We are happy you have joined us in our exploration of the fundamental principles of biology. Biology is the scientific study of life. Biologists are scientists who study living organisms.

Life is everywhere. Biologists study the human body and figure out how it works when it is healthy, and compare that to the way it works when things go wrong. They study the bacteria that live in your digestive system and explore the reasons why these bacteria are critical to your health. They study mice and flies and yeast and plants and learn about how living organisms are alike, and how they are different.

Biology montage. Photographs donated by Eric Guinther, 2004. Wikimedia.

Different kinds of biologists study different things. Cell biologists are currently researching the causes and symptoms of various types of cancer, enabling doctors to find cures and treatments. Ecologists are biologists who specialize in studying the way that living organisms interact with their environments. They examine important issues such as acid rain and observe what happens to the health of living systems when acid rain falls. There are even specialized biologists, called astrobiologists, who study conditions on other planets and design experiments to determine whether or not life could exist in other places in our solar system.

Understanding biology can help us understand ourselves and the environment around us. For example, understanding how climate change affects ecosystems will help identify the ways in which sustainable food production can keep up with a growing human population. Biological research is constantly adding to our understanding of human health and disease, and often results in treatments that lead to longer, healthier, and more productive lives. Biological research can also help address the growing demand for renewable energy and sustainable resource use.

Being a Critical Consumer of Information

Every day we are bombarded with information about health issues, new vaccines and medicines, ecological problems, and other issues related to biological research. This information comes at us from a myriad of diverse sources, including friends, healthcare providers, the media, your neighbors, and the Internet. As you gain a deeper understanding of life and the processes that sustain it, you will be able to more effectively sort through and interpret this deluge of information, and make informed decisions about your health and how you interact with the environment.

Every day, we are bombarded with reports of new discoveries in biology that are exciting, relevant, and sometimes controversial. See University of Oxford (2012, June 18)

After completing this course, you will have a basic understanding of biological principles and how they relate to your life.

Portions of this course are built on materials developed and generously provided by University of Maryland University College, made available with permission under a CC-BY-NC license. Direct use of specific activities and media elements are noted throughout the course.

The purpose of this course introduction is to prepare you conceptually and technically for the course. Since you may not have experienced an online course like this before, we will start with a short section describing the course and offer some learning strategies that will help you use the materials most efficiently. Finally, we will discuss what biology is all about — the "big picture" — our framework for exploring the relationship between the themes in biological research and the fundamental concepts and principles included in this course.

Information in this course is organized into units. Each unit begins with an introduction that orients you toward the major themes you’ll explore in that section. The unit introduction will also show you how the content fits into the course as a whole. Each unit consists of several modules. Modules are like chapters in a book, and when you start a new module, you will see the list of learning outcomes you will achieve after completing that section of the course. Each module consists of several pages designed to help you achieve the learning outcomes. The introduction highlights what you will learn and how it relates to the big picture. The following pages make up the informational “meat” of the module. This explanatory content consists of short passages of text with information, examples, images, and explanations. As you work through the content, you will have many opportunities to practice what you are learning. The practice usually takes one of two forms:

• “Learn By Doing” activities give you the chance to practice the concept that you are learning, with hints and targeted feedback to guide you if you struggle.
• “Did I Get This?” activities give you the opportunity to do a quick "self-check" to assess your own understanding of the material before completing a graded quiz.

Directed feedback during these learning activities will help you stay on track as you assimilate new information. Most modules will also include an “Application Spotlight” that gives you the opportunity to apply your understanding of the module’s content to a specific case study or real-life example.

After completing a module, you will have a chance to demonstrate what you learned by taking a graded quiz. The module quizzes will assess and reinforce your learning as you progress through the unit. When you complete all the modules in a unit, you can participate in a “My Response” activity, where you will assess your own understanding of the unit content. After reflecting on your ability to achieve the learning objectives, you will have a chance to submit questions to your instructor, and then you will conclude your activities with a unit quiz.

Other Course Features

You can navigate through this course using the navigation bar at the top of the screen, the course syllabus, the course outline, and the page number box. All are accessible on any page in the course.

Also provided is an Appendix, which includes information such as a glossary of key terms and their definitions, a table illustrating the various ways biologists represent chemical structures, and an interactive image of the cell (the smallest unit of life).

This course is divided into 10 units. This first unit, "Biology: The Science of Life," lays the foundation upon which the rest of the course is built. This unit begins by defining biology and characterizing its relationship to other fields of scientific study. It then elaborates on a few of the themes that emerge over and over throughout this course. Finally, in this unit you will explore the nature of science. This introduction represents the toolkit you’ll need to understand the rest of the course, and will enable you to create context for all the new information you will learn.

The diagram above represents the "Big Picture" of biology. It illustrates how the course is organized and depicts the relationships between the main topics you will learn about as you progress through the material. You will find that as you go, the material is telling a story. It is a story based on the research and collaboration of centuries of scientific thinkers. The story begins with the smallest particles of matter: atoms. Atoms are the building blocks of all matter and they can be put together, like Legos, to form molecules. A special class of molecules called biomolecules are the “legos” used to build the structures required for life. The fundamental unit of life is the cell, and all cells are made of biomolecules. The cell is the first level of organization to display all the characteristics of life. Cells, and all living organisms, require energy to function. Organisms capture and use energy through a chain of chemical reactions called metabolic processes. The energy that cells capture through metabolism can be used to do work, including the work required for reproduction. All living organisms reproduce, passing their genetic information from generation to generation. This results in a unity and diversity of all living organisms, because we all share a common ancestor. Some organisms are more likely to survive than others, and this leads to evolutionary processes that result in the incredible diversity of life you see around you. The final chapter in the story reminds us that the diversity of life exists within a rich context of interactions, causes, and effects. Life does not take place in a vacuum; instead, living organisms rely intimately on other living organisms, as well as in the nonliving environment. All matter, living and nonliving, exists within a delicate interconnected balance, and humans are just one part of this biosphere.

This is a fascinating story and one that inspires a deep understanding and appreciation of the living world within us and around us. As we study the fundamental principles of biology, we will systematically explore the following characteristics of life.

Biology is the scientific study of life and is the branch of science that studies living organisms and the way organisms interact with their environments. The subject is vast and includes topics as diverse as acid rain, evolution, and genetically modified foods. In this module, you will investigate the definition of life and explore some of the characteristics of living systems.

Biologists study many varieties of living organisms. Clockwise from top left: salmonella bacteria; a koala bear; a fern plant; fly amanita, a poisonous fungus; the red-eyed tree frog; a tarantula. Source: Andrew Colvin; August, 2010; Wikipedia.

Biologists study how humans and other living organisms interact with their environment. A couple from Northern Thailand. The husband is carrying the stem of a banana plant, which will be fed to their pigs. Source: Manuel Jobi Weltenbummler, 2007, Wikipedia.

Have you ever gotten sick with the flu and said something like, “I’ve come down with a bug,” or “I’ve got the flu bug”? In fact, the flu (short for influenza) is not really caused by a “bug” at all. It is caused by a virus, and there is some controversy in the scientific community regarding whether or not viruses are alive. But what are viruses, really? And how would you determine whether or not they are alive? In this lesson, you’ll learn more about what viruses are, so you can figure out if they are actually alive.

Components of a Virus

Viruses contain genetic material within a protein or membrane coat.

Viruses contain genetic information in the form of either DNA or RNA. The genetic information is surrounded by a protein coat called a capsid. Some viruses also have a membrane structure surrounding their genetic information. Viruses are tiny particles and they lack the machinery necessary for growth and reproduction. In order to reproduce, a virus must infect a host cell and hijack the host cell’s machinery. In other words, a virus cannot reproduce without using the tools of another cell.

So are viruses alive? There is much debate on the subject. Complete the following activity and draw your own conclusions.

Throughout the study of biology, several themes emerge. These recurrent concepts will continually appear as we delve deeper into the scientific study of life. As we progress through the course, we will highlight the lessons that help to illustrate these six themes:

1. Structure determines function.
2. Living organisms maintain homeostasis.
3. Energy flows through living systems; matter is recycled.
4. Life’s components are interconnected and interdependent.
5. Organisms grow, develop, and reproduce.
6. Evolutionary processes explain both the unity and adaptive diversity of life.

In this module, we will explore an overview of each of these themes separately.

Biologists describe how organisms are put together (structure) and explain how organisms stay alive, move, grow, reproduce, and do other activities (function). In biological systems, the structure of a cell or body part is tightly linked to its function within the life of the organism.

The structure of something is determined by two factors: its three-dimensional shape, and the materials from which it is made. The structure that something takes directly influences its possible functions. Consider a piece of wood. Depending on how it is shaped, it could be used as a spear for hunting, a cup for drinking, a pipe for smoking, or even a flute for playing music. The wood also possesses unique properties that influence how it can be used. For example, the piece of wood could never function as a hot air balloon, no matter what kind of shape it took. It would always be too heavy to lift off the ground.

At the smallest levels of biological organization, the structure of a molecule determines its function within a cell. In this course, you might investigate the structure of a molecule and then learn what it does. It will help you to remind yourself: the structure and the function of this molecule are connected.

Enzymes are molecules found within a cell that speed up the rate of the chemical reactions necessary to support life. Enzymes break down food molecules, help build muscle proteins, can destroy toxins, and much more. An enzyme’s ability to function depends directly on its three-dimensional shape. If exposed to excessive heat or harsh chemical conditions, enzymes unravel and change shape. When this occurs, the enzymes stop working and the chemical reactions of life slow down or cease.

At a larger scale, the structure of a cell is directly linked to its function within the body of a multicellular organism. Compare the following images of some different cell types and explore how structure relates to function at the cellular level.

First division of a sea urchin cell just after egg and sperm join to start the life cycle. The cells are relatively large, because they are full of nutrients that will be used to feed the developing animal. Otherwise, there is little noticeable structure to the cells. Their main function at this point is simply to divide, laying the groundwork for future more specialized generations of cells within the body. (Source: Evelyn Spiegel and Louisa Howard, The Cell Image Library)

Developing nerve cells in the spinal cord of an embryo. When mature, the reddish structures will connect to other cells to relay nerve signals. Right now they are exploring the environment, responding to chemical signals, and growing toward their destinations. This function is supported by the branching “hand-like” structure; these cell structures are chemically “feeling their way along” through the embryo. The long thin yellow structures will act as cables, carrying signals over long distances — just as their structure suggests.

Lining of a human oviduct, or fallopian tube. This view shows several cells. Together they form a lining. They are shaped to form a sealed surface. Broom-like structures sprout from the exposed surface of each cell. These beat against the fluid in the tube, creating a gentle current that moves the egg cell toward the uterus, where it may implant to begin a pregnancy.

Hair cells in the inner ear of a guinea pig. These cells are shaped so that they are easily disturbed by vibrations. When they are flexed, a signal passes to nerve cells that take the message to the brain, where it is interpreted as sound. (Source: Dr. David Furness, Wellcome Images)

Structure also determines function at higher levels of biological organization. Your body’s organs function as they do because of how tissues are put together, forming filters, pumps, levers, surfaces for gas exchange, and pipes for air and fluid flow. And, of course, the entire body of an organism is suited to its lifestyle and environment. For example, the earthworm is well-suited for burrowing: it is slimy, muscular, flexible, and cylindrical. Yet there are many surprising details in the worm’s structure. The next time you get the chance, feel an earthworm. Pinch it carefully near the head with one hand, then rub your free forefinger against its belly. You’ll notice prickly hairs on the worm’s underside. And you’ll find that you only feel them when you move your finger toward the worm’s head: the hairs are set at an angle, enabling the worm to grip the soil to and move it forward through the earth.

You can probably imagine other ways to use different shapes and materials to build a functional body that enables Structo to overcome many different challenges. Environmental pressures have led (and continue to lead) to the evolution of organisms with a virtually infinite range of such combinations.

In fact, organisms are so well adapted to their environments that humans are now looking to them for inspiration. Today, a fast-growing field called biomimicry brings biologists together with engineers to develop new products based on solutions found in nature. One of the earliest products of this approach was the invention of Velcro (the hook and loop attachment) by Swiss engineer Georges de Mestral. He was inspired by the burrs that got stuck in his dog’s fur. To learn more, visit the Biomimicry Institute.

Living organisms detect and respond to changes in the conditions of their external environment. In response to threats and opportunities, organisms may move or change their activities. For example, plant stems can grow toward a source of light. Over time, the trunks of trees strengthen when they are flexed by the wind. Animals, of course, respond to stimuli with a huge range of behaviors from the hibernation of bears to your own development of “goosebumps” on a chilly day.

In contrast to the extreme variability of the outside world, the interior of a cell is a remarkably constant environment. For example, cells typically keep their internal pH (acidity) within a narrow range. This is important because changes in pH can cause molecules like enzymes to change their shapes. As you already know, a molecule’s shape (or structure) determines its function. If its shape changes, it may lose function. Because of this, many of the chemical reactions of life will not work properly if cell conditions change too much.

The ability or tendency of organisms and cells to maintain stable internal conditions is called homeostasis. The term homeostasis comes from the Greek words homeo (same, alike) and stasis (standing). It describes how life stands in one place despite many changes in the surrounding world.

Environmental conditions can also affect cellular homeostasis. If the cell’s surroundings change quickly, conditions inside the cell may be temporarily disturbed. Organisms react to these changes in a corrective way: they detect changes and do something to oppose them. For example, when you get cold, your muscles start to contract in rapid bursts, causing you to shiver. The process of shivering then generates heat that warms you back up again. As a result of this and other adjustments, your temperature is maintained close to 99 degrees F (Fahrenheit) [37 degrees C (Celsius)]. At this temperature, your enzymes work very efficiently.

Homeostasis is an important theme in biology. All living systems use resources to maintain homeostasis. When cells fail to maintain homeostasis, disease results. Ultimately, if homeostasis is not restored, an organism will die.

All organisms grow and develop. Growth is just an increase in size. In development, structure and function change in an orderly way as an organism passes through its life cycle. An individual’s pattern of development is partly determined by genetic instructions. DNA, the molecule of inheritance, encodes proteins and other molecules that build cells and make them work. You can think of genes as “recipes” for proteins. Each cell has a huge library of thousands of recipes in its DNA. But most of the recipes don’t get used in any given cell. Chemical controls tell the “cooks” whether to make a given protein, or ignore its recipe and make something else. Therefore, even though your cells share the same DNA, their activities change radically in different parts of your body and at different stages of development.

In this time-lapse video, a few days of development are sped up for your viewing pleasure. In the earliest frames you can see large cells dividing. With each division the individual cells get smaller. Chemical signals in each cell are passed to its descendants and to nearby cells. As a result, DNA is turned “on” or “off” in each cell, leading to different shapes and structures. Toward the middle and end of the video, individual cells are much too tiny to see. Specialized cell types form. Cells move from place to place, grow, die to create gaps, and divide to create bulges. In this way, body structures begin to emerge.

Reproduction occurs when an individual organism passes on its genetic information to a newly independent organism, or offspring. Individual organisms have a limited life span. All are subject to extreme events that bring death, such as being eaten by a predator. Even if they avoid such a fate, most organisms decline in health and die toward the end of their typical life span. Reproduction maintains genetic information by passing it to new individuals. Offspring resemble their parent(s) and reproduction maintains the continuity of life over time.

Evolution is a scientific theory that explains how and why life changes over time. Evolution provides the explanation for why all living organisms share profound similarities, and yet, the life forms on our planet are so incredibly diverse. The two fundamental tenets of evolution are shared ancestry and natural selection.

Shared Ancestry

As you learned previously in this module, reproduction results in the passing of characteristics from parents to offspring and maintains the continuity of life. You can see this in a family photograph: offspring resemble their parents and siblings resemble each other. Biologists look at all life on the planet and see the same patterns.

According to evolutionary thinking, life forms are similar because of their shared ancestry. All cells have DNA as the molecule of inheritance and they also share many other detailed features. Organisms and cells always come from parents, and this is where they get their genetic information. Trace this process back in time, and it is reasonable to suppose that all life forms inherited DNA and many other features from a long-ago common ancestor. The unity of life is very striking when we examine molecules, which can be almost identical in species as different as bacteria and whales. This unity of structure and function is also evident when we compare skeletons, kidneys, or hearts among animals.

Charles Darwin’s Sketch of the Tree of Life

Sketching in his notebook in 1837, Charles Darwin created the first diagram of a phylogenetic tree. It shows several life forms related to each other by ancestry. The neighboring “twigs” in the lettered groups are similar species. Eventually Darwin would propose that ALL life forms find a place on one tree, and that it began with one or just a few very simple life forms long ago.

learn by doing

Natural Selection

The second major idea of evolution is that of natural selection. Natural selection helps explain how groups of organisms become well-suited, or adapted, to their surroundings. Individuals are always a bit different from their parents and from each other, partly because of changes to their genes. These differences may be helpful or harmful to the individuals that inherit them. In nature, individuals often have very low odds of surviving to reproduce. Individuals with slightly harmful or even average characteristics might be less likely to make it, and those with traits that fit in very well with the local habitat will have the greatest chance to survive and reproduce. This sorting process goes on generation after generation. Each time only a tiny fraction of those born are well-suited and lucky enough to pass their genes along; the others die, leaving no descendants. As generations of time pass, inherited features that help organisms produce offspring become more common within a population. Harmful features that reduce reproduction become less common. Many experiments have demonstrated the effects of natural selection on populations in the laboratory and in nature. The process of natural selection is one way that scientists have explained the vast diversity of life on our planet.

Dandelions Illustrate Features of Natural Selection

This photo shows a crowd of dandelions, all striving to reproduce. Each plant may produce hundreds of seeds, but only a few of them are likely to grow up to produce seeds of their own. In each generation there is a great sorting process, with most offspring (in this case, seeds and seedlings) dying young. Only a few survive to reproduce themselves. These survivors are probably quite well-suited to local conditions, and they will produce offspring with similar traits.

learn by doing

did I get this

Science is a powerful tool used to understand the natural world. It is the process that has resulted in the knowledge we are exploring in this course. However, the process of science does have limitations. In other words, there are some questions that science cannot be used to answer. For example, science cannot answer questions about supernatural things. It also cannot be used to make moral or aesthetic judgments. While questions of these types may be important for humans to explore, the process of science cannot be used to study them.

In this module, the process of science will be discussed in more detail. Then you will learn about how to design a quality scientific experiment. Finally, you will have the opportunity to practice identifying examples of science and to compare those to examples of pseudoscience, or things that claim to be scientific, but are not.

You’ve successfully identified a hypothesis for the University of Washington’s study on HPV: People who get the HPV vaccine will not get HPV.

The next step is to design an experiment that will test this hypothesis. There are several important factors to consider when designing a scientific experiment. First, scientific experiments must have an experimental group. This is the group that receives the experimental treatment necessary to address the hypothesis.

The experimental group receives the vaccine, but how can we know if the vaccine made a difference? Many things may change HPV infection rates in a group of people over time. To clearly show that the vaccine was effective in helping the experimental group, we need to include in our study an otherwise similar control group that does not get the treatment. We can then compare the two groups and determine if the vaccine made a difference. The control group shows us what happens in the absence of the factor under study.

However, the control group cannot get “nothing.” Instead, the control group often receives a placebo. A placebo is a procedure that has no expected therapeutic effect — such as giving a person a sugar pill or a shot containing only plain saline solution with no drug. Scientific studies have shown that the “placebo effect” can alter experimental results because when individuals are told that they are or are not being treated, this knowledge can alter their actions or their emotions, which can then alter the results of the experiment.

Moreover, if the doctor knows which group a patient is in, this can also influence the results of the experiment. Without saying so directly, the doctor may show — through body language or other subtle cues — his or her views about whether the patient is likely to get well. These errors can then alter the patient’s experience and change the results of the experiment. Therefore, many clinical studies are “double blind.” In these studies, neither the doctor nor the patient knows which group the patient is in until all experimental results have been collected.

Both placebo treatments and double-blind procedures are designed to prevent bias. Bias is any systematic error that makes a particular experimental outcome more or less likely. Errors can happen in any experiment: people make mistakes in measurement, instruments fail, computer glitches can alter data. But most such errors are random and don’t favor one outcome over another. Patients’ belief in a treatment can make it more likely to appear to “work.” Placebos and double-blind procedures are used to level the playing field so that both groups of study subjects are treated equally and share similar beliefs about their treatment.

A variable is a characteristic of a subject (in this case, of a person in the study) that can vary over time or among individuals. Sometimes a variable takes the form of a category, such as male or female; often a variable can be measured precisely, such as body height. Ideally, only one variable is different between the control group and the experimental group in a scientific experiment. Otherwise, the researchers will not be able to determine which variable caused any differences seen in the results. For example, imagine that the people in the control group were, on average, much more sexually active than the people in the experimental group. If, at the end of the experiment, the control group had a higher rate of HPV infection, could you confidently determine why? Maybe the experimental subjects were protected by the vaccine, but maybe they were protected by their low level of sexual contact.

To avoid this situation, experimenters make sure that their subject groups are as similar as possible in all variables except for the variable that is being tested in the experiment. This variable, or factor, will be deliberately changed in the experimental group. The one variable that is different between the two groups is called the independent variable. An independent variable is known or hypothesized to cause some outcome. Imagine an educational researcher investigating the effectiveness of a new teaching strategy in a classroom. The experimental group receives the new teaching strategy, while the control group receives the traditional strategy. It is the teaching strategy that is the independent variable in this scenario. In an experiment, the independent variable is the variable that the scientist deliberately changes or imposes on the subjects.

Dependent variables are known or hypothesized consequences; they are the effects that result from changes or differences in an independent variable. In an experiment, the dependent variables are those that the scientist measures before, during, and particularly at the end of the experiment to see if they have changed as expected. The dependent variable must be stated so that it is clear how it will be observed or measured. Rather than comparing “learning” among students (which is a vague and difficult to measure concept), an educational researcher might choose to compare test scores, which are very specific and easy to measure.

In any real-world example, many, many variables MIGHT affect the outcome of an experiment, yet only one or a few independent variables can be tested. Other variables must be kept as similar as possible between the study groups and are called control variables. For our educational research example, if the control group consisted only of people between the ages of 18 and 20 and the experimental group contained people between the ages of 30 and 35, we would not know if it was the teaching strategy or the students' ages that played a larger role in the results. To avoid this problem, a good study will be set up so that each group contains students with a similar age profile. In a well-designed educational research study, student age will be a controlled variable, along with other possibly-important factors like gender, past educational achievement, and pre-existing knowledge of the subject area.

Matter is anything that has mass and takes up space. The chair you are sitting in is made of atoms. The food you ate for lunch was built from atoms. Even the air you breathe is made of atoms. In this unit, we will learn more about atoms, the fundamental unit of matter.

All matter is made of atoms. There are 92 different kinds of atoms that can be put together in unique ways, resulting in all the diverse things you see around you.

The cell is the fundamental unit of life; therefore, you might think that your study of biology should begin with the cell. In fact, before you can truly understand how a cell functions, you must understand the building blocks from which cells are made. In the Introduction to Biology module, you learned that all life exhibits a hierarchical organization. While cells are the first level of organization that displays all the properties of life, their component parts (atoms and molecules) are not alive, as illustrated in the inverted pyramid below.

To make sense of how cells work, you must constantly return to their parts (atoms and molecules) and the interactions among them. This is why a clear understanding of some chemistry is essential to understanding how life functions. This unit will focus on the atom. You will learn how atoms combine to form different molecules, making up all the diverse matter you see around you. In this unit, you will explore only nonliving components of the hierarchy of life.

In this module, you will learn about the basic structure of the atom, the fundamental unit of matter. Living things are made up of atoms arranged in a complex and nonrandom way. This is one of the common features of all living organisms. The atom is the smallest level in the hierarchy of life that we will explore in this course. Understanding the properties of atoms allows us to predict and understand how atoms interact with one another to build molecules, such as hormones and DNA. In addition, an understanding of atoms allows us to predict how cells will react to different therapeutic drugs and toxins in the environment.

The Atom

All living and nonliving things are composed of matter. Matter can be defined as anything that occupies space and has mass. The mass of an object is a measure of how much matter it has (that is, how much “stuff” is in it). Mass is not exactly the same as weight, but here on Earth we can measure and compare the masses of different objects by weighing them.

When we explore matter scientifically, we find that it takes on many different structures as we zoom in at smaller and smaller scales. Everyday objects are mostly mixtures of molecules, which in turn are made up of atoms. Even air is a mixture of molecules. The atom is a good focal point for understanding matter; all matter is composed of atoms.

Atoms are unimaginably small. Even within a single microscopic cell, there is room for not just billions, but trillions or even hundreds of trillions of atoms. Amazingly, however, physicists now understand that most of the volume of an atom is actually made up of empty space. The atoms themselves are made of even smaller subatomic particles called protons, neutrons, and electrons. We cannot look at the parts of atoms with a microscope; they are simply too small. However, physicists have learned a great deal about atoms and subatomic particles through indirect methods. One model of the atom is shown in the diagram below.

Diagram of an Atom

Atoms contain protons and neutrons, which are found in the nucleus (center) of the atom. Atoms also contain electrons, which are found outside the nucleus. This is a model of a lithium atom.

did I get this

Elements (atoms) are characterized by their atomic structure, which is made up of subatomic particles: protons, neutrons, and electrons. Protons and neutrons reside in the nucleus (center) of the atom and have a mass of one atomic mass unit (amu) each. Electrons are found outside of the nucleus, in zones that are called “shells.” Electrons have almost no mass.

Diagram of atom

Atoms contain protons and neutrons, which are found in the nucleus (center) of the atom. Atoms also contain electrons, which are found outside the nucleus. This is a model of a lithium atom.

The mass of an atom is called the atomic mass. When calculating atomic mass, we pay attention only to the protons and neutrons; the electrons have almost no mass. The atomic mass is the sum of the number of protons and the number of neutrons. By summing the atomic mass of all the atoms in a molecule, one can estimate the molecular mass of the molecule, which is expressed in atomic mass units (called Daltons). Each of the heavy particles (neutron, proton) weighs one atomic mass unit, so a Helium (He) atom, which has two protons, two neutrons, and two electrons, weighs about four atomic mass units; that is, two protons plus two neutrons.

In addition to location and mass, each subatomic particle has a property called “charge.” Charge can be “positive” or “negative.” Items with the same charge tend to repel each other and items with opposite charges tend to attract each other. Protons have a positive charge and neutrons have no charge, giving the nucleus a positive overall charge. Each electron has a negative charge that is equal in strength to the positive charge of a proton. Electrons and the protons of the nucleus attract each other, and this is the force that keeps the atom together, much like the force of gravity keeps the moon in orbit around Earth.

Scientists have learned to use isotopes in many different ways. For example, stable isotopes can be used to trace chemical reactions through a food web. For example, if a stable isotope is used in fertilizer, that same isotope will later show up in the tissues of plants, then in animals, and finally in decomposers as the nutrient moves through the food web. Other isotopes are unstable and they tend to decay (or break down into other isotopes) at a constant rate. Scientists have learned how to use unstable isotopes to determine the age of fossils or artifacts. Finally, some isotopes are radioactive. Radioactive isotopes emit energy in the form of radiation when they decay into different isotopes.

Radioactive isotopes can be used to visualize certain tissues for medical diagnosis. One example of this is radioactive iodine, which tends to concentrate in the thyroid gland. It emits radiation as it breaks down to another isotope of iodine. Special cameras can pick up this radiation and use it to create an image of the thyroid gland to determine if the patient's thyroid is functioning normally. If there is abnormal activity in the thyroid gland, this can indicate cancer.

Another example of radioactive isotopes is positron-emission tomography (PET). In PET, a patient ingests sugar that is marked with a radioactive isotope. Cells that are using a lot of sugar (or need a lot of energy) will absorb more of the radioactive isotope. The patient is then moved into a PET scanner, where the radioactive isotopes are visualized and the machine translates the data into an image. This can help in a variety of applications, from cancer and Alzheimer’s disease diagnosis to addiction research (see image).

Positron-Emission Tomography (PET)Images

PET brain scans show chemical differences in the brain between addicts and nonaddicts. The normal images in the bottom row come from nonaddicts; the abnormal images in the top row come from patients with addiction disorders. These PET brain scans show that addicts have fewer than average dopamine receptors in their brains, so that weaker dopamine signals are sent between cells. Source: Nora Volkow, March 2001, Wikipedia.

Atoms are the smallest units of an element that retain all the properties of the element. Atoms combine to form a larger and more complex entity called a molecule. Molecules are composed of two or more atoms held together by covalent bonds.

Chemical bonds are attractions between atoms that hold atoms and molecules together. There are three types of chemical bonds that are important in biology: covalent bonds, ionic bonds, and hydrogen bonds. Covalent bonds are very stable, while ionic and hydrogen bonds are less stable. The relatively weaker ionic bonds and hydrogen bonds allow reversible interactions between different molecules in biological systems.

Joining atoms together builds molecules that are more complex and larger than the individual atoms that compose them. The table below illustrates some similarities and differences among ionic, covalent and hydrogen bonds.

The most stable situation for an atom is to have its outer shell completely filled with electrons. It is not easy to explain why this is true, but it is a rule of thumb that predicts how atoms will react with each other. Recall from the discussion on electrons, in the Atoms module, that the first electron shell is full with two electrons, and the second and third shells are full with eight electrons. Atoms tend to bond to other atoms in such a way that both atoms have filled outer shells as a result of the interaction.

Ionic bonds are the interactions between ions of opposite charges. Atoms form ions when they either take up or release electrons in order to fill their outer shell. Elements in the outer columns of the periodic table often react in this manner; elements like sodium tend to lose electrons and become cations (positively charged ions), whereas elements like chlorine tend to gain electrons and become anions (negatively charged ions).

In fact, the reaction between sodium and chlorine is a great example of ionic bonding, and produces a compound you have in your kitchen — table salt. Chlorine (Cl) has an atomic number of 17, so it has 7 electrons in its outermost shell. Chlorine needs one more electron to have a full outer shell.

Sodium (Na) has an atomic number of 11, with one electron in its outermost shell. Sodium needs to get rid of an electron, and then it will have a full outer shell.

By losing an electron, sodium becomes a cation with a positive charge (+1). By gaining an electron, chlorine becomes an anion with a negative charge (-1). Now each ion has a net charge and the two charges are opposite. The ions attract one another. The electrostatic interaction between the sodium ion and the chlorine ion is an ionic bond .

Instead of transferring their electrons completely, atoms may remain in very close contact and share electrons so that their outer shells are filled. In essence, a shared electron is counted “twice” and participates in a larger shell that joins the two atoms. A single pair of shared electrons makes a single covalent bond. Atoms can share two pairs of electrons (in a double bond), or even three pairs of electrons (in a triple bond).

This sharing of electrons is called a covalent bond.

Carbon, for example, has an atomic number of 6 (see the figure below). The outer shell of carbon has 4 electrons. Carbon can share an electron with four other atoms. Hydrogen has an atomic number of 1. It has a single electron in its outermost shell, and can share this electron with one other atom. A carbon atom can form a covalent bond with four hydrogen atoms to form a molecule called methane, CH_{4 .} In a methane molecule, carbon effectively has a “full” second shell (8 electrons) and each hydrogen has a “full” second shell (two electrons).

Example 1: Carbon and hydrogen react to form methane (CH₄). Each hydrogen requires one covalent bond to fill its first electron shell. Each carbon requires four bonds to fill its second shell. Exaample 2: Nitrogen and hydrogen form ammonium (NH₃). The three unpaired electrons on the nitrogen atom (N) in ammonia, represented as single dots, form bonds with three hydrogen atoms.

Nitrogen, another example, has an atomic number of 7 (see the figure above). The outer shell of carbon has 5 electrons. Nitrogen can share an electron with three other atoms. Hydrogen has an atomic number of 1. It has a single electron in its outermost shell, and can share this electron with one other atom. A nitrogen atom can form a covalent bond with three hydrogen atoms to form a molecule called ammonia, NH₃ . In an ammonia molecule, nitrogen effectively has a “full” second shell (8 electrons) and each hydrogen has a “full” second shell (two electrons).

Recall that in a covalent bond, the electrons are shared between two atoms. However, the two atoms don’t necessarily share the electrons equally. Some atoms are more likely to draw the shared electrons closer to themselves. Atoms have a high electronegativity if they tend to draw the electrons towards them. Electronegativity increases as one moves from the left to the right across the periodic table. Hydrogen is moderately electronegative, with a value of 2.1, carbon is somewhat more electronegative, with a value of 2.5, and fluorine is the most electronegative atom, with a value of 4.0.

Electronegativities of Biologically Important Atoms

Image modified from Chart of Each Element's Electronegativity, UC Davis ChemWiki by University of California.

The degree of unequal electron sharing depends on the difference in electronegativity of the atoms involved in the bond. For example, in carbon-carbon bonds, both atoms have the same electronegativity, so the electrons are equally shared between the two carbons. In contrast, a carbon-oxygen bond involves two atoms that have different electronegativities. The less electronegative atom (carbon) will donate part of its electrons to the more electronegative atom (oxygen), resulting in a partial positive charge on the carbon (indicated by δ⁺) and a partial negative charge on the oxygen (indicated by δ^-). The size of the partial charges is proportional to the difference between the electronegativities of the two bonded atoms. Bonds in which electrons are unequally shared between the atoms are called polar covalent bonds.

Throughout this course, you will be studying many different molecules. Many of the important molecules of life, like DNA, proteins, and even ordinary water, share a key characteristic: they all form hydrogen bonds.

Hydrogen bonds are not like the covalent bonds you just learned about. They do not join atoms into molecules. Instead, they are the attraction of an electronegative atom to a hydrogen that is covalently bonded to another electronegative atom. This involves the attraction of the hydrogen with a partial positive charge to the electronegative atom with a partial negative charge. Only hydrogen covalently bonded to an electronegative atom can participate in hydrogen bonding.

Hydrogen bonding has a significant effect on the properties of molecules. For example, the structure of the DNA molecule is in part held together by hydrogen bonds. Hydrogen bonds also create coils and other structures within the complex protein molecules that are essential to life’s diversity. Finally, water behaves the way it does because of the hydrogen bonds that attract water molecules to each other.

Water

The water molecule is a very important example of a molecule that can form hydrogen bonds. It is the hydrogen bonding of the water molecules that gives water many of its unique and life-sustaining properties. One water molecule consists of two hydrogen atoms covalently bonded to a oxygen atom.

Recall that in a covalent bond, the electrons are shared between two atoms. However, the two atoms don’t necessarily share the electrons equally. Some atoms are more likely to draw the shared electrons closer to themselves. These atoms have a high electronegativity. Both oxygen and nitrogen are molecules with a high electronegativity.

In a water molecule, oxygen is more electronegative than hydrogen. This means that oxygen has a greater affinity or attraction for the shared electron pair than hydrogen does. Because of this, the electrons tend to spend more time close to the oxygen atom and they spend less time close to the hydrogen atom. As a result, the oxygen becomes slightly negative and each hydrogen atom develops a slightly positive charge. Whenever two atoms with different electronegativities form a covalent bond, we say that the bond between the atoms is polar, with each atom carrying a partial charge. Oxygen and nitrogen are the two highly electronegative elements that are often bonded to hydrogen in biological molecules. O-H and N-H bonds are strongly polar, and this sets the stage for hydrogen bonding.

δ^- and δ⁺ represent a partial negative and partial positive charge, respectively.

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Hydrogen bonding is the attraction of an electronegative atom for a hydrogen that is covalently bonded to another electronegative atom. This involves the attraction of a hydrogen with a partial positive charge to an atom with a partial negative charge. However, only hydrogen covalently bonded to an electronegative atom can participate in hydrogen bonding.

In water, the partially positive hydrogen atoms are attracted to the partially negative oxygen atoms of neighboring water molecules. Hydrogen bonds are responsible for many of the unique properties of water. We’ll explore this in more detail in the next module. Watch the following animation that illustrates hydrogen bonding.

Adjust the volume on your computer and click the play button.

Biologists have different ways of representing chemical structures. Each type conveys different information.

Have you ever wondered why scientists spend time looking for water on other planets? It is because, at least here on Earth, water is essential to life. Evidence of water on Mars, and some of the moons of Saturn and Jupiter, increases the odds that life may exist there. Here on Earth, water is one of the most abundant molecules. The water content of our bodies and our cells ranges from 70 to 95 percent. All of life’s chemical reactions take place in watery fluid. Without water, life as we know it simply would not exist.

There are four properties of water that make it such a unique and important molecule:

1. Water is an excellent solvent and can dissolve a wide range of substances.
2. Water is cohesive.
3. Water’s temperature tends to remain stable.
4. Solid water (ice) is less dense than liquid water.

These properties of water are due to the hydrogen bonds formed between water molecules. Hydrogen bonds are discussed in the Chemical Bonds module.

Solutions are homogeneous mixtures. This means that you can sample any part of the solution and the composition of the solution will be the same.

Solutions have two components:

• solvent: the component of the solution in the greatest quantity.
• solutes: the component(s) present in lower quantities.

If you add some salt to water, you are making a solution. Water is the solvent and the salt is the solute. Solutions can have more than one solute. If you add sugar to your salt solution, both sugar and salt would be the solutes of the solution. Solutions in which water is the solvent are called aqueous solutions. The inside of our cells and our body fluids are examples of aqueous solutions. When a solute is added to a solvent and a solution is formed; the solute is described as “dissolving” in the solvent.

Substances that will dissolve in water are hydrophilic or water-loving. What kinds of molecules are hydrophilic? Ionic substances like table salt (NaCl) are hydrophilic. They split into positive and negative ions and dissolve in water. Polar water molecules surround the charged particles, breaking them away and pulling them into the fluid.

Polar molecules also are hydrophilic. Polar water molecules readily surround and dissolve polar molecules or molecules with polar functional groups. Examples include sugars and alcohols, which have hydroxyl groups. Molecules that do not dissolve in water are hydrophobic (from the Greek word meaning water-fearing or water-hating). Nonpolar molecules are hydrophobic. Examples include hydrocarbons and fatty acids with their abundant nonpolar C-H bonds. Have you ever tried to mix water and oil? Oils and fats are nonpolar and will not form a solution with water.

Oil Spill in San Francisco Bay

About 58,000 gallons of oil spilled from a South Korea-bound container ship when it struck a tower supporting the San Francisco-Oakland Bay Bridge in dense fog on 11/07/07. Brocken Inaglory, Nov, 2007; Wikimedia Commons.

Next we will examine hydrophobic molecules more closely. Substances with hydrophobic molecules will not dissolve in water and instead will tend to separate from water.

Some molecules are hydrophobic, which literally means fear (phobia) of water (hydro). These molecules do not like to dissolve in water. When hydrophobic molecules are mixed with water, they will tend to separate into distinct phases (or layers), one containing water and the other containing the hydrophobic molecules. This makes it very difficult, for example, to “wash” oil off of waterfowl after an oil spill.

Birds killed as a result of oil from the Exxon Valdez spill. Photo in the public domain courtesy of the Exxon Valdez Oil Spill Trustee Council.

Things composed of hydrophobic molecules generally include oils, fats, and greasy substances. Materials containing hydrophobic substances are often used for removal of oil from water and management of oil spills. Other molecules are hydrophilic, which means love (philic) of water, and readily dissolve in water.

Chemical Structures

Now that you know some common hydrophobic and hydrophilic molecules, let’s look at their structures to understand why they interact with water in different ways.

learn by doing

The additional atoms that are found only on glucose are electronegative, meaning that they will withdraw some of the electrons from the atoms that form bonds with them. The electronegative atom will have a slight negative charge, and the atom that it is bonded to it will have a slight positive charge. The unequal distribution of electrons makes the bond a polar bond.

Water is a polar molecule. The electronegative oxygen draws the electron from hydrogen toward it, causing the hydrogens to have slight positive charge and the oxygen to have a slight negative charge.

learn by doing

The interaction between a polar bond on water and polar bonds on hydrophilic molecules is given a special name — the hydrogen bond, because it involves a hydrogen that forms a bridge between the two molecules. Hydrogen bonds are fairly stable, so quite a bit of energy is released when they are formed. The release of energy helps hydrophilic molecules like glucose dissolve in water. Since hydrophilic molecules contain polar bonds, they are often referred to as polar molecules.

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Amphipathic Molecules

Molecules that contain a very polar part and a very nonpolar part are called amphipathic. The polar part interacts with water, forming strong interactions, while the nonpolar part doesn’t interact with water because of the hydrophobic effect. In order to accomplish this, amphipathic molecules usually undergo spontaneous self-assembly into structures that expose the polar part to water and keep the nonpolar section away from water. One example of amphipathic molecules are fatty acids.

Fatty Acids Molecule

The carboxylate group (COOH) on the left interacts strongly with water, while the remaining part of the molecule is very hydrophobic and is forced away from water. Fatty acids form structures in solution called micelles. These spherical structures have the hydrophilic part exposed to water on the surface of the sphere and bury the hydrophobic part in the center of the sphere.

Schematic of a spherical micelle.

You might be wondering why triglycerides are not amphipathic, given that they are similar to fatty acids, with a polar group of atoms and a nonpolar group. The reason is that the polar region of triglycerides interacts weakly with water because there is no free -OH group.

Have you ever filled up a glass of water to the very top and then slowly added a few more drops? Before it overflows, the water forms a dome-like shape above the rim of the glass. This water can stay above the edges of the glass because of the property of cohesion. In cohesion, water molecules are attracted to each other (because of hydrogen bonding), keeping the molecules together. Cohesion allows surface tension, the capacity of a liquid’s surface to resist being ruptured when placed under tension or stress. When water is sprinkled onto a solid surface, surface tension causes the water to remain in compact droplets instead of spreading out into a thin film.

Water drops exhibit cohesion. The water molecules attract each other strongly, and this force counteracts the force of gravity pulling water down against the leaf.

When you drop a small scrap of paper onto a droplet of water, the paper floats on top of the water droplet, even though the object is denser (heavier) than the water. This occurs because of the surface tension that is created by the water molecules. Cohesion and surface tension keep the water molecules intact and the item floating on the top. Many insects are specially adapted to exploit surface tension, which allows them to literally “walk on water.”

Water Strider

The surface tension of water helps insects, such as this water strider, remain afloat.

These cohesive forces are related to water’s property of adhesion, or the attraction between water molecules and other molecules. This is observed when water “climbs” up a straw placed in a glass of water. You will notice that the water appears to be higher on the sides of the straw than in the middle. This is because the water molecules are attracted to the straw and therefore adhere to it.

Capillary Action

If a thin glass tube is placed in water, the water moves up the tube in a process called capillary action. Capillary action is the result of adhesion of water to the sides of a glass tube and cohesion of water molecules to each other.

Cohesive and adhesive forces are important for sustaining life. For example, because of these forces, water can flow up tubes within plants. These tubes connect the roots of plants to their leaves, and carry water to plant tissues. Adhesion helps water cling to the walls of the tubes, and cohesion keeps the water in an intact column. Without these properties of water, tall plants would be unable to receive the water and nutrients they require, and they would die.

Imagine you have placed a metal pan containing water on the stove. You transfer heat energy to the pan. If you touch the metal pan after a few minutes, it is warm or even hot to the touch, but the water does not yet feel warm. The metal’s temperature changes much more quickly than that of the water, even though both substances are receiving heat from the same source. Temperature is a measure of the vibrational energy of molecules within a substance; it reflects how fast the molecules are jiggling around. If you add heat to metal, the molecules respond quickly with an increase in their “jiggling” and the temperature increases rapidly. If you add the same amount of heat to water, the molecules respond much less quickly. Why is water’s temperature so resistant to change?

Hydrogen Bonds in Water

Water has many hydrogen bonds; each molecule can form hydrogen bonds with up to four other molecules. It takes a lot of energy to break all of these bonds.

When water is heated, a large part of the heat energy goes into breaking the hydrogen bonds between the water molecules. Only a small part actually increases the kinetic energy of the water molecules. Imagine a rack of billiard (pool) balls. When the cue ball strikes them, energy is transferred and the balls “break,” rolling in every direction. What would happen if the balls were connected by rubber bands? They would not move nearly as much. Similarly, the hydrogen bonds among water molecules make it hard to increase their “jiggling.” As heat is added, hydrogen bonds are broken and water warms up, but due to the hydrogen bonding, the water’s temperature changes only slowly. When water cools down, it releases a great deal of heat as hydrogen bonds are re-established. This effect is particularly strong when water freezes; water molecules are joined in a regular crystal structure by stable hydrogen bonds. As these bonds form, heat is released to the surrounding environment. You may have noticed that snowy days are often not quite as cold as the dry clear days of winter. This is yet another example of the way that water moderates temperature.

We use detergents to remove oily dirt from things. We use dish detergent to remove the grease on dishes, laundry detergent for oils on our clothes, and shampoo for oils in our hair. Detergents make the hydrophobic oils soluble so that the dirt can be rinsed away. How does this happen?

All detergents are amphipathic molecules; they have a polar, water-loving (hydrophilic) part and a nonpolar, water-hating (hydrophobic) part, which allows them to dissolve in both water and oils. The chemical structure of a common detergent, sodium dodecyl sulfate (SDS), is shown below. The hydrophilic part of DS interacts favorably with water by hydrogen bonding and electrostatic (charge-charge) interactions between the negative charge on the DS and the partial positive charges on the polar water molecules. The hydrophobic part has no polar atoms to form favorable interactions with the water.

The molecular structure of sodium dodecyl sulfate (SDS), a common detergent.

When placed in water, detergents spontaneously form organized spherical structures called micelles. In a micelle, the hydrophilic part of the detergent is on the surface of the sphere and interacts with the water. The center of the sphere contains the hydrophobic part of the detergent, hidden from the water. A cross section image and a three-dimensional structure of a micelle are shown below. When a micelle comes in contact with oily (hydrophobic) compounds, the oils dissolve into the interior of the micelle and can be washed away with the micelle.

One of the ways that scientists can measure the pH of a solution is to use indicator paper. This is special paper that is infused with dyes that change color when placed in an acid or a base. The most simple indicator paper is called litmus paper. Litmus paper comes in two colors — red and blue.

• Red litmus paper turns blue in the presence of a base (it does not change color in the presence of an acid).
• Blue litmus paper turns red in the presence of an acid (it does not change color in the presence of a base).

In the presence of a neutral solution, red litmus paper remains red, and blue litmus paper remains blue.

If an acid gives a hydrogen ion (H⁺) in solution and a base accepts a hydrogen ion by giving a hydroxide ion (OH^-), you may be wondering what will happen when an acid and a base are combined. Let’s consider the combination of equal amounts of hydrochloric acid (HCl), a strong acid, and sodium hydroxide (NaOH), a strong base. When the hydrogen ion (H⁺) is released from hydrochloric acid, and the hydroxide ion (OH^-) is released from sodium hydroxide, the two ions combine to form water (HOH). Water, as you know, has a neutral pH, so the process of combining an acid and a base is called neutralization. Remember, in a neutral solution (like water) the number of hydrogen ions equals the number of hydroxide ions. The remaining sodium ion (Na⁺) from the sodium hydroxide and the remaining chloride ion (Cl^-) from the hydrochloric acid also stay in solution as dissolved table salt (NaCl). This process can be written as it is below:

Notice that the same four atoms (H, Cl, Na, and OH) are found on each side of the equation. Using this example we can generalize the process of neutralization as follows:

The process of neutralization also gives off heat, indicating that chemical potential energy is being released during the course of the reaction. Neutralization has many useful applications. One such application in the laboratory is to neutralize strong acids or bases so that they can safely be disposed of. As you will learn later in this course, the addition of acids and bases to the environment leads to ecosystem damage, so before a strong acid or base can be disposed of, it must be neutralized (to make water and salt) to prevent injuries or environmental damage. In your everyday life you may be familiar with acid and base neutralization through your lawn care and gardening activities. Grass grows best in a very mildly acidic soil (pH 6.5 to 7). So if your soil is too acidic (less than pH 6.5), you would need to add a compound like limestone (a basic mineral) to your soil to neutralize the excess acidity and correct the pH level. Likewise, if your soil is too basic (pH above 7), you would need to add sulfur, which interacts with water in the soil to form sulfuric acid, to help neutralize the excess base in the soil.

Another common application of neutralization is the standard volcano science fair project, where a mixture of vinegar (an acid) and baking soda (a base) are combined to make the volcano "erupt." In this case, the reaction releases some carbon dioxide gas, generating fizz and fun.

If you ever come into contact with a strong acid or base and receive a chemical burn, DO NOT attempt your own science experiment to try and neutralize the compound. The damage to your skin is already occurring and can be exacerbated by adding more chemicals; a vigorous neutralization reaction could cause further harm through the release of heat, causing a physical burn on top of the chemical burn already suffered. Your safest option is to wash the affected area under a heavy stream of running water, and to seek medical attention for your burn. The goal is to remove the agent causing the burn to prevent further damage.

Living organisms are quite sensitive to even small changes in pH. The chemical reactions of life are tuned to a specific and often narrow pH range; outside this range, the reactions will not proceed normally. Therefore, organisms have mechanisms that work to maintain a constant pH level. This is true both at the cellular level and at the level of the whole organism. Maintaining a stable pH in a living organism is an important part of homeostasis. Homeostasis refers to the ability of an organism (or cell) to maintain stable internal conditions despite constantly changing environmental conditions.

While maintaining a pH close to neutral is usually the goal of homeostasis, there are certain conditions and parts of organisms that are maintained at a lower (more acidic) pH. For instance, the process of digestion is aided by the presence of stomach acid (pH 2). Not only does stomach acid help to break down the compounds in our food, it also helps to prevent disease by killing many of the bacteria and viruses found in food and water. Lysosomes, digestive organelles found in eukaryotic cells, have an internal pH of about 5. Again this acidic environment is used to break down cellular food, waste, and even invading bacteria. Likewise, the surface of our skin is acidic (pH of 4.5 to 6), which helps to support the growth of our normal bacterial flora, as well as to help prevent the growth of pathogenic bacteria.

When the normal pH levels of the body are disrupted, there are detriments to the health of the organism. For instance, the female vaginal tract is moderately acidic, with a pH between 3.8 and 4.5. When the pH increases in this area of the body (becomes more basic), women are more prone to bacterial infections of the vagina. Conversely, if the pH decreases (becomes more acidic), women are more prone to yeast infections.

Example

Diabetic Ketoacidosis

A higher-stakes example of loss of pH regulation occurs in diabetic ketoacidosis. In people with diabetes, cells cannot take up glucose (sugar) from the blood efficiently. As a result, cells switch from using glucose (sugar) as a fuel source and use fatty acids (fats) instead. When fatty acids are broken down, ketone acids are produced as a by-product. In healthy individuals, a small amount of ketone acids are released by normal metabolic processes; for example, if you are losing weight, fat breakdown will add some ketone acids to your bloodstream. This poses no problem because your blood is buffered, and your liver and kidneys are able to remove the excess acids before they cause problems. However, in people with diabetes, chronic release of ketone acids can overwhelm these systems. Ketone acids build up in the blood and urine, leading to a condition called ketoacidosis. The presence of excess ketone acids lowers the body’s pH, leading to several health problems as detailed on the figure below. If the pH balance is not restored, diabetics in ketoacidosis can face serious harm and even death. Treatment consists of restoring proper insulin levels in the body (so that carbohydrates can be absorbed by cells and used as a fuel source) and ensuring proper hydration (to help the kidneys flush out the excess ketones).

Symptoms of Acidosis

This figure shows the symptoms of acidosis in the body broken down by organ system. Notice that the symptoms range from mild to severe. In the long term, these symptoms can become life threatening.

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While it is clear that the regulation of pH in living organisms is crucial to their survival, the pH in the environment is just as important to maintaining life on this planet. Different environments have different pH levels, and organisms that live in those locations have adapted to those conditions. When environmental pH levels are disrupted, the health and vitality of the ecosystem becomes threatened.

Example

Seawater

As you have learned, seawater is slightly basic at pH 8. The oceans and the organisms that live in them play a critical role in maintaining the balance of oxygen and carbon dioxide on this planet. You will learn more about this in the Photosynthesis / Cellular Respiration module in the Metabolism unit. With the increased burning of fossil fuels in the modern industrial society, more man-made carbon dioxide (CO₂) is being released into the environment than ever before. Much of this carbon dioxide is absorbed by the oceans. When carbon dioxide is absorbed into water, carbonic acid is produced. This then dissociates to produce bicarbonate ions and hydrogen ions, and the pH of the ocean is lowered. Acidification of the ocean threatens the health of the organisms that call the ocean home. Many marine life forms, including reef-building corals, are harmed or killed when ocean water is acidified. As carbon dioxide levels in the atmosphere continue to climb, there is great concern about the worsening impact of ocean acidification.

Effects of Acid on Coral Reefs

Figure A shows a healthy vibrant coral reef. Notice the bright colors and water clarity. Figure B shows a dying coral reef. Notice the dull, black color of the reef and the poor water quality. Coral reefs are made up of millions of tiny living organisms and provide shelter, food, and nesting grounds to other marine animals. The death of coral reefs due to ocean acidification and other factors is a matter of grave concern to marine biologists and to those who depend on ocean ecosystems.

In the Introduction to Chemistry unit, you learned that atoms are the building blocks of all matter. You also learned that atoms can be linked together with chemical bonds, to form molecules that have their own unique properties. In this unit, you will take a closer look at a special group of molecules that form the backbone of living structures: the biological macromolecules. Biological macromolecules are special molecules that contain carbon atoms covalently bonded with hydrogen atoms.

Atoms are the building blocks of all matter. Biological macromolecules are formed when atoms of carbon, hydrogen, oxygen, nitrogen, phosphorus, and other elements bond with each other in unique and varied ways. Biological macromolecules are the raw materials used to build living organisms.

There are four classes of biological macromolecules that we will study in this course: carbohydrates, lipids, proteins and nucleic acids. These macromolecules are probably already familiar to you, because they make up the nutrients you ingest every time you eat. In this way, you provide your cells with the building materials and energy necessary to sustain life. In the next unit, we will use these fundamental building blocks to form the cell, the first level of organization that shows all the characteristics of life.

In chemistry, the word “organic” has a special meaning. It is different from the grocery-store meaning, where “organic” refers to foods that are grown in a particular way and are free of pesticides. In fact, many of the chemical pesticides that an organic farmer would never use are actually organic molecules.

An organic molecule is any molecule that contains a carbon to hydrogen (C-H) covalent bond. They are often complex and many store a lot of chemical potential energy. Examples of organic molecules include glucose, methane, DNA, protein, and fat.

All the molecules discussed in the "Introduction to Chemistry" unit were inorganic molecules. Molecules like water, oxygen gas, carbon dioxide, and ionic salts like sodium chloride fall into this category. Most inorganic substances are relatively stable, simple, and store little chemical potential energy. What exactly are organic molecules? All organic molecules have several common properties that help distinguish them from inorganic molecules:

1. All organic molecules contain carbon atoms bonded to hydrogen (C-H bonds). Organic molecules often contain oxygen, nitrogen, phosphorus, or sulfur as well.
2. Atoms within organic molecules are connected by covalent bonds.
3. Organic molecules are modular. Smaller organic molecules (monomers) can be linked together to make larger organic molecules (polymers). Larger organic molecules consist of a carbon/oxygen/nitrogen/phosphorus skeleton (backbone) with other atoms branching off from this structure.
4. Organic molecules are typically produced by living cells and are found in large amounts only in living things or in their remains. However, it is important to remember that some molecules produced by living things are inorganic. Humans have developed ways to synthesize organic chemicals artificially.

In this module, you will learn more about how to recognize organic molecules. You’ll also explore in more detail the important characteristics of organic molecules.

All organic molecules contain carbon atoms covalently bonded to hydrogen (C-H bonds). They can also contain oxygen, nitrogen, or sulfur. In the next activity, you will practice determining whether or not a chemical structure is an organic molecule.

Functional groups are parts of organic molecules that have specific properties or functions. Because organic molecules can contain more than one type of functional group, a particular molecule may have multiple properties. Identifying functional groups in molecules is an important skill, because once you identify a molecule’s functional groups, you can predict many aspects of its biological behavior.

Functional groups can be divided into three groups based on their physical properties. There are the nonpolar groups, the polar groups, and the charged groups.

Nonpolar Functional Groups

Functional groups in this category are also referred to as hydrophobic (water-hating) groups. They only contain carbon and hydrogen, and lack electronegative atoms such as nitrogen, oxygen, and sulfur. Nonpolar functional groups are often found on amino acid side chains of proteins, and they also make up a major part of most lipid molecules. The hydrophobic nature of nonpolar functional groups often affects the shape of molecules containing these groups. For example, proteins will fold so that nonpolar groups are clustered together and are not in contact with water. Some lipids bury the nonpolar section of the molecule by forming lipid bilayers, which shape the boundaries of all cells.

The key nonpolar functional groups are:

Also, long chain alkanes, (CH₂)_n, found in lipids, are among the nonpolar functional groups.

Polar Functional Groups

Polar functional groups contain electronegative atoms like nitrogen (N), oxygen (O), and sulfur (S). The presence of electronegative atoms in a functional group results in an unequal distribution of charges on the atoms, causing the bonds to become polar. Because polar bonds interact favorably with water, compounds with polar functional groups also interact favorably with water, making them hydrophilic, or water-loving. In addition to interacting favorably with water, the polar atoms can also participate in chemical reactions and polar functional groups are usually responsible for the catalytic properties of enzymes.

The key polar functional groups are:

Some compounds contain both nonpolar and polar functional groups; molecules of this type are referred to as amphipathic molecules. Phospholipids and soaps are examples of amphipathic molecules.

Charged Functional Groups

Charged functional groups are acids, meaning that they form ions by the release of hydrogen ions (H+), which are also called protons. Depending on the specific functional group, these groups of molecules lose a hydrogen ion (or deprotonate) and become either charged or neutral as a result. Charged functional groups play key roles in biological systems. For example, many proteins bind to DNA (or RNA) by utilizing the electrostatic interaction between positive charges on the protein and negative charges on the DNA or RNA. Note that when these groups are in their uncharged state, they can be considered to be polar functional groups.

The key charged functional groups are:

A special case of the phosphate group is a phosphate diester, which links together nucleotides in DNA and RNA. The phosphate diester is always negatively charged at neutral pH.

Carbohydrates are organic molecules that consist of carbon, hydrogen, and oxygen atoms in a 1:2:1 ratio. The most abundant class of macromolecules found in living systems, carbohydrates are the primary source of energy in living systems. Large complex carbohydrates can be used to store energy. For example, a potato is full of starch, which is a complex carbohydrate that the potato plant uses to store energy. When you eat the complex carbohydrate, your body breaks the large molecules into their smaller subunits (sugars), which you will then use to fuel your own body’s energy needs.

Carbohydrates can also be used as structural building materials. Cellulose is an example of a complex carbohydrate used in plants for structural support. Within plant cell walls, cellulose molecules form chains that provide high tensile strength. In some plants, cellulose is also included in a secondary cell wall, which adds rigidity and waterproofing. This helps tree bark, plant leaf stalks, and other structures resist wind and other physical forces in the environment.

Office of Biological and Environmental Research, U.S. Department of Energy Office of Science. http://genomicscience.energy.gov

Cellulose, while indigestible to humans, is an important part of our diets because it makes up dietary fiber, which has been linked to lowered risk of diabetes and heart disease. In this module, you will take a closer look at the structure and function of these important macromolecules.

The paper you write on, the bowl of cereal you eat for breakfast, and the energy you use to walk up a flight of stairs all come from carbohydrates. Rice, wheat, and corn are some of humanity’s most important crops; these foods are the primary source of energy for much of our population. All three of these foods are high in carbohydrates.

A carbohydrate is an organic molecule that contains carbon, hydrogen, and oxygen. Carbohydrates are either simple (often referred to as sugars) or complex. Simple carbohydrates (sugars) are made up of only one or two sugar monomers. Each monomer has the proportion of carbon to hydrogen to oxygen in the ratio of 1:2:1, or (CH₂O). You can see why these compounds are called carbohydrates; in a monomer, each carbon is “hydrated.” Complex carbohydrates are made up of more than two sugar monomers linked together. Carbohydrates can be further subclassified, again on the basis of structure, depending on the number of monomers in each molecule: monosaccharides and disaccharides (simple carbohydrates) and polysaccharides (complex carbohydrates).

Simple carbohydrates are quickly and easily accessed to generate energy the cell can use, while complex carbohydrates are used to store energy for a longer period of time. Some complex carbohydrates are also used as structural components. Carbohydrates also play a role in cell signaling and recognition within multicellular organisms.

Indigestible carbohydrates, which cannot be degraded by human digestive enzymes, are referred to as dietary fiber. Cellulose, mentioned above as a major component of plant cell walls, is one of the largest contributors of dietary fiber. Pectin is another structural carbohydrate found in most plants, especially apples and citrus fruits, and is commonly used as a gelling agent to make jams and jellies. A diet high in fiber has several benefits. Dietary fiber plays a role in maintaining regular digestive functioning, slowing the absorption of sugar into the bloodstream, and reducing bad cholesterol. So the old saying “an apple a day keeps the doctor away” does have some truth to it, since there are proven health benefits associated with the consumption of foods that are high in fiber, like apples. Other foods that are high in fiber are oatmeal, popcorn, raspberries, black beans, lentils, and peas, to name a few.

For a quick boost of energy, simple sugars are the carbohydrate of choice; diabetics will oftentimes carry a sugary food or drink with them in case their blood sugar level drops too low. However, excessively high blood sugar levels can be equally dangerous. Accordingly, doctors routinely suggest that diabetics eat a diet high in fiber to help manage their diabetes, since fiber helps to slow the absorption of sugar into the bloodstream, which helps diabetics to prevent spikes in blood sugar. In contrast with simple sugars, complex carbohydrates are broken down by the body more slowly and energy is released in a stepwise fashion.

Lipids are a diverse group of macromolecules united by their hydrophobic, nonpolar nature. We are most familiar with the lipids known as fats. Fats are used to store energy for later use. They also provide structural support and cushioning for many animals. Some dietary fats are healthier than others. In this module, you will learn about the differences between saturated, unsaturated, and trans fats.

People are most familiar with fats, but there are other types of molecules that are not fats, but are lipids. Cholesterol is a familiar example of a lipid that is not actually a fat. You will learn more about cholesterol in this module as well.

Lipids include a diverse group of compounds that are united by two common features. First, they are largely nonpolar in nature. This is because they are hydrocarbons that include many nonpolar carbon-carbon or carbon-hydrogen bonds. Second, because lipids are nonpolar, they are also hydrophobic (water-hating), or insoluble in water.

Lipids perform many different functions in a cell. Cells store energy for long-term use in the form of fats. Lipids also provide insulation from the environment for plants and animals. For example, they help keep aquatic birds and mammals dry because of their hydrophobic nature. Lipids are also the building blocks of many hormones and are an important constituent of the cell’s plasma membrane. Lipids include fats, oils, waxes, phospholipids, and steroids.

Summary of Lipid Structures and Functions

Because lipids are such a diverse group of biomolecules, we will study them in four categories. Examine the following table for a general understanding of lipid structure and function.

Waxes are nonpolar lipids that form protective layers on plants and animals. For example, waxes cover the feathers of some aquatic birds to keep the feathers dry. Plants, on the other hand, often have leaves coated with waxes to prevent water from evaporating off the plant surface. Because of their hydrophobic nature, waxes prevent water from sticking on the surface of these structures.

Wax: "Esterified" Fatty Acid Chain

Chemical structure of cetyl palmitate, a typical wax ester.

The chemical structure of a wax is linked to its function. Waxes are the simplest lipids in nature, consisting of two long hydrocarbon chains linked in the middle by an ester group. It is this structure that enables waxes to function the way they do in living systems.

Steroids are a family of lipids based on a molecular structure with four fused carbon rings. This family of lipids includes many hormones and cholesterol. Hormones (such as estrogen and testosterone) are used by some animals as long-distance messengers. This means that they are produced by cells in one part of the body and affect cells in a different part of the body.

Steroids — including cholesterol, testosterone, vitamin D₂, and cortisol — are characterized by four fused hydrocarbon rings. The chemical groups attached to these carbon rings are what distinguishes different types of steroids: (A) shows a molecule of cholesterol; (B) shows a molecule of testosterone; (C) shows cortisol; and ( D) shows vitamin D₂.

Cholesterol is an example of a familiar steroid that plays many important roles in your body. While most people are familiar with cholesterol, they often don’t realize how important it is for healthy function. In fact, most of the cholesterol in your body is synthesized by your liver. Cholesterol has many functions. Cholesterol is used to build steroid hormones, including testosterone and estradiol, which are secreted by the sex organs. Cholesterol is also the precursor to vitamins D and K. Some cholesterol is converted to bile salts, which help in the absorption of fats from the digestive system into the body. Cholesterol is also used by animals to maintain the proper consistency of the cell membrane, which is the structure that surrounds every cell. Other organisms use different steroids for this function. For example, plants use a steroid called stigmasterol, while fungi use ergosterol.

A diet rich in saturated fats may contribute to formation of plaques in the arteries (atherosclerosis) and increase your risk of heart disease. To reduce this risk, it is recommended that you replace some foods rich in saturated fats (e.g. fatty cuts of pork, beef, and high-fat dairy products like butter) with foods that provide unsaturated fats (available in foods like olive oil, canola oil, seafood, and walnuts). Such a shift is believed to help improve blood cholesterol levels and may reduce your risk of cardiovascular disease.

Physical Properties of Saturated and Unsaturated Fats

In the diagram above, you see the physical behavior of two different triglycerides (with saturated and unsaturated fatty acids) at three distinct temperatures. Figure 1 shows that at a temperature of 0^oC (freezing), both types of fatty acids stack neatly. At 16^oC (Fig. 2), the unsaturated fatty acids lose the tightly stacked formation and become more mobile. At 70^oC, the saturated fatty acids also become mobile (Fig.3). At 27^oC (room temperature) and at 37^oC (body temperature), triglycerides with unsaturated fatty acids are liquid oils, whereas saturated fats remain solid.

Phospholipids are an important class of lipids found in the membranes of all cells and organelles. A phospholipid contains only two fatty acids attached to a glycerol, which in turn is bound to a phosphate group. Together, the phosphate and the glycerol make up the “head” of the phospholipid. The fatty acids make up the molecule’s “tail.” The phosphate group carries a negative charge and is therefore hydrophilic. The tail, on the other hand, is made up of nonpolar fatty acids and, like other lipids, is hydrophobic. Thus phospholipids, like fatty acids, are amphipathic. An amphipathic molecule has both a hydrophilic end and a hydrophobic end.

A phospholipid is made of two fatty acids and a phosphate group attached to glycerol.

For simplicity, phospholipids are often drawn as a circle to indicate the phosphate group and 2 chains to indicate the fatty acids.

Remember that hydrophilic molecules dissolve in water and hydrophobic ones do not. But phospholipids have a “split personality” in this regard. How do they behave in water? When small numbers of phospholipids are in an aqueous solution they will self-assemble into micelles, structures that exclude water molecules from the hydrophobic tails while keeping the hydrophilic head in contact with the aqueous solution. If enough phospholipids are present, they will form a bilayer. This is the favored formation because it is the most stable orientation for phospholipids in a water solution. View the animation that demonstrates the formation of micelles and bilayers.

With their “split personality,” phospholipids are able to play a very important role in biology. Phospholipids, together with other molecules in smaller quantities, form membranes that surround the cell and intracellular organelles such as mitochondria. The cell membrane is a fluid, semipermeable bilayer that separates the cell's contents from the environment. See animation below.

Although some cholesterol is essential for healthy physiological functioning, excess cholesterol can lead to health problems. Because cholesterol is hydrophobic, it cannot be easily transported through the body in the blood stream. A carrier is required to transport cholesterol around the body to the cells that need it. These carriers are called lipoproteins. You can think of lipoproteins as cholesterol boats that carry cholesterol to the body’s cells (where it can be used to build or repair cell membranes or synthesize steroid hormones). Lipoproteins that carry cholesterol to the cell for use are called low-density lipoproteins (or LDL). LDL is often referred to as “bad” cholesterol, because excess LDL levels have been linked to plaque deposition in the arteries, which can result in heart disease. Another type of lipoprotein, known as high-density lipoprotein (or HDL) transports cholesterol to the liver, where it is often turned into bile salts and excreted. HDL is often referred to as “good” cholesterol, because high blood concentrations of HDL have been linked to a decreased risk of heart disease. Exercise and proper diet can increase HDL levels. Increasing intake of unsaturated fats and decreasing intake of saturated fats is also a good strategy for increasing HDL levels.

Proteins are the most functionally diverse group of biomolecules we will examine in this unit. Critical to our diet, protein can be found in animal products like meats and cheeses, as well as in plant products like beans and grains. Kwashiorkor, which causes a distinct swelling of the abdomen, is often seen in malnourished children who lack sufficient protein in their diets. Proteins are also found in many toxins, such as the incredibly poisonous toxin produced by the bacterial species Clostridium botulinum. Studies have shown that just one teaspoon of this poison, which is a protein, would be enough to kill 20 percent of the world’s population! This module will take a closer look at the structure of a protein and examine how protein structure enables such a wide range of diverse functions.

Proteins are macromolecules built from amino acids. There are 20 different amino acids that can be joined in a myriad of ways to produce molecules with an enormous variety of possible structures that can perform a huge number of critical cellular functions. The following list represents just a sampling of the many things proteins can do in living systems.

1. Proteins can catalyze chemical reactions by accelerating the rate at which chemical reactions take place in the cell. Proteins that catalyze reactions are called enzymes.
2. Proteins play a role in the storage, replication, transmission, and regulation of genetic information (DNA). Some proteins bind to DNA and either reduce the expression of a gene, or activate the expression of a gene.
3. Proteins can help move substances in and out of the cell. These proteins can be embedded in the cell membrane, where they act as transporters.
4. Some soluble proteins can transport materials throughout the body. Hemoglobin is a protein that is found in high concentrations in red blood cells. Hemoglobin carries oxygen from our lungs to our tissues.
5. Proteins can recognize specific molecules. Protein receptors found in the lining of your nose recognize and bind to chemicals in the air, which triggers a message to the brain indicating the presence of a certain smell.
6. Proteins can facilitate mechanical movement. Special proteins found in muscle cells use the energy in ATP to flex your muscles.
7. Proteins can help maintain structure in an organism. The cellular cytoskeleton consists of proteins that form long fibrous scaffolding in cells that helps the cell maintain its shape.

Take a look at this diagram to see even more ways that proteins are used in your body.

Source: The Structures of Life, National Institute of General Medical Sciences.

Amino acids are the building blocks of proteins. A protein is composed of a series of amino acids attached end-to-end via covalent bonds. Consequently, a protein looks like a string of beads, with each bead representing an amino acid. The bond between the amino acids is referred to as the peptide bond.

Amino acids, represented here by circles, are the building blocks of proteins. When amino acids are attached to each other via peptide bonds, they form a protein. Proteins can be made up of a number of different amino acids, represented in this figure by the open and filled circles.

An amino acid is a small organic chemical that is made up of four parts. There is a nitrogen-containing amino group on one end of an amino acid. The other end of an amino acid has a carboxylic acid group. These two groups (the amino group and the carboxylic acid group) are the reason for the name “amino acid.” The amino and carboxylic acid groups are linked by a single carbon atom called the alpha carbon. Finally, there is a variable “R group” also attached to the alpha carbon. The amino acids differ in the nature of the R group that is attached to the central alpha carbon. There are 20 different R groups commonly found in nature. In this way, all amino acids are identical except for the different R groups (also called side chains) attached to the alpha carbon. The properties of different proteins depend entirely on the sequence, or arrangement, of the amino acids.

There are many ways to represent an amino acid. Take a look at some of the representations below.

This is a building block diagram.

This image reminds you that the blocks are representing chemical structures.

Two amino acids are shown: alanine and serine. The building block diagram for each amino acid is on the left and the chemical structure is on the right. Note that only the side chain (R group) differs between the two: in alanine, it consists of a nonpolar CH3 group; in serine, one of the hydrogens has been replaced by a polar -OH group

Proteins are built when amino acids are linked end-to-end by covalent bonds. The covalent bonds that link amino acids are called peptide bonds. A peptide bond is formed when the amino group of one amino acid reacts with the carboxylic acid of another amino acid. After a peptide bond forms, the three conserved parts of the two amino acids (the nitrogen group, the alpha carbon and the carboxylic acid) are all linked, forming the main chain, or backbone, of the protein. The variable side chains of each amino acid (the R groups) project out from the main chain.

Two amino acids join to form a dipeptide. Longer chains of connected amino acids are often called polypeptides. When polypeptides are synthesized, new amino acids are added only to the carboxylic acid end of the existing chain. A completed polypeptide is directional; it has two different ends. One end has a free amino group, while the other end has a free carboxylic acid group. When amino acids in a protein are counted, the numbering starts with the amino acid that has the free amino group. The last amino acid is also the last one that was added when the chain was built: it has a free carboxylic acid group.

Peptide bond formation. The left side shows a building block representation; the right side shows chemical structures. Note that the serine is flipped upside down in the right diagram for ease of presentation. The amino group of the second amino acid (serine) forms a peptide bond with the carbon that is part of the carboxylic acid group of the first amino acid (alanine), releasing a water molecule. The atoms that become the water molecule are highlighted in yellow. There is now a dipeptide ("di" means "two"). The resultant dipeptide consists of a continuous chain of main-chain atoms (pink highlight), from which the side chains project. When building a dipeptide, any pair of amino acids can be linked together in any order. This variability and the different chemical properties of each amino acid result in a vast number of very different proteins with very different functions.

The order of the amino acids in a particular protein is determined by information encoded in the cell's genes, and the order of amino acids is referred to as the sequence of the protein. An example of a protein sequence is shown below where the one-letter abbreviations are used for each of the 20 amino acids used in cellular protein synthesis. By convention, the first amino acid is at the end with the free amino group and the last amino acid is at the end with the carboxylic acid group.

Example

Human Myoglobin

The linear chain of amino acids will spontaneously fold into a three-dimensional shape, which is usually the active form of the protein. For example, look at the drawing of the three-dimensional structure of myoglobin (shown on the left). You can manipulate the 3D structure using the Jmol image on the right.

Many folded proteins bind small organic molecules that assist the protein in performing its function. For example, the heme group in myoglobin (colored gray in the right image) is not part of the protein chain, but fits within a pocket in the myoglobin protein. Myoglobin is responsible for binding oxygen in muscles. Heme groups also are present in the oxygen transport protein, hemoglobin.

Protein Folding

Proteins spontaneously fold to form their functional three-dimensional shape, reaching the lowest energy state, because this is the most stable state. The folding process can be reversible, meaning that a folded protein can unfold and then refold. However, unfolding can also be irreversible, where the unfolded protein chains tangle with each other, forming an aggregate and precipitating out of solution. This is often referred to as a denatured state. Conditions that cause proteins to unfold and denature are extremes of temperature and pH. Cooking denatures proteins by heating so they unfold and denature. The same effect occurs when proteins are exposed to the low pH in your stomach. This helps your body digest the proteins found in your food, and it helps kill ingested bacteria and viruses.

The folded structure of one particular protein is similar for all molecules in solution. Heating the sample can cause the protein to unfold. In the unfolded state, each molecule has a different shape. The unfolded protein can either refold, or the chains can aggregate or tangle, forming the insoluble denatured form. The polypeptide sequence is the same for all three forms of the protein.

learn by doing

The Hydrophobic Effect on Folding

Although many factors stabilize the final shape of a protein, the most important factor is the hydrophobic effect. Amino acids with nonpolar (hydrophobic) side chains are driven into the central core of the protein because they are repelled by the water. This is known as the hydrophobic effect, and it results in proteins that have amino acids with hydrophilic side chains on the surface of the protein. The folded protein reaches the lowest energy state, which is the most stable, by folding in a way that will optimize the burial of nonpolar amino acid side chains while still leaving the polar groups on the surface. Therefore, the shape of the folded form of the protein depends on the order of the hydrophobic amino acids in the protein.

Example

Consider a short 12 amino acid protein consisting of polar (white) and nonpolar (black) amino acids. This polypeptide will fold to bury most of the nonpolar amino acids, removing them from contact with water, giving the lowest energy state. Other structures are possible, but these will be higher energy (and consequently less stable) because they expose more nonpolar amino acid side chains to water.

The unfolded form of a 12 amino acid peptide is shown on the left. Notice that the first amino acid is polar, followed by a nonpolar one, and then two polar ones. Two possible folded structures are shown on the right. The top structure exposes four nonpolar side chains to the water, while the lower structure only exposes three nonpolar side chains to the water. This indicates that the lower structure would be the most stable folded structure. The red line shows the path of the main-chain atoms.

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The biological function of most proteins involves binding to something else. The binding event may be the first step in transport, signaling, regulation, or an enzyme-catalyzed reaction. Molecules that bind to proteins without being modified are called ligands. Although ligands are usually small molecules, they can also be larger than the protein to which they are binding. For example, when proteins bind to DNA, it is the DNA that is the ligand. Oxygen is a ligand when it binds to hemoglobin (a protein) during oxygen transport to the tissues. Molecules found on the surface of bacterial cells are ligands when antibodies (proteins) in your blood bind to them during an immune response. Sometimes ligands are given special names to remind us of their function. For example: enzyme inhibitors are ligands that bind to and inhibit enzymes; antigens are ligands that are recognized by antibodies (which are proteins).

The ligand binds to the protein by interacting with amino acids in the protein’s binding site.Binding proteins have binding sites for their ligand (L).

Binding proteins have amino acids in their binding site that are complementary to the ligand. Generally, a higher degree of complementarity leads to tighter binding and a more specific interaction. The molecules can be complementary in these different ways:

• The shape of the ligand matches the shape of the ligand binding pocket on the protein. The better the match, the stronger the bond between the ligand and the protein.
• Any charges on the ligand molecule can be aligned close to opposite charges on the protein's binding site. Remember, opposite charges attract each other.
• Hydrogen bonds often form between the ligand and the protein binding site.
• Nonpolar ligands bind more favorably to nonpolar surfaces on the protein.

The interactions between proteins and their ligands are incredibly diverse, but they all share some basic ground rules. Protein-ligand binding is:

• Reversible — bound ligands can be released by the protein.
• Concentration dependent — the level of binding depends on the ligand concentration. As the ligand concentration increases, so does the amount of protein bound.
• Limited — once all of the proteins are ligand bound, no additional ligand can bind and the protein is said to be saturated.

Enzymes are proteins that have the ability to bind substrate in their active site and then chemically modify the bound substrate, converting it to a different molecule — the product of the reaction. Substrates bind to enzymes just like ligands bind to proteins. However, when substrates bind to enzymes, they undergo an enzyme-induced chemical change, and are converted to products.

The substrate binds to the enzyme by interacting with amino acids in the binding site. The binding site on enzymes is often referred to as the active site because it contains amino acids that both bind the substrate and aid in its conversion to product.

Compare the protein-ligand interaction to the enzyme-substrate interaction. Notice that both binding proteins and enzymes have binding sites for their ligands (L) and substrates (S), respectively. This area of the enzyme is called the active site because it also contains amino acids that are important for the conversion of substrate to product.

You can often recognize that a protein is an enzyme by its name. Many enzyme names end with “-ase.” For example, the enzyme lactase is used to break down the sugar lactose, found in mammalian milk. Other enzymes are known by a common name, such as pepsin, which is an enzyme that aids in the digestion of proteins in your stomach by breaking the peptide bonds in the proteins.

Enzymes are catalysts, meaning that they make a reaction go faster, but the enzymes themselves are not altered by the overall reaction. Examine this image to see how enzymes work.

Simplified enzymatic reaction. The substrate reversibly binds to the active site of the enzyme, forming the enzyme-substrate (ES) complex. The bound substrate is converted to product by catalytic groups in the active site, forming the enzyme-product complex (EP). The bound products are released, returning the enzyme to its unbound form, ready to catalyze another round of converting substrate to product.

The amino acids in the active site of enzymes play two roles, and sometimes those roles overlap. Some of the amino acids in the active site are responsible for binding of the substrate and others are responsible for facilitating the chemical reaction. Enzymes are generally quite specific for their substrates. Although lactase and pepsin both catalyze the same type of reaction, breaking a bond using water (hydrolysis: "hydro" means "water" and "lysis" means "to break"), lactase only functions when lactose is its substrate and pepsin can only break peptide bonds.

Enzymes catalyze many different types of chemical reactions. Some of the reactions are synthetic and result in products that are more complex than the original substrates. This is often done by binding two substrates together. Synthetic metabolic pathways like this are called anabolic pathways.

Other enzymes catalyze reactions that reduce the substrate to simpler products. These enzymes catalyze reactions in catabolic pathways.

Example

An example of an enzyme that is involved in catabolism is lactase. Lactase is produced in the intestinal tract of mammals and breaks the sugar in milk, lactose, down into the monosaccharides glucose and galactose so that they can be metabolized to produce energy.

The enzyme lactase breaks lactose into the monosaccharides galactose and glucose by adding a water molecule to the bond between the two sugars.

Unfortunately, in many adults the ability to produce lactase is diminished. Without adequate lactase, ingested lactose from milk and cheese is not broken down and absorbed in the small intestine. Instead, the lactose goes to the large intestine, where it is converted into large volumes of carbon dioxide (CO₂) gas by the bacteria in the large intestine. These individuals are lactose intolerant and should avoid eating foods with high milk content.

did I get this

In all chemical reactions, there is an initial input of energy that is required before the reaction can occur. If this initial energy requirement (called the activation energy or energy barrier) is small, then the reaction will happen quickly and easily. If the activation energy is large, then the reaction will take longer to occur. Enzymes function to reduce the activation energy required for a chemical reaction to occur.

First, the enzyme binds to the substrate and slightly distorts its shape. The change in shape activates the substrate molecule and decreases the total activation energy required for the substrate to be turned into product. As the number of activated substrate molecules increases, so does the conversion of substrate to product. An analogy for this effect is a ski hill, with skiers at the bottom of one side of the hill representing substrates, skiers on the top of the hill representing activated substrates, and the products being the number of skiers that ski down the other side. If the height of the hill is lowered (due to the presence of the enzyme), then more skiers can make it to the top, increasing the number that ski down to become products.

A noncatalyzed reaction is shown on the left and an enzyme-catalyzed reaction is shown on the right. The enzyme reduces the energy barrier required to activate the substrate, allowing more substrates to become activated, which increases the rate of product formation. Note that the energy difference between the substrate and the product is not changed by the enzyme.

The activity of an enzyme (its ability to convert substrate to product), depends on a number of parameters that are listed below. Many of these parameters can help control the activities of enzymes to optimize the utilization of cellular resources.

• Temperature: As the temperature increases, the kinetic energy of the substrate molecules increases, allowing more substrate molecules to become activated and increasing the reaction rate. This is equivalent to more skiers having the energy to surmount the activation energy and reach the top of the hill. Many enzymes have optimal activity at the temperature of the organism. However, there is a limit to how much you can increase the rate of the reaction by changing the temperature. If the temperature is too high, the enzyme unfolds, denatures, and becomes inactive.
• pH: Protein structure can be affected by the pH of the solution surrounding it. If a protein group that is important for substrate binding or catalysis can be protonated or deprotonated, then changing the pH is likely to affect the enzyme activity. Different enzymes are functional at different pH levels. Pepsin is a digestive enzyme secreted by the stomach lining that is activated by the low pH in the stomach. Salivary amylase, on the other hand, is denatured and nonfunctional in the stomach environment.
• Substrate concentration: As the substrate concentration increases, the number of substrate molecules that bind to the enzyme also increases. This leads to increased substrate activation.
• Presence of inhibitors: Inhibitors can reduce the activity of enzymes through two different mechanisms. Competitive inhibitors bind to the active site and prevent the substrate from attaching to the binding site. Since less substrate can bind to the enzyme, the activity is reduced. Noncompetitive inhibitors (also called mixed-type) do not bind to the active site, but bind elsewhere on the enzyme. However, the bound inhibitor changes the shape of the active site, reducing the activity of the enzyme. Drugs to treat disease often inhibit enzyme activity. For example, one of the drugs used to treat HIV is a competitive inhibitor of a specific viral enzyme, while another anti-HIV drug is a noncompetitive inhibitor of a different viral enzyme.
• Presence of activators: Activators, like noncompetitive inhibitors, also change the shape of the active site by binding elsewhere on the enzyme, but in this case the enzyme is converted from an inactive form to an active form. In this way, activators increase enzyme activity.

In 1953, a group of scientists contributed to one of the most significant scientific discoveries in history when they determined the structure of DNA, a nucleic acid that is the hereditary material in a cell.

Nucleic acids are macromolecules that carry out two main functions in the cell: storage of genetic information and synthesis of proteins. Two types of nucleic acids specialize in these functions: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material that stores information for making proteins in all living organisms. Some viruses store their genetic information in RNA instead of DNA. This may seem like an exception to the universal use of DNA as genetic material; however, recall that viruses are not cellular, and are not considered living organisms.

A nucleic acid consists of a chain of nucleotides. There are different kinds of nucleotides that can be linked to build the different nucleic acids. DNA is probably the most familiar nucleic acid, but in this module, you will also learn about RNA. The nucleotides that are used to build RNA molecules are different from the nucleotides that are used to build DNA. You'll also take a look at a very special nucleotide — ATP, which acts as the energy currency of the cell.

All DNA found in living organisms comes in sets of two polymers or strands, usually referred to as double-stranded DNA. Some viruses are an exception to this rule and contain single-stranded DNA as their genetic material. The discovery that DNA structure is a double helix (two strands wound around each other) is considered one of the greatest discoveries in science. Understanding of the structure of DNA opened up a whole new realm of biological and biomedical research (molecular biology) and led to the development of new technologies in science and medicine. Let’s examine the structure of DNA using the activity below.

DNA structure is an antiparallel double helix: the two DNA strands run in opposite directions. The sugar-phosphate backbone is on the outside, and the bases are on the inside of the helix. The two strands are held together by base pairing: hydrogen bonding between specific bases. Adenine (a purine) always pairs with thymine (a pyrimidine); guanine (a purine) always pairs with cytosine (a pyrimidine). These base pairing rules (A-T, G-C) are very important to the structure and function of DNA.

Two of the most important nucleic acids are DNA and RNA. DNA contains the instructions for building proteins. RNA, on the other hand, is involved in actually building the proteins. Because of these different functions, the structures of the two molecules are very different.

Compare DNA and RNA and answer the questions about these structures.

In this module you learned that nucleotides are the monomers that make up the nucleic acid polymers. Adenosine triphosphate (ATP) is a nucleotide. It consists of a single adenosine (the base adenine and the sugar ribose), linked to three phosphate ions. However, ATP has another essential function: it acts as a general energy source for most cellular activities. You will learn in detail about ATP in the unit dedicated to metabolism.

ATP is a relatively unstable molecule; consequently, it is never used for the long-term storage of energy in the cell. This job goes to other more stable compounds, like fats and sugars. However, ATP is specialized for direct and rapid transfers of energy. The bond between the second and the third phosphates can be broken in a reaction producing ADP (adenosine diphosphate). The energy released in this reaction can be used for chemical reactions or cellular work. Conversely, if there is a surplus of energy, specialized reactions can produce ATP from ADP and phosphate, storing the energy temporarily before being used for other processes.

The ADP generated when energy is released is recycled back to ATP using energy gained from the metabolic process. Large amounts of ATP are consumed while providing energy for biological functions.

The cell is the first level of organization that exhibits all the properties of life. Made up of biological macromolecules, the cell’s unique structure enables it to carry out the functions of life.

In the "Biological Macromolecules" unit, you explored matter and learned how atoms can be combined to form molecules that, through their own unique structures, are able to carry out specific functions. You learned that proteins, such as enzymes, are able to function like little molecular machines. However, enzymes and other biological macromolecules made of matter do not possess the properties of life. In fact, it is only after we combine these molecular building blocks to form a cell that we finally see the emergent property of life. Take a moment to review examples of each level of organization forming these building blocks using the activity below.

One of the hallmarks of living systems is the ability to maintain homeostasis, or a relatively constant internal state. The cell is the first level of complexity able to maintain homeostasis, and it is the unique structure of the cell that enables this critical function.

In this unit, you will learn about the cell and all the parts that make it functional. You will also focus on the cell membrane, which is the structure that surrounds the cell and separates its internal environment from the external environment. This separation enables the cell to maintain homeostasis and exhibit the emergent property of life.

The microscopes we use today are far more advanced than those used in the 1600s by Antony van Leeuwenhoek, a Dutch shopkeeper who had great skill in crafting lenses. Despite the limitations of his now-ancient lenses, van Leeuwenhoek observed the movements of bacteria, other single-celled organisms, and sperm. He labeled these moving microbes “animalcules.”

In a 1665 publication called Micrographia, experimental scientist Robert Hooke coined the term “cell” for the box-like structures he observed when viewing cork tissue through a lens. Later, he confirmed van Leeuwenhoek’s 1678 discovery of bacteria and protozoa. Later advances in lenses and microscope construction enabled other scientists to see some components inside cells.

By the late 1830s, scientists had closely examined many plant and animal tissues under the microscope. Comparing notes, botanist Matthias Schleiden and zoologist Theodor Schwann realized that cells were found in every tissue they had studied. They proposed the Unified Cell Theory, which states that all living things are composed of one or more cells, and that the cell is the basic unit of life. You, for instance, are made of approximately 60 trillion cells, all of which originated from one single cell, the fertilized cell produced when an egg from your mother was fertilized by the sperm cell from your father.

However, there were still controversies between those who believed in the existence of a vital force able to “create” life (spontaneous generation) and those who supported biogenesis, which claims that living cells can arise only from pre-existing cells. A series of experiments by Louis Pasteur and Rudolf Virchow showed that living organisms could only come from other living organisms. The currently accepted tenets of Cell Theory are:

1. All known living things are composed of one or more cells.
2. All new cells are created by pre-existing cells dividing in two and reproducing.
3. The cell is the most basic unit of structure and function in all living organisms.

Modern cell theorists assert that all functions essential to life occur within the cell and that during cell division the cell contains and transmits to the next generation the information necessary to conduct and regulate cell functioning.

Using special technology, biologists can capture images of living cells. The yellow and blue fibers in these cells are made of proteins and the green circles in the middle are nuclei (singular: nucleus), which hold the cell’s DNA. Image by: Torsten Wittmann, NIGMS Image Gallery.

In spite of the fact that all cells share certain characteristics, there is incredible diversity in structure and function among different cells. The human body alone contains trillions of cells of more than 200 different types, each with a unique structure and function. Cells are categorized into two types: Prokaryotes are small, simple, single-cell organisms; bacteria are the most prevalent kind. Eukaryotes are larger, and most often they are multicellular organisms, including plants, animals, and fungi. Eukaryotic cells are about 15 times wider than the typical prokaryotic cell, and up to 1,000 times greater in volume. The images below show examples of a prokaryote and single-celled eukaryotic organisms.

Prokaryotic MRSA Bacteria Cells Methicillin-resistant Staphylococcus aureus (commonly known as MRSA) is an antibiotic-resistant of bacteria, shown here in yellow. These bacteria are being ingested by a white blood cell, shown here in purplish blue. Source: National Institute of Allergy and Infectious Diseases /National Institutes of Health (NIAID/NIH)

Eukaryotic Single-Celled Organisms These two cells are both single-celled organisms, also known as protists. The Didinium (bottom right) is stalking the Paramecium (top left), and will eventually catch and eat the larger cell. Image by: Gregory Antipa (San Francisco State University).

You have already learned that cells are made up of organelles, molecules, atoms, and subatomic particles. These parts assemble into various structures to perform specific functions within the cell. Organelles are specialized structures formed when a specific set of molecules bonds, providing a subunit within a membrane-like enclosure that performs particular functions within the cell. Some structures are the same for both prokaryotic and eukaryotic cell types and some structures are different. The remainder of this page will focus on a handful of structures that all cells have in common. Then, later in this module, you will learn about the structures and characteristics of each cell type in more detail.

Structures Common to All Cells

There are several parts (referred to as structures) common to all cells regardless of the cell type. All cells are surrounded by a cell membrane. The cell membrane provides a barrier between the interior and exterior of the cell and it regulates the flow of substances in and out of the cell. All cells also have cytoplasm, which is the fluid that occupies the space inside the cell. Cytoplasm is the space in which the chemical reactions that enable life take place. All cells also contain DNA, which is often called the “master molecule” of the cell because it contains the instructions for synthesizing all of the cell’s proteins. As you already know, proteins are the raw materials used to build many important structures in living systems. Finally, both prokaryotes and eukaryotes contain ribosomes. Ribosomes are the molecular machines that use the instructions contained in the DNA to build all the proteins needed by the cell.

The following table summarizes the major structures found in cells and the primary function of each structure. In addition, it lists the types of cells in which each structure is found. (There are many other important structures and features of cells. The table below shows only the most important structures.)

The Most Important Structures Found in Prokaryotic and Eukaryotic Cells

By University of Maryland University College CC-BY-NC

The essential differences and similarities among prokaryotic and eukaryotic cells are:

• All cells contain DNA (chromosomes), membranes, cytoplasm, and ribosomes.
• Prokaryotes do NOT contain a nucleus or any other organelle.
• Chloroplasts exist only in eukaryotic plant cells.

Check your understanding of cell structures with the following activity and then learn more about the structures and characteristics of each cell type on the next page.

Every cell on Earth belongs to one of two categories:

1. Prokaryotic cells
2. Eukaryotic cells

Prokaryotic cells were the first cells to appear on our planet. All prokaryotes alive today are unicellular (one-celled), and include bacteria (singular form is "bacterium") and archaea (singular form is "archaean"). Prokaryotes are small cells that don't have a nucleus or membrane-bound organelles.

Eukaryotic cells appeared 1.5 billion years after prokaryotes. The main difference between the two is that eukaryotes have a central control structure, called the nucleus (plural form is "nuclei"), where DNA is housed. In prokaryotes, the main DNA molecule (bacterial chromosome) is present in a region called the nucleoid, but the nucleoid lacks a surrounding membrane. Smaller DNA molecules called plasmids can be also found in prokaryotes. Prokaryotic DNA is circular, in contrast to the linear structure of eukaryotic DNA.

Both eukaryotic and prokaryotic cells have a cell or plasma membrane, which surrounds and defines the inner environment of the cell. The cell membrane is made of a phospholipid bilayer containing a variety of proteins and additional components. The cell membrane is responsible for mediating interactions between the cell and its environment. The Cell Membrane module contains a more detailed discussion of the structure and function of the cell membrane.

Typical Animal Cell (Eukaryotic)

Bacteria Cell (Prokaryotic) Note: these images are not drawn to scale. A typical eukaryotic cell is 10 times bigger than the typical prokaryotic cell.

Prokaryotic cells have a simpler structure than eukaryotic cells, and they range in diameter from 0.1 to 5.0 µm (micrometers). Most prokaryotes have a protective layer called the cell wall that is made of peptidoglycan, which is a combination of polysaccharides and amino acids. Prokaryotes also have a cell membrane and cytoplasm. Many prokaryotes also have external appendages such as a flagellum. The cytoplasm contains the DNA and the ribosomes, where protein synthesis takes place. Several types of RNA are involved in the process of protein synthesis, and ribosomal RNA (rRNA) is the main component of ribosomes. Both prokaryotes and eukaryotes have ribosomes, but they are different. Prokaryotic ribosomes are smaller and lighter than their eukaryotic counterparts.

Comparison of cell sizes

Relative sizes of cells and their contents. Notice that the scale shown is logarithmic.

Note that certain abiotic entities such as viruses and prions (infectious proteins causing diseases such as mad cow disease) are also studied in biology. However, they are not cells, and while they may exhibit certain characteristics of life, they do so only in certain conditions.

All eukaryotes contain a nucleus. Animals and plants are familiar eukaryotes; in fact, all large complex organisms are eukaryotes. Fungi (the singular form is "fungus"), which include molds and mushrooms, are also eukaryotes. There are even single-celled eukaryotes, called protists. All eukaryotes have a nucleus, but they can also have other cell structures in common.

One simplified but useful analogy of a cell is that of a factory. Just as in a factory, cells have a wall or membrane providing a protective enclosure, a planning center where the product blueprints are stored, a source of energy, an assembly line for production, packaging and shipping facilities, storage facilities, etc.

The Plant Cell as a Factory

In this visual, a plant cell is compared to a factory. Each functional unit of the factory is compared to a cellular organelle. Even though cells can have many different functions, the function often relies on the production of different types of proteins. In this way, a cell is like a protein-producing factory. We will refer back to this analogy as we discuss the functions of different cellular organelles.

Organelles

Eukaryotic cells contain compartments with specialized functions called organelles. Organelles are surrounded by membranes. Organelles are similar to the specialized work areas in the factory above. Because a cell is a protein-producing factory, we can take a closer look at the different organelles and see how they function toward this goal.

Nucleus: Control Center

The nucleus is the control center of the cell and it stores the DNA, which contains the instructions for how to build all the protein products required by the cell. The nucleus is like the factory command center, which stores the instructions needed to build its product. A single molecule of DNA is called a chromosome. The chromosomes are like the different books in the factory’s control center. The nucleus is surrounded by a double-layered membrane called the nuclear envelope. The nuclear envelope is studded with pores that allow information from inside the nucleus to enter the cytoplasm. You can imagine that a factory command center would not be very effective if it did not have doors or windows through which to pass information to the rest of the factory.

Ribosome: Protein Production

There are several important structures found within the nucleus. The most visible of these is the nucleolus. In contrast to other organelles, the nucleolus is not bound by a membrane. Instead, it is an aggregate of molecules where ribosomes, another type of nonmembranous organelle, are assembled. Most organelles, including ribosomes (after they are built in the nucleus), are found in the cytoplasm, which is the substance found between the nucleus and the cell membrane (number eight in the cell factory diagram). The cytoplasm is analogous to the factory floor, where all the work takes place.

Mitochondria: Power Plant

All this work requires energy. Most factories need some sort of power plant that converts fuel into a form of energy that can be captured to do work. In the cell, this job is accomplished by organelles called mitochondria (singular form is "mitochondrion"), which take fuel in the form of sugar (glucose) and convert it to usable energy — ATP.

Chloroplasts: Sugar Production

Plant cells have an additional type of organelle — chloroplasts, which exist only in plant cells — involved in energy transfer. The chloroplasts provide sugar. Chloroplasts capture energy from the sun and use that energy to build sugar molecules. Mitochondria then harvest the energy stored in the sugar molecules and use it to do work. The chloroplasts and mitochondria are the organelles responsible for providing energy for all cellular functions.

Endoplasmic Reticulum: Product Assembly

Factories often have assembly lines that put together the company’s product. In the cell, proteins and other cellular components are put together, or assembled, by the endoplasmic reticulum (ER), a series of sacs and tubes. In eukaryotes, ribosomes are associated with the "rough ER," which gets its name from the beaded appearance that the ribosomes give it. The smooth ER (without ribosomes) can have different functions depending on the cell type, but it is often the site for the synthesis of lipids.

Vacuoles: Storage

The Golgi apparatus is the packaging and shipping center of the cell, where the proteins that were built by the ER assembly line are delivered to different parts of the cell, or in multicellular organisms, to different parts of the body. Often the Golgi apparatus packages proteins in vesicles and vacuoles, which are membrane-bound sacs that function in storage and transport. Vesicles are specialized for transport and some other functions. Their membranes can fuse with the plasma membrane, allowing them to empty their contents into the extracellular space. Vesicles also may fuse with the membranes of the endoplasmic reticulum and Golgi apparatus, allowing them to empty their contents into those organelles. Lysosomes are specialized vesicles found only in animal cells. Lysosomes contain powerful digestive enzymes that can recycle cellular parts or destroy external invaders. Vacuoles are specialized mainly for storage. Their membranes do not fuse with the membranes of other cellular components.

Both animal and plant cells are eukaryotic cells. However, they both contain some specialized structures. Plants have chloroplasts and a rigid cell wall. Chloroplasts are unique organelles able to harvest solar energy to make sugars from carbon dioxide. This process, called photosynthesis, is the basis of life as we know it on our planet. This process is possible due to the presence of special pigments, called chlorophylls, which are found in the chloroplasts.

The cell wall is a porous structure that protects, supports, and gives shape to the cell. The plant cell wall is different from that of prokaryotes, and it is mainly formed by polysaccharides, particularly cellulose. Plant cells can also have a central vacuole, which can be a place of storage, degradation, defense, and even physical support for the cell. Even though plants have a cell wall, this does not mean they don’t have a cell membrane. All cells have a cell membrane. Some, like plant cells, just have a cell wall as well.

Eukaryotic Plant Cell

A typical eukaryotic plant cell. Compare this to the image of the animal cell. Notice that each plant cell has a cell wall, chloroplasts, and a central vacuole, but lacks cilia, lysosomes, and a centrosome.

Eukaryotic Animal Cell

A typical eukaryotic animal cell. No cell looks exactly like this one, but this figure orients you to the organelles and other components discussed. Cilia are not present in all animal cells, but are in some.

The structures shown above are parts of a “generic” eukaryotic cell. While most eukaryotic cells will present these structures, variations occur depending on the function of the cell. Think about cars — while most cars have the same parts, there will be differences between a sedan and an off-road vehicle. Among animal cells, extreme examples of specialization include red blood cells (containers of hemoglobin to transport oxygen; see picture on the left) and nerve cells (dedicated to transmission and integration of signals; picture on the right).

Blood Cells Human red blood cell, platelet, and white blood cell. Observe the flattened disk shape of the red blood cell, which allows it to easily pass through small blood vessels.

Nerve Cell Mouse neurons (nerve cells). Observe the many projections connecting cells with each other, allowing communication and transmission of signals.

The cell membrane must be a dynamic structure if the cell is to grow and respond to environmental changes. The fluidity of the membrane is demonstrated in the following animation.

Maintaining Proper Fluidity of the Membrane

To keep their membranes fluid across a range of temperatures, cells alter the composition of their membranes. Phospholipids with differing fatty acid tails have different levels of mobility in the membrane. The right ratio of saturated to unsaturated fatty acids keeps the membrane fluid at any temperature conducive to life. For example, winter wheat responds to decreasing temperatures by increasing the amount of unsaturated fatty acids in cell membranes. The unsaturated fatty acid tails keep membranes fluid because they are kinked and resistant to packing. In animal cells, the membrane is made up of mostly saturated fatty acids, so it is relatively stable (not too fluid). Cholesterol plays a key role in keeping animal cell membranes fluid across a range of temperatures. At high temperatures, cholesterol molecules interfere with phospholipid movement and reduce membrane fluidity. At low temperatures, cholesterol keeps the saturated fatty acid tails from packing and maintains adequate fluidity. Other sterols play a similar role in the cell membranes of plants, fungi, and even some prokaryotes. Fungi, for example, use ergosterol.

Structure of Cholesterol

Cholesterol in the membrane maintains the correct fluidity.

The cellular or plasma membrane is a lipid bilayer composed of phospholipids and associated proteins, specialized lipids, and carbohydrates. The composition of the plasma membrane varies according to the type and function of the cell.

Components of the Membrane

The plasma membrane is a complex structure containing many different macromolecules. Wikicommons

In order to carry out their functions, some proteins need to be embedded in the membrane. These proteins are called integral proteins (“integral” because they are “integrated” into the membrane). For example, a membrane protein that transports materials into or out of the cell needs to completely span the membrane. On the other hand, a protein that binds the cell to another can simply be attached to the outer surface of the membrane. Proteins that are attached to the inner or outer surface of a membrane are called peripheral proteins.

Membrane Proteins

Prokaryotes are an enormously diverse group of organisms. However, they can be organized into two primary groups: bacteria and archaea. While both bacteria and archaea are prokaryotes (both groups lack nuclei), the archaeans have some interesting structural characteristics in the cell membrane that have unique functional significance.

The cell membranes found in both eukaryotic and bacterial cells consist of a phospholipid bilayer that separates the internal environment of the cell from its external environment and regulates the materials that pass in and out of the cell. This enables the cell to maintain internal homeostasis, regardless of changing external conditions. You already know that cell membranes can be structurally different, to enable different functions. For example, some bacteria live in the frozen Arctic Circle. They are able to maintain membrane fluidity because of an increased concentration of unsaturated fatty acid tails found within the membrane phospholipids.

The Archaean Cell Membrane

Archaeans are often found living in extreme environments such as high temperature, pH, or salinity, and as such, are often called “extremophiles” (loving extreme conditions). How can their cell membranes stay intact in such conditions? The cell membrane must have a unique structure to withstand these conditions.

Grand Prismatic Spring, Yellowstone National Park

Archaea were first found in extreme environments, such as volcanic hot springs like Grand Prismatic Spring, Hot Springs, Midway and Lower Geyser Basin, Yellowstone National Park. The picture on the right shows an aerial view of the spring. Photo by Jim Peaco, National Park Service, July, 2001, Public Domain.

You will explore characteristics of the archaean cell membrane in the following activities. First, you need to orient yourself to the phospholipid found in a bacterial cell. You might want to review the structure of phospholipids.

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You figured out that the structure of the archaean phospholipid is significantly different from the structure of the bacterial phospholipid. These structural differences lead to functional differences that enable archaeans to survive in extreme environments. This is an excellent example of how structure determines function at the cellular level of organization.

The cell membrane provides a semipermeable barrier between the inside and the outside of the cell. The phospholipid bilayer structure of the membrane allows selected ions and organic molecules to pass through the plasma membrane and regulates the movement of molecular substances. This characteristic of the membrane, known as selective permeability, acts as a filter that allows only selected substances that are needed for the survival and functioning of the cell in and out. The movement of molecular substances across the membrane can occur passively without the cell exerting energy or it can occur through the cell's use of energy to transport substances. Selective permeability affects the energy required to transport substances in and out of the cell. This page will explore the conditions under which molecules can pass across the membrane passively through diffusion.

The size, polarity, and charge of a substance will determine whether or not the substance can cross the cell membrane by diffusion. The cholesterol was an example of a lipid, and is highly soluble in the nonpolar environment of the lipid bilayer. You saw, in the animation above, the cholesterol freely passing into the hydrophobic environment of the membrane. Cholesterol distributes freely in the membrane and then some fraction will dissolve in the aqueous environment of the cytoplasm. Water, on the other hand, while polar, is small enough to cross the membrane at a slow rate. Note that specialized transport proteins in certain cell membranes can provide a channel for the water, greatly increasing its rate of crossing the membrane. The lipid bilayer is much less permeable to the ion, because of its charge and larger size. As a general rule, charged molecules are much less permeable to the lipid bilayer.

Cells must be able to move large polar and charged molecules across the lipid bilayer of the membrane in order to carry out life processes. To allow these molecules, which are not soluble in the lipid bilayer, to pass across the hydrophobic barrier, it is necessary to provide ports, channels, or holes through the membrane. The molecules will still move spontaneously down a concentration gradient from high to low concentration. These channels can either remain open at all times, allowing the molecules to move freely according to the concentration gradient, or they can be gated channels that open and close in response to the needs of the cell. In most cases these channels are very discriminatory and will only allow specific molecules to pass. The process of moving impermeable molecules across a membrane (down their concentration gradients) using channels or pores is referred to as facilitated diffusion. Because the molecules are moving down a concentration gradient, the process is driven by simple diffusion and does not require the input of additional energy from the cell. The following simulation depicts the facilitated diffusion of glucose across the membrane using the glucose permease transporter.

In some cases it is necessary to move molecules against their concentration gradient. The eukaryotic cell has many compartments within it, each surrounded by a membrane. In most cases, the environment within the compartment is different from the environment in the cytoplasm. An example is the lysosome, an organelle whose function is to digest macromolecules delivered either from outside the cell or from other compartments within the cell. To carry out this function, the lysosome maintains a very low internal pH compared to that of the cytoplasm. Thus, there is a steep pH gradient across the lysosome's membrane. This contrasts with the equilibrium state, in which the concentration of hydrogen ions would be the same inside and outside the lysosome.

To decrease the pH inside the lysosome, the concentration of protons will need to be greater inside the lysosome than in the cytoplasm. To accomplish this, protons will need to move from a low concentration to a high concentration. This is a nonspontaneous process and requires the cell to do work to move the ions "uphill" against the concentration gradient. To do work, the cell must expend energy and actively move (pump) the ions. This process is referred to as active transport. The source of energy for this process in most biological systems is the hydrolysis of ATP.

The animation that follows illustrates an example of an active transporter that uses energy from the molecule ATP to transport sodium (Na+) ions out of the cell and potassium (K+) ions into the cell. Both ions are moved against their concentration gradients. The main stages of the process are:

1. Three Na+ ions from inside the cell bind to the transporter.
2. A molecule of ATP binds to the transporter, providing the energy needed to change the shape of the transporter. This allows the Na+ to cross the membrane and exit the cell, against its concentration gradient.
3. Two K+ ions from outside the cell bind to the transporter.
4. The transporter changes shape again, bringing the K+ into the cell.

Observe the active transport of sodium and potassium molecules using ATP.

Facilitated diffusion and active transport are not the only ways that materials can enter or leave cells. Through the processes of endocytosis and exocytosis, materials can be taken up or ejected in bulk, without passing through the cell's plasma membrane.

In endocytosis, material is engulfed within an infolding of the plasma membrane and then brought into the cell within a cytoplasmic vesicle. To begin endocytosis, a particle encounters the cell surface and produces a dimple or pit in the membrane. The pit deepens, invaginates further, and finally pinches off to form a vesicle in the cytoplasm of the cell. Note that during the process the inside surface of the newly formed vesicle is the same as the exterior surface of the cell. Thus the integrity of the cytoplasm and the orientation of the plasma membrane are preserved. Once internalized, a new vesicle containing solid materials may fuse with a lysosome so that its solid contents are digested. The resulting molecules may be released to the cytoplasm for use within the cell.

There are two general forms of endocytosis: phagocytosis and pinocytosis. Phagocytosis is the uptake of large solid particles such as bacteria or cellular debris. Pinocytosis is the uptake of fluid and any small molecules dissolved within it. Cells are also capable of recognizing specific particles and engulfing them in a more targeted way, a process called receptor-mediated endocytosis. In this case, the particle first binds to a membrane protein receptor on the surface of the cell. Binding of the target particle induces the cell to engulf it.

Exocytosis is just the reverse of endocytosis. In exocytosis, an internal vesicle fuses with the plasma membrane and releases its contents to the outside. The balance of exocytosis and endocytosis preserves the size of the plasma membrane and keeps the cell's size constant. The following animation depicts endocytosis.

How are endocytosis and exocytosis important to everyday life? Immune cells protect animals by recognizing and destroying foreign objects such as bacteria. Disease-causing bacteria are recognized by proteins called receptors on the surface of the immune cell. The phagocytic immune cell will then engulf the bacterial cells (phagocytosis). The vesicle that contains these bacterial cells is called a phagosome ("phago" means "eating" and "-some" refers to "body"). The phagosome next fuses with lysosomes. Finally, the digested bacterial products are excreted through the process of exocytosis.

Phagocytosis of a Bacterium

Cells continually encounter changes in their external environment. Most cells have a similar blend of solutes within them, but external fluids can vary dramatically, from pure water to brine or syrup. What will happen if there is a strong concentration gradient between a cell's interior and the fluid outside? As you know, molecules will tend to move down their concentration gradients until equilibrium is reached. You might think that solutes will flow into our out of the cell until the solute concentrations are equal across the membrane. However, not all molecules can pass through the cell membrane. The plasma membrane (lipid bilayer) is significantly less permeable to most solutes than it is to water. Therefore the WATER tends to flow in a way that establishes an equal concentration of solutes on either side of the membrane. The water flows down its own concentration gradient, with a net movement toward the region that has a higher concentration of solutes. This movement of water across a semipermeable membrane in response to an imbalance of solute is called osmosis.

Osmosis in an Animal Cell

The figure shows red blood cells immersed in three different solutions. The black dots represent sodium ions. Inside the red blood cell, the concentration of sodium is equal under all three conditions (shown as four dots). In the hypertonic solution, the concentration of sodium is higher outside (8 dots) than inside the cell. Water tends to leave the cell, flowing down its own concentration gradient. In the isotonic solution, the sodium concentration is the same inside and outside the cell. Water molecules enter and leave the cell at the same rate and the system is in equilibrium. In the hypotonic solution, there is a relatively low concentration of sodium (two dots) on the outside of the cell. Water is more concentrated outside the cell and tends to flow in. As water enters, sodium is diluted inside the cell, bringing the cytoplasm's sodium concentration closer to that of the external solution. But if too much water enters, the cell can burst (lyse).

Cells may find themselves in three different sorts of solutions. The terms isotonic, hypertonic, and hypotonic refer to the concentration of solutes outside the cell relative to the solute concentration inside the cell. In an isotonic solution, solutes and water are equally concentrated within and outside the cell. The cell is bathed in a solution with a solute concentration that is similar to its own cytoplasm. Many medical preparations (saline solutions for nasal sprays, eye drops, and intravenous drugs) are designed to be isotonic to our cells. A hypotonic solution has a low solute concentration and a high concentration of water compared to the cell's cytoplasm. Distilled (pure) water is the ultimate hypotonic solution. If a cell is placed in a hypotonic solution, it will tend to gain water. The solutes will "stay put" within the cell, but water molecules will diffuse such that their net flow is toward the area with a higher concentration of solutes. A hypertonic solution has a high solute concentration (lower water concentration) compared to the cell cytoplasm. Very salty or sugary solutions (brines or syrups) are hypertonic to living cells. If a cell is placed in such a solution, water tends to flow spontaneously out of the cell.

Cystic fibrosis is an inherited condition that affects the respiratory and digestive systems in children and adults. While there is no cure for the condition, in the 1950’s, people diagnosed with cystic fibrosis were lucky if they lived long enough to go to elementary school. Medical research has made an enormous difference in the life expectancy of people with cystic fibrosis, and today, they routinely live into their thirties and forties.

A diagnosis of cystic fibrosis (CF) is suspected if a patient has chronic weight loss accompanied by problems with the respiratory system. Most people with the condition are diagnosed by the time they are two years old. A century ago, cystic fibrosis was diagnosed when a doctor licked the forehead of a patient and found it to be unusually salty. While the medical equipment used to diagnose the condition today is much more professional, the same symptoms are identified. People with CF exhibit a variety of symptoms ^[1] that may include:

• persistent coughing often heavy with mucous;
• frequent respiratory infections;
• wheezing and shortness of breath;
• excessive appetite but poor weight gain;
• unusually salty-tasting skin; and
• greasy, bulky stools.

Cystic fibrosis is caused by a malfunctioning transport protein called Cystic Fibrosis Transmembrane Conductance Regulator (CFTR). CFTR is a channel that allows for the passage of chloride ions (Cl-) into and out of the cell. CFTR is located in the cells that line the respiratory tract, the pancreas, and sweat glands. It allows for the movement of Cl- into or out of a cell. CFTR is an active transporter and requires energy in the form of ATP to function.

Effect of Malfunctioning Membrane Transporters

People with cystic fibrosis have respiratory difficulties, usually caused by unusually thick mucus in the respiratory tubes in the lungs. In the lungs, CFTR transporters secrete chloride ions into the center of the respiratory tubes. This increases the concentration of solutes in the mucus lining the tubes, which in turn causes water to flow into the space inside the tubes (yellow). Under normal conditions, this process allows for a runny mucus to line the tubes.

Human Lungs

The lungs function by allowing air to flow through a series of tubes (yellow) that culminate in tiny sacs where gas exchange occurs. The yellow tubes are lined with special cells that have CFTR transporters in them that secrete chloride ions into the air tubes.

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Energy can be converted from one form to another. In the image below, the chemical energy in the wood is converted to light and heat. After the fire dies, the heat and light have dissipated and are no longer available for living organisms. Energy in our biosphere is a one-way system: It comes from the sun, is captured by living organisms, and eventually is released back out as heat.

Biological Energy Transformations

Energy cannot be created or destroyed. Instead, energy is transformed from one form to another. Imagine that you climb a mountain trail ending in a steep cliff. Your body’s movement (kinetic energy) is fueled by chemical energy from your food. As you move uphill, your body’s chemical potential energy decreases (you break down molecules and use up stored food energy). At the same time, your body’s gravitational potential energy increases. This kind of potential energy can be released by letting an object drop from a height. A fall from the top of the cliff would do a great deal of “work,” so watch your step!

Chemical to Gravitational Energy

Converting chemical energy to gravitational energy. © Copyright Iain Lees and licensed for reuse under the CC BY-SA 2.0 licence.

Where does chemical energy in food come from? The sun provides solar energy, the energy source for most living things. Plants and other photosynthetic organisms can use solar energy to build sugar molecules from simpler raw materials (carbon dioxide and water). A sugar molecule stores chemical energy in the bonds that join its atoms. The energy stored in sugar can be released and used to build other types of biological molecules (proteins, lipids, etc.), which also contain stored chemical energy in their complex structures.

Energy from the sun can be converted into chemical energy (in sugars) by photosynthetic organisms. This chemical energy can then be used to do other work like building the components needed for growth.

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To us, it seems that the sun has burned forever and will always keep shining. However, the sun is fueled by nuclear energy generated by atoms colliding in its incredibly hot core. Eventually, the supply of fuel in the sun will be depleted and our sun’s long life will end. This illustrates an inescapable fact about energy: it tends to lose quality over time. It dissipates, spreading out in space, and loses its intensity.

Heat is the energy possessed by any substance because of the random jiggling of its molecules and atoms. It is a low form of energy, disorderly, and spreads out rapidly through most materials. Every kind of energy conversion generates at least some heat energy as a byproduct. For example, the breakdown and use of chemical energy in food also releases heat. Heat can be helpful in keeping our bodies warm, but for the most part heat energy is a loss: an energy waste that cannot be recovered. No organism can capture heat and use it to do work or to make food. Instead, heat seeps out of organisms and eventually into space, leaving the biosphere forever.

Adenosine triphosphate, or ATP, is an organic molecule that acts as the direct energy source for almost all cellular activities. ATP consists of a single adenosine molecule (composed of an adenine bound to a ribose sugar) linked to three phosphate ions.

ATP consists of a single adenosine molecule (green rectangle) linked to three phosphate ions (orange circles).

ATP is a relatively unstable molecule. Consequently it is never used for the long-term storage of energy in the cell. This job goes to other more stable compounds, like fats and sugars. ATP is specialized for direct and rapid transfers of energy. It is because of this instability that ATP is such a good energy currency for the cell (it’s easy to “spend” this energy). ATP is like cash, while long-term energy storage molecules (such as fats and sugars) are more like a savings account.

Most life on Earth is fueled by solar energy through the process of photosynthesis. Photosynthetic organisms use sunlight to make organic molecules from simple raw materials (carbon dioxide and water). Cellular respiration and other processes break down organic molecules and use the energy released to build ATP molecules. ATP then transfers energy to drive many important processes in cells including movement, transport, and synthesis. In this way, the energy from the sun is transformed to chemical energy in molecules such as glucose and ATP. Eventually energy is released in forms like motion, heat, sound, or light.

Catabolic Reactions Release Energy and Reduce Complexity

In the figure above, a larger molecule on the left is broken down into smaller and simpler components. As high-energy bonds are broken and replaced by lower-energy bonds, energy is released. Some of this energy may be captured to do cellular work.

Anabolic reactions use energy to build more complex molecules from relatively simple raw materials. “Anabolic” and “catabolic” sound similar but are opposites. To remember the difference, it may help to think about how “anabolic steroids” promote the buildup of muscle mass. All of the complex molecules of life — carbohydrates, lipids, proteins, nucleic acids — are generated by anabolic reactions. Anabolic reactions are central to processes like photosynthesis, protein synthesis, and DNA replication.

At this point, you may wonder why the cell has to break down complex molecules in order to build them up again. Different cells use and require different biomolecules for their specialized functions. For example, carbohydrates are good sources of energy. In plants, carbohydrates are usually stored as starch. In animals, they are stored as glycogen. Both are polymers of glucose, but they have different structures, and an animal cell cannot readily store or access starch. When an athlete “carbo-loads” the evening before a race, starches from foods like pasta are digested to simple sugars in a catabolic reaction. They are then rebuilt as glycogen (in an anabolic reaction) in the muscles and liver. That way, there is some extra energy stored and easily accessible for the muscle cells to use for the big race. Biomolecules are broken down to raw materials, then rebuilt in a different form to meet the needs of the organism. One molecule that is unique to your cells is DNA. No other organism (except an identical twin) has the same DNA as you, so your cells need to build it anew in order to pass it on to the next generation

Photosynthesis is an anabolic process you’ll learn more about in this unit. Protein synthesis is an amazing feat of anabolism. Protein chains (polypeptides) are produced by linking together relatively simple amino acid monomers. In one polypeptide, thousands of amino acids may be strung together, and several different polypeptides may fold and bind to each other to form a large and complex protein molecule.

Anabolic Reactions Use Energy to Build Complex Molecules

In the figure above, several smaller components are joined by bonds to form larger, more complex molecules. Energy inputs are required to do this work.

Plants, algae, and some bacteria can use light energy to turn carbon dioxide and water into simple sugars through the process of photosynthesis. These sugars can act as “building blocks” for the synthesis of other organic molecules, or they can store energy for later use. While the process of photosynthesis stores chemical energy for later use, most photosynthetic organisms access the stored energy the same way consumers do: they break down the sugars to build ATP using the process of cellular respiration, which occurs in subcellular organelles called mitochondria.

Photosynthetic producers have evolved an effective system for absorbing light and converting it into chemical energy. This biochemical solar energy system begins with a diverse array of (mostly green) pigments that are embedded in membranes. In plants and algae, these pigments are contained within specialized subcellular organelles called chloroplasts.

You may want to review the Cell Structures page.

The main purpose of photosynthesis is to convert energy from sunlight and store it as bond energy within sugars. Photosynthesis uses pigments (such as chlorophyll) in the chloroplasts to absorb light energy. This energy is used to produce sugars from carbon dioxide, while oxygen is given off as a byproduct. You will examine the function of pigments in more detail later.

Photosynthesis Transforms Light to Chemical Energy in Sugar

Light energy enables photosynthesis. This process requires the participation of chlorophyll pigment; in plants it occurs mainly in leaves.

Some photosynthetic organisms (such as most algae and cyanobacteria) live in water. Their cells are equipped with pigments to absorb light, and they absorb water and other nutrients directly across the cell membrane. They are faced with a challenge involving the attenuation (loss) of light energy with increasing depth. As a result, many algae and cyanobacteria have adaptations that keep them floating near the water’s surface.

Kelp Float to Reach Light

These kelp are anchored below and use air bladders for the top of the plant to reach the water’s surface.

Land plants face a different set of challenges. Plant leaves are the main location of photosynthesis. They are often large, flat structures that are adapted for maximum light absorption. In many plants, leaves also are held high above the ground by tall stems. Growing tall is an adaptation that helps a plant get high-intensity sunlight, because short plants are more likely to be shaded by taller ones.

Plants Grow Tall to Compete for Light

Land plant leaves are often broad and flat, maximizing the surface area for light absorption. Many species also grow upward to gain access to high-intensity sunlight. Note also how the leaves are arranged: few gaps are left unfilled in this tree’s canopy.

Land plants also face the risk of drying out. Plants have evolved traits that protect their above-ground portions from excess water loss. For example, plant leaves are sealed with a layer of waxy material called cuticle. Protected in this way, leaves cannot efficiently absorb water when it rains. Instead, land plants absorb water from the ground (through their roots).

Plants must then transport water upward to leaves and other tissues. This is quite a challenge for a tall plant. Plants have no moving parts that could power a pump, so their circulatory systems must work on different principles. Plants use specialized cells to move water. These cells are essentially long, thin tubes that transport water from the roots all the way up to hollow cavities in the leaves. Evaporation of water from leaves provides negative pressure that sucks water up the tubes. The thick cell wall that allows the tube cells to function without collapsing also provides the plant with structural stability. “Wood” is mainly the structural material that remains after these cells have died. Ultimately, an adaptation for moving water helps woody plants grow even taller than their less sturdy cousins, further enhancing their access to light.

Microscopic image of wood

Under a microscope, you can see the individual transport cells that make up the wood.

The adaptations of plants have long been a subject of biological study. One of the first questions asked by early scientists was, “How do plants get their resources for growth?”

Photosynthesis: A Summary

Photosynthesis is summarized in the diagram above. The sun provides energy that enables carbon dioxide and water to react to form glucose. Oxygen gas is a byproduct of this process.

We know that plants require light. But “light” is a complex form of energy. Visible light is just a small part of a much broader spectrum including many forms of electromagnetic radiation. In many ways, light behaves as a wave. Different colors of light have different wavelengths. In a given period of time, short wavelengths deliver more energy to a surface than longer wavelengths. Thus blue light is higher in energy than red light.

Sunlight Includes All Colors of Visible Light

A rainbow vividly demonstrates that sunlight includes a range of light colors and wavelengths, from blue (shorter wavelengths) to red (longer wavelengths). Raindrops act as prisms, separating the wavelengths and making the colors apparent. © Copyright Rod Trevaskus and licensed for reuse under this Creative Commons Licence.

Are all wavelengths of light equally useful for photosynthesis? In 1883, a scientist named George Engelmann designed an experiment to answer this question. He shined a light through a prism to separate the different wavelengths so that they landed on different zones along the length of filaments of Spirogyra, a type of green algae. Examine the following image depicting Engelmann’s results.

Engelmann's Action Spectrum Experiment

Pigments are colored substances that absorb light energy. Why does a pigment look red, green, purple, or blue? A given pigment absorbs only a limited set of light wavelengths. For example, a red pigment absorbs green and blue wavelengths. Red light, by contrast, is NOT absorbed: it is either reflected or transmitted through a solution containing the pigment.

Pigments Absorb Some Wavelengths and Reflect Others

The green chlorophyll pigment appears green because it reflects and transmits light in the green wavelength range. Blue and red light, by contrast, are absorbed.

What happens to light energy that is absorbed by a pigment? In keeping with the law of conservation of energy, this energy does not disappear. Instead, it excites electrons in the pigment, boosting them to higher energy levels. In plants, the excited electrons from some pigments are transferred to other molecules, where they start the transformation of light energy into chemical potential energy.

If excited electrons are not removed from a pigment molecule, they will eventually “fall” back to their starting point. At this point, the pigment will release energy. In some pigments, a portion of the released energy is emitted as light. If you expose these fluorescent pigments to light and then place them in a dark place, they will glow. All pigments release at least some of the energy they absorbed from light as heat.

O₂ is a product of photosynthesis. This product is essential for many living organisms, including humans and any other organisms that go through cellular respiration. When photosynthesis became widespread in the early Earth’s oceans, it generated excess oxygen gas that changed the Earth’s atmosphere. This increase in atmospheric oxygen concentration eventually changed the face of our planet as organisms that couldn’t adapt died off and new organisms evolved.

As we have emphasized thus far, cells juggle energy through opposing reactions. Photosynthesis is an anabolic pathway fueled by solar energy that allows the synthesis of organic molecules from simple raw materials. Catabolic pathways reverse this process. They break molecules down into simpler components. The centrally important catabolic pathway that is complementary to photosynthesis is cellular respiration. Although there are may other catabolic reactions occurring in any cell, cellular respiration supplies the vast majority of ATP molecules required for cellular work in aerobic organisms.

If you compare the summary reactions of photosynthesis and cellular respiration, you will see that cellular respiration is photosynthesis “running in reverse”:

Cellular Respiration Breaks Down Sugar and Captures Energy within ATP

Sugar and oxygen gas are converted to carbon dioxide and water in cellular respiration. In the process, heat is released and ADP is phosphorylated to produce ATP.

Cellular respiration is a key pathway in the metabolism of all aerobic organisms. On the macro scale, respiration refers to breathing: taking in oxygen and removing CO₂. But ultimately, the reason we need to breathe is to provide the oxygen needed to carry out cellular respiration in our cells and to remove the carbon dioxide produced as a byproduct.

Three important things happen during cellular respiration:

1. The carbon-containing molecules used as cellular fuel are broken down and converted to CO₂.
2. Electrons and hydrogen ions (H+) are produced as sugar is broken down and energy is harvested; oxygen (O₂) combines with these byproducts to produce water (H₂O).
3. The energy released when carbon-containing molecules are broken down is captured and used to generate ATP molecules; some energy is also lost as heat.

In eukaryotes, the breakdown of sugar begins in the cytoplasm (cytosol), while the consumption of oxygen and the generation of CO₂ and ATP synthesis happen inside specialized membrane-bound organelles called mitochondria.

Combustion vs. Respiration

Energy is released in small portions, so that some of the released energy can be captured in chemical bonds, ultimately as ATP. The process can be regulated at different steps, allowing cells more control over the process.

Combustion vs. Respiration

Both combustion and respiration release the same amount of energy. However, because combustion happens all at once, much of that energy is released as heat and light and cannot be captured by the cells. The stepwise process of respiration releases energy slowly so cells can capture the energy in ATP.

did I get this

Many Fuels Feed into Cellular Respiration

In addition to carbohydrates, fats and proteins can also be used as fuels for cellular respiration. However, these fuels must first be partially broken down, and they feed in at intermediate steps within the pathway.

As you may recall, photosynthesis occurs in some bacteria; in eukaryotes it occurs in cells that contain chloroplasts. Such cells are found in algae and in the leaves and stems of plants. Photosynthetic organisms use light energy and simple building blocks (carbon dioxide and water) to make their own food. Cellular respiration is very widespread. It is completed in mitochondria, bacteria-like organelles that are found in protists, fungi, plants, and animals. Although the details of the two pathways are different, the overall reaction of cellular respiration is photosynthesis running in reverse. Cellular respiration extracts the stored energy from food molecules, uses it to “charge up” ATP, and releases carbon dioxide and water as wastes.

Photosynthesis and Cellular Respiration Recycle Carbon and Transfer Energy

In the last two sections, the topics of photosynthesis and cellular respiration have been introduced and discussed as independent processes. The focus of this module is on how the two processes are part of one larger cycle. There is a yin-yang relationship between the two processes — the product of one process is the starting material for the other.

In the image below, you see a summary of photosynthesis. But photosynthesis does not occur in a vacuum. In fact, it is inevitably PAIRED WITH cellular respiration in most producers. They take most of the glucose they have produced and break it right down again in their own cells.

Photosynthesis Summary Reaction: CO₂ and H₂O to Glucose Using Light Energy

In the diagram above, photosynthesis is summarized. Carbon dioxide and water are joined to form glucose using light energy. Oxygen gas is also a byproduct of this process.

A full representation joins photosynthesis to cellular respiration in a cycle. The products of one reaction are the starting materials for the other.

Cellular respiration and photosynthesis are interdependent. The glucose and oxygen produced by photosynthesis are used up in cellular respiration. Energy is transferred to “charge up” ATP, and heat, carbon dioxide, and water are released as waste products. The carbon dioxide and water are then available as raw materials for photosynthesis.

Cycling Between Photosynthesis and Cellular Respiration

This is how the cycling between photosynthesis and cellular respiration occurs: in photosynthesis, carbon dioxide and water, in the presence of light energy, are converted to make glucose and oxygen; while in cellular respiration, the products of photosynthesis (glucose and oxygen) are metabolized to make energy in the form of ATP and heat, releasing carbon dioxide and water. Because each process starts where the other ends, they form a cycle.

The photosynthesis / cellular respiration cycle isn’t restricted to the cells of an individual plant. To the contrary, it is a global cycle that makes all life on Earth interdependent. A growing photosynthetic producer carries out more photosynthesis than cellular respiration. Thus, it releases excess oxygen into the atmosphere and stores carbohydrates and other molecules in its body as growth. These materials are essential to virtually all other life forms on Earth. This interdependence is depicted in the diagram below.

Photosynthesis -Cellular Respiration Cycle

This image shows the cycling between the products of photosynthesis and cellular respiration. The two processes are intimately linked.

The cycling that occurs between photosynthesis and cellular respiration is vital to the health of planet Earth. If there was no way for the carbon dioxide produced through cellular respiration to be utilized, respiring organisms (like humans, dogs, and even grass) would soon die of asphyxiation. Additionally, photosynthetic organisms are the base of almost every food chain on the planet, so without these organisms, mass starvation would ensue. Luckily, this planet is full of photosynthetic organisms. All of the breathable oxygen on Earth comes from photosynthesis. Just over half of the oxygen is produced by phytoplankton — drifting photosynthetic algae and bacteria — in the oceans. The rest comes from plants (trees, grass, etc.) on the land. Without this vital connection between photosynthesis and cellular respiration, life as we know it would cease to exist.

Cycling Between Photosynthesis and Cellular Respiration

An understanding of this balance is important in the modern world, with global warming in the headlines. Since the late 1700's, the amount of carbon dioxide in the Earth’s atmosphere has been rising. This indicates that the natural recycling of carbon has been upset. The main source of excess carbon dioxide in our atmosphere is the burning of fossil fuels, which were created by photosynthesis millions of years ago. Meanwhile, deforestation removes photosynthetic organisms (trees) from the surface of the planet. Taken together, these human activities have changed Earth’s atmosphere. The carbon dioxide concentration of Earth’s air has increased by more than 35 percent since the 1700's. Such changes are very likely changing Earth’s climate, and pollution and deforestation also have other detrimental effects on environmental health. We will return to explore these topics further in the Ecology unit. You will need to use your understanding of photosynthesis and respiration to fully grasp these issues.

In the previous modules, you learned about metabolic pathways in cells — those “freeways” that shuttle energy and carbon in different directions. Metabolic pathways can be either anabolic or catabolic. Anabolic pathways build things up and catabolic pathways break them back down again, sometimes as a source of energy, other times to obtain building materials. Among the main pathways of the cell are photosynthesis and cellular respiration, although there are a variety of alternative pathways such as fermentation.

Regardless of their purpose, all metabolic pathways share four important features:

1. Many pathways are universal among living organisms. When you look at life, you may see a great deal of diversity. Those who study metabolism, by contrast, see a huge degree of overlap among the cells of all living things. Many of the fundamental enzymes that keep our cells working are found in only slightly different forms in creatures as varied as zebrafish, fruit flies, yeast, and nematode worms. This is partly why studies on model organisms can teach us so much about our own biology.

Example

These organisms all use very similar metabolic pathways

Metabolic pathways (such as cellular respiration) are nearly universal. These organisms all use similar pathways.

2. Each pathway contains multiple intermediate products, and there are small molecular differences between the intermediates. Pathways proceed in “baby steps.” A chemical change that can be written and balanced as a single reaction may, in a real pathway, require dozens of reaction steps!

   A sample metabolic pathway

   This pathway shows the production of the end product “D” from the starting substrate “A.” In this reaction, A is the substrate of enzyme 1, which produces B. Enzyme 2 then uses B as its substrate to produce C. Enzyme 3 then uses C as its substrate to produce D.
3. Each step within the pathway, or the conversion from one intermediate to the next, is catalyzed by an enzyme. Thousands of enzymes catalyze reactions in human cells. Each enzyme conducts a single chemical reaction. The coordination of many enzymes working together can produce a variety of outcomes.

   Another sample metabolic pathway

   Each enzyme within the pathway is specific to one reaction. The coordinated effort of many enzymes can produce a variety of final products.
4. Each pathway is regulated to ensure the optimal use of resources and to maintain the health of the cell. For example, if there is plenty of ATP in a cell, the cellular respiration pathway (which produces ATP as its final product) will slow down. In a complex web of cause and effect, pathways influence themselves and each other. The net effect in a healthy cell is the maintenance of homeostasis. Stockpiles of raw materials, intermediates, and finished products are maintained at optimal levels, and the chemistry of the cell cytosol is also regulated, as are extracellular fluids.

   Many metabolic pathways are reversible, which means that certain chemical reactions can go “either way,” depending on the needs of the cell. For example, some of the reactions that are part of cellular respiration (which is a catabolic pathway) can become anabolic when there is a surplus of energy. A small number of steps utilize different enzymes in the forward versus the reverse direction. These enzymes are regulated in a coordinated fashion such that a pathway operates in only direction at time.

   Catabolic and Anabolic Reactions

   Animals use fats and complex carbohydrates such as glycogen for long-term energy storage. When energy is needed, catabolic pathways degrade lipids and glycogen to glucose or other intermediates of the cellular respiration pathway, resulting in ATP production. When there is excess ATP (for example after eating a meal rich in fats and sugars), parts of the cellular respiration pathway go “in reverse” to provide building blocks for the anabolic reactions building up lipids and glycogen.

At the heart of metabolism are enzymes. These proteins embrace substrates, quickly generating products. One or more substrates bind to an enzyme’s active site. As a result, activation energy is reduced and the reaction proceeds much more quickly than it otherwise would. Without enzymes, metabolism would grind to a halt. Furthermore, the structural characteristics of enzymes allow the regulation of their function, thus allowing the regulation of the metabolic pathways they participate in. You may want to review the functions of enzyme proteins.

Metabolic pathways are regulated in order to maintain maximum efficiency or in response to environmental changes.

There are two major methods of pathway regulation. The first method involves changing the amount of the enzymes in the pathway. Since the reactions are catalyzed by the enzymes, if the enzyme is not present, the pathway is effectively shut off. Enzyme levels are usually altered by controlling the amount of mRNA produced from the gene that encodes the enzyme. You will explore how enzyme levels are regulated in the section on transcription.

Regulation of pathways by altering the amount of enzymes in the pathway is usually too slow to meet the second-by-second regulation needs of the organism. Consequently, many pathways are regulated by increasing or decreasing the activity of an enzyme due to the binding of a small regulatory compound. Typically, only a few steps in the pathway are regulated, and the regulated steps typically occur near the beginning of the pathway to prevent the accumulation of intermediates, which are seldom of use to the cell. Think of an assembly line: the speed of production will change depending on how much of the starting material is available, how quickly each of the workers completes the task, and how much of the final product is needed. Similarly, pathways are influenced by the availability of the starting materials, the activity of each enzyme in the pathway, and the concentration of product already present in the cell.

Example

Glucose and Cellular Respiration

Let’s look at an example of a metabolic pathway and explore one mechanism that regulates it. You may remember that cellular respiration is an essential catabolic pathway. Cellular respiration starts with a pathway called glycolysis, which degrades three-carbon glucose into a three-carbon molecule called pyruvate. Glucose can come from ingested carbohydrates, or from degradation of glycogen, a polysaccharide. When there is an excess of carbohydrates, they are stored as glycogen in an anabolic pathway.

Glycolysis is the first stage of cellular respiration, in which glucose is degraded to a three-carbon compound called pyruvate. In this process, ATP is formed. As with all pathways, glycolysis has several steps. The on-off switch of the pathway is found at the third enzyme (represented by a traffic light), which is inhibited by high levels of ATP. Synthesis and degradation of glycogen, a polymer of glucose commonly found in animal cells, occurs through an early intermediate of glycolysis.

Six general mechanisms can regulate the rate of each step in a pathway. The mechanisms differ in how rapidly they can respond to changes in the environment. Each of them is discussed below, with the more rapid forms of regulation at the top of the list.

1. Substrate availability. If the substrate concentration increases, the rate of a reaction will increase. Put simply, substrates must collide with enzymes to initiate binding. Such collisions will occur more often if the substrate is highly concentrated. Note that too much of the substrate can saturate the enzyme, so above a certain amount of substrate, the reaction speed will not increase anymore.
2. Competitive inhibition. An inhibitor “competes” with the substrate for the active site. If the inhibitor binds first, the substrate is blocked from entering and the enzyme is inhibited (cannot complete any reactions). Competitive inhibitors are often used as drugs to block an undesirable metabolic pathway. For example, sulfa antibiotics are competitive inhibitors of the bacterial pathway that produces folic acid, an essential molecule for nucleic acid synthesis. Products of a reaction are often competitive inhibitors, because they bind to the active site.
3. Noncompetitive control. This mechanism is similar to competitive control, except in this case substances bind to a site away from the active site. Binding can either enhance or inhibit the enzyme’s function by changing the shape of the active site. This is the example that you saw above with glycolysis.
4. Feedback inhibition. Both competitive and noncompetitive controls are often set up so that a product inhibits its own production by inhibiting enzymes at an early step in the synthesis process. This regulates the pathway: the product “turns off” its own production by inhibiting an enzyme on its own “assembly line.” This prevents the overproduction of a substance and also prevents the waste of resources on unnecessary intermediate products. Feedback inhibition is observed when a product inhibits an earlier step in the pathway. Product inhibition occurs when the product inhibits the enzyme that was directly involved in making that product.
5. Modification of the enzyme. Chemical modification of enzymes (such as adding a phosphate group) can cause a change in the shape of the active site of the enzyme. The change may either increase or decrease enzyme activity. This is similar to noncompetitive control, except in this case the enzyme is chemically modified and control does not involve the binding of a large molecule to the enzyme.
6. Changing enzyme concentrations. Enzyme levels can be increased by 1) conversion of inactive forms of the enzyme to active forms, or 2) regulating the synthesis of the enzyme. An example of the former is blood clotting, where inactive precursors of clotting enzymes become activated, in a cascade, by blood vessel damage. This permits a very quick response to bleeding: all the necessary factors are present and require only an activating signal. Similarly, many digestive enzymes are activated only when they reach their destination (for example, gastric fluid of low pH). Elsewhere they are inactive — and thus do not digest the organ that secretes them. It takes longer to adjust enzyme levels by regulating the activity of genes that produce them. Such changes are most often seen in response to longer-term changes in the environment. For example, bacteria turn genes for digestive enzymes on and off depending on the nutrients that are available to them. Many animal genes are produced only during certain stages of development.

In summary, metabolic pathways are dynamic processes, continuously changing in response to environmental changes and cellular (or organismal) needs, while avoiding waste of resources. How much substrate or enzyme is available will determine the rate of reactions. Moreover, extreme “fine-tuning” of metabolism is possible through changes in enzyme activity due to the binding of inhibitors. This is a prime example of the relationship between structure and function.

To this point, you have learned much about how pathways work. They proceed as a series of steps catalyzed by enzymes. They are regulated by factors that modify enzymes or alter the expression of genes.

In living organisms, metabolic processes are tightly regulated under normal conditions. The cell, and the organism as a whole (e.g., the human body), tend to respond to external influences in ways that maintain a relatively stable internal environment. This ability or tendency is called homeostasis and depends on a complex set of stabilizing responses.

Cells live in dynamic environments. Therefore, it takes work to keep conditions stable in a cell. Precise regulation enables the cell (or body) to establish consistent internal conditions. Factors like pH, ion concentrations, and levels of various substrates and products are held within narrow bounds. This unique environment allows a diverse set of reactions to take place. Many of these chemical reactions are essential for life and all of them help maintain overall health.

Many humans are able to maintain a stable adult body weight over a large number of years. Although it may seem perfectly normal, this is an amazing feat of metabolic regulation. As you eat, foods are broken down and metabolized. But the energy stored in the food’s chemical bonds cannot be destroyed. Simply put, if more calories are consumed than are required for growth, activity, and maintenance, the excess energy is stored within the body. This energy is stored when enzymes catalyze the formation of new chemical bonds to create specific kinds of macromolecules (i.e., glycogen, fat, and protein), which tends to increase overall body mass. On the other hand, if not enough food calories are consumed, the body will begin to break down its own tissues as a source of energy, and will decline in mass as a result.

Note that when “calories” are being discussed in reference to food consumption, the word "calorie" actually refers to a kilocalorie. One kilocalorie is the amount of energy required to raise the temperature of one kilogram of water by one degree Celsius. It is the unit typically used when discussing human nutrition and energy balance. For your reference, a typical adult male requires about 2,500 calories per day; a female of average size might require 2,000 calories daily. The body’s calorie requirement declines with age, and depends on many factors, including body size, sex, and physical activity.

As you have seen, the balance between caloric intake and output must be held within narrow limits to maintain a steady body weight. Yet some humans do this without conscious effort. How does this remarkable balancing act work?

First, consider what happens over the course of a typical day. After a meal, extra calories are initially stored in the liver and muscles as glycogen (a complex carbohydrate). Glycogen is broken down and used to supply glucose for intense exercise, and to provide glucose while we sleep. Breakfast provides fuel to rebuild some of the body’s glycogen stores that were depleted overnight. Thus, over short time scales, glycogen storage is an efficient way to provide glucose when it’s needed between meals.

Over longer time periods, body fat is used to store excess energy. When glycogen stores are full, the body switches over to storing the excess energy as fat. Remember that energy is stored within chemical bonds, and so it is the chemical bonds within glycogen and fat molecules that contain energy. Fat is an efficient way for the body to store extra calories, because it is able to pack more calories per unit mass when compared with carbohydrates or proteins (see Figure 8.2 below). You can think of body fat as a long-term, highly compacted energy reserve.

Fat Stores Maximum Energy per Unit of Mass

At 9 kilocalories per gram, fat stores more than twice as much energy per unit mass than proteins or carbohydrates.

learn by doing

In this unit ^[1] , you will learn about another major cell process — cell division, or cell reproduction. The word "reproduction" is used in many different scientific and nonscientific settings. Regardless of the setting, though, reproduction has the same basic meaning. Reproduction is defined as "the act of making a copy of the original." With this in mind, the word reproduction can be applied to many different situations. Some of these include parents having a baby, you photocopying a page in your textbook, and a museum staff member making print copies of a famous oil painting.

In each case, a relatively close copy of the original has been made. The same principle applies in cell reproduction—making new cells that closely resemble the original cell. Cell reproduction is a complex process that involves many intricate, highly regulated steps. Like metabolism, each of these steps must occur in a particular order.

Cell reproduction is important for three reasons:

1. It provides new cells for growth, the replacement of dead cells, and healing.
2. In cells, it ensures the inheritance of genetic information from parent cell to offspring cell.
3. In organisms, it ensures the inheritance of genetic information from one generation to the next.

In this unit, you will learn about how cells carry out these critical processes. Your understanding of the information this unit will lay the foundation for understanding heredity and molecular genetics.

Chromosomes are thread-like structures located inside cells. In eukaryotic cells, the chromosomes are contained inside an organelle called a nucleus . In prokaryotic cells, they are located in a particular area of the cytoplasm. Chromosomes are made up of two major parts: DNA and proteins. Both DNA and proteins are large molecules. Envision the general makeup of a chromosome, as shown in the following diagram.

By University of Maryland University College CC-BY-NC.

DNA is the molecule that stores and transmits inherited genetic information. This information includes the directions that tell a cell how to make proteins. Information is stored in DNA in segments called genes. In the diagram above, the ruler represents the entire DNA molecule. The genes are represented as short segments of the ruler. You will learn more about the structure and function of genes in the Molecular Genetics unit.

The blobs of clay in the diagram above represent histone protein molecules. These proteins associate with DNA in a very precise way. First, they couple with DNA at regularly spaced intervals. Notice in the diagram above that the blobs of clay (histones) are located at equally spaced intervals along the ruler. Second, they help to wind the DNA molecule into an organized and compact structure. The following diagram shows how histones wind DNA into a compact structure called a chromosome.

By University of Maryland University College CC-BY-NC.

The winding function of histones plays a very important role in cells. It allows the DNA to be condensed into organized bundles (chromosomes) that can easily be moved around the cell. Because the DNA is wound around the histones in such an organized way, the DNA can be easily wound up and unwound at various points during the cell cycle. For example, chromosomes must unwind slightly when a new copy of DNA is made. Then, the chromosomes become very tightly wound as the cell gets ready to divide during mitosis or meiosis. Without an organized compaction system, the long pieces of DNA in chromosomes could easily become "knotted" and tangled. Think of a long piece of string. Knots can easily form in the string if it is not carefully wound up into a ball. Keeping the DNA organized is critical, especially when you consider that the DNA in one human cell is three feet long when it is stretched out straight. This is quite amazing when you realize that this must fit into a cell so small that it cannot be seen with the naked eye. This feat is achieved by two different winding processes. One of these is the winding of DNA around histone molecules. As a result of this winding, the DNA molecule becomes shorter than before it was wound around the histone molecules.

Now look at an image of the relationship between DNA and histones in chromosomes that is more realistic than what is shown in our ruler-and-clay diagram above. When the DNA becomes tightly wound around the histone proteins, imagine that the chromosome looks as illustrated below.

The chromosomes in somatic cells and germ cells are present in pairs. One chromosome in each pair is descended from the organism's father. The other chromosome in the pair is descended from the organism's mother. Each member of a chromosome pair is called a homologue. Together, these two chromosomes make up a pair of homologous chromosomes. The words homologue and homologous both begin with the prefix "homo-," which means "the same or similar." So the two chromosomes in each pair contain the same set of instructions. The following diagram shows the relationship between homologues and homologous chromosomes.

Somatic cells produced through mitosis are diploid. “Di-” means “two,” and diploid cells contain two copies of every chromosome. Chromosomes are the condensed form of chromatin, the combination of DNA and proteins that fill the eukaryotic nucleus. Humans have a total of 46 chromosomes in their diploid cells. One way to write this is "2n = 46." Humans who have more or less than 46 chromosomes sometimes survive, but usually have life-altering conditions, such as Down syndrome. Down syndrome is caused by having three copies of chromosome 21, instead of the usual two copies.

Gametes are haploid cells. They contain only one copy of each chromosome. In human haploid gametes, there are 23 chromosomes. One way to write this is "1n = 23." As you learned in the previous activity, two haploid cells can combine, through the process of fertilization, to form a diploid zygote. The diploid zygote then goes through mitosis to form the diploid somatic cells of the organism.

Remember that germ cells, found in the ovaries and testes, give rise to gametes. In other words, germ cells go through meiosis to produce gametes. Germ cells are diploid cells. When they go through meiosis, the end result is four unique haploid daughter cells. These haploid cells can be fertilized by other haploid cells to produce diploid cells again.

Number of Chromosomes in Diploid and Haploid Cells

By University of Maryland University College CC-BY-NC.

The table below summarizes the characteristics of somatic cells, germ cells, and gametes.

Every living organism goes through various stages of development. For example, human beings go through these stages of development: fetus, infant, child, youth, teenager, young adult, adult. Remember from earlier that cells are living things. They, too, go through a set of programmed stages.

The cell cycle is the "life cycle" of a cell. It is the set of stages that a cell goes through during its lifetime. Cells go through five major stages of development: G1, S, G2, M, and cytokinesis. The events that occur during stages G1, S, and G2 are nearly the same in all types of cells. Together, these three stages of the cell cycle are called "interphase." The events that occur during stages M and cytokinesis are different, depending upon the type of cell. The diagram below shows an overview of the stages in a cell's life cycle:

Overview of the Cell Cycle

By University of Maryland University College CC-BY-NC.

Notice in the diagram above that we start with one cell on the left side. This is called the parent cell. It is called this because, like a human parent, it reproduces—it makes new cells that are copies of itself. The parent cell goes through the five stages of development in this order—G1, S, G2, M, and cytokinesis.

At the end of the development process, two new cells are produced. These cells represent the next generation of cells in this lineage (just as your parents represent one generation and you represent the next generation). Each of the new cells is called a daughter cell. Do not be confused by the use of the word daughter—it does not mean that these are female cells. Regardless of whether they are male or female cells, the newly produced cells are called daughter cells.

Notice that the parent cell no longer exists—but the parent cell did not die. Rather, the contents of the parent cell have been split into two new cells. Each of the new cells contains a portion of the original parent cell. Previously, we compared the cell cycle to the phases of human development. Notice here a very important difference between the two: The far end of human development is marked by the death of the individual. The end of the cell cycle, however, results in the formation of new cells.

In the diagram "Overview of the Cell Cycle" above, look closely at the parent cell and the two daughter cells. Notice that they look the same. Once again, we revisit the theme of cycles in nature that we discussed above. The cycle generates cells that resemble the cells we started with. In addition, the new cells undergo the same development-and-division process that their parental cell did. For these two reasons, we call this the cell cycle, and draw it like a circle. Similarly, human beings have children, who then have children themselves. (You may have heard this called the circle of life.) Cells do the same thing through the cell cycle. The following diagram shows the cell cycle in circular form.

Overview of the Cell Cycle

By University of Maryland University College CC-BY-NC.

In cell replication, chromosomes are moved to new locations. Like packing household materials into a box before moving, condensing the chromosomes helps with this process. Chromosomes are condensed by wrapping them more tightly around histones (proteins found in the nucleus).

If a cell is going to reproduce, more DNA is needed. During mitosis, one cell divides into two cells containing identical genetic material. This requires twice as much DNA, because there must be one complete set for each daughter cell. Meiosis also requires the DNA to be replicated. DNA replication (or DNA synthesis) occurs in the synthesis (S) stage of the cell cycle.

After a chromosome has replicated, the two copies remain attached at a point called the centromere. Each copy of the chromosome is called a chromatid.

Before cell division, DNA is copied and condensed.

During cell division, each chromatid moves to one of the two daughter cells. Keeping the two copies of a single chromosome attached helps the sorting process. In human cells, there are a total of 46 chromosomes. After the S stage of the cell cycle, these chromosomes have replicated and there are now 92 total pieces of DNA. The process of mitosis must sort these into 2 identical piles of 46 chromosomes. The cell keeps the matching pairs attached to keep track of which chromosomes need to be sent to opposite poles.

This is rather like sorting a sock drawer. If all the socks are loose in the drawer, it can be challenging to find the identical mate to a sock. But if the sock mates are folded together, each bundle contains both mates in the set.

Overview of Mitosis

By University of Maryland University College CC-BY-NC.

Both mitosis and meiosis must keep track of the chromatids on a chromosome. In the Meiosis module, you will learn that meiosis must also keep track of homologous chromosomes. A diploid cell has two copies of each chromosome — one copy from each parent. These chromosome pairs are called homologous because they have the same genes, but may have different versions of that gene. For example, a homologous pair of chromosomes may have a gene for hair color. One chromosome in this homologue may contain a “blond” version of that gene and the other homologue may contain the “brown” version. Each gamete that is produced will get either the homologue with the brown version or the homologue with the blond version.

Use the activities on this page to review the process of mitosis. Do the activities as many times as you’d like, until you feel comfortable with the whole process.

The cell cycle is highly regulated. There are many checkpoints that are used to determine if the cell should or should not continue through the stages of the cell cycle. Many different environmental and internal signals are involved in determining whether or not a cell will complete division.

Checkpoints occur throughout the cell cycle. These checkpoints control whether or not a cell will continue dividing. Image adapted from a diagram by LadyofHats: Mariana Ruiz Villarreal in the public domain.

A healthy cell has many genes that produce proteins involved in the process of regulating cell division. Some of these genes produce proteins that encourage cell division. These proteins would be produced under circumstances where the cell should divide. For example, if you scrape your knee, the cells in that area need to be replaced. Other genes produce proteins that inhibit cell division. For example, healthy human cells grown on a petri dish would stop growing when they filled the dish. This is also an essential component of regulation. Cells that continue dividing when they should not can cause cancer.

Cancer cells do not respond to proper regulatory signals and divide when they should not divide. Image from the National Cancer Institute in the public domain.

Numerous research projects in the past and present are investigating cell cycle genes. Some of these research projects are focused on cancer treatments and cures and others are focused on understanding the biology of this process. Because much of this research is focused on cancer, the terminology used is generally focused on relationship to the disease.

For example, genes that inhibit cell division are classified as tumor suppressor genes. If these genes are working properly, a cell will not divide uncontrollably because these genes will stop the process. Genes that encourage cell division are called proto-oncogenes. If these genes are working properly, a cell will not receive the message to divide unless it should be dividing.

Mutations could cause these genes to stop working properly. Mutations are errors in DNA that can result from genetic predisposition or environmental factors. Mutagens are chemicals in the environment that produce mutations. Carcinogens are specifically those mutagens that have shown that they can cause cancer. Cigarettes, for example, contain carcinogens that can alter the DNA and disrupt proper regulation of the cell cycle.

Current efforts to decrease the use of cigarettes are correlated with a decrease in lung cancer. Image from the National Cancer Institute in the public domain. Chart illustrates a correlation between smoking and lung cancer in US males, showing a 20-year time lag between increased smoking rates and increased incidence of lung cancer.

The development of cancer requires mutations in BOTH proto-oncogenes and tumor suppressor genes. A malfunctioning proto-oncogene is called an oncogene because it promotes the development of cancer. The root “proto-” refers to "before" and the root “onco-” refers to "cancer." A defective tumor suppressor gene can no longer suppress tumors. Cancer is the result of numerous mutations in multiple genes involved in regulating the cell cycle.

There are two ways for organisms to reproduce: asexual and sexual. Many organisms, such as bacteria, fungi, and even some plants and animals reproduce asexually. During asexual reproduction, all of the genes in a cell are passed to its daughter cells. This means that the resulting cells are clones, or identical copies of the parental cell.

Asexual reproduction is efficient and fast. However, it only provides one set of genes to adapt to the environment. Think about trying to guess a number. Do you have a better chance of guessing the number if you get one guess or if you get two guesses? Sexual reproduction, in which the genes of two parents are combined, results in more genetic variability. This enables offspring to deal more successfully with environmental change. However, sexual reproduction is a more complex process and results in a smaller number of offspring. Interestingly, certain organisms that can reproduce both asexually and sexually will choose sexual reproduction only when environmental conditions are not optimal. That way, a smaller number of more variable, and thus more adaptable, offspring is produced. In optimal conditions, however, asexual reproduction is the favored mechanism.

As you learned, genetic information is contained in DNA, which in eukaryotic cells is bound to special proteins called histones. The combination of DNA and histone proteins is called chromatin. During the S phase of the cell cycle, the chromatin is loose, to facilitate DNA replication. Chromatin can condense to form chromosomes during nuclear division. Chromosomes have a typical appearance and can be organized in a karyotype.

Human Karyotype of a Male

Humans have 23 pairs of chromosomes (2n = 46). Of those 23 pairs, 22 are autosomes, and the 23rd pair are sex chromosomes. Sex chromosomes can be of two types: X and Y. Males have one X and one Y chromosome (XY), while women have two copies of the X chromosome (XX).

In sexual reproduction, two reproductive cells called gametes fuse in the process of fertilization. In order to avoid the duplication of the chromosome number, gametes are formed through a special form of cell division, meiosis, which halves the number of chromosomes. Cells with a single set of chromosomes are haploid (n), in contrast to the somatic (body) cells, which are diploid (2n). The fusion of the gametes during fertilization restores the diploid chromosome number in the first cell of the new individual, the zygote.

By University of Maryland University College CC-BY-NC

In the human life cycle, haploid gametes produced during meiosis fuse to form a diploid zygote, which goes through the process of mitosis to grow into an adult human. When the adult human produces haploid gametes, the process can be repeated.

Meiosis II begins with two haploid cells, each containing too much DNA. The events in meiosis II are almost identical to the events of mitosis.

In Meiosis II (which is essentially like mitosis), the sister chromatids separate from each other. Thus, as the result of meiosis, four haploid cells are produced. Note that those four cells are not always viable. In humans, male germ cells will produce four viable sperm cells. However, in the case of females, only one of the four will survive as an egg.

The end result of meiosis is four unique haploid daughter cells. Genetic variability is introduced in various ways during meiosis:

1. Crossing over during prophase 1: crossing over introduces novel combinations of traits among offspring.
2. Segregation of chromosomes into gametes: the maternal and the paternal copy of each chromosome pair will segregate to different gametes. However, which goes to which cell is a random process. Thus, the possible number of combinations is astounding: in the case of humans, with 23 chromosomes, it is 2²³ (8,388,608).

When you add that fertilization is also a random process, you can get an idea of the incredible number of combinations of possible offspring showing up even in one family.

Why do children look like their parents? How do rose growers get so many different colors of roses — pink, red, white, yellow, purple, peach, striped, and many more? How can there be different-colored puppies within one litter?

Inheritance is the way that organisms pass traits to their offspring. Because offspring possess some (or all) of the genetic information from their parents, they also share many traits in common with their parents.

In the Cell Division unit, you learned that cells pass on a complete set of genetic information (contained in the DNA), which is transmitted from parent cells to daughter cells. This genetic information helps determine many of the characteristics of the offspring. In humans, for instance, DNA is responsible for a child’s height and skin pigmentation. It also helps determine the overall health of the child by regulating many physiological characteristics, such as the condition of the heart and lungs, as well as brain and blood chemistry.

How much of our physiological makeup is determined by genetics, and how much is determined by other factors, such as personal choice and environment? This question is a source of ongoing debate in both scientific and philosophical communities. Environmental factors can influence our DNA, and our DNA can influence how we react to environmental factors. If we are ever able to answer this question, the answer will likely be complex.

In this unit, you will focus on the direct links between genetic information and visible traits. This will help you to learn how genetic information can be passed from one generation to the next and how these genes affect the later generation. We will introduce simple examples of traits that are clearly visible and have a direct correlation to genetics.

The Cell unit discussed the components of the cell. One of these components is the DNA, which is arranged into one or more chromosomes. Each chromosome contains many genes. A gene is a region of a chromosome that has a specific function. For example, genes can contain information required to make a protein. How this happens will be discussed in the Molecular Genetics Unit.

DNA carries the information about how proteins are built, and proteins carry out many of the reactions necessary for living organisms. The Proteins module discussed the variety of roles proteins can play in a living organism. Some proteins produced by living organisms determine the traits we can observe. These visible traits are called the phenotype of an organism.

For example, protein enzymes in plants catalyze production of the pigments, resulting in flowers of different colors. The color of the flower is one of the observable traits, or the phenotype of the plant. The genetic information that produces these traits is called the genotype of an organism. Depending on the pigment production, the flowers can have red, blue, or white color. Flower color is determined by specific genes in the cells. The variations in the same gene are called alleles. In our example, different alleles of the pigment-producing gene can result in more or less pigment, and, consequently, in darker or light flower color.

In this unit, you will learn about the genotype and phenotype of diploid organisms. Diploid cells have two copies of each chromosome; haploid cells have only one copy of each chromosome. Because diploid cells have two copies of each chromosome, they also have two copies of every gene. One set of chromosomes (and, therefore, one copy of each gene) is from the mother (or egg) and one set is from the father (or sperm). Diploid cells can have two of the same alleles of a gene, or they can have two different alleles of a gene. Cells that have the same allele are called homozygous (“homo” meaning "same," and “zygous” referring to the reproductive cells produced from meiosis). These cells are called homozygous because all of their reproductive cells (gametes) will have identical alleles. Cells with different alleles are called heterozygous (“hetero” meaning "different") because they will produce reproductive cells that have different alleles of this gene.

By U.S. National Library of Medicine (Gregor Mendel) Public Domain

Gregor Mendel was a nineteenth-century Augustinian monk in Bohemia, a country in Europe that is now part of the Czech Republic. In 1853, Mendel left the monastery for two years to study at the University of Vienna, where he learned about mathematics and botany. When he returned to the monastery, he began investigating how plants passed on their characteristics to their offspring. He was conducting this research only a few years before Charles Darwin published On the Origin of Species.

Mendel set out to understand inheritance by breeding pea plants. By collecting peas from pods produced after fertilizing two parent pea plants, Mendel could then grow those peas into new pea plants and see how these offspring resemble or differ from the parent plants. The heritable characteristics that Mendel studied included seed color and shape, pod color and shape, flower color and position, and stem length. Each of the traits that Mendel studied occurs only in two forms, or phenotypes. For instance, pea flower color is a trait that can exhibit either the purple phenotype or the white phenotype.

So if we know the phenotype, and we know that those two varieties would always result in same-color flowers, we can deduce that all individuals (plants) in that population (purple or white) have the same alleles for the gene that determines flower color.

Next, Mendel crossed the purple variety with the white variety. He manipulated his plants so he could control which plant pollinated which. In plants, pollen is the male gamete, landing on the flower to fuse with the ovule—the female gamete. The resulting zygote will give rise to the seed, or embryo.

When Mendel crossed purple and white flowers, the first generation of plants, which he designated “F1,” were all purple. Somehow, purple was “stronger,” or dominant over the white. So if the alleles of the purple flowers were symbolized by “B," then the allele corresponding to white flowers was “weaker” and is symbolized by “b.” If the genotype of the parent purple flower is BB, then the genotype of the parent white plant will be bb.

Let’s see what happened during that first cross. You will use a tool called a Punnett square, which graphically shows the possible combinations of the gametes of the parents. In a Punnett square, you place the possible gametes from each parent along the top and left side of the square. What you are representing here is the Law of Segregation: during meiosis I, the chromosome pair separates, resulting in haploid gametes. Each gamete will have only one allele.

Then you combine the possible gametes with each other to see all possible combinations, as shown in this example.

As you can see, 100 percent of the offspring have the Bb genotype, but 100 percent also show the purple phenotype. You might expect the offspring to show a phenotype that somehow blends the parental phenotypes. Sometimes this happens, but in the case of these pea plants' flower color, the purple allele (B) is dominant over the white allele (b). Stated another way, the white allele (b) is recessive to the purple allele (B).

In many, but not all, cases it is possible to pinpoint a phenotype to one allele. Remember, alleles are variants of genes, and genes code for proteins. In this example, the purple color may be due to an enzyme that produces a purple pigment. If the allele codes for a mutated enzyme that does not perform as expected, the resulting flower would be white. A flower with BB or Bb genotype has the normal enzyme — purple pigment is produced — and even the heterozygous flower, which has only one allele for the normal enzyme, produces enough pigment for the flower to be purple. The bb flower, on the other hand, has no functioning enzyme, so the flower remains white.

There are some easily observable human traits that follow the Mendelian inheritance pattern, showing a dominant and a recessive allele. Examples include unattached earlobes (dominant) versus attached earlobes (recessive). The widow’s peak hairline, a cleft chin, rolling tongue, and hitchhiker’s thumb are others. Does the ability to roll your tongue make you more fit for survival? Not really! One common misconception is that dominant traits are more favorable from an evolutionary point of view. Another is that dominant traits are more common. We cannot stress enough that traits, and particularly human traits, are determined by complex interactions between genes and environment. In the early days of genetics, simple observable traits were used to describe inheritance patterns. Once the molecular basis of inheritance was established, scientists could tackle more complex interactions. You will learn more about this in the Molecular Genetics unit.

There are around seven billion people on our planet, and everybody looks at least a little different from everyone else. Siblings are different from each other, and even identical twins—who are genetically identical—can show different traits over time. However, when we look at families over several generations, it becomes obvious that certain traits appear generation after generation. How can this extraordinary variability be explained?

In the previous module you learned about the inheritance patterns (Mendelian and non-Mendelian) that were studied using models such as peas, snapdragons, and dogs. Another organism that is often used is the fruit fly Drosophila. Common to these organisms is that they are relatively easy to breed and cross under controlled conditions. They also have a relatively short lifespan, which allows the tracking of traits for many generations. In the case of humans, genetic analysis is much more complicated. We live under a variety of conditions, so the environmental influences are much stronger. Humans choose their mates freely, families are usually smaller, and our lifespan is the same as that of the geneticists. Much information about transmission of human traits comes from the study of pedigrees, a chart of genetic connections similar to a family tree. In this module, you’ll learn how to read pedigrees. You’ll also look at the different patterns and factors that affect human inheritance.

Many human traits are clear-cut and easy to test. These include the ability to bend back the thumb nearly 90 degrees (known as “hitchhiker’s thumb”), to roll the tongue into a U-shape, and to taste a bitter chemical called phenylthiocarbamide. While these traits do not have considerable implications on human health and species survival, many others do. Some of them are related to disorders such as sickle cell anemia, hemophilia, Tay-Sachs disease, and Down syndrome, to name a few.

Left, a tongue-rolling girl. Tongue rolling is a dominant trait that follows Mendelian inheritance. By Gideon Tsang (Rolled tongue flikr) CC BY-SA 2.0 Right: Queen Victoria and the royal family. Hemophilia, a blood clotting disorder transmitted by sex-linked inheritance, affected 18 of Queen Victoria’s 69 descendants. By M.W. Ridley (Queen Victoria and Royal Family) Public Domain

Some human traits (like the tongue-rolling ability) follow Mendelian patterns, which means they are controlled by a single gene. One of the alleles is dominant, and the other is recessive. Human genetic disorders following a Mendelian pattern are the least common. Most of those tend to be recessive, meaning that the defective allele causing the disorder is recessive. That means only homozygous recessive individuals will show the disorder. The heterozygotes will be carriers, so while they carry the defective allele (and sometimes even express it, as in the sickle cell trait), they phenotypically do not present the full disorder. Other disorders may be dominant, wherein the defective allele causing the disorder is dominant. In this case, the presence of only one allele is enough to provoke the appearance of the disorder, and only homozygous recessive individuals show the healthy phenotype.

As you remember from the Meiosis module, of the 23 pairs of chromosomes found in a human somatic cell, 22 are autosomes, and the 23rd pair are sex chromosomes. Sex chromosomes are of two types: X and Y. Males have one X and one Y chromosome (XY), and females have two copies of the X chromosome (XX). If the gene responsible for the disorder is present on the autosomes, it is called an autosomal disorder. The term “autosomal” refers to chromosomes that are not sex determining. On the other hand, if the responsible gene is present on a sex chromosome, it is called a sex-linked disorder. Due to the fact that the male Y chromosome is very small and contains only genes related to sex determination, sex-linked disorders are due to defective alleles on the X chromosome. The following table shows the inheritance patterns of some human genetic disorders and abnormalities.

In humans, determination of sex is dependent on a special pair of chromosomes called the sex chromosomes. The other 22 pairs are called autosomes.

There are two types of sex chromosomes — X and Y. The X chromosome is large and carries many genes unrelated to sex. The Y chromosome, on the other hand, is much smaller and carries only the genes containing the instructions for “maleness,” which are molecular signals that instruct the fetal gonads (sex organs) to develop as testes and not ovaries. In the absence of the Y chromosome, a fetus develops as female.

Females have two copies of the X chromosome (XX), while males carry one X and one Y (XY). When gametes are formed, females will have only gametes that contain the X chromosome; males will have some gametes with X and others with Y. For a male baby, a Y gamete from the father has to meet the mother’s gamete. So the determination of a baby’s sex depends on which gamete the father contributes.

About one out of every ten men is color-blind. People who are color-blind are unable to distinguish between certain colors, especially green and red. On the other hand, only about one out of every 200 women is color-blind. Why is there such a drastic difference between the sexes?

In 1910, an American geneticist named Thomas Hunt Morgan made an observation that began to shed some light on this question. One morning, when peering through a hand lens at a male fruit fly, he noticed that it didn’t look right. Instead of having the normally brilliant red eyes of wild-type Drosophila melanogaster, this fly had white eyes. Morgan was particularly interested in how traits were inherited and distributed in developing organisms, and he wondered what caused this fly's eyes to deviate from the norm.

A fruitfly (Drosophila melanogaster) displaying the normal red-eyed phenotype. By André Karwath (Drosophila melanogaster - side) CC-BY-SA-2.5

He bred the white-eyed male with several true-bred, red-eyed females and obtained all red-eyed flies in the first generation. (Remember, true-bred organisms have a homozygous genotype.)

Morgan did crosses between the F1 hybrids, and he observed the following: 75 percent of the offspring were red-eyed, and 25 percent were white-eyed. So far, the results supported the Mendelian pattern of 3:1. But then he noticed something odd: all of the white-eyed flies were male.

Morgan wondered why the white-eye trait was associated with the male sex. In Morgan’s time, the idea that an additional pair of chromosomes was responsible for sex determination had just emerged. There were two plausible possibilities: either the trait was somehow linked to the sex chromosome, or the white-eyed trait was lethal for females, meaning that females with the phenotype would not develop past the egg stage. Morgan conducted a series of crosses using the F2 generation, and obtained some white-eyed females also, showing that the white-eyed characteristic was not lethal for females.

In a famous subsequent experiment, Morgan crossed white-eyed females with white-eyed males, obtaining only white-eyed offspring. This cross confirmed that the eye color trait was linked to the female sex chromosome. Because of this, the males are what is called hemizygous for this trait: they have only one allele present, which is in the X chromosome. The Y chromosome does not have the same genes as the X chromosome. Males have no heterozygous option: they either have the dominant allele (red-eyed) or the recessive allele (white-eyed).

The trait of white eyes in fruit flies is a sex-linked trait. It is located on a sex chromosome, so it occurs at different rates in males and females. Because it is located on the X chromosome, it is more specifically called an X-linked gene. In humans, the trait of color blindness results from a gene on the X chromosome. So do some more serious diseases, including Duchenne muscular dystrophy, which causes progressive muscle weakness. People with this disorder rarely live past the age of 25. A gene on the X chromosome codes for a muscle protein that is missing in people with Duchenne muscular dystrophy.

Human chromosomes are numbered from largest to smallest. Each of the 22 pairs of autosomal chromosomes have an identifying number, from 1 to 22; chromosome 1 is the biggest and chromosome 22 is the smallest. As you already know, the pair of sex chromosomes are named either X or Y. The chromosomes of a cell can be visualized using a process that takes a picture of the cell during mitosis, when chromosomes are easily visible. The picture that is produced is called a karyotype.

A karyotype visualizes the chromosomes of a cell. By National Human Genome Research Institute (Sky spectral karyotype) Public Domain

Karyotypes can be used to identify chromosomal abnormalities in cells or in developing fetuses. Amniocentesis is a medical procedure used to sample fetal cells from a pregnant mother. These cells, which are rapidly dividing, can be used to create a karyotype of the fetus. This karyotype can then help identify potential chromosomal abnormalities in the developing child. Abnormalities could include extra chromosomes, missing chromosomes, and even extra or missing pieces of chromosomes.

By National Human Genome Research Institute (Down Syndrome Karyotype) Public Domain

This karyotype has an extra chromosome 21. This condition is called “trisomy 21” because the cell has three ("tri") of these chromosomes instead of the usual two. This condition is more commonly called “Down syndrome.” There are relatively few examples of such large-scale chromosomal anomalies. Down syndrome results from an extra copy of one of the smallest chromosomes. Extra or missing copies of sex chromosomes can also result in viable embryos. Embryos with extra or missing chromosomes are often nonviable, and other chromosomal anomalies are not generally seen.

Aneuploidy is the condition of having too many or too few chromosomes, which results from errors in meiosis. If crossing-over does not occur correctly, the chromosomes can have extra pieces or missing pieces. If the chromosomes do not separate properly during anaphase, the resulting cells can have extra or missing chromosomes. This improper separation of chromosomes is called nondisjunction. Nondisjunction can occur in either meiosis I or meiosis II.

The following activity looks at aneuploidy that results from nondisjunction in Meiosis I.

Nondisjunction can also occur at Meiosis II. Complete the following activity to learn more.

Pedigrees are maps that can be used to trace genetic traits through generations of individuals. Pedigrees use the following symbols:

• Males are symbolized by squares.
• Females are symbolized by circles.
• Mated individuals are connected by a horizontal line, and children are connected to them by vertical branches extending down from the line.
  
• Individuals expressing a genetic trait are shaded; individuals not expressing the trait are not shaded.
  

Pedigrees can be used to determine if the trait being studied is dominant, recessive, or X-linked. A trait is recessive if a child anywhere in the family has the trait and both parents do not. This must be the case because if the child has the trait and the parents do not, the only possible genotype option is:

It would not be possible for an affected individual to show a dominant trait that was not expressed in his or her parents, because this sets up an impossible situation where the child would have an allele that could not come from either parent:

If there is no case where a child expresses the trait but neither parent does, then the pedigree is likely to be dominant. In a real-world situation, researchers would need to look at hundreds of individuals to be sure that this conclusion is statistically significant. But for the purposes of this activity, you will look at only a few individuals.

A trait that is significantly more common in males than females is likely to be X-linked. Again, in a real-world situation a much larger sample size would be needed to be sure of these conclusions. The X-linked traits used here are also recessive, so you will notice that they show both characteristics of being X-linked (mostly males) and characteristics of being recessive (child demonstrating a trait that neither parent has).

Progeria (Hutchinson-Gilford Progeria Syndrome, HGPS)

Child with progeria. HGPS is a childhood disorder caused by mutations in one of the major architectural proteins of the cell nucleus. In HGPS patients, the cell nucleus has dramatically aberrant morphology (bottom, right) rather than the uniform shape typically found in healthy individuals (top, right). By P Scaffidi (Hutchinson-Gilford Progeria Syndrome) CC BY 2.5

HGPS is an extremely rare (one case per eight million live births) autosomal dominant disorder characterized by accelerated aging. The disorder is caused in the gene coding for lamin A, a protein involved in chromosome organization. The defective protein accumulates in the nuclear membrane of the cells, affecting many cellular processes. Symptoms start before age two, with thinning skin and weak muscles and bones. Aging is estimated to be eight to 10 times faster than normal. Patients die in their teens from stroke or heart attack. How do people “get” progeria? It is important to remember that because progeria patients die at a very young age, progeria is not inherited, but only appears as a random mutation. This explains its fortunately very low incidence.

In the Classical Genetics unit, you learned about the mechanisms of inheritance, focusing mostly on the organism and population levels in the hierarchy of life. In the Molecular Genetics unit, you will learn about the molecular basis of traits that characterize the organisms. You will develop an understanding on the molecular level of how genetic information is organized and used by living organisms.

DNA carries all the information needed to build living organisms. Information in DNA is used to build proteins, which cause the physical traits, or phenotypes, of an organism. The central dogma describes how the information in the DNA is used to build a molecule of mRNA, which provides instructions to the ribosome for building the proteins that cause the physical traits.

If we compare traits of individuals within species, we find that they share certain traits, but they also show many differences among individuals. Fore example, rice (pictured below) shows variation in shape and color of seeds/grains. People also come in different shapes and sizes. What determines physical traits that characterize a person: hair color, eye color, height, weight? How about behavior: some people are risk-takers, others get easily anxious; some people love to be in large noisy crowds, others prefer quiet and solitude. What is more important in determining physical and behavioral traits — genetics or environment? This classic “nature vs. nurture” argument should not be phrased as “either/or,” because the answer is “both.” The interactions between genes and environment determine the traits.

Rice seed collection. Source: BY Kleomarlo (Rice diversity) CC-BY-2.0

A better question to ask is “To what extent is each trait determined by genetics and to what extent by environment?” The answer will vary by trait and is still being researched. It is not a trivial question to answer, and the numbers below are only rough estimates.

In Molecular Genetics, first you will learn about the storage, transmission, and expression of genetic information (central dogma of molecular biology), whereby the information content in DNA sequences, called genes, is ultimately converted to a protein. Then you will look at the structure of genes and genomes and at the interactions between genes and the environment. Finally, you will examine how humans are able to manipulate genes through biotechnology.

If you look at people around you, you will probably notice a fairly large variation in height. Some people are taller than you, while others are shorter than you. Consider this trait as an example that you want to understand on the molecular level. What kinds of molecules may be involved in determining a person’s height? If you and your parents are relatively short (or tall), you may say that you inherited the short (or tall) stature from your parents. What molecule is involved in the transmission of information from one generation to the next? DNA. How does information contained in DNA affect your height? One possible explanation is that your DNA contains a gene encoding a protein called growth hormone. This protein is produced by the pituitary gland, travels to other tissues, and delivers a signal for the cells to grow and divide. Changes in the amount of protein produced or the sequence of amino acids in the protein can affect the function. If bone and muscle cells receive only a small number of signal molecules, the person will end up with a short stature. If they receive a large number of signal molecules, the person may end up being very tall. For a signaling protein (hormone) to deliver the signal, there must be a protein that can bind the hormone and receive the signal (receptor protein). The variation in height will result from any of the following:

• The amount of signaling protein produced.
• The amount of receptor produced in different tissues.
• How tightly the hormone and the receptor bind to each other; small variations in specific amino acids of either molecule can change the binding interaction.

Note that a person who inherits “tall” genes may never grow very tall because of illness or inadequate nutrition. Conversely, a person who inherits a faulty growth hormone gene may grow relatively tall if he or she is treated with growth hormone. These are examples of how environment and genes interact to produce traits and phenotypes.

In this module, you will learn about how genetic information is stored in DNA and copied for the next generation. You will also look at a practical application of the process of DNA replication called the polymerase chain reaction (PCR). In the next module, you will learn how the genetic information stored in genes is expressed, resulting in the variety of traits and phenotypes of all organisms.

Nucleic acids are macromolecules that carry out two main functions in the cell: storage of genetic information and synthesis of proteins. Two types of nucleic acids specialize in these functions: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material that stores information for making proteins in all living organisms. Some viruses store their genetic information in RNA instead of DNA. This may seem as an exception to the universal use of DNA as genetic material; however, viruses are not cellular, and are not considered living organisms. DNA is found in the nucleus of eukaryotes and in two cellular organelles: chloroplasts, and mitochondria.

Location of DNA in Cells

Location of DNA in Prokaryotic Cells

In prokaryotes, DNA is not enclosed in a separate compartment, but found in the cytoplasm.

Bacteria Cell

Regardless of where DNA is stored in the cell, it contains instructions for building proteins. For protein synthesis to occur, genetic information stored in DNA must first be copied into RNA. In eukaryotic cells, RNA is transported to the cytoplasm, where protein synthesis takes place. Thus, while both RNA and DNA can contain instructions for making proteins, DNA is used for storage of this information, while RNA is directly involved in making proteins.

To understand in more detail how nucleic acids function in transmission of genetic information and in protein synthesis, you must first consider the structures of these molecules and the relationship between structure and function.

The genetic information of an organism is stored in DNA molecules. How can one kind of molecule contain all the instructions for making complicated living beings like ourselves? What component or feature of DNA can contain this information? It has to come from the nitrogen bases, because, as you already know, the backbone of all DNA molecules is the same. But there are only four bases found in DNA : G, A, C, and T. The sequence of these four bases can provide all the instructions needed to build any living organism. It might be hard to imagine that 4 different “letters” can communicate so much information. But think about the English language, which can represent a huge amount of information using just 26 letters. Even more profound is the binary code used to write computer programs. This code contains only ones and zeros, and think of all the things your computer can do. The DNA alphabet can encode very complex instructions using just four letters, though the messages end up being really long. For example, the E. coli bacterium carries its genetic instructions in a DNA molecule that contains more than five million nucleotides. The human genome (all the DNA of an organism) consists of around three billion nucleotides divided up between 23 DNA molecules, or chromosomes.

The information stored in the order of bases is organized into genes: each gene contains information for making a functional product. The genetic information is first copied to another nucleic acid polymer, RNA (ribonucleic acid), preserving the order of the nucleotide bases. Genes that contain instructions for making proteins are converted to messenger RNA (mRNA). Some specialized genes contain instructions for making functional RNA molecules that don’t make proteins. These RNA molecules function by affecting cellular processes directly; for example some of these RNA molecules regulate the expression of mRNA. Other genes produce RNA molecules that are required for protein synthesis, transfer RNA (tRNA) and ribosomal RNA (rRNA).

In order for DNA to function effectively at storing information, two key processes are required. First, information stored in the DNA molecule must be copied, with minimal errors, every time a cell divides. This ensures that both daughter cells inherit the complete set of genetic information from the parent cell. Second, the information stored in the DNA molecule must be translated, or expressed. In order for the stored information to be useful, cells must be able to access the instructions for making specific proteins, so the correct proteins are made in the right place at the right time.

Both copying and reading the information stored in DNA relies on base pairing between two nucleic acid polymer strands. Recall that DNA structure is a double helix (see figure below).

DNA Structure (B-helix)

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The sugar deoxyribose with the phosphate group forms the scaffold or backbone of the molecule (highlighted in yellow in the figure above). Bases point inward. Complementary bases form hydrogen bonds with each other within the double helix. See how the bigger bases (purines) pair with the smaller ones (pyrimidines). This keeps the width of the double helix constant. More specifically, A pairs with T and C pairs with G. As we discuss the function of DNA in subsequent sections, keep in mind that there is a chemical reason for specific pairing of bases.

To illustrate the connection between information in DNA and an observable characteristic of an organism, let’s consider a gene that provides the instructions for building the hormone insulin. Insulin is responsible for regulating blood sugar levels. The insulin gene contains instructions for assembling the protein insulin from individual amino acids. Changing the sequence of nucleotides in the DNA molecule can change the amino acids in the final protein, leading to protein malfunction. If insulin does not function correctly, it might be unable to bind to another protein (insulin receptor). On the organismal level of organization, this molecular event (change of DNA sequence) can lead to a disease state — in this case, diabetes.

Before a cell can divide, it must first make a copy or replica of its DNA through a process called DNA replication. This process occurs during the S phase of the cell cycle, so by the time the cell enters the mitotic phase, there are two copies of the DNA molecule. This process of DNA replication takes place in the nucleus of the cell in eukaryotes, where the DNA molecule is found. It also occurs in the mitochondria in animal cells and chloroplasts in plant cells.

Think about this: it is critical that the copies of the DNA are exactly like the original, so the daughter cells are identical to the parent cells. There may be changes to DNA sequence by mutations (as you will see in another section), and meiosis introduces some genetic variability when gametes are produced. But for unicellular organisms or for somatic cells, DNA replication is a process that requires high fidelity.

The process of DNA replication is catalyzed by a type of enzyme called DNA polymerase (poly meaning many, mer meaning pieces, and ase meaning enzyme; so an enzyme that attaches many pieces of DNA). Observe the figure below: the double helix of the original DNA molecule separates (blue) and new strands are made to match the separated strands. The result will be two DNA molecules, each containing an old and a new strand. Therefore, DNA replication is called semiconservative. The term semiconservative refers to the fact that half of the original molecule (one of the two strands in the double helix) is “conserved” in the new molecule. The original strand is referred to as the template strand because it provides the information, or template, for the newly synthesized strand.

By Madprime(wikipedia) (DNA replication split horizontal) CC BY-SA 2.0

DNA replication relies on the double-stranded nature of the molecule. One double stranded DNA molecule, when replicated, will become two double-stranded molecules, each containing one original strand and one newly synthesized strand. You remember that the two strands of DNA run antiparallel: one from the 5’ to the 3’, and the other from the 3’ to the 5’. The synthesis of the new DNA strand can only happen in one direction: from the 5’ to the 3’ end. In other words, the new bases are always added to the 3’ end of the newly synthesized DNA strand. So if the new nucleotide is always added to the 3’ end of an existing nucleotide, where does the first nucleotide come from? In fact, DNA polymerase needs an “anchor” to start adding nucleotides: a short sequence of DNA or RNA that is complementary to the template strand will work to provide a free 3’ end. This sequence is called a primer.

How does DNA polymerase know in what order to add nucleotides? Specific base pairing in DNA is the key to copying the DNA: if you know the sequence of one strand, you can use base pairing rules to build the other strand. Bases form pairs (base pairs) in a very specific way. The figure shows how A (adenine) pairs with T (thymine) and G (guanine) pairs with C (cytosine). It is important to remember that this binding is specific: T pairs with A, but not with C. The molecular recognition occurs because of the ability of bases to form specific hydrogen bonds: atoms align just right to make hydrogen bonds possible. Also note that a larger base (purine, A or G) always pairs with a smaller base (pyrimidine, C or T).

By Madeleine Price Ball (DNA chemical structure) CC-BY-SA-2.0

Now that you understand the basics of DNA replication, we can add a bit of complexity. The two strands of DNA have to be temporarily separated from each other; this job is done by a special enzyme, helicase, that helps unwind and separate the DNA helices. Another issue is that the DNA polymerase only works in one direction along the strand (5’ to 3’), but the double-stranded DNA has two strands oriented in opposite directions. This problem is solved by synthesizing the two strands slightly differently: one new strand grows continuously, the other in bits and pieces. Short fragments of RNA are used as primers for the DNA polymerase.

By Mariana Ruiz (DNA replication) Public Domain

Much of our DNA contains a number of short DNA segments that are repeated over and over again at different locations in our genome. The number of these tandem repeats at each location in the genome can differ from individual to individual, with 5 to 20 percent of individuals having the same number of tandem repeats at the same location.

Illustration of the variation in tandem repeats in the human population. Two chromosomes are shown, and the tandem repeats in each chromosome are shown as yellow (chromosome 1) or blue boxes (chromosome 2). The two individuals have the same number of tandem repeats on chromosome 1, but a different number of repeats on chromosome 2.

Variations in the number of tandem repeats are detected by the polymerase chain reaction, using primers that bind to unique sequences on the edges of the repeat.

Amplification of repetitive DNA by PCR. The region of DNA containing the repeats is shown on the top; the PCR product is on the bottom.

If the two DNA samples show a different number of repeats, then the samples must have come from two different individuals. If two DNA samples show the same number of repeats at one location, then there is a chance that the two DNA samples came from the same individual. This is not a very reliable indication that the DNA samples came from the same individual, since a significant fraction of people can have the same number of tandem repeats at any one location in the chromosome. To increase the reliability of a positive match between the two samples, a total of 13 different locations of tandem repeats are amplified, and the number of repeats at each location are compared. If any of the 13 locations differ in the number of repeats, the two DNA samples came from different individuals. However, if all 13 agree, there is a greater than 99.99 percent probability that the two DNA samples came from the same individual. There is still a 0.01 percent chance that the DNA came from two different people who just happened to have the same number of tandem repeats at each of the 13 different locations.

In the previous module, you learned how genetic information is stored in DNA and how it is passed in its totality to the next generation through the process of DNA replication. You also read about PCR, a practical application of the DNA synthesis process. In this module, we will focus on how this information is expressed. Information contained in DNA is organized into genes, and each gene contains instructions for making a functional product: an RNA molecule or a protein. This process of making the functional gene product is gene expression. Different cells can contain the same DNA, but they express different genes and produce different proteins according to their function. For example, red blood cells produce the protein hemoglobin, which is required for delivery of oxygen throughout the body. Nerve cells contain the same DNA, but the hemoglobin gene is not expressed. Instead, nerve cells make RNA copies of the genes that encode proteins required for signaling.

Both a nerve cell (left) and a red blood cell (right) develop from cells that have identical DNA, but the expression of different genes leads to structural and functional differences between the cells.

Even cells of the same type may express different genes and therefore produce different proteins, depending on their needs or environmental conditions. For example, pancreatic beta cells produce insulin when blood sugar levels are increased. Weightlifting increases muscle mass because it increases the production of proteins in the muscle cell. Sex hormones are not produced until the beginning of puberty.

Multiple proteins expressed at specific levels at specific times in the cell determine the phenotype. In this module, we will consider each of these processes in more detail, and we will conclude by looking at how changes in DNA sequence can affect the proteins encoded by DNA.

The flow of information in a cell is described by the central dogma of molecular biology.

In eukaryotic cells, DNA stores the genetic information, which is passed from generation to generation through the process of DNA replication. During replication, the whole sequence of DNA is copied. In order for the information stored in DNA to be used by a living cell, the information must be expressed (gene expression). First, DNA is transcribed into one form of RNA called messenger RNA, or mRNA, through the process of transcription; then mRNA can be translated into an amino acid sequence forming a protein through the process of translation. The ribosome translates the RNA sequence into a protein sequence, using three nucleotide bases to encode each amino acid DNA also encodes two other RNA molecules, transfer RNA (tRNA) and ribosomal RNA (rRNA). Although these RNA molecules do not directly encode proteins, they are both required for protein synthesis.

Transcription and translation are often confused. Transcription is copying the information without changing the language. This word comes from the same root as scribe, a word that describes someone who made copies of books in medieval times. DNA and RNA are considered the same chemical “language” because their monomers are nucleotides.

Now, compare transcription to translation. Just as translators of books change information from one language to another, the cellular process of translation changes information from the language of nucleic acids (using nucleotides as the monomers) into the language of proteins (using amino acids as monomers).

A scribe copying information by Meister des Maréchal de Boucicaut; artwork in the public domain. On right, a dictionary used to translate from the language of English to Spanish.

Note that there are exceptions to the central dogma. It is thought that during the dawn of life, RNA was the first molecule to store genetic information, and certain viruses still have RNA as their nucleic acid component. In fact, certain viruses (among them the human immunodeficiency virus, or HIV) have an enzyme capable of making DNA using RNA as a template. However, you will recall that viruses are not cells, so it is safe to say that cells use DNA as their genetic material, and the flow of information goes as follows:

Gene expression, a process that is central to all living cells, can be summarized as a list of the following steps:

• the DNA double helix is separated
• an enzyme called RNA polymerase moves along one strand and transcribes the information from one strand of DNA into a strand of RNA
• the ribosome translates the RNA sequence into a protein sequence.

In eukaryotes, DNA and ribosomes reside in separate compartments, so an additional step is required: the transportation of RNA out of the nucleus and into the cytoplasm.

The animation below illustrates the process of gene expression in eukaryotes. Watch the animation, and then label still frames of the animation in the Learn By Doing activity.

During gene expression, information stored in DNA is first copied (or transcribed) into RNA in a process called transcription. Only one of the two DNA strands is transcribed, and the order of bases in RNA is determined by the base pairing of the ribonucleotides with the DNA. In RNA, the base T is absent and U is present instead. As you know, A pairs with T, but because T is replaced by U in RNA, A pairs with U in RNA. If the transcribed DNA strand has the sequence

and the bottom stand is used as a template to produce the RNA copy, the sequence of the RNA will be

Note that it the transcribed RNA has exactly the same sequence as the upper DNA strand, but with T replaced by U.

Genetic Code Table

This table summarizes the amino acids that result from each codon on mRNA. The first letter in the codon is on the left. The second is on the top, and the third is on the right.

learn by doing

The genetic code table allows us to convert the information contained in a nucleic acid into an amino acid sequence. How does the cell do this during translation? Translation from one language to another requires a dictionary, a book that connects words in two different languages. In the cell, we need a molecule that connects codons and amino acids. That molecule is transfer RNA (tRNA). Each tRNA contains three bases that can pair with a particular codon in mRNA (complementary base pairing). Each tRNA also carries a specific amino acid. The tRNA binds mRNA via base pairing and brings the correct amino acids to the growing polypeptide chain.

By Boumphreyfr(Wikipedia) (Peptide syn) CC BY-SA 3.0

The last type of RNA molecule that is critical for translation is ribosomal RNA (rRNA). rRNAs are components of the ribosome. The ribosome is a large macromolecular complex composed of rRNA and ribosomal proteins. The ribosome catalyzes the formation of peptide bonds between the amino acids. Some ribosomes are located in the cytosol and translate cytosolic proteins. Some ribosomes are attached to membranes; these ribosomes translate proteins destined to be inserted into the membrane or secreted outside the cell.

To summarize, three types of RNA carry out distinct roles in translation: mRNA encodes the protein, tRNA brings amino acids to mRNA, and rRNA is a component of the ribosome required for catalysis.

In the exercise below, you will simulate the process of transcription and translation and build a small protein. Complete the activity and then answer the questions below.

None of the processes discussed so far are free of errors. Errors can be made during transcription if incorrect nucleotides are incorporated into the growing RNA strands. Errors can happen during translation if incorrect amino acids are inserted into a growing protein, or if translation is terminated too soon. Errors during gene expression have generally short-lived effects and can be overcome by additional RNA or protein synthesis.

Errors during DNA replication can have a much longer lasting effect. If incorrect nucleotides are incorporated into a newly synthesized DNA strand, the error may be passed on to future generations. Such heritable changes are referred to as mutations. Some mutations happen due to large scale rearrangements of DNA molecules that involve thousands or millions of nucleotides. We will limit our discussion here to small-scale changes that involve one or a few nucleotides in the coding sequence of a gene. These mutations include substitution of a single nucleotide base and insertion or deletion of one or more bases.

Let us consider how different types of mutations affect the proteins encoded by DNA. The sentence below represents a protein-coding gene. Each three letter word carries some meaning – equivalent to each amino acid being encoded by a three-letter codon in DNA.

• Silent mutations. A silent mutation changes the letter, but not the meaning. Recall that the genetic code is redundant: multiple combinations of three bases can encode the same amino acid.

• Missense mutations. A missense mutation changes a letter in DNA and also changes the encoded amino acid. It changes the meaning of the message as below:

• Nonsense mutations. A nonsense mutation changes an amino acid codon to a stop codon, terminating transcription:

• Frameshift mutations. A frameshift mutation occurs when one or two bases are inserted into or deleted from a sequence. As a result, subsequent codons are read incorrectly in new groupings of three bases each:

Deletion of one nucleotide: introduces frame shift

Deletion of three nucleotides removes information, but no frame shift.

There are many possible variations on the mutation types above. For example, three bases may be deleted in a group corresponding to one existing codon. In this rare instance, there would be no frame shift but a single amino acid would be missing from the encoded protein:

Next, we apply the classification above to an actual mutation observed in human DNA.

The activity below deals with a mutation in the gene that encodes the oxygen transport protein hemoglobin. The mutation causes hemoglobin to form long rods inside red blood cells. As a result, it is difficult for the cells to pass through blood vessels. This leads to a disease called sickle cell anemia in many of those who inherit the mutation.

You have probably seen Siamese cats--those graceful creatures with darker fur on their faces, tails, and paws. This is an example of a phenotype dependent on the interaction between genes and environment. Modern Siamese cats have a defective tyrosinase enzyme; tyrosinase is involved in the synthesis of melanin, the dark pigment of the skin. This defective enzyme is inactive at normal body temperatures, but it becomes active in cooler areas of the skin. This results in dark coloration in the coolest parts of the body, including the extremities and the face, which is cooled by the passage of air through the sinuses.

By Cindy McCravey (Neighbor's Siamese) CC BY 2.0

In this module, we will explore the connection between DNA and phenotype on the molecular level. We will start by clarifying the distinctions between genes, genomes, alleles, and other related terms. We will compare prokaryotic and eukaryotic genes and genomes, and we will look at how DNA is packaged into chromosomes with the help of specialized proteins. We will consider how gene expression can be regulated in the cell by interactions with other genes and environment.

Throughout the genetics unit, we have been using the terms gene, allele, and DNA, along with several other related terms. Before we go on, we need to clarify the relationships among these terms. First, we need to distinguish between terms that relate to actual molecules and terms that relate to the information content of those molecules. The macromolecule that carries genetic information is DNA, which in the eukaryotic cell binds specialized proteins to create compact structures called chromosomes.

All the hereditary information contained within an organism is called a genome. The genome includes genes and noncoding DNA sequences. The human genome, for example, contains the DNA sequence (information) of 22 autosomal chromosomes, as well as the two sex chromosomes X and Y. The field of study that focuses on the properties of genomes is called genomics, which is related to but distinct from genetics, which focuses on individual genes or a group of genes.

By KES47 (Chromosome en) CC BY 3.0

Genes carry the information required to produce a functional product (protein or RNA). The information is contained in the order of bases in the DNA. This information is “read” by the cell to produce, first RNA, and then a protein, during a process called gene expression. When a protein affects an observable characteristic of an organism (remember, observable characteristics represent an organism’s phenotype), the gene encoding that particular protein can be linked to that characteristic or character (e.g., hair color, eye color, or height). Traits are specific variations in characteristics (e.g., black hair or blue eyes). For example, the gene encoding growth hormone (a protein) affects the height of an individual; in this case, height is the characteristic, and tall or short stature are the traits. Some genes can be linked to the development of diseases. Nearly all observable characteristics depend upon multiple genes. Therefore, when we hear someone refer to the “obesity gene,” “Alzheimer’s gene,” “breast cancer gene,” and so on, it is important to realize that these labels imply (or should imply) one of the multiple genes that contribute to each of these conditions.

What is the connection between genes and traits? We must now consider alleles, which are observed variations in the sequence of bases for a particular gene. Two alleles of a gene may differ by a single base. On one end of the spectrum, an allele may refer to a total deletion of a gene. A diploid organism has two alleles of each gene, one from the organism’s mother and one from its father. The combination of the two alleles of a particular gene is the genetic determinant of the phenotypic traits of the organism. Note that in addition to genetic factors, environment also contributes to traits. We will consider environmental effects in a later section.

The arrows in the diagram show the relationships among the key terms gene, allele, trait, and character (or characteristic). The characteristic of eye color is used as an example to illustrate these relationships. Eye color depends upon production of the pigment melanin. Pigment production depends upon transport of tyrosine (the amino acid required to produce melanin) across the cell membrane. The transporter protein is encoded by the gene OCA2. A person with brown eyes produces functional transporter protein and plenty of pigment, leading to dark eye color. A mutation G to A in position 1559 of the coding DNA sequence of OCA2 leads to amino acid change in the transport protein; instead of alanine in position 481, threonine is present. This leads to reduced function of the transporter, which in turn results in decreased production of melanin. When the second allele is a deletion, an albino phenotype results (pale blue eyes, pale skin and hair color).

What is the difference between allele and mutation? Any change in the DNA of an organism is called a mutation. Mutations can be advantageous, harmful, or neutral (in which case they have no effect on the phenotype). Mutations include large deletions and rearrangements in the DNA, but they can also be changes in a single base. Mutation is a more general term than allele because mutation does not necessarily involve a specific gene, but can include deletion or rearrangement of multiple genes. Multiple alleles of a gene arise by mutation, and they will be passed on to the offspring and will persist in the population.

In the previous module, we mentioned different kinds of genes. Some genes produce functional RNA (rRNA and tRNAs), but most genes code for proteins. Remember that a gene is information residing in the order of bases in a DNA molecule. The general organization of information of any gene can be represented as follows:

In this module, we will focus on the structure of the protein-coding genes. A protein-coding gene contains information for making the mRNA that is translated into a protein. First, let’s consider what kind of information in the mRNA is required to produce a protein during translation, and then we will step back and look at the information in the gene that is required for transcription.

To encode a protein, mRNA needs a protein-coding region and regulatory regions. The coding region of the gene (and the coding region of mRNA) has to start with a start codon: ATG in DNA and AUG in mRNA code for the amino acid methionine, Met. The coding region of a gene always ends with a stop codon TAA, TAG, or TGA (in mRNA, these will have a U instead of a T). The sequence between start and stop codons should contain nucleotides in multiples of three, encoding the sequence of amino acids in the protein. The untranslated regulatory regions (denoted by UTR) include a site for the ribosome to bind before the start codon (5’ UTR) and a region after the stop codon (3’ UTR). Both 5’ and 3’ UTRs can bind specific proteins involved in regulation of translation (how fast new protein product is built, how fast mRNA is degraded).

Note that mRNA in the figure above starts with 5’ UTR, not with the start codon. The start codon signals the start of translation, not transcription. Next, we will consider DNA regions required for transcription.

Genes include regulatory regions at the beginning and the end of the transcribed DNA:

1. The promoter region of the gene “promotes” transcription by binding RNA polymerase.
2. The terminator region signals the end of transcription.
3. Regulatory regions before and after the transcribed region bind regulatory proteins. These proteins activate or inhibit transcription, depending on the signals from within the cell or from the environment.

Putting the regulatory signals associated with RNA production together with those signals on the mRNA, we can represent the central dogma of molecular biology with the following diagram:

After considering individual genes, let’s zoom out and consider a more global view: how genes are organized into genomes.

The prokaryotic genome resides on a circular piece of double-stranded DNA; there is no membrane to separate DNA from the rest of the cell. Most bacterial genomes are several million nucleotides long. The E. coli genome, for example, is approximately 5 million nucleotides long. Although this is a relatively small genome, the physical length of the DNA is longer than the length of the bacterial cell. In order to condense the DNA into a smaller size, the DNA is supercoiled. In supercoiled DNA, the double helix of the DNA contains additional turns beyond the normal one turn per 10 base pairs. These additional twists introduce strain into the DNA that is relieved by large-scale twists in the entire DNA molecule, or supercoils. A good model for supercoiling is an old-fashioned spiral phone cord. If you form the cord into a circle, and then rotate or twist one of the free ends relative to the other, you will introduce supercoils into the cord.

Many bacteria contain smaller, circular DNA molecules, called plasmids, in addition to the large DNA molecule that is their chromosome. Plasmids can replicate independently of the large DNA and can be transferred to other cells. Some naturally occurring plasmids carry genes encoding toxins and proteins that make bacteria resistant to antibiotics.

By Spaully(Wikipedia) (Plasmid) CC BY-SA 2.5

Plasmids provide a very useful tool for biotechnology. Scientists use them to insert “foreign” genes into bacteria so they can use the bacteria as “factories” to produce desired proteins. For example, to study a human disease caused by a malfunction in a specific protein, scientists need a large amount of the protein for experiments. Instead of purifying protein from human cells, scientists can combine coding DNA from the human genome with bacterial regulatory DNA regions on a plasmid, and introduce the plasmid carrying human gene into the bacteria. Growing a large amount of bacterial cells is much easier than obtaining large amounts of human cells. Combining DNA from different organisms is called recombinant DNA technology.

A eukaryotic genome resides on multiple linear DNA molecules in the nucleus. Each of these DNA molecules is called a chromosome. Eukaryotic cells also contain DNA in mitochondria and chloroplasts; mitochondrial and chloroplast genomes are circular like those of bacteria, and are typically considered separately from eukaryotic genomes.

In general, eukaryotic genomes are much larger than prokaryotic genomes, and they contain a lot more noncoding DNA. This presents a problem of packaging for eukaryotic -cells: how are they to fit very large DNA into a small compartment? Although eukaryotic DNA is supercoiled, this isn’t enough to solve the packaging problem. Eukaryotic cells use special proteins (histones) to wind up DNA and fold it into nucleosomes, which are compact structures. DNA can be transcribed in this state. Further packaging of DNA into highly compact fibers makes genes inaccessible for transcription, leading to gene silencing. Gene silencing is an important way of regulating gene expression.

Packaging of DNA in Eukaryotes. Nucleosomes are formed by DNA looping around a collection of proteins called histones. Genes that are actively undergoing transcription can be found in nucleosomes. In the case of inactive (silenced) genes, the DNA is further compacted into thick fibers of the DNA-histone complex. By Richard Wheeler (Chromatin Structures) CC BY-SA 3.0

The shape of the chromosomes changes throughout the cell cycle. For example, when a cell needs to divide, DNA is further compacted by the addition of scaffolding proteins that help divide copies of the chromosomes equally. The most compact shape of the chromosomes can be observed during cell division.

The shape of the chromosomes changes throughout the cell cycle. For example, when a cell needs to divide, DNA is further compacted by the addition of scaffolding proteins that help divide copies of the chromosomes equally. The most compact shape of the chromosomes can be observed during cell division. By Richard Wheeler (Chromatin Structures) CC BY-SA 3.0

How DNA is Packaged

In the previous sections of this module, we discussed the structure and organization of genes and genomes. Throughout the molecular genetics module, we have been pointing out the connections between genotype and phenotype. Here, we will discuss the other important factor in determining the phenotype of an organism: environment. The effects of environment on phenotype can be fairly subtle or pretty dramatic. In certain groups of cold-blooded animals, such as Nile crocodiles, sex is determined by an environmental factor: average temperature during the middle third of the incubation period. Males will only hatch at temperatures between 89.1° and 94.1°F. Nests with higher or lower temperatures will produce predominantly females.

How does environment exert its influence on phenotype? Recall that at the molecular and cellular levels, phenotype depends on the molecules produced by the cell. Production of all molecules is catalyzed by protein enzymes that are encoded by the genome of the organism. Ultimately, if phenotype depends on protein function, then the environment must have a way of modifying the amount and the activity of proteins. Using the central dogma of molecular biology, we can deduce that environment may affect protein function at the level of protein, mRNA, or DNA.

By Michael Bodega (6-year old tortoise shell cat) Public Domain

Epigenetic regulation and inheritance has been linked to cancer and obesity, aging and longevity, and other important processes. It is the key mechanism for interactions between genes and environment. Unlike the genome, which remains fairly unchanged throughout an organism’s life cycle, the epigenome (consisting of the pattern of DNA methylation and histone modifications) is dynamic, responds to the environment, and can be heritable.

In summary, environment can influence phenotype by interacting with the genome in the following ways:

1. Environmental signals can change gene expression by affecting regulatory proteins.
2. Environmental signals can change DNA packaging, which affects gene expression.
3. Environmental mutagens can cause mutations in DNA.

In this spotlight, we will explore in more detail changes in gene expression (transcription) due to changes in the environment. Eukaryotes have complex regulatory mechanisms; consequently, we will focus on gene regulation in prokaryotes. However, common principles of regulation are used by both prokaryotic and eukaryotic organisms, and an understanding of regulation in prokaryotes will help you understand eukaryotic regulation in future studies.

Many bacterial genes are expressed at the same time as part of an operon. The expression of the genes in the operon is controlled by a repressor protein. The repressor protein will bind to the regulatory region at a DNA sequence. This sequence is the operator. When the repressor is bound to the DNA, RNA polymerase cannot transcribe the structural genes because it is blocked by the repressor protein bound on the DNA; under these conditions, none of the enzymes required for the pathway is produced. Whether or not the repressor binds to the operator is controlled by the binding of a small molecule to the repressor. The small molecule is either the compound that enters the pathway (for catabolic, or degradative pathways) or the compound that is produced by the pathway (for anabolic, or synthetic pathways). The compound binds to the repressor protein and causes the repressor either to bind to the DNA (this is called positive control), turning off transcription, or to be released from the operator site on the DNA (this is called negative control), turning on transcription. You will explore both of these control mechanisms in the spotlight below.

The Bacterial Operon. The operon contains the promoter (green box), the operator sequence (red box), and two or more structural genes that code for structural proteins. If the operon is associated with metabolic pathways, the structural proteins would be the enzymes in the pathway. In addition to the genes in the operon, there is a separate gene that codes for the repressor protein, so its transcription is independent of the transcription of the operon. The repressor protein controls the expression of genes in the operon by binding to the operator DNA sequence, blocking the ability of RNA polymerase to transcribe the structural genes (A-C) for the operon. When the repressor is not bound to its operator, RNA polymerase can transcribe the operon and it will produce one long mRNA transcript, containing the coding information for the structural proteins.

Lac Operon

Bacteria can use a wide variety of carbon sources as fuel to extract energy for growth. Two common carbon sources are the sugars glucose and lactose (milk sugar). Glucose is a monosaccharide containing one six-membered ring, while lactose is a disaccharide made of glucose linked to galactose.

It is less efficient for bacteria to use lactose as an energy source because they must take additional steps to convert lactose into a form that can be used to extract energy. Each of these steps requires the synthesis of an enzyme, which is costly to the bacteria. Consequently, bacteria prefer to use glucose rather than lactose as a fuel source when both sugars are present. However, when lactose is present and glucose is not, the bacteria “turn on,” or synthesize, the enzymes required for lactose metabolism, allowing the bacteria to use lactose for energy.

The genes for lactose metabolism are contained in an operon known as the lac operon. The lac operon is controlled by the lac repressor, which is produced from the lacI gene. The lacI gene has its own promoter; consequently, low levels of the lac repressor protein are present all of the time. Three structural genes in the operon, lacZ, lacY, and lacA, encode enzymes required for lactose metabolism.

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learn by doing

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Thus far, we have described what happens when either glucose is present or lactose is present. If both are present, glucose is used first by the bacteria, and only very small amounts of the enzymes for lactose metabolism are made. Complete the following Learn by Doing to understand how glucose turns off the lac operon, even if lactose is present.

learn by doing

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Regulation of Biosynthetic Pathways

The enzymes for the synthesis of the amino acid tryptophan are contained in the Trp operon. The structure of this operon is shown below. The trp repressor binds the amino acid tryptophan, the end product of the biosynthesis of tryptophan (trp). As you can see, it has the same structure as the lac operon, but it contains more genes for the biosynthesis of trp.

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The ability to manipulate DNA has led to dramatic changes in medicine, agriculture, and many other aspects of society. For example, genes from other species are transferred into crop plants and livestock to provide them with desired traits. And many drugs are produced by bacteria, yeast, or other organisms that have been engineered to express human genes.

In this module, you will learn about how biotechnology is used to produce human growth hormone (huGH) for medical applications. HuGH is a protein made of 191 amino acids. It is necessary for the normal growth and metabolism of an individual. Worldwide, one in 4,000 to 10,000 individuals is born without the ability to make sufficient human growth hormone, causing a host of medical problems. These people can be helped with growth hormone injections, but growth hormone from other species (pigs, cattle) cannot be used. Only human growth hormone will produce the desired effects. Historically, the only source of human growth hormone was a small amount that could be extracted from recently deceased individuals (cadavers). this severely limited the supply that was available for medical use.

You will also learn about how biotechnology has solved this problem and decreased the cost of medical treatments that significantly improve the quality of life for many people.

The basic steps in producing human growth hormone (HuGH) in bacteria are:

1. generation of a synthetic gene
2. inserting this gene into a bacterial expression plasmid,
3. introducing the plasmid into bacteria,
4. production and purification of the human growth hormone.

The synthetic gene provides the information that specifies the order of the amino acids in HuGH. The expression plasmid is a large closed circular piece of DNA. Various DNA sequences on the expression plasmid are required for maintenance of the plasmid in the cells. These sequences are present on all plasmids, regardless of the type of protein that is being made. The plasmid also contains DNA sequences (promoter for RNA polymerase, lac operator) that are required for the production of the mRNA that encodes HuGH. The bacterial cell provides the protein synthesizing machinery so that the mRNA can be translated to a protein. In order for the protein to be correctly made the mRNA must contain a ribosome binding site, a start codon, and a stop codon.

More recently, proteins used for medical treatment are produced in yeast or cultured mammalian cells that are grown in synthetic growth media. Protein production in yeast or mammalian cells avoids the possibility of having toxic bacterial impurities in the final product. The overall steps in producing the protein in yeast or mammalian cells are very similar to the steps described here, however the overall cost of producing the protein may be somewhat higher.

Growth of mammalian cells in tissue culture. The sterile plastic dish holds synthetic media (red liquid) that supports the growth of mammalian cells

Steps in the production of Human Growth Hormone in Bacteria.

1. A synthetic gene is made that can be translated into the amino acid sequence of the human growth hormone.
2. This gene is inserted in the correct location in a closed circular piece of DNA (an expression plasmid) by use of restriction sites.
3. The expression plasmid is introduced into bacteria.
4. The bacteria are grown to a high cell density, and then lactose is added to induce the production of human growth hormone.

The first step in producing HuGH is to generate a synthetic gene whose nucleotide sequence codes for the amino acid sequence of the growth hormone. This sequence would contain the start codon, codons representing each amino acid in the growth hormone, and a stop codon. To do this, the known amino acid sequence for human growth hormone must be “back-translated” to a nucleic acid sequence. Since most amino acids can be coded for by more than one mRNA codon, this process is ambiguous. Because the genetic code is universal it would be possible to use the human codons to encode the sequence of amino acids. However, the host organism (which is bacteria in this example) often prefer certain codons over others, so the preferred codons must be used to optimize protein expression.

We will synthesize our HuGH gene using a chemical method called solid-phase synthesis. In this method, the first base of our DNA sequence is attached to a small glass bead. The next base is then added to the first, and so on, until the sequence is completed at which point the DNA is released from the glass bead. Any desired DNA sequence can be generated by this method. Current technology limits this approach to about 200 bases. If our gene is longer, we have to make it in segments and then join the individual segments together.

Chemical synthesis of DNA. The first base (A) is attached to a glass bead (blue sphere). The next base (G) is added, followed by the third base (T). This process is repeated until the entire DNA strand is completed. The linkage to the glass bead is then broken, and the completed DNA molecule is released. In contrast to the direction of synthesis by DNA polymerases (5’->3’), the chemical synthesis of DNA is in the reverse direction, beginning at the 3’ end. The above diagram shows the synthesis of 5’-TGA-3’.

In addition to the codons, it is necessary to add additional sequences to the end of the gene to facilitate the insertion of our synthetic gene into the expression plasmid. These sequences are called restriction sites. Consequently the complete gene is:

After you have generated your synthetic gene, you must insert the gene into an expression plasmid so it can be placed inside a living bacterial cell and translated into the HuGH protein. We will look at that step in detail on the next page. For now, let’s assume that has been accomplished. Here we want to focus on the properties of the expression plasmid.

An expression plasmid is a closed circular molecule of DNA that has several unique properties associated with its DNA sequences. There are three general types of sequences that are found on expression vectors:

1. Sequences involved in maintaining the plasmid in the cell.
   • First, the expression plasmid contains a section of DNA that is an origin of replication. This ensures that when it is placed into a bacterial host cell, it will be successfully replicated. The origin of replication on the plasmid is similar to the origin of replication that is found on the bacterial chromosome.
   • The expression plasmid must also contain a section of DNA that encodes a protein that will confer antibiotic resistance on the bacterial cells that contain the plasmid. This provides a method to select the bacterial cells that contain the plasmid, because if they have the plasmid, they will be able to grow in the presence of an antibiotic while cells that do not have the plasmid will die.
2. Sequences that allow the insertion of the synthetic DNA into the plasmid.
   • These are short DNA sequences that are recognized by restriction endonucleases, in the case of this plasmid they are the EcoR1 and BamH1 sites. Restriction endonucleases cut the DNA at these sequences, allowing the insertion of the synthetic gene between the sites. The actual mechanism is discussed in the next section.
3. Sequences involved in transcribing the DNA to mRNA.
   • The expression plasmid must also contain a promoter that is recognized by RNA polymerase. This promoter is adjacent to the growth hormone gene and will enable the transcription of the growth hormone gene into mRNA.
   • The expression plasmid must contain a DNA sequence that allows a repressor protein to bind. The repressor protein can then act as an on-off switch for mRNA production. An on/off switch is important because the production of growth hormone can interfere with cell division and the production of the growth hormone should be off until a sufficient number of cells are obtained. The most common repressor protein that is used is the lac repressor. The lac repressor binds to a specific DNA sequence called the lac operator. You may want to review the properties of the lac operon. The addition of an inducer molecule, such as lactose, will cause the repressor to fall off of the DNA, allowing RNA polymerase to produce mRNA. It is important that the operator sequence is placed between the promoter and the DNA that encodes the mRNA so that mRNA cannot be made unless an inducer is added.
4. Sequences involved in translating the mRNA to Protein
   • The expression plasmid must have a DNA sequence that will encode a ribosome binding site on the mRNA. This sequence, which will be found at the beginning of the mRNA, will allow the mRNA to bind to the bacterial ribosome, initiating the process of protein synthesis. This segment must be part of the mRNA and it has to occur just before the start codon to position the mRNA correctly on the ribosome.

Summary of DNA sequences in the expression plasmid and their role in mRNA and protein production.

The step of inserting our synthetic DNA into the plasmid use two very important enzymes, restriction enzymes and DNA ligase. Restriction endonucleases are enzymes that recognize specific DNA sequences, such as GAATTC, and cut both strands of the DNA within these sequences. Typically four or six bases are recognized. Restriction enzymes are isolated from a number of bacterial species and the name of the enzyme reflects the original species. For example, the restriction enzyme EcoR1 was isolated from Escherichia coli. The normal biological function of restriction endonucleases is to protect the bacterial species from viruses by digesting the viral DNA as it enters the cell. Of course, the bacteria shouldn’t digest their own DNA. Consequently, they have companion enzymes called DNA methylases, which add methyl groups to the bacterial DNA, protecting it from digestion.

There are hundreds of different restriction enzymes, each of which recognizes and cleaves a different DNA sequence or “restriction site”. Examples of two such enzymes are shown below. A shorthand notation for the recognition site is given below each name. The “^” symbol indicates the site of cleavage. The DNA sequence that they recognize is shown on the left and the products of the digestion are shown on the right. The fragments that are produced after cleavage can contain single stranded overhangs (e.g. EcoR1) or have blunt ends, such as with PvuII.

The DNA sequences that are recognized by restriction endonucleases have a unique property in that the sequence on the top strand is identical to the sequence on the bottom strand, i.e. in the case of EcoR1 the sequence of the top strand is 5’-GAATTC. Taking the complement of that sequence to generate the bottom strand gives: 5’ GAATTC. The other notable feature is that the cutting position is in the same location on both strands. Using EcoR1 as an example, the enzyme cuts between the G and the A. The symmetry in the recognition sequence and the cutting location is due to the fact that the active form of these enzymes contain two identical polypeptide chains. You can imagine that one chain recognizes and cleaves the top strand. The second chain, because it is identical to the first, recognizes the same sequence on the other strand and cleaves in the same location.

Cartoon diagram of EcoR1. The two blue rectangles represent the two identical subunits of the enzyme. The red arrow marks the cleavage location.

If the restriction enzyme does not cut at the center of its recognition sequence the cleavage products will contain short single-stranded segments of DNA. These are often called “sticky-ends” because they can stick to other DNA molecules that have complementary sticky ends. Enzymes that cut in the middle of their recognition sequences produce blunt end fragments.

Below, the formation of sticky ends after EcoR1 cleavage is illustrated.

Because cleavage does not occur in the middle of the recognition sequence, the products have short single strand segments (highlighted). These sticky ends can “stick” to complementary single-stranded DNA sequences using normal DNA basepairing (A-T, G-C).

The presence of sticky ends on DNA fragments makes it easy to join DNA fragments. If two fragments are both cut with the same restriction enzyme, they will have complementary sticky ends. These will align and bind loosely to each other: hydrogen bonds will form between complementary bases.

At this point, the two fragments are not firmly held together by covalent bonds; the sugar-phosphate backbone is still broken on both strands. DNA ligases can be used to rejoin DNA after it has been cut with the restriction enzyme. This reaction requires energy (usually ATP) and requires that the two pieces of DNA that are being joined are close to each other. Since the sticky ends hold the two ends close together it is easy for DNA ligase to join the fragments, reforming the phosphodiester bonds on both strands.

Although most of the time DNA fragments are joined using sticky ends, it is possible to join fragments that are blunt ended. This is more difficult however because there are no hydrogen bonds to hold the DNA fragments together.

Insertion of the Human Growth Hormone Gene Into the Expression plasmid

Restriction endonucleases and DNA ligase are used to insert the synthetic gene into the correct location in the expression plasmid, just after the ribosome binding site.

The expression plasmid would have two different restriction sites after the ribosome binding site to facilitate the insertion of the synthetic gene. To utilize these sites it would be necessary to include these restriction sites at the end of our synthetic gene. The expression plasmid and the synthetic fragment would be cut with the restriction enzymes, mixed, and then treated with DNA ligase to re-seal the phosphodiester backbone:

Detailed process of joining the huGH gene to the expression plasmid. Both the plasmid and the huGH gene are cut with EcoR1 (G^AATTC) and BamHI (G^GATCC), generating sticky ends on both DNAs (bold text). After mixing the cut plasmid and huGH gene, the sticky ends pair by hydrogen bonding (highlight), bringing the DNA molecules close so that they can be ligated by DNA ligase.

Combined expression plasmid - synthetic gene before ligation. The paired sticky ends are highlighted in yellow.

Once the synthetic gene has been successfully spliced into the expression plasmid, the complete expression plasmid must be taken into the bacterial cell. This is a delicate process that must take place under special conditions. In these conditions, the expression plasmid is mixed with bacterial cells, allowing some of the cells to take up one circular DNA molecule. The origin of replication on the expression plasmid will cause the bacteria to replicate the plasmid along with its own chromosomal DNA. It is not possible to determine which cells have taken up the expression plasmid. Consequently, the cells are grown in the presence of an antibiotic and only those cells who have obtained the expression plasmid will live because of the gene for antibiotic resistance that is also present on the expression plasmid.

Thus far you have learned a great deal about how cells function. In the genetics units you’ve learned how biological information is inherited and used. You are beginning to appreciate that each cell and organism is a complex and highly integrated unit.

Life changes and evolves over time. Evolution considers how life changes from one generation to the next and how these changes accumulate over very long periods.

Evolution builds on what you already know. It is a scientific theory that explores life on a different scale and provides another layer of explanation (Table 1). First, it goes beyond the brief lifetimes of individual organisms. Instead, evolution considers how life changes from one generation to the next and how these changes accumulate over very long time scales. Second, evolution is focused on collections of individuals: populations, species, and larger taxonomic groups (for example, birds or flowering plants). Evolution also adds another layer of explanation to biological thinking. So far we have focused mainly on “how” questions. How does a cell maintain homeostasis? How is information passed from parents to offspring, and how is that information used to construct living cells? Evolution helps us answer “why” questions: Why do cells of very different organisms have so much in common? Why are cave fish blind? Rather than taking the features of life as a starting point, evolution asks why those features exist today and how they originated in the past.

People have been grappling with questions about the origins of life for nearly as long as we have been in existence. Every society has addressed these questions based on the information that was available at that time and place. Before the Scientific Revolution, people used many different sources of information to answer questions about the origins of life. Some of their ideas were based on direct observations, but many of them involved supernatural beings or spiritual forces. Stories were told to explain how the world and humans were made, but also to address questions of meaning: why the world exists and what human life is “for.” Ideas were passed down as oral tradition (myth and folklore) or in the written documents of organized religions. Scientific study is much more narrowly focused on close examination of processes and objects in the natural world. In order for an explanation to be considered scientific, it must be based on verifiable observations. It must be possible to test it through observations or experiments. Ideas or explanations that do not meet these criteria are not necessarily “bad” or “wrong,” but they are unscientific.

Scientific and non-scientific views are separate but potentially complementary ways of knowing. Scientific methods can be used to answer direct, factual questions about “what is” and “what probably was” through a clear procedure of observation and testing. Through an ongoing process scientists select ideas that best fit the available data. No religious tradition revealed the existence and function of DNA to humans: that was the fruit of scientific study and reasoning. However, answers derived from science are limited. They do not necessarily help with ultimate questions of meaning (why the Universe exists in the first place, what humans should be or do). Non-scientific ways of looking at the world (religion, philosophy) are more directly focused on these questions. Many scientists embrace religious ideas about the meaning and ultimate origins of life. However, they do not publish these ideas in scientific journals or used them to explain their detailed observations of the natural world.

In this course, we will focus on how the scientific community understands evolution and the origins of life. Like the community of science itself, we will restrict our scope to fairly narrow questions of how and when things probably happened, based on what we can observe today. Other explanations are better suited to philosophy or religion courses; they help us explore broader questions about why the Universe exists and what our place is within it.

Before defining the modern theory of evolution, we will consider its historic roots. You probably know that the scholar most widely recognized as the author of the theory of evolution was Charles Darwin. The first statement of modern evolutionary theory was his book On the Origin of Species, published in 1859. But Darwin didn’t make up the theory from nothing, and he wasn’t the first to ask questions about the ultimate origins of life. How did science deal with life’s big “why” questions before evolutionary theory developed? What clues led scientists to propose and embrace evolution? To gain some insights into these questions, explore the Learn By Doing activity below.

After Darwin, science has continued to reinforce, refine, and modify the theory of evolution. Two major developments were particularly important. In the early 1900s, scientists rediscovered Mendel’s genetic principles and applied them to evolution. Theorists developed models of how the gene pool of a population could change over time. Field biologists observed such changes in fruit flies and other short-lived organisms. Lab experiments also demonstrated the effects of natural selection. With a focus on genetics, these advances reinforced the idea of natural selection. In 1953 James Watson and Francis Crick discovered the structure of DNA. This laid the groundwork for an explosion of information that continues today. Inherited information now can be analyzed directly and in detail. Comparisons of DNA in different species support their common ancestry. DNA analysis also pinpoints the genetic mutations that produce new adaptive traits in organisms. To Learn More: A comprehensive database of Darwin-related publications, images, commentary and more are available free online at http://darwin-online.org.uk/. A more detailed history of evolutionary thought is available from the University of California Museum of Paleontology at http://evolution.berkeley.edu/evolibrary/article/0_0_0/history_01.

Before we begin our exploration of microevolution, let’s review a few principles that we have already covered in this course. The principles of evolution are based in genes; therefore, it is important that we remember that genes are segments of DNA that have "meaning." Genes are sequences of DNA that encode particular RNA and protein molecules, which work together to give a cell and an organism its characteristics and functions, whether they be physical, chemical, or behavioral. Most genes have multiple forms, called alleles,, discussed previously in the Heredity module of the Classical Genetics unit. For example, pea plants have a gene that determines seed color, and the different forms (alleles) of that gene are "green seed" and "yellow seed."

When you studied inheritance, you often were thinking about crosses: two individuals mating to produce offspring. As we study microevolution, we will be backing up to think about how inheritance works within larger groups. You will need to understand and use the following terms: species, population, and gene pool. The illustration below shows an example of how a species, population, and gene pool are related.

All humans are members of the same species. A group of people on an island, as shown on the left, make up a population. That same group of people also make up a gene pool. A gene pool is the sum total of all alleles available within a species at a specific location and time. By University of Maryland University College CC-BY-NC

In this course we will define a species as a group of organisms whose members can and will breed with each other to produce fertile offspring. A population is all the individuals of the same species that occupy the same area and are likely to breed with one another. Some examples of a population might be all the people that live in your state, all of the frogs that live near a pond, all of the grizzly bears that live in Denali National Park, or all the dandelions that live in your hometown.

There are two defining aspects to a population. A population is strictly composed of members of the same species. For example, a population would always consist of people or of grizzly bears, but never of both people and grizzly bears. Second, the members of a population occupy the same area. Scientists define the area based upon the problem they are studying. In evolutionary studies, biologists try to define populations based on actual patterns of breeding, so that individuals most often breed within their population groups; migration and mixing between populations is less frequent.

You might wonder how a species and a population are different from one another. Populations are subsets of a species. The dandelions in Boston, Massachusetts and those in Annapolis, Maryland belong to separate populations. They are not likely to breed with one another because their pollen doesn't travel that far. However, the Boston dandelions and the Annapolis dandelions do belong to the same species. They could breed with one another if conditions allowed. For example, breeding could occur if a human being carried dandelion pollen from Boston to Annapolis.

The gene pool is all of the genes and alleles present in a population at some point in time. Just as the genotype is the genetic composition of an individual, the gene pool is the genetic composition of a population.

The pea plant example only looks at one trait of the plants, seed color, but there are many other genes present in this population. A gene pool includes all of the genes and alleles in a population, not just those for a particular trait. So the gene pool for this pea plant population actually contains genes and alleles that influence thousands of different traits. Some of these traits are visible, such as plant height and flower color. Other genes may determine how resistant the plants are to diseases and pests, how they respond to drought or freezing, and many more features that are important to peas - and to gardeners.

What is microevolution?

The word evolution means change, and things that change are said to "evolve." These terms are commonly used in our everyday lives (a work project evolves from the original idea to a finished product, people dealing with a tragedy evolve as they learn to cope), but in these settings they have a very different meaning than in biology. In biology, the words evolution and evolve are used in a precise way. These words apply to changes that occur in the gene pool of a population. Evolution occurs in populations, not in individual organisms. In biological terms, for example, individual people don't evolve, but the human race does. When evolution occurs in a population, different alleles (and genotypes) become more or less frequent within the gene pool. As a result, we observe a gradual change in the inherited characteristics of the population as one generation succeeds another.

Evolution of corn

Over time, a wild grass has evolved to modern corn. Initial corn varieties had small ears with few kernels; modern corn has much larger, fuller ears. These changes were guided by human breeders and are a form of evolution. Source: Nicolle Rager Fuller, National Science Foundation. By Nicolle Rager Fuller, National Science Foundation (Maize) Public Domain

Microevolution of an insect population

Evolution occurs when an insect population is exposed to an insecticide. In the first generation, one insect (red) contains an allele that makes it resistant to the insecticide. This heritable variation is already present due to past random mutations. When the insecticide is applied, selection occurs: the red insect survives while the majority of the non-resistant insects die off (solid blue arrow). Surviving insects reproduce and generations pass with continued selection due to insecticide use. After generations of adaptation (dashed diagonal arrow) the resistant insects (red) make up a larger portion of the population. The insecticide is less effective against these insects because of the increased proportion of resistant individuals within the population. By Delldot(Wikipedia) (Pest resistance labelled light) CC BY-SA 3.0

Microevolution occurs when the type or frequency of the alleles and genotypes in a population change over one to many generations of time. But what does that actually mean? Let's look at a hypothetical example. We’ll observe two different populations of foxes, one in Maryland and one in Wisconsin. We’ll narrow our focus to a single gene with two alleles that determine coat thickness. And we will visit the populations at two different times.

As you can see from the Fox population example, evolution is not determined by the increase or decrease in the number of individuals within a population. Both populations saw an increase in the total number of foxes from 1962 to 2202. Microevolution occurs when there are changes in the genetic makeup of the population: when the frequency (percentage) of each genotype changes over time.

This example of microevolution covers a few hundred years, but in organisms that have shorter generation times, like bacteria, microevolution can be observed on an even smaller time scale. Antibiotic resistance has become a major problem for the medical community worldwide.

Now that we have a better understanding of what microevolution is, we must consider in more detail how microevolution happens. What are the mechanisms that allow for changes in the gene pool over time? In this page we will learn about selection, a central process in evolution. Selection occurs whenever some genetic types in a population reproduce more than others in a given environment. We will discuss three types of selection: natural, sexual, and artificial.

Sexual selection

Sexual selection is a subtype of natural selection. In natural selection, some genetic types in a population reproduce more than others because they are more likely to survive or because they obtain more resources. In sexual selection, some types reproduce more than others because they have traits that allow them to:

• find or attract more mates
• choose higher-quality mates
• win in competitions over mates

Can you think of some traits in animals or plants that would increase their likelihood of mating? Here are some examples.

Male peafowls (i.e. peacocks) have elaborate tail plumage to attract a mate. By Pruneau(Wikipedia) (Peafowl) CC BY-SA 2.0

Female peafowl are more likely to mate with males that have fuller, more colorful, and more grandiose tail plumage. During mating season, males display their plumage when females are in the area in the hopes of attracting the females for mating. The males with the better tail feathers are more likely to successfully mate and pass on their genes.

Male elk grow antlers each year. As the elk age, their antlers get larger and more full with each successive year. These antlers not only help to attract mates, but also allow the elk to fight off rival males. This image shows two male elk sparring during the rut. By FWS (Elk Fighting) Public Domain

These are just two examples of many thousands of traits that are driven by natural selection in nature. Whenever the males and females of a species are noticeably different in appearance, sexual selection is probably at work. Some additional examples of sexually selected traits include:

• birds who perform dances and construct elaborate “bowers” to attract mates
• male walruses and elephant seals that battle over access to females
• whales that “sing” haunting mating songs

The typical pattern in sexual selection is that males compete with each other for mates; sometimes they do so through displays that are meant to attract females, while in other cases they may battle each other directly. Females tend to choose mates carefully.

The perplexing thing about sexual selection is that the showy traits that are used to attract a mate can also interfere with survival. For instance, the elaborate plumage of the peacock can make the males more likely targets for predators. Elk with larger antlers may get them stuck in fences or brambles, which can lead to the untimely death of the stuck elk. And fighting is never good for survival.

So why do these dangerous traits exist? First, survival is only a means to an end: individuals that fail to mate have zero fitness, even if they are very good survivors. The gene pool will contain traits of those who have survived, yes, but also of those who have mated successfully. Second, many sexually selected traits (e.g. elaborate plumage, bright colors, large antlers) are known to be indicative of a healthier mate. Males who can “carry off” a good display and a successful battle are also fit in other ways. Females who are choosy are doubly successful in their own reproduction: they produce “sexy sons” who will themselves be successful in mating, and they also produce offspring that are generally healthy.

Sexual selection is a powerful force in evolution. To understand the impact of sexual selection consider what happens to the genes of the individual who does not mate.

In this image consider twin brothers, Matt and Mark. Mark gets married at the age of 24 while Matt does not. By the time the brothers are 45 years old, Mark has mated and has children. His genes have been passed on to the next generation. When the brothers are 72, Matt is still unmarried and has no children while Mark has grandchildren.

In the figure above, Mark’s genes have been passed down to a second generation because his children have mated and have children of their own. Mark is successful evolutionarily speaking and his alleles have become more common through his reproduction and that of his offspring. The evolutionary success of Matt’s genes is zero because he has no offspring. Sexual selection is a powerful driving force within evolution.

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Artificial Selection

Selection occurs whenever some genetic types in a population reproduce more than others in a given environment. In natural selection, the types that succeed are those that survive and/or grow the best. In sexual selection, mating success is key. In artificial selection, humans decide which types reproduce best: we deliberately breed certain individuals with desired traits.

Artificial selection is sometimes referred to as selective breeding. It has been in use for thousands of years as humans have domesticated plants and animals to suit their needs. As we discussed at the beginning of this module, corn as we know it today (with large, full ears) has been selectively bred by humans from its wild grass ancestor (with small, sparse ears). In the same way, dairy cows have been selectively bred to produce more milk; beef cattle have been bred to have more muscle; horses have been bred to run faster; tomatoes have been bred to produce larger fruit; and wild mustard has been bred to produce cabbage, Brussels sprouts, kale, broccoli, cauliflower, and kohlrabi.

There is perhaps no better example of artificial selection than the domestic dog. Dogs are descended from gray wolves, but after thousands of years of humans directing the breeding of dogs, we have well over one hundred different breeds. There are dogs with good noses that can track game and search for missing persons. Some dogs have been bred to herd or protect domestic animals. Some dog breeds are known for happy personalities and soft fur that make them great companions while others are known for their strength and intelligence which makes them good guard or police dogs. Consider the image below to get a sense of the power of artificial selection.

Examples of modern dog breeds all descended from the gray wolf (center). The dogs range in size from less than 10 lb (4.5 kg) to over 100 lb (45 kg). Many of these breeds are now kept as family pets, but their body structures and inherited behavior routines also suit them to many different “jobs” including tracking game, pointing at game birds, retrieving ducks, herding or guarding sheep or cattle, pulling sleds, racing, guarding the home, or catching rats.

Selective breeding is not as simple as it may appear. Let’s say you take a dairy cow who is a high milk producer. You mate her with a male who has the red spotted coat you like. Unfortunately, you are not guaranteed to get a female calf who is a high milk producer and has red spots. You are not just dealing with the two traits you desire in a dairy cow (high milk yield and red spots), but every trait (i.e. every allele) that each parent cow has. When you breed these two animals, the offspring will have some combination of all of the parents’ traits. Because of this, it often takes many generations of artificial selection to consistently produce offspring with the desired traits.

In the process of selecting for desired traits, undesirable traits often “tag along”, and thus we see an increased likelihood of genetic disorders in many domestic animals. This is a result of inbreeding (mating of individuals that are closely related). For example, inbreeding among dalmatians has resulted in a tendency toward aggressive behavior. Additionally, sometimes selective breeding can magnify a desired trait to such an extreme that it interferes with survival or reproduction. American domestic turkeys have been bred to have larger breast muscles to satisfy consumers’ preference for white meat. As a result of generations of selective breeding, today’s male turkeys are literally too large-chested to mount and copulate with female turkeys. To produce more turkeys, farmers must artificially inseminate females. In this and other examples, selective breeding can produce plant and animal varieties that are totally dependent on our care and intervention, exhibiting traits that would never be adaptive in the wild.

Artificial selection is a powerful tool that drives the evolution of domesticated plants and animals, but it is one that must be utilized with great thought and consideration so as to avoid the problems that come with inbreeding. Does it surprise you that farmers and animal breeders need to understand a good deal about biology to be successful in their professions?

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We have just learned how natural selection, sexual selection, and artificial selection can change the gene pool of a population and result in evolution. In this section we will consider other processes that can change the gene pool of a population: mutation, gene flow, and genetic drift.

Remember from the gene expression module that a mutation is a permanent, irreversible, and heritable change in DNA. We often think of mutations as a “bad” thing, in part because of how they are portrayed in TV shows and movies. Mutant creatures are often bizarre (three eyed fish in Lake Springfield of The Simpsons) or dangerous (mutant dinosaurs of Jurassic Park). Even when the mutations create superheros like the Teenage Mutant Ninja Turtles or Spider Man, the mutation is never really portrayed as a good thing. While a certain amount of that bad reputation is deserved, as some mutations do indeed have negative consequences for living organisms, not all mutations are "bad." All of the following are true statements about mutations:

• Mutations alter RNA and may alter protein molecules. If a protein molecule is changed, the altered molecule may work just the same as the original, it may be totally nonfunctional, or it may work more efficiently than before.
• Some mutations cause genetic disorders, abnormalities, and cancer, while others merely contribute to normal variation of traits in a species (such as freckles, widow’s peaks, and eye color variations).
• Some mutations are harmful because they encode a trait that decreases an organism's chances of survival, while others are beneficial because they encode an adaptive trait that increases an organism's chances of survival.
• The effect of a mutation upon an organism can depend upon the environment in which the organism lives. In fact, some mutations that have no immediate effect on survival can be maintained in a gene pool, and as conditions change become advantageous or disadvantageous long after the initial mutation occurred.

Mutations in genes are random and have the potential to change the gene pool of a population. When parents produce sperm or eggs, errors (mutations) can occur so that the gametes carry new versions (alleles) of existing genes. Fertilization, growth, and development can result in an adult individual that carries a new allele and is able to pass it on to offspring. Technically, the birth of a single individual carrying a new mutation qualifies as microevolution: as soon as the new allele appears, the gene pool has been altered.

Let's consider for a moment the gene that encodes the alpha-amylase enzyme. This enzyme is found in saliva and begins the process of digesting starches in your mouth. Assume that you were born with a new mutant version of the alpha-amylase gene. You produce a form of the enzyme that very efficiently digests starch. No one else in the world carries this form of the alpha-amylase gene in their cells. So as a result of this mutation, a new allele has been introduced in the gene pool of your population and of the entire human race. The type and frequency of the alleles and genotypes in your population has changed (ever so slightly)… so evolution has occurred. Will this change have a meaningful effect on the entire population or species? That depends on what happens next.

The alleles and genotypes in a gene pool can also change via two processes that are sometimes confused with one another: gene flow and genetic drift. Gene flow refers to the movement of alleles from one population to another, as a result of migration followed by breeding. Remember that when living organisms move from one place to another, they take their alleles with them! Consider the average height difference between people in East Asia (e.g. China) and those in Western nations (Europe and the Americas). As westerners migrate to East Asia, the gene pool there changes to include more alleles that confer tall height. Conversely, alleles characteristic of Asian populations move along with immigrants to the United States. Gene flow involves breeding between two or more populations and it tends to make them more similar to each other.

Genetic drift refers to random events that change the frequency of alleles and genotypes in a population. It is similar to selection in some ways. Recall that in selection, certain genetic types become more frequent in the population because they survive well, grow well, mate successfully, or even just because humans like them and choose to breed them. In genetic drift, certain genetic types become more frequent through dumb luck.

Genetic drift often reduces the diversity of a gene pool and has the biggest effect when there is a low number of organisms in the population. In two different situations, genetic drift can profoundly affect a gene pool. The first is known as the bottleneck effect. When events like fires, earthquakes, hurricanes, and other disasters kill a large percent of the population, the surviving population is unlikely to have the same gene pool as the original population. It is very likely that some alleles will be underrepresented or overrepresented in the surviving population as compared to the original. An analogy may help. Half the cards in a deck are red (hearts and diamonds) and the other half are black (spades and clubs). But if you draw six cards from the deck at random, will you always get 3 red and 3 black cards? No. You might well draw six black or six red cards. Similarly, consider a grove of 1000 oak trees. If a flash flood washes away and kills 900 of the trees, the alleles of these trees have been lost from the population gene pool. Compared to the original group, the 100 lucky survivors will have higher percentages of some genetic types, a lower percentage of others, and some alleles might be entirely missing. The flood altered the population’s gene pool in a random way.

Genetic drift can also occur through the founder effect. In the founder effect, a small number of individuals from a population settle in a new area. This small group is not likely to contain all of the alleles of the original population, just as is seen with the survivors in the bottleneck effect. Imagine a field of dandelions. Dandelions are self-fertile, so they do not require cross pollination from other dandelions to produce offspring. If just one of the white fluffy dandelion seeds is carried by the breeze to a new location that does not have dandelions, the plant from this single seed could start a new population. As a result of the founder effect, however, the gene pool of the new population would be very limited. It would have only those alleles that were found in the original seed, drawn at random from a much larger source population.

As you can see from the examples presented here, mutations, gene flow and genetic drift are mechanisms that can alter the gene pool of a population leading to microevolution. While these mechanisms of evolution have been presented separately from the mechanisms of natural, artificial, and sexual selection, in reality it is likely that several or all of these mechanisms are at work at any given time to drive evolution. Evolution is a complicated process. It involves some relatively predictable elements (selection and gene flow) but also has many unpredictable aspects (mutation, genetic drift).

Microevolution and Infectious Diseases

Many species have very short generation times ranging from minutes (some bacteria) to a few weeks or months (many insects, some weeds). We can track evolutionary changes in populations of these organisms. They may change in ways that are important to us. For example, disease organisms may shift to human hosts, evolve to evade vaccines, or evolve to resist drugs. Pests and weeds may also evolve in ways that make them more harmful or harder to control. Scientists and doctors can use what we know about microevolution and the mechanisms that drive evolution to help tackle these problems in the “real world” not just in the realm of academia.

In our first example of microevolution and infectious disease, we will explore the Human Immunodeficiency Virus (HIV), which causes Acquired Immune Deficiency Syndrome (AIDS). In AIDS, HIV disables the human immune system by depleting CD4 T-cells. The HIV virus prefers to infect these cells. HIV is an interesting virus in that it uses RNA to encode its genetic material instead of DNA like most viruses.

A schematic diagram of an HIV virus particle. By Daniel Beyer (multiplication of HIV) CC BY-SA 3.0

HIV has special enzymes to help it make copies of itself within the host cell. Some of these are reverse transcriptase, integrase, and protease. Each one is essential to the virus:

• Reverse transcriptase converts the HIV virus RNA into DNA that can be recognized by the infected human cell’s DNA replication machinery as well as human RNA polymerase.
• Integrase inserts the DNA made from the HIV RNA (using reverse transcriptase) into one of the human chromosomes. In this way, the virus (which is not living - see Application Spotlight: Viruses) tricks the human host cell into producing more viral RNA, which the virus cannot do itself.
• HIV’s protease cuts the viral proteins that are manufactured by the host cell into their functional forms.

AIDS was first recognized and tied to the HIV virus in the early 1980s. At that time a diagnosis of HIV infection was considered a death sentence as there were no available treatments. The first breakthrough in HIV treatment came about in 1986 when zidovudine (also known as AZT) was introduced in the United States. AZT works by blocking the activity of the HIV reverse transcriptase enzyme. AZT was hailed as a HUGE medical breakthrough, and it worked well at keeping the viral infection in check. AZT would remain the only treatment available for HIV until the early 1990s when other reverse transcriptase inhibitor drugs as well as drugs that inhibited the HIV protease were introduced. With AZT and the new drugs available the scientific and medical communities thought that the struggles of managing this disease were over! Having HIV was no longer a death sentence! Infected patients could simply be given any one of these drugs, and live fairly normal lives as long as they continued treatment. However, by the mid 1990s, it became apparent that there was a problem. Patients whose infections had been well controlled (even for many years) started once again to exhibit symptoms of AIDS and their health deteriorated rapidly. While this turn of events may seem perplexing, the explanation has everything to do with microevolution.

By the late 1990s, doctors and scientists came to the conclusion that in order to continue to treat HIV effectively, they needed to approach the problem from multiple fronts - as you just discovered in the above Learn By Doing activity. New drugs were developed that targeted different parts of the virus, current drugs were administered together, and when it became clear that a drug was no longer working for a patient, the patient was given a different one. The end result of all of this work was the development of what is known today as Highly Active Antiretroviral Therapy or HAART. HAART generally consists of one protease inhibitor given in concert with one or two other anti-HIV drugs that target different aspects of the virus. To date, there are over 30 drugs approved for use in the treatment of HIV.

HIV Viral Replication Cycle and HAART Drug Targets

This figure shows the replication cycle of the HIV virus with the current drug targets indicated with an X. By Daniel Beyer (multiplication of HIV) CC BY-SA 3.0

While doctors and scientists have made great strides in combating HIV, the “war” on this virus is far from over. In 2010, there were approximately 34 million people infected with HIV worldwide and 1.8 million deaths associated with HIV. Rates of HIV infection and the death toll from AIDS are disproportionately high in Sub-Saharan Africa and in other areas without access to HAART. Even in wealthier nations, the problem of drug resistance continues. As of 2009 researchers were tracking 93 different common drug-resistance mutations worldwide. Today the World Health Organization (WHO) and other groups are working to raise HIV awareness, reduce infection rates, and increase access to drugs among those already infected. Researchers are also working to develop new drugs and vaccines.

Now that we have learned how our understanding of evolution can be used to help fight HIV, let’s see if we can apply that knowledge to an even more complicated infectious disease: malaria. Malaria is an ancient disease that has been around for over 50,000 years! Malaria is caused by four parasites of the Plasmodium genus: Plasmodium falciparum, Plasmodium vivax, Plasmodium ovale, and Plasmodium malariae. These protists (eukaryotes) have complicated life-cycles that require both a mosquito host and a human host, and the parasite undergoes many developmental stages within these two hosts. Humans become infected with the malarial parasites when they are bitten by an infected mosquito. Similarly, uninfected mosquitoes can pick up the parasites when they ingest blood from an infected human.

Life Cycle of Malarial Parasites

This diagram shows a detailed overview of the life cycle of the Plasmodium parasites that cause malaria. You need not learn the details, but the diagram helps you to see the complexity of the Plasmodium life cycle. By CDC (Malaria) Public Domain

Because of its complex life cycle and the eukaryotic nature of this organism, malaria has been a difficult disease to combat. However, this complexity also means that there are more potential ways to intervene, prevent, and treat this disease. The parasite could be targeted with anti-malarial drugs in the human host. Other methods could be used to prevent the parasite from surviving in the mosquito host. Or measures can be taken to prevent the human host from being bitten by mosquitoes.

This diagram shows the interactions between the Plasmodium parasite, the human host, and the insect host that all contribute to malaria disease and serve as potential targets for preventive measures or treatments.

We have now explored two corners of the “Interactions in Malaria” triangle - the mosquito vector and the malaria parasite. As you can see from the question above, there are several ways in which malarial parasites can evolve resistance to anti-malarial medications. This is a real world problem in the fight against malaria. Resistance to almost every drug available to prevent or treat malaria has been reported, and the rates of resistance are only increasing. Insecticide resistant mosquitoes are also contributing to the problem because many areas where malaria is rampant rely heavily on pesticide control of the mosquito populations to curtail the spread of malaria. If the mosquitoes are no longer killed by the pesticide, then there will be more mosquitoes around to transmit malaria.

The last corner of our triangle is the human host. The alleles of many human genes have been determined to alter a person’s susceptibility to malarial infections. The most famous and arguably the most important is the sickle cell allele. People homozygous for the sickle-cell allele suffer from sickle cell anemia. Their red blood cells are misshapen, resembling a sickle.

Images of Normal and Sickle Red Blood Cells

Sickle-cell disease is indicated by the presence of sickle shaped red blood cells. As shown here, normal, healthy red blood cells are round and plump while sickle red blood cells are “C” shaped and somewhat flattened. By United States, National Human Genome Research Institute (Sickle Cell) Public Domain

A sickle is a “C”-shaped farm tool that is used to help cut down crops. The deformed red bloods cells in sickle cell anemia get their name from this agricultural tool. By Thamizhpparithi Maari (Sickle) CC BY-SA 3.0

Sickle cell anemia is caused by a recessive allele (we will call it “a”). Three genotypes are possible:

Good work. You’ve cracked the mystery! There is a situation called heterozygote advantage at work here. Why does a gene that alters red blood cells have anything to do with malaria? The malaria parasite spends a large part of its life cycle in red blood cells. The red blood cells of those with the Aa genotype are less hospitable to Plasmodium than those of an average (AA) individual. For example, in an Aa person the red blood cells may sickle in response to being invaded by Plasmodium. This will lead to the death of the newly invaded red blood cell, and the parasites will die with it.

Malaria is a serious disease with an estimated 216 million cases and over 600,000 deaths in 2010. In Sub-Saharan Africa, where malaria rates are highest, a child under the age of five dies every minute from this disease. Doctors and scientists are working to help prevent and treat this disease by designing new treatments, developing vaccines, working to prevent mosquitoes from transmitting the malaria parasites, and by studying the interrelatedness between the parasite, the insect host and the human host. At the center of the connection between parasite, insect, and human lies evolution.

HIV and malaria are just two examples where an understanding of evolutionary principles has proven to be a critical component in the effort to fight infectious disease. Other prominent examples include tuberculosis, methicillin-resistant Staphylococcus aureus (MRSA), avian influenza, and pertussis. Evolution is at work all around us, and every population of every organism is subjected to it.

Thus far, we have been exploring how subtle changes can occur within a population. We’ve seen that these changes can lead to adaptation. The genetic makeup of populations also can change through migration and interbreeding (gene flow) and even through the vagaries of chance (genetic drift). But how does this relate to macroevolution? For example, can microevolution possibly explain the origin of new and different species?

Macroevolution is a long-term process and includes the origin and extinction of species and larger taxonomic groups. However, each and every event of macroevolution occurs through the processes of microevolution you just studied. The two processes are continuous and are part of a unified whole.

As you should recall, microevolution occurs at the population level. But a population is only a part of a larger collection that we refer to here as a biological lineage. A lineage is a group of populations that evolves independently of other groups. Members of the same lineage can move between its populations. Mating may occur between members of different populations in the same lineage. Lineages change as their member populations evolve and exchange genes and individuals with each other. To get a clearer sense for the nature of a biological lineage, do the Learn By Doing activity below.

To recap, a lineage is a group of populations that can exchange genes and individuals and that evolves as a unit as shown in the Figure below. The lineage evolves through changes that occur in its component populations.

Evolution within a biological lineage.

Within a biological lineage, evolution occurs as the component populations evolve. The diagram shows evolution of a biological lineage starting at an arbitrary reference point (“baseline generation”). Each chevron represents a snapshot of the lineage at one point in time. Circles (A-F) represent populations of various sizes linked by gene flow (white lines). Population (A) goes extinct. A mutation produces a new adaptive trait that spreads first through population E, then moves through gene flow to the remaining populations.

In practice, biologists often use the term “species” to describe a biological lineage. The definition of “species” you learned earlier in this Unit fits the idea of a lineage. Consider the Roseate Spoonbill (Platalea ajaja). These birds use their sensitive, flat bills to capture small animal prey in shallow water. There are populations of Roseate Spoonbill in coastal and wetland areas within South America, Central America, and the U.S. Gulf Coast. Individual Spoonbills can move from one population to another, taking their genes and adaptive traits with them. Changes in the genetic makeup of one population can affect the genetic makeup of other populations over time, so the species as a whole evolves as a unit. Yet the evolution of the Roseate Spoonbill does not affect the genetic makeup of other bird species. Five additional species of Spoonbill live in different parts of Africa, Australia, and Eurasia. Each is a distinct biological lineage.

Roseate Spoonbill, Platalea ajaja.

By John James Audubon (Roseate Spoonbill) Public domain

Speciation is the formation of new biological lineages. It occurs when an existing species splits or branches into two or more new species that evolve independently of each other. Over very long periods of time, repeated branching of a lineage can create groups of related species called clades. A clade is a complete group of all species that descend from some common ancestor. The six species of Spoonbill form a clade; all of them share unique adaptive traits not found in other birds, most notably the distinctive bill. They all likely descended from a single ancestral species that possessed these unique features.

Two additional members of the Spoonbill clade, genus Platalea. Royal Spoonbill (left), Eurasian Spoonbill (right). All spoonbill species have a similar bill shape and mode of feeding, but species vary in distribution, behavior, genetics, coloration, structure, and plumage. Left image by Fir0002(Wikipedia) (Royal Spoonbill mouth open) GFDL 1.2. Right image by Andreas Trepte (Eurasian Spoonbill) CC BY-SA 2.5.

In the early 1700s, Carolus Linnaeus established the modern system for naming and classifying organisms. In it, species are placed in nested groups based on their shared characteristics. Species correspond to biological lineages. Higher levels of classification are the genus, family, order, class, phylum, and kingdom. Each level is nested within the next higher level; all members of a genus, for example, are members of the same family, order, and so on. Below, the Linnaean hierarchy is shown for the Roseate Spoonbill.

Table 2.Linnean classification is a system of nested groups.

How does this classification system relate to macroevolution? Today, biologists strive to place closely related species (members of a clade) within the same taxonomic groups. We hypothesize that the members of a genus had a recent common ancestor; members of genera within a family can be traced to an earlier common ancestor; and so forth. Thus the taxonomic system is not merely a convenient way to organize species. It partly reflects our understanding of how biological diversity has evolved over time.

The idea of common ancestry is very strongly supported by many lines of evidence. Like plagiarized term papers, our genes contain many sequences that closely match those in other species. Body structures and patterns of embryological development tell the same story. And fossils provide a historic record of the traits of our ancestors. You will see some such evidence in this Module.

To Learn More / Credits:

All taxonomic data based on current status in the Integrated Taxonomic Information System, http://www.itis.gov/

Speciation is the formation of new species. We will assume in this course that a species is a biological lineage, although there can be considerable debate among biologists about how species are best defined in practice.

How can new species form? Recall that changes that occur in the genetic makeup of one lineage do not directly influence the genetics of another lineage as we move forward through time. Therefore speciation is the establishment of a new group that does not exchange individuals or genes with its source lineage.

What could break up a biological lineage? Species can form if they are isolated from the source lineage by geography. This is called allopatric speciation. Allopatric translates to “different country.” Species may also form through genetic or other changes that create a subgroup within a lineage that does not breed or exchange individuals with the source population. A new species “pops up” right within, and surrounded by, its parent species. This is called sympatric speciation (translates to “same-country”).

Allopatric speciation begins when populations are separated in space by some kind of geographic barrier. It can occur if geological changes break a species’ range into separate “islands” of habitat. The diagram below illustrates this process:

Allopatric speciation can occur if a geologic change creates a barrier to dispersal (movement). The barrier stops or greatly reduces gene flow between groups of populations. As they evolve independently, the groups diverge, eventually forming separate species.

Allopatric speciation can occur in another way as well: through long-distance dispersal and colonization of a new habitat. We can see the result of this process in islands far out at sea: a few hardy colonists “make it” to an island to start a population; after many generations they are distinct from their cousins on the mainland. This mechanism is illustrated in the diagram below:

Allopatric speciation can occur if a few individuals manage to disperse over a barrier and start a new population that is distant from the source species. As they evolve independently, the groups diverge, eventually forming separate species.

The map of the world is a jigsaw puzzle of broken-up habitats (continents, oceans, islands, mountain ranges, lakes, caves, river systems, forests, deserts...) occupied by different regional or local species. Allopatric speciation helps us make sense of these patterns: as Earth’s landscapes were reshaped and broken up by geologic processes, living lineages also became separated and diverged into locally adapted species.

In some cases many closely-related species all live in the same geographic area and there is no known barrier that divides them today or in the recent geologic past. These species likely formed through sympatric speciation, which occurs without help from a physical barrier to dispersal. The diagram below shows a general model for sympatric speciation:

Sympatric speciation occurs when a subgroup arises within a species. It lives in the same area but does not breed freely with the original species. Eventually the subgroup may diverge enough to become a separate species.

How could sympatric speciation happen? The drive to reproduce generally maintains the integrity of species by assuring that all their populations will exchange genes with each other. Sympatric speciation goes against this tendency; it requires the formation of a group of finicky, “cliquish” breeders. Most of the well-known examples involve genetic errors that produce offspring with extra chromosomes, a condition known as polyploidy. Sometimes polyploid types form new species that can breed with each other but are incompatible with the original species. Second, changes in ecology and breeding habits can also isolate a group within a species.

To Learn More:

Hoeck, P.E.A. and others. 2010. Differentiation with drift: a spatio-temporal genetic analysis of Galápagos mockingbird populations (Mimus spp.) Philosophical Transactions of the Royal Society of London B Biological Sciences 365: 1127–1138. doi:10.1098/rstb.2009.0311

You have probably noticed certain features that “run in families:” dark curly hair, an oddly shaped ear, bushy eyebrows, freckles... Siblings are often similar in appearance because they have inherited their genes from a common source.

In evolutionary biology, the same principle is extended to related lineages. Species with a recent common ancestor are close relatives, like brother and sister. Their lineages split apart not too long ago. Other species are much more distantly related, like second cousins. They can be traced to a common ancestor, but this ancestor lived very long ago. We can tell their degree of relationship by looking at homologous features: shared features that were inherited from the same source and reflect common ancestry. Two species that are closely related share many homologous features. Species that are distantly related share only a few.

Not every similarity between two species is homologous. We are looking for features that were inherited from a common source. Therefore the features should be based in genes (not acquired through learning, for example). Homologous features will also be similar in their details; there should be more than a passing resemblance.

An analogy might help you to recognize what we’re getting at here. Two students are brought into a professor’s office. They are shown their term papers, side by side. Bill’s paper begins: “Phylogenetic biology is the exhaustive comparison of taxonomic units in an attempt to elucidate the ancestral relationships among all life forms on the planet Earth.” Sarah’s paper starts with the exact same sentence. At several points, the papers have identical or extremely similar wording.

The students are charged with plagiarism. Both claim to have written their own papers. After all, the professor asked for a paper on phylogenetic biology, so of course the papers will be similar! The professor counters this with a quick calculation: the odds that two students’ papers would have such similar language by chance are one in several trillion. The academic integrity board agrees: either one student copied from the other, or they both copied language from the same outside source.

In biology, the same sorts of judgments are made about similarities among species. When inherited features are very similar in their details, biologists assume they were likely inherited from a common source. One classic example involves the skeletal structure of vertebrates.

Color-coded homologous features of vertebrate forelimbs. Forelimbs serve different functions in humans (arm), dogs (front leg), birds (wing), and whales (flipper). Yet their underlying structure is similar. Here the major bone categories are matched by color. Notice that the digits (“finger bones”) are partially fused in dogs; in the bird the digits are more extensively fused and reshaped. By Волков Владислав Петрович (Homology vertebrates) CC0 1.0

It seems unlikely that these four animals (not to mention thousands of others) would develop such similar limb structures by chance. It also does not appear to be necessary. Why should a whale flipper have embedded fingers, wrist bones, and three major limb bones? If adaptive evolution was starting “from scratch,” it might “design” a flipper with just a few bony plates. Instead, evidence supports the idea that all four-limbed vertebrates descend from a common ancestor; they all inherit their curious and specific arrangement of limb bones from that source. In separate lineages, adaptation has reshaped the limbs and suited them to very different functions. At first glance, a whale flipper and a hummingbird wing have little in common, but the details of the structures point to shared ancestry. Let’s take a moment to assess your understanding of homologous features.

Homologous Molecules and Cellular Structures

It is not just four-limbed animals that are related. According to current evolutionary thinking, all life on Earth is related by ancestry. You, a bacterium, a fly, a fern, and a Portabello mushroom all belong to a single clade. To some, this is a difficult or even preposterous concept. What could you and a bacterium or mushroom possibly have in common? And if you do have something in common, why do biologists think it was inherited from the same source?

We may look very different, but unifying features are evident within our cells. For example, all cells contain DNA. And to make use of their genes, all cells have ribosomes: clusters of protein and RNA that carry out the synthesis of proteins.

A model of the small subunit of the ribosome in Thermus thermophilus, a bacterium that lives in hot springs. The structure shown is composed of RNA (pink) and proteins (blue). In a functioning ribosome, this unit is paired with a larger structure. By David S. Goodsell, RCSB Protein Data Bank (10 small subunit) Public Domain

Every cell has ribosomes, but each organism’s ribosomes are built according to a slightly different set of specifications. Here, then, is a characteristic that we can compare and contrast among every single living species. That is just what Carl Woese, a microbiologist at the University of Illinois, set out to do in the 1970s. He obtained gene sequences for ribosomes of a wide range of species. He focused on part of the small subunit, shown above for one species of heat-loving bacterium. Amazingly, he could line up matching gene sequences (long series of the nucleotide bases A,G,C,T) among various microbes, plants, animal, and fungi. This was painstaking work, done without the aid of modern computers and software.

In 1990 Woese published a paper proposing a change in the classification system. He reported that there were consistent differences in ribosomal gene sequences among three major groups. Above the level of Kingdom, he proposed three Domains of life. Two of them are made up of prokaryotes (Bacteria and Archaea). The third is called Eukarya and includes all organisms whose cells have nuclei, including fungi, animals, plants, and several groups of protists. Woese’s data have since been greatly expanded, and the new data are consistent with the idea that the three Domains are the first three branches on a unified tree of life.

Why do scientists think that the chemical similarities of cells reflect shared ancestry? As with vertebrate limb structure, the genetic similarities among life forms are more than a passing resemblance. DNA sequences are detailed, complex, and contain a great deal of information. In a court of law, DNA evidence can be used to tie a suspect to a crime scene sample: it is extremely unlikely that two long DNA sequences would show an exact match unless they came from the same source. In evolutionary biology, the same sort of reasoning applies: long chunks of DNA sequences match closely among species and are evidence for shared ancestry. Thus we can now analyze inherited characteristics that have been present for not just millions but billions of years. In these ancient gene sequences we see the deepest roots of the tree of life.

Homologous features are the key sources of information for the construction of phylogenetic trees. A phylogenetic tree, or phylogeny, is a diagram that shows how a biological lineage may have branched and formed clades over time. A tree diagram is a hypothesis about how different species are related and is subject to change as more data are gathered and as analysis techniques improve. To get a feel for how phylogenetic trees work and what they mean, do the following activity.

As you have learned, shared characteristics can be used to organize species into groups, with clades defined by unique inherited traits. Unfortunately, this procedure is often quite difficult: there are millions of species to organize and an infinite number of possible characteristics to compare! Many traits may be lost or reversed over time. Consider the examples of tetrapods with one or both pairs of limbs reduced or missing (snakes, some lizards, whales and dolphins, manatees, seals, etc.). Some changes also occur quite predictably as adaptations to special environments. In the Arctic, foxes, birds, mink, hares, bears, and more all have snow-white winter coats or feathers. They are not closely related and did not all inherit their winter coloration from a common ancestor. Instead, “snow white winter color” developed independently in each of these lineages at different times and starting with different mutations.

Unlike many physical or behavioral traits, DNA sequences are an excellent source of data on relationships. By looking at DNA, biologists have a way to directly and objectively compare inherited information. For example, virtually all eukaryote species have a gene in their mitochondria that codes for cytochrome C oxidase, an enzyme that is vital to the process of aerobic respiration. This widespread gene is quite similar in most species, but mutations do occur and tend to be preserved within a lineage. Subunit 2 is a portion of the cytochrome C oxidase protein; its gene is composed of about 700 nucleotide base pairs. What does this gene say about the relationships among Carp, Salamander, Sea Turtle, Human, and Mouse? The image below gives a glimpse of the data.

Comparison of cytochrome C oxidase subunit 2 for Common Carp, Tiger Salamander, Green Sea Turtle, Human, and House Mouse. Highlighted nucleotides are identical for at least 4 of the 5 species. The image shows only the first 100 bases in the sequence; the full sequence contains a total of almost 700 bases. Image generated using Geneious software v5.6, http://www.geneious.com

As you can see, there is a great deal of similarity in this gene among the five species. This shouldn’t be too surprising: they are all vertebrate animals, close relatives in the grand scheme of life’s diversity. There are clearly sections of the gene where all the bases tend to agree; other regions show more differences. Do the differences between the genes match our expectations about how Carp, Salamander, Sea Turtle, Human, and Mouse are related? It is not easy for a human to sort through the sequences and count differences one by one, but a computer can complete this task in a flash. Below is a summary of how the full gene sequence for each species compares to that of the Common Carp:

At least from the Carp’s perspective, the genetic data agree with our tree: the Tiger Salamander is Carp’s closest match; Sea Turtle is in between; and Mouse and Human are more distant!

Using modern computers and a variety of analytical techniques, biologists can now compare vast amounts of genetic data among hundreds or even thousands of species. They can sometimes even include DNA sequence data extracted from fossils! The result has been a huge improvement in our ability to identify the clades within the tree of life.

To Learn More

Tree of Life web project: http://tolweb.org/tree/

Travels in the Great Tree of Life, Peabody Museum: http://archive.peabody.yale.edu/exhibits/treeoflife/index.html

Wellcome Trust Tree of Life website: http://www.wellcometreeoflife.org/

Discovery in Model Organism																																																																Application to Humans
A microscopic view of a fission yeast culture. Image by David O. Morgan, The Cell Cycle: Principles of Control. No Restriction. Proteins that control cell division were discovered in the 1970s through research in yeast (single-celled fungi) and sea urchins. Roles of cyclins and cyclin-dependent kinases (CDKs) were found by studying mutant yeast strains with unusual patterns of cell division.																																																																A young girl receiving chemotherapy. National Cancer Institute, Bill Branson (Photographer). Public Domain Cell cycle controls are lost or disrupted in cancer. Several drugs known as CDK inhibitors have been developed for use in chemotherapy as seen above. Continued research in yeast, mice, and humans is being used to refine and improve these treatments.
Image by Bob Goldstein, UNC Chapel Hill. CC BY-SA 3.0 Microscopic roundworms (C. elegans) normally live for 3 weeks. Those with mutations in certain genes can live twice as long.																																																																Naples (1890s) Old couple. Photo in public domain. One of the genes identified in C. elegans FOXO) has an allele that is associated with long life in humans. Several related proteins work in a pathway that involves insulin signaling; therapies that target this pathway may help extend healthy lifespan in humans.
A knockout mouse (left) that is a model of obesity, compared with a normal mouse. Image by Lexicon Genetics Incorporated, Public Domain. Thousands of strains of laboratory mice show specific diseases and disorders like the obese mouse (left) compared to a normal phenotype mouse above. Research on obese mice led to the discovery of leptin, a hormone involved in the regulation of hunger.																																																																Illustration of obesity and waist circumference. From left to right, the "healthy" man has a 33 inch (84 cm) waist, the "overweight" man a 45 inch (114 cm) waist, and the "obese" man a 60 inch (152cm) waist. Infographic: FDA/Renée Gordon. Public Domain.(1) [1] Some obese humans produce too little leptin or have nonfunctional leptin receptors in their brains, and thus are prone to overeating. Drugs may help restore healthy appetite control in some of these people.

References / To Learn More:

Willcox, B.J. and others. 2008. FOXO3A genotype is strongly associated with human longevity. Proceedings of the National Academy of Sciences 105: 13987-13992.

Spencer, G. 2002. Background on mouse as a model organism. National Human Genome Research Institute website.

Partridge, L. and others. 2011. The new science of ageing. Philosophical Transactions of the Royal Society of London Biological Sciences 366: 6-8.

National Science Foundation / American Museum of Natural History. 2000. Assembling the Tree of Life: Harnessing Life’s History to Benefit Science and Society.

Population ecology is focused on how populations — of plants, animals, bacteria, and other types of organisms — change over time. A population is a group that includes all individuals of a particular species within a given area at one point in time.

Population size, often represented by the variable N, is the total number of individuals in a population at a particular point in time. Population size can be an abstract concept, particularly for small organisms whose numbers can be astronomical. A single species of mosquito in a swamp might easily number in the millions or even billions of individuals. It is often better and more practical to describe such populations in terms of their density.

Population density is the total number of individuals of a species per unit area or volume within a specified habitat or region. In many cases this number can be pictured and measured more easily than population size itself. It also can be used to compare populations that occupy areas of different size, allowing you to judge where a population is more or less crowded.

As illustrated by the case of Valley Forge’s deer population, population size and density are dynamic, or changeable, numbers. As humans we care about changes in the density and sizes of other populations. We notice when the density of mosquitoes skyrockets after a summer rain. We are concerned about the population sizes and densities of animals we hunt, fish we harvest for food, and endangered species we seek to conserve. Much of population ecology is directed toward predicting, understanding, and controlling changes that occur in the populations of other species over time.

Why We Care about Populations

In this image a mother white-tailed deer (Odocoileus virginianus) and her two fawns forage in a suburban yard in Pennsylvania. These fawns, if both survive to adulthood, will replace the mother and her mate. If the mother produces additional successful offspring over her lifetime, the population will grow. Most people enjoy watching deer, but overabundant deer can damage gardens, pose a road hazard, and cause other problems for humans. By Glenn Brinette (Deer) CC BY 2.0

Populations change through four primary processes. New members can arise by birth through reproduction of existing population members. In the photo on the previous page, a white-tailed deer has given birth to two offspring (family sizes vary widely among species). New population members may also immigrate (move into the population) from other areas outside the boundaries set by the researcher. A population declines through the death of its existing members. The population may also decrease if members emigrate (move away to areas outside the boundaries enclosing the population). To simplify calculations ecologists often assume that a population is closed - that emigration and immigration do not occur. For this course we will adopt this idea and assume that, unless otherwise stated, the populations we analyze are closed.

Researchers studying populations usually describe birth and death in terms of rates so that they can compare different populations to each other on a similar basis. According toFederal Bureau of Investigation Uniform Crime Report statistics, in 2010 there were roughly 530 cases of murder in New York City and about 180 murder cases in New Orleans, Louisiana. Think New York City is more dangerous? Raw numbers don’t tell the full story. In 2010, New York City had a population of over 8 million people compared to New Orleans’ population of about 350,000. Therefore the rate of murder was almost 8 times greater in New Orleans than in NYC.

By calculating rates we can make fair comparisons between populations regardless of their size. The simplest way to do this is by using per capita (literally “per head”) rates where population size is included in the denominator of a rate calculation. Per capita rates can be calculated for events like birth and death or even occurrences like murders or car accidents. In each case, the calculation is equivalent.

If N = population size at the beginning of a time period, the per capita rate of some event is calculated as shown below for birth and death rates:

per capita rate of birth =

per capita rate of death =

Now you have some mathematical tools for describing a population’s status in terms of its size, density, and birth and death rates. As we will see in the next page, the rates of birth and death can be very helpful in projecting how a population will change over time.

(1) Source: "The City of New York, Summary of Vital Statistics 2009"

Now that we know a bit about how to describe a population, how can we figure out how its numbers will change over time? Let’s consider the relatively simple case of a closed population, where there is no immigration or emigration. We can predict how a population’s size will change over time simply by taking the difference between the rates of birth and death:

• per capita rate of change = per capita rate of birth − per capita rate of death

A population will grow if its rate of birth is greater than its rate of death. The population will remain constant if the two rates are equal—that is, if births are balanced by deaths. It will decrease if the rate of death is greater than the rate of birth.

Think of a population as a parade of generations, with each new crop of offspring replacing the previous generation. For sexual species, the average female must produce two offspring that live to reproduce: one to replace herself, and another to replace her mate. Yet we know that most species attempt to produce more—often far more—than one or two offspring. Furthermore, they often attempt to live for several reproductive seasons, each time generating another set of offspring. As long as conditions permit good survival and successful reproduction, any population’s size will inevitably increase.

For any population, the actual quantity of increase (number added to the population) will depend on how many you already have in the group. It can be calculated as follows:

• total number added per unit time = per capita rate of increase * starting N

That is, the per captita rate of increase multiplied by the starting population size (N).

Now you see that a rate of increase predicts how much a population will grow, and that all species tend to increase if given good conditions for growth. Below are a table and a graph that continue the process of growth for the Valley Forge NHP deer population, using our estimated annual per capita growth rate of 0.39 deer added per deer per year.

Exponential Model of Valley Forge NHP Deer Population

The population is projected to grow at a constant annual rate of increase (0.39 deer added per deer per year, or 39% annual growth). Each year, the starting N is updated to reflect the growth of the previous year. For example, the starting population for 1986 (236) = the base population from 1985 (170) plus the growth from 1985 (66). Although the per capita rate of growth remains constant, the number added each year increases with the base population.

Year	N at Start of Year	Number Added
1985	170	66
1986	236	92
1987	328	128
1988	457	178
1989	635	247
1990	882	344
1991	1226	478
1992	1704	665
1993	2369	924
1994	3293	1284
1995	4577	1785

Exponential growth

Exponential growth of the Valley Forge NHP deer population assuming continued growth at a constant annual rate of increase (0.39 deer added per deer per year or 39% annual growth).

The table and graph above depict a pattern of change called exponential growth. In exponential growth, a quantity grows by a constant percentage each time step. As the quantity gets larger, so does the actual amount of growth that occurs. Some familiar examples of exponential growth involve finances. A bank account may earn 1% of its value in interest each year.When the bank account’s value is $100, 1% amounts to a dollar. But if the account already contains $1 million, a gain of 1% brings in $10,000!

You can recognize exponential growth as a pattern in which the numbers increase faster and faster with each time step. A series of numbers with this property would be 2, 4, 8, 16, 32, 64, and so on. Visually, you can imagine exponential growth as a snowball rolling down a hill, picking up snow as it goes: the bigger it gets, the faster it grows. A wildfire spreading through dry grass might also grow exponentially. In a graph, exponential growth shows up as a J-shaped curve.If you imagine the graph as a staircase, each individual step is taller than the one that came before it.

A contrasting model of growth is linear growth. Here a quantity grows by a constant number (not percentage) in each time interval. A series of numbers with this growth pattern would be 2, 4, 6, 8, 10, 12, and so on. Each time step the quantity increases by 2, no matter how big it might already be. In a graph, linear growth appears as a straight line. A staircase is linear: the risers are evenly spaced and you gain a set amount of height with each subsequent step.

Compared to linear growth, the exponential growth pattern is a better starting point for predicting how populations will change over time. It captures a little bit of reality, in that a bigger group will have more individuals capable of producing offspring. However, it is important to emphasize that the table and graph above are based on a “what-if” exercise. They show numbers generated by a model of how populations increase. This model assumes that the growth rate will remain constant and predicts how the population will change if this condition is met.

did I get this

All populations have the potential and tendency to increase. For sexual species, each adult female must produce two adult offspring to replace herself and her mate and thereby maintain a steady population size. But if conditions are right, individuals of any type of organism will produce offspring in excess of this replacement number.

The exponential model of growth predicts what will happen if this potential is realized each generation for an extended period of time. The population will grow faster and faster the larger it gets, producing a characteristic J-shaped curve on a graph of population size over time.

What actually happened to the deer population at Valley Forge NHP from 1985 onward? Data are not available for the late 1980s or early 1990s. However, the record that is available looks like this:

Estimated changes in deer population at Valley Forge NHP. Data are not available for the time period from 1985 to 1996.Source:

A few things are evident in the graph. First, the population did not increase to over 4500 by 1995 as predicted by the simple exponential growth model. Instead, it increased to about 1400 until the early 2000s and then began to fluctuate.

The exponential growth model assumes that populations will maintain constant rates of birth, death, and increase as they grow larger. In reality, we often see that populations stop growing—and sometimes even crash—due to the effects of limiting factors. Limiting factors are biotic or abiotic factors that limit populations by reducing birth rates, increasing death rates, or both. Limiting factors may also increase rates of emigration or decrease immigration.

Sometimes limiting factors act in an unpredictable way to reduce population sizes. Hard freezes, fires, droughts, and floods are all examples of factors that could act to quickly reduce a population. These factors most strongly affect small-bodied organisms that are easy to kill such as insects, microbes, and weedy plants. Their populations often show an erratic boom-and-bust pattern: population sizes shoot up when times are good and crash when conditions are bad. Ecologists agree that it is difficult to predict or model the changes in such populations, except by taking into account the weather or other outside factors known to control them.

Other types of limiting factors act more gradually and have their greatest effects when populations are crowded. Scarce resources, limited space, and infectious diseases are important examples. These factors often play the greatest role in limiting large-bodied organisms with extended life spans such as large animals and woody plants. For example, deer survive frost well but are more likely to starve in a hard winter if there are many mouths to feed. Over time, populations of such species limit themselves: they remain close to a stable size called the carrying capacity. When a population is at its carrying capacity, it does not tend to increase or decrease but tends to stay essentially the same over many generations.

At least in principle, we can predict what will happen to a self-limiting population over time: it should grow until it reaches its carrying capacity and then remain stable. This pattern of change is calledlogistic growth. It is simple to describe logistic growth with a math equation that allows a population to grow when it is small but causes it to level off when it reaches a predetermined value (the carrying capacity). A logistic model for the Valley Forge NHP is shown below, superimposed on the actual population data from the park.

Logistic model and observed population sizes for deer at Valley Forge NHP.

In purple (diamond symbols) are the observed population sizes for deer at Valley Forge NHP. Based on these data, a logistic growth model was developed assuming that the carrying capacity = 1312 deer and the average annual per capita rate of increase over the period was 0.23, or 23%. The logistic model output is plotted with a green line / square symbols.

A graph of logistic growth shows up as a slightly S-shaped curve. Initial growth is relatively slow because the population is small and has few individuals to give birth. At moderate population sizes the population grows fastest: there are many parents but the effects of crowding are not yet severe. As the population approaches its carrying capacity, the effects of crowding start to reduce its growth. The rate of growth slows and then stops.

Principles of population ecology are critically important to many enterprises including game and fisheries management, conservation of rare and endangered species, and pest control. How can a population be “managed”? Managers seek to control conditions for survival and reproduction.

Management of threatened or endangered species may simply involve increasing birth and reducing death rates as much as possible, though this is often easier said than done. To help such species, conservationists may breed them in captivity and release individuals back into the wild. Captive breeding programs have been used to aid in the recovery of many species, including the peregrine falcon and the black-footed ferret. Most endangered species management focuses on improving survival rates (reducing death rates) by banning harvest of these species or trade in their products, by eliminating introduced predators, or by improving habitat conditions.

The situation is more complicated when the goal is to manage a resource so that it can be harvested. Consider a population of fish that supports a commercial fishery. Here, the goal is to maximize the harvest rate while maintaining a healthy population size. How can principles of population ecology help in choosing the best rate of harvest?

The general idea is that a population is like a bank account. Every so often, we can remove the interest that has accumulated in a bank account. This can continue indefinitely so long as we do not remove any of the principal that is earning the interest. Similarly, every so often we can remove a population’s growth without causing the population to decline: it will be reset to its beginning level and the harvested individuals will be replaced by further reproduction and growth. Ideally, we should be able to find the population size that provide the maximum level of growth (and harvest) each year. Population modeling can help with this effort.

As you have just seen, the logistic model indicates that a harvestable population should be maintained at a moderate size of about half its carrying capacity. At this point there is a large increment of growth each year and these individuals can be harvested. This is the general framework used by fisheries managers as they seek to maintain and improve the productivity of fish populations. They often set regulations and allowable harvest limits to try to keep populations close to the “sweet spot” at about 50% of carrying capacity.

Fishery managed to maximize harvest.

This idealized diagram shows a fish population managed to maximize the sustainable harvest. The average size of the population is maintained at 50% of the carrying capacity. Each year, the annual growth is harvested (glowing dashed lines = harvest). The surviving population grows at a maximum rate and rebounds to enable another harvest.

Population models help officials manage fisheries for maximum benefits to commercial fishermen and recreational anglers. However, this approach can be risky. Models are not the same as reality. Outside factors such as weather events, disease epidemics, and so on can sometimes unpredictablydecimate fish populations. With fewer adults in the population, the population cannot rebound after a harvest that would normally be sustainable. Even just one bad year can set up a series of events in which the population dwindles over time. Because of this unpredictability, many fisheries managers try to maintain populations at a level that is a bit “too high” (say, 75% of carrying capacity) and limit harvest rates accordingly. This reduces the amount of fish that can be harvested but it also reduces the risk that harvests will drive the population downward.

Endangered species and fisheries management are just a few of the areas in which principles of population ecology are applied to solve real-world problems. Pest management is often a very challenging exercise because pest species tend to reproduce very rapidly and show a boom-and-bust pattern of growth. Even if we can induce a bust—say, by spraying an insecticide—the population is likely to rebound with another boom unless we can reduce the birth rate. Effective pest management often requires that several strategies be used together with careful monitoring of the pest population.

Population management can also raise ethical issues. It involves life-and-death decisions that can be very emotionally charged. At Valley Forge NHP, park managers recognized the need to act as deer populations climbed past 1,000 and serious ecological damage began to occur. The park’s plant diversity was severely threatened by the high deer numbers; few tree seedlings or wildflowers were able to survive except within small fenced areas (deer exclosures).

Most agreed that something should be done, but how should the deer population be controlled? It would be unsafe to allow the public to hunt in the park. Some citizens argued that birth control injections should be used to manage the population, but evidence indicated that this would be expensive and ineffective. After extensive deliberation and community input, a deer control program was begun. In the winters of 2010 and 2011, sharpshooters were contracted to kill deer at the park; meat was provided to an area food bank. Sharpshooters removed 600 deer in 2010 and 377 deer in 2011. As a result, the deer population fell from 1,277 in 2009 to 374 in the spring of 2012. Initial data indicate that many tree, shrub, and wildflower species are already beginning to recover as a result.

To learn more / sources: Valley Forge NHP White-Tailed Deer Management Page

Until now, we have focused on specific populations responding to limiting factors such as weather, crowding, or fishing by humans. Community ecology broadens the focus to explore how populations of different species interact with each other. An ecological community is the collection of all interacting species populations within some defined area. Because animals move in and out of any given area, it can be tricky to determine what populations belong within a community. For example, birds such as herons may interact with pond communities by removing fish. They are therefore included as part of the pond community because they can have an important effect on pond life.

Scientists learn about species interactions first by direct observation. For example, it is simple enough to discover a predator-prey relationship by watching a lion take down an antelope, or by finding prey in a predator’s stomach. However, community ecologists often want to go a step further and determine the consequences of an interaction. How will a community change if a new species is added, or if an existing population dies out? To find out, ecologists may do comparative observations or experiments, as we will see in this module.

In several examples we will also see that community ecology is important to people. Managers of nature preserves and wildlife parks seek to increase or maintain the diversity of native species in the areas under their care. Community interactions may also control the abundance of pests, disease agents, pollinators, fish, game animals, and other species that have a direct effect on human well-being.

An ecological community can be described in many different ways. One statistic that is often of interest is the species richness of a community: the number of different species of organisms present in a given area. Some communities, such as tropical rainforest or coral reef communities, have high species richness with thousands of species of plants, animals, and microorganisms coexisting in a small area. Other communities with harsher conditions (deserts, arctic tundra, salt lakes) may hold far fewer species. Within any region, a given type of habitat will have a fairly predictable level of species richness. Human activities that alter living conditions, such as pollution or habitat destruction, can change the membership of communities and usually will cause species richness to drop. Thus a naturally high level of species richness is one indicator that a community is healthy and relatively unaffected by human activities.

An interspecific interaction is an effect of one population on another in a community. Although we are often focused on how one population affects the size of another, ecologists also may look at how species interact in terms of their activity, growth rates, body size, or other aspects of their well-being. Interactions are classified according to their consequences for each species involved. The most important types of interactions are summarized in the table below.

In a community, any pair of species may potentially interact. However, some interactions are much clearer and more easily predictable than others.

Direct interactions occur when two species make contact and affect each other’s well-being without the participation of any third species. Some pairs of species are intimately and physically connected, with a smaller species (symbiont) living in or on the body of a larger species (host). These direct interactions are described using the term symbiosis,which translates to “together living.” In other cases the contact between direct interactors is more fleeting, as when a bee visits a flower or when a hawk swoops down on its prey.

Mutualistic, or mutually beneficial, relationships are widespread and important features of communities. Sometimes mutualism also involves symbiosis. Many animals and plants are host to microorganisms that provide them with vital functions. In other cases, equally important mutualistic transactions are carried out at a distance: not all mutualisms are symbiotic. Plants, for example, reward animals for transportation services that allow them to mate (pollination) and travel as seeds (seed dispersal). Animals also may help each other in subtle ways.

Predation can be broadly defined as any win-lose interaction, though it is most commonly used to describe situations where one species kills and eats another. You are no doubt familiar with many spectacular examples, as when a pack of wolves takes down a moose. More subtle examples of predation also exist. Sometimes the predator will eat only part of the prey, allowing it to live another day. Though we often use the term “herbivory” for the consumption of plants, the moose might itself be considered a predator if it harms the plants on which it feeds. Many forms of predation involve symbiosis. Such interactions are called parasitism and may involve animal or a plant hosts that provide both habitat and food to their harmful symbionts.

Competition is a lose-lose, or mutually harmful, relationship between two species. Two species are competitors if each would be better off alone. Clear examples of competition are often seen among plants that require very similar resources, such as light, water, and certain mineral nutrients. Animals may compete for space, sometimes fighting directly for territory or simply excluding each other from living sites. Animals that eat similar foods may also sometimes make life harder for each other, though here the degree of competition is often limited because each species may eat slightly different foods.

Whenever ecologists study species interactions, they try to get clear data answering “what-if” questions. What happens to prey populations if a predator is removed from a community, or if a new predator shows up? Do two species really compete; that is, do they each do better if they are alone than if they are living together in a habitat? Can a species and its mutualist live apart, or are the two species entirely dependent on each other? Sometimes we can learn about these issues simply by observing what happens when introduced species—species brought into an area by human activity—establish themselves in a community. We can also see what happens to the larger community if a particular population is eradicated by human activity. On a smaller scale, ecologists sometimes carry out true experiments. In these studies ecologists deliberately manipulate the presence or abundance of species in enclosures or in natural environments and then track what happens to other species as a result.

Explore some examples of species interactions below. In each case you may be asked to identify the type of interaction—mutualism, predation, or competition—and to clarify exactly how the species interact.

Ecological interactions range from harmful to helpful and can take on many forms. Some interactions involve exchanges of materials; others are more subtle and involve services or behaviors. Mutualistic interactions often develop when two partners have complementary abilities. For example, aphids are excellent plant sap drillers but ants are much tougher and more mobile, so the trade between aphid and ant is quite logical. Predation is a nearly universal interaction: almost every organism is food for something else, and most animals eat living prey of some kind. Competition often develops where individuals or species have similar requirements, like the plants that will crowd together in a dense Alabama thicket if conditions permit it.

Ecological communities can be dizzyingly complex. A community may be home to thousands of species, and every single one of them may be linked to several others through a variety of interactions. Among all this complexity, ecologists have worked to discover the most meaningful and important interactions: those that determine the stability and diversity of the whole community.

One way to simplify the problem is to focus on a few particularly important species. Species that are physically dominant (largest and/or most abundant) in communities are sometimes called foundation species. They include the most abundant trees within terrestrial forests, common grasses within grasslands, and reef-building corals. Foundation species directly provide habitat and often food for most of the other species in the community. Anything that threatens their well-being is likely to harm many other species as well.

Along the coast of western North America, rocky areas are often home to a spectacular community called the kelp forest. It is dominated by kelp, big brown algae (seaweeds) whose fronds can stretch to dozens of meters in length. Kelp are clearly the foundation species of the kelp forest: they provide food and shelter to a huge diversity of fish and invertebrates including such economically important species as lobster and rockfish.

Kelp and sardines off the California coast

Kelp fronds shown here are surrounded by sardines and provide food and cover for a wide range of marine animals. By NOAA (Kelp and Sardines) CC BY-SA 2.0

Most communities are clearly dependent on one or a few foundation species. But not every important species has effects that are so obvious. In ecological communities, many interactions are indirect.Indirect interactions, sometimes called “ripple effects,” occur through chains of cause and effect. The effect of one species on another is said to be indirect if one or more additional species are involved in the interaction as intermediaries. Complexity of this sort is a source of fascination and challenge for ecologists attempting to unravel how communities work.

Indirect interactions can produce surprises in communities. Some species, called keystone species, may be very influential in communities even though they are not particularly abundant or large. In architecture, a keystone is a single wedge-shaped stone at the top of a stone arch that maintains the integrity of the structure; its removal will cause both sides of the arch to collapse. A keystone species, then is a species that has an unexpectedly strong effect on community stability or diversity. Keystone species play unique roles and are not easily replaced by other species within the community. We often discover their importance only after they are eliminated by human actions.

Within kelp forests, human hunting revealed the importance of a keystone species. The story begins with urchins, which are abundant bottom-dwelling grazers and scavengers. Kelp are tough and fast-growing, but urchins (animals related tostarfish) can eat them with their hard rasp-like mouth parts. Urchins are protected by their prickly spines and a hard outer shell. In the absence of factors controlling their abundance, urchins can increase to very high densities, producing what are sometimes called “urchin barrens” devoid of kelp. Unlike kelp forests, urchin barrens do not support much life.

Purple sea urchins

A thick aggregation of purple sea urchins at a tidepool in California. By Steve Jurvetson (Purple Urchins) CC BY 2.0

What factors normally keep urchins in check? In the cold waters off the west coast of Alaska and Canada, evidence points to one factor as particularly critical: the presence of sea otters. Historically, humans hunted sea otters for their fur, nearly eliminating them by the late 1800s. More recently, sea otters have been reintroduced to many areas where they had been absent. Since the 1980s, researchers, including James Estes of the University of California Santa Cruz, have been tracking sea otter numbers and documenting their effects on marine communities in Alaska and off the coast of British Columbia. They have found that the sea otter is a keystone species in the kelp forest.

Sea otters are uniquely suited to eating the urchins. With their dexterous paws and long incisors, they can crack open the urchins, eating the soft flesh inside. Sometimes they even use rocks as tools to crush tough prey. After eating an urchin, a sea otter discards its empty shell, or test. A study published in 2011 by Estes and Jane Watson reported that when broken tests sink to the bottom, remaining urchins will flee from the immediate area. Thus, sea otters can reduce urchin numbers and change urchin behavior. In this way, otters safeguard kelp and help to maintain healthy kelp forests.

California Sea Otter resting within a group off the coast of California. Note the large teeth, which are used to break into sea urchins and help explain the unique keystone role of sea otters in Alaskan and Canadian kelp forests. A frond of kelp is wrapped around the otter’s abdomen. Note that kelp forests in California do not appear to depend as directly on sea otters as those in Alaska or Canada. A wider range of factors may act to control urchin numbers along the California coast. Left image by Mike Baird (California Sea Otter) CC BY 2.0 Right Image by Mike Baird (California Sea Otter resting) CC BY 2.0

Kelp forests provide a glimpse into the many facets of community ecology. They are complex, with more than twenty species of kelp plus hundreds of animal species. They also are structured in an understandable way, with some species interactions more important than others. As ecologists continue to unravel community interactions, we are improving in our ability to predict how communities will respond to factors like hunting. Kelp forests are a treasured resource for recreational diving and fishing. Kelp also are harvested for use in aquaculture and industry. The science of ecology can help us learn more about kelp forests and supports our efforts to safeguard these dazzling communities.

Source and To Learn More:Whipple, WJ and RL Beschta. 2012. Trophic cascades in Yellowstone: The first 15 years after wolf reintroduction. Biological Conservation 145: 205-213.

Up to this point, we have focused on the living components of the environment. Consider a suburban backyard that is home to diverse species, including robins, squirrels, ants, oak trees, grass, rabbits, daisies, spiders, toads, mushrooms, and raccoons. These living, or biotic, components together make up an ecological community. Its populations affect each other directly and indirectly as we just explored. But each population also interacts with a host of nonliving factors. A grass plant, for instance, requires light, carbon dioxide gas, soil nutrients, and water. It is affected by temperature and by factors like snow cover or fires. In turn, it influences nonliving factors as well. Its roots, for example, hold soil in place.

To fully appreciate an organism’s role in the environment, we must go beyond the web of life. We must also consider nonliving, or abiotic, components of the environment: rocks, water, gases in the air, chemicals in soil and water, light, temperature, wind, and waves. The combination of biotic and abiotic components forms an ecosystem. A community is restricted to the populations of living organisms in an area; an ecosystem also includes all of the nonliving physical and chemical factors that are important to these populations.

In a healthy ecosystem, there is a continuous flow of energy that provides resources to sustain a diverse community of life. As we will explore in this module, energy starts in a nonliving form, usually as sunlight, and is captured and stored as chemical energy by producers. It then moves through chains of consumers, dissipating as heat along the way. A continuing supply of solar energy keeps this system in motion.

As they take up and release energy, growing organisms also absorb chemical nutrients and release chemical wastes. There is a continuous exchange of material between the living and nonliving portions of the ecosystem. Each chemical element retains its integrity but takes on many different forms as chemical bonds are formed and broken. To see how this material recycling takes place, think about a leaf on a tree. Its living tissue contains organic molecules rich in carbon (C), hydrogen (H), nitrogen (N), oxygen (O), phosphorus (P), sulfur (S), and other elements. In autumn, the leaf dies and falls to the ground. Over time, the leaf decays. Bacteria and fungi feed on the leaf material. In the process, its large organic molecules are broken down to simpler inorganic molecules. Focusing on just one element, the nitrogen atoms that were in the leaf are now released to the soil as ammonium (NH₄⁺). To complete the cycle back to life, plants take up ammonium through their roots and use its nitrogen to make proteins and nucleic acids. Thus, nitrogen has cycled between the biotic and abiotic components of the ecosystem.

Energy and nutrients take many complicated paths through an ecosystem. Feeding relationships are a good place to start; they describe how atoms and calories move through the living community. Take as an example the simple act of eating a tomato. A tomato plant grows and produces fruit only if it has plenty of light and nutrients. Chemical energy is stored in the bonds that join together the tomato’s organic molecules. After you eat and digest a tomato, some of its molecules are broken down into their subunits. Your cells can use some of that energy to make new molecules or run processes in your cells. Much of it is released as heat.

The simple example above illustrates two transfers of energy: sunlight → tomato and tomato → human. Every organism in an ecosystem must obtain its energy through one or more such transfers. Some organisms are close to the source of energy (the tomato); others are several steps down the line (a hawk that eats a bird that ate a caterpillar that ate the tomato plant). We can break a community up into a series of food-based groups called trophic levels. Trophic level 1 is composed of producers that form the base of all ecosystems. Organisms in level 1 are eaten by organisms in level 2; organisms in level 2 are eaten by organisms in level 3; organisms in level 3 are by organisms in level 4, and so on.

The energy that fuels most ecosystems comes from the sun. Photosynthetic producers such as plants are found in trophic level 1. Organisms in level 1 do not consume other living organisms to obtain nutrients. They can make simple organic food molecules from inorganic raw materials using light energy from the sun. Plants, algae, and cyanobacteria are the photosynthetic producers that make up trophic level 1 in most ecosystems. Organisms in level 2 and beyond are called consumers because they obtain food by eating plants or by eating organisms that have eaten plants. Animals, fungi, and many microbes are consumers. Consumers are identified as primary, secondary and tertiary depending on their trophic level. Cows eat grass and are primary consumers. When you consume a salad, you too are acting as a primary consumer. Humans who eat meat from cattle act as secondary consumers.

In addition to the chains of consumers that eat living prey, many consumers feed on dead organic material. Dead plants, dead animals, shed parts of animals such as fur or skin, shed parts of plants such as leaves, and feces all contain nutrients and calories. Animals that feed on dead organic matter are called detritivores; some of them specialize on eating dead animals (e.g., vultures) and others feed on dead plant material (e.g., earthworms, which consume decaying leaves). Bacteria and fungi that colonize dead material and absorb food molecules from it are called decomposers. Detritivores and decomposers extract remaining calories and nutrients found in dead organisms and dung. In the process, they release simple inorganic wastes to the environment, making chemical elements available to producers.

A food chain is a group of organisms that are joined in a linear series of feeding relationships. Each species in a food chain gains energy from a single source and is, in turn, a source of energy to at most one consumer as shown in the picture below:

CAPTION: A simple food chain diagram. Light energy flows from the sun. The plant uses that energy to produce food energy. The grasshopper eats the plant leaves. The mouse eats the grasshopper and the snake eats the mouse.

In the food chain above, the plant is the producer, the grasshopper is the primary consumer, the mouse the secondary consumer and the snake is the top predator or tertiary consumer. Food chains help us trace the flow of energy and materials through ecosystems. Based on the transfers shown above, plants are in trophic level 1, grasshoppers are in trophic level 2, mice are in level 3, and snakes are in level 4. Each level is dependent on the previous level as a source of food and may provide nutrients and energy to a subsequent level.

Food chains are not very realistic. In real ecosystems, food chains overlap and are interconnected as food webs. Consumers rarely specialize on only one type of food. Many of them are omnivores, feeding on more than one trophic level. Mice, for example, may eat:

• plant seeds or fruits (acting as primary consumers, trophic level 2)
• grasshoppers (acting as secondary consumers, trophic level 3)
• dead snakes or snake eggs (acting as level 5 consumers)

In addition, most organisms are fed upon by more than one species. A mice could be eaten by a snake, but it could also be eaten by an owl, a hawk, or a house cat. A complete food web shows all of these possible feeding relationships. In diagrams that depict food chains or food webs, the arrow points from the organism being eaten to the organism doing the eating. In other words, the arrows follow the flow of energy and nutrients through the ecosystem.

We have seen how food chains, trophic levels, and food webs can be used to describe how energy and materials move through an ecosystem. Although they are not as realistic as food webs, food chains and trophic levels do provide us with some important insights. They help us understand, for example, why top predators are rare and why meat costs more than grain.

All organisms require energy for growth, reproduction, and metabolism. But as energy flows through a food web, much of it is lost at each transfer along the way. Let’s trace how energy moves through a simple ecosystem consisting of tomato plants, caterpillars, and birds.

Transfer 1: sunlight → tomato plant. Most of the sunlight energy that reaches the plant is reflected or absorbed and re-emitted as heat. Some is captured by photosynthesis. Most of this is used by the plant for aerobic respiration and ATP generation; ultimately this energy is released as heat. Only about 1% of the incoming solar energy is stored as calories in the molecules within the tissues of the growing plant.

Energy transfer from the sun to producers

Of the available solar energy (100%), producers capture and store only about 1% as growth that is then available as food calories to primary consumers in the ecosystem. The rest of the energy (99%) is reflected as light or released as heat.

Transfer 2: tomato plant → caterpillar. Much of the energy in the leaf material eaten by a caterpillar is not digested and is excreted in feces. Of the energy that is absorbed, most is used in aerobic respiration and is released as heat. Only about 10% is stored as calories in the molecules (fats, proteins, etc.) that make up the tissues of the caterpillar.

Transfer 3: caterpillar → bird. Some of the energy in the caterpillar is excreted in the bird’s feces. Most of what is absorbed is used in aerobic respiration and is released as heat. Only about 10% is stored as calories in the tissues of the bird.

Energy transfer through consumers

Of the food calories ingested, consumers store only about 10% as growth that is then available as food calories to consumers in the next trophic level. The rest is excreted in feces (calories in undigested food) or is released as heat.

If you are a bird-eating consumer such as a snake or hawk, very little energy is available to you. Based on the estimates above, you would have access to only 0.01% of the solar energy that fuels the ecosystem as a whole.

As you can see, only about 1% of incoming solar energy is stored as calories in the tissues of growing photosynthetic producers. This energy is then passed up to higher trophic levels through a series of transfers. On average, only about 10% of the available energy in one trophic level is incorporated and stored as calories in the bodies of the next level up. The rest of the energy is released undigested in feces or is dissipated as heat. The result is that all ecosystems show a pattern known as the energy pyramid in which energy availability decreases with increasing trophic level. The bottom of the pyramid contains producers (usually plants or algae). Each trophic level of consumers (level 2 and above) becomes progressively smaller. The amount of energy available to consumers at the top of the pyramid is much smaller that what is available to organisms at lower levels.

The diagram below shows each trophic level as a block of color. In keeping with real patterns as seen in many ecosystems, each block’s area is 10% or one-tenth that of the preceding block. That leaves mighty slim pickings for level 5!

Ecosystem energy pyramid

A realistically scaled energy pyramid. Blocks are scaled so that their area shows the amount of energy available to each trophic level. 90% of energy is lost as heat or waste with each transfer in a food chain.

In real ecosystems, energy availability can be measured in many different ways. The mass of organisms at each trophic level can be measured, or their total annual calorie requirements can be estimated. In either case, the overall energy pyramid pattern remains quite consistent. This helps to explain why huge hunting grounds support only small numbers of top-level predators such as killer whales, great white sharks, or tigers.

The energy pyramid also has implications for humans. Our diet is very flexible. Strict vegetarians live on trophic level 2. Those who eat a lot of animal products live closer to trophic level 3. When grain is fed to animals much of its calorie content is used by the animals themselves, and only a small fraction is available to us in the food that is produced. Therefore people who eat a diet rich in animal products generally have a greater total environmental impact—in terms of crops consumed, fertilizers used, land area farmed, etc.—than those who eat plant foods. And as seen in the largely vegetarian traditional diets of rural China or India, a given land area can support more people at lower cost if they live on trophic level 2.

Energy enters ecosystems as sunlight and dissipates from all living things as heat. Producers (trophic level 1) have access to the greatest amount of energy (sunlight). As they grow, they store up food calories that supply all consumers with energy. Consumers feed on producers directly (trophic level 2) or feed on each other through a series of transfers that can be described as a food chain. The amount of energy available to consumers declines by about 90% with each transfer, so top predators at the end of long food chains tend to be rare.

In the past, the science of ecology focused on nonhuman species. Rather than studying cities or farms, ecologists have worked in “wild” places like forests, mountain streams, coral reefs, and grasslands. Ecologists sought to unravel how plants and animals in these places interacted with each other. The activities of humans were viewed as a separate issue, outside the normal set of processes at work in “natural” communities and ecosystems.

Today, however, ecologists recognize that humans have an influence on all communities and ecosystems. In some ways, we are simply participants in and members of ecosystems. Like other animals, we feed on the bodies of plants and other animals; excrete gaseous, liquid, and solid wastes; and disturb small areas of soil when we travel across the landscape on foot. In most of our activities, however, humans have impacts that go far beyond those of other animal species. What makes us different?

• Population size. As we will discuss in this unit, Earth’s total human population now exceeds 7 billion. Our total biomass is far greater than that of all wild large animals (megafauna) combined, as is the biomass of our domestic animals. We require huge volumes of food and water simply to meet our most basic needs.
• Affluence and consumption levels. Today, over a billion humans live in high-income nations where most citizens enjoy a standard of living that goes far beyond basic nutrition. Many of us live in sturdy temperature-controlled buildings and have indoor plumbing, electric lights, washing machines, refrigerators, electronic gadgets, and automobiles. These items all require resources and generate wastes in their production, use, and disposal.
• High-impact technologies. Until about 1800, most human activities were accomplished by the labor of humans and domestic animals. Biodegradable materials were used. Impacts on ecosystems took a long time to develop and much of the damage was repaired through natural processes. Today, humans have harnessed outside energy sources (fossil fuels, explosives, wind and flowing water, nuclear energy, and the like) to perform work at an unprecedented scale. Humans now can rapidly transform landscapes and intervene in basic natural processes. Advanced technologies have also produced persistent (nonbiodegradable) chemical toxins and radioactive wastes.

Each of the above factors promotes greater environmental impact if all other factors are held equal. In real societies, however, all three factors change over time and influence each other. This leads to some surprising patterns of impact. For example, some environmental conditions are better in high-income nations than in lower-income countries. In general, the air and water are cleaner, industries are better-regulated, and forests are less heavily exploited in higher-income nations. We can account for this in two ways. First, goods can be consumed in one place but generate their impacts elsewhere. With global trade, many of the impacts of consumption occur in developing nations where goods are produced, dumped, or recycled. Second, more advanced technology is not always more disruptive; technology can also be developed to reduce impact. Examples of advanced low-impact technologies include renewable energy technologies (solar panels, windmill generators), biodegradable plastics, smokestack “scrubbers” that remove pollutants from power plant emissions, and energy-efficient appliances and buildings.

Although there are many competing priorities, environmental concerns have become more prominent in our society since the 1970s. Corporations have adopted environmental goals as part of their mission statements. Nonprofit groups advocate for the environment. Government programs promote specific environmental goals. We use buzzwords like “sustainability” and “stewardship.” Products and ideas are marketed as being “ecosafe,” “earth-friendly,” or “green.”

As a consumer, voter, employee, or business leader, you have some control over environmental impact in your daily decisions. You should have a clear sense for what sustainability really means. Sustainable technologies meet human needs—economic and social—and preserve the productivity or biodiversity of ecosystems over a long period of time. In any given case, different options may maximize individual economic benefit, public welfare, or environmental integrity. The most sustainable choice often involves finding a compromise among these competing priorities.

One step toward sustainability is the careful use of renewable resources: those that are replenished quickly enough to replace what we consume. Resources are renewed through growth or other ongoing processes. Most products of plants and animals are potentially renewable, so long as we do not consume them too quickly. Many physical processes (solar energy input, river flow, tidal flow, wind, flow of heat from Earth’s interior) also occur at a high and sustained rate.Nonrenewable resources, by contrast, are replenished very slowly. Such a resource can be thought of as a fixed stock. Once depleted, a nonrenewable resource cannot be replaced in useful quantities. Most mineral resources and fossil fuels are nonrenewable. Over time, if humans continue to use these resources they will become increasingly scarce. A second factor in sustainability involves the disposal or ultimate fate of materials and wastes we produce. Biodegradable materials are more sustainable over time because natural decomposition processes will break them down and recycle any nutrients they contain. Nonbiodegradable materials tend to accumulate over time and may cause negative environmental impacts. Some examples include plastics and persistent toxic chemicals.

Renewable resources can be used in a sustainable way so long as the rate of use does not exceed the rate of renewal. Nonrenewable resources cannot be used indefinitely and technologies that rely heavily on them are unsustainable. In the table below we summarize several examples of renewable and nonrenewable resources.

Over time, human activities may have permanent negative effects on the environment’s capacity to support life or provide resources to future generations. Ultimately the degree and nature of our impact will depend on how population size, affluence levels, and technologies change in the future. We will explore these issues in more depth in this module. In the next page, we will examine the history of the global human population, tracing some of the factors that have enabled our dramatic expansion in numbers and in impact.

To grasp our collective impact as human beings, we must begin with some analysis of our population’s size and technological reach. How many of us are there? How did we get to our current abundance and affluence? What were some of the major milestones along the way?

Based on fossil and genetic evidence, the first anatomically modern Homo sapiens arose in Africa about 200,000 years ago. The history of humanity can be divided into three broad periods that represent widely differing ways of life. We will call them the Stone Age, the Agricultural Age, and the Industrial Age.

Stone Age. By 50,000 years ago, humans had developed many features of Stone Age technology and culture. By 20,000 years ago, modern humans had dispersed through much of the world. Stone Age humans obtained food by fishing, hunting wild game, and gathering wild plant products. Food sources were unreliable and most humans were nomadic, traveling widely to find food. Shelter, clothing, and tools were made from stone, animal hides, and wood. Fire was used as a source of heat and to modify the landscape for better hunting or travel. Human labor was the main energy source.

Agricultural Age. This age started around 10,000 years ago. It involved many (though not all) human cultures worldwide and extended through the late 1700s. People began to domesticate plants and animals. Food supplies became more reliable and abundant and diets expanded to include grains, poultry, meat and dairy products from livestock, improved fruits and nuts, and more. Agricultural Age humans stayed close to productive farms and pastures and built the first permanent towns and cities. Humans began to extract and forge metal to make durable tools, weapons, and ornaments. Energy sources expanded to include labor from farm animals such as oxen and horses. Windmills and water mills were also used as a source of power. Some cultures developed extensive water control systems for irrigation of crops. Governments, organized religions, and written languages flourished.

Industrial Age. The Industrial Age began in Europe in the 1700s and continues today. Agriculture continued to improve and cities continued to grow. Global trade moved people and ideas around the world. Science helped to spark new technologies. Machines harnessed external sources of energy to accomplish all kinds of work. Fossil fuels became the main source of energy for transportation, farm work, heating, cooling, manufacturing, mining, and other activities. Scientific principles were applied to improve public health, beginning with vast improvements to sanitation in cities. Sewage treatment, safe municipal water supplies, public garbage disposal, and soap are all Industrial Age innovations. Modern medical practices, including aseptic surgery, antibiotics, and vaccinations, were developed. At the same time, the reliability and quality of food supplies continued to improve.

Thus the world’s humans have gone through dramatic changes in their technologies and living conditions. In the activity below, explore and learn more about how rates of birth, death, and population growth changed as a result.

History of environmental impacts

Thus far, we have seen how human technology and population size have changed over the past 200,000 years. How have humans impacted the environment over this time span? Humans have had an impact on Earth’s ecosystems at every stage of our history.

During the Stone Age, for example, human use of fire may have had a profound effect on many ecosystems.By setting forest and grassland fires, humans favor fire-adapted plant and animal species. Hunting may have depleted some food resources and probably contributed to past animal extinctions as well.

During the Agricultural Age, humans cleared forests and created dams and irrigation systems. These actions harmed many species and benefited others. In some cases, resources like forests or fertile soils were depleted on a local or regional scale, contributing to the collapse of human societies. Throughout this history, however, human impacts on the environment were limited in their scope and severity.

Starting with the Industrial Revolution, human impacts on the environment have intensified. Many of them have become particularly extreme since about 1950. Human activities generate impacts through three major mechanisms summarized below.

• Physical disturbance. Humans reshape the physical structure of ecosystems by clearing forests, suppressing or setting fires, building roads and cities, mining, maintaining croplands, and building water control structures such as dams. This leads to biodiversity loss. It may also increase our exposure to forest fires, floods, droughts, soil erosion, landslides, and other physical hazards.
• Resource depletion. Currently, the average citizen of a developed nation consumes an average of 16 tons of minerals, ores, fossil fuels, and biomass per year. Shortages may result if humans use resources at an unsustainable rate. Wild plants and animals may be harvested to the point of extinction. Degradation of soil can lead to crop failures. Minerals and fossil fuels may be depleted to the point where their extraction becomes increasingly expensive and disruptive.
• Pollution. Humans release materials that harm biodiversity or human health. Pollution may occur whenhumans greatly increase the levels of naturally occurring materials in the air, water, or soil. Other pollutants are novel synthetic chemical compounds, usually derived from petrochemicals, that are toxic and persist in the environment.

The scope of human actions and impacts is truly mind-boggling. The map below illustrates our global impact using a “human footprint index” that summarizes several different indicators.

Humanity’s global environmental footprint. Areas least impacted by human activities are shown in green and more heavily impacted regions are red, purple, and black. This index is based on several different indicators of human presence and activity: human population density, physical habitat disruption (built-up areas, nighttime lights, land use/land cover), and accessibility (coastlines, roads, railroads, navigable rivers). By Center for International Earth Science Information Network (CIESIN), Columbia University and Wildlife Conservation Society, the Bronx Zoo, New York. By SEDAC (Human Footprint) Public Domain

We humans are incredibly ingenious as individuals. But as part of an organized culture that has accumulated knowledge since the Stone Age, our power is far greater. Consider a gadget like a laptop computer. No one human really knows how to make a laptop, and certainly no individual could manufacture one from scratch working alone. Instead, thousands of individuals must contribute specialized knowledge to make the parts and assemble them in a working unit. Making a laptop also depends on extraction of metals and oil from deposits around the world, and requires heavy inputs of fossil energy. Similar feats of cooperation and innovation allow us to make airplanes, smart phones, heart monitors, reliable automobiles, and thousands of other useful objects. Unfortunately, we also have the power to do great damage to the environment and its ability to sustain life. We simplify and reshape ecosystems. We overuse resources so that they become scarce and costly. We make atomic weapons and synthesize chemicals that are both persistent and toxic. We overload natural geochemical cycles, leading to the accumulation of wastes. These and other impacts will be described further in this module.

Next we will focus on one particular aspect of human impact that is very relevant to the field of biology: how humans have changed biodiversity on a global scale.

From earliest childhood, humans are fascinated by the diversity of life. Tourists flock to African savannas, coral reefs, and tropical rain forests, cameras at the ready. Kids’ picture books are populated with bright, beautiful, and bizarre animal drawings. Television nature programs, zoos, botanical gardens, and natural history museums provide an up-close look at the real thing. At some level each of us feels interested in, inspired by, or connected to nature in some form. And we are saddened to learn that much of this diversity is threatened by human activity. What is at stake? What has been lost? What can we do to protect what’s left?

What is biodiversity and Why Does it Matter?

Biodiversity is simply the diversity of life in an area. As seen in the photo below, it can be measured at a number of different levels.

• Genetic diversity is the inherited variation among individuals within a single species or population. It provides the raw material for evolution.
• Species richness is the number of different species within a community.
• Ecosystem diversity is the variety of distinct ecosystem types (habitats) within a region. In some places a wide array of habitats can form a diverse patchwork of life.

This scene in Romania illustrates diversity at several different levels. Within one species of flower there is genetic diversity. Within the meadow community there is a rich blend of species. At the landscape level there is a patchwork of distinct ecosystem types (grassland and forest). Many central European meadows have very high plant species diversityand are maintained by grazing and/or mowing. By Joadl (Botzia) CC-BY-SA-3.0

Earth is home to a diverse and vibrant riot of life. Over the past 400 years, biologists have discovered, described, and named over 1.3 million species of animals, plants, fungi, protists, and prokaryotes. Millions more exist but have not yet been described.

Biodiversity is of great value to humans. Functioning natural ecosystems supply us with countless benefits, many of which we take for granted. When was the last time you paid—or even expressed thanks—for oxygen? Some of the most important benefits provided by ecosystems and by specific wild species within them include:

• Removal of excess nutrients, pathogens, and organic waste from sewage.
• Addition of oxygen and removal of carbon dioxide from the atmosphere.
• Physical protection of soils, unstable slopes, and coastlines by plants.
• Pollination of crops by wild animals including insects.
• Recreational opportunities for wildlife viewing, hunting, angling, and more.
• Products like lumber, fish, shellfish, fruits, mushrooms, latex for rubber, etc.
• Specific biochemicals that can be developed to produce pharmaceuticals and other valuable new products.

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Threats to Biodiversity

As a whole, biodiversity may seem limitless. But when we look at specific communities and species, we can see evidence to the contrary. Biodiversity is reduced when populations are eliminated from local communities (local extinction). Local extinctions can severely disrupt ecological communities and may even lead to additional extinctions. This is particularly likely if keystone species are lost, as you learned in the community ecology module. Over time, local extinctions can lead to the loss of an entire species when the last reproducing group dies out (global extinction). Global extinction is irreversible: When a species goes extinct, we lose all future opportunities to learn from it, use it, and appreciate it.

Human activities have affected biodiversity for thousands of years. In fact, human hunting is one probable cause for the extinction of many large animal species that ended about 10,000 years ago. We may never know for sure if humans caused the demise of the woolly mammoth or the saber-toothed tiger, but we can be quite sure that our activities severely threaten many species today. Tracking and clarifying this problem is a major challenge for ecologists. Below is a diagram showing how many species are threatened (or already extinct) among some well-studied groups of plants and animals.

Numbers of species in various status categories in 2010. Of the groups assessed, amphibians had the highest number of species that are threatened to some degree. High fractions of threatened species were found among tropical reef-building corals and among cycads, a group of tropical trees. Source: Global Biodiversity Outlook 3.0, Convention on Biological Diversity. Data from assessments by the International Union for the Conservation of Nature, a global coalition of scientists and nonprofit organizations. By Convention on Biological Diversity (CBD). (Figure 4) Public Domain

Extinction is a naturally occurring process; thousands of species known only from fossils attest to that fact. However, current rates of endangerment and extinction are much faster than those estimated from a study of the fossil record. Today, the vast majority of extinctions can be clearly attributed to the environmental impacts generated by human activities. The major causes of extinction can be categorized as follows:

• Habitat loss. Human activities destroy or change habitat so that it no longer supports the growth and reproduction of a species. This is widely acknowledged as the most important direct threat to biodiversity worldwide. Habitats that have been profoundly changed by human activities include forests (clearing), grasslands (plowing and overgrazing), rivers (damming), and wetlands (draining).
• Introduced species. Humans move species out of their natural range and into a new area. The new species prey upon, compete with, change habitat for, or otherwise harm native species, resulting in their extinction. This is a particularly important threat on islands and other isolated habitats, where introduced predators may decimate native prey species that are not adapted to their presence.
• Overharvesting. Human harvesting—hunting, fishing, logging, gathering, and so on—removes individuals more quickly than they can be replaced by natural reproduction. This was historically a major threat in North America and Europe, but today most fish and wildlife resources are fairly well-protected. Open ocean fisheries and tropical mammals, by contrast, are heavily impacted by human harvesting today. For example, an estimated 80% of the world’s major ocean fisheries were fully exploited, overexploited, depleted, or recovering from depletion in 2005.
• Pollution. Wastes generated by human activities change habitat conditions or threaten the health of organisms directly. Nutrient pollution, for example, is a global problem that harms the diversity of aquatic and some terrestrial communities. Pollution of the atmosphere by greenhouse gases generates climate change, a problem so complex and severe that it is often counted as a separate threat category.

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In summary, species and communities worldwide face many threats. Very often, a single species will be affected by multiple factors. In most cases, humans do not set out to deliberately eradicate species. Instead, we cause extinction inadvertently when our actions generate unexpected consequences.

In the past, humans were often unaware of the effects of their actions or did not try to change course until it was too late. Today, with advances in technology and ecological science, we can do much better. We have begun to effectively regulate or prohibit harvesting, reduce some forms of pollution, protect remaining habitats, and control introduced species. As a result, the status of many populations in high-income nations or in priority areas is improving. In the United States, several species, including the American beaver, the American bison, and the gray wolf, have been protected from overharvesting and have recovered and returned to much of their former range. The bald eagle and peregrine falcon were nearly driven extinct by the pesticide DDT and related compounds that entered food chains, concentrated in the birds, and impaired their introduction. Both species have recovered strongly since DDT was banned for use in the U.S. in 1972. As seen in the graph below, these and similar cases have led to an overall increase in many vertebrate animal populations within high-income nations in North America, Europe, Australia, and Japan since 1970.

The Living Planet Index is based on population sizes of vertebrate species that are monitored over time. Values represent the change in average population sizes over time. Positive values indicate that populations have increased; negative values indicate population declines relative to the 1970 baseline. Since 1970, the Living Planet Index shows slight progress in high-income nations and biodiversity declines elsewhere. By Living Planet Report 2012. By WWF (Living reports) Public Domain

Much of the world’s remaining biodiversity is in the tropics within low- and moderate-income nations. Here, the biodiversity situation remains much more troubling. Resources for conservation efforts are limited and high rates of human population growth continue to drive habitat destruction and overharvesting in many of these nations. Poaching (illegal hunting), forest destruction, poorly regulated mining, overfishing, and destructive farming and livestock grazing practices are all contributing to biodiversity decline that threatens thousands of unique and irreplaceable species. On the positive side, conservationists are working very hard to protect wild habitats within “biodiversity hotspots” that harbor a large diversity of species. Nongovernmental organizations from high-income nations are spearheading these efforts. Through investments and education, they are working with communities to develop sustainable businesses that provide income while protecting the integrity of local ecosystems.

To Learn More / References:

Global Biodiversity Outlook 3.0

Living Planet Report 2012

In this page we will focus on human effects on the atmosphere and climate as a chief example of our ecosystem-level impacts. You have probably heard and learned about global warming and global climate change. Through this course we aim to help you improve your knowledge about the science behind this issue and clear up any misconceptions you may have about it.

A continuing increase in Earth’s ocean and land surface temperatures since the early 1900s is known as global warming. The phrase “global warming” may leave the false impression that the Earth simply gets a bit cozier over time as this process continues. Earth’s climate is a complex system. As the climate warms, temperatures are not evenly adjusted upward by a fixed number of degrees across seasons and locations. Instead, we are also seeing many dramatic weather anomalies in recent decades, including strong hurricanes and tornadoes, protracted droughts, unusually severe heat waves, and even record snowfalls. Instead of global warming, some like to say we are experiencing “global weirding.” Anthropogenic global climate change is a more appropriate description of how climate is responding to human activities on a global scale. It is the full range of climatic disruptions that have occurred as a probable result of human alteration of the atmosphere. In other words, it is recent climate warming—and weirdness—that is probably caused by humans. The case for global climate change can be summarized as follows:

1. Greenhouse gases are known to slow the escape of heat from Earth, and in this way they warm the climate through a mechanism called the greenhouse effect.
2. Humans have dramatically increased levels of greenhouse gases in the atmosphere.
3. The climate has warmed in parallel with and as a result of these changes in the atmosphere.

Let’s look at some of this theory and evidence, beginning by thinking about how the Earth’s overall temperature is determined.

Earth’s Energy Budget and the Greenhouse Effect

Energy enters the Earth system—its land, water, and air—as sunlight. Some of the light is reflected back into space, but much of it is absorbed by land and water. When materials absorb light, they warm up. Over time, they release energy as heat, also known as infrared radiation. Eventually, all of the energy that entered as sunlight escapes back into space as infrared radiation. Energy that enters the Earth system as light is balanced by energy that exits as heat.

If the Earth had no atmosphere, heat would escape very rapidly. The Earth’s night-time surface temperatures would be like those on the moon: −153° Celsius, −243° Fahrenheit. Below is a diagram showing what Earth’s energy balance might look like if there were no clouds to reflect light and no gases that could interfere with heat’s escape.

Hypothetical energy budget for Earth with no clouds (which reflect 20% of incoming solar radiation) and with no greenhouse gases in the atmosphere. Heat radiation would not be delayed on its trip to space, and Earth’s surface would have low and very quickly changing temperatures. By NASA. Public Domain

Lucky for us, Earth has an atmosphere comprising gases that make our atmosphere act something like an insulating blanket. The atmosphere is a mixture of many different gases that are held close to Earth’s surface by gravity. The two most abundant gases in the atmosphere are N₂,or nitrogen gas (78% of air by volume), and O₂, or oxygen gas (21%). These gases are transparent to light and to heat radiation; that is, they do not interfere with sunlight energy coming into Earth or with the heat radiating back into space. Several much less abundant gases, however, do have a major effect on Earth’s energy budget. These greenhouse gases absorb and reemit heat waves (infrared radiation). Three important greenhouse gases are water vapor (H₂O), carbon dioxide (CO₂), and methane (CH₄). Much of the heat (infrared) radiation that leaves Earth’s surface is absorbed by greenhouse gases and reemitted back toward Earth. As a result, these gases retain heat in the atmosphere. Instead of escaping immediately to space, heat is delayed near the Earth’s surface and continues to warm our atmosphere.

Energy budget for Earth with its current atmosphere. Much of the incoming sunlight is reflected by Earth’s surface (about 10%) and clouds (about 20%). The rest of the energy (70%) is absorbed by materials in the air, land, and water and is then reemitted as heat. Only a small fraction of the emitted heat (about 12% of the total incoming sunlight energy) escapes directly. The rest is absorbed by greenhouse gases in the atmosphere and reemitted. This energy remains close to the Earth’s surface for a longer period of time, thereby maintaining a warmer and more stable climate. Data derived from two publications in 2009 summarizing 10 years’ worth of data and presented by NASA. Public Domain

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As you just learned, greenhouse gases in the Earth’s atmosphere retain heat and keep surface temperatures warm and relatively steady over time. This phenomenon is called the greenhouse effect. It is a natural part of the Earth’s climate system and helps make our planet livable. Currently, however, the greenhouse effect is strengthened by a high and increasing level of greenhouse gases in the atmosphere. Evidence indicates that human activity is responsible for this increase.

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Human activities have increased levels of greenhouse gases in the atmosphere.

In terms of its total effect on climate, the most significant greenhouse gas is carbon dioxide. As of May 2012, the concentration of carbon dioxide in the atmosphere is about 397 ppm (parts per million). How does this compare to past levels?

• Today’s level is 26% higher than the level in 1958; levels have been increasing steadily since that time based on monthly measurements that have been taken at Mauna Loa observatory in Hawaii and at many other locations worldwide.

Increase in carbon dioxide at Mauna Loa Observatory in Hawaii since from 1958 to June 2012. By Dr. Pieter Tans, NOAA/ESRL Full Mauna Loa CO2 record Public Domain.

• The current level is almost twice as high as the long term average over the past several hundred thousand years. These data come from analysis of bubbles of air trapped in ice. Glacial ice has annual layers and can be dated, allowing researchers to look back in time as they drill deeper into the ice. The longest records now come from ice cores extending over 3 km deep into an Antarctic glacier. Throughout the 800,000-year period of record, CO₂ levels never exceeded 300 ppm and were typically around 220 ppm.

The graph above shows carbon dioxide data from an ice core extending 400,000 years into the past; more recent data double that time span but show a similar pattern. Carbon dioxide has fluctuated between about 170 ppm and 300 ppm; at no point did it approach the current level of nearly 400 ppm. By NOAA evidence CO2 Public Domain

The situation is similar for other greenhouse gases including methane and nitrous oxide, each of which has increased dramatically since about 1900.

Levels of three important greenhouse gases have all increased greatly starting at around 1900. Values are in parts per million (ppm) or parts per billion (ppb) which indicates the number of molecules of each gas in a million or billion molecules of mixed air. By U.S. Global Change Research Program. (Greenhouse Gases) Public Domain

Clearly, greenhouse gases are increasing. And you already know that human population and impact have increased greatly through the Industrial Age, so it is natural to suspect that human activities are the cause of recent changes in atmospheric gases. Many lines of evidence confirm this. Specific human activities and practices are known to emit greenhouse gases and are also known to have increased in step with rising greenhouse gas concentrations.

• CO₂: burning of fossil fuels, deforestation. Burning of coal, oil, and natural gas transfers carbon from long-term storage in the Earth’s crust and adds CO₂ directly to the air. Deforestation reduces the overall rate of photosynthesis and plant growth. It also returns carbon stored in wood and soil to the atmosphere when wood is burned or when soils are warmed up, encouraging decomposition.
• Methane (CH₄): fossil fuel production and transport, rice paddy agriculture, ruminant livestock, landfilling of garbage, sewage treatment. Methane-releasing decomposers (prokaryotes in the domain Archaea) thrive under wet, low-oxygen conditions. Humans create methane emissions by favoring the activity of these decomposers. Ruminant livestock—cattle, goats, and so on—have this type of prokaryotes in their stomachs and release methane as flatulence. Methane is also emitted when natural gas escapes from wells or pipelines. In the future climate change itself may also lead to big methane releases due to melting of permafrost and other releases from long-term storage.
• Nitrous oxide (N₂O): agriculture, exhaust from internal combustion engines. Humans add extra nitrous oxide (N₂O) to the air through use of artificial fertilizers and other agricultural practices. Nitrous oxide is also produced when fuels or biomass are burned; high temperatures encourage a reaction between N₂ and O₂ gases in the air. Therefore the exhaust from internal combustion engines is a source of nitrous oxide.

Many ongoing natural processes also influence levels of greenhouse gases, but these processes have not changed in a way that can account for the extra CO₂ in the air. Typically natural processes cancel each other out; they are part of cycle that is more or less in balance. Human activities, by contrast, have a history of rapid increase that tracks very closely with the observed increase in the air’s greenhouse gas levels over the past century.

Global human carbon dioxide emissions from burning fossil fuels and from cement production. Direct emissions have increased rapidly since 1950 in step with increases in atmospheric carbon dioxide. Graph by Mak Thorpe using data from the Carbon Dioxide Information Analysis Center. By Mak Thorpe. (Global Carbon Emissions) CC-BY-SA

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The Climate has warmed in association with increased greenhouse gas levels.

As previously discussed, greenhouse gases absorb and reemit heat. There is a clear theoretical basis for the idea that increases in greenhouse gas levels should warm the climate. There is also an abundance of direct evidence that climate has warmed in association with higher concentrations of greenhouse gases over time. Coinciding with the observed increase in greenhouse gases, scientists have documented substantial increases in the average temperatures of Earth’s air and oceans, particularly since about 1950.

Carbon dioxide and temperature in the Industrial Age. As greenhouse gas concentrations have increased (shown here: carbon dioxide, the most important greenhouse gas), average global temperature levels have also risen. By U.S. Global Change Research Program Global Climate Change 4 Public Domain

Many other ongoing natural processes have an influence on the climate. Why do scientists think greenhouse gas increases are the factor driving the recent warming? Again, natural processes have not changed in a way that can explain the observed warming of the climate. For example, the sun’s energy output changes over time, and this can influence our climate. But these changes cannot account for recent global warming. In fact, the sun’s energy output was considerably lower than normal from 2005 to 2010, but the climate continued to warm over that period.

Taken together, thousands of observations and trends provide evidence for global climate change and indicate some of its consequences for life on planet Earth. The following are a few of the many strong indicators of change:

Warm weather and ocean temperatures. In a record of weather and ocean temperature data stretching back to 1900, the top five warmest years were 2005, 2010, 1998, 2003, and 2002. Studies based on weather stations and ocean temperature measurements around the world have repeatedly found a trend of increasing temperatures since about 1900 with steep increases since around 1970. The data for land weather stations are summarized in the graph below. As average temperatures have increased, so has the frequency of extreme heat waves. These are particularly dangerous in low-income nations like India, where people lack air conditioning.

Average temperatures from long term weather records since 1800 show an increasing trend, particularly since the 1970s. In this graph, data from a number of different studies are compared. The black line (labeled “Berkeley”) is based on 1.6 billion records from 39,000 different weather stations and 16 different data archives. The study was led by a “climate skeptic” who processed the data to correct for biases and errors he had thought were leading to false conclusions in other analyses. Yet the results paralleled those of other studies by NASA, NOAA, HadCRU, indicating an increase of about 0.9° Celsius since the 1950s. By Berkeley Earth Surface Temperature project. Temperature graph Public Domain

Sea level rise. The average sea level has increased by an estimated 0.2 m since 1900, both because the ocean water is expanding as it warms and because glaciers on land are melting. Sea level rise is expected to continue and accelerate with continued warming of the climate. Particularly when coupled with more intense storms, increasing sea levels threaten human settlements and natural ecosystems in low-lying coastal areas worldwide.

Ice and permafrost melting. The extent and thickness of floating sea ice in the Arctic has declined in recent decades. Based on satellite data, the area covered by thick multiyear ice decreased by about half between 1980 and 2012. A majority of mountain glaciers are also shrinking in thickness and area over time. Perpetually frozen soils (permafrost) have been melting to increasing depths each summer in the Arctic. Such changes have many implications. Sea ice is important to the ecology of polar bears and other arctic animals; it acts as a platform for travel and foraging. Mountain glaciers supply summer melt water to major river systems in Asia and elsewhere; glacier retreat may reduce the reliability of water supplies for irrigation and other uses. And melting of permafrost leads to landslides and releases additional greenhouse gases to the atmosphere.

A comparison showing how Pederson Glacier in Alaska has retreated since 1920; land and vegetation have also filled in what was previously a lagoon habitat. By NOAA Pederson Glacier Public domain

Increased intensity or duration of drought. Climate change is likely to reduce rainfall in some regions. Even if rainfall does not decline, warmer temperatures lead directly to drier soils and lower water levels by speeding up evaporation and boosting the rate at which plants use water. Record-breaking droughts and wildfire seasons are some indicators that this effect is already under way in some regions. Droughts threaten human well-being by limiting crop production and by reducing the availability of water for municipal use, navigation, power generation, and recreation.

Changes in species distributions. Many species’ geographic ranges are shifting, following climate conditions toward historically cooler areas as their existing habitats get warmer. Species are shifting toward the poles: further north in the Northern Hemisphere and further south in the Southern Hemisphere. In mountainous regions, species’ distributions are shifting upward to higher elevations. Range shifts may lead to endangerment of species, loss of species that provide economic resources, and northward spread of tropical pathogens and their vectors (particularly mosquitoes).

Changes in seasonal patterns of life. As the climate warms, springtime events—leaf emergence and flowering, nesting and migration of birds, etc.—are occurring at earlier dates than in the past. A 2003 study reviewed data from studies on 172 different species of plants, birds, butterflies, and amphibians and found that springtime events had shifted toward earlier dates by an average of 2.3 days per ten years; most of the studies extended over a period of about 50 years. Such shifts can disrupt community interactions, particularly since some species respond more quickly than others to changes in climate. Studies have found that some birds arrive at summer breeding grounds only to find that their prey (insects) have already completed their life cycles. Similarly, some butterfly species are in trouble because their food plants are developing tough leaves and beginning to wither earlier in the season, before the caterpillars have hatched. To learn more about how butterflies are responding to climate changes view the video in the “Changing Planet” series by NBC Learn on “ The Adaption of Butterflies .”

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We began this module by considering how three factors have changed over time: human population size, affluence or material consumption, and human use of high-impact technologies. Next we examined how these factors have led, through various mechanisms, to effects on biodiversity and climate. But what does all this say about the future? Here we will conclude by looking at how population, affluence, and technology may change, and how these changes are likely to affect humanity’s impact on the global environment.

Use this table as a quick reference for the major elements.

The following is a list of the key terms discussed in this Introduction to Biology course and their meaning.