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What is energy? Where does your energy come from? Can energy be recycled?
This team of ants is breaking down a dead tree. A classic example of teamwork. And all that work takes energy. In fact, each chemical reaction - the chemical reactions that allow the cellsin those ants to do the work - needs energy to get started. And all that energy comes from the food the ants eat. Whatever eats the ants gets their energy from the ants. Energy passes through an ecosystem in one direction only.
Chemical Reactions and Energy
Chemical reactions always involve energy. Energy is a property of matter that is defined as the ability to do work. When methane burns, for example, it releases energy in the form ofheat and light. Other chemical reactions absorb energy rather than release it.
Exothermic Reactions
A chemical reaction that releases energy (as heat) is called an exothermic reaction. This type of reaction can be represented by a general chemical equation:
Reactants → Products + Heat
In addition to methane burning, another example of an exothermic reaction is chlorine combining with sodium to form table salt. This reaction also releases energy.
Endothermic Reaction
A chemical reaction that absorbs energy is called an endothermic reaction. This type of reaction can also be represented by a general chemical equation:
Reactants + Heat → Products
Did you ever use a chemical cold pack? The pack cools down because of an endothermic reaction. When a tube inside the pack is broken, it releases a chemical that reacts with waterinside the pack. This reaction absorbs heat energy and quickly cools down the pack.
Activation Energy
All chemical reactions need energy to get started. Even reactions that release energy need a boost of energy in order to begin. The energy needed to start a chemical reaction is calledactivation energy. Activation energy is like the push a child needs to start going down a playground slide. The push gives the child enough energy to start moving, but once she starts, she keeps moving without being pushed again. Activation energy is illustrated inFigure below.
Activation Energy. Activation energy provides the “push” needed to start a chemical reaction. Is the chemical reaction in this figure an exothermic or endothermic reaction?
Why do all chemical reactions need energy to get started? In order for reactions to begin, reactant molecules must bump into each other, so they must be moving, and movement requires energy. When reactant molecules bump together, they may repel each other because of intermolecular forces pushing them apart. Overcoming these forces so the molecules can come together and react also takes energy.
An overview of activation energy can be viewed at http://www.youtube.com/watch?v=VbIaK6PLrRM (1:16).
As you view Activation energy, focus on these concepts:
1. the role of activation energy,
2. what an energy diagram demonstrates.
Summary
• Chemical reactions always involve energy. A chemical reaction that releases energy is an exothermic reaction, and a chemical reaction that absorbs energy is an endothermic reaction. The energy needed to start a chemical reaction is the activation energy.
Explore More
Use this resource to answer the questions that follow.
1. What is energy?
2. Why do living organisms need energy?
3. What is the main difference between potential and kinetic energy?
4. What is the original source of most energy used by living organisms on Earth?
Review
1. What is an exothermic reaction?
2. What is the general chemical equation for an endothermic reaction?
3. What is the activation energy?
4. Why do all chemical reactions require activation energy? | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/01%3A_Introduction_to_Biology/1.15%3A_Energy_and_Biochemical_Reactions.txt |
What do you get when you cross biology and chemistry?
Hummingbirds, with their tiny bodies and high levels of activity, have the highest metabolic rates of any animals — roughly a dozen times that of a pigeon and a hundred times that of an elephant. The metabolic rate, or rate of metabolism, has to do with the amount of energy the organism uses. And that energy is used to drive the chemical reactions in cells — or thebiochemical reactions. And, of course, it is all the biochemical reactions that allow the cells function properly, and maintain life.
Biochemical Reactions
Biochemical reactions are chemical reactions that take place inside the cells of living things. The field of biochemistry demonstrates that knowledge of chemistry as well as biology is needed to understand fully the life processes of organisms at the level of the cell. The sum of all the biochemical reactions in an organism is called metabolism. It includes both exothermic and endothermic reactions.
Types of Biochemical Reactions
Exothermic reactions in organisms are called catabolic reactions. These reactions break down molecules into smaller units and release energy. An example of a catabolic reaction is the breakdown of glucose, which releases energy that cells need to carry out life processes.Endothermic reactions in organisms are called anabolic reactions. These reactions build up bigger molecules from smaller ones. An example of an anabolic reaction is the joining of amino acids to form a protein. Which type of reactions—catabolic or anabolic—do you think occur when your body digests food?
Summary
• Biochemical reactions are chemical reactions that take place inside the cells of organisms.
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Use this resource to answer the questions that follow.
• How to Contrast Biochemical Reactions Inside the Body and Chemical Reactions in the Chemistry Laboratory at www.wikihow.com/Contrast-Biochemical-Reactions-Inside-the-Body-and-Chemical-Reactions-in--the-Chemistry-Laboratory.
1. Define metabolic reactions.
2. What catalyzes most biochemical reactions inside the body?
3. What yield is typical in most enzyme catalyzed biochemical reactions?
Review
1. What are biochemical reactions?
2. What is metabolism?
3. Describe catabolic reactions?
4. What is an example of a biochemical reaction?
1.17: Enzymes
What is a biological catalyst?
This super fast train can obviously reach great speeds. And there's a lot of technology that helps this train go fast. Speaking of helping things go fast brings us to enzymes. Life could not exist without enzymes. Essentially, enzymes are biological catalysts that speed upbiochemical reactions.
Enzymes
Enzymes and Biochemical Reactions
Most chemical reactions within organisms would be impossible under the conditions in cells. For example, the body temperature of most organisms is too low for reactions to occur quickly enough to carry out life processes. Reactants may also be present in such low concentrations that it is unlikely they will meet and collide. Therefore, the rate of mostbiochemical reactions must be increased by a catalyst. A catalyst is a chemical that speeds up chemical reactions. In organisms, catalysts are called enzymes. Essentially, enzymes are biological catalysts.
Like other catalysts, enzymes are not reactants in the reactions they control. They help the reactants interact but are not used up in the reactions. Instead, they may be used over and over again. Unlike other catalysts, enzymes are usually highly specific for particular chemical reactions. They generally catalyze only one or a few types of reactions.
Enzymes are extremely efficient in speeding up reactions. They can catalyze up to several million reactions per second. As a result, the difference in rates of biochemical reactions with and without enzymes may be enormous. A typical biochemical reaction might take hours or even days to occur under normal cellular conditions without an enzyme, but less than a second with an enzyme.
Enzymes, an overview of these proteins, can be viewed at http://www.youtube.com/watch?v=E90D4BmaVJM (9:43).
As you view Enzymes, focus on these concepts:
1. the role of enzymes in nature,
2. other uses of enzymes.
Importance of Enzymes
Enzymes are involved in most of the biochemical reactions that take place in organisms. About 4,000 such reactions are known to be catalyzed by enzymes, but the number may be even higher. Enzymes allow reactions to occur at the rate necessary for life.
In animals, an important function of enzymes is to help digest food. Digestive enzymes speedup reactions that break down large molecules of carbohydrates, proteins, and fats into smaller molecules the body can use. Without digestive enzymes, animals would not be able to break down food molecules quickly enough to provide the energy and nutrients they need to survive.
Summary
• Enzymes are biological catalysts. They speed up biochemical reactions.
• Enzymes are involved in most of the chemical reactions that take place in organisms.
Explore More
Use this resources to answer the questions that follow.
1. What is the function of enzymes?
2. What type of compound are enzymes?
3. What determines an enzyme's function?
4. How many different enzymes may be in the cytoplasm of a bacterium? How many copies of each enzyme are there?
Review
1. What are enzymes?
2. Are enzymes reactants? Explain your answer.
3. What happens to an enzyme after a biochemical reaction?
4. Explain why organisms need enzymes to survive. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/01%3A_Introduction_to_Biology/1.16%3A_Types_of_Biochemical_Reactions.txt |
Do cells have one enzyme with lots of functions, or many enzymes, each with just one function?
Enzymes. Magical proteins necessary for life. So how do enzymes work? How do they catalyze just one specific biochemical reaction? In a puzzle, only two pieces will fit together properly. Understanding that is one of the main steps in understanding how enzymes work.
Enzyme Function
How do enzymes speed up biochemical reactions so dramatically? Like all catalysts, enzymes work by lowering the activation energy of chemical reactions. Activation energy is the energy needed to start a chemical reaction. This is illustrated in Figure below. The biochemical reaction shown in the figure requires about three times as much activation energy without the enzyme as it does with the enzyme.
An animation of how enzymes work can be seen at http://www.youtube.com/watch?v=CZD5xsOKres (2:02).
As you view Enzyme Animation, focus on this concept:
1. how enzymes function.
The reaction represented by this graph is a combustion reaction involving the reactants glucose (C6H12O6) and oxygen (O2). The products of the reaction are carbon dioxide (CO2) and water (H2O). Energy is also released during the reaction. The enzyme speeds up the reaction by lowering the activation energy needed for the reaction to start. Compare the activation energy with and without the enzyme.
Enzymes generally lower activation energy by reducing the energy needed for reactants to come together and react. For example:
• Enzymes bring reactants together so they don’t have to expend energy moving about until they collide at random. Enzymes bind both reactant molecules (called the substrate), tightly and specifically, at a site on the enzyme molecule called the active site (Figurebelow).
• By binding reactants at the active site, enzymes also position reactants correctly, so they do not have to overcome intermolecular forces that would otherwise push them apart. This allows the molecules to interact with less energy.
• Enzymes may also allow reactions to occur by different pathways that have lower activation energy.
The active site is specific for the reactants of the biochemical reaction the enzyme catalyzes. Similar to puzzle pieces fitting together, the active site can only bind certain substrates.
This enzyme molecule binds reactant molecules—called substrate—at its active site, forming an enzyme-substrate complex. This brings the reactants together and positions them correctly so the reaction can occur. After the reaction, the products are released from the enzyme’s active site. This frees up the enzyme so it can catalyze additional reactions.
The activities of enzymes also depend on the temperature, ionic conditions, and the pH of the surroundings. Some enzymes work best at acidic pHs, while others work best in neutral environments.
• Digestive enzymes secreted in the acidic environment (low pH) of the stomach help break down proteins into smaller molecules. The main digestive enzyme in the stomach is pepsin, which works best at a pH of about 1.5. These enzymes would not work optimally at other pHs. Trypsin is another enzyme in the digestive system, which breaks protein chains in food into smaller parts. Trypsin works in the small intestine, which is not an acidic environment. Trypsin's optimum pH is about 8.
• Biochemical reactions are optimal at physiological temperatures. For example, mostbiochemical reactions work best at the normal body temperature of 98.6˚F. Many enzymes lose function at lower and higher temperatures. At higher temperatures, an enzyme’s shape deteriorates. Only when the temperature comes back to normal does the enzyme regain its shape and normal activity.
Summary
• Enzymes work by lowering the activation energy needed to start biochemical reactions.
• The activities of enzymes depend on the temperature, ionic conditions, and the pH of the surroundings.
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Explore More I
Use this resource to answer the questions that follow.
1. What are enzymes?
2. How many jobs in the cell can one enzyme do?
3. What is the substrate?
4. How does an enzyme interact with a substrate?
5. List four factors that can regulate enzyme activity?
Review
1. How do enzymes speed up biochemical reactions?
2. Where is the active site located? Explain the role of the active site?
3. Complete this sentence: The activities of enzymes depends on the __________, __________ conditions, and the __________ of the surroundings.
4. Distinguish between the conditions needed for the proper functioning of pepsin and trypsin. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/01%3A_Introduction_to_Biology/1.18%3A_Enzyme_Function.txt |
Dihydrogen oxide or dihydrogen monoxide. Does this chemical sound dangerous?
Another name for this compound is…water. Water can create some absolutely beautiful sights. Iguassu Falls is the largest series of waterfalls on the planet, located in Brazil, Argentina, and Paraguay. And water is necessary for life. The importance of water to life cannot be emphasized enough. All life needs water. Life started in water. Essentially, without this simple three atom molecule, life would not exist.
Water
Water, like carbon, has a special role in living things. It is needed by all known forms of life. Water is a simple molecule, containing just three atoms. Nonetheless, water’s structure gives it unique properties that help explain why it is vital to all living organisms.
Water, Water Everywhere
Water is a common chemical substance on planet Earth. In fact, Earth is sometimes called the "water planet" because almost 75% of its surface is covered with water. If you look at Figure below, you will see where Earth’s water is found. The term water generally refers to its liquid state, and water is a liquid over a wide range of temperatures on Earth. However, water also occurs on Earth as a solid (ice) and as a gas (water vapor).
Most of the water on Earth consists of saltwater in the oceans. What percent of Earth’s water is fresh water? Where is most of the fresh water found?
Structure and Properties of Water
No doubt, you are already aware of some of the properties of water. For example, you probably know that water is tasteless and odorless. You also probably know that water is transparent, which means that light can pass through it. This is important for organisms that live in the water, because some of them need sunlight to make food.
Chemical Structure of Water
To understand some of water’s properties, you need to know more about its chemical structure. As you have seen, each molecule of water consists of one atom of oxygen and twoatoms of hydrogen. The oxygen atom in a water molecule attracts negatively-chargedelectrons more strongly than the hydrogen atoms do. As a result, the oxygen atom has a slightly negative charge, and the hydrogen atoms have a slightly positive charge. A difference in electrical charge between different parts of the same molecule is called polarity, making water a polar molecule. The diagram in Figure below shows water’s polarity.
Water Molecule. This diagram shows the positive and negative parts of a water molecule. It also depicts how a charge, such as on an ion (Na or Cl, for example) can interact with a water molecule.
Opposites attract when it comes to charged molecules. In the case of water, the positive (hydrogen) end of one water molecule is attracted to the negative (oxygen) end of a nearby water molecule. Because of this attraction, weak bonds form between adjacent water molecules, as shown in Figure below. The type of bond that forms between molecules is called a hydrogen bond. Bonds between molecules are not as strong as bonds within molecules. There are just many more hydrogen bonds in water (between water molecules) than there are covalent bonds within a molecule. The hydrogen bonds may not be strong, but in water they are strong enough to hold together nearby molecules.
Hydrogen Bonding in Water Molecules. Hydrogen bonds form between nearby water molecules. How do you think this might affect water’s properties?
Properties of Water
Hydrogen bonds between water molecules explain some of water’s properties. For example, hydrogen bonds explain why water molecules tend to stick together. Have you ever watched water drip from a leaky faucet or from a melting icicle? If you have, then you know that water always falls in drops rather than as separate molecules. The dew drops in Figure below are another example of water molecules sticking together.
Droplets of Dew. Drops of dew cling to a spider web in this picture. Can you think of other examples of water forming drops? (Hint: What happens when rain falls on a newly waxed car?)
Hydrogen bonds cause water to have a relatively high boiling point of 100°C (212°F). Because of its high boiling point, most water on Earth is in a liquid state rather than in a gaseous state. Water in its liquid state is needed by all living things. Hydrogen bonds also cause water to expand when it freezes. This, in turn, causes ice to have a lower density (mass/volume) than liquid water. The lower density of ice means that it floats on water. For example, in cold climates, ice floats on top of the water in lakes. This allows lake animals such as fish to survive the winter by staying in the water under the ice.
Water and Life
The human body is about 70% water (not counting the water in body fat, which varies from person to person). The body needs all this water to function normally. Just why is so much water required by human beings and other organisms? Water can dissolve many substancesthat organisms need, and it is necessary for many biochemical reactions. The examples below are among the most important biochemical processes that occur in living things, but they are just two of many ways that water is involved in biochemical reactions.
• Photosynthesis—In this process, cells use the energy in sunlight to change carbon dioxide and water to glucose and oxygen. Water is a reactant in this process. The reactions ofphotosynthesis can be represented by the chemical equation
6CO2 + 6H2O + Energy → C6H12O6 + 6O2.
• Cellular respiration—In this process, cells break down glucose in the presence of oxygen and release carbon dioxide, water (a product), and energy. The reactions of cellular respiration can be represented by the chemical equation
C6H12O6 + 6O2 → 6CO2 + 6H2O + Energy.
Water is involved in many other biochemical reactions. As a result, just about all life processes depend on water. Clearly, life as we know it could not exist without water.
Summary
• Water is needed by all known forms of life.
• Due to the difference in the distribution of charge, water is a polar molecule.
• Hydrogen bonds hold adjacent water molecules together.
• Water is involved in many biochemical reactions. As a result, just about all life processes depend on water.
Explore More
Use these resources to answer the questions that follow.
Explore More I
1. How do hydrogen and oxygen bind to form water?
2. Why is water a polar molecule?
3. Describe the bond between water molecules.
Explore More II
1. Describe two properties of water that make it important to life.
2. Why is the specific heat of water important?
3. Why does ice float?
Review
1. Where is most of Earth’s water found?
2. What percent of Earth’s water is fresh water?
3. What is polarity? Describe the polarity of water.
4. How could you demonstrate to a child that solid water is less dense than liquid water?
5. Explain how water’s polarity is related to its boiling point.
6. Explain why metabolism in organisms depends on water. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/01%3A_Introduction_to_Biology/1.19%3A_Water_and_Life.txt |
Acids and bases. Why are these important in biology?
It comes back to a number of biological processes. For example, enzymes work best at specific levels of acids or bases. Take your stomach, a very acidic environment. The enzymes that work in that environment could not work in your mouth. What would your food taste like if your mouth was also a very acidic environment?
Acids and Bases
Water is the main ingredient of many solutions. A solution is a mixture of two or moresubstances that has the same composition throughout. Some solutions are acids and some are bases. To understand acids and bases, you need to know more about pure water. In pure water (such as distilled water), a tiny fraction of water molecules naturally breaks down to form ions. An ion is an electrically charged atom or molecule. The breakdown of water is represented by the chemical equation
2 H2O → H3O+ + OH-
The products of this reaction are a hydronium ion (H3O+) and a hydroxide ion (OH-). The hydroxide ion, which has a negative charge, forms when a water molecule gives up a positively charged hydrogen ion (H+). The hydronium ion, which has positive charge, forms when another water molecule accepts the hydrogen ion.
Acidity and pH
The concentration of hydronium ions in a solution is known as acidity. In pure water, the concentration of hydronium ions is very low; only about 1 in 10 million water molecules naturally breaks down to form a hydronium ion. As a result, pure water is essentially neutral. Acidity is measured on a scale called pH, as shown in Figure below. Pure water has a pH of 7, so the point of neutrality on the pH scale is 7.
Acidity and the pH Scale Water has a pH of 7, so this is the point of neutrality on the pH scale. Acids have a pH less than 7, and bases have a pH greater than 7. Approximate pHs of examples are shown.
Acids
If a solution has a higher concentration of hydronium ions than pure water, it has a pH lower than 7. A solution with a pH lower than 7 is called an acid. As the hydronium ion concentration increases, the pH value decreases. Therefore, the more acidic a solution is, the lower its pH value is. Did you ever taste vinegar? Like other acids, it tastes sour. Stronger acids can be harmful to organisms. For example, stomach acid would eat through the stomach if it were not lined with a layer of mucus. Strong acids can also damage materials, even hard materials such as glass.
Bases
If a solution has a lower concentration of hydronium ions than pure water, it has a pH higher than 7. A solution with a pH higher than 7 is called a base. Bases, such as baking soda, have a bitter taste. Like strong acids, strong bases can harm organisms and damage materials. For example, lye can burn the skin, and bleach can remove the color from clothing.
Acids and Bases in Organisms
Acids and bases are important in living things because most enzymes can do their job only at a certain level of acidity. Cells secrete acids and bases to maintain the proper pH for enzymes to work. For example, every time you digest food, acids and bases are at work in your digestive system. Consider the acidic environment of the stomach. The acidic environment helps with the digestion of food. The enzyme pepsin, which helps break down proteins in the stomach can only function optimally in the low pH environment. The stomach secretes a strong acid that allows pepsin to work, and the stomach to do its job. However, when stomach contents enter the small intestine, the acid must be neutralized. This is because enzymes in the small intestine need a basic environment in order to work. An organ called the pancreas secretes a strong base into the small intestine, and this base neutralizes the acid.
Summary
• A solution is a mixture of two or more substances that has the same composition throughout. Some solutions are acids, some are bases.
• Pure water has a pH of 7, so the point of neutrality on the pH scale is 7.
• Acids have a higher concentration of hydronium ions than pure water, and a pH lower than 7.
• Bases have a lower concentration of hydronium ions than pure water, and a pH higher than 7.
• Acids and bases are important in living organisms because most enzymes function best at a specific pH.
Explore More
Use these resources to answer the questions that follow.
Explore More I
1. What is the definition of pH?
2. What is a strong acid?
3. What is the pH scale?
4. What is the pH range of most cellular processes?
5. Use the pH slider to find the pH of
1. digestive juices.
2. Windex.
3. soapy water.
4. sea water.
5. beer.
6. vinegar.
Review
1. What is the pH of a neutral solution?
2. Distinguish between an acid and a base.
3. Describe an example of an acid or a base that is involved in human digestion.
4. Assume that you test an unknown solution and find that it has a pH of 7.2. What type of solution is it? How do you know?
5. Are the following acids or bases?
1. milk
2. coffee
3. soap | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/01%3A_Introduction_to_Biology/1.20%3A_Acids_and_Bases_in_Biology.txt |
Covers the cell, cell transport, metabolism, division, and reproduction.
Thumbnail: A diagram of a typical prokaryotic cell. (Public Domain; LadyofHats).
02: Cell Biology
Saltwater Fish vs. Freshwater Fish?
Fish cells, like all cells, have semi-permeable membranes. Eventually, the concentration of "stuff" on either side of them will even out. A fish that lives in salt water will have somewhat salty water inside itself. Put it in the freshwater, and the freshwater will, through osmosis, enter the fish, causing its cells to swell, and the fish will die. What will happen to a freshwater fish in the ocean?
Osmosis
Imagine you have a cup that has 100ml water, and you add 15g of table sugar to the water. The sugar dissolves and the mixture that is now in the cup is made up of a solute (the sugar) that is dissolved in the solvent (the water). The mixture of a solute in a solvent is called asolution.
Imagine now that you have a second cup with 100ml of water, and you add 45 grams of table sugar to the water. Just like the first cup, the sugar is the solute, and the water is the solvent. But now you have two mixtures of different solute concentrations. In comparing two solutions of unequal solute concentration, the solution with the higher solute concentration is hypertonic, and the solution with the lower solute concentration is hypotonic. Solutions of equal solute concentration are isotonic. The first sugar solution is hypotonic to the second solution. The second sugar solution is hypertonic to the first.
You now add the two solutions to a beaker that has been divided by a selectively permeable membrane, with pores that are too small for the sugar molecules to pass through, but are big enough for the water molecules to pass through. The hypertonic solution is on one side of the membrane and the hypotonic solution on the other. The hypertonic solution has a lower water concentration than the hypotonic solution, so a concentration gradient of water now exists across the membrane. Water molecules will move from the side of higher water concentration to the side of lower concentration until both solutions are isotonic. At this point, equilibrium is reached.
Osmosis is the diffusion of water molecules across a selectively permeable membrane from an area of higher concentration to an area of lower concentration. Water moves into and out of cells by osmosis. If a cell is in a hypertonic solution, the solution has a lower water concentration than the cell cytosol, and water moves out of the cell until both solutions are isotonic. Cells placed in a hypotonic solution will take in water across their membrane until both the external solution and the cytosol are isotonic.
A cell that does not have a rigid cell wall, such as a red blood cell, will swell and lyse (burst) when placed in a hypotonic solution. Cells with a cell wall will swell when placed in a hypotonic solution, but once the cell is turgid (firm), the tough cell wall prevents any more water from entering the cell. When placed in a hypertonic solution, a cell without a cell wall will lose water to the environment, shrivel, and probably die. In a hypertonic solution, a cell with a cell wall will lose water too. The plasma membrane pulls away from the cell wall as it shrivels, a process called plasmolysis. Animal cells tend to do best in an isotonic environment, plant cells tend to do best in a hypotonic environment. This is demonstrated inFigure below.
Unless an animal cell (such as the red blood cell in the top panel) has an adaptation that allows it to alter the osmotic uptake of water, it will lose too much water and shrivel up in a hypertonic environment. If placed in a hypotonic solution, water molecules will enter the cell, causing it to swell and burst. Plant cells (bottom panel) become plasmolyzed in a hypertonic solution, but tend to do best in a hypotonic environment. Water is stored in the central vacuole of the plant cell.
Osmotic Pressure
When water moves into a cell by osmosis, osmotic pressure may build up inside the cell. If a cell has a cell wall, the wall helps maintain the cell’s water balance. Osmotic pressure is the main cause of support in many plants. When a plant cell is in a hypotonic environment, the osmotic entry of water raises the turgor pressure exerted against the cell wall until the pressure prevents more water from coming into the cell. At this point the plant cell is turgid (Figure below). The effects of osmotic pressures on plant cells are shown in Figure below.
The central vacuoles of the plant cells in this image are full of water, so the cells are turgid.
In contrast, the vacuoles take up much less space when the tissue is placed in hypertonic solution, see below.
The action of osmosis can be very harmful to organisms, especially ones without cell walls. For example, if a saltwater fish (whose cells are isotonic with seawater), is placed in fresh water, its cells will take on excess water, lyse, and the fish will die. Another example of a harmful osmotic effect is the use of table salt to kill slugs and snails.
Diffusion and osmosis are discussed at http://www.youtube.com/watch?v=aubZU0iWtgI(18:59).
Controlling Osmosis
Organisms that live in a hypotonic environment such as freshwater, need a way to prevent their cells from taking in too much water by osmosis. A contractile vacuole is a type of vacuole that removes excess water from a cell. Freshwater protists, such as the paramecium shown in Figure below, have a contractile vacuole. The vacuole is surrounded by several canals, which absorb water by osmosis from the cytoplasm. After the canals fill with water, the water is pumped into the vacuole. When the vacuole is full, it pushes the water out of the cell through a pore.
The contractile vacuole is the star-like structure within the paramecia.
Summary
• Osmosis is the diffusion of water.
• In comparing two solutions of unequal solute concentration, the solution with the higher solute concentration is hypertonic, and the solution with the lower concentration is hypotonic. Solutions of equal solute concentration are isotonic.
• A contractile vacuole is a type of vacuole that removes excess water from a cell.
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Explore More I
Use this resource to answer the questions that follow.
1. What is osmosis?
2. What does salt do to water?
3. What is a hypotonic solution? What happens to water in a hypotonic solution?
4. What is a hypertonic solution? What happens to water in a hypertonic solution?
5. What happens to water in an isotonic solution?
• Osmosis
Review
1. What is osmosis? What type of transport is it?
2. How does osmosis differ from diffusion?
3. What happens to red blood cells when placed in a hypotonic solution?
4. What will happen to a salt water fish if placed in fresh water? | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/02%3A_Cell_Biology/2.01%3A_Osmosis.txt |
What's the same between a bacterial cell and one of your cells?
There are many different types of cells, but they all have certain parts in common. As this image of human blood shows, cells come in different shapes and sizes. The shapes and sizes directly influence the function of the cell. Yet, all cells - cells from the smallest bacteria to those in the largest whale - do some similar functions, so they do have parts in common.
Common Parts of Cells
Discovery of Cells
The first time the word cell was used to refer to these tiny units of life was in 1665 by a British scientist named Robert Hooke. Hooke was one of the earliest scientists to study living things under a microscope. The microscopes of his day were not very strong, but Hooke was still able to make an important discovery. When he looked at a thin slice of cork under his microscope, he was surprised to see what looked like a honeycomb. Hooke made the drawing in Figure below to show what he saw. As you can see, the cork was made up of many tiny units, which Hooke called cells.
Cork Cells. This is what Robert Hooke saw when he looked at a thin slice of cork under his microscope. What type of material is cork? Do you know where cork comes from?
Soon after Robert Hooke discovered cells in cork, Anton van Leeuwenhoek in Holland made other important discoveries using a microscope. Leeuwenhoek made his own microscope lenses, and he was so good at it that his microscope was more powerful than othermicroscopes of his day. In fact, Leeuwenhoek’s microscope was almost as strong as modern light microscopes.
Using his microscope, Leeuwenhoek discovered tiny animals such as rotifers. Leeuwenhoek also discovered human blood cells. He even scraped plaque from his own teeth and observed it under the microscope. What do you think Leeuwenhoek saw in the plaque? He saw tiny living things with a single cell that he named animalcules (“tiny animals”). Today, we call Leeuwenhoek’s animalcules bacteria.
The Cell Theory
The Cell Theory is one of the fundamental theories of biology. For two centuries after the discovery of the microscope by Robert Hooke and Anton van Leeuwenhoek, biologists found cells everywhere. Biologists in the early part of the 19th century suggested that all living things were made of cells, but the role of cells as the primary building block of life was not discovered until 1839 when two German scientists, Theodor Schwann, a zoologist (studies animals), and Matthias Jakob Schleiden, a botanist (studies plants), suggested that cells were the basic unit of structure and function of all life. Later, in 1858, the German doctor Rudolf Virchow observed that cells divide to produce more cells. He proposed that all cells arise only from other cells. The collective observations of all three scientists form the Cell Theory, which states that:
• all organisms are made up of one or more cells,
• all the life functions of an organism occur within cells,
• all cells come from preexisting cells.
Cell Diversity
Cells with different functions often have different shapes. The cells pictured in Figure beloware just a few examples of the many different shapes that cells may have. Each type of cell in the figure has a shape that helps it do its job. For example, the job of the nerve cell is to carry messages to other cells. The nerve cell has many long extensions that reach out in all directions, allowing it to pass messages to many other cells at once. Do you see the tail-like projections on the algae cells? Algae live in water, and their tails help them swim. Pollen grains have spikes that help them stick to insects such as bees. How do you think the spikes help the pollen grains do their job? (Hint: Insects pollinate flowers.)
As these pictures show, cells come in many different shapes. How are the shapes of these cells related to their functions?
Four Common Parts of a Cell
Although cells are diverse, all cells have certain parts in common. The parts include a plasma membrane, cytoplasm, ribosomes, and DNA.
1. The plasma membrane (also called the cell membrane) is a thin coat of lipids that surrounds a cell. It forms the physical boundary between the cell and its environment, so you can think of it as the ‘‘skin’’ of the cell.
2. Cytoplasm refers to all of the cellular material inside the plasma membrane, other than the nucleus. Cytoplasm is made up of a watery substance called cytosol, and contains other cell structures such as ribosomes.
3. Ribosomes are structures in the cytoplasm where proteins are made.
4. DNA is a nucleic acid found in cells. It contains the genetic instructions that cells need to make proteins.
These parts are common to all cells, from organisms as different as bacteria and human beings. How did all known organisms come to have such similar cells? The similarities show that all life on Earth has a common evolutionary history.
A nice introduction to the cell is available at http://www.youtube.com/watch?v=Hmwvj9X4GNY (21:03).
Summary
• Cells come in many different shapes. Cells with different functions often have different shapes.
• Although cells comes in diverse shapes, all cells have certain parts in common. These parts include the plasma membrane, cytoplasm, ribosomes, and DNA.
Explore More
Use this resource to answer the questions that follow.
1. Describe each of the following:
1. plasma membrane
2. cytosol
3. cytoplasm
4. ribosomes
5. DNA
Review
1. Who coined the term cell, in reference to the tiny structures seen in living organisms?
2. Who identified animalcules? What are animalcules?
3. What are the three main parts of the cell theory?
4. List the four parts common to all cells.
5. What are the cell structures where proteins are made?
6. What is the role of DNA? | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/02%3A_Cell_Biology/2.02%3A_Common_Parts_of_the_Cell.txt |
How many different types of cells are there?
There are many different types of cells. For example, in you there are blood cells and skin cells and bone cells and even bacteria. Here we have drawings of bacteria and human cells. Can you tell which depicts various types of bacteria? However, all cells - whether from bacteria, human, or any other organism - will be one of two general types. In fact, all cells other than bacteria will be one type, and bacterial cells will be the other. And it all depends on how the cell stores its DNA.
Two Types of Cells
There is another basic cell structure that is present in many but not all living cells: the nucleus. The nucleus of a cell is a structure in the cytoplasm that is surrounded by a membrane (the nuclear membrane) and contains, and protects, most of the cell's DNA. Based on whether they have a nucleus, there are two basic types of cells: prokaryotic cells and eukaryotic cells. You can watch animations of both types of cells at the link below.www.learnerstv.com/animation/animation.php?ani=162&cat=biology
Prokaryotic Cells
Prokaryotic cells are cells without a nucleus. The DNA in prokaryotic cells is in the cytoplasm rather than enclosed within a nuclear membrane. Prokaryotic cells are found in single-celled organisms, such as bacteria, like the one shown in Figure below. Organisms with prokaryotic cells are called prokaryotes. They were the first type of organisms to evolve and are still the most common organisms today.
Prokaryotic Cell. This diagram shows the structure of a typical prokaryotic cell, a bacterium. Like other prokaryotic cells, this bacterial cell lacks a nucleus but has other cell parts, including a plasma membrane, cytoplasm, ribosomes, and DNA. Identify each of these parts in the diagram.
Bacteria are described in the following video http://www.youtube.com/watch?v=TDoGrbpJJ14(18:26).
Eukaryotic Cells
Eukaryotic cells are cells that contain a nucleus. A typical eukaryotic cell is shown in Figurebelow. Eukaryotic cells are usually larger than prokaryotic cells, and they are found mainly in multicellular organisms. Organisms with eukaryotic cells are called eukaryotes, and they range from fungi to people.
Eukaryotic cells also contain other organelles besides the nucleus. An organelle is a structure within the cytoplasm that performs a specific job in the cell. Organelles called mitochondria, for example, provide energy to the cell, and organelles called vacuoles store substances in the cell. Organelles allow eukaryotic cells to carry out more functions than prokaryotic cells can. This allows eukaryotic cells to have greater cell specificity than prokaryotic cells.Ribosomes, the organelle where proteins are made, are the only organelles in prokaryotic cells.
Eukaryotic Cell. Compare and contrast the eukaryotic cell shown here with the prokaryotic cell. What similarities and differences do you see?
In some ways, a cell resembles a plastic bag full of Jell-O. Its basic structure is a plasmamembrane filled with cytoplasm. Like Jell-O containing mixed fruit, the cytoplasm of the cell also contains various structures, such as a nucleus and other organelles. You can also explore the structures of an interactive animal cell at this link:http://www.cellsalive.com/cells/cell_model.htm.
Summary
• Prokaryotic cells are cells without a nucleus.
• Eukaryotic cells are cells that contain a nucleus.
• Eukaryotic cells have other organelles besides the nucleus. The only organelles in a prokaryotic cell are ribosomes.
Practice
Use these resources to answer the questions that follow.
Explore More I
1. What types of organisms are prokaryotic?
2. What organisms have eukaryotic cells?
3. Compare prokaryotic to eukaryotic cells.
4. Describe where the DNA is located in a prokaryotic cell.
Explore More II
1. Which cells have a nucleus?
2. Which cells usually form unicellular organisms?
3. Which cells have ribosomes?
4. Which cells have mitochondria?
5. Which cells have DNA?
Review
1. What is the cell nucleus?
2. What is the main difference between prokaryotic and eukaryotic cells?
3. Give an example of a prokaryotic cell.
4. Define organelle.
5. What is the advantage of having organelles? | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/02%3A_Cell_Biology/2.03%3A_Prokaryotic_and_Eukaryotic_Cells.txt |
What is a virus? Is it even a living organism?
This alien-looking thing is a virus. But is it prokaryotic or eukaryotic? Or neither? Or both? A virus is essentially genetic material surrounded by protein. That's it. So, is a virus prokaryotic or eukaryotic? Or neither? Or both?
Viruses: Prokaryotes or Eukaryotes?
Viruses, like the one depicted in Figure below, are tiny particles that may cause disease. Human diseases caused by viruses include the common cold and flu. Do you think viruses are prokaryotes or eukaryotes? The answer may surprise you. Viruses are not cells at all, so they are neither prokaryotes nor eukaryotes.
Cartoon of a flu virus. The flu virus is a tiny particle that may cause illness in humans. What is a virus? Is it a cell? Is it even alive?
Viruses contain DNA but not much else. They lack the other parts shared by all cells, including a plasma membrane, cytoplasm, and ribosomes. Therefore, viruses are not cells, but are they alive? All living things not only have cells; they are also capable of reproduction. Viruses cannot reproduce by themselves. Instead, they infect living hosts, and use the hosts’ cells to make copies of their own DNA. Viruses also do not have their own metabolism or maintain homeostasis. For these reasons, most scientists do not consider viruses to be living things.
An overview of viruses can be seen at http://www.youtube.com/watch?v=0h5Jd7sgQWY(23:17).
Summary
• Viruses are neither prokaryotic or eukaryotic.
• Viruses are not made of cells. Viruses cannot replicate on their own.
• Most scientists do not consider viruses to be living.
Explore More
Use this resource to answer the questions that follow.
1. Briefly describe a virus.
2. Why are viruses considered parasites?
3. Describe the outside covering of a virus.
4. What do the lytic and lysogenic cycles describe?
Review
1. What is a virus?
2. Explain why viruses are not considered to be living.
2.05: Phospholipid Bilayers
All cells have a plasma membrane. This membrane surrounds the cell. So what is its role?
Can molecules enter and leave the cell? Yes. Can anything or everything enter or leave? No. So, what determines what can go in or out? Is it the nucleus? The DNA? Or the plasma membrane?
The Plasma Membrane
The plasma membrane (also known as the cell membrane) forms a barrier between the cytoplasm inside the cell and the environment outside the cell. It protects and supports the cell and also controls everything that enters and leaves the cell. It allows only certain substances to pass through, while keeping others in or out. The ability to allow only certain molecules in or out of the cell is referred to as selective permeability or semipermeability. To understand how the plasma membrane controls what crosses into or out of the cell, you need to know its composition.
The plasma membrane is discussed at http://www.youtube.com/watch?v=-aSfoB8Cmic (6:16).
A Phospholipid Bilayer
The plasma membrane is composed mainly of phospholipids, which consist of fatty acids and alcohol. The phospholipids in the plasma membrane are arranged in two layers, called aphospholipid bilayer. As shown in Figure below, each phospholipid molecule has a head and two tails. The head “loves” water (hydrophilic) and the tails “hate” water (hydrophobic). The water-hating tails are on the interior of the membrane, whereas the water-loving heads point outwards, toward either the cytoplasm or the fluid that surrounds the cell.
Molecules that are hydrophobic can easily pass through the plasma membrane, if they are small enough, because they are water-hating like the interior of the membrane. Molecules that are hydrophilic, on the other hand, cannot pass through the plasma membrane—at least not without help—because they are water-loving like the exterior of the membrane, and are therefore excluded from the interior of the membrane.
Phospholipid Bilayer. The phospholipid bilayer consists of two layers of phospholipids, with a hydrophobic, or water-hating, interior and a hydrophilic, or water-loving, exterior. The hydrophilic (polar) head group and hydrophobic tails (fatty acid chains) are depicted in the single phospholipid molecule. The polar head group and fatty acid chains are attached by a 3-carbon glycerol unit.
See Insights into cell membranes via dish detergent at http://ed.ted.com/lessons/insights-into-cell-membranes-via-dish-detergent-ethan-perlstein for additional information on the cell membrane.
Summary
• The plasma membrane forms a barrier between the cytoplasm and the environment outside the cell. The plasma membrane has selective permeability.
• The plasma membrane is primarily composed of phospholipids arranged in a bilayer, with the hydrophobic tails on the interior of the membrane, and the hydrophilic heads pointing outwards.
Explore More
Use these resources to answer the questions that follow.
Explore More I
1. What are the two main components of the cell membrane?
2. Describe the types of proteins that live in the cell membrane.
3. Describe the orientation of the phospholipid molecule in the cell membrane.
Explore More II
1. Are all cells surrounded by a membrane?
2. Why are phospholipids considered an amphipathic molecule?
3. What is a glycolipid?
4. Describe the role of cholesterol in the cell membrane.
Explore More III
1. What are the roles of the plasma membrane?
2. What are the functions of proteins associated with the cell membrane?
3. Why is the structure of the cell membrane described as "fluid mosaic"?
Review
1. Describe the role of the plasma membrane.
2. What is meant by semipermeability?
3. Describe the composition of the plasma membrane.
4. Explain why hydrophobic molecules can easily cross the plasma membrane, while hydrophilic molecules cannot. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/02%3A_Cell_Biology/2.04%3A_Viruses.txt |
Can anything or everything move in or out of the cell?
No. It is the semipermeable plasma membrane that determines what can enter and leave the cell. So, if not everything can cross the membrane, how do certain things get across?
Membrane Proteins
The plasma membrane contains molecules other than phospholipids, primarily other lipids and proteins. The green molecules in Figure below, for example, are the lipid cholesterol. Molecules of cholesterol help the plasma membrane keep its shape. Many of the proteins in the plasma membrane assist other substances in crossing the membrane.
The plasma membranes also contain certain types of proteins. A membrane protein is a protein molecule that is attached to, or associated with, the membrane of a cell or an organelle. Membrane proteins can be put into two groups based on how the protein is associated with the membrane.
Integral membrane proteins are permanently embedded within the plasma membrane. They have a range of important functions. Such functions include channeling or transporting molecules across the membrane. Other integral proteins act as cell receptors. Integral membrane proteins can be classified according to their relationship with the bilayer:
• Transmembrane proteins span the entire plasma membrane. Transmembrane proteins are found in all types of biological membranes.
• Integral monotopic proteins are permanently attached to the membrane from only one side.
Some integral membrane proteins are responsible for cell adhesion (sticking of a cell to another cell or surface). On the outside of cell membranes and attached to some of the proteins are carbohydrate chains that act as labels that identify the cell type. Shown in Figure below are two different types of membrane proteins and associated molecules.
Peripheral membrane proteins are proteins that are only temporarily associated with the membrane. They can be easily removed, which allows them to be involved in cell signaling. Peripheral proteins can also be attached to integral membrane proteins, or they can stick into a small portion of the lipid bilayer by themselves. Peripheral membrane proteins are often associated with ion channels and transmembrane receptors. Most peripheral membrane proteins are hydrophilic.
Some of the membrane proteins make up a major transport system that moves molecules and ions through the polar phospholipid bilayer.
The Fluid Mosaic Model
In 1972 S.J. Singer and G.L. Nicolson proposed the now widely accepted Fluid Mosaic Modelof the structure of cell membranes. The model proposes that integral membrane proteins are embedded in the phospholipid bilayer, as seen in Figure above. Some of these proteins extend all the way through the bilayer, and some only partially across it. These membrane proteins act as transport proteins and receptors proteins.
Their model also proposed that the membrane behaves like a fluid, rather than a solid. The proteins and lipids of the membrane move around the membrane, much like buoys in water. Such movement causes a constant change in the "mosaic pattern" of the plasma membrane.
A further description of the Fluid Mosaic Model can be viewed athttp://www.youtube.com/watch?v=Qqsf_UJcfBc (1:27).
Extensions of the Plasma Membrane
The plasma membrane may have extensions, such as whip-like flagella or brush-like cilia. In single-celled organisms, like those shown in Figure below, the membrane extensions may help the organisms move. In multicellular organisms, the extensions have other functions. For example, the cilia on human lung cells sweep foreign particles and mucus toward the mouth and nose.
Flagella and Cilia. Cilia and flagella are extensions of the plasma membrane of many cells.
Summary
• The plasma membrane has many proteins that assist other substances in crossing the membrane.
• The Fluid Mosaic Model depicts the biological nature of the plasma membrane.
• Cilia and flagella are extensions of the plasma membrane.
Explore More
Use these resources to answer the questions that follow.
Explore More I
1. What is the major role of many membrane proteins?
2. How much of a cell's genetic material may code for membrane proteins?
3. What are transmembrane proteins, and what is their main function?
4. How can a protein "tunnel" form through the membrane?
5. How can a protein "channel" form through the membrane?
Explore More II
1. How may water molecules enter the cell?
2. How may ions enter the cell?
3. What type(s) of protein(s) identify the cell?
4. What molecule is found in the membrane of animal cells but not plant cells?
Review
1. What is the main difference between the two main types of proteins associated with the plasma membrane?
2. What are two functions of integral membrane proteins?
3. Discuss the Fluid Mosaic Model.
4. What are flagella and cilia? | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/02%3A_Cell_Biology/2.06%3A_Membrane_Proteins.txt |
Does a cell have, or even need, a "skeleton"?
What do you get if you take some tubing, and make the tubes smaller and smaller and smaller? You get very small tubes, or microtubes. Very small tubes, or microtubules, together with microfilaments, form the basis of the "skeleton" inside the cell.
The Cytoplasm and Cytoskeleton
The cytoplasm consists of everything inside the plasma membrane of the cell, excluding the nucleus in a eukaryotic cell. It includes the watery, gel-like material called cytosol, as well as various structures. The water in the cytoplasm makes up about two thirds of the cell’s weight and gives the cell many of its properties.
Functions of the Cytoplasm
The cytoplasm has several important functions, including:
1. suspending cell organelles.
2. pushing against the plasma membrane to help the cell keep its shape.
3. providing a site for many of the biochemical reactions of the cell.
The Cytoskeleton
The cytoskeleton is a cellular "scaffolding" or "skeleton" that crisscrosses the cytoplasm. All eukaryotic cells have a cytoskeleton, and recent research has shown that prokaryotic cells also have a cytoskeleton. The eukaryotic cytoskeleton is made up of a network of long, thin protein fibers and has many functions. It helps to maintain cell shape. It holds organelles in place, and for some cells, it enables cell movement. The cytoskeleton also plays important roles in both the intracellular movement of substances and in cell division. Certain proteins act like a path that vesicles and organelles move along within the cell. The threadlike proteins that make up the cytoskeleton continually rebuild to adapt to the cell's constantly changing needs. Three main kinds of cytoskeleton fibers are microtubules, intermediate filaments, and microfilaments.
• Microtubules, shown in Figure below (a), are hollow cylinders and are the thickest of the cytoskeleton structures. They are most commonly made of filaments which are polymers of alpha and beta tubulin, and radiate outwards from an area near the nucleus called the centrosome. Tubulin is the protein that forms microtubules. Two forms of tubulin, alpha and beta, form dimers (pairs) which come together to form the hollow cylinders. The cylinders are twisted around each other to form the microtubules. Microtubules help the cell keep its shape. They hold organelles in place and allow them to move around the cell, and they form the mitotic spindle during cell division. Microtubules also make up parts of cilia and flagella, the organelles that help a cell move.
• Microfilaments, shown in Figure below (b), are made of two thin actin chains that are twisted around one another. Microfilaments are mostly concentrated just beneath the cell membrane, where they support the cell and help the cell keep its shape. Microfilaments form cytoplasmatic extensions, such as pseudopodia and microvilli, which allow certain cells to move. The actin of the microfilaments interacts with the protein myosin to cause contraction in muscle cells. Microfilaments are found in almost every cell, and are numerous in muscle cells and in cells that move by changing shape, such as phagocytes (white blood cells that search the body for bacteria and other invaders).
• Intermediate filaments differ in make-up from one cell type to another. Intermediate filaments organize the inside structure of the cell by holding organelles and providing strength. They are also structural components of the nuclear envelope. Intermediate filaments made of the protein keratin are found in skin, hair, and nails cells.
(a) The eukaryotic cytoskeleton. Microfilaments are shown in red, microtubules in green, and the nuclei are in blue. By linking regions of the cell together, the cytoskeleton helps support the shape of the cell. (b) Microscopy of microfilaments (actin filaments), shown in green, inside cells. The nucleus is shown in blue.
Cytoskeleton Structure
Microtubules Intermediate Filaments Microfilaments
Fiber Diameter About 25 nm 8 to 11 nm Around 7 nm
Protein Composition Tubulin, with two subunits, alpha and beta tubulin One of different types of proteins such as lamin, vimentin, and keratin Actin
Shape Hollow cylinders made of two protein chains twisted around each other Protein fiber coils twisted into each other Two actin chains twisted around one another
Main Functions Organelle and vesicle movement; form mitotic spindles during cell reproduction; cell motility (in cilia and flagella) Organize cell shape; positions organelles in cytoplasm structural support of the nuclear envelope and sarcomeres; involved in cell-to-cell and cell-to-matrix junctions Keep cellular shape; allows movement of certain cells by forming cytoplasmatic extensions or contraction of actin fibers; involved in some cell-to-cell or cell-to-matrix junctions
Representation
The cytoskeleton is discussed in the following video: http://www.youtube.com/watch?v=5rqbmLiSkpk (4:50).
Summary
• The cytoplasm consists of everything inside the plasma membrane of the cell.
• The cytoskeleton is a cellular "skeleton" that crisscrosses the cytoplasm. Three main cytoskeleton fibers are microtubules, intermediate filaments, and microfilaments.
• Microtubules are the thickest of the cytoskeleton structures and are most commonly made of filaments which are polymers of alpha and beta tubulin.
• Microfilament are the thinnest of the cytoskeleton structures and are made of two thin actin chains that are twisted around one another.
Explore More
Use this resource to answer the following questions.
1. What is the role of the cytoskeleton?
2. What is the subunit of microfilaments and microtubules?
3. Describe the main function of microtubules.
4. What is the role of microtubules during mitosis?
5. How are microtubules associated with locomotion?
6. Describe the roles of microfilaments.
Review
1. What is the difference between cytoplasm and cytosol?
2. List two roles of the cytoplasm.
3. Name the three main types of cytoskeleton fibers.
4. List two functions of the eukaryotic cytoskeleton. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/02%3A_Cell_Biology/2.07%3A_Cytoplasm_and_Cytoskeletons.txt |
Where does the DNA live?
The answer depends on if the cell is prokaryotic or eukaryotic. The main difference between the two types of cells is the presence of a nucleus. And in eukaryotic cells, DNA lives in the nucleus.
The Nucleus
The nucleus is a membrane-enclosed organelle found in most eukaryotic cells. The nucleus is the largest organelle in the cell and contains most of the cell's genetic information (mitochondria also contain DNA, called mitochondrial DNA, but it makes up just a small percentage of the cell’s overall DNA content). The genetic information, which contains the information for the structure and function of the organism, is found encoded in DNA in the form of genes. A gene is a short segment of DNA that contains information to encode an RNA molecule or a protein strand. DNA in the nucleus is organized in long linear strands that are attached to different proteins. These proteins help the DNA coil up for better storage in the nucleus. Think how a string gets tightly coiled up if you twist one end while holding the other end. These long strands of coiled-up DNA and proteins are called chromosomes. Each chromosome contains many genes. The function of the nucleus is to maintain the integrity of these genes and to control the activities of the cell by regulating gene expression. Gene expression is the process by which the information in a gene is "decoded" by various cell molecules to produce a functional gene product, such as a protein molecule or an RNA molecule.
The degree of DNA coiling determines whether the chromosome strands are short and thick or long and thin. Between cell divisions, the DNA in chromosomes is more loosely coiled and forms long, thin strands called chromatin. Before the cell divides, the chromatin coil up more tightly and form chromosomes. Only chromosomes stain clearly enough to be seen under a microscope. The word chromosome comes from the Greek word chroma (color), and soma(body), due to its ability to be stained strongly by dyes.
The Nuclear Envelope
The nuclear envelope is a double membrane of the nucleus that encloses the genetic material. It separates the contents of the nucleus from the cytoplasm. The nuclear envelope is made of two lipid bilayers, an inner membrane and an outer membrane. The outer membrane is continuous with the rough endoplasmic reticulum. Many tiny holes called nuclear pores are found in the nuclear envelope. These nuclear pores help to regulate the exchange of materials (such as RNA and proteins) between the nucleus and the cytoplasm.
The Nucleolus
The nucleus of many cells also contains a non-membrane bound organelle called anucleolus, shown in Figure below. The nucleolus is mainly involved in the assembly of ribosomes. Ribosomes are organelles made of protein and ribosomal RNA (rRNA), and they build cellular proteins in the cytoplasm. The function of the rRNA is to provide a way of decoding the genetic messages within another type of RNA (called mRNA), into amino acids. After being made in the nucleolus, ribosomes are exported to the cytoplasm, where they direct protein synthesis.
The eukaryotic cell nucleus. Visible in this diagram are the ribosome-studded double membranes of the nuclear envelope, the DNA (as chromatin), and the nucleolus. Within the cell nucleus is a viscous liquid called nucleoplasm, similar to the cytoplasm found outside the nucleus. The chromatin (which is normally invisible), is visible in this figure only to show that it is spread throughout the nucleus.
Summary
• The nucleus is a membrane-enclosed organelle, found in most eukaryotic cells, which stores the genetic material (DNA).
• The nucleus is surrounded by a double lipid bilayer, the nuclear envelope, which is embedded with nuclear pores.
• The nucleolus is inside the nucleus, and is where ribosomes are made.
Explore More
Use this resource to answer the following questions.
1. What are the roles of the nucleus?
2. What is the nuclear envelope?
3. Describe chromatin.
4. What is the nucleolus?
5. What type of molecules move into the nucleus through the nuclear pores?
Review
1. What is the role of the nucleus of a eukaryotic cell?
2. Describe the nuclear membrane.
3. What are nuclear pores?
4. What is the role of the nucleolus? | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/02%3A_Cell_Biology/2.08%3A_Cell_Nucleus.txt |
Sperm cells and muscle cells need lots of energy. What do they have in common?
They have lots of mitochondria. Mitochondria are called the power plants of the cell, as these organelles are where most of the cell's energy is produced. Cells that need lots of energy have lots of mitochondria.
Other Organelles
In addition to the nucleus, eukaryotic cells have many other organelles, including ribosomes and mitochondria. Ribosomes are present in all cells.
Ribosomes
Ribosomes are small organelles and are the sites of protein synthesis (or assembly). They are made of ribosomal protein and ribosomal RNA, and are found in both eukaryotic and prokaryotic cells. Unlike other organelles, ribosomes are not surrounded by a membrane. Each ribosome has two parts, a large and a small subunit, as shown in Figure below. The subunits are attached to one another. Ribosomes can be found alone or in groups within the cytoplasm. Some ribosomes are attached to the endoplasmic reticulum (ER) (as shown in Figure below), and others are attached to the nuclear envelope.
The two subunits that make up a ribosome, small organelles that are intercellular protein factories.
Ribozymes are RNA molecules that catalyze chemical reactions, such as translation.Translation is the process of ordering the amino acids in the assembly of a protein, and translation will be discussed more in another concept. Briefly, the ribosomes interact with other RNA molecules to make chains of amino acids called polypeptide chains, due to the peptide bond that forms between individual amino acids. Polypeptide chains are built from the genetic instructions held within a messenger RNA (mRNA) molecule. Polypeptide chains that are made on the rough ER (discussed below) are inserted directly into the ER and then are transported to their various cellular destinations. Ribosomes on the rough ER usually produce proteins that are destined for the cell membrane.
Ribosomes are found in both eukaryotic and prokaryotic cells. Ribosomes are not surrounded by a membrane. The other organelles found in eukaryotic cells are surrounded by a membrane.
Mitochondria
A mitochondrion (mitochondria, plural), is a membrane-enclosed organelle that is found in most eukaryotic cells. Mitochondria are called the "power plants" of the cell because they are the sites of cellular respiration, where they use energy from organic compounds to make ATP (adenosine triphosphate). ATP is the cell's energy source that is used for such things such as movement and cell division. Some ATP is made in the cytosol of the cell, but most of it is made inside mitochondria. The number of mitochondria in a cell depends on the cell’s energy needs. For example, active human muscle cells may have thousands of mitochondria, while less active red blood cells do not have any.
(a): Electron micrograph of a single mitochondrion, within which you can see many cristae. Mitochondria range from 1 to 10 μm in size. (b): This model of a mitochondrion shows the organized arrangement of the inner and outer membranes, the protein matrix, and the folded inner mitochondrial membranes.
As Figure above (a) and (b) show, a mitochondrion has two phospholipid membranes. The smooth outer membrane separates the mitochondrion from the cytosol. The inner membrane has many folds, called cristae. The fluid-filled inside of the mitochondrion, called matrix, is where most of the cell’s ATP is made.
Although most of a cell's DNA is contained in the cell nucleus, mitochondria have their own DNA. Mitochondria are able to reproduce asexually, and scientists think that they are descended from prokaryotes. According to the endosymbiotic theory, mitochondria were once free-living prokaryotes that infected or were engulfed by ancient eukaryotic cells. The invading prokaryotes were protected inside the eukaryotic host cell, and in turn the prokaryote supplied extra ATP to its host.
Summary
• Ribosomes are small organelles and are the site of protein synthesis. Ribosomes are found in all cells.
• Mitochondria are where energy from organic compounds is used to make ATP.
Explore More
Use this resource to answer the following questions.
1. List three characteristics of mitochondria.
2. Describe how mitochondria originated?
3. What is the general function of proteins embedded within the mitochondria inner membrane?
4. What occurs in the mitochondrial matrix?
5. How do mitochondria divide?
Review
1. What is the function of a ribosome?
2. What is a significant difference between the structure of a ribosome and other organelles?
3. Identify the reason why mitochondria are called "power plants" of the cell.
4. Describe the structure of a mitochondrion. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/02%3A_Cell_Biology/2.09%3A_Ribosomes_and_Mitochondria.txt |
Does a cell have its own ER?
Yes, but in this case, the ER is not just for emergencies. True, there might be times when the cell responds to emergency conditions and the functions of the ER may be needed, but usually the cell's ER is involved in normal functions. Proteins are also made on the outside of the ER, and this starts a whole process of protein transport, both around the inside of the cell and to the cell membrane and out.
Other Organelles
In addition to the nucleus, eukaryotic cells have many other organelles, including the endoplasmic reticulum, Golgi apparatus, vesicles, vacuoles, and centrioles.
Endoplasmic Reticulum
The endoplasmic reticulum (ER) (plural, reticuli) is a network of phospholipid membranes that form hollow tubes, flattened sheets, and round sacs. These flattened, hollow folds and sacs are called cisternae. The ER has two major functions:
• Transport: Molecules, such as proteins, can move from place to place inside the ER, much like on an intracellular highway.
• Synthesis: Ribosomes that are attached to ER, similar to unattached ribosomes, make proteins. Lipids are also produced in the ER.
There are two types of endoplasmic reticulum, rough endoplasmic reticulum (RER) and smooth endoplasmic reticulum (SER).
• Rough endoplasmic reticulum is studded with ribosomes, which gives it a "rough" appearance. These ribosomes make proteins that are then transported from the ER in small sacs called transport vesicles. The transport vesicles pinch off the ends of the ER. The rough endoplasmic reticulum works with the Golgi apparatus to move new proteins to their proper destinations in the cell. The membrane of the RER is continuous with the outer layer of the nuclear envelope.
• Smooth endoplasmic reticulum does not have any ribosomes attached to it, and so it has a smooth appearance. SER has many different functions, some of which include lipid synthesis, calcium ion storage, and drug detoxification. Smooth endoplasmic reticulum is found in both animal and plant cells and it serves different functions in each. The SER is made up of tubules and vesicles that branch out to form a network. In some cells there are dilated areas like the sacs of RER. Smooth endoplasmic reticulum and RER form an interconnected network.
Image of nucleus, endoplasmic reticulum and Golgi apparatus, and how they work together. The process of secretion from endoplasmic reticuli to Golgi apparatus is shown.
Golgi Apparatus
The Golgi apparatus is a large organelle that is usually made up of five to eight cup-shaped, membrane-covered discs called cisternae, as shown in Figure above. The cisternae look a bit like a stack of deflated balloons. The Golgi apparatus modifies, sorts, and packages different substances for secretion out of the cell, or for use within the cell. The Golgi apparatus is found close to the nucleus of the cell, where it modifies proteins that have been delivered in transport vesicles from the RER. It is also involved in the transport of lipids around the cell. Pieces of the Golgi membrane pinch off to form vesicles that transport molecules around the cell. The Golgi apparatus can be thought of as similar to a post office; it packages and labels "items" and then sends them to different parts of the cell. Both plant and animal cells have a Golgi apparatus. Plant cells can have up to several hundred Golgi stacks scattered throughout the cytoplasm. In plants, the Golgi apparatus contains enzymes that synthesize some of the cell wall polysaccharides.
Vesicles
A vesicle is a small, spherical compartment that is separated from the cytosol by at least one lipid bilayer. Many vesicles are made in the Golgi apparatus and the endoplasmic reticulum, or are made from parts of the cell membrane. Vesicles from the Golgi apparatus can be seen in Figure above. Because it is separated from the cytosol, the space inside the vesicle can be made to be chemically different from the cytosol. Vesicles are basic tools of the cell for organizing metabolism, transport, and storage of molecules. Vesicles are also used as chemical reaction chambers. They can be classified by their contents and function.
• Transport vesicles are able to move molecules between locations inside the cell. For example, transport vesicles move proteins from the rough endoplasmic reticulum to the Golgi apparatus.
• Lysosomes are vesicles that are formed by the Golgi apparatus. They contain powerful enzymes that could break down (digest) the cell. Lysosomes break down harmful cell products, waste materials, and cellular debris and then force them out of the cell. They also digest invading organisms such as bacteria. Lysosomes also break down cells that are ready to die, a process called autolysis.
• Peroxisomes are vesicles that use oxygen to break down toxic substances in the cell. Unlike lysosomes, which are formed by the Golgi apparatus, peroxisomes self-replicate by growing bigger and then dividing. They are common in liver and kidney cells that break down harmful substances. Peroxisomes are named for the hydrogen peroxide (H2O2) that is produced when they break down organic compounds. Hydrogen peroxide is toxic, and in turn is broken down into water (H2O) and oxygen (O2) molecules.
Vacuoles
Vacuoles are membrane-bound organelles that can have secretory, excretory, and storage functions. Many organisms will use vacuoles as storage areas and some plant cells have very large vacuoles. Vesicles are much smaller than vacuoles and function in transporting materials both within and to the outside of the cell.
Centrioles
Centrioles are rod-like structures made of short microtubules. Nine groups of three microtubules make up each centriole. Two perpendicular centrioles make up the centrosome. Centrioles are very important in cellular division, where they arrange the mitotic spindles that pull the chromosome apart during mitosis.
Summary
• The endoplasmic reticulum (ER) is involved in the synthesis of lipids and synthesis and transport of proteins.
• The Golgi apparatus modifies, sorts, and packages different substances for secretion out of the cell, or for use within the cell.
• Vesicles are also used as chemical reaction chambers. Transport vesicles, lysosomes, and peroxisomes are types of vesicles.
• Vacuoles have secretory, excretory, and storage functions.
• Centrioles are made of short microtubules and are very important in cell division.
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Use this resource to answer the questions that follow.
• Organelles and Their Functions at biology.unm.edu/ccouncil/Biol...ries/Cell.html.
1. Describe rough and smooth ER.
2. Why is the ER described as the "highways and road systems?"
3. Why is the Golgi apparatus similar to a post office?
4. Vesicles and vacuoles can be referred to as “warehouses, water towers or garbage dumps.” Explain this.
Review
1. List five organelles eukaryotes have that prokaryotes do not have.
2. Explain how the following organelles ensure that a cell has the proteins it needs: nucleus, rough ER, vesicles, and Golgi apparatus.
3. What is the main difference between rough endoplasmic reticulum and smooth endoplasmic reticulum?
4. Describe the three types of vesicles. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/02%3A_Cell_Biology/2.10%3A_Other_Cell_Organelles.txt |
What do plants have to do that animals don't?
Many plant cells are green. Why? Plant cells also usually have a distinct shape. The rigid exterior around the cells is necessary to allow the plants to grow upright. Animal cells do not have these rigid exteriors. There are other distinct differences between plant and animal cells. These will be the focus of this concept.
Plant Cells
Special Structures in Plant Cells
Most organelles are common to both animal and plant cells. However, plant cells also have features that animal cells do not have: a cell wall, a large central vacuole, and plastids such as chloroplasts.
Plants have very different lifestyles from animals, and these differences are apparent when you examine the structure of the plant cell. Plants make their own food in a process called photosynthesis. They take in carbon dioxide (CO2) and water (H2O) and convert them into sugars. The features unique to plant cells can be seen in Figure below.
In addition to containing most of the organelles found in animal cells, plant cells also have a cell wall, a large central vacuole, and plastids. These three features are not found in animal cells.
The Cell Wall
A cell wall is a rigid layer that is found outside the cell membrane and surrounds the cell. The cell wall contains not only cellulose and protein, but other polysaccharides as well. The cell wall provides structural support and protection. Pores in the cell wall allow water and nutrients to move into and out of the cell. The cell wall also prevents the plant cell from bursting when water enters the cell.
Microtubules guide the formation of the plant cell wall. Cellulose is laid down by enzymes to form the primary cell wall. Some plants also have a secondary cell wall. The secondary wall contains a lignin, a secondary cell component in plant cells that have completed cell growth/expansion.
The Central Vacuole
Most mature plant cells have a central vacuole that occupies more than 30% of the cell's volume. The central vacuole can occupy as much as 90% of the volume of certain cells. The central vacuole is surrounded by a membrane called the tonoplast. The central vacuole has many functions. Aside from storage, the main role of the vacuole is to maintain turgor pressure against the cell wall. Proteins found in the tonoplast control the flow of water into and out of the vacuole. The central vacuole also stores the pigments that color flowers.
The central vacuole contains large amounts of a liquid called cell sap, which differs in composition to the cell cytosol. Cell sap is a mixture of water, enzymes, ions, salts, and othersubstances. Cell sap may also contain toxic byproducts that have been removed from the cytosol. Toxins in the vacuole may help to protect some plants from being eaten.
Plastids
Plant plastids are a group of closely related membrane-bound organelles that carry out many functions. They are responsible for photosynthesis, for storage of products such as starch, and for the synthesis of many types of molecules that are needed as cellular building blocks. Plastids have the ability to change their function between these and other forms. Plastids contain their own DNA and some ribosomes, and scientists think that plastids are descended from photosynthetic bacteria that allowed the first eukaryotes to make oxygen. The main types of plastids and their functions are:
• Chloroplasts are the organelle of photosynthesis. They capture light energy from the sun and use it with water and carbon dioxide to make food (sugar) for the plant. The arrangement of chloroplasts in a plant’s cells can be seen in Figure below.
• Chromoplasts make and store pigments that give petals and fruit their orange and yellow colors.
• Leucoplasts do not contain pigments and are located in roots and non-photosynthetic tissues of plants. They may become specialized for bulk storage of starch, lipid, or protein. However, in many cells, leucoplasts do not have a major storage function. Instead, they make molecules such as fatty acids and many amino acids.
Plant cells with visible chloroplasts.
Chloroplasts
Chloroplasts capture light energy from the sun and use it with water and carbon dioxide to produce sugars for food. Chloroplasts look like flat discs and are usually 2 to 10 micrometers in diameter and 1 micrometer thick. A model of a chloroplast is shown in Figure below. The chloroplast is enclosed by an inner and an outer phospholipid membrane. Between these two layers is the intermembrane space. The fluid within the chloroplast is called the stroma, and it contains one or more molecules of small, circular DNA. The stroma also has ribosomes. Within the stroma are stacks of thylakoids, sub-organelles that are the site of photosynthesis. The thylakoids are arranged in stacks called grana (singular: granum). A thylakoid has a flattened disk shape. Inside it is an empty area called the thylakoid space or lumen. Photosynthesis takes place on the thylakoid membrane.
Within the thylakoid membrane is the complex of proteins and light-absorbing pigments, such as chlorophyll and carotenoids. This complex allows capture of light energy from many wavelengths because chlorophyll and carotenoids both absorb different wavelengths of light. These will be further discussed in the "Photosynthesis" concept.
The internal structure of a chloroplast, with a granal stack of thylakoids circled.
Summary
• Plant cells have a cell wall, a large central vacuole, and plastids such as chloroplasts.
• The cell wall is a rigid layer that is found outside the cell membrane and surrounds the cell, providing structural support and protection.
• The central vacuole maintains turgor pressure against the cell wall.
• Chloroplasts capture light energy from the sun and use it with water and carbon dioxide to produce sugars for food.
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Use this resource to answer the questions that follow.
1. What is the role of the chloroplast?
2. Which evolved first, photosynthesis to the chloroplast?
3. What is the significance of the thylakoid membrane?
4. Why do plant cells need a cell wall?
5. What is turgor pressure? How is turgor pressure maintained by the plant?
Review
1. List three structures that are found in plant cells but not in animal cells.
2. Identify two functions of plastids in plant cells.
3. What are the roles of the cell wall and the central vacuole?
4. Describe the chloroplast structure. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/02%3A_Cell_Biology/2.11%3A_Plant_Cell_Structures.txt |
Why be organized?
It can be said organization leads to efficiency. And in you, cells are organized into tissues, which are organized into organs, which are organized into organ systems, which form you. And it can be said that the human body is a very organized and efficient system.
Organization of Cells
Biological organization exists at all levels in organisms. It can be seen at the smallest level, in the molecules that made up such things as DNA and proteins, to the largest level, in an organism such as a blue whale, the largest mammal on Earth. Similarly, single celled prokaryotes and eukaryotes show order in the way their cells are arranged. Single-celled organisms such as an amoeba are free-floating and independent-living. Their single-celled "bodies" are able to carry out all the processes of life, such as metabolism and respiration, without help from other cells. Some single-celled organisms, such as bacteria, can group together and form a biofilm. A biofilm is a large grouping of many bacteria that sticks to a surface and makes a protective coating over itself. Biofilms can show similarities to multicellular organisms. Division of labor is the process in which one group of cells does one job (such as making the "glue" that sticks the biofilm to the surface), while another group of cells does another job (such as taking in nutrients). Multicellular organisms carry out their life processes through division of labor. They have specialized cells that do specific jobs. However, biofilms are not considered multicellular organisms and are instead called colonial organisms. The difference between a multicellular organism and a colonial organism is that individual organisms from a colony or biofilm can, if separated, survive on their own, while cells from a multicellular organism (e.g., liver cells) cannot.
Colonial algae of the genus Volvox.
Colonial Organisms
Colonial organisms were probably one of the first evolutionary steps towards multicellular organisms. Algae of the genus Volvox are an example of the border between colonial organisms and multicellular organisms.
Each Volvox, shown in Figure above, is a colonial organism. It is made up of between 1,000 to 3,000 photosynthetic algae that are grouped together into a hollow sphere. The sphere has a distinct front and back end. The cells have eyespots, which are more developed in the cells near the front. This enables the colony to swim towards light.
Origin of Multicellularity
The oldest known multicellular organism is a red algae Bangiomorpha pubescens, fossils of which were found in 1.2 billion-year-old rock. As the first organisms were single-celled, these organisms had to evolve into multicellular organisms.
Scientists think that multicellularity arose from cooperation between many organisms of the same species. The Colonial Theory proposes that this cooperation led to the development of a multicellular organism. Many examples of cooperation between organisms in nature have been observed. For example, a certain species of amoeba (a single-celled protist) groups together during times of food shortage and forms a colony that moves as one to a new location. Some of these amoebas then become slightly differentiated from each other. Volvox, shown in Figure above, is another example of a colonial organism. Most scientists accept that the Colonial Theory explains how multicellular organisms evolved.
Multicellular organisms are organisms that are made up of more than one type of cell and have specialized cells that are grouped together to carry out specialized functions. Most life that you can see without a microscope is multicellular. As discussed earlier, the cells of a multicellular organism would not survive as independent cells. The body of a multicellular organism, such as a tree or a cat, exhibits organization at several levels: tissues, organs, and organ systems. Similar cells are grouped into tissues, groups of tissues make up organs, and organs with a similar function are grouped into an organ system.
Levels of Organization in Multicellular Organisms
The simplest living multicellular organisms, sponges, are made of many specialized types of cells that work together for a common goal. Such cell types include digestive cells, tubular pore cells, and epidermal cells. Though the different cell types create a large, organized, multicellular structure — the visible sponge — they are not organized into true interconnected tissues. If a sponge is broken up by passing it through a sieve, the sponge will reform on the other side. However, if the sponge’s cells are separated from each other, the individual cell types cannot survive alone. Simpler colonial organisms, such as members of the genusVolvox, as shown in Figure above, differ in that their individual cells are free-living and can survive on their own if separated from the colony.
This roundworm, a multicellular organism, was stained to highlight the nuclei of all the cells in its body (red dots).
A tissue is a group of connected cells that have a similar function within an organism. More complex organisms such as jellyfish, coral, and sea anemones have a tissue level of organization. For example, jellyfish have tissues that have separate protective, digestive, and sensory functions.
Even more complex organisms, such as the roundworm shown in Figure above, while also having differentiated cells and tissues, have an organ level of development. An organ is a group of tissues that has a specific function or group of functions. Organs can be as primitive as the brain of a flatworm (a group of nerve cells), as large as the stem of a sequoia (up to 90 meters, or 300 feet, in height), or as complex as a human liver.
The most complex organisms (such as mammals, trees, and flowers) have organ systems. Anorgan system is a group of organs that act together to carry out complex related functions, with each organ focusing on a part of the task. An example is the human digestive system, in which the mouth ingests food, the stomach crushes and liquifies it, the pancreas and gall bladder make and release digestive enzymes, and the intestines absorb nutrients into theblood.
Summary
• Single-celled organisms are able to carry out all the processes of life without help from other cells.
• Multicellular organisms carry out their life processes through division of labor. They have specialized cells that do specific jobs.
• The Colonial Theory proposes that cooperation among cells of the same species led to the development of a multicellular organism.
• Multicellular organisms, depending on their complexity, may be organized from cells to tissues, organs, and organ systems.
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Use these resources to answer the questions that follow.
Explore More I
1. Why are multicellular organisms highly organized?
2. What is a tissue?
3. How many tissue types are there in animals?
Explore More II
1. What is the difference between an organ and an organ system?
2. How many organ systems do humans have?
Review
1. What is a multicellular organism?
2. What is a cell feature that distinguishes a colonial organism from a multicellular organism?
3. What is the difference between a cell and a tissue?
4. Describe the top two levels of organization of an organism. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/02%3A_Cell_Biology/2.12%3A_Organization_of_Cells.txt |
What will eventually happen to these dyes?
They will all blend together. The dyes will move through the water until an even distribution is achieved. The process of moving from areas of high amounts to areas of low amounts is called diffusion.
Passive Transport
Probably the most important feature of a cell’s phospholipid membranes is that they are selectively permeable or semipermeable. A membrane that is selectively permeable has control over what molecules or ions can enter or leave the cell, as shown in Figure below. The permeability of a membrane is dependent on the organization and characteristics of the membrane lipids and proteins. In this way, cell membranes help maintain a state of homeostasis within cells (and tissues, organs, and organ systems) so that an organism can stay alive and healthy.
A selectively permeable membrane allows certain molecules through, but not others.
Transport Across Membranes
The molecular make-up of the phospholipid bilayer limits the types of molecules that can pass through it. For example, hydrophobic (water-hating) molecules, such as carbon dioxide (CO2) and oxygen (O2), can easily pass through the lipid bilayer, but ions such as calcium (Ca2+) and polar molecules such as water (H2O) cannot. The hydrophobic interior of the phospholipid bilayer does not allow ions or polar molecules through because these molecules are hydrophilic, or water loving. In addition, large molecules such as sugars and proteins are too big to pass through the bilayer. Transport proteins within the membrane allow these molecules to pass through the membrane, and into or out of the cell. This way, polar molecules avoid contact with the nonpolar interior of the membrane, and large molecules are moved through large pores.
Every cell is contained within a membrane punctuated with transport proteins that act as channels or pumps to let in or force out certain molecules. The purpose of the transport proteins is to protect the cell's internal environment and to keep its balance of salts, nutrients, and proteins within a range that keeps the cell and the organism alive.
There are three main ways that molecules can pass through a phospholipid membrane. The first way requires no energy input by the cell and is called passive transport. The second way requires that the cell uses energy to pull in or pump out certain molecules and ions and is called active transport. The third way is through vesicle transport, in which large molecules are moved across the membrane in bubble-like sacks that are made from pieces of the membrane.
Passive transport is a way that small molecules or ions move across the cell membrane without input of energy by the cell. The three main kinds of passive transport are diffusion,osmosis, and facilitated diffusion.
Diffusion
Diffusion is the movement of molecules from an area of high concentration of the molecules to an area with a lower concentration. The difference in the concentrations of the molecules in the two areas is called the concentration gradient. Diffusion will continue until this gradient has been eliminated. Since diffusion moves materials from an area of higher concentration to the lower, it is described as moving solutes "down the concentration gradient." The end result of diffusion is an equal concentration, or equilibrium, of molecules on both sides of the membrane.
If a molecule can pass freely through a cell membrane, it will cross the membrane by diffusion (Figure below).
Molecules move from an area of high concentration to an area of lower concentration until an equilibrium is met. The molecules continue to cross the membrane at equilibrium, but at equal rates in both directions.
Summary
• The cell membrane is selectively permeable, allowing only certain substances to pass through.
• Passive transport is a way that small molecules or ions move across the cell membrane without input of energy by the cell. The three main kinds of passive transport are diffusion,osmosis, and facilitated diffusion.
• Diffusion is the movement of molecules from an area of high concentration of the molecules to an area with a lower concentration.
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Use this resource to answer the questions that follow.
• Passive Transport at www.northland.cc.mn.us/biolog...s/passive1.swf.
1. What is diffusion?
2. What does concentration gradient refer to?
3. Name two factors that influence the rate of diffusion?
Review
1. Define semipermeable.
2. What is diffusion?
3. What is a concentration gradient?
4. What is meant by passive transport? | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/02%3A_Cell_Biology/2.13%3A_Diffusion.txt |
Can you help me move?
What is one of the questions no one likes to be asked? Sometimes the cell needs help moving things as well, or facilitating the diffusion process. And this would be the job of a special type of protein.
Facilitated Diffusion
What happens if a substance needs assistance to move across or through the plasma membrane? Facilitated diffusion is the diffusion of solutes through transport proteins in the plasma membrane. Facilitated diffusion is a type of passive transport. Even though facilitated diffusion involves transport proteins, it is still passive transport because the solute is moving down the concentration gradient.
Small nonpolar molecules can easily diffuse across the cell membrane. However, due to the hydrophobic nature of the lipids that make up cell membranes, polar molecules (such as water) and ions cannot do so. Instead, they diffuse across the membrane through transport proteins. A transport protein completely spans the membrane, and allows certain molecules or ions to diffuse across the membrane. Channel proteins, gated channel proteins, and carrier proteins are three types of transport proteins that are involved in facilitated diffusion.
A channel protein, a type of transport protein, acts like a pore in the membrane that lets water molecules or small ions through quickly. Water channel proteins (aquaporins) allow water to diffuse across the membrane at a very fast rate. Ion channel proteins allow ions to diffuse across the membrane.
A gated channel protein is a transport protein that opens a "gate," allowing a molecule to pass through the membrane. Gated channels have a binding site that is specific for a given molecule or ion. A stimulus causes the "gate" to open or shut. The stimulus may be chemical or electrical signals, temperature, or mechanical force, depending on the type of gated channel. For example, the sodium gated channels of a nerve cell are stimulated by a chemical signal which causes them to open and allow sodium ions into the cell. Glucose molecules are too big to diffuse through the plasma membrane easily, so they are moved across the membrane through gated channels. In this way glucose diffuses very quickly across a cell membrane, which is important because many cells depend on glucose for energy.
A carrier protein is a transport protein that is specific for an ion, molecule, or group of substances. Carrier proteins "carry" the ion or molecule across the membrane by changing shape after the binding of the ion or molecule. Carrier proteins are involved in passive and active transport. A model of a channel protein and carrier proteins is shown in Figure below.
Facilitated diffusion through the cell membrane. Channel proteins and carrier proteins are shown (but not a gated-channel protein). Water molecules and ions move through channel proteins. Other ions or molecules are also carried across the cell membrane by carrier proteins. The ion or molecule binds to the active site of a carrier protein. The carrier protein changes shape, and releases the ion or molecule on the other side of the membrane. The carrier protein then returns to its original shape.
An animation depicting facilitated diffusion can be viewed at http://www.youtube.com/watch?v=OV4PgZDRTQw (1:36).
Ion Channels
Ions such as sodium (Na+), potassium (K+), calcium (Ca2+), and chloride (Cl-), are important for many cell functions. Because they are charged (polar), these ions do not diffuse through the membrane. Instead they move through ion channel proteins where they are protected from the hydrophobic interior of the membrane. Ion channels allow the formation of a concentration gradient between the extracellular fluid and the cytosol. Ion channels are very specific, as they allow only certain ions through the cell membrane. Some ion channels are always open, others are "gated" and can be opened or closed. Gated ion channels can open or close in response to different types of stimuli, such as electrical or chemical signals.
Summary
• Facilitated diffusion is the diffusion of solutes through transport proteins in the plasma membrane. Channel proteins, gated channel proteins, and carrier proteins are three types of transport proteins that are involved in facilitated diffusion.
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Use this resource to answer the questions that follow.
• Facilitated Diffusion atwww.physiologyweb.com/lecture_notes/membrane_transport/facilitated_diffusion.html.
1. Define facilitative diffusion.
2. Describe the alternating access model.
3. What is meant by the occluded state?
4. What occurs after the occluded state?
Review
1. What is facilitated diffusion?
2. What is a transport protein? Give three examples.
3. Assume a molecule must cross the plasma membrane into a cell. The molecule is very large. How will it be transported into the cell?
4. Explain how carrier proteins function?
5. Explain the role of ion channels. Why are ion channels necessary? | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/02%3A_Cell_Biology/2.14%3A_Facilitated_Diffusion.txt |
Need to move something really heavy?
If you did, it would take a lot of energy. Sometimes, moving things into or out of the cell also takes energy. How would the cell move something against a concentration gradient? It starts by using energy.
Active Transport
In contrast to facilitated diffusion, which does not require energy and carries molecules or ions down a concentration gradient, active transport pumps molecules and ions against a concentration gradient. Sometimes an organism needs to transport something against a concentration gradient. The only way this can be done is through active transport, which uses energy that is produced by respiration (ATP). In active transport, the particles move across a cell membrane from a lower concentration to a higher concentration. Active transport is the energy-requiring process of pumping molecules and ions across membranes "uphill" - against a concentration gradient.
• The active transport of small molecules or ions across a cell membrane is generally carried out by transport proteins that are found in the membrane.
• Larger molecules such as starch can also be actively transported across the cell membrane by processes called endocytosis and exocytosis.
Homeostasis and Cell Function
Homeostasis refers to the balance, or equilibrium, within the cell or a body. It is an organism’s ability to keep a constant internal environment. Keeping a stable internal environment requires constant adjustments as conditions change inside and outside the cell. The adjusting of systems within a cell is called homeostatic regulation. Because the internal and external environments of a cell are constantly changing, adjustments must be made continuously to stay at or near the set point (the normal level or range). Homeostasis is a dynamic equilibrium rather than an unchanging state. The cellular processes discussed in both the Diffusion andActive Transport concepts all play an important role in homeostatic regulation. You will learn more about homeostasis in other concepts.
Summary
• Active transport is the energy-requiring process of pumping molecules and ions across membranes against a concentration gradient.
• Active transport processes help maintain homeostasis.
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Use this resource to answer the questions that follow.
• Active Transport at www.northland.cc.mn.us/biolog...ns/active1.swf.
1. What is the role of ion pumps?
2. Why is ATP necessary with ion pumps?
3. What is cotransport?
4. Why must one molecule be pumped across the membrane during cotransport?
Explore More III
• Active Transport
Review
1. What is active transport?
2. Explain how cell transport helps an organism maintain homeostasis.
2.16: Sodium-Potassium Pump
What is this incredible object?
Would it surprise you to learn that it is a human cell? The image represents an active human nerve cell. How nerve cells function will be the focus of another concept. However, active transport processes play a significant role in the function of these cells. Specifically, it is the sodium-potassium pump that is active in the axons of these nerve cells.
The Sodium-Potassium Pump
Active transport is the energy-requiring process of pumping molecules and ions across membranes "uphill" - against a concentration gradient. To move these molecules against their concentration gradient, a carrier protein is needed. Carrier proteins can work with a concentration gradient (during passive transport), but some carrier proteins can move solutes against the concentration gradient (from low concentration to high concentration), with an input of energy. In active transport, as carrier proteins are used to move materials against their concentration gradient, these proteins are known as pumps. As in other types of cellular activities, ATP supplies the energy for most active transport. One way ATP powers active transport is by transferring a phosphate group directly to a carrier protein. This may cause the carrier protein to change its shape, which moves the molecule or ion to the other side of the membrane. An example of this type of active transport system, as shown in Figure below, is the sodium-potassium pump, which exchanges sodium ions for potassium ions across the plasma membrane of animal cells.
The sodium-potassium pump system moves sodium and potassium ions against large concentration gradients. It moves two potassium ions into the cell where potassium levels are high, and pumps three sodium ions out of the cell and into the extracellular fluid.
As is shown in Figure above, three sodium ions bind with the protein pump inside the cell. The carrier protein then gets energy from ATP and changes shape. In doing so, it pumps the three sodium ions out of the cell. At that point, two potassium ions from outside the cell bind to the protein pump. The potassium ions are then transported into the cell, and the process repeats. The sodium-potassium pump is found in the plasma membrane of almost every human cell and is common to all cellular life. It helps maintain cell potential and regulates cellular volume.
A more detailed look at the sodium-potassium pump is available at http://www.youtube.com/watch?v=C_H-ONQFjpQ (13:53) and http://www.youtube.com/watch?v=ye3rTjLCvAU (6:48).
The Electrochemical Gradient
The active transport of ions across the membrane causes an electrical gradient to build up across the plasma membrane. The number of positively charged ions outside the cell is greater than the number of positively charged ions in the cytosol. This results in a relatively negative charge on the inside of the membrane, and a positive charge on the outside. This difference in charges causes a voltage across the membrane. Voltage is electrical potential energy that is caused by a separation of opposite charges, in this case across the membrane. The voltage across a membrane is called membrane potential. Membrane potential is very important for the conduction of electrical impulses along nerve cells.
Because the inside of the cell is negative compared to outside the cell, the membrane potential favors the movement of positively charged ions (cations) into the cell, and the movement of negative ions (anions) out of the cell. So, there are two forces that drive the diffusion of ions across the plasma membrane—a chemical force (the ions' concentration gradient), and an electrical force (the effect of the membrane potential on the ions’ movement). These two forces working together are called an electrochemical gradient, and will be discussed in detail in "Nerve Cells" and "Nerve Impulses" concepts.
Summary
• Active transport is the energy-requiring process of pumping molecules and ions across membranes against a concentration gradient.
• The sodium-potassium pump is an active transport pump that exchanges sodium ions for potassium ions.
Explore More
Use this resource to answer the questions that follow.
1. Are there more sodium ions on the outside of cells or the inside?
2. Are there more potassium ions on the outside of cells or the inside?
3. Describe the role of ATP in active transport.
4. What happens after the pump is phosphorylated?
5. What happens after dephosphorylation?
Review
1. What is active transport?
2. What type of protein is involved in active transport?
3. Describe how the sodium-potassium pump functions.
4. What is the electrochemical gradient? | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/02%3A_Cell_Biology/2.15%3A__Active_Transport.txt |
What does a cell "eat"?
Is it possible for objects larger than a small molecule to be engulfed by a cell? Of course it is. This image depicts a cancer cell being attacked by a cell of the immune system. Cells of the immune system consistently destroy pathogens by essentially "eating" them.
Vesicle Transport
Some molecules or particles are just too large to pass through the plasma membrane or to move through a transport protein. So cells use two other active transport processes to move these macromolecules (large molecules) into or out of the cell. Vesicles or other bodies in the cytoplasm move macromolecules or large particles across the plasma membrane. There are two types of vesicle transport, endocytosis and exocytosis (illustrated in Figure below). Both processes are active transport processes, requiring energy.
Illustration of the two types of vesicle transport, exocytosis and endocytosis.
Endocytosis and Exocytosis
Endocytosis is the process of capturing a substance or particle from outside the cell by engulfing it with the cell membrane. The membrane folds over the substance and it becomes completely enclosed by the membrane. At this point a membrane-bound sac, or vesicle, pinches off and moves the substance into the cytosol. There are two main kinds of endocytosis:
• Phagocytosis, or cellular eating, occurs when the dissolved materials enter the cell. The plasma membrane engulfs the solid material, forming a phagocytic vesicle.
• Pinocytosis, or cellular drinking, occurs when the plasma membrane folds inward to form a channel allowing dissolved substances to enter the cell, as shown in Figure below. When the channel is closed, the liquid is encircled within a pinocytic vesicle.
Transmission electron microscope image of brain tissue that shows pinocytotic vesicles. Pinocytosis is a type of endocytosis.
Exocytosis describes the process of vesicles fusing with the plasma membrane and releasing their contents to the outside of the cell, as shown in Figure below. Exocytosis occurs when a cell produces substances for export, such as a protein, or when the cell is getting rid of a waste product or a toxin. Newly made membrane proteins and membrane lipids are moved on top the plasma membrane by exocytosis. For a detailed animation of cellular secretion, see http://vcell.ndsu.edu/animations/constitutivesecretion/first.htm.
Illustration of an axon releasing dopamine by exocytosis.
Summary
• Active transport is the energy-requiring process of pumping molecules and ions across membranes against a concentration gradient.
• Endocytosis is the process of capturing a substance or particle from outside the cell by engulfing it with the cell membrane, and bringing it into the cell.
• Exocytosis describes the process of vesicles fusing with the plasma membrane and releasing their contents to the outside of the cell.
• Both endocytosis and exocytosis are active transport processes.
Explore More
Use this resource to answer the questions that follow.
1. What is bulk transport?
2. Describe how exocytosis occurs?
3. What are the types of endocytosis?
4. Some types of endocytosis are non-specific processes. What does this mean?
5. Describe the process of receptor-mediated endocytosis.
Review
1. What is the difference between endocytosis and exocytosis?
2. Why is pinocytosis a form of endocytosis?
3. Are vesicles involved in passive transport? Explain. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/02%3A_Cell_Biology/2.17%3A_Exocytosis_and_Endocytosis.txt |
Name one major difference between a plant and an animal.
There are many differences, but in terms of energy, it all starts with sunlight. Plants absorb the energy from the sun and turn it into food. You can sit in the sun for hours and hours. You will feel warm, but you're not going to absorb any energy. You have to eat to obtain your energy.
Autotrophs vs. Heterotrophs
Living organisms obtain chemical energy in one of two ways.
Autotrophs, shown in Figure below, store chemical energy in carbohydrate food molecules they build themselves. Food is chemical energy stored in organic molecules. Food provides both the energy to do work and the carbon to build bodies. Because most autotrophs transform sunlight to make food, we call the process they use photosynthesis. Only three groups of organisms - plants, algae, and some bacteria - are capable of this life-giving energy transformation. Autotrophs make food for their own use, but they make enough to support other life as well. Almost all other organisms depend absolutely on these three groups for the food they produce. The producers, as autotrophs are also known, begin food chains which feed all life. Food chains will be discussed in the "Food Chains and Food Webs" concept.
Heterotrophs cannot make their own food, so they must eat or absorb it. For this reason, heterotrophs are also known as consumers. Consumers include all animals and fungi and many protists and bacteria. They may consume autotrophs or other heterotrophs or organic molecules from other organisms. Heterotrophs show great diversity and may appear far more fascinating than producers. But heterotrophs are limited by our utter dependence on those autotrophs that originally made our food. If plants, algae, and autotrophic bacteria vanished from earth, animals, fungi, and other heterotrophs would soon disappear as well. All life requires a constant input of energy. Only autotrophs can transform that ultimate, solar source into the chemical energy in food that powers life, as shown in Figure below.
Photosynthetic autotrophs, which make food using the energy in sunlight, include (a) plants, (b) algae, and (c) certain bacteria.
Photosynthesis provides over 99 percent of the energy for life on earth. A much smaller group of autotrophs - mostly bacteria in dark or low-oxygen environments - produce food using the chemical energy stored in inorganic molecules such as hydrogen sulfide, ammonia, or methane. While photosynthesis transforms light energy to chemical energy, this alternate method of making food transfers chemical energy from inorganic to organic molecules. It is therefore called chemosynthesis, and is characteristic of the tubeworms shown in Figure below. Some of the most recently discovered chemosynthetic bacteria inhabit deep ocean hot water vents or “black smokers.” There, they use the energy in gases from the Earth’s interior to produce food for a variety of unique heterotrophs: giant tube worms, blind shrimp, giant white crabs, and armored snails. Some scientists think that chemosynthesis may support life below the surface of Mars, Jupiter's moon, Europa, and other planets as well. Ecosystems based on chemosynthesis may seem rare and exotic, but they too illustrate the absolute dependence of heterotrophs on autotrophs for food.
A food chain shows how energy and matter flow from producers to consumers. Matter is recycled, but energy must keep flowing into the system. Where does this energy come from? Though this food chains "ends" with decomposers, do decomposers, in fact, digest matter from each level of the food chain? (see the "Flow of Energy" concept.)
Tubeworms deep in the Galapagos Rift get their energy from chemosynthetic bacteria living within their tissues. No digestive systems needed!
Making and Using Food
The flow of energy through living organisms begins with photosynthesis. This process stores energy from sunlight in the chemical bonds of glucose. By breaking the chemical bonds in glucose, cells release the stored energy and make the ATP they need. The process in which glucose is broken down and ATP is made is called cellular respiration.
Photosynthesis and cellular respiration are like two sides of the same coin. This is apparent from Figure below. The products of one process are the reactants of the other. Together, the two processes store and release energy in living organisms. The two processes also work together to recycle oxygen in Earth’s atmosphere.
This diagram compares and contrasts photosynthesis and cellular respiration. It also shows how the two processes are related.
Photosynthesis
Photosynthesis is often considered to be the single most important life process on Earth. It changes light energy into chemical energy and also releases oxygen. Without photosynthesis, there would be no oxygen in the atmosphere. Photosynthesis involves many chemical reactions, but they can be summed up in a single chemical equation:
6CO2 + 6H2O + Light Energy → C6H12O6 + 6O2.
Photosynthetic autotrophs capture light energy from the sun and absorb carbon dioxide and water from their environment. Using the light energy, they combine the reactants to produce glucose and oxygen, which is a waste product. They store the glucose, usually as starch, and they release the oxygen into the atmosphere.
Cellular Respiration
Cellular respiration actually “burns” glucose for energy. However, it doesn’t produce light or intense heat as some other types of burning do. This is because it releases the energy in glucose slowly, in many small steps. It uses the energy that is released to form molecules of ATP. Cellular respiration involves many chemical reactions, which can be summed up with this chemical equation:
C6H12O6 + 6O2 → 6CO2 + 6H2O + Chemical Energy (in ATP)
Cellular respiration occurs in the cells of all living things. It takes place in the cells of both autotrophs and heterotrophs. All of them burn glucose to form ATP.
Summary
• Autotrophs store chemical energy in carbohydrate food molecules they build themselves. Most autotrophs make their "food" through photosynthesis using the energy of the sun.
• Heterotrophs cannot make their own food, so they must eat or absorb it.
• Chemosynthesis is used to produce food using the chemical energy stored in inorganic molecules.
Explore More
Use this resource to answer the questions that follow.
1. Define autotroph and heterotroph.
2. What position do autotrophs fill in a food chain?
3. Give examples of autotrophs and heterotrophs.
4. Describe energy production in photoautotrophs.
5. What is a chemoheterotroph?
Review
1. Compare autotrophs to heterotrophs, and describe the relationship between these two groups of organisms.
2. Name and describe the two types of food making processes found among autotrophs. Which is quantitatively more important to life on earth?
3. Describe the flow of energy through a typical food chain (describing "what eats what"), including the original source of that energy and its ultimate form after use. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/02%3A_Cell_Biology/2.18%3A__Autotrophs_and_Heterotrophs.txt |
Needs lots of energy?
To run a marathon, probably. Where does this extra energy come from? Carbohydrate loading is a strategy used by endurance athletes to maximize the storage of energy, in the form of glycogen, in the muscles. Glycogen forms an energy reserve that can be quickly mobilized to meet a sudden need for glucose, which is then turned into ATP through the process ofcellular respiration.
Glucose and ATP
Energy-Carrying Molecules
You know that the fish you had for lunch contained protein molecules. But do you know that the atoms in that protein could easily have formed the color in a dragonfly’s eye, the heart of a water flea, and the whiplike tail of a Euglena before they hit your plate as sleek fish muscle? Food consists of organic (carbon-containing) molecules which store energy in the chemical bonds between their atoms. Organisms use the atoms of food molecules to build larger organic molecules including proteins, DNA, and fats (lipids) and use the energy in food to power life processes. By breaking the bonds in food molecules, cells release energy to build new compounds. Although some energy dissipates as heat at each energy transfer, much of it is stored in the newly made molecules. Chemical bonds in organic molecules are a reservoir of the energy used to make them. Fueled by the energy from food molecules, cells can combine and recombine the elements of life to form thousands of different molecules. Both the energy (despite some loss) and the materials (despite being reorganized) pass from producer to consumer – perhaps from algal tails, to water flea hearts, to dragonfly eye colors, to fish muscle, to you!
The process of photosynthesis, which usually begins the flow of energy through life, uses many different kinds of energy-carrying molecules to transform sunlight energy into chemical energy and build food. Some carrier molecules hold energy briefly, quickly shifting it like a hot potato to other molecules. This strategy allows energy to be released in small, controlled amounts. An example starts in chlorophyll, the green pigment present in most plants, which helps convert solar energy to chemical energy. When a chlorophyll molecule absorbs light energy, electrons are excited and "jump" to a higher energy level. The excited electrons then bounce to a series of carrier molecules, losing a little energy at each step. Most of the "lost" energy powers some small cellular task, such as moving ions across a membrane or building up another molecule. Another short-term energy carrier important to photosynthesis, NADPH, holds chemical energy a bit longer but soon "spends" it to help to build sugar.
Two of the most important energy-carrying molecules are glucose and adenosine triphosphate, commonly referred to as ATP. These are nearly universal fuels throughout the living world and are both key players in photosynthesis, as shown below.
Glucose
A molecule of glucose, which has the chemical formula C6H12O6, carries a packet of chemical energy just the right size for transport and uptake by cells. In your body, glucose is the "deliverable" form of energy, carried in your blood through capillaries to each of your 100 trillion cells. Glucose is also the carbohydrate produced by photosynthesis, and as such is the near-universal food for life.
Glucose is the energy-rich product of photosynthesis, a universal food for life. It is also the primary form in which your bloodstream delivers energy to every cell in your body.
ATP
ATP molecules store smaller quantities of energy, but each releases just the right amount to actually do work within a cell. Muscle cell proteins, for example, pull each other with the energy released when bonds in ATP break open (discussed below). The process of photosynthesis also makes and uses ATP - for energy to build glucose! ATP, then, is the useable form of energy for your cells. ATP is commonly referred to as the "energy currency" of the cell.
Why do we need both glucose and ATP?
Why don’t plants just make ATP and be done with it? If energy were money, ATP would be a quarter. Enough money to operate a parking meter or washing machine. Glucose would be a ten dollar bill – much easier to carry around in your wallet, but too large to do the actual work of paying for parking or washing. Just as we find several denominations of money useful, organisms need several "denominations" of energy – a smaller quantity for work within cells, and a larger quantity for stable storage, transport, and delivery to cells. (Actually a glucose molecule would be about \$9.50, as under the proper conditions, up to 38 ATP are produced for each glucose molecule.)
Let’s take a closer look at a molecule of ATP. Although it carries less energy than glucose, its structure is more complex. The "A" in ATP refers to the majority of the molecule, adenosine, a combination of a nitrogenous base and a five-carbon sugar. The "TP" indicates the three phosphates, linked by bonds which hold the energy actually used by cells. Usually, only the outermost bond breaks to release or spend energy for cellular work.
An ATP molecule, shown in the Figure below, is like a rechargeable battery: its energy can be used by the cell when it breaks apart into ADP (adenosine diphosphate) and phosphate, and then the "worn-out battery" ADP can be recharged using new energy to attach a new phosphate and rebuild ATP. The materials are recyclable, but recall that energy is not!
How much energy does it cost to do your body’s work? A single cell uses about 10 million ATP molecules per second, and recycles all of its ATP molecules about every 20-30 seconds.
An arrow shows the bond between two phosphate groups in an ATP molecule. When this bond breaks, its chemical energy can do cellular work. The resulting ADP molecule is recycled when new energy attaches another phosphate, rebuilding ATP.
A explanation of ATP as "biological energy" is found at http://www.youtube.com/watch?v=YQfWiDlFEcA.
Summary
• Glucose is the carbohydrate produced by photosynthesis. Energy-rich glucose is delivered through your blood to each of your cells.
• ATP is the usable form of energy for your cells.
Explore More
Use this resource to answer the questions that follow.
1. What is the role of ATP?
2. What are the components of an ATP molecule?
3. Why do cells require chemical energy?
4. How does ATP hold energy?
5. How does ATP drive cellular processes?
Review
1. The fact that all organisms use similar energy-carrying molecules shows one aspect of the grand "Unity of Life." Name two universal energy-carrying molecules, and explain why most organisms need both carriers rather than just one.
2. A single cell uses about 10 million ATP molecules per second. Explain how cells use the energy and recycle the materials in ATP.
3. ATP and glucose are both molecules that organisms use for energy. They are like the tank of a tanker truck that delivers gas to a gas station and the gas tank that holds the fuel for a car. Which molecule is like the tank of the delivery truck, and which is like the gas tank of the car? Explain your answer. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/02%3A_Cell_Biology/2.19%3A_Glucose_and_ATP.txt |
What do pancakes and chloroplasts have in common?
The chloroplast is the site of photosynthesis. Part of the photosynthesis reactions occur in an internal membrane within the organelle. The chloroplast contains many of these internal membranes, making photosynthesis very efficient. These internal membranes stack on top of each other, just like a stack of pancakes.
Stages of Photosynthesis
Photosynthesis occurs in two stages, which are shown in Figure below.
1. Stage I is called the light reactions. This stage uses water and changes light energy from the sun into chemical energy stored in ATP and NADPH (another energy-carrying molecule). This stage also releases oxygen as a waste product.
2. Stage II is called the Calvin cycle. This stage combines carbon from carbon dioxide in the air and uses the chemical energy in ATP and NADPH to make glucose.
The two stages of photosynthesis are the light reactions and the Calvin cycle. Do you see how the two stages are related?
Before you read about these two stages of photosynthesis in greater detail, you need to know more about the chloroplast, where the two stages take place.
The Chloroplast
Chloroplasts: Theaters for Photosynthesis
Photosynthesis, the process of turning the energy of sunlight into ‘‘food,’’ is divided into two basic sets of reactions, known as the light reactions and the Calvin cycle, which uses carbon dioxide. As you study the details in other concepts, refer frequently to the chemical equation of photosynthesis: 6CO2 + 6H2O + Light Energy → C6H12O6 + 6O2. Photosynthesis occurs in the chloroplast, an organelle specific to plant cells.
If you examine a single leaf of a Winter Jasmine leaf, shown in Figure below, under a microscope, you will see within each cell dozens of small green ovals. These are chloroplasts, the organelles which conduct photosynthesis in plants and algae. Chloroplasts closely resemble some types of bacteria and even contain their own circular DNA and ribosomes. In fact, the endosymbiotic theory holds that chloroplasts were once independently living bacteria (prokaryotes). So when we say that photosynthesis occurs within chloroplasts, we speak not only of the organelles within plants and algae, but also of some bacteria – in other words, virtually all photosynthetic autotrophs.
High power microscopic photo of the upper part of a Winter Jasmine leaf. Viewed under a microscope, many green chloroplasts are visible.
Each chloroplast contains neat stacks called grana (singular, granum). The grana consist of sac-like membranes, known as thylakoid membranes. These membranes contain photosystems, which are groups of molecules that include chlorophyll, a green pigment. The light reactions of photosynthesis occur in the thylakoid membranes. The stroma is the space outside the thylakoid membranes, as shown in Figure below. This is where the reactions of the Calvin cycle take place. In addition to enzymes, two basic types of molecules - pigments and electron carriers – are key players in this process and are also found in the thylakoid membranes.
You can take a video tour of a chloroplast at Encyclopedia Britannica: Chloroplast:www.britannica.com/EBchecked/...in-plant-cells.
A chloroplast consists of thylakoid membranes surrounded by stroma. The thylakoid membranes contain molecules of the green pigment chlorophyll.
Electron carrier molecules are usually arranged in electron transport chains (ETCs). These accept and pass along energy-carrying electrons in small steps (Figure below). In this way, they produce ATP and NADPH, which temporarily store chemical energy. Electrons in transport chains behave much like a ball bouncing down a set of stairs – a little energy is lost with each bounce. However, the energy “lost” at each step in an electron transport chain accomplishes a little bit of work, which eventually results in the synthesis of ATP.
This figure shows the light reactions of photosynthesis. This stage of photosynthesis begins with photosystem II (so named because it was discovered after photosystem I). Find the two electrons (2 e-) in photosystem II, and then follow them through the electron transport chain (also called the electron transfer chain) to the formation of NADPH. Where do the hydrogen ions (H+) come from that help make ATP?
Summary
• Photosynthesis occurs in the chloroplast, an organelle specific to plant cells.
• The light reactions of photosynthesis occur in the thylakoid membranes of the chloroplast.
• Electron carrier molecules are arranged in electron transport chains that produce ATP and NADPH, which temporarily store chemical energy.
Explore More
Use this resource to answer the questions that follow.
1. What are the functions of a plant's leaves?
2. Where do the photosynthetic reactions occur?
3. What is a stomata? What is their role?
4. Describe the internal structure of a chloroplast.
5. What reactions occur in the thylakoid membranes?
Review
1. Describe the chloroplast's role in photosynthesis.
2. Explain how the structure of a chloroplast (its membranes and thylakoids) makes its function (the chemical reactions of photosynthesis) more efficient.
3. Describe electron carriers and the electron transport chain. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/02%3A_Cell_Biology/2.20%3A_Chloroplasts.txt |
Oxygen has been described as a ‘‘waste product’’. How is this possible?
Essentially, oxygen is a waste product of the light reactions of photosynthesis. It is a ‘‘leftover’’ from a necessary part of the process. All the oxygen that is necessary to maintain most forms of life just happens to come about during this process.
Photosynthesis Stage I: The Light Reactions
An overview of photosynthesis is available at http://www.youtube.com/watch?v=-rsYk4eCKnA(13:37).
Chloroplasts Capture Sunlight
Every second, the sun fuses over 600 million tons of hydrogen into 596 tons of helium, converting over 4 tons of helium (4.3 billion kg) into light and heat energy. Countless tiny packets of that light energy travel 93 million miles (150 million km) through space, and about 1% of the light which reaches the Earth’s surface participates in photosynthesis. Light is the source of energy for photosynthesis, and the first set of reactions which begin the process requires light – thus the name, light reactions, or light-dependent reactions.
When light strikes chlorophyll (or an accessory pigment) within the chloroplast, it energizes electrons within that molecule. These electrons jump up to higher energy levels; they have absorbed or captured, and now carry, that energy. High-energy electrons are “excited.” Who wouldn’t be excited to hold the energy for life?
The excited electrons leave chlorophyll to participate in further reactions, leaving the chlorophyll “at a loss”; eventually they must be replaced. That replacement process also requires light, working with an enzyme complex to split water molecules. In this process ofphotolysis (“splitting by light”), H2O molecules are broken into hydrogen ions, electrons, and oxygen atoms. The electrons replace those originally lost from chlorophyll. Hydrogen ions and the high-energy electrons from chlorophyll will carry on the energy transformation drama after the light reactions are over.
The oxygen atoms, however, form oxygen gas, which is a waste product of photosynthesis. The oxygen given off supplies most of the oxygen in our atmosphere. Before photosynthesis evolved, Earth’s atmosphere lacked oxygen altogether, and this highly reactive gas was toxic to the many organisms living at the time. Something had to change! Most contemporary organisms rely on oxygen for efficient respiration. So plants don’t just “restore” the air, they also had a major role in creating it!
To summarize, chloroplasts “capture” sunlight energy in two ways. Light ‘‘excites’’ electrons in pigment molecules, and light provides the energy to split water molecules, providing more electrons as well as hydrogen ions.
Light Energy to Chemical Energy
Excited electrons that have absorbed light energy are unstable. However, the highly organized electron carrier molecules embedded in chloroplast membranes order the flow of these electrons, directing them through electron transport chains (ETCs). At each transfer, small amounts of energy released by the electrons are captured and put to work or stored. Some is also lost as heat with each transfer, but overall the light reactions are extremely efficient at capturing light energy and transforming it into chemical energy.
Two sequential transport chains harvest the energy of excited electrons, as shown in Figure below.
(1) First, they pass down an ETC, which captures their energy and uses it to pump hydrogen ions by active transport into the thylakoids. These concentrated ions store potential energy by forming a chemiosmotic or electrochemical gradient – a higher concentration of both positive charge and hydrogen inside the thylakoid than outside. (The gradient formed by the H+ ions is known as a chemiosmotic gradient.) Picture this energy buildup of H+ as a dam holding back a waterfall. Like water flowing through a hole in the dam, hydrogen ions “slide down” their concentration gradient through a membrane protein which acts as both ion channel and enzyme. As they flow, the ion channel/enzyme ATP synthase uses their energy to chemically bond a phosphate group to ADP, making ATP.
(2) Light re-energizes the electrons, and they travel down a second electron transport chain (ETC), eventually bonding hydrogen ions to NADP+ to form a more stable energy storage molecule, NADPH. NADPH is sometimes called “hot hydrogen,” and its energy and hydrogen atoms will be used to help build sugar in the second stage of photosynthesis.
Membrane architecture: The large colored carrier molecules form electron transport chains which capture small amounts of energy from excited electrons in order to store it in ATP and NADPH. Follow the energy pathways: light → electrons → NADPH (blue line) and light → electrons → concentrated H+ → ATP (red line). Note the intricate organization of the chloroplast.
NADPH and ATP molecules now store the energy from excited electrons – energy which was originally sunlight – in chemical bonds. Thus chloroplasts, with their orderly arrangement of pigments, enzymes, and electron transport chains, transform light energy into chemical energy. The first stage of photosynthesis – light-dependent reactions or simply light reactions – is complete.
For a detailed discussion of photosynthesis, see http://www.youtube.com/watch?v=GR2GA7chA_c (20:16) and http://www.youtube.com/watch?v=yfR36PMWegg (18:51).
Summary
• The light reactions capture energy from sunlight, which they change to chemical energy that is stored in molecules of NADPH and ATP.
• The light reactions also release oxygen gas as a waste product.
Explore More
Use this resource to answer the questions that follow.
1. How long does it take solar photons of light to reach Earth?
2. What happens when chlorophyll is struck by sunlight?
3. What is the immediate fate of the energy absorbed by chlorophyll?
4. What is a by-product of the light reactions?
Review
1. Summarize what happens during the light reactions of photosynthesis.
2. What is the chemiosmotic gradient?
3. Explain the role of the first electron transport chain in the formation of ATP during the light reactions of photosynthesis. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/02%3A_Cell_Biology/2.21%3A_Light_Reactions_of_Photosynthesis.txt |
Other than being green, what do all these fruits and vegetables have in common?
They are full of energy. Energy in the form of glucose. The energy from sunlight is briefly held in NADPH and ATP, which is needed to drive the formation of sugars such as glucose. And this all happens in the Calvin cycle.
The Calvin Cycle
Making Food “From Thin Air”
You’ve learned that the first, light-dependent stage of photosynthesis uses two of the three reactants, water and light, and produces one of the products, oxygen gas (a waste product of this process). All three necessary conditions are required – chlorophyll pigments, the chloroplast “theater,” and enzyme catalysts. The first stage transforms light energy into chemical energy, stored to this point in molecules of ATP and NADPH. Look again at the overall equation below. What is left?
Waiting in the wings is one more reactant, carbon dioxide, and yet to come is the star product, which is food for all life – glucose. These key players perform in the second act of the photosynthesis drama, in which food is “made from thin air!”
The second stage of photosynthesis can proceed without light, so its steps are sometimes called “light-independent” or “dark” reactions (though the term ‘‘dark’’ reactions can be misleading). Many biologists honor the scientist, Melvin Calvin, who won a 1961 Nobel Prize for working out this complex set of chemical reactions, naming it the Calvin cycle.
The Calvin cycle has two parts. First carbon dioxide is ‘‘fixed’’. Then ATP and NADPH from the light reactions provide energy to combine the fixed carbons to make sugar.
The Calvin cycle is discussed at http://www.youtube.com/watch?v=slm6D2VEXYs (13:28)
Carbon Dioxide is “Fixed”
Why does carbon dioxide need to be fixed? Was it ever broken?
Life on Earth is carbon-based. Organisms need not only energy but also carbon atoms for building bodies. For nearly all life, the ultimate source of carbon is carbon dioxide (CO2), an inorganic molecule. CO2 makes up less than 1% of the Earth’s atmosphere.
Animals and most other heterotrophs cannot take in CO2 directly. They must eat other organisms or absorb organic molecules to get carbon. Only autotrophs can build low-energy inorganic CO2 into high-energy organic molecules like glucose. This process is carbon fixation.
Stomata on the underside of leaves take in CO2 and release water and O2. Guard cells close the stomata when water is scarce. Leaf cross-section (above) and stoma (below).
Plants have evolved three pathways for carbon fixation.
The most common pathway combines one molecule of CO2 with a 5-carbon sugar called ribulose biphosphate (RuBP). The enzyme which catalyzes this reaction (nicknamed RuBisCo) is the most abundant enzyme on earth! The resulting 6-carbon molecule is unstable, so it immediately splits into two 3-carbon molecules. The 3 carbons in the first stable molecule of this pathway give this largest group of plants the name “C3.”
Dry air, hot temperatures, and bright sunlight slow the C3 pathway for carbon fixation. This is because stomata, tiny openings under the leaf which normally allow CO2 to enter and O2 to leave, must close to prevent loss of water vapor (Figure above). Closed stomata lead to a shortage of CO2. Two alternative pathways for carbon fixation demonstrate biochemical adaptations to differing environments.
Plants such as corn solve the problem by using a separate compartment to fix CO2. Here CO2combines with a 3-carbon molecule, resulting in a 4-carbon molecule. Because the first stable organic molecule has four carbons, this adaptation has the name C4. Shuttled away from the initial fixation site, the 4-carbon molecule is actually broken back down into CO2, and when enough accumulates, RuBisCo fixes it a second time! Compartmentalization allows efficient use of low concentrations of carbon dioxide in these specialized plants.
See http://www.youtube.com/watch?v=7ynX_F-SwNY (16:58) for further information.
Cacti and succulents such as the jade plant avoid water loss by fixing CO2 only at night. These plants close their stomata during the day and open them only in the cooler and more humid nighttime hours. Leaf structure differs slightly from that of C4 plants, but the fixation pathways are similar. The family of plants in which this pathway was discovered gives the pathway its name, Crassulacean Acid Metabolism, or CAM (Figure below). All three carbon fixation pathways lead to the Calvin cycle to build sugar.
See http://www.youtube.com/watch?v=xp6Zj24h8uA (8:37) for further information.
Even chemical reactions adapt to specific environments! Carbon fixation pathways vary among three groups. Temperate species (maple tree, left) use the C3 pathway. C4 species (corn, center) concentrate CO2 in a separate compartment to lessen water loss in hot bright climates. Desert plants (jade plant, right) fix CO2 only at night, closing stomata in the daytime to conserve water.
How Does the Calvin Cycle Store Energy in Sugar?
As Melvin Calvin discovered, carbon fixation is the first step of a cycle. Like an electron transport chain, the Calvin cycle, shown in Figure below, transfers energy in small, controlled steps. Each step pushes molecules uphill in terms of energy content. Recall that in the electron transfer chain, excited electrons lose energy to NADPH and ATP. In the Calvin cycle, NADPH and ATP formed in the light reactions lose their stored chemical energy to build glucose.
Use the Figure below to identify the major aspects of the process:
• the general cycle pattern
• the major reactants
• the products
Overview of the Calvin Cycle Pathway.
First, notice where carbon is fixed by the enzyme nicknamed RuBisCo. In C3, C4, and CAM plants, CO2 enters the cycle by joining with 5-carbon ribulose bisphosphate to form a 6-carbon intermediate, which splits (so quickly that it isn’t even shown!) into two 3-carbon molecules.
Now look for the points at which ATP and NADPH (made in the light reactions) add chemical energy (“Reduction” in the diagram) to the 3-carbon molecules. The resulting “half-sugars” can enter several different metabolic pathways. One recreates the original 5-carbon precursor, completing the cycle. A second combines two of the 3-carbon molecules to form glucose, universal fuel for life.
The cycle begins and ends with the same molecule, but the process combines carbon and energy to build carbohydrates – food for life.
So, how does photosynthesis store energy in sugar? Six “turns” of the Calvin cycle use chemical energy from ATP to combine six carbon atoms from six CO2 molecules with 12 “hot hydrogens” from NADPH. The result is one molecule of glucose, C6H12O6.
Summary
• The reactions of the Calvin cycle add carbon (from carbon dioxide in the atmosphere) to a simple five-carbon molecule called RuBP.
• These reactions use chemical energy from NADPH and ATP that were produced in the light reactions.
• The final product of the Calvin cycle is glucose.
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Use this resource to answer the questions that follow.
1. What molecule "starts" the Calvin cycle? What is transferred onto this molecule?
2. What happens to the energy from NADPH?
3. What is the first 6-carbon sugar to form during this process? What happens to this sugar?
Review
1. What happens during the carbon fixation step of the Calvin cycle?
2. What is special about RuBisCo?
3. What are stomata?
4. Explain what might happen if the third step of the Calvin cycle did not occur. Why?
5. What is the main final product of the Calvin cycle? How many turns of the Calvin cycle are needed to produce this product? | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/02%3A_Cell_Biology/2.22%3A__Calvin_Cycle.txt |
What is photosynthesis?
The process of using the energy in sunlight to make food (glucose). Is it really as simple as that? Of course not. As you have seen, photosynthesis includes many steps all conveniently condensed into one simple equation. In the five concepts describing photosynthesis, this process has been presented in an introductory fashion. Obviously, much more details could have been included, though those are beyond the scope of these concepts.
Photosynthesis
Summary
The following 10 points summarize photosynthesis.
• 6CO2 + 6H2O + Light Energy → C6H12O6 + 6O2
• Autotrophs store chemical energy in carbohydrate food molecules they build themselves. Most autotrophs make their "food" through photosynthesis using the energy of the sun.
• Photosynthesis occurs in the chloroplast, an organelle specific to plant cells.
• The light reactions of photosynthesis occur in the thylakoid membranes of the chloroplast.
• Electron carrier molecules are arranged in electron transport chains that produce ATP and NADPH, which temporarily store chemical energy.
• The light reactions capture energy from sunlight, which they change to chemical energy that is stored in molecules of NADPH and ATP.
• The light reactions also release oxygen gas as a waste product.
• The reactions of the Calvin cycle add carbon (from carbon dioxide in the atmosphere) to a simple five-carbon molecule called RuBP.
• The Calvin cycle reactions use chemical energy from NADPH and ATP that were produced in the light reactions.
• The final product of the Calvin cycle is glucose.
FAQs
• What is photosynthesis?
The process of using the energy in sunlight to make food (glucose). But of course it is much more complex than that simple statement. Photosynthesis is a multistep biochemical pathway that uses the energy in sunlight to fix carbon dioxide, transferring the energy into carbohydrates, and releasing oxygen in the process.
• What is NADPH?
Nicotinamide adenine dinucleotide phosphate, an energy carrier molecule produced in the light reactions of photosynthesis. NADPH is the reduced form of the electron acceptor NADP+. At the end of the light reactions, the energy from sunlight is transferred to NADP+, producing NADPH. This energy in NADPH is then used in the Calvin cycle.
• Where do the protons used in the light reactions come from?
The protons used in the light reactions come from photolysis, the splitting of water, in which H2O molecules are broken into hydrogen ions, electrons, and oxygen atoms. In addition, the energy from sunlight is used to pump protons into the thylakoid lumen during the first electron transport chain, forming a chemiosmotic gradient.
• How do you distinguish between the Calvin cycle and the Krebs cycle?
The Calvin cycle is part of the light-independent reactions of photosynthesis. The Calvin cycle uses ATP and NADPH. The Krebs cycle is part of cellular respiration. This cycle makes ATP and NAPH.
• Do photosynthesis and cellular respiration occur at the same time in a plant?
Yes. Photosynthesis occurs in the chloroplasts, whereas cellular respiration occurs in the mitochondria. Photosynthesis makes glucose and oxygen, which are then used as the starting products for cellular respiration. Cellular respiration makes carbon dioxide and water (and ATP), which are the starting products (together with sunlight) for photosynthesis.
Common Misconceptions
• A common student misconception is that plants photosynthesize only during daylight and conduct cellular respiration only at night. Some teaching literature even states this. Though it is true the light reactions can only occur when the sun is out, cellular respiration occurs continuously in plants, not just at night.
• The “dark reactions” of photosynthesis are a misnomer that often leads students to believe that photosynthetic carbon fixation occurs at night. This is not true. It is preferable to use the term Calvin cycle or light-independent reactions instead of dark reactions.
• Though the final product of photosynthesis is glucose, the glucose is conveniently stored as starch. Starch is approximated as (C6H10O5)n, where n is in the thousands. Starch is formed by the condensation of thousands of glucose molecules.
Explore More
Use this resource to answer the questions that follow.
1. Why is it more appropriate to say chloroplasts, rather than chlorophyll, are necessary for photosynthesis?
2. Why is much more than six water molecules necessary for photosynthesis?
3. Do plants absorb any green light? Explain your answer. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/02%3A_Cell_Biology/2.23%3A_Photosynthesis_Summary.txt |
Is it possible to live in temperatures over 175°F?
It is if you're a Pompeii worm. The Pompeii worm, the most heat-tolerant animal on Earth, lives in the deep ocean at super-heated hydrothermal vents. Covering this deep-sea worm's back is a fleece of bacteria. These microbes contain all the genes necessary for life in extreme environments.
Chemosynthesis
Why do bacteria that live deep below the ocean’s surface rely on chemical compounds instead of sunlight for energy to make food?
Most autotrophs make food by photosynthesis, but this isn’t the only way that autotrophs produce food. Some bacteria make food by another process, which uses chemical energy instead of light energy. This process is called chemosynthesis. In chemosynthesis, one or more carbon molecules (usually carbon dioxide or methane, CH4) and nutrients is converted into organic matter, using the oxidation of inorganic molecules (such as hydrogen gas, hydrogen sulfide (H2S) or ammonia (NH3)) or methane as a source of energy, rather than sunlight. In hydrogen sulfide chemosynthesis, in the presence of carbon dioxide and oxygen,carbohydrates (CH2O) can be produced:
CO2 + O2 + 4H2S → CH2O + 4S + 3H2O
Many organisms that use chemosynthesis are extremophiles, living in harsh conditions, such as in the absence of sunlight and a wide range of water temperatures, some approaching the boiling point. Some chemosynthetic bacteria live around deep-ocean vents known as “black smokers.” Compounds such as hydrogen sulfide, which flow out of the vents from Earth’s interior, are used by the bacteria for energy to make food. Consumers that depend on these bacteria to produce food for them include giant tubeworms, like those pictured in Figure below. These organisms are known as chemoautotrophs. Many chemosynthetic microorganisms are consumed by other organisms in the ocean, and symbiotic associations between these organisms and respiring heterotrophs are quite common.
Tubeworms deep in the Galapagos Rift get their energy from chemosynthetic bacteria. Tubeworms have no mouth, eyes or stomach. Their survival depends on a symbiotic relationship with the billions of bacteria that live inside them. These bacteria convert the chemicals that shoot out of the hydrothermal vents into food for the worm.
Summary
• Chemosynthesis is a process in which some organisms use chemical energy instead of light energy to produce "food."
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Use this resource to answer the questions that follow.
1. What is chemosynthesis?
2. What are hydrothermal vents?
3. Why do hydrothermal vent regions have high biomass?
4. What type of organisms are found in a hydrothermal vent region?
Review
1. What is chemosynthesis?
2. Why do bacteria that live deep below the ocean’s surface rely on chemical compounds instead of sunlight for energy to make food?
3. Describe the habitats of extremophiles?
2.25: Anaerobic vs Aerobic Respiration
How long can you hold your breath?
With or without air? In terms of producing energy, that is the key question. Can cellular respiration occur without air? It can, but it does have limitations.
The Presence of Oxygen
There are two types of cellular respiration (see Cellular Respiration concept): aerobic and anaerobic. One occurs in the presence of oxygen (aerobic), and one occurs in the absence of oxygen (anaerobic). Both begin with glycolysis - the splitting of glucose.
Glycolysis (see "Glycolysis" concept) is an anaerobic process - it does not need oxygen to proceed. This process produces a minimal amount of ATP. The Krebs cycle and electron transport do need oxygen to proceed, and in the presence of oxygen, these process produce much more ATP than glycolysis alone.
Scientists think that glycolysis evolved before the other stages of cellular respiration. This is because the other stages need oxygen, whereas glycolysis does not, and there was no oxygen in Earth’s atmosphere when life first evolved about 3.5 to 4 billion years ago. Cellular respiration that proceeds without oxygen is called anaerobic respiration.
Then, about 2 or 3 billion years ago, oxygen was gradually added to the atmosphere by early photosynthetic bacteria (cyanobacteria). After that, living things could use oxygen to break down glucose and make ATP. Today, most organisms make ATP with oxygen. They follow glycolysis with the Krebs cycle and electron transport to make more ATP than by glycolysis alone. Cellular respiration that proceeds in the presence of oxygen is called aerobic respiration.
Summary
• Cellular respiration always begins with glycolysis, which can occur either in the absence or presence of oxygen.
• Cellular respiration that proceeds in the absence of oxygen is anaerobic respiration.
• Cellular respiration that proceeds in the presence of oxygen is aerobic respiration.
• Anaerobic respiration evolved prior to aerobic respiration.
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Use this resource to answer the questions that follow.
1. What is the main difference between aerobic and anaerobic respiration?
2. What cells perform anaerobic respiration?
3. Compare the amount of ATP released by both aerobic and anaerobic respiration.
4. What are the two stages of anaerobic respiration?
Review
1. Define aerobic and anaerobic respiration.
2. What process is common to both aerobic and anaerobic respiration?
3. Why do scientists think that glycolysis evolved before the other stages of cellular respiration? | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/02%3A_Cell_Biology/2.24%3A_Chemosynthesis.txt |
Why eat?
Because we're hungry. Not necessarily. But biologically speaking…we eat to get energy. The food we eat is broken down, the glucose extracted, and that energy is converted into ATP.
Cellular Respiration
What happens to the energy stored in glucose during photosynthesis? How do living things make use of this stored energy? The answer is cellular respiration. This process releases theenergy in glucose to make ATP (adenosine triphosphate), the molecule that powers all the work of cells.
An introduction to cellular respiration can be viewed at http://www.youtube.com/watch?v=2f7YwCtHcgk (14:19).
Stages of Cellular Respiration
Cellular respiration involves many chemical reactions. The reactions can be summed up in this equation:
C6H12O6 + 6O2 → 6CO2 + 6H2O + Chemical Energy (in ATP)
The reactions of cellular respiration can be grouped into three stages: glycolysis (stage 1), the Krebs cycle, also called the citric acid cycle (stage 2), and electron transport (stage 3).Figure below gives an overview of these three stages, which are further discussed in the concepts that follow. Glycolysis occurs in the cytosol of the cell and does not require oxygen, whereas the Krebs cycle and electron transport occur in the mitochondria and do require oxygen.
Cellular respiration takes place in the stages shown here. The process begins with a molecule of glucose, which has six carbon atoms. What happens to each of these atoms of carbon?
Structure of the Mitochondrion: Key to Aerobic Respiration
The structure of the mitochondrion is key to the process of aerobic (in the presence of oxygen) cellular respiration, especially the Krebs cycle and electron transport. A diagram of a mitochondrion is shown in Figure below.
The structure of a mitochondrion is defined by an inner and outer membrane. This structure plays an important role in aerobic respiration.
As you can see from Figure above, a mitochondrion has an inner and outer membrane. The space between the inner and outer membrane is called the intermembrane space. The space enclosed by the inner membrane is called the matrix. The second stage of cellular respiration, the Krebs cycle, takes place in the matrix. The third stage, electron transport, takes place on the inner membrane.
Summary
• Cellular respiration takes the energy stored in glucose and transfers it to ATP.
• Cellular respiration has three stages: glycolysis: the Krebs cycle and electron transport.
• The inner and outer membranes of the mitochondrion play an important roles in aerobic respiration.
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Explore More I
Use this resource to answer the questions that follow.
1. What are the three stages of cellular respiration?
2. What is the outcome of glycolysis?
3. What is produced during the Krebs cycle?
4. What occurs during the electron transport system?
Review
1. Define cellular respiration.
2. What are the three stages of cellular respiration?
3. Describe the structure of the mitochondrion and discuss the importance of this structure in cellular respiration.
4. Assume that a new species of organism has been discovered. Scientists have observed its cells under a microscope and determined that they lack mitochondria. What type of cellular respiration would you predict that the new species uses? Explain your prediction.
5. When you exhale onto a cold window pane, water vapor in your breath condenses on the glass. Where does the water vapor come from? | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/02%3A_Cell_Biology/2.26%3A_Cellular_Respiration.txt |
How do you slice a molecule of glucose in half?
With sharp knives? Not really. But you essentially slice it in half through glycolysis. This is an extremely important part of cellular respiration. It happens all the time, both with and without oxygen. And in the process, transfers some energy to ATP.
Cellular Respiration Stage I: Glycolysis
The first stage of cellular respiration is glycolysis. It does not require oxygen, and it does not take place in the mitochondrion - it takes place in the cytosol of the cytoplasm.
When was the last time you enjoyed yogurt on your breakfast cereal, or had a tetanus shot? These experiences may appear unconnected, but both relate to bacteria which do not use oxygen to make ATP. In fact, tetanus bacteria cannot survive if oxygen is present. However,Lactobacillus acidophilus (bacteria which make yogurt) and Clostridium tetani (bacteria which cause tetanus or lockjaw) share with nearly all organisms the first stage of cellular respiration, glycolysis. Because glycolysis is universal, whereas aerobic (oxygen-requiring) cellular respiration is not, most biologists consider it to be the most fundamental and primitive pathway for making ATP.
Splitting Glucose
The word glycolysis means “glucose splitting,” which is exactly what happens in this stage.Enzymes split a molecule of glucose into two molecules of pyruvate (also known as pyruvic acid). This occurs in several steps, as shown in Figure below. You can watch an animation of the steps of glycolysis at this link: http://www.youtube.com/watch?v=6JGXayUyNVw.
In glycolysis, glucose (C6) is split into two 3-carbon (C3) pyruvate molecules. This releases energy, which is transferred to ATP. How many ATP molecules are made during this stage of cellular respiration?
Results of Glycolysis
Energy is needed at the start of glycolysis to split the glucose molecule into two pyruvate molecules. These two molecules go on to stage II of cellular respiration. The energy to split glucose is provided by two molecules of ATP. As glycolysis proceeds, energy is released, and the energy is used to make four molecules of ATP. As a result, there is a net gain of two ATP molecules during glycolysis. During this stage, high-energy electrons are also transferred to molecules of NAD+ to produce two molecules of NADH, another energy-carrying molecule. NADH is used in stage III of cellular respiration to make more ATP.
A summary of glycolysis can be viewed at http://www.youtube.com/watch?v=FE2jfTXAJHg.
Summary
• The first stage of cellular respiration is glycolysis. It does not require oxygen.
• During glycolysis, one glucose molecule is split into two pyruvate molecules, using 2 ATP while producing 4 ATP and 2 NADH molecules.
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Explore More I
Use this resource to answer the questions that follow.
1. What is the meaning of glycolysis?
2. What is used in step 1 of glycolysis?
3. What are isomers?
4. What is used in step 3 of glycolysis?
5. How many carbon atoms are in one glyceraldehyde phosphate?
6. What is produced in step 6?
7. What is produced in step 7?
8. What is produced in step 10?
9. How many ATPs are used and produced during glycolysis?
Review
1. What is glycolysis?
2. Describe what happens during glycolysis. How many ATP and NADH molecules are gained during this stage?
3. Defend this statement: ‘‘Glycolysis is a universal and ancient pathway for making ATP’’. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/02%3A_Cell_Biology/2.27%3A_Glycolysis.txt |
What type of acid do these fruits contain?
Citric acid. Citric acid is also the first product formed in the Krebs cycle, and therefore this acid occurs in the metabolism of virtually all living things.
Cellular Respiration Stage II: The Krebs Cycle
Recall that glycolysis, stage I of cellular respiration, produces two molecules of pyruvate. These molecules enter the matrix of a mitochondrion, where they start the Krebs cycle. The reactions that occur next are shown in Figure below. You can watch an animated version at this link: http://www.youtube.com/watch?v=p-k0biO1DT8.
The Krebs cycle starts with pyruvic acid from glycolysis. Each small circle in the diagram represents one carbon atom. For example, citric acid is a six carbon molecule, and OAA (oxaloacetate) is a four carbon molecule. Follow what happens to the carbon atoms as the cycle proceeds. In one turn through the cycle, how many molecules are produced of ATP? How many molecules of NADH and FADH2 are produced?
Before the Krebs cycle begins, pyruvic acid, which has three carbon atoms, is split apart and combined with an enzyme known as CoA, which stands for coenzyme A. The product of this reaction is a two-carbon molecule called acetyl-CoA. The third carbon from pyruvic acid combines with oxygen to form carbon dioxide, which is released as a waste product. High-energy electrons are also released and captured in NADH.
Steps of the Krebs Cycle
The Krebs cycle itself actually begins when acetyl-CoA combines with a four-carbon molecule called OAA (oxaloacetate) (see Figure above). This produces citric acid, which has six carbonatoms. This is why the Krebs cycle is also called the citric acid cycle.
After citric acid forms, it goes through a series of reactions that release energy. The energy is captured in molecules of NADH, ATP, and FADH2, another energy-carrying compound. Carbon dioxide is also released as a waste product of these reactions.
The final step of the Krebs cycle regenerates OAA, the molecule that began the Krebs cycle. This molecule is needed for the next turn through the cycle. Two turns are needed because glycolysis produces two pyruvic acid molecules when it splits glucose. Watch the OSU band present the Krebs cycle: http://www.youtube.com/watch?v=FgXnH087JIk.
Results of the Krebs Cycle
After the second turn through the Krebs cycle, the original glucose molecule has been broken down completely. All six of its carbon atoms have combined with oxygen to form carbon dioxide. The energy from its chemical bonds has been stored in a total of 16 energy-carrier molecules. These molecules are:
• 4 ATP (including 2 from glycolysis)
• 10 NADH (including 2 from glycolysis)
• 2 FADH2
The Krebs cycle is reviewed at http://www.youtube.com/watch?v=juM2ROSLWfw.
Summary
• The Krebs cycle is the second stage of cellular respiration.
• During the Krebs cycle, energy stored in pyruvate is transferred to NADH and FADH2, and some ATP is produced.
• See the Krebs Cycle at http://johnkyrk.com/krebs.html for a detailed summary.
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Use this resource to answer the questions that follow.
• The Citric Acid Cycle at virtuallabs.stanford.edu/other/biochem/TCA.swf.
1. Where does the Krebs cycle occur in the cell?
2. What is the first product of this cycle?
3. How many reactions does it take to complete the cycle?
4. How many NADHs and FADH2s are produced during the Krebs cycle?
Review
1. What is the Krebs cycle?
2. What are the products of the Krebs cycle?
3. Explain why two turns of the Krebs cycle are needed for each molecule of glucose. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/02%3A_Cell_Biology/2.28%3A_Krebs_Cycle.txt |
Train, truck, boat or plane?
Ways to transport. To make ATP, energy must be ‘‘transported’’ - first from glucose to NADH, and then somehow passed to ATP. How is this done? With an electron transport chain.
Cellular Respiration Stage III: Electron Transport
Electron transport is the final stage of aerobic respiration. In this stage, energy from NADH and FADH2, which result from the Krebs cycle, is transferred to ATP. Can you predict how this happens? (Hint: How does electron transport occur in photosynthesis?)
See http://www.youtube.com/watch?v=1engJR_XWVU for an overview of the electron transport chain.
Transporting Electrons
High-energy electrons are released from NADH and FADH2, and they move along electron transport chains, like those used in photosynthesis. The electron transport chains are on the inner membrane of the mitochondrion. As the high-energy electrons are transported along the chains, some of their energy is captured. This energy is used to pump hydrogen ions(from NADH and FADH2) across the inner membrane, from the matrix into the intermembrane space. Electron transport in a mitochondrion is shown in Figure below.
Electron-transport chains on the inner membrane of the mitochondrion carry out the last stage of cellular respiration.
Making ATP
The pumping of hydrogen ions across the inner membrane creates a greater concentration of the ions in the intermembrane space than in the matrix. This chemiosmotic gradient causes the ions to flow back across the membrane into the matrix, where their concentration is lower.ATP synthase acts as a channel protein, helping the hydrogen ions cross the membrane. It also acts as an enzyme, forming ATP from ADP and inorganic phosphate. After passing through the electron-transport chain, the “spent” electrons combine with oxygen to formwater. This is why oxygen is needed; in the absence of oxygen, this process cannot occur.
How much ATP is produced? The two NADH produced in the cytoplasm produces 2 to 3 ATP each (4 to 6 total) by the electron transport system, the 8 NADH produced in the mitochondriaproduces three ATP each (24 total), and the 2 FADH2 adds its electrons to the electron transport system at a lower level than NADH, so they produce two ATP each (4 total). This results in the formation of 34 ATP during the electron transport stage.
A summary of this process can be seen at the following sites: http://www.youtube.com/watch?v=fgCcFXUZRk (17:16) and http://www.youtube.com/watch?v=W_Q17tqw_7A (4:59).
Summary
• Electron transport is the final stage of aerobic respiration. In this stage, energy from NADH and FADH2 is transferred to ATP.
• During electron transport, energy is used to pump hydrogen ions across the mitochondrial inner membrane, from the matrix into the intermembrane space.
• A chemiosmotic gradient causes hydrogen ions to flow back across the mitochondrial membrane into the matrix, through ATP synthase, producing ATP.
• See Mitochondria at http://johnkyrk.com/mitochondrion.html for a detailed summary.
Explore More
Use this resource to answer the questions that follow.
1. What happens as electrons are passed along the ETC from NADH to oxygen?
2. What happens as electrons are passed along the ETC from FADH2 to oxygen?
3. What is the significance of the proton gradient within the mitochondria?
Review
1. Summarize the overall task of Stage III of aerobic respiration.
2. Explain the chemiosmotic gradient.
3. What is the maximum number of ATP molecules that can be produced during the electron transport stage of aerobic respiration? | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/02%3A_Cell_Biology/2.29%3A_Electron_Transport.txt |
When you combine grapes and yeast, what have you begun to make?
Wine. It may be slightly more complicated than that, but you need to start with grapes and yeast, and allow a natural fermentation process to occur. Essentially, this is respiration without oxygen.
Anaerobic Respiration: Fermentation
Today, most living things use oxygen to make ATP from glucose. However, many living things can also make ATP without oxygen. This is true of some plants and fungi and also of many bacteria. These organisms use aerobic respiration when oxygen is present, but when oxygen is in short supply, they use anaerobic respiration instead. Certain bacteria can only useanaerobic respiration. In fact, they may not be able to survive at all in the presence of oxygen.
An important way of making ATP without oxygen is called fermentation. It involves glycolysis, but not the other two stages of aerobic respiration. Many bacteria and yeasts carry out fermentation. People use these organisms to make yogurt, bread, wine, and biofuels. Human muscle cells also use fermentation. This occurs when muscle cells cannot get oxygen fast enough to meet their energy needs through aerobic respiration.
There are two types of fermentation: lactic acid fermentation and alcoholic fermentation. Both types of fermentation are described below. You can also watch animations of both types at this link: http://www.cst.cmich.edu/users/schul1te/animations/fermentation.swf.
Lactic Acid Fermentation
In lactic acid fermentation, pyruvic acid from glycolysis changes to lactic acid. This is shown in Figure below. In the process, NAD+ forms from NADH. NAD+, in turn, lets glycolysiscontinue. This results in additional molecules of ATP. This type of fermentation is carried out by the bacteria in yogurt. It is also used by your own muscle cells when you work them hard and fast.
Lactic acid fermentation produces lactic acid and NAD+. The NAD+ cycles back to allow glycolysis to continue so more ATP is made. Each circle represents a carbon atom.
Did you ever run a race and notice that your muscles feel tired and sore afterward? This is because your muscle cells used lactic acid fermentation for energy. This causes lactic acid to build up in the muscles. It is the buildup of lactic acid that makes the muscles feel tired and sore.
Alcoholic Fermentation
In alcoholic fermentation, pyruvic acid changes to alcohol and carbon dioxide. This is shown in Figure below. NAD+ also forms from NADH, allowing glycolysis to continue making ATP. This type of fermentation is carried out by yeasts and some bacteria. It is used to make bread, wine, and biofuels.
Alcoholic fermentation produces ethanol and NAD+. The NAD+ allows glycolysis to continue making ATP.
Have your parents ever put corn in the gas tank of their car? They did if they used gas containing ethanol. Ethanol is produced by alcoholic fermentation of the glucose in corn or other plants. This type of fermentation also explains why bread dough rises. Yeasts in bread dough use alcoholic fermentation and produce carbon dioxide gas. The gas forms bubbles in the dough, which cause the dough to expand. The bubbles also leave small holes in the bread after it bakes, making the bread light and fluffy. Do you see the small holes in the slice of bread in Figure below?
The small holes in bread are formed by bubbles of carbon dioxide gas. The gas was produced by alcoholic fermentation carried out by yeast.
Gut Fermentation
Behind every fart is an army of gut bacteria undergoing some crazy biochemistry. These bacteria break down the remains of digested food through fermentation, creating gas in the process. Learn what these bacteria have in common with beer brewing athttp://youtu.be/R1kxajH629A?list=PLzMhsCgGKd1hoofiKuifwy6qRXZs7NG6a.
Summary
• Fermentation is making ATP without oxygen, which involves glycolysis only.
• Fermentation recycles NAD+, and produces 2 ATPs.
• In lactic acid fermentation, pyruvic acid from glycolysis changes to lactic acid. This type of fermentation is carried out by the bacteria in yogurt, and by your own muscle cells.
• In alcoholic fermentation, pyruvic acid changes to alcohol and carbon dioxide. This type of fermentation is carried out by yeasts and some bacteria.
Explore More
Use this resource to answer the questions that follow.
1. What is fermentation?
2. Why do yeast ferment?
3. Name four food produced using fermentation.
4. What happens in ethanol fermentation?
5. When does fermentation occur in animals? What type of fermentation is this?
Review
1. What is fermentation?
2. Name two types of fermentation.
3. What is the main advantage of aerobic respiration? Of anaerobic respiration?
4. What process produces fuel for motor vehicles from living plant products? What is the waste product of this process?
5. Compare and contrast lactic acid fermentation and alcoholic fermentation. Include examples of organisms that use each type of fermentation.
2.31: Anaerobic and Aerobic Respiration
Why oxygen?
Oxygen is the final electron acceptor at the end of the electron transport chain of aerobic respiration. In the absence of oxygen, only a few ATP are produced from glucose. In the presence of oxygen, many more ATP are made.
Aerobic vs. Anaerobic Respiration: A Comparison
Aerobic respiration, which takes place in the presence of oxygen, evolved after oxygen was added to Earth’s atmosphere. This type of respiration is useful today because the atmosphere is now 21% oxygen. However, some anaerobic organisms that evolved before the atmosphere contained oxygen have survived to the present. Therefore, anaerobic respiration, which takes place without oxygen, must also have advantages.
Advantages of Aerobic Respiration
A major advantage of aerobic respiration is the amount of energy it releases. Without oxygen, organisms can split glucose into just two molecules of pyruvate. This releases only enough energy to make two ATP molecules. With oxygen, organisms can break down glucose all the way to carbon dioxide. This releases enough energy to produce up to 38 ATP molecules. Thus, aerobic respiration releases much more energy than anaerobic respiration.
The amount of energy produced by aerobic respiration may explain why aerobic organisms came to dominate life on Earth. It may also explain how organisms were able to become multicellular and increase in size.
Advantages of Anaerobic Respiration
One advantage of anaerobic respiration is obvious. It lets organisms live in places where there is little or no oxygen. Such places include deep water, soil, and the digestive tracts of animals such as humans (see Figure below).
E. coli bacteria are anaerobic bacteria that live in the human digestive tract.
Another advantage of anaerobic respiration is its speed. It produces ATP very quickly. For example, it lets your muscles get the energy they need for short bursts of intense activity (seeFigure below). Aerobic respiration, on the other hand, produces ATP more slowly.
The muscles of these hurdlers need to use anaerobic respiration for energy. It gives them the energy they need for the short-term, intense activity of this sport.
Summary
• Aerobic respiration produces much more ATP than anaerobic respiration.
• Anaerobic respiration occurs more quickly than aerobic respiration.
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Use this resource to answer the questions that follow.
1. What is the significance of oxygen during cellular respiration?
2. Which is more efficient: aerobic or anaerobic respiration?
3. What is the difference in ATP production between aerobic and anaerobic respiration?
4. Why was anaerobic respiration sufficient when it first evolved?
Review
1. What is the main advantage of aerobic respiration? Of anaerobic respiration?
2. Tanya is on the high school track team and runs the 100-meter sprint. Marissa is on the cross-country team and runs 5-kilometer races. Explain which type of respiration the muscle cells in each runner’s legs use. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/02%3A_Cell_Biology/2.30%3A_Fermentation.txt |
Where do cells come from?
No matter what the cell, all cells come from preexisting cells through the process of cell division. The cell may be the simplest bacterium or a complex muscle, bone, or blood cell. The cell may comprise the whole organism, or be just one cell of trillions.
Cell Division
You consist of a great many cells, but like all other organisms, you started life as a single cell. How did you develop from a single cell into an organism with trillions of cells? The answer is cell division. After cells grow to their maximum size, they divide into two new cells. These new cells are small at first, but they grow quickly and eventually divide and produce more new cells. This process keeps repeating in a continuous cycle.
Cell division is the process in which one cell, called the parent cell, divides to form two new cells, referred to as daughter cells. How this happens depends on whether the cell is prokaryotic or eukaryotic.
Cell division is simpler in prokaryotes than eukaryotes because prokaryotic cells themselves are simpler. Prokaryotic cells have a single circular chromosome, no nucleus, and few other organelles. Eukaryotic cells, in contrast, have multiple chromosomes contained within a nucleus, and many other organelles. All of these cell parts must be duplicated and then separated when the cell divides. A chromosome is a molecule of DNA, and will be the focus of a subsequent concept.
Cell Division in Prokaryotes
Most prokaryotic cells divide by the process of binary fission. A bacterial cell dividing this way is depicted in Figure below. You can also watch an animation of binary fission at this link:http://en.Wikipedia.org/wiki/File:Binary_fission_anim.gif.
Binary Fission in a Bacterial Cell. Cell division is relatively simple in prokaryotic cells. The two cells are dividing by binary fission. Green and orange lines indicate old and newly-generated bacterial cell walls, respectively. Eventually the parent cell will pinch apart to form two identical daughter cells. Left, growth at the center of bacterial body. Right, apical growth from the ends of the bacterial body.
Binary fission can be described as a series of steps, although it is actually a continuous process. The steps are described below and also illustrated in Figure below. They include DNA replication, chromosome segregation, and finally the separation into two daughter cells.
• Step 1: DNA Replication. Just before the cell divides, its DNA is copied in a process called DNA replication. This results in two identical chromosomes instead of just one. This step is necessary so that when the cell divides, each daughter cell will have its own chromosome.
• Step 2: Chromosome Segregation. The two chromosomes segregate, or separate, and move to opposite ends (known as "poles") of the cell. This occurs as each copy of DNA attaches to different parts of the cell membrane.
• Step 3: Separation. A new plasma membrane starts growing into the center of the cell, and the cytoplasm splits apart, forming two daughter cells. As the cell begins to pull apart, the new and the original chromosomes are separated. The two daughter cells that result are genetically identical to each other and to the parent cell. New cell wall must also form around the two cells.
Steps of Binary Fission. Prokaryotic cells divide by binary fission. This is also how many single-celled organisms reproduce.
Cell Division in Eukaryotes
Cell division is more complex in eukaryotes than prokaryotes. Prior to dividing, all the DNA in a eukaryotic cell’s multiple chromosomes is replicated. Its organelles are also duplicated. Then, when the cell divides, it occurs in two major steps:
1. The first step is mitosis, a multi-phase process in which the nucleus of the cell divides. During mitosis, the nuclear membrane breaks down and later reforms. The chromosomes are also sorted and separated to ensure that each daughter cell receives a diploid number (2 sets) of chromosomes. In humans, that number of chromosomes is 46 (23 pairs). Mitosis is described in greater detail in a subsequent concept.
2. The second major step is cytokinesis. As in prokaryotic cells, the cytoplasm must divide. Cytokinesis is the division of the cytoplasm in eukaryotic cells, resulting in two genetically identical daughter cells.
Summary
• Cell division is part of the life cycle of virtually all cells. Cell division is the process in which one cell divides to form two new cells.
• Most prokaryotic cells divide by the process of binary fission.
• In eukaryotes, cell division occurs in two major steps: mitosis and cytokinesis.
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Use this resource to answer the questions that follow.
1. Cell division has how many steps? What are they?
2. How do prokaryotic cells divide? How do eukaryotic cells divide?
3. Describe the process of binary fission.
4. Compare the cells before and after the mitotic division.
5. What is cytokinesis?
Review
1. Describe binary fission.
2. What is mitosis?
3. Contrast cell division in prokaryotes and eukaryotes. Why are the two types of cell division different? | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/02%3A_Cell_Biology/2.32%3A_Cell_Division.txt |
What is a cell's life like?
The eukaryotic cell spends most of its "life" in interphase of the cell cycle, which can be subdivided into the three phases, G1, S and G2. During interphase, the cell does what it is supposed to do. Though cells have many common functions, such as DNA replication, they also have certain specific functions. That is, during the life of a heart cell, the cell would obviously perform certain different activities than a kidney cell or a liver cell.
The Cell Cycle
Cell division is just one of several stages that a cell goes through during its lifetime. The cell cycle is a repeating series of events that include growth, DNA synthesis, and cell division. The cell cycle in prokaryotes is quite simple: the cell grows, its DNA replicates, and the cell divides. In eukaryotes, the cell cycle is more complicated.
The Eukaryotic Cell Cycle
The diagram in Figure below represents the cell cycle of a eukaryotic cell. As you can see, the eukaryotic cell cycle has several phases. The mitotic phase (M) actually includes both mitosis and cytokinesis. This is when the nucleus and then the cytoplasm divide. The other three phases (G1, S, and G2) are generally grouped together as interphase. During interphase, the cell grows, performs routine life processes, and prepares to divide. These phases are discussed below. You can watch a eukaryotic cell going through these phases of the cell cycle at the following link: http://www.cellsalive.com/cell_cycle.htm.
Eukaryotic Cell Cycle. This diagram represents the cell cycle in eukaryotes. The First Gap, Synthesis, and Second Gap phases make up interphase (I). The M (mitotic) phase includes mitosis and cytokinesis. After the M phase, two cells result.
Interphase
Interphase of the eukaryotic cell cycle can be subdivided into the following three phases, which are represented in Figure above:
• Growth Phase 1 (G1): during this phase, the cell grows rapidly, while performing routine metabolic processes. It also makes proteins needed for DNA replication and copies some of its organelles in preparation for cell division. A cell typically spends most of its life in this phase. This phase is sometimes referred to as Gap 1.
• Synthesis Phase (S): during this phase, the cell’s DNA is copied in the process of DNA replication.
• Growth Phase 2 (G2): during this phase, the cell makes final preparations to divide. For example, it makes additional proteins and organelles. This phase is sometimes referred to as Gap 2.
Control of the Cell Cycle
If the cell cycle occurred without regulation, cells might go from one phase to the next before they were ready. What controls the cell cycle? How does the cell know when to grow, synthesize DNA, and divide? The cell cycle is controlled mainly by regulatory proteins. These proteins control the cycle by signaling the cell to either start or delay the next phase of the cycle. They ensure that the cell completes the previous phase before moving on. Regulatory proteins control the cell cycle at key checkpoints, which are shown in Figure below. There are a number of main checkpoints.
• The G1 checkpoint, just before entry into S phase, makes the key decision of whether the cell should divide.
• The S checkpoint determines if the DNA has been replicated properly.
• The mitotic spindle checkpoint occurs at the point in metaphase where all thechromosomes should have aligned at the mitotic plate.
Checkpoints in the eukaryotic cell cycle ensure that the cell is ready to proceed before it moves on to the next phase of the cycle.
Cancer and the Cell Cycle
Cancer is a disease that occurs when the cell cycle is no longer regulated. This may happen because a cell’s DNA becomes damaged. Damage can occur due to exposure to hazards such as radiation or toxic chemicals. Cancerous cells generally divide much faster than normal cells. They may form a mass of abnormal cells called a tumor (see Figure below). The rapidly dividing cells take up nutrients and space that normal cells need. This can damage tissues and organs and eventually lead to death.
These cells are cancer cells, growing out of control and forming a tumor.
Cancer is discussed in the video at http://www.youtube.com/watch?v=RZhL7LDPk8w.
Summary
• The cell cycle is a repeating series of events that cells go through. It includes growth, DNA synthesis, and cell division. In eukaryotic cells, there are two growth phases, and cell division includes mitosis.
• The cell cycle is controlled by regulatory proteins at three key checkpoints in the cycle. The proteins signal the cell to either start or delay the next phase of the cycle.
• Cancer is a disease that occurs when the cell cycle is no longer regulated. Cancer cells grow rapidly and may form a mass of abnormal cells called a tumor.
• See the Cell Cycle at http://www.cellsalive.com/cell_cycle.htm for a detailed summary.
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Use this resources to answer the questions that follow.
• The Cell Cycle at outreach.mcb.harvard.edu/anim.../cellcycle.swf.
1. When does the cell's genetic material replicate?
2. What is G2? What happens during G2?
3. What occurs after the G2 phase?
4. What is G1?
Review
1. Identify the phases of the eukaryotic cell cycle.
2. What happens during interphase?
3. Define cancer.
4. Cells go through a series of events that include growth, DNA synthesis, and cell division. Why are these events best represented by a cycle diagram?
5. Explain how the cell cycle is regulated.
6. Why is DNA replication essential to the cell cycle? | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/02%3A_Cell_Biology/2.33%3A_Cell_Cycle.txt |
How is it assured that every cell in your body has the same DNA?
Chromosomes, like those shown here, must form prior to cell division, to ensure that each daughter cell receives a complete set of genetic material. Essentially, each new cell receives half of each "X-shaped" chromosome.
Chromosomes
In eukaryotic cells, the nucleus divides before the cell itself divides. The process in which the nucleus divides is called mitosis. Before mitosis occurs, a cell’s DNA is replicated. This is necessary so that each daughter cell will have a complete copy of the genetic material from the parent cell. How is the replicated DNA sorted and separated so that each daughter cell gets a complete set of the genetic material? To understand how this happens, you need to know more about chromosomes.
Chromosomes are coiled structures made of DNA and proteins. Chromosomes are the form of the genetic material of a cell during cell division. It is this coiled structure that ensures proper segregation of the chromosomes during cell division. During other phases of the cell cycle, DNA is not coiled into chromosomes. Instead, it exists as a grainy material calledchromatin.
The vocabulary of DNA: chromosomes, chromatids, chromatin, transcription, translation, and replication is discussed at http://www.youtube.com/watch?v=s9HPNwXd9fk (18:23).
Chromatids and the Centromere
DNA condenses and coils into the familiar X-shaped form of a chromosome, shown in Figure below, only after it has replicated. (You can watch DNA coiling into a chromosome at the link below.) Because DNA has already replicated, each chromosome actually consists of two identical copies. The two copies are called sister chromatids. They are attached to one another at a region called the centromere. A remarkable animation can be viewed at http://www.hhmi.org/biointeractive/m...ing_vo2-sm.mov.
Chromosome. After DNA replicates, it forms chromosomes like the one shown here.
Chromosomes and Genes
The DNA of a chromosome is encoded with genetic instructions for making proteins. These instructions are organized into units called genes. Most genes contain the instructions for a single protein. There may be hundreds or even thousands of genes on a single chromosome.
Human Chromosomes
Human cells normally have two sets of chromosomes, one set inherited from each parent. There are 23 chromosomes in each set, for a total of 46 chromosomes per cell. Each chromosome in one set is matched by a chromosome of the same type in the other set, so there are actually 23 pairs of chromosomes per cell. Each pair consists of chromosomes of the same size and shape that also contain the same genes. The chromosomes in a pair are known as homologous chromosomes.
Summary
• Chromosomes are coiled structures made of DNA and proteins.
• Chromosomes form after DNA replicates; prior to replication, DNA exists as chromatin.
• Chromosomes contain genes, which code for proteins.
• Human cells normally have 46 chromosomes, made up of two sets of chromosomes, one set inherited from each parent.
• See Chromosomes at http://johnkyrk.com/chromosomestructure.html for a detailed summary.
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Use this resource to answer the questions that follow.
1. What is a chromosome? What makes up a chromosome?
2. How many chromosomes do people usually have?
3. Can changes in the number of chromosomes affect health and development?
Review
1. What are chromosomes? When do they form?
2. Identify the chromatids and the centromere of a chromosome.
3. Explain how chromosomes are related to chromatin. Why are chromosomes important for mitosis?
4. How many chromosomes are in a normal human cell? | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/02%3A_Cell_Biology/2.34%3A_Chromosomes.txt |
What is meant by the "division of the nucleus"?
What do you think this colorful picture shows? If you guessed that it’s a picture of a cell undergoing cell division, you are right. But more specifically, the image is a lung cell stained with fluorescent dyes undergoing mitosis, during early anaphase.
Mitosis and Cytokinesis
During mitosis, when the nucleus divides, the two chromatids that make up each chromosome separate from each other and move to opposite poles of the cell. This is shown in Figure below. You can watch an animation of the process at the following link:http://www.biology.arizona.edu/Cell_bio/tutorials/cell_cycle/MitosisFlash.html.
Mitosis is the phase of the eukaryotic cell cycle that occurs between DNA replication and the formation of two daughter cells. What happens during mitosis?
Mitosis actually occurs in four phases. The phases are called prophase, metaphase, anaphase, and telophase. They are shown in Figure below and described in greater detail in the following sections.
Mitosis in the Eukaryotic Cell Cycle. Mitosis is the multi-phase process in which the nucleus of a eukaryotic cell divides.
Prophase
The first and longest phase of mitosis is prophase. During prophase, chromatin condenses into chromosomes, and the nuclear envelope, or membrane, breaks down. In animal cells, thecentrioles near the nucleus begin to separate and move to opposite poles (sides) of the cell. As the centrioles move, a spindle starts to form between them. The spindle, shown in Figurebelow, consists of fibers made of microtubules.
Spindle. The spindle starts to form during prophase of mitosis. Kinetochores on the spindle attach to the centromeres of sister chromatids.
Metaphase
During metaphase, spindle fibers attach to the centromere of each pair of sister chromatids (see Figure below). The sister chromatids line up at the equator, or center, of the cell. This is also known as the metaphase plate. The spindle fibers ensure that sister chromatids will separate and go to different daughter cells when the cell divides.
Chromosomes, consisting of sister chromatids, line up at the equator or middle of the cell during metaphase.
Anaphase
During anaphase, sister chromatids separate and the centromeres divide. The sister chromatids are pulled apart by the shortening of the spindle fibers. This is like reeling in a fish by shortening the fishing line. One sister chromatid moves to one pole of the cell, and the other sister chromatid moves to the opposite pole. At the end of anaphase, each pole of the cell has a complete set of chromosomes.
Telophase
During telophase, the chromosomes begin to uncoil and form chromatin. This prepares the genetic material for directing the metabolic activities of the new cells. The spindle also breaks down, and new nuclear membranes (nuclear envelope) form.
Cytokinesis
Cytokinesis is the final stage of cell division in eukaryotes as well as prokaryotes. During cytokinesis, the cytoplasm splits in two and the cell divides. Cytokinesis occurs somewhat differently in plant and animal cells, as shown in Figure below. In animal cells, the plasma membrane of the parent cell pinches inward along the cell’s equator until two daughter cells form. In plant cells, a cell plate forms along the equator of the parent cell. Then, a new plasma membrane and cell wall form along each side of the cell plate.
Cytokinesis is the final stage of eukaryotic cell division. It occurs differently in animal (left) and plant (right) cells.
The phases of mitosis are discussed in the video: http://www.youtube.com/watch?v=LLKX_4DHE3I.
The four phases of mitosis. Can you describe what happens in each phase?
Summary
• Cell division in eukaryotic cells includes mitosis, in which the nucleus divides, and cytokinesis, in which the cytoplasm divides and daughter cells form.
• Mitosis occurs in four phases, called prophase, metaphase, anaphase, and telophase.
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Explore More I
Use this resource to answer the questions that follow.
1. During which phase of mitosis do the spindle fibers align the chromosomes along the middle of the cell?
2. During which phase of mitosis do poteins attach to the centromeres creating the kinetochores?
3. During which phase of mitosis does chromatin in the nucleus begins to condense?
4. During which phase of mitosis do the paired chromosomes separate at the kinetochores?
5. During which phase of mitosis do new membranes form around the daughter nuclei?
Review
1. List the phases of mitosis.
2. What happens during prophase of mitosis?
3. During which phase of mitosis do sister chromatids separate?
4. Describe what happens during cytokinesis in animal cells.
5. If a cell skipped metaphase during mitosis, how might this affect the two daughter cells?
6. Explain the significance of the spindle fibers in mitosis. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/02%3A_Cell_Biology/2.35%3A_Mitosis_and_Cytokinesis.txt |
One parent or two?
That is the main difference between sexual and asexual reproduction. Sexual reproduction just means combining genetic material from two parents. Asexual reproduction produces offspring genetically identical to the one parent.
Reproduction: Asexual vs. Sexual
Cell division is how organisms grow and repair themselves. It is also how many organisms produce offspring. For many single-celled organisms, reproduction is a similar process. The parent cell simply divides to form two daughter cells that are identical to the parent. In many other organisms, two parents are involved, and the offspring are not identical to the parents. In fact, each offspring is unique. Look at the family in Figure below. The children resemble their parents, but they are not identical to them. Instead, each has a unique combination of characteristics inherited from both parents.
Family Portrait: Mother, Daughter, Father, and Son. Children resemble their parents, but they are never identical to them. Do you know why this is the case?
Reproduction is the process by which organisms give rise to offspring. It is one of the defining characteristics of living things. There are two basic types of reproduction: asexual reproduction and sexual reproduction.
Asexual Reproduction
Asexual reproduction involves a single parent. It results in offspring that are genetically identical to each other and to the parent. All prokaryotes and some eukaryotes reproduce this way. There are several different methods of asexual reproduction. They include binary fission, fragmentation, and budding.
• Binary fission occurs when a parent cell splits into two identical daughter cells of the same size.
• Fragmentation occurs when a parent organism breaks into fragments, or pieces, and each fragment develops into a new organism. Starfish, like the one in Figure below, reproduce this way. A new starfish can develop from a single ray, or arm. Starfish, however, are also capable of sexual reproduction.
• Budding occurs when a parent cell forms a bubble-like bud. The bud stays attached to the parent cell while it grows and develops. When the bud is fully developed, it breaks away from the parent cell and forms a new organism. Budding in yeast is shown in Figure below.
Binary Fission in various single-celled organisms (left). Cell division is a relatively simple process in many single-celled organisms. Eventually the parent cell will pinch apart to form two identical daughter cells. In multiple fission (right), a multinucleated cell can divide to form more than one daughter cell. Multiple fission is more often observed among protists.
Starfish reproduce by fragmentation and yeasts reproduce by budding. Both are types of asexual reproduction.
Asexual reproduction can be very rapid. This is an advantage for many organisms. It allows them to crowd out other organisms that reproduce more slowly. Bacteria, for example, may divide several times per hour. Under ideal conditions, 100 bacteria can divide to produce millions of bacterial cells in just a few hours! However, most bacteria do not live under ideal conditions. If they did, the entire surface of the planet would soon be covered with them. Instead, their reproduction is kept in check by limited resources, predators, and their own wastes. This is true of most other organisms as well.
Sexual Reproduction
Sexual reproduction involves two parents. As you can see from Figure below, in sexual reproduction, parents produce reproductive cells—called gametes—that unite to form an offspring. Gametes are haploid cells. This means they contain only half the number ofchromosomes found in other cells of the organism. Gametes are produced by a type of cell division called meiosis, which is described in detail in a subsequent concept. The process in which two gametes unite is called fertilization. The fertilized cell that results is referred to as a zygote. A zygote is diploid cell, which means that it has twice the number of chromosomesas a gamete.
Mitosis, Meiosis and Sexual Reproduction is discussed at http://www.youtube.com/watch?v=kaSIjIzAtYA.
Cycle of Sexual Reproduction. Sexual reproduction involves the production of haploid gametes by meiosis. This is followed by fertilization and the formation of a diploid zygote. The number of chromosomes in a gamete is represented by the letter n. Why does the zygote have 2n, or twice as many, chromosomes?
Summary
• Asexual reproduction involves one parent and produces offspring that are genetically identical to each other and to the parent.
• Sexual reproduction involves two parents and produces offspring that are genetically unique.
• During sexual reproduction, two haploid gametes join in the process of fertilization to produce a diploid zygote.
• Meiosis is the type of cell division that produces gametes.
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Use this resource to answer the questions that follow.
1. How do the offspring of asexual reproduction compare to the parent?
2. How do the offspring of sexual reproduction compare to the parents?
3. How do the following organism reproduce?
1. brittle stars
2. Salmonella
3. cactus
4. sunflower
5. garden strawberry
6. coast redwood tree
7. grizzly bear
Review
1. What are three types of asexual reproduction?
2. Define gamete and zygote. What number of chromosomes does each have (in humans)?
3. What happens during fertilization?
4. Compare and contrast asexual and sexual reproduction. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/02%3A_Cell_Biology/2.36%3A_Asexual_vs._Sexual_Reproduction.txt |
How do you make a cell with half the DNA?
Meiosis. This allows cells to have half the number of chromosomes, so two of these cells can come back together to form a new organism with the complete number of chromosomes. This process not only helps produce gametes, it also ensures genetic variation.
Meiosis
The process that produces haploid gametes is meiosis. Meiosis is a type of cell division in which the number of chromosomes is reduced by half. It occurs only in certain special cells of the organisms. During meiosis, homologous chromosomes separate, and haploid cells form that have only one chromosome from each pair. Two cell divisions occur during meiosis, and a total of four haploid cells are produced. The two cell divisions are called meiosis I and meiosis II. The overall process of meiosis is summarized in Figure below. You can watch an animation of meiosis at this link: http://www.youtube.com/watch?v=D1_-mQS_FZ0.
Overview of Meiosis. During meiosis, homologous chromosomes separate and go to different daughter cells. This diagram shows just the nuclei of the cells. Notice the exchange of genetic material that occurs prior to the first cell division.
Phases of Meiosis
Meiosis I begins after DNA replicates during interphase of the cell cycle. In both meiosis I and meiosis II, cells go through the same four phases as mitosis - prophase, metaphase, anaphase and telophase. However, there are important differences between meiosis I and mitosis. The flowchart in Figure below shows what happens in both meiosis I and II.
Phases of Meiosis. This flowchart of meiosis shows meiosis I in greater detail than meiosis II. Meiosis I—but not meiosis II—differs somewhat from mitosis. Compare meiosis I in this flowchart with the earlier figure featuring mitosis. How does meiosis I differ from mitosis?
Compare meiosis I in this flowchart with the figure from the Mitosis and Cytokinesis concept. How does meiosis I differ from mitosis? Notice at the beginning of meiosis (prophase I), homologous chromosomes exchange segments of DNA. This is known as crossing-over, and is unique to this phase of meiosis.
The phases of meiosis are discussed at http://www.youtube.com/watch?v=ijLc52LmFQg(27:23).
Meiosis I
1. Prophase I: The nuclear envelope begins to break down, and the chromosomes condense. Centrioles start moving to opposite poles of the cell, and a spindle begins to form. Importantly, homologous chromosomes pair up, which is unique to prophase I. In prophase of mitosis and meiosis II, homologous chromosomes do not form pairs in this way. Crossing-over occurs during this phase (see the Genetic Variation concept).
2. Metaphase I: Spindle fibers attach to the paired homologous chromosomes. The paired chromosomes line up along the equator (middle) of the cell. This occurs only in metaphase I. In metaphase of mitosis and meiosis II, it is sister chromatids that line up along the equator of the cell.
3. Anaphase I: Spindle fibers shorten, and the chromosomes of each homologous pair start to separate from each other. One chromosome of each pair moves toward one pole of the cell, and the other chromosome moves toward the opposite pole.
4. Telophase I and Cytokinesis: The spindle breaks down, and new nuclear membranes form. The cytoplasm of the cell divides, and two haploid daughter cells result. The daughter cells each have a random assortment of chromosomes, with one from each homologous pair. Both daughter cells go on to meiosis II. The DNA does not replicate between meiosis I and meiosis II.
Meiosis II
1. Prophase II: The nuclear envelope breaks down and the spindle begins to form in each haploid daughter cell from meiosis I. The centrioles also start to separate.
2. Metaphase II: Spindle fibers line up the sister chromatids of each chromosome along the equator of the cell.
3. Anaphase II: Sister chromatids separate and move to opposite poles.
4. Telophase II and Cytokinesis: The spindle breaks down, and new nuclear membranes form. The cytoplasm of each cell divides, and four haploid cells result. Each cell has a unique combination of chromosomes.
Mitosis, Meiosis and Sexual Reproduction is discussed at http://www.youtube.com/watch?v=kaSIjIzAtYA (18:23).
You can watch an animation of meiosis at this link: http://www.youtube.com/watch?v=D1_-mQS_FZ0.
Summary
• Meiosis is the type of cell division that produces gametes.
• Meiosis involves two cell divisions and produces four haploid cells.
• Sexual reproduction has the potential to produce tremendous genetic variation in offspring. This is due in part to crossing-over during meiosis.
• See Meiosis at http://johnkyrk.com/meiosis.html for a detailed summary.
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Use these resources to answer the questions that follow.
Explore More I
1. Give a complete definition of meiosis.
2. What comprises the 46 chromosomes in a human female?
3. How do chromosomes pair in prophase I?
4. What does not occur between meiosis I and meiosis II? Why is this significant?
5. How many chromosomes are in the cells at the end of meiosis I and meiosis II?
Review
1. What is meiosis?
2. Compare the events of metaphase I to metaphase II?
3. Create a diagram to show how crossing-over occurs and how it creates new gene combinations on each chromosome.
4. Explain why sexual reproduction results in genetically unique offspring.
5. Explain how meiosis I differs from mitosis. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/02%3A_Cell_Biology/2.37%3A_Meiosis.txt |
What's the biggest cell on Earth?
The ostrich egg - unfertilized, of course. Yes, this egg, just like a human ovum, is just one cell. The egg shell membrane encloses the nucleus containing the genetic material and the cytoplasm.
Gametogenesis
At the end of meiosis, four haploid cells have been produced, but the cells are not yet gametes. The cells need to develop before they become mature gametes capable offertilization. The development of haploid cells into gametes is called gametogenesis.
How much DNA is in a gamete? The sperm cell forms by meiosis and spermatogenesis. Because it forms by meiosis, the sperm cell has only half as much DNA as a body cell. Notice the three distinct segments: a head piece, a flagella tail and a midpiece of mostly mitochondria. What is the role of each section?
Gametogenesis may differ between males and females. Male gametes are called sperm. Female gametes are called eggs. In human males, for example, the process that produces mature sperm cells is called spermatogenesis. During this process, sperm cells grow a tail and gain the ability to “swim,” like the human sperm cell shown in Figure below. In human females, the process that produces mature eggs is called oogenesis. Just one egg is produced from the four haploid cells that result from meiosis. The single egg is a very large cell, as you can see from the human egg in Figure below.
A human sperm is a tiny cell with a tail. A human egg is much larger. Both cells are mature haploid gametes that are capable of fertilization. What process is shown in this photograph? Notice the sperm with the head piece containing the genetic material, a flagella tail that propels the sperm, and a midpiece of mostly mitochondria, supplying ATP.
Spermatogenesis and Oogenesis
During spermatogenesis, primary spermatocytes go through the first cell division of meiosis to produce secondary spermatocytes. These are haploid cells. Secondary spermatocytes then quickly complete the meiotic division to become spermatids, which are also haploid cells. The four haploid cells produced from meiosis develop a flagellum tail and compact head piece to become mature sperm cells, capable of swimming and fertilizing an egg. The compact head, which has lost most of its cytoplasm, is key in the formation of a streamlined shape. The middle piece of the sperm, connecting the head to the tail, contains many mitochondria, providing energy to the cell. The sperm cell essentially contributes only DNA to the zygote.
On the other hand, the egg provides the other half of the DNA, but also organelles, building blocks for compounds such as proteins and nucleic acids, and other necessary materials. The egg, being much larger than a sperm cell, contains almost all of the cytoplasm a developing embryo will have during its first few days of life. Therefore, oogenesis is a much more complicated process than spermatogenesis.
Oogenesis begins before birth and is not completed until after fertilization. Oogenesis begins when oogonia (singular, oogonium), which are the immature eggs that form in the ovaries before birth and have the diploid number of chromosomes, undergo mitosis to form primary oocytes, also with the diploid number. Oogenesis proceeds as a primary oocyte undergoes the first cell division of meiosis to form secondary oocytes with the haploid number of chromosomes. A secondary oocyte only undergoes the second meiotic cell division to form a haploid ovum if it is fertilized by a sperm. The one egg cell that results from meiosis contains most of the cytoplasm, nutrients, and organelles. This unequal distribution of materials produces one large cell, and one cell with little more than DNA. This other cell, known as a polar body, eventually breaks down. The larger cell undergoes meiosis II, once again producing a large cell and a polar body. The large cell develops into the mature gamete, called an ovum (Figure below). The unequal distribution of the cytoplasm during oogenesis is necessary as the zygote that results from fertilization receives all of its cytoplasm from the egg. So the egg needs to have as much cytoplasm as possible.
Maturation of the ovum. Notice only one mature ovum, or egg, forms during meiosis from the primary oocyte. Three polar bodies may form during oogenesis. These polar bodies will not form mature gametes. Conversely, four haploid spermatids form during meiosis from the primary spermatocyte.
Summary
• Meiosis is a step during spermatogenesis and oogenesis.
• Spermatogenesis produces four haploid sperm cells, while oogenesis produces one mature ovum.
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Use this resource to answer the questions that follow.
1. What is gametogenesis?
2. Compare sperm to eggs.
3. What is spermiogenesis? What happens during spermatogenesis?
4. What is oogenesis?
5. When do the primary oocytes form?
Review
1. What is gametogenesis, and when does it occur?
2. What are the main differences between oogenesis and spermatogenesis?
3. How many chromosomes are in a human oogonia?
4. Why is there unequal distribution of the cytoplasm during oogenesis? | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/02%3A_Cell_Biology/2.38%3A__Gametogenesis.txt |
What helps ensure the survival of a species?
Genetic variation. It is this variation that is the essence of evolution. Without genetic differences among individuals, "survival of the fittest" would not be likely. Either all survive, or all perish.
Genetic Variation
Sexual reproduction results in infinite possibilities of genetic variation. In other words, sexual reproduction results in offspring that are genetically unique. They differ from both parents and also from each other. This occurs for a number of reasons.
• When homologous chromosomes form pairs during prophase I of meiosis I, crossing-over can occur. Crossing-over is the exchange of genetic material between homologous chromosomes. It results in new combinations of genes on each chromosome.
• When cells divide during meiosis, homologous chromosomes are randomly distributed to daughter cells, and different chromosomes segregate independently of each other. This called is called independent assortment. It results in gametes that have unique combinations of chromosomes.
• In sexual reproduction, two gametes unite to produce an offspring. But which two of the millions of possible gametes will it be? This is likely to be a matter of chance. It is obviously another source of genetic variation in offspring. This is known as random fertilization.
All of these mechanisms working together result in an amazing amount of potential variation. Each human couple, for example, has the potential to produce more than 64 trillion genetically unique children. No wonder we are all different!
See Sources of Variation at http://learn.genetics.utah.edu/content/variation/sources/ for additional information.
Crossing-Over
Crossing-over occurs during prophase I, and it is the exchange of genetic material between non-sister chromatids of homologous chromosomes. Recall during prophase I, homologous chromosomes line up in pairs, gene-for-gene down their entire length, forming a configuration with four chromatids, known as a tetrad. At this point, the chromatids are very close to each other and some material from two chromatids switch chromosomes, that is, the material breaks off and reattaches at the same position on the homologous chromosome (Figure below). This exchange of genetic material can happen many times within the same pair of homologous chromosomes, creating unique combinations of genes. This process is also known as recombination.
Crossing-over. A maternal strand of DNA is shown in red. A paternal strand of DNA is shown in blue. Crossing over produces two chromosomes that have not previously existed. The process of recombination involves the breakage and rejoining of parental chromosomes (M, F). This results in the generation of novel chromosomes (C1, C2) that share DNA from both parents.
Independent Assortment and Random Fertilization
In humans, there are over 8 million configurations in which the chromosomes can line up during metaphase I of meiosis. It is the specific processes of meiosis, resulting in four unique haploid cells, that result in these many combinations. This independent assortment, in which the chromosome inherited from either the father or mother can sort into any gamete, produces the potential for tremendous genetic variation. Together with random fertilization, more possibilities for genetic variation exist between any two people than the number of individuals alive today. Sexual reproduction is the random fertilization of a gamete from the female using a gamete from the male. In humans, over 8 million (223) chromosome combinations exist in the production of gametes in both the male and female. A sperm cell, with over 8 million chromosome combinations, fertilizes an egg cell, which also has over 8 million chromosome combinations. That is over 64 trillion unique combinations, not counting the unique combinations produced by crossing-over. In other words, each human couple could produce a child with over 64 trillion unique chromosome combinations!
See How Cells Divide: Mitosis vs. Meiosis at http://www.pbs.org/wgbh/nova/miracle/divide.html for an animation comparing the two processes.
Summary
• Sexual reproduction has the potential to produce tremendous genetic variation in offspring.
• This variation is due to independent assortment and crossing-over during meiosis, and random union of gametes during fertilization.
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Use this resource to answer the questions that follow.
1. What is meant by genetic variation?
2. Would natural selection occur without genetic variation? Explain your response.
3. What causes genetic variation?
4. How would genetic variation result in a change in phenotype?
5. What are the sources of genetic variation? Explain your response.
Review
1. What is crossing-over and when does it occur?
2. Describe how crossing-over, independent assortment, and random fertilization lead to genetic variation.
3. How many combinations of chromosomes are possible from sexual reproduction in humans?
4. Create a diagram to show how crossing-over occurs and how it creates new gene combinations on each chromosome. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/02%3A_Cell_Biology/2.39%3A_Genetic_Variation.txt |
Young to old. A life cycle?
Not in the biological sense. Life cycles describe the amount of DNA present at a specific stage or time in the life of an organism. Is there a haploid or diploid amount of DNA? That is the key question.
Life Cycles
Sexual reproduction occurs in a cycle. Diploid parents produce haploid gametes that unite and develop into diploid adults, which repeat the cycle. This series of life stages and events that a sexually reproducing organism goes through is called its life cycle. Sexually reproducing organisms can have different types of life cycles. Three are represented in Figure below and described following sections.
Life cycles can vary in sexually reproducing organisms. Three types of sexual life cycles are shown here. Do you see how they differ? The letter n indicates haploid stages of the life cycles, and 2n indicates diploid stages.
Haploid Life Cycle
The haploid life cycle is the simplest life cycle. It is found in many single-celled eukaryotic organisms. Organisms with a haploid life cycle spend the majority of their lives as haploid gametes. When the haploid gametes fuse, they form a diploid zygote. It quickly undergoes meiosis to produce more haploid gametes that repeat the life cycle.
Diploid Life Cycle
Organisms with a diploid life cycle spend the majority of their lives as diploid adults. When they are ready to reproduce, they undergo meiosis and produce haploid gametes. Gametes then unite in fertilization and form a diploid zygote, which immediately enters G1 of the cell cycle. Next, the zygote's DNA is replicated. Finally, the processes of mitosis and cytokinesis produce two genetically identical diploid cells. Through repeated rounds of growth and division, this organism becomes a diploid adult and the cycle continues. Can you think of an organism with a diploid life cycle? (Hint: What type of life cycle do humans have?)
Alternation of Generations
Plants, algae, and some protists have a life cycle that alternates between diploid and haploid phases, known as alternation of generations. In plants, the life cycle alternates between the diploid sporophyte and haploid gametophyte. Spore forming cells in the diploid sporophyte undergo meiosis to produce spores, a haploid reproductive cell. Spores can develop into an adult without fusing with another cell. The spores give rise to a multicellular haploid gametophyte, which produce gametes by mitosis. The gametes fuse, producing a diploid zygote, which grow into the diploid sporophyte. These life cycles may be quite complicated. You can read about them in additional concepts.
Summary
• A life cycle is the sequence of stages an organisms goes through from one generation to the next. Organisms that reproduce sexually can have different types of life cycles, such as haploid or diploid life cycles.
Summary of all three life cycles.
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Use this resource to answer the questions that follow.
1. What is a life cycle?
2. Describe the basic stages of the life cycles for all organisms.
3. Explain why butterflies have complex life cycles.
Review
1. What is a life cycle?
2. An adult organism produces gametes that quickly go through fertilization and form diploid zygotes. The zygotes mature into adults, which live for many years. Eventually the adults produce gametes and the cycle repeats. What type of life cycle does this organism have? Explain your answer.
3. Which life cycle is the simplest? Why?
4. Describe the alternation of generations life cycle. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/02%3A_Cell_Biology/2.40%3A_Reproductive_Life_Cycles.txt |
Covers Mendelian and non-Mendelian genetics, human genetics, and biotechnology.
03: Genetics
What's so interesting about pea plants?
These purple-flowered plants are not just pretty to look at. Plants like these led to a huge leap forward in biology. The plants are common garden pea plants, and they were studied in the mid-1800s by an Austrian monk named Gregor Mendel. With his careful experiments, Mendel uncovered the secrets of heredity, or how parents pass characteristics to their offspring.
You may not care much about heredity in pea plants, but you probably care about your own heredity. Mendel’s discoveries apply to you as well as to peas—and to all other living things that reproduce sexually.
Mendel and His Pea Plants
People have long known that the characteristics of living things are similar in parents and their offspring. Whether it’s the flower color in pea plants or nose shape in people, it is obvious that offspring resemble their parents. However, it wasn’t until the experiments of Gregor Mendel that scientists understood how characteristics are inherited. Mendel’s discoveries formed the basis of genetics, the science of heredity. That’s why Mendel is often called the "father of genetics." It’s not common for a single researcher to have such an important impact on science. The importance of Mendel’s work was due to three things: a curious mind, sound scientific methods, and good luck. You’ll see why when you read about Mendel’s experiments.
An introduction to heredity can be seen at http://www.youtube.com/watch?v=eEUvRrhmcxM(17:27).
Gregor Mendel was born in 1822 and grew up on his parents’ farm in Austria. He did well in school and became a monk. He also went to the University of Vienna, where he studied science and math. His professors encouraged him to learn science through experimentation and to use math to make sense of his results. Mendel is best known for his experiments with the pea plant Pisum sativum (see Figure below). You can watch a video about Mendel and his research at the following link: http://www.biography.com/people/gregor-mendel-39282.
Gregor Mendel. The Austrian monk Gregor Mendel experimented with pea plants. He did all of his research in the garden of the monastery where he lived.
Blending Theory of Inheritance
During Mendel’s time, the blending theory of inheritance was popular. This is the theory that offspring have a blend, or mix, of the characteristics of their parents. Mendel noticed plants in his own garden that weren’t a blend of the parents. For example, a tall plant and a short plant had offspring that were either tall or short but not medium in height. Observations such as these led Mendel to question the blending theory. He wondered if there was a different underlying principle that could explain how characteristics are inherited. He decided to experiment with pea plants to find out. In fact, Mendel experimented with almost 30,000 pea plants over the next several years! At the following link, you can watch an animation in which Mendel explains how he arrived at his decision to study inheritance in pea plants:http://www.dnalc.org/view/16170-Animation-3-Gene-s-don-t-blend-.html.
Why Study Pea Plants?
Why did Mendel choose common, garden-variety pea plants for his experiments? Pea plants are a good choice because they are fast growing and easy to raise. They also have several visible characteristics that may vary. These characteristics, which are shown in Figure below, include seed form and color, flower color, pod form and color, placement of pods and flowers on stems, and stem length. Each characteristic has two common values. For example, seed form may be round or wrinkled, and flower color may be white or purple (violet).
Mendel investigated seven different characteristics in pea plants. In this chart, cotyledons refer to the tiny leaves inside seeds. Axial pods are located along the stems. Terminal pods are located at the ends of the stems.
Controlling Pollination
To research how characteristics are passed from parents to offspring, Mendel needed to control pollination. Pollination is the fertilization step in the sexual reproduction of plants.Pollen consists of tiny grains that are the male gametes of plants. They are produced by a male flower part called the anther (see Figure below). Pollination occurs when pollen is transferred from the anther to the stigma of the same or another flower. The stigma is a female part of a flower. It passes the pollen grains to female gametes in the ovary.
Flowers are the reproductive organs of plants. Each pea plant flower has both male and female parts. The anther is part of the stamen, the male structure that produces male gametes (pollen). The stigma is part of the pistil, the female structure that produces female gametes and guides the pollen grains to them. The stigma receives the pollen grains and passes them to the ovary, which contains female gametes.
Pea plants are naturally self-pollinating. In self-pollination, pollen grains from anthers on one plant are transferred to stigmas of flowers on the same plant. Mendel was interested in the offspring of two different parent plants, so he had to prevent self-pollination. He removed the anthers from the flowers of some of the plants in his experiments. Then he pollinated them by hand with pollen from other parent plants of his choice. When pollen from one plant fertilizes another plant of the same species, it is called cross-pollination. The offspring that result from such a cross are called hybrids.
Summary
• Gregor Mendel experimented with pea plants to learn how characteristics are passed from parents to offspring.
• Mendel’s discoveries formed the basis of genetics, the science of heredity.
• Cross-pollination produces hybrids.
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Use this resource to answer the questions that follow.
1. What did Gregor Mendel discover about "factors", which are genes?
2. Briefly state Mendel's three laws.
Review
1. What is the blending theory of inheritance? Why did Mendel question this theory?
2. List the seven characteristics that Mendel investigated in pea plants.
3. How did Mendel control pollination in pea plants?
4. What are hybrids? | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/03%3A_Genetics/3.01%3A_Mendel%27s_Pea_Plants.txt |
Peas. Some round and some wrinkled. Why?
That's what Mendel asked. He noticed peas were always round or wrinkled, but never anything else. Seed shape was one of the traits Mendel studied in his first set of experiments.
Mendel’s First Set of Experiments
Mendel first experimented with just one characteristic of a pea plant at a time. He began with flower color. As shown in Figure below, Mendel cross-pollinated purple- and white-flowered parent plants. The parent plants in the experiments are referred to as the P (for parent)generation. You can explore an interactive animation of Mendel’s first set of experiments at this link: http://www2.edc.org/weblabs/Mendel/mendel.html.
This diagram shows Mendel's first experiment with pea plants. The F1 generation results from cross-pollination of two parent (P) plants, and contained all purple flowers. The F2 generation results from self-pollination of F1 plants, and contained 75% purple flowers and 25% white flowers. This type of experiment is known as a monohybrid cross.
F1 and F2 Generations
The offspring of the P generation are called the F1 (for filial, or “offspring”) generation. As you can see from Figure above, all of the plants in the F1 generation had purple flowers. None of them had white flowers. Mendel wondered what had happened to the white-flower characteristic. He assumed some type of inherited factor produces white flowers and some other inherited factor produces purple flowers. Did the white-flower factor just disappear in the F1 generation? If so, then the offspring of the F1 generation—called the F2 generation—should all have purple flowers like their parents.
To test this prediction, Mendel allowed the F1 generation plants to self-pollinate. He was surprised by the results. Some of the F2 generation plants had white flowers. He studied hundreds of F2 generation plants, and for every three purple-flowered plants, there was an average of one white-flowered plant.
Law of Segregation
Mendel did the same experiment for all seven characteristics. In each case, one value of the characteristic disappeared in the F1 plants and then showed up again in the F2 plants. And in each case, 75 percent of F2 plants had one value of the characteristic and 25 percent had the other value. Based on these observations, Mendel formulated his first law of inheritance. This law is called the law of segregation. It states that there are two factors controlling a given characteristic, one of which dominates the other, and these factors separate and go to different gametes when a parent reproduces.
Summary
• Mendel first researched one characteristic at a time. This led to his law of segregation. This law states that each characteristic is controlled by two factors, which separate and go to different gametes when an organism reproduces.
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Use this resource to answer the questions that follow.
1. What is a pure line?
2. What did Mendel always see in the F1 generation?
3. What did Mendel always see in the F2 generation?
4. Summarize Mendel's conclusions from these experiments.
Review
1. Describe in general terms Mendel’s first set of experiments.
2. State Mendel's first law.
3. Assume you are investigating the inheritance of stem length in pea plants. You cross-pollinate a short-stemmed plant with a long-stemmed plant. All of the offspring have long stems. Then, you let the offspring self-pollinate. Describe the stem lengths you would expect to find in the second generation of offspring. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/03%3A_Genetics/3.02%3A_Mendel%27s_First_Set_of_Experiments.txt |
Round and green, round and yellow, wrinkled and green, or wrinkled and yellow?
Can two traits be inherited together? Or are all traits inherited separately? Mendel asked these questions after his first round of experiments.
Mendel’s Second Set of Experiments
After observing the results of his first set of experiments, Mendel wondered whether different characteristics are inherited together. For example, are purple flowers and tall stems always inherited together? Or do these two characteristics show up in different combinations in offspring? To answer these questions, Mendel next investigated two characteristics at a time. For example, he crossed plants with yellow round seeds and plants with green wrinkled seeds. The results of this cross, which is a dihybrid cross, are shown in Figure below.
This chart represents Mendel's second set of experiments. It shows the outcome of a cross between plants that differ in seed color (yellow or green) and seed form (shown here with a smooth round appearance or wrinkled appearance). The letters R, r, Y, and y represent genes for the characteristics Mendel was studying. Mendel didn’t know about genes, however. Genes would not be discovered until several decades later. This experiment demonstrates that in the F2 generation, 9/16 were round yellow seeds, 3/16 were wrinkled yellow seeds, 3/16 were round green seeds, and 1/16 were wrinkled green seeds.
F1 and F2 Generations
In this set of experiments, Mendel observed that plants in the F1 generation were all alike. All of them had yellow and round seeds like one of the two parents. When the F1 generation plants self-pollinated, however, their offspring—the F2 generation—showed all possible combinations of the two characteristics. Some had green round seeds, for example, and some had yellow wrinkled seeds. These combinations of characteristics were not present in the F1 or P generations.
Law of Independent Assortment
Mendel repeated this experiment with other combinations of characteristics, such as flower color and stem length. Each time, the results were the same as those in Figure above. The results of Mendel’s second set of experiments led to his second law. This is the law of independent assortment. It states that factors controlling different characteristics are inherited independently of each other.
Summary
• After his first set of experiments, Mendel researched two characteristics at a time. This led to his law of independent assortment. This law states that the factors controlling different characteristics are inherited independently of each other.
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Use this resource to answer the questions that follow.
1. What is a dihybrid?
2. What is a dihybrid cross?
3. What were the parental phenotypes for the seeds Mendel used in his dihybrid cross?
4. What were Mendel's results in the F2 generation of his dihybrid cross?
5. What is Mendel's second law? State this law.
Explore More II
• The Geniverse Lab at www.concord.org/activities/geniverse-lab.
Review
1. What was Mendel investigating with his second set of experiments? What was the outcome?
2. State Mendel’s second law.
3. If a purple-flowered, short-stemmed plant is crossed with a white-flowered, long-stemmed plant, would all of the purple-flowered offspring also have short stems? Why or why not? | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/03%3A_Genetics/3.03%3A_Mendel%27s_Second_Set_of_Experiments.txt |
Do you look like your parents?
You probably have some characteristics or traits in common with each of your parents. Mendel's work provided the basis to understand the passing of traits from one generation to the next.
Mendel’s Laws and Genetics
You might think that Mendel's discoveries would have made a big impact on science as soon as he made them. But you would be wrong. Why? Because Mendel's work was largely ignored. Mendel was far ahead of his time and working from a remote monastery. He had no reputation among the scientific community and no previously published work.
Mendel’s work, titled Experiments in Plant Hybridization, was published in 1866, and sent to prominent libraries in several countries, as well as 133 natural science associations. Mendel himself even sent carefully marked experiment kits to Karl von Nageli, the leading botanist of the day. The result - it was almost completely ignored. Von Nageli instead sent hawkweed seeds to Mendel, which he thought was a better plant for studying heredity. Unfortunately hawkweed reproduces asexually, resulting in genetically identical clones of the parent.
Charles Darwin published his landmark book on evolution in 1869, not long after Mendel had discovered his laws. Unfortunately, Darwin knew nothing of Mendel's discoveries and didn’t understand heredity. This made his arguments about evolution less convincing to many people. This example demonstrates the importance for scientists to communicate the results of their investigations.
Rediscovering Mendel’s Work
Mendel’s work was virtually unknown until 1900. In that year, three different European scientists — named Hugo De Vries, Carl Correns, and Erich Von Tschermak-Seysenegg — independently arrived at Mendel’s laws. All three had done experiments similar to Mendel’s. They came to the same conclusions that he had drawn almost half a century earlier. Only then was Mendel’s actual work rediscovered.
As scientists learned more about heredity - the passing of traits from parents to offspring - over the next few decades, they were able to describe Mendel’s ideas about inheritance in terms of genes. In this way, the field of genetics was born. At the link that follows, you can watch an animation of Mendel explaining his laws of inheritance in genetic terms.http://www.dnalc.org/view/16182-Animation-4-Some-genes-are-dominant-.html
Genetics of Inheritance
Today, we known that characteristics of organisms are controlled by genes on chromosomes(see Figure below). The position of a gene on a chromosome is called its locus. In sexually reproducing organisms, each individual has two copies of the same gene, as there are two versions of the same chromosome (homologous chromosomes). One copy comes from each parent. The gene for a characteristic may have different versions, but the different versions are always at the same locus. The different versions are called alleles. For example, in pea plants, there is a purple-flower allele (B) and a white-flower allele (b). Different alleles account for much of the variation in the characteristics of organisms.
Chromosome, Gene, Locus, and Allele. This diagram shows how the concepts of chromosome, gene, locus, and allele are related. What is the different between a gene and a locus? Between a gene and an allele?
During meiosis, homologous chromosomes separate and go to different gametes. Thus, the two alleles for each gene also go to different gametes. At the same time, different chromosomes assort independently. As a result, alleles for different genes assort independently as well. In these ways, alleles are shuffled and recombined in each parent’s gametes.
Genotype and Phenotype
When gametes unite during fertilization, the resulting zygote inherits two alleles for each gene. One allele comes from each parent. The alleles an individual inherits make up the individual’s genotype. The two alleles may be the same or different. As shown in Tablebelow, an organism with two alleles of the same type (BB or bb) is called a homozygote. An organism with two different alleles (Bb) is called a heterozygote. This results in three possible genotypes.
Alleles Genotypes Phenotypes
BB (homozygote) purple flowers
B (purple) Bb (heterozygote) purple flowers
b (white) bb (homozygote) white flowers
The expression of an organism’s genotype produces its phenotype. The phenotype refers to the organism’s characteristics, such as purple or white flowers. As you can see from Tableabove, different genotypes may produce the same phenotype. For example, BB and Bbgenotypes both produce plants with purple flowers. Why does this happen? In a Bbheterozygote, only the B allele is expressed, so the b allele doesn’t influence the phenotype. In general, when only one of two alleles is expressed in the phenotype, the expressed allele is called the dominant allele. The allele that isn’t expressed is called the recessive allele.
How Mendel Worked Backward to Get Ahead
Mendel used hundreds or even thousands of pea plants in each experiment he did. Therefore, his results were very close to those you would expect based on the rules of probability (see "Probability and Inheritance" concept). For example, in one of his first experiments with flower color, there were 929 plants in the F2 generation. Of these, 705 (76 percent) had purple flowers and 224 (24 percent) had white flowers. Thus, Mendel’s results were very close to the 75 percent purple and 25 percent white you would expect by the laws of probability for this type of cross.
Of course, Mendel had only phenotypes to work with. He knew nothing about genes and genotypes. Instead, he had to work backward from phenotypes and their percents in offspring to understand inheritance. From the results of his first set of experiments, Mendel realized that there must be two factors controlling each of the characteristics he studied, with one of the factors being dominant to the other. He also realized that the two factors separate and go to different gametes and later recombine in the offspring. This is an example of Mendel’s good luck. All of the characteristics he studied happened to be inherited in this way.
Mendel also was lucky when he did his second set of experiments. He happened to pick characteristics that are inherited independently of one another. We now know that these characteristics are controlled by genes on nonhomologous chromosomes. What if Mendel had studied characteristics controlled by genes on homologous chromosomes? Would they be inherited together? If so, how do you think this would have affected Mendel’s conclusions? Would he have been able to develop his second law of inheritance?
To better understand how Mendel interpreted his findings and developed his laws of inheritance, you can visit the following link. It provides an animation in which Mendel explains how he came to understand heredity from his experimental results.http://www.dnalc.org/view/16154-Animation-2-Genes-Come-in-Pairs.html
Summary
• Mendel’s work was rediscovered in 1900. Soon after that, genes and alleles were discovered. This allowed Mendel’s laws to be stated in terms of the inheritance of alleles.
• The gene for a characteristic may have different versions. These different versions of a gene are known as alleles.
• Alleles for different genes assort independently during meiosis.
• The alleles an individual inherits make up the individual’s genotype. The individual may be homozygous (two of the same alleles) or heterozygous (two different alleles).
• The expression of an organism’s genotype produces its phenotype.
• When only one of two alleles is expressed, the expressed allele is the dominant allele, and the allele that isn’t expressed is the recessive allele.
• Mendel used the percentage of phenotypes in offspring to understand how characteristics are inherited.
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Use these resources to answer the questions that follow.
1. What is a gene?
2. The gene for flower color in pea plants can occur in the white or red form. What are these two different forms of the same gene?
3. How many copies of a gene are in a gamete?
4. How many copies of a gene are in a zygote?
5. State Mendel's law of segregation.
Review
1. If Darwin knew of Mendel’s work, how might it have influenced his theory of evolution? Do you think this would have affected how well Darwin’s work was accepted?
2. Explain Mendel’s laws in genetic terms, that is, in terms of chromosomes, genes, and alleles.
3. Explain the relationship between genotype and phenotype. How can one phenotype result from more than one genotype? | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/03%3A_Genetics/3.04%3A_Mendel%27s_Laws_and_Genetics.txt |
What are the odds of landing on 25 again?
Not as high as inheriting an allele from a parent. Probability plays a big role in determining the chance of inheriting an allele from a parent. It is similar to tossing a coin. What's the chance of the coin landing on heads?
Probability
Assume you are a plant breeder trying to develop a new variety of plant that is more useful to humans. You plan to cross-pollinate an insect-resistant plant with a plant that grows rapidly. Your goal is to produce a variety of plant that is both insect resistant and fast growing. What percentage of the offspring would you expect to have both characteristics? Mendel’s laws can be used to find out. However, to understand how Mendel’s laws can be used in this way, you first need to know about probability.
Probability is the likelihood, or chance, that a certain event will occur. The easiest way to understand probability is with coin tosses (see Figure below). When you toss a coin, the chance of a head turning up is 50 percent. This is because a coin has only two sides, so there is an equal chance of a head or tail turning up on any given toss.
Tossing a Coin. Competitions often begin with the toss of a coin. Why is this a fair way to decide who goes first? If you choose heads, what is the chance that the toss will go your way?
If you toss a coin twice, you might expect to get one head and one tail. But each time you toss the coin, the chance of a head is still 50 percent. Therefore, it’s quite likely that you will get two or even several heads (or tails) in a row. What if you tossed a coin ten times? You would probably get more or less than the expected five heads. For example, you might get seven heads (70 percent) and three tails (30 percent). The more times you toss the coin, however, the closer you will get to 50 percent heads. For example, if you tossed a coin 1000 times, you might get 510 heads and 490 tails.
Probability and Inheritance
The same rules of probability in coin tossing apply to the main events that determine thegenotypes of offspring. These events are the formation of gametes during meiosis and the union of gametes during fertilization.
Probability and Gamete Formation
How is gamete formation like tossing a coin? Consider Mendel’s purple-flowered pea plants again. Assume that a plant is heterozygous for the flower-color allele, so it has the genotypeBb (see Figure below). During meiosis, homologous chromosomes, and the alleles they carry, segregate and go to different gametes. Therefore, when the Bb pea plant forms gametes, theB and b alleles segregate and go to different gametes. As a result, half the gametes produced by the Bb parent will have the B allele and half will have the b allele. Based on the rules of probability, any given gamete of this parent has a 50 percent chance of having the B allele and a 50 percent chance of having the b allele.
Formation of gametes by meiosis. Paired alleles always separate and go to different gametes during meiosis.
Probability and Fertilization
Which of these gametes joins in fertilization with the gamete of another parent plant? This is a matter of chance, like tossing a coin. Thus, we can assume that either type of gamete—one with the B allele or one with the b allele—has an equal chance of uniting with any of the gametes produced by the other parent. Now assume that the other parent is also Bb. If gametes of two Bb parents unite, what is the chance of the offspring having one of each allele like the parents (Bb)? What is the chance of them having a different combination of alleles than the parents (either BB or bb)? To answer these questions, geneticists use a simple tool called a Punnett square, which is the focus of the next concept.
Summary
• Probability is the chance that a certain event will occur. For example, the probability of a head turning up on any given coin toss is 50 percent.
• Probability can be used to predict the chance of gametes and offspring having certain alleles.
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Use this resource to answer the questions that follow.
• Rules of Probability for Mendelian Inheritanceat www.boundless.com/biology/textbooks/boundless-biology-textbook/mendel-s-experiments-and-heredity-12/mendel-s-experiments-and-the-laws-of-probability-94/rules-of-probability-for-mendelian-inheritance-413-11640/.
1. Distinguish between the product rule and the sum rule.
2. Define probability.
3. How can you determine the probability of two independent events that occur together?
Review
1. Define probability. Apply the term to a coin toss.
2. How is gamete formation like tossing a coin?
3. With a BB homozygote, what is the chance of a gamete having the B allele? The b allele? | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/03%3A_Genetics/3.05%3A_Probability_and_Inheritance.txt |
What do you get when you cross an apple and an orange?
Though the above fruit may not result, it would be nice to scientifically predict what would result. Predicting the possible genotypes and phenotypes from a genetic cross is often aided by a Punnett square.
Punnett Squares
A Punnett square is a chart that allows you to easily determine the expected percentage of different genotypes in the offspring of two parents. An example of a Punnett square for pea plants is shown in Figure below. In this example, both parents are heterozygous for flowercolor (Bb). The gametes produced by the male parent are at the top of the chart, and the gametes produced by the female parent are along the side. The different possible combinations of alleles in their offspring are determined by filling in the cells of the Punnett square with the correct letters (alleles). At the link below, you can watch an animation in which Reginald Punnett, inventor of the Punnett square, explains the purpose of his invention and how to use it. http://www.dnalc.org/view/16192-Animation-5-Genetic-inheritance-follows-rules-.html
An explanation of Punnett squares can be viewed at http://www.youtube.com/watch?v=D5ymMYcLtv0 (25:16). Another example of the use of a Punnett square can be viewed athttp://www.youtube.com/watch?v=nsHZbgOmVwg (5:40).
This Punnett square shows a cross between two heterozygotes, Bb. Do you know where each letter (allele) in all four cells comes from? Two pea plants, both heterozygous for flower color, are crossed. The offspring will show the dominant purple coloration in a 3:1 ratio. Or, about 75% of the offspring will be purple.
Predicting Offspring Genotypes
In the cross shown in Figure above, you can see that one out of four offspring (25 percent) has the genotype BB, one out of four (25 percent) has the genotype bb, and two out of four (50 percent) have the genotype Bb. These percentages of genotypes are what you would expect in any cross between two heterozygous parents. Of course, when just four offspring are produced, the actual percentages of genotypes may vary by chance from the expected percentages. However, if you considered hundreds of such crosses and thousands of offspring, you would get very close to the expected results, just like tossing a coin.
Predicting Offspring Phenotypes
You can predict the percentages of phenotypes in the offspring of this cross from their genotypes. B is dominant to b, so offspring with either the BB or Bb genotype will have the purple-flower phenotype. Only offspring with the bb genotype will have the white-flower phenotype. Therefore, in this cross, you would expect three out of four (75 percent) of the offspring to have purple flowers and one out of four (25 percent) to have white flowers. These are the same percentages that Mendel got in his first experiment.
Determining Missing Genotypes
A Punnett square can also be used to determine a missing genotype based on the other genotypes involved in a cross. Suppose you have a parent plant with purple flowers and a parent plant with white flowers. Because the b allele is recessive, you know that the white-flowered parent must have the genotype bb. The purple-flowered parent, on the other hand, could have either the BB or the Bb genotype. The Punnett square in Figure below shows this cross. The question marks (?) in the chart could be either B or b alleles.
Punnett Square: Cross Between White-Flowered and Purple-Flowered Pea Plants. This Punnett square shows a cross between a white-flowered pea plant and a purple-flowered pea plant. Can you fill in the missing alleles? What do you need to know about the offspring to complete their genotypes?
Can you tell what the genotype of the purple-flowered parent is from the information in the Punnett square? No; you also need to know the genotypes of the offspring in row 2. What if you found out that two of the four offspring have white flowers? Now you know that the offspring in the second row must have the bb genotype. One of their b alleles obviously comes from the white-flowered (bb) parent, because that’s the only allele this parent has. The other b allele must come from the purple-flowered parent. Therefore, the parent with purple flowers must have the genotype Bb.
Punnett Square for Two Characteristics
When you consider more than one characteristic at a time, using a Punnett square is more complicated. This is because many more combinations of alleles are possible. For example, with two genes each having two alleles, an individual has four alleles, and these four alleles can occur in 16 different combinations. This is illustrated for pea plants in Figure below. In this cross, known as a dihybrid cross, both parents are heterozygous for pod color (Gg) and pod form (Ff).
Punnett Square for Two Characteristics. This Punnett square represents a cross between two pea plants that are heterozygous for two characteristics. G represents the dominant allele for green pod color, and g represents the recessive allele for yellow pod color. F represents the dominant allele for full pod form, and f represents the recessive allele for constricted pod form.
Summary
• A Punnett square is a chart that allows you to determine the expected percentages of different genotypes in the offspring of two parents.
• A Punnett square allows the prediction of the percentages of phenotypes in the offspring of a cross from known genotypes.
• A Punnett square can be used to determine a missing genotype based on the other genotypes involved in a cross.
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Explore More I
Use this resource to answer the questions that follow.
1. What is a Punnett square?
2. What do the boxes in a Punnett square represent?
3. What is the size of a Punnett square used in a dihybrid cross?
4. Define the following terms: alleles, genotype, phenotype, genome.
Review
1. What is a Punnett square? How is it used?
2. Draw a Punnett square of an Ss x ss cross. The S allele codes for long stems in pea plants and the s allele codes for short stems. If S is dominant to s, what percentage of the offspring would you expect to have each phenotype?
3. What letter should replace the question marks (?) in this Punnett square? Explain how you know.
4. How do the Punnett squares for a monohybrid cross and a dihybrid cross differ?
5. What are the genotypes of gametes of a AaBb self-pollination?
6. Mendel carried out a dihybrid cross to examine the inheritance of the characteristics for seed color and seed shape. The dominant allele for yellow seed color is Y, and the recessive allele for green color is y. The dominant allele for round seeds is R, and the recessive allele for a wrinkled shape is r. The two plants that were crossed were F1 dihybrids RrYy. Identify the ratios of traits that Mendel observed in the F2 generation. Create a Punnett square to help you answer the question. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/03%3A_Genetics/3.06%3A_Punnett_Squares.txt |
Green, blue, brown, black, hazel, violet, or grey. What color are your eyes?
Of course human eyes do not come in multi-color, but they do come in many colors. How do eyes come in so many colors? That brings us to complex inheritance patterns, known as non-Mendelian inheritance. Many times inheritance is more complicated than the simple patterns observed by Mendel.
Non-Mendelian Inheritance
The inheritance of characteristics is not always as simple as it is for the characteristics that Mendel studied in pea plants. Each characteristic Mendel investigated was controlled by one gene that had two possible alleles, one of which was completely dominant to the other. This resulted in just two possible phenotypes for each characteristic. Each characteristic Mendel studied was also controlled by a gene on a different (nonhomologous) chromosome. As a result, each characteristic was inherited independently of the other characteristics. Geneticists now know that inheritance is often more complex than this.
A characteristic may be controlled by one gene with two alleles, but the two alleles may have a different relationship than the simple dominant-recessive relationship that you have read about so far. For example, the two alleles may have a codominant or incompletely dominant relationship. The former is illustrated by the flower in Figure below, and the latter in Figure below.
Codominance
Codominance occurs when both alleles are expressed equally in the phenotype of the heterozygote. The red and white flower in the figure has codominant alleles for red petals and white petals.
Codominance. The flower has red and white petals because of codominance of red-petal and white-petal alleles.
Incomplete Dominance
Incomplete dominance occurs when the phenotype of the offspring is somewhere in between the phenotypes of both parents; a completely dominant allele does not occur. For example, when red snapdragons (CRCR) are crossed with white snapdragons (CWCW), the F1hybrids are all pink heterozygotes for flower color (CRCW). The pink color is an intermediate between the two parent colors. When two F1 (CRCW) hybrids are crossed they will produce red, pink, and white flowers. The genotype of an organism with incomplete dominance can be determined from its phenotype (Figure below).
Incomplete Dominance. The flower has pink petals because of incomplete dominance of a red-petal allele and a recessive white-petal allele.
Multiple Alleles
Many genes have multiple (more than two) alleles. An example is ABO blood type in humans. There are three common alleles for the gene that controls this characteristic. The alleles IAand IB are dominant over i. A person who is homozygous recessive ii has type O blood. Homozygous dominant IAIA or heterozygous dominant IAi have type A blood, and homozygous dominant IBIB or heterozygous dominant IBi have type B blood. IAIB people have type AB blood, because the A and B alleles are codominant. Type A and type B parents can have a type AB child. Type A and type B parents can also have a child with Type O blood, if they are both heterozygous (IBi, IAi).
• Type A blood: IAIA, IAi
• Type B blood: IB IB, IB i
• Type AB blood: IAIB
• Type O blood: ii
Polygenic Characteristics
Polygenic characteristics are controlled by more than one gene, and each gene may have two or more alleles. The genes may be on the same chromosome or on nonhomologous chromosomes.
• If the genes are located close together on the same chromosome, they are likely to be inherited together. However, it is possible that they will be separated by crossing-over during meiosis, in which case they may be inherited independently of one another.
• If the genes are on non homologous chromosomes, they may be recombined in various ways because of independent assortment.
For these reasons, the inheritance of polygenic characteristics is very complicated. Such characteristics may have many possible phenotypes. Skin color and adult height are examples of polygenic characteristics in humans. Do you have any idea how many phenotypes each characteristic has?
Human Adult Height. Like many other polygenic traits, adult height has a bell-shaped distribution.
Effects of Environment on Phenotype
Genes play an important role in determining an organism’s characteristics. However, for many characteristics, the individual’s phenotype is influenced by other factors as well. Environmental factors, such as sunlight and food availability, can affect how genes are expressed in the phenotype of individuals. Here are just two examples:
• Genes play an important part in determining our adult height. However, factors such as poor nutrition can prevent us from achieving our full genetic potential.
• Genes are a major determinant of human skin color. However, exposure to ultraviolet radiation can increase the amount of pigment in the skin and make it appear darker.
Summary
• Many characteristics have more complex inheritance patterns than those studied by Mendel. They are complicated by factors such as codominance, incomplete dominance, multiple alleles, and environmental influences.
Explore More
Use this resource to answer the questions that follow.
1. Flower color in carnations demonstrates what type of inheritance?
2. What is the genotype of a pink carnation?
3. What are the alleles for blood type in humans?
4. How is skin color in humans determined?
5. Define pleiotropy.
Review
1. A classmate tells you that a person can have type AO blood. Do you agree? Explain.
2. Mendelian inheritance does not apply to the inheritance of alleles that result in incomplete dominance and codominance. Explain why this is so.
3. Describe the relationship between environment and phenotype.
4. Mendel investigated stem length, or height, in pea plants. What if he had investigated human height instead? Why would his results have been harder to interpret? | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/03%3A_Genetics/3.07%3A_Non-Mendelian_Inheritance.txt |
All these ACGTs. What are they?
Over three billion of them from a human form the human genome - the human genetic material - all the information needed to encode a human being. It would take about 9.5 years to read out loud - without stopping - the more than three billion pairs of bases in one person's genome.
The Human Genome
What makes each one of us unique? You could argue that the environment plays a role, and it does to some extent. But most would agree that your parents have something to do with your uniqueness. In fact, it is our genes that make each one of us unique – or at least genetically unique. We all have the genes that make us human: the genes for skin and bones, eyes and ears, fingers and toes, and so on. However, we all have different skin colors, different bone sizes, different eye colors and different ear shapes. In fact, even though we have the same genes, the products of these genes work a little differently in most of us. And that is what makes us unique.
The human genome is the genome - all the DNA - of Homo sapiens. Humans have about 3 billion bases of information, divided into roughly 20,000 to 22,000 genes, which are spread among non-coding sequences and distributed among 24 distinct chromosomes (22autosomes plus the X and Y sex chromosomes) (below). The genome is all of the hereditary information encoded in the DNA, including the genes and non-coding sequences.
Human Genome, Chromosomes, and Genes. Each chromosome of the human genome contains many genes as well as noncoding intergenic (between genes) regions. Each pair of chromosomes is shown here in a different color.
Thanks to the Human Genome Project, scientists now know the DNA sequence of the entire human genome. The Human Genome Project is an international project that includes scientists from around the world. It began in 1990, and by 2003, scientists had sequenced all 3 billion base pairs of human DNA. Now they are trying to identify all the genes in the sequence. The Human Genome Project has produced a reference sequence of the human genome. The human genome consists of protein-coding exons, associated introns and regulatory sequences, genes that encode other RNA molecules, and other DNA sequences (sometimes referred to as "junk" DNA), which are regions in which no function as yet been identified.
You can watch a video about the Human Genome Project and how it cracked the "code of life" at this link: http://www.pbs.org/wgbh/nova/genome/program.html.
Our Molecular Selves video discusses the human genome, and is available athttp://www.genome.gov/25520211 or http://www.youtube.com/watch?v=_EK3g6px7Ik.Genome, Unlocking Life's Code is the Smithsonian's National Museum of Natural History exhibit of the human genome. See http://unlockinglifescode.org to visit the exhibit.
ENCODE: The Encyclopedia of DNA Elements
In September 2012, ENCODE, The Encyclopedia of DNA Elements, was announced. ENCODE was a colossal project, involving over 440 scientists in 32 labs the world-over, whose goal was to understand the human genome. It had been thought that about 80% of the human genome was "junk" DNA. ENCODE has established that this is not true. Now it is thought that about 80% of the genome is active. In fact, much of the human genome is regulatory sequences, on/off switches that tell our genes what to do and when to do it. Dr. Eric Green, director of the National Human Genome Research Institute of the National Institutes of Health which organized this project, states, "It's this incredible choreography going on, of a modest number of genes and an immense number of ... switches that are choreographing how those genes are used."
It is now thought that at least three-quarters of the genome is involved in making RNA, and most of this RNA appears to help regulate gene activity. Scientists have also identified about 4 million sites where proteins bind to DNA and act in a regulatory capacity. These new findings demonstrate that the human genome has remarkable and precise, and complex, controls over the expression of genetic information within a cell.
See ENCODE data describes function of human genome athttp://www.genome.gov/27549810 for additional information.
Summary
• The human genome consists of about 3 billion base pairs of DNA.
• In 2003, the Human Genome Project finished sequencing all 3 billion base pairs.
Explore More
Use this resource to answer the questions that follow.
1. What were 3 goals of the Human Genome Project?
2. How many genes are on chromosome #1?
3. How big is the human genome?
4. How much genetic variation is there among people?
5. How much of the genome is not part of any gene?
Review
1. Describe the human genome.
2. What has the Human Genome Project achieved?
3. Describe the makeup of the human genome. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/03%3A_Genetics/3.08%3A_Human_Genome.txt |
Coiled bundles of DNA and proteins, containing hundreds or thousands of genes. What are these things?
Chromosomes. These ensure that each cell receives the proper amount of DNA during cell division. And usually people have 46 of them, 23 from each parent.
Chromosomes and Genes
Each species has a characteristic number of chromosomes. Chromosomes are coiled structures made of DNA and proteins called histones (Figure below). Chromosomes are the form of the genetic material of a cell during cell division. See the "Chromosomes" section for additional information.
The human genome has 23 pairs of chromosomes located in the nucleus of somatic cells. Each chromosome is composed of genes and other DNA wound around histones (proteins) into a tightly coiled molecule.
The human species is characterized by 23 pairs of chromosomes, as shown in Figure below. You can watch a short animation about human chromosomes at this link:http://www.dnalc.org/view/15520-DNA-is-organized-into-46-chromosomes-including-sex-chromosomes-3D-animation.html.
Human Chromosomes. Humans have 23 pairs of chromosomes. Pairs 1-22 are autosomes. Females have two X chromosomes, and males have an X and a Y chromosome.
Autosomes
Of the 23 pairs of human chromosomes, 22 pairs are autosomes (numbers 1–22 in Figureabove). Autosomes are chromosomes that contain genes for characteristics that are unrelated to sex. These chromosomes are the same in males and females. The great majority of human genes are located on autosomes. At the link below, you can click on any human chromosome to see which traits its genes control.http://www.ornl.gov/sci/techresources/Human_Genome/posters/chromosome/chooser.shtml
Sex Chromosomes
The remaining pair of human chromosomes consists of the sex chromosomes, X and Y. Females have two X chromosomes, and males have one X and one Y chromosome. In females, one of the X chromosomes in each cell is inactivated and known as a Barr body. This ensures that females, like males, have only one functioning copy of the X chromosome in each cell.
As you can see from Figure above and Figure above, the X chromosome is much larger than the Y chromosome. The X chromosome has about 2,000 genes, whereas the Y chromosome has fewer than 100, none of which are essential to survival. (For comparison, the smallest autosome, chromosome 22, has over 500 genes.) Virtually all of the X chromosome genes are unrelated to sex. Only the Y chromosome contains genes that determine sex. A single Y chromosome gene, called SRY (which stands for sex-determining region Y gene), triggers an embryo to develop into a male. Without a Y chromosome, an individual develops into a female, so you can think of female as the default sex of the human species. Can you think of a reason why the Y chromosome is so much smaller than the X chromosome? At the link that follows, you can watch an animation that explains why:www.hhmi.org/biointeractive/g...evolution.html.
Human Genes
Humans have an estimated 20,000 to 22,000 genes. This may sound like a lot, but it really isn’t. Far simpler species have almost as many genes as humans. However, human cells use splicing and other processes to make multiple proteins from the instructions encoded in a single gene. Of the 3 billion base pairs in the human genome, only about 25 percent make up genes and their regulatory elements. The functions of many of the other base pairs are still unclear. To learn more about the coding and noncoding sequences of human DNA, watch the animation at this link: www.hhmi.org/biointeractive/d...sequences.html.
The majority of human genes have two or more possible alleles, which are alternative forms of a gene. Differences in alleles account for the considerable genetic variation among people. In fact, most human genetic variation is the result of differences in individual DNA bases within alleles.
Summary
• Humans have 23 pairs of chromosomes. Of these, 22 pairs are autosomes.
• The X and Y chromosomes are the sex chromosomes. Females have two X chromosomes, and males have one X and one Y.
• Human chromosomes contain a total of 20,000 to 22,000 genes, the majority of which have two or more alleles.
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Use this resource to answer the questions that follow.
1. What is a chromosome?
2. What is the role of chromosomes during cell division?
3. Do all living things have the same types of chromosomes?
4. What are centromeres? What is their role?
5. What are telomeres? What is their role?
Review
1. Describe human chromosomes.
2. Compare and contrast human autosomes and sex chromosomes.
3. What is SRY?
4. Why are females the "default sex" of the human species? | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/03%3A_Genetics/3.09%3A_Human_Chromosomes_and_Genes.txt |
What does it mean to be linked?
For a pair of hands, the above image may suggest a certain type of linkage. For genes, it might suggest that they are very hard to separate.
Linkage
Genes that are located on the same chromosome are called linked genes. Alleles for these genes tend to segregate together during meiosis, unless they are separated by crossing-over.Crossing-over occurs when two homologous chromosomes exchange genetic material during meiosis I. The closer together two genes are on a chromosome, the less likely their alleles will be separated by crossing-over. At the following link, you can watch an animation showing how genes on the same chromosome may be separated by crossing-over:www.biostudio.com/d_%20Meioti...ed%20Genes.htm.
Linkage explains why certain characteristics are frequently inherited together. For example, genes for hair color and eye color are linked, so certain hair and eye colors tend to be inherited together, such as blonde hair with blue eyes and brown hair with brown eyes. What other human traits seem to occur together? Do you think they might be controlled by linked genes?
Sex-Linked Genes
Genes located on the sex chromosomes are called sex-linked genes. Most sex-linked genes are on the X chromosome, because the Y chromosome has relatively few genes. Strictly speaking, genes on the X chromosome are X-linked genes, but the term sex-linked is often used to refer to them.
Sex-linked traits are discussed at http://www.youtube.com/watch?v=-ROhfKyxgCo (14:19).
Mapping Linkage
Linkage can be assessed by determining how often crossing-over occurs between two genes on the same chromosome. Genes on different (nonhomologous) chromosomes are not linked. They assort independently during meiosis, so they have a 50 percent chance of ending up in different gametes. If genes show up in different gametes less than 50 percent of the time (that is, they tend to be inherited together), they are assumed to be on the same (homologous) chromosome. They may be separated by crossing-over, but this is likely to occur less than 50 percent of the time. The lower the frequency of crossing-over, the closer together on the same chromosome the genes are presumed to be. Frequencies of crossing-over can be used to construct a linkage map like the one in Figure below. A linkage map shows the locations of genes on a chromosome.
Linkage Map for the Human X Chromosome. This linkage map shows the locations of several genes on the X chromosome. Some of the genes code for normal proteins. Others code for abnormal proteins that lead to genetic disorders. Which pair of genes would you expect to have a lower frequency of crossing-over: the genes that code for hemophilia A and G6PD deficiency, or the genes that code for protan and Xm?
Summary
• Linked genes are located on the same chromosome.
• Sex-linked genes are located on a sex chromosome, and X-linked genes are located on the X chromosome.
• The frequency of crossing-over between genes is used to construct linkage maps that show the locations of genes on chromosomes.
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Explore More I
Use these resources to answer the questions that follow.
1. What is recombination?
2. What determines the amount of recombination between two genes?
3. What are recombinant gametes?
4. What is a centimorgan?
Explore More II
• T. H. Morgan at www.dnalc.org/resources/nobel/morgan.html.
Review
1. What are linked genes?
2. Explain how you would construct a linkage map for a human chromosome. What data would you need?
3. People with red hair usually have very light skin. What might be a genetic explanation for this observation?
4. How often does crossing-over occur between non-linked genes? Explain your answer. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/03%3A_Genetics/3.10%3A_Genetic_Linkage.txt |
What number can you see?
Red-green colorblindness is a common inherited trait in humans. About 1 in 10 men have some form of color blindness, however, very few women are color blind. Why?
Mendelian Inheritance in Humans
Characteristics that are encoded in DNA are called genetic traits. Different types of human traits are inherited in different ways. Some human traits have simple inheritance patterns like the traits that Gregor Mendel studied in pea plants. Other human traits have more complex inheritance patterns.
Mendelian inheritance refers to the inheritance of traits controlled by a single gene with two alleles, one of which may be dominant to the other. Not many human traits are controlled by a single gene with two alleles, but they are a good starting point for understanding human heredity. How Mendelian traits are inherited depends on whether the traits are controlled by genes on autosomes or the X chromosome.
Autosomal Traits
Autosomal traits are controlled by genes on one of the 22 human autosomes. Consider earlobe attachment. A single autosomal gene with two alleles determines whether you have attached earlobes or free-hanging earlobes. The allele for free-hanging earlobes (F) is dominant to the allele for attached earlobes (f). Other single-gene autosomal traits include widow’s peak and hitchhiker’s thumb. The dominant and recessive forms of these traits are shown in Figure below. Which form of these traits do you have? What are your possible genotypes for the traits?
The chart in Figure below is called a pedigree. It shows how the earlobe trait was passed from generation to generation within a family. Pedigrees are useful tools for studying inheritance patterns.
You can watch a video explaining how pedigrees are used and what they reveal at this link:http://www.youtube.com/watch?v=HbIHjsn5cHo.
Having free-hanging earlobes is an autosomal dominant trait. This figure shows the trait and how it was inherited in a family over three generations. Shading indicates people who have the recessive form of the trait. Look at (or feel) your own earlobes. Which form of the trait do you have? Can you tell which genotype you have?
Other single-gene autosomal traits include widow's peak and hitchhiker's thumb. The dominant and recessive forms of these traits are shown in Figure below. Which form of these traits do you have? What are your possible genotypes for the traits?
Widow's peak and hitchhiker's thumb are dominant traits controlled by a single autosomal gene.
Sex-Linked Traits
Traits controlled by genes on the sex chromosomes are called sex-linked traits, or X-linked traits in the case of the X chromosome. Single-gene X-linked traits have a different pattern of inheritance than single-gene autosomal traits. Do you know why? It’s because males have just one X chromosome. In addition, they always inherit their X chromosome from their mother, and they pass it on to all their daughters but none of their sons. This is illustrated in Figurebelow.
Inheritance of Sex Chromosomes. Mothers pass only X chromosomes to their children. Fathers always pass their X chromosome to their daughters and their Y chromosome to their sons. Can you explain why fathers always determine the sex of the offspring?
Because males have just one X chromosome, they have only one allele for any X-linked trait. Therefore, a recessive X-linked allele is always expressed in males. Because females have two X chromosomes, they have two alleles for any X-linked trait. Therefore, they must inherit two copies of the recessive allele to express the recessive trait. This explains why X-linked recessive traits are less common in females than males. An example of a recessive X-linked trait is red-green color blindness. People with this trait cannot distinguish between the colors red and green. More than one recessive gene on the X chromosome codes for this trait, which is fairly common in males but relatively rare in females (Figure below). At the following link, you can watch an animation about another X-linked recessive trait called hemophilia A:http://www.dnalc.org/view/16315-Animation-13-Mendelian-laws-apply-to-human-beings-.html.
Pedigree for Color Blindness. Color blindness is an X-linked recessive trait. Mothers pass the recessive allele for the trait to their sons, who pass it to their daughters.
Summary
• A minority of human traits are controlled by single genes with two alleles.
• They have different inheritance patterns depending on whether they are controlled by autosomal or X-linked genes.
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Explore More I
Use these resources to answer the questions that follow.
1. A homozygous freckled man marries a non-freckled woman. If freckles are dominant, will their children have freckles? Explain your answer.
2. Using F and f, what are the genotypes of the parents? What are the genotypes of their gametes?
Explore More II
• Pedigree Analysis
Review
• Describe the inheritance pattern for a single-gene autosomal dominant trait, such as free-hanging earlobes.
• Draw a pedigree for hitchhiker’s thumb. Your pedigree should cover at least two generations and include both dominant and recessive forms of the trait. Label the pedigree with genotypes, using the letter H to represent the dominant allele for the trait and the letter h to represent the recessive allele.
• Why is a recessive X-linked allele always expressed in males?
• What is necessary for a recessive X-linked allele to be expressed in females?
• What is an example of a recessive X-linked trait? | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/03%3A_Genetics/3.11%3A_Mendelian_Inheritance_in_Humans.txt |
Is being short-statured inherited?
It can be. Achondroplasia is the most common form of dwarfism in humans, and it is caused by a dominant mutation. The mutation can be passed from one generation to the next.
Genetic Disorders
Many genetic disorders are caused by mutations in one or a few genes. Other genetic disorders are caused by abnormal numbers of chromosomes.
Genetic Disorders Caused by Mutations
The Table below lists several genetic disorders caused by mutations in just one gene. Some of the disorders are caused by mutations in autosomal genes, others by mutations in X-linked genes. Which disorder would you expect to be more common in males than females? You can watch a video about the human genome, genetic disorders, and mutations at this link:http://www.pbs.org/wgbh/nova/programs/ht/rv/2809_03.html.
You can click on any human chromosome at this link to see the genetic disorders associated with it:http://www.ornl.gov/sci/techresource.../chooser.shtml.
Genetic Disorder Direct Effect of Mutation Signs and Symptoms of the Disorder Mode of Inheritance
Marfan syndrome defective protein in connective tissue heart and bone defects and unusually long, slender limbs and fingers autosomal dominant
Sickle cell anemia abnormal hemoglobin protein in red blood cells sickle-shaped red blood cells that clog tinyblood vessels, causing pain and damaging organs and joints autosomal recessive
Vitamin D-resistant rickets lack of a substance needed for bones to absorb minerals soft bones that easily become deformed, leading to bowed legs and other skeletal deformities X-linked dominant
Hemophilia A reduced activity of a protein needed for blood clotting internal and external bleeding that occurs easily and is difficult to control X-linked recessive
Few genetic disorders are controlled by dominant alleles. A mutant dominant allele is expressed in every individual who inherits even one copy of it. If it causes a serious disorder, affected people may die young and fail to reproduce. Therefore, the mutant dominant allele is likely to die out of the population.
A mutant recessive allele, such as the allele that causes sickle cell anemia (see Figure belowand the link that follows), is not expressed in people who inherit just one copy of it. These people are called carriers. They do not have the disorder themselves, but they carry the mutant allele and can pass it to their offspring. Thus, the allele is likely to pass on to the next generation rather than die out. http://www.dnalc.org/resources/3d/17-sickle-cell.html
Sickle-Shaped and Normal Red Blood Cells. Sickle cell anemia is an autosomal recessive disorder. The mutation that causes the disorder affects just one amino acid in a single protein, but it has serious consequences for the affected person. This photo shows the sickle shape of red blood cells in people with sickle cell anemia.
Cystic Fibrosis and Tay-Sachs disease are two additional severe genetic disorders. They are discussed in the following video: http://www.youtube.com/watch?v=8s4he3wLgkM (9:31). Tay-Sachs is further discussed at http://www.youtube.com/watch?v=1RO0LOgHbIo (3:13) andhttp://www.youtube.com/watch?v=6zNj5LdDuTA (2:01).
Chromosomal Disorders
Mistakes may occur during meiosis that result in nondisjunction. This is the failure of replicated chromosomes to separate during meiosis (the animation at the link below shows how this happens). Some of the resulting gametes will be missing a chromosome, while others will have an extra copy of the chromosome. If such gametes are fertilized and form zygotes, they usually do not survive. If they do survive, the individuals are likely to have serious genetic disorders. Table below lists several genetic disorders that are caused by abnormal numbers of chromosomes. Most chromosomal disorders involve the X chromosome. Look back at the X and Y chromosomes and you will see why. The X and Y chromosomes are very different in size, so nondisjunction of the sex chromosomes occurs relatively often. learn.genetics.utah.edu/conte...der/index.html
Genetic Disorder Genotype Phenotypic Effects
Down syndrome extra copy (complete or partial) of chromosome 21 (see Figure below) developmental delays, distinctive facial appearance, and other abnormalities (see Figurebelow)
Turner’s syndrome one X chromosome but no other sex chromosome (XO) female with short height and infertility (inability to reproduce)
Triple X syndrome three X chromosomes (XXX) female with mild developmental delays and menstrual irregularities
Klinefelter’s syndrome one Y chromosome and two or more X chromosomes (XXY, XXXY) male with problems in sexual development and reduced levels of the male hormone testosterone
(left) Trisomy 21 (Down Syndrome) Karyotype. A karyotype is a picture of a cell's chromosomes. Note the extra chromosome 21. (right) Child with Down syndrome, exhibiting characteristic facial appearance.
Diagnosing Genetic Disorders
A genetic disorder that is caused by a mutation can be inherited. Therefore, people with a genetic disorder in their family may be concerned about having children with the disorder. Professionals known as genetic counselors can help them understand the risks of their children being affected. If they decide to have children, they may be advised to have prenatal(“before birth”) testing to see if the fetus has any genetic abnormalities. One method of prenatal testing is amniocentesis. In this procedure, a few fetal cells are extracted from the fluid surrounding the fetus, and the fetal chromosomes are examined.
Treating Genetic Disorders
The symptoms of genetic disorders can sometimes be treated, but cures for genetic disorders are still in the early stages of development. One potential cure that has already been used with some success is gene therapy. This involves inserting normal genes into cells with mutant genes. At the following link, you can watch the video ‘‘Sickle Cell Anemia: Hope fromGene Therapy’’, to learn how scientists are trying to cure sickle-cell anemia with gene therapy. www.pubinfo.vcu.edu/secretsof...list_frame.asp
If you could learn your risk of getting cancer or another genetic disease, would you? Though this is a personal decision, it is a possibility. A number of companies now makes it easy to order medical genetic tests through the Web. See Genetic Testing through the Web athttp://www.kqed.org/quest/televisi...hrough-the-web.
Summary
• Many genetic disorders are caused by mutations in one or a few genes.
• Other genetic disorders are caused by abnormal numbers of chromosomes.
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Use this resource to answer the questions that follow.
1. How do mutations affect proteins?
2. What is a single-gene disorder?
3. What is a chromosomal disorder?
4. What is a complex disorder?
5. Give an example of a chromosomal disorder.
Review
1. Describe a genetic disorder caused by a mutation in a single gene.
2. What causes Down syndrome?
3. What is nondisjunction?
4. What is gene therapy?
5. Explain why genetic disorders caused by abnormal numbers of chromosomes most often involve the X chromosome. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/03%3A_Genetics/3.12%3A_Genetic_Disorders.txt |
So how does a scientist work with DNA?
It always starts with the sequence. Once the sequence is known, so much more can be done. Specific regions can be isolated, cloned, amplified, and then used to help us.
Biotechnology Methods
Biotechnology is the use of technology to change the genetic makeup of living things for human purposes. Generally, the purpose of biotechnology is to create organisms that are useful to humans or to cure genetic disorders. For example, biotechnology may be used to create crops that resist insect pests or yield more food, or to create new treatments for human diseases.
Biotechnology: The Invisible Revolution can be seen at http://www.youtube.com/watch?v=OcG9q9cPqm4.
What does biotechnology have to do with me? Is discussed in the following video:http://www.youtube.com/watch?v=rrT5BT_7HdI (10:01).
Biotechnology uses a variety of techniques to achieve its aims. Two commonly used techniques are gene cloning and the polymerase chain reaction.
Gene Cloning
Gene cloning is the process of isolating and making copies of a gene. This is useful for many purposes. For example, gene cloning might be used to isolate and make copies of a normal gene for gene therapy. Gene cloning involves four steps: isolation, ligation, transformation, and selection. You can watch an interactive animation about gene cloning at this link:http://www.teachersdomain.org/asset/...int_geneclone/.
1. In isolation, an enzyme (called a restriction enzyme) is used to break DNA at a specific base sequence. This is done to isolate a gene.
2. During ligation, the enzyme DNA ligase combines the isolated gene with plasmid DNAfrom bacteria. (A plasmid is circular DNA that is not part of a chromosome and can replicate independently.) Ligation is illustrated in Figure below. The DNA that results is called recombinant DNA.
3. In transformation, the recombinant DNA is inserted into a living cell, usually a bacterial cell. Changing an organism in this way is also called genetic engineering.
4. Selection involves growing transformed bacteria to make sure they have the recombinant DNA. This is a necessary step because transformation is not always successful. Only bacteria that contain the recombinant DNA are selected for further use.
Ligation. DNA ligase joins together an isolated gene and plasmid DNA. This produces recombinant DNA.
Recombinant DNA technology is discussed in the following videos and animations:http://www.youtube.com/watch?v=x2jUMG2E-ic (4.36), http://www.youtube.com/watch?v=Jy15BWVxTC0 (0.50), http://www.youtube.com/watch?v=sjwNtQYLKeU (7.20),http://www.youtube.com/watch?v=Fi63VjfhsfI (3:59).
The experiments of Stanley Cohen and Herbert Boyer, pioneers of genetic engineering, are explained in the video at https://www.youtube.com/watch?v=nfC689ElUVk. More on these pioneers can be found at http://www.dnalc.org/view/16033-Stanley-Cohen-and-Herbert-Boyer-1972.html.
Polymerase Chain Reaction
The polymerase chain reaction (PCR) makes many copies of a gene or other DNA segment. This might be done in order to make large quantities of a gene for genetic testing. PCR involves three steps: denaturing, annealing, and extension. The three steps are illustrated in Figure below. They are repeated many times in a cycle to make large quantities of the gene. You can watch animations of PCR at these links:
1. Denaturing involves heating DNA to break the bonds holding together the two DNA strands. This yields two single strands of DNA.
2. Annealing involves cooling the single strands of DNA and mixing them with short DNA segments called primers. Primers have base sequences that are complementary to segments of the single DNA strands. As a result, bonds form between the DNA strands and primers.
3. Extension occurs when an enzyme (Taq polymerase or Taq DNA polymerase) adds nucleotides to the primers. This produces new DNA molecules, each incorporating one of the original DNA strands.
The Polymerase Chain Reaction. The polymerase chain reaction involves three steps. High temperatures are needed for the process to work. The enzyme Taq polymerase is used in step 3 because it can withstand high temperatures.
Summary
• Biotechnology is the use of technology to change the genetic makeup of living things for human purposes.
• Gene cloning is the process of isolating and making copies of a DNA segment such as a gene.
• The polymerase chain reaction makes many copies of a gene or other DNA segment.
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Use this resource and the videos associated with this resource to answer the questions that follow.
• Polymerase Chain Reaction at www.dnalc.org/resources/spotlight/index.html.
1. Who developed PCR?
2. What does PCR allow?
3. Describe the 3 steps involved in PCR.
4. Approximately how many copies of a specific segment of DNA can be made by PCR?
Review
1. Define biotechnology.
2. What is recombinant DNA?
3. Identify the steps of gene cloning.
4. What is the purpose of the polymerase chain reaction?
5. Describe the three steps of PCR. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/03%3A_Genetics/3.13%3A_Biotechnology.txt |
Why would anyone grow plants like this?
Developing better crops is a significant aspect of biotechnology. Crops that are resistant to damage from insects or droughts must have a significant role in the world's future. And it all starts in the lab.
Applications of Biotechnology
Methods of biotechnology can be used for many practical purposes. They are used widely in both medicine and agriculture. To see how biotechnology can be used to solve crimes, watch the video "Justice DNA—Freeing the Innocent" at the following link:www.pubinfo.vcu.edu/secretsof...list_frame.asp.
Applications in Medicine
In addition to gene therapy for genetic disorders, biotechnology can be used to transform bacteria so they are able to make human proteins. Figure below shows how this is done to produce a cytokine, which is a small protein that helps fight infections. Proteins made by the bacteria are injected into people who cannot produce them because of mutations.
Genetically Engineering Bacteria to Produce a Human Protein. Bacteria can be genetically engineered to produce a human protein, such as a cytokine. A cytokine is a small protein that helps fight infections.
Insulin was the first human protein to be produced in this way. Insulin helps cells take up glucose from the blood. People with type 1 diabetes have a mutation in the gene that normally codes for insulin. Without insulin, their blood glucose rises to harmfully high levels. At present, the only treatment for type 1 diabetes is the injection of insulin from outside sources. Until recently, there was no known way to make insulin outside the human body. The problem was solved by gene cloning. The human insulin gene was cloned and used to transform bacterial cells, which could then produce large quantities of human insulin.
Pharmacogenomics
We know that, thanks to our DNA, each of us is a little bit different. Some of those differences are obvious, like eye and hair color. Others are not so obvious, like how our bodies react to medication. Researchers are beginning to look at how to tailor medical treatments to our genetic profiles, in a relatively new field called pharmacogenomics. Some of the biggest breakthroughs have been in cancer treatment. For additional information on this “personalized medicine,” listen to www.kqed.org/quest/radio/pers...ed-medicineand see www.kqed.org/quest/blog/2009/...ized-medicine/.
Synthetic Biology
Imagine living cells acting as memory devices, biofuels brewing from yeast, or a light receptor taken from algae that makes photographs on a plate of bacteria. The new field of synthetic biology is making biology easier to engineer so that new functions can be derived from living systems. Find out the tools that synthetic biologists are using and the exciting things they are building at www.kqed.org/quest/television...thetic-biology.
Applications in Agriculture
Biotechnology has been used to create transgenic crops. Transgenic crops are genetically modified with new genes that code for traits useful to humans. The diagram in Figure below shows how a transgenic crop is created. You can learn more about how scientists create transgenic crops with the interactive animation "Engineer a Crop: Transgenic Manipulation" at this link: http://www.pbs.org/wgbh/harvest/engineer/transgen.html.
Creating a Transgenic Crop. A transgenic crop is genetically modified to be more useful to humans. The bacterium transfers the T-DNA (from the Ti plasmid) fragment with the desired gene into the host plant's nuclear genome.
Transgenic crops have been created with a variety of different traits, such as yielding more food, tasting better, surviving drought, and resisting insect pests. Scientists have even created a transgenic purple tomato that contains a cancer-fighting compound and others that have high levels of antioxidants (see Figure below). Seehttp://extension.oregonstate.edu/...tomato-debuts-‘indigo-rose’ for more information. To learn how scientists have used biotechnology to create plants that can grow in salty soil, watch the video "Salt of the Earth - Engineering Salt-tolerant Plants" at this link:http://www.sosq.vcu.edu/videos.aspx.
Transgenic Purple Tomato. A purple tomato is genetically modified to contain a cancer-fighting compound. A gene for the compound was transferred into normal red tomatoes.
Biotechnology in agriculture is discussed at http://www.youtube.com/watch?v=IY3mfgbe-0c(6:40).
Applications in Forensic Science
Biotechnology has also had tremendous impacts in the forensic sciences. Can DNA Demand a Verdict (http://learn.genetics.utah.edu/content/science/forensics/) discusses how DNA analysis is used to solve crimes. Also see Gel Electrophoresis athttps://www.youtube.com/watch?v=Pk5hCRE_28g to see how biotechnology helps with solving crimes.
Summary
• Biotechnology can be used to transform bacteria so they are able to make human proteins, such as insulin.
• It can also be used to create transgenic crops, such as crops that yield more food or resist insect pests.
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Explore More I
Use this resource to answer the questions that follow.
• Modern Biotechnology at www.biotechlearn.org.nz/theme..._biotechnology.
1. Give an example of early biotechnology.
2. Give an example of modern biotechnology.
3. Describe one use of biotechnology in:
1. medicine,
2. agriculture,
3. forensics.
Review
1. What are transgenic crops?
2. Make a flow chart outlining the steps involved in creating a transgenic crop.
3. Explain how bacteria can be genetically engineered to produce a human protein. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/03%3A_Genetics/3.14%3A_Biotechnology_Applications.txt |
Right or wrong? Good or bad? Legal or illegal?
The completion of The Human Genome Project is one of the most important scientific events of the past 50 years. However, is knowing all of our DNA a good thing? The advancement of biotechnology has raised many interesting ethical, legal and social questions.
Ethical, Legal, and Social Issues
Imagine someone analyzes part of your DNA. Who controls that information? What if your health insurance company found out you were predisposed to develop a devastating genetic disease. Might they decide to cancel your insurance? Privacy issues concerning genetic information is an important issue in this day and age.
ELSI stands for Ethical, Legal and Social Issues. It's a term associated with the Human Genome project. This project didn't only have the goal to identify all the genes in the human genome, but also to address the ELSI that might arise from the project. Rapid advances in DNA-based research, human genetics, and their applications have resulted in new and complex ethical and legal issues for society.
Concerns from Biotechnology
The use of biotechnology has raised a number of ethical, legal, and social issues. Here are just a few:
• Who owns genetically modified organisms such as bacteria? Can such organisms be patented like inventions?
• Are genetically modified foods safe to eat? Might they have unknown harmful effects on the people who consume them?
• Are genetically engineered crops safe for the environment? Might they harm other organisms or even entire ecosystems?
• Who controls a person’s genetic information? What safeguards ensure that the information is kept private?
• How far should we go to ensure that children are free of mutations? Should a pregnancy be ended if the fetus has a mutation for a serious genetic disorder?
Addressing such issues is beyond the scope of this concept. The following example shows how complex the issues may be:
A strain of corn has been created with a gene that encodes a natural pesticide. On the positive side, the transgenic corn is not eaten by insects, so there is more corn for people to eat. The corn also doesn’t need to be sprayed with chemical pesticides, which can harm people and other living things. On the negative side, the transgenic corn has been shown to cross-pollinate nearby milkweed plants. Offspring of the cross-pollinated milkweed plants are now known to be toxic to monarch butterfly caterpillars that depend on them for food. Scientists are concerned that this may threaten the monarch species as well as other species that normally eat monarchs.
As this example shows, the pros of biotechnology may be obvious, but the cons may not be known until it is too late. Unforeseen harm may be done to people, other species, and entire ecosystems. No doubt the ethical, legal, and social issues raised by biotechnology will be debated for decades to come. For a recent debate about the ethics of applying biotechnology to humans, watch the video at the link below. In the video, a Harvard University professor of government and a Princeton University professor of bioethics debate the science of “perfecting humans.” http://www.youtube.com/watch?v=-BPna-fSNOE
Summary
• Biotechnology has raised a number of ethical, legal, and social issues. For example, are genetically modified foods safe to eat, and who controls a person’s genetic information?
Explore More
Use this resource to answer the questions that follow.
1. What is the ELSI program focus of the Human Genome Project?
Review
1. Identify three ethical, legal, or social issues raised by biotechnology.
2. State your view on an ELSI issue, and develop a logical argument to support your view. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/03%3A_Genetics/3.15%3A_Ethical_Legal_and_Social_Issues_of_Biotechnology.txt |
Covers molecular biology, DNA, protein synthesis, gene regulation, and mutations.
04: Molecular Biology
Is it always DNA to RNA to proteins?
The central dogma of molecular biology. Coined by Francis Crick. And in his own words, "I called this idea the central dogma, for two reasons, I suspect. I had already used the obvious word hypothesis in the sequence hypothesis, and in addition I wanted to suggest that this new assumption was more central and more powerful."
Central Dogma of Molecular Biology
Your DNA, or deoxyribonucleic acid, contains the genes that determine who you are. How can this organic molecule control your characteristics? DNA contains instructions for all theproteins your body makes. Proteins, in turn, determine the structure and function of all yourcells. What determines a protein’s structure? It begins with the sequence of amino acids that make up the protein. Instructions for making proteins with the correct sequence of amino acids are encoded in DNA.
DNA is found in chromosomes. In eukaryotic cells, chromosomes always remain in the nucleus, but proteins are made at ribosomes in the cytoplasm. How do the instructions in DNA get to the site of protein synthesis outside the nucleus? Another type of nucleic acid is responsible. This nucleic acid is RNA, or ribonucleic acid. RNA is a small molecule that can squeeze through pores in the nuclear membrane. It carries the information from DNA in the nucleus to a ribosome in the cytoplasm and then helps assemble the protein. In short:
DNA → RNA → Protein
Discovering this sequence of events was a major milestone in molecular biology. It is called the central dogma of molecular biology. You can watch a video about the central dogma and other concepts in this lesson at this link: http://www.youtube.com/watch?v=ZjRCmU0_dhY(8:07).
The vocabulary of DNA, including the two processes involved in the central dogma, transcription and translation, is discussed at http://www.youtube.com/watch?v=s9HPNwXd9fk (18:23).
An overview of protein synthesis can be viewed at http://www.youtube.com/watch?v=-ygpqVr7_xs (10:46).
Summary
• The central dogma of molecular biology states that DNA contains instructions for making a protein, which are copied by RNA.
• RNA then uses the instructions to make a protein.
• In short: DNA → RNA → Protein, or DNA to RNA to Protein.
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Explore More I
Use this resource to answer the questions that follow.
• What Makes a Firefly Glow? at learn.genetics.utah.edu/conte...n/dna/firefly/.
1. What happens during transcription?
2. What happens to the mRNA after transcription?
3. What is a ribosome?
4. What happens during translation?
Review
1. State the central dogma of molecular biology.
2. What are transcription and translation?
3. Explain the central dogma of molecular biology.
4.02: DNA the Genetic Material
The spiral structure in the picture is a large organic molecule. What type of organic molecule is it?
Here’s a hint: molecules like this one determine who you are. They contain genetic information that controls your characteristics. They determine your eye color, facial features, and other physical attributes. What molecule is it?
You probably answered "DNA." Today, it is commonly known that DNA is the genetic material. For a long time, scientists knew such molecules existed. They were aware that genetic information was contained within organic molecules. However, they didn’t know which type of molecules play this role. In fact, for many decades, scientists thought that proteins were the molecules that carry genetic information. In this section, you will learn how scientists discovered that DNA carries the code of life.
DNA, the Genetic Material
DNA, deoxyribonucleic acid, is the genetic material in your cells. It was passed on to you from your parents and determines your characteristics. The discovery that DNA is the genetic material was another important milestone in molecular biology.
Griffith Searches for the Genetic Material
Many scientists contributed to the identification of DNA as the genetic material. In the 1920s, Frederick Griffith made an important discovery. He was studying two different strains of a bacterium, called R (rough) strain and S (smooth) strain. He injected the two strains into mice. The S strain killed (virulent) the mice, but the R strain did not (non-virulent) (see Figure below). Griffith also injected mice with S-strain bacteria that had been killed by heat. As expected, the killed bacteria did not harm the mice. However, when the dead S-strain bacteria were mixed with live R-strain bacteria and injected, the mice died.
Griffith’s Experimental Results. Griffith showed that a substance could be transferred to harmless bacteria and make them deadly.
Based on his observations, Griffith deduced that something in the killed S strain was transferred to the previously harmless R strain, making the R strain deadly. He called this process transformation, as something was "transforming" the bacteria from one strain into another strain. What was that something? What type of substance could change the characteristics of the organism that received it?
Avery’s Team Makes a Major Contribution
In the early 1940s, a team of scientists led by Oswald Avery tried to answer the question raised by Griffith’s results. They inactivated various substances in the S-strain bacteria. They then killed the S-strain bacteria and mixed the remains with live R-strain bacteria. (Keep in mind, the R-strain bacteria usually did not harm the mice.) When they inactivated proteins, the R-strain was deadly to the injected mice. This ruled out proteins as the genetic material. Why? Even without the S-strain proteins, the R strain was changed, or transformed, into the deadly strain. However, when the researchers inactivated DNA in the S strain, the R strain remained harmless. This led to the conclusion that DNA is the substance that controls the characteristics of organisms. In other words, DNA is the genetic material. You can watch an animation about the research of both Griffith and Avery at this link:http://www.dnalc.org/view/16375-Animation-17-A-gene-is-made-of-DNA-.html.
Hershey and Chase Seal the Deal
The conclusion that DNA is the genetic material was not widely accepted at first. It had to be confirmed by other research. In the 1950s, Alfred Hershey and Martha Chase did experiments with viruses and bacteria. Viruses are not made of cells. They are basically DNA inside a protein coat. To reproduce, a virus must insert its own genetic material into a cell (such as a bacterium). Then it uses the cell’s machinery to make more viruses. The researchers used different radioactive elements to label the DNA and proteins in viruses. This allowed them to identify which molecule the viruses inserted into bacteria. DNA was the molecule they identified. This confirmed that DNA is the genetic material.
Summary
• The work of several researchers led to the discovery that DNA is the genetic material.
• Along the way, Griffith discovered the process of transformation.
Explore More
I) Bacteria and viruses have DNA too at
www.dnalc.org/resources/nobel/hershey.html
1. What is a bacteriophage?
2. How do phages reproduce?
3. Why was DNA labeled with radioactive phosphorus?
4. After the experiment, where was the radioactive phosphorus found?
5. What is the genetic material? Why?
Review
1. List the research that determined that DNA is the genetic material.
2. What is transformation?
3. What happened to the R-strain bacteria when Avery and his colleagues inactivated DNA in the S strain bacteria? | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/04%3A_Molecular_Biology/4.01%3A_Central_Dogma_of_Molecular_Biology.txt |
How do these four structures form DNA?
In an extremely elegant model, that's how. As you will soon see, the model predicts how the DNA sequence can code for proteins, and how the molecule can be replicated.
DNA Structure and Replication
Chargaff's Rules
Other important discoveries about DNA were made in the mid-1900s by Erwin Chargaff. He studied DNA from many different species. He was especially interested in the four different nitrogen bases of DNA: adenine (A), guanine (G), cytosine (C), and thymine (T) (see Figure below). Chargaff found that concentrations of the four bases differed from one species to another. However, within each species, the concentration of adenine was always about the same as the concentration of thymine. The same was true of the concentrations of guanine and cytosine. These observations came to be known as Chargaff’s rules. The significance of the rules would not be revealed until the structure of DNA was discovered.
Nitrogen Bases in DNA. The DNA of all species has the same four nitrogen bases.
The Double Helix
After DNA was found to be the genetic material, scientists wanted to learn more about it. James Watson and Francis Crick are usually given credit for discovering that DNA has adouble helix shape, like a spiral staircase (see Figure below). The discovery was based on the prior work of Rosalind Franklin and other scientists, who had used X rays to learn more about DNA’s structure. Franklin and these other scientists have not always been given credit for their contributions. You can learn more about Franklin’s work by watching the video at this link: http://www.youtube.com/watch?v=s3whouvZYG8 (7:47).
The DNA molecule has a double helix shape. This is the same basic shape as a spiral staircase. Do you see the resemblance? Which parts of the DNA molecule are like the steps of the spiral staircase?
The double helix shape of DNA, together with Chargaff’s rules, led to a better understanding of DNA. DNA, as a nucleic acid, is made from nucleotide monomers, and the DNA double helix consists of two polynucleotide chains. Each nucleotide consists of a sugar (deoxyribose), a phosphate group, and a nitrogen-containing base (A, C, G, or T).
Scientists concluded that bonds (hydrogen bonds) between complementary bases hold together the two polynucleotide chains of DNA. Adenine always bonds with its complementary base, thymine. Cytosine always bonds with its complementary base, guanine. If you look at the nitrogen bases in Figure above, you will see why. Adenine and guanine have a two-ring structure. Cytosine and thymine have just one ring. If adenine were to bind with guanine and cytosine with thymine, the distance between the two DNA chains would be variable. However, when a one-ring molecule binds with a two-ring molecule, the distance between the two chains is kept constant. This maintains the uniform shape of the DNA double helix. These base pairs (A-T or G-C) stick into the middle of the double helix, forming, in essence, the steps of the spiral staircase.
DNA Replication
Knowledge of DNA’s structure helped scientists understand how DNA replicates. DNA replication is the process in which DNA is copied. It occurs during the synthesis (S) phase of the eukaryotic cell cycle. DNA replication begins when an enzyme, DNA helicase, breaks the bonds between complementary bases in DNA (see Figure below). This exposes the bases inside the molecule so they can be “read” by another enzyme, DNA polymerase, and used to build two new DNA strands with complementary bases, also by DNA polymerase. The two daughter molecules that result each contain one strand from the parent molecule and one new strand that is complementary to it. As a result, the two daughter molecules are both identical to the parent molecule. DNA replication is a semi-conservative process because half of the parent DNA molecule is conserved in each of the two daughter DNA molecules.
The process of DNA replication is actually much more complex than this simple summary. You can see a detailed animation of the process at this link: http://www.youtube.com/watch?v=-mtLXpgjHL0 (2:05).
DNA Replication. DNA replication is a semi-conservative process. Half of the parent DNA molecule is conserved in each of the two daughter DNA molecules.
Summary
• Chargaff's rules state that the amount of A is similar to the amount of T, and the amount of G is similar to the amount of C.
• Watson and Crick discovered that DNA has a double helix shape, consisting of two polynucleotide chains held together by bonds between complementary bases.
• DNA replication is semi-conservative: half of the parent DNA molecule is conserved in each of the two daughter DNA molecules.
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Use these resources to answer the questions that follow.
Explore More I
1. Describe the structure of DNA.
2. The phrase ‘‘sides of the ladder’’ refers to what structure(s)?
3. Why is there a specific pairing pattern among the bases?
4. Why are the two strands of the double helix ‘‘perfect and specific compliments’’?
5. List three functions of DNA that are based on its structure.
Explore More II
1. Why must DNA be replicated?
2. When does replication occur?
3. Describe the first step of replication.
4. Why is each strand of DNA able to serve as a template for replication?
5. Explain the meaning of semi-conservative replication.
Explore More III
• Build a DNA Molecule at learn.genetics.utah.edu/conte.../dna/builddna/.
Review
1. What are Chargaff’s rules?
2. Identify the structure of the DNA molecule.
3. What are nucleotides? What makes up a nucleotide?
4. Why is DNA replication said to be semi-conservative?
5. Create a diagram that shows how DNA replication occurs.
6. What is complementary base pairing? Explain why complementary base pairing is necessary to maintain the double helix shape of the DNA molecule. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/04%3A_Molecular_Biology/4.03%3A_DNA_Structure_and_Replication.txt |
RNA, the other nucleic acid, that's how. Specifically mRNA. RNA, the middle player in the central dogma. This image is an abstract representation of tRNA. Without tRNA, mRNA, and rRNA, proteins cannot be made.
RNA
DNA alone cannot ‘‘tell’’ your cells how to make proteins. It needs the help of RNA, ribonucleic acid, the other main player in the central dogma of molecular biology. Remember, DNA ‘‘lives’’ in the nucleus, but proteins are made on the ribosomes in the cytoplasm. How does the genetic information get from the nucleus to the cytoplasm? RNA is the answer.
RNA vs. DNA
RNA, like DNA, is a nucleic acid. However, RNA differs from DNA in several ways. In addition to being smaller than DNA, RNA also
• consists of one nucleotide chain instead of two,
• contains the nitrogen base uracil (U) instead of thymine,
• contains the sugar ribose instead of deoxyribose.
Types of RNA
There are three main types of RNA, all of which are involved in making proteins.
1. Messenger RNA (mRNA) copies the genetic instructions from DNA in the nucleus, and carries the instructions to the cytoplasm.
2. Ribosomal RNA (rRNA) helps form ribosomes, the organelle where proteins are assembled.
3. Transfer RNA (tRNA) brings amino acids to ribosomes, where they are joined together to form proteins.
Shown are the three types of RNA and their roles: (1) mRNA contains the genetic message, (2) tRNA transfers the amino acids to the ribosome, (3) rRNA is the main component of the ribosome. More on the roles of the RNAs will be discussed in these concepts: ‘‘Transcription of DNA to RNA’’, ‘‘Genetic Code’’, and ‘‘Translation of RNA to Protein’’.
Summary
• RNA differs from DNA in several ways.
• There are three main types of RNA: messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA).
• Each type plays a different in role in making proteins.
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Use these resources to answer the questions that follow.
Explore More I
1. What is the role of RNA?
2. What are the components of an RNA nucleotide?
3. How does the structure of RNA differ from that of DNA?
4. What is an advantage of being single-stranded?
Review
1. What are the three main types of RNA? Describe their roles.
2. Compare and contrast DNA and RNA.
4.05: Transcription of DNA to RNA
How does a cell use the information in its DNA?
To transcribe means ‘‘to paraphrase or summarize in writing’’. The information in DNA is transcribed - or summarized - into a smaller version - RNA - that can be used by the cell. This process is called transcription.
Transcription
The process in which cells make proteins is called protein synthesis. It actually consists of two processes: transcription and translation. Transcription takes place in the nucleus. It uses DNA as a template to make an RNA molecule. RNA then leaves the nucleus and goes to a ribosome in the cytoplasm, where translation occurs. Translation reads the genetic code in mRNA and makes a protein.
Transcription is the first part of the central dogma of molecular biology: DNA → RNA. It is the transfer of genetic instructions in DNA to messenger RNA (mRNA). During transcription, a strand of mRNA is made that is complementary to a strand of DNA. Figure below shows how this occurs. You can watch an animation of the process at this link:www.biostudio.com/d_%20Transcription.htm.
Overview of Transcription. Transcription uses the sequence of bases in a strand of DNA to make a complementary strand of mRNA. Triplets are groups of three successive nucleotide bases in DNA. Codons are complementary groups of bases in mRNA.
Steps of Transcription
Transcription takes place in three steps: initiation, elongation, and termination. The steps are illustrated in Figure below.
1. Initiation is the beginning of transcription. It occurs when the enzyme RNA polymerase binds to a region of a gene called the promoter. This signals the DNA to unwind so the enzyme can ‘‘read’’ the bases in one of the DNA strands. The enzyme is now ready to make a strand of mRNA with a complementary sequence of bases.
2. Elongation is the addition of nucleotides to the mRNA strand. RNA polymerase reads the unwound DNA strand and builds the mRNA molecule, using complementary base pairs. There is a brief time during this process when the newly formed RNA is bound to the unwound DNA. During this process, an adenine (A) in the DNA binds to an uracil (U) in the RNA.
3. Termination is the ending of transcription, and occurs when RNA polymerase crosses a stop (termination) sequence in the gene. The mRNA strand is complete, and it detaches from DNA.
Steps of Transcription. Transcription occurs in the three steps - initiation, elongation, and termination - shown here.
Processing mRNA
In eukaryotes, the new mRNA is not yet ready for translation. It must go through additional processing before it leaves the nucleus. This may include splicing, editing, and polyadenylation. These processes modify the mRNA in various ways. Such modifications allow a single gene to be used to make more than one protein.
• Splicing removes introns from mRNA (see Figure below). Introns are regions that do not code for proteins. The remaining mRNA consists only of regions that do code for proteins, which are called exons. You can watch a video showing splicing in more detail at this link:http://vcell.ndsu.edu/animations/mrnasplicing/movie-flash.htm. Ribonucleoproteins are nucleoproteins that contains RNA. Small nuclear ribonuclearproteins are involved in pre-mRNA splicing.
• Editing changes some of the nucleotides in mRNA. For example, the human protein called APOB, which helps transport lipids in the blood, has two different forms because of editing. One form is smaller than the other because editing adds a premature stop signal in the mRNA.
• Polyadenylation adds a “tail” to the mRNA. The tail consists of a string of As (adenine bases). It signals the end of mRNA. It is also involved in exporting mRNA from the nucleus. In addition, the tail protects mRNA from enzymes that might break it down.
Splicing. Splicing removes introns from mRNA. UTR is an untranslated region of the mRNA.
Summary
• Transcription is the DNA → RNA part of the central dogma of molecular biology.
• Transcription occurs in the nucleus.
• During transcription, a copy of mRNA is made that is complementary to a strand of DNA. In eukaryotes, mRNA may be modified before it leaves the nucleus.
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Explore More I
Use this resource to answer the questions that follow.
1. What is transcription?
2. Describe the three stages of transcription.
3. What is a transcription factor?
4. What is a promoter?
Explore More II
• What is a Gene? at learn.genetics.utah.edu/content/begin/dna/
Review
1. What is protein synthesis?
2. What enzyme is involved in transcription?
3. Describe transcription.
4. Describe splicing. Distinguish introns from exons.
5. How may mRNA be modified before it leaves the nucleus? | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/04%3A_Molecular_Biology/4.04%3A_RNA.txt |
How do you go from four letters to 20 amino acids?
You need a code. And the code that changes the information embedded in DNA and RNA into ordered amino acids and proteins is the genetic code. And every living organism uses the same genetic code.
The Genetic Code
How is the information in a gene encoded? The answer is the genetic code. The genetic code consists of the sequence of nitrogen bases—A, C, G, U—in an mRNA chain. The four bases make up the “letters” of the genetic code. The letters are combined in groups of three to form code “words,” called codons. Each codon stands for (encodes) one amino acid, unless it codes for a start or stop signal.
There are 20 common amino acids in proteins. There are 64 possible codons, more than enough to code for the 20 amino acids. The genetic code is shown in Figure below. To see how scientists cracked the genetic code, go to this link: http://www.dnalc.org/view/16494-Animation-22-DNA-words-are-three-letters-long-.html.
The Genetic Code. To find the amino acid for a particular codon, find the cell in the table for the first and second bases of the codon. Then, within that cell, find the codon with the correct third base. For example CUG codes for leucine, AAG codes for lysine, and GGG codes for glycine.
Reading the Genetic Code
As shown in Figure above, the codon AUG codes for the amino acid methionine. This codon is also the start codon that begins translation. The start codon establishes the reading frame of mRNA. The reading frame is the way the letters are divided into codons. After the AUG start codon, the next three letters are read as the second codon. The next three letters after that are read as the third codon, and so on. This is illustrated in Figure below. The mRNA molecule is read, codon by codon, until a stop codon is reached. UAG, UGA, and UAA are all stop codons. They do not code for any amino acids. Stop codons are also known as termination codons.
Reading the Genetic Code. The genetic code is read three bases at a time. Codons are the code words of the genetic code. Which amino acid does codon 2 in the drawing stand for?
Characteristics of the Genetic Code
The genetic code has a number of important characteristics.
• The genetic code is universal. All known living organisms use the same genetic code. This shows that all organisms share a common evolutionary history.
• The genetic code is unambiguous. Each codon codes for just one amino acid (or start or stop). What might happen if codons encoded more than one amino acid?
• The genetic code is redundant. Most amino acids are encoded by more than one codon. In Figure above, how many codons code for the amino acid threonine? What might be an advantage of having more than one codon for the same amino acid?
Summary
• The genetic code consists of the sequence of bases in DNA or RNA.
• Groups of three bases form codons, and each codon stands for one amino acid (or start or stop).
• The codons are read in sequence following the start codon until a stop codon is reached.
• The genetic code is universal, unambiguous, and redundant.
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Explore More I
Use this resource to answer the questions that follow.
1. What is the genetic code?
2. How many nucleotides make a codon?
3. What was the first codon deciphered in the genetic code? What amino acid does this codon code for?
4. How many possible codon combinations are there in the genetic code?
5. How many stop signals are there in the genetic code?
6. The genetic code is degenerate. Explain this statement.
Review
1. What is the genetic code?
2. What are codons? How many codons are there?
3. Use the genetic code to translate the following segment of RNA into a sequence of five amino acids: GUC-GCG-CAU-AGC-AAG
4. The genetic code is universal, unambiguous, and redundant. Explain what this means. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/04%3A_Molecular_Biology/4.06%3A_Genetic_Code.txt |
RNA to proteins. How?
You must translate. To go from one language to another. Spanish to English, French to German, or nucleotides to amino acids. Which type is the translation of molecular biology? Obviously, the type of translating discussed here translates from the language of nucleotides to the language of amino acids.
Translation
Translation is the second part of the central dogma of molecular biology: RNA → Protein. It is the process in which the genetic code in mRNA is read, one codon at a time, to make a protein. Figure below shows how this happens. After mRNA leaves the nucleus, it moves to a ribosome, which consists of rRNA and proteins. The ribosome reads the sequence of codons in mRNA. Molecules of tRNA bring amino acids to the ribosome in the correct sequence.
Translation of the codons in mRNA to a chain of amino acids occurs at a ribosome. Notice the growing amino acid chain attached to the tRNAs and ribosome. Find the different types of RNA in the diagram. What are their roles in translation?
To understand the role of tRNA, you need to know more about its structure. Each tRNA molecule has an anticodon for the amino acid it carries. An anticodon is a sequence of 3 bases, and is complementary to the codon for an amino acid. For example, the amino acid lysine has the codon AAG, so the anticodon is UUC. Therefore, lysine would be carried by a tRNA molecule with the anticodon UUC. Wherever the codon AAG appears in mRNA, a UUC anticodon on a tRNA temporarily binds to the codon. While bound to the mRNA, the tRNA gives up its amino acid. Bonds form between adjacent amino acids as they are brought one by one to the ribosome, forming a polypeptide chain. The chain of amino acids keeps growing until a stop codon is reached. To see how this happens, go the link below.http://www.youtube.com/watch?v=B6O6uRb1D38 (1:29)
The tRNA structure is a very important aspect in its role. Though the molecule folds into a 3-leaf clover structure, notice the anticodon arm in the lower segment of the molecule, with the amino acid attached at the opposite end of the molecule (acceptor stem). It is the anticodon that determines which codon in the mRNA the tRNA will bind to.
After a polypeptide chain is synthesized, it may undergo additional processes. For example, it may assume a folded shape due to interactions among its amino acids. It may also bind with other polypeptides or with different types of molecules, such as lipids or carbohydrates. Many proteins travel to the Golgi apparatus to be modified for the specific job they will do. You can see how this occurs by watching the animation at this link:http://vcell.ndsu.edu/animations/proteinmodification/movie-flash.htm.
Summary
• Translation is the RNA → Protein part of the central dogma.
• Translation occurs at a ribosome.
• During translation, a protein is synthesized using the codons in mRNA as a guide.
• All three types of RNA play a role in translation.
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Explore More I
Use this resource to answer the questions that follow.
1. In addition to the mRNA, translation needs what three components?
2. Describe the structure of a ribosome.
3. Describe the structure and role of a tRNA molecule.
4. Define codon and anticodon.
5. How does termination occur?
Review
1. Outline the steps of translation.
2. Discuss the structure of a tRNA molecule, and its role in translation.
3. How are transcription and translation related to the central dogma of molecular biology? | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/04%3A_Molecular_Biology/4.07%3A_Translation_of_RNA_to_Protein.txt |
What causes albinism?
This rare albino alligator must have the specific "instructions," or DNA, to have this quality. The cause of albinism is a mutation in a gene for melanin, a protein found in skin and eyes. Such a mutation may result in no melanin production at all or a significant decline in the amount of melanin.
Mutations
A change in the sequence of bases in DNA or RNA is called a mutation. Does the word mutation make you think of science fiction and bug-eyed monsters? Think again. Everyone has mutations. In fact, most people have dozens or even hundreds of mutations in their DNA. Mutations are essential for evolution to occur. They are the ultimate source of all new genetic material - new alleles - in a species. Although most mutations have no effect on the organisms in which they occur, some mutations are beneficial. Even harmful mutations rarely cause drastic changes in organisms.
Types of Mutations
There are a variety of types of mutations. Two major categories of mutations are germline mutations and somatic mutations.
• Germline mutations occur in gametes. These mutations are especially significant because they can be transmitted to offspring and every cell in the offspring will have the mutation.
• Somatic mutations occur in other cells of the body. These mutations may have little effect on the organism because they are confined to just one cell and its daughter cells. Somatic mutations cannot be passed on to offspring.
Mutations also differ in the way that the genetic material is changed. Mutations may change the structure of a chromosome or just change a single nucleotide.
Chromosomal Alterations
Chromosomal alterations are mutations that change chromosome structure. They occur when a section of a chromosome breaks off and rejoins incorrectly or does not rejoin at all. Possible ways these mutations can occur are illustrated in Figure below. Go to this link for a video about chromosomal alterations: http://www.youtube.com/watch?v=OrXRSqa_3lU (2:18).
Chromosomal Alterations. Chromosomal alterations are major changes in the genetic material.
Chromosomal alterations are very serious. They often result in the death of the organism in which they occur. If the organism survives, it may be affected in multiple ways. An example of a human chromosomal alteration is the mutation that causes Down Syndrome. It is a duplication mutation that leads to developmental delays and other abnormalities.
Point Mutations
A point mutation is a change in a single nucleotide in DNA. This type of mutation is usually less serious than a chromosomal alteration. An example of a point mutation is a mutation that changes the codon UUU to the codon UCU. Point mutations can be silent, missense, or nonsense mutations, as shown in Table below. The effects of point mutations depend on how they change the genetic code. You can watch an animation about nonsense mutations at this link:www.biostudio.com/d_%20Nonsen...20Mutation.htm.
Type Description Example Effect
Silent mutated codon codes for the same amino acid CAA (glutamine) → CAG (glutamine) none
Missense mutated codon codes for a different amino acid CAA (glutamine) → CCA (proline) variable
Nonsense mutated codon is a premature stop codon CAA (glutamine) → UAA (stop) usually serious
Frameshift Mutations
A frameshift mutation is a deletion or insertion of one or more nucleotides that changes the reading frame of the base sequence. Deletions remove nucleotides, and insertions add nucleotides. Consider the following sequence of bases in RNA:
AUG-AAU-ACG-GCU = start-asparagine-threonine-alanine
Now, assume an insertion occurs in this sequence. Let’s say an A nucleotide is inserted after the start codon AUG:
AUG-AAA-UAC-GGC-U = start-lysine-tyrosine-glycine
Even though the rest of the sequence is unchanged, this insertion changes the reading frame and thus all of the codons that follow it. As this example shows, a frameshift mutation can dramatically change how the codons in mRNA are read. This can have a drastic effect on the protein product.
Summary
• Germline mutations occur in gametes. Somatic mutations occur in other body cells.
• Chromosomal alterations are mutations that change chromosome structure.
• Point mutations change a single nucleotide.
• Frameshift mutations are additions or deletions of nucleotides that cause a shift in the reading frame.
Explore More
Use this resource to answer the questions that follow.
1. What is a point mutation?
2. What are the effects of a point mutation?
3. What is a frameshift mutation?
4. What causes a frameshift?
5. Who identified point mutations?
Review
1. Identify three types of chromosomal alterations.
2. Distinguish among silent, missense, and nonsense point mutations.
3. What is a frameshift mutation? What causes this type of mutation?
4. Assume that a point mutation changes the codon AUU to AUC. Why is this a silent mutation?
5. Look at the following mutation: AUG-GUC-CCU-AAA → AUG-AGU-CCC-UAA-A. The base A was inserted following the start codon AUG. Describe how this mutation affects the encoded amino acid sequence.
6. Compare and contrast germline mutations and somatic mutations.
4.09: Mutation Causes
What does radiation contamination do?
It mutates DNA. The Chernobyl disaster was a nuclear accident that occurred on April 26, 1986. It is considered the worst nuclear power plant accident in history. A Russian publication concludes that 985,000 excess cancers occurred between 1986 and 2004 as a result of radioactive contamination. The 2011 report of the European Committee on Radiation Risk calculates a total of 1.4 million excess cancers occurred as a result of this contamination.
Causes of Mutation
Mutations have many possible causes. Some mutations seem to happen spontaneously without any outside influence. They can occur when mistakes are made during DNA replication or transcription. Other mutations are caused by environmental factors. Anything in the environment that can cause a mutation is known as a mutagen. Examples of mutagens are pictured in Figure below. For a video about mutagens, go the link below.http://www.youtube.com/watch?v=0wrNxCGKCws (0:36)
Examples of Mutagens. Types of mutagens include radiation, chemicals, and infectious agents. Do you know of other examples of each type of mutagen shown here?
Spontaneous Mutations
There are five common types of spontaneous mutations. These are described in the Tablebelow.
Mutation Description
Tautomerism a base is changed by the repositioning of a hydrogen atom
Depurination loss of a purine base (A or G)
Deamination spontaneous deamination of 5-methycytosine
Transition a purine to purine (A to G, G to A), or a pyrimidine to pyrimidine (C to T, T to C) change
Transversion a purine becomes a pyrimidine, or vice versa
The Chernobyl Disaster: Follow-up
Though the area immediately around the Chernobyl disaster may not be safe for human life for thousands of years, the Exclusion Zone around the Chernobyl nuclear power station has become a haven for wildlife. As humans were evacuated from the area 25 years ago, existing animal populations multiplied and rare species not seen for centuries have returned or have been reintroduced, for example lynx, wild boar, wolf, Eurasian brown bear, European bison, Przewalski's horse, and eagle owl. The Exclusion Zone is so lush with wildlife and greenery that in 2007 the Ukrainian government designated it a wildlife sanctuary. It is now one of the largest wildlife sanctuaries in Europe.
Summary
• Mutations are caused by environmental factors known as mutagens.
• Types of mutagens include radiation, chemicals, and infectious agents.
• Mutations may be spontaneous in nature.
Explore More
Use this resource to answer the questions that follow.
1. When do most mutations develop?
2. What happens to most of the mutations that develop naturally?
3. Where in the genome do most mutations occur?
4. Are most mutations bad? Explain your answer.
5. What is meant by DNA repair?
Review
1. Define mutation and mutagen.
2. List three examples of mutagens.
3. Distinguish between a transition and a transversion. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/04%3A_Molecular_Biology/4.08%3A_Mutation_Types.txt |
Is this rat hairless?
Yes. Why? The result of a mutation, a change in the DNA sequence. The effects of mutations can vary widely, from being beneficial, to having no effect, to having lethal consequences, and every possibility in between.
Effects of Mutations
The majority of mutations have neither negative nor positive effects on the organism in which they occur. These mutations are called neutral mutations. Examples include silent point mutations. They are neutral because they do not change the amino acids in the proteins they encode.
Many other mutations have no effect on the organism because they are repaired beforeprotein synthesis occurs. Cells have multiple repair mechanisms to fix mutations in DNA. One way DNA can be repaired is illustrated in Figure below. If a cell’s DNA is permanently damaged and cannot be repaired, the cell is likely to be prevented from dividing.
DNA Repair Pathway. This flow chart shows one way that damaged DNA is repaired in E. coli bacteria.
Beneficial Mutations
Some mutations have a positive effect on the organism in which they occur. They are calledbeneficial mutations. They lead to new versions of proteins that help organisms adapt to changes in their environment. Beneficial mutations are essential for evolution to occur. They increase an organism’s changes of surviving or reproducing, so they are likely to become more common over time. There are several well-known examples of beneficial mutations. Here are just two:
1. Mutations in many bacteria that allow them to survive in the presence of antibiotic drugs. The mutations lead to antibiotic-resistant strains of bacteria.
2. A unique mutation is found in people in a small town in Italy. The mutation protects them from developing atherosclerosis, which is the dangerous buildup of fatty materials in blood vessels. The individual in which the mutation first appeared has even been identified.
Harmful Mutations
Imagine making a random change in a complicated machine such as a car engine. The chance that the random change would improve the functioning of the car is very small. The change is far more likely to result in a car that does not run well or perhaps does not run at all. By the same token, any random change in a gene's DNA is likely to result in a protein that does not function normally or may not function at all. Such mutations are likely to be harmful. Harmful mutations may cause genetic disorders or cancer.
• A genetic disorder is a disease caused by a mutation in one or a few genes. A human example is cystic fibrosis. A mutation in a single gene causes the body to produce thick, sticky mucus that clogs the lungs and blocks ducts in digestive organs. You can watch a video about cystic fibrosis and other genetic disorders at this link:http://www.youtube.com/watch?v=8s4he3wLgkM (9:31).
• Cancer is a disease in which cells grow out of control and form abnormal masses of cells. It is generally caused by mutations in genes that regulate the cell cycle. Because of the mutations, cells with damaged DNA are allowed to divide without limits. Cancer genes can be inherited. You can learn more about hereditary cancer by watching the video at the following link: http://www.youtube.com/watch?v=LWk5FplsKwM (4:29)
Albino Redwoods, Ghosts of the Forest
What happens if a plant does not have chlorophyll? They would lack the part of the leaf that makes them green. So these plants could be referred to as albino. This would have to result from a genetic mutation. Do these plants die because they cannot photosynthesize? Not necessarily. What can these plants tell us about the biochemistry, genetics and physiology of plants?
See Science on the SPOT: Albino Redwoods, Ghosts of the Forest athttp://science.kqed.org/quest/video/science-on-the-spot-albino-redwoods-ghosts-of-the-forest/, Science on the SPOT: Revisiting Albino Redwoods, Biological Mystery athttp://science.kqed.org/quest/video/science-on-the-spot-revisiting-albino-redwoods-biological-mystery/, and Science on the SPOT: Revisiting Albino Redwoods, Cracking the Code at http://science.kqed.org/quest/video/science-on-the-spot-revisiting-albino-redwoods-cracking-the-code/ for more information.
Summary
• Mutations are essential for evolution to occur because they increase genetic variation and the potential for individuals to differ.
• The majority of mutations are neutral in their effects on the organisms in which they occur.
• Beneficial mutations may become more common through natural selection.
• Harmful mutations may cause genetic disorders or cancer.
Explore More
Explore More I
Use these resources to answer the questions that follow.
1. Define genetic disorders.
2. What are the two primary types of genetic aberrations?
3. What is a carrier?
Explore More II
1. What are the results of a mutation or defect in a single gene?
2. Describe the causes and effects of cystic fibrosis, Huntington's Disease, and hemophilia.
Explore More III
1. What is a chromosomal disorder?
2. When and how do chromosomal errors occur?
3. Describe an inversion and translocation.
4. Describe the causes of Cri-du-chat Syndrome and Down Syndrome.
Review
1. Why are mutations essential for evolution to occur?
2. What is a genetic disorder?
3. What is cancer? What usually causes cancer? | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/04%3A_Molecular_Biology/4.10%3A_Mutation_Effects.txt |
Can your expression change at any moment?
As you know, a person's expression can change moment by moment. The expression that is demonstrated is usually appropriate for that moment's feelings. Gene expression is the use of a gene whose product is necessary for that moment. It may be a moment during development, it may be a moment of increased anxiety, or it may be in response to an environmental change. Whenever a particular protein is needed, gene expression provides it.
Gene Expression
Each of your cells has at least 20,000 genes. In fact, all of your cells have the same genes. Do all of your cells make the same proteins? Obviously not. If they did, then all your cells would be alike. Instead, you have cells with different structures and functions. This is because different cells make different proteins. They do this by using, or expressing, different genes. Using a gene to make a protein is called gene expression.
How Gene Expression is Regulated
Gene expression is regulated to ensure that the correct proteins are made when and where they are needed. Regulation may occur at any point in the expression of a gene, from the start of transcription to the processing of a protein after translation. Following is a list of stages where gene expression is regulated:
• Chemical and structural modification of DNA or chromatin
• Transcription
• Translation
• Post-transcriptional modification
• RNA transport
• mRNA degradation
• Post-translational modifications
As shown in Figure below, transcription is controlled by regulatory proteins binding to the DNA. Specifically, gene regulation at the level of transcription controls when transcription occurs as well as how much RNA is created. A regulatory protein, or a transcription factor, is a protein involved in regulating gene expression. It is usually bound to a cis-regulatory element, which is part of the DNA. Regulatory proteins often must be bound to a cis-regulatory element to switch a gene on (activator), or to turn a gene off (repressor).
Transcription of a gene by RNA polymerase can be regulated by at least five mechanisms:
• Specificity factors (proteins) alter the specificity of RNA polymerase for a promoter or set of promoters, making it more or less likely to bind to the promoter and begin transcription.
• Activator proteins enhance the interaction between RNA polymerase and a particular promoter.
• Repressor proteins bind to non-coding sequences on the DNA that are close to or overlap the promoter region, impeding RNA polymerase's progress along the strand.
• Basal factors are transcription factors that help position RNA polymerase at the start of a gene.
• Enhancers are sites on the DNA strand that are bound by activators in order to loop the DNA, bringing a specific transcription factor to the initiation complex. An initiation complex is composed of RNA polymerase and transcription factors.
As the organism grows more sophisticated, gene regulation becomes more complex, though prokaryotic organisms possess some highly regulated systems. Some human genes are controlled by many activators and repressors working together. Obviously, a mutation in a cis-regulatory region, such as the promoter, can greatly affect the proper expression of a gene. It may keep the gene permanently off, such that no protein can be made, or it can keep the gene permanently on, such that the corresponding protein is constantly made. Both of these can have detremental effects on the cell.
Regulation of Transcription. Regulatory proteins bind to regulatory elements to control transcription. The regulatory elements are embedded within the DNA.
Summary
• Gene transcription is controlled by regulatory proteins that bind to regulatory elements on DNA.
• The proteins usually either activate or repress transcription.
Explore More
Use this resource to answer the questions that follow.
• What is Gene Expression? at www.news-medical.net/health/What-is-Gene-Expression.aspx.
1. What is gene expression?
2. What is necessary to begin transcription?
3. What is produced as the DNA is "read?"
4. Where is the promoter for a gene located in relation to the transcription start site?
Review
1. What is gene expression?
2. Why is gene expression regulated?
3. List three stages where gene expression is regulated.
4. Describe how regulatory proteins regulate gene expression.
5. Compare activators to repressors. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/04%3A_Molecular_Biology/4.11%3A_Gene_Expression.txt |
On or off?
When it comes to genes, that is an important question. And if you're a single-celled organism like a bacterium, conserving energy by not producing unnecessary proteins is very important.
Prokaryotic Gene Regulation
Transcription is regulated differently in prokaryotes and eukaryotes. In general, prokaryotic regulation is simpler than eukaryotic regulation.
The Role of Operons
Regulation of transcription in prokaryotes typically involves operons. An operon is a region ofDNA that consists of one or more genes that encode the proteins needed for a specific function. The operon also includes a promoter and an operator. The operator is a region of the operon where regulatory proteins bind. It is located near the promoter and helps regulate transcription of the operon genes.
The Lac Operon
A well-known example of operon regulation involves the lac operon in E. coli bacteria (see Figure below and the video at the link below). The lac operon consists of a promoter, an operator, and three genes that encode the enzymes needed to digest lactose, the sugar found in milk. The lac operon is regulated by lactose in the environment. The Lac Operon video at http://www.youtube.com/watch?v=oBwtxdI1zvk explains the operon in further detail.
• When lactose is absent, a repressor protein binds to the operator. The operator is located between the promoter and the three lac operon genes. The protein blocks the binding of RNA polymerase to the promoter. As a result, the lac genes are not expressed.
• When lactose is present, the repressor protein does not bind to the operator. This allows RNA polymerase to bind to the promoter and begin transcription. As a result, the lac genes are expressed, and lactose is digested.
Why might it be beneficial to express genes only when they are needed? (Hint: synthesizing proteins requires energy and materials.)
The three genes of the lac operon are lacZ, lacY, and lacA. They encode proteins needed to digest lactose. The genes are expressed only in the presence of lactose.
Summary
• Regulation of transcription in prokaryotes typically involves an operon, such as the lac operon in E. coli.
• The lac operon is regulated by proteins that behave differently depending on whether lactose is present or absent.
Explore More
Explore More I
Use this resource to answer the questions that follow.
1. How do bacteria break large sugars into smaller ones?
2. What is the role of lactose in gene regulation?
3. What happens when lactose is present? Or absent?
4. What is the operator?
5. What does "operon" refer to?
Explore More II
Gene Machine: The Lac Operon at http://phet.colorado.edu/en/simulation/gene-machine-lac-operon.
Review
1. What is an operon?
2. Why might it be beneficial to express genes only when they are needed?
3. What is the role of an operon's operator?
4. What happens to the lac operon in the absence of lactose?
5. Draw a diagram to show how the lac operon is regulated.
4.13: Eukaryotic Gene Regulation
On or Off? On or Off? On or Off?
That is the key question. Gene regulation in eukaryotes is a highly regulated process usually involving many proteins, which either bind to each other or bind to the DNA.
Eukaryotic Gene Regulation
In eukaryotic cells, the start of transcription is one of the most complicated parts of gene regulation. There may be many regulatory proteins and regulatory elements involved. Regulation may also involve enhancers. Enhancers are distant regions of DNA that can loop back to interact with a gene’s promoter.
The TATA Box
Different types of cells have unique patterns of regulatory elements that result in only the necessary genes being transcribed. That’s why a skin cell and nerve cell, for example, are so different from each other. However, some patterns of regulatory elements are common to all genes, regardless of the cells in which they occur. An example is the TATA box, so named because it has a core sequence of TATAAA. This is a regulatory element that is part of the promoter of most eukaryotic genes. A number of regulatory proteins bind to the TATA box, forming a multi-protein complex. It is only when all of the appropriate proteins are bound to the TATA box that RNA polymerase recognizes the complex and binds to the promoter. Once RNA polymerase binds, transcription begins. To see a video showing the role of the TATA box in the initiation of transcription, go to this link: http://www.youtube.com/watch?v=6tqPsI-9aQA.
Regulation During Development
The regulation of gene expression is extremely important during the development of an organism. Regulatory proteins must turn on certain genes in particular cells at just the right time so the organism develops normal organs and organ systems. Homeobox genes are an example of genes that regulate development. They code for regulatory proteins that switch on whole series of major developmental genes. In insects, homeobox genes called hox genes ensure that body parts such as limbs develop in the correct place. Figure below shows how a mutation in a hox gene can affect an insect’s development. Other organisms, including humans, also have how genes. You can learn more about homeobox genes at this link:http://www.youtube.com/watch?v=LFG-aLidT8s.
Effect of Hox Gene Mutation. Scientists caused a mutation in a hox gene of this fruit fly. As a result of the mutation, a leg grew out of its head where an antenna should have developed.
Gene Expression and Cancer
The mutations that cause cancer generally occur in two types of regulatory genes: tumor-suppressor genes and proto-oncogenes (see Figure below). These genes produce regulatory proteins that control the cell cycle. When the genes mutate, cells with mutations divide rapidly and without limits, potentially resulting in a tumor and cancer.
How Cancer Develops. This flow chart shows how a series of mutations in tumor-suppressor genes and proto-oncogenes leads to cancer.
Summary
• Regulation of transcription in eukaryotes is generally more complex than in prokaryotes. It involves unique regulatory elements in different cells as well as common regulatory elements such as the TATA box.
• Regulation is especially important during development. It may involve regulatory genes such as homeobox genes that switch other regulatory genes on or off.
• Mutations in regulatory genes that normally control the cell cycle cause cancer.
Explore More
Use this resource to answer the questions that follow.
• Master genes control basic body plans at www.dnalc.org/resources/nobel/lewis_nauulein_wieschaus.html.
1. How were genes that control early embryonic development identified?
2. Describe the polarity of the fertilized egg, as it relates to protein expression.
3. What does "segmentation" refer to in the developing fly?
4. What is a gap mutant?
5. Describe the antennapedia mutant.
6. What is a homeobox protein?
Review
1. Identify the TATA box and its function in transcription.
2. What is a homeobox gene?
3. Why is gene regulation especially important during development?
4. What are tumor-suppressor genes and proto-oncogenes?
5. Sketch how an insect with a mutated hox gene might look. Explain your sketch. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/04%3A_Molecular_Biology/4.12%3A_Prokaryotic_Gene_Regulation.txt |
There are millions and millions of species, so classifying organisms into proper categories can be a difficult task. To make it easier for all scientists to do, a classification system had to be developed.
Linnaean Classification
The evolution of life on Earth over the past 4 billion years has resulted in a huge variety of species. For more than 2,000 years, humans have been trying to classify the great diversity of life. The science of classifying organisms is called taxonomy. Classification is an important step in understanding the present diversity and past evolutionary history of life on Earth.
All modern classification systems have their roots in the Linnaean classification system. It was developed by Swedish botanist Carolus Linnaeus in the 1700s. He tried to classify all living things that were known at his time. He grouped together organisms that shared obvious physical traits, such as number of legs or shape of leaves. For his contribution, Linnaeus is known as the “father of taxonomy.” You can learn more about Linnaeus and his system of classification by watching the video at this link: http://teachertube.com/viewVideo.php?video_id=169889.
The Linnaean system of classification consists of a hierarchy of groupings, called taxa(singular, taxon). Taxa range from the kingdom to the species (see Figure below). The kingdom is the largest and most inclusive grouping. It consists of organisms that share just a few basic similarities. Examples are the plant and animal kingdoms. The species is the smallest and most exclusive grouping. It consists of organisms that are similar enough to produce fertile offspring together. Closely related species are grouped together in a genus.
Linnaean Classification System: Classification of the Human Species. This chart shows the taxa of the Linnaean classification system. Each taxon is a subdivision of the taxon below it in the chart. For example, a species is a subdivision of a genus. The classification of humans is given in the chart as an example.
Binomial Nomenclature
Perhaps the single greatest contribution Linnaeus made to science was his method of naming species. This method, called binomial nomenclature, gives each species a unique, two-word Latin name consisting of the genus name and the species name. An example is Homo sapiens, the two-word Latin name for humans. It literally means “wise human.” This is a reference to our big brains.
Why is having two names so important? It is similar to people having a first and a last name. You may know several people with the first name Michael, but adding Michael’s last name usually pins down exactly whom you mean. In the same way, having two names uniquely identifies a species.
Revisions in Linnaean Classification
Linnaeus published his classification system in the 1700s. Since then, many new species have been discovered. The biochemistry of many organisms has also become known. Eventually, scientists realized that Linnaeus’s system of classification needed revision.
A major change to the Linnaean system was the addition of a new taxon called the domain. Adomain is a taxon that is larger and more inclusive than the kingdom. Most biologists agree there are three domains of life on Earth: Bacteria, Archaea, and Eukaryota (see Figure below). Both Bacteria and Archaea consist of single-celled prokaryotes. Eukaryota consists of all eukaryotes, from single-celled protists to humans. This domain includes the Animalia (animals), Plantae (plants), Fungi (fungi), and Protista (protists) kingdoms.
This phylogenetic tree is based on comparisons of ribosomal RNA base sequences among living organisms. The tree divides all organisms into three domains: Bacteria, Archaea, and Eukarya. Humans and other animals belong to the Eukarya domain. From this tree, organisms that make up the domain Eukarya appear to have shared a more recent common ancestor with Archaea than Bacteria.
Summary
• Classification is an important step in understanding life on Earth.
• All modern classification systems have their roots in the Linnaean classification system.
• The Linnaean system is based on similarities in obvious physical traits. It consists of a hierarchy of taxa, from the kingdom to the species.
• Each species is given a unique two-word Latin name.
• The recently added domain is a larger and more inclusive taxon than the kingdom.
Explore More
Use this resource to answer the questions that follow.
1. Why is the Linnaean taxonomic system useful as a classification system?
2. Because wolves and dogs share many similarities, they also share what part of their scientific name?
3. Mammalia is what category of classification?
4. What is necessary for two species to be in the same genus?
Review
1. What is taxonomy?
2. Define taxon and give an example.
3. What is binomial nomenclature? Why is it important?
4. What is a domain? What are the three domains of life on Earth?
5. Create a taxonomy, modeled on the Linnaean classification system, for a set of common objects, such as motor vehicles, tools, or office supplies. Identify the groupings that correspond to the different taxa in the Linnaean system. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/05%3A_Evolution/5.01%3A_Linnaean_Classification.txt |
Why is balance important?
To these individuals, the importance of maintaining balance is obvious. If balance, or equilibrium, is maintained within a population's genes, can evolution occur? No. But maintaining this type of balance today is difficult.
The Hardy-Weinberg Theorem
Godfrey Hardy was an English mathematician. Wilhelm Weinberg was a German doctor. Each worked alone to come up with the founding principle of population genetics. Today, that principle is called the Hardy-Weinberg theorem. It shows that allele frequencies do not change in a population if certain conditions are met. Such a population is said to be in Hardy-Weinberg equilibrium. The conditions for equilibrium are:
1. No new mutations are occurring. Therefore, no new alleles are being created.
2. There is no migration. In other words, no one is moving into or out of the population.
3. The population is very large.
4. Mating is at random in the population. This means that individuals do not choose mates based on genotype.
5. There is no natural selection. Thus, all members of the population have an equal chance of reproducing and passing their genes to the next generation.
When all these conditions are met, allele frequencies stay the same. Genotype frequencies also remain constant. In addition, genotype frequencies can be expressed in terms of allele frequencies, as the Table below shows. For a further explanation of this theorem, see Solving Hardy Weinberg Problems at http://www.youtube.com/watch?v=xPkOAnK20kw.
Hardy and Weinberg used mathematics to describe an equilibrium population (p = frequency of A, q = frequency of a, so p + q = 1): p2 + 2pq + q2 = 1. Using the genotype frequencies shown in Table below, if p = 0.4, what is the frequency of the AA genotype?
Genotype Genotype Frequency
AA p2
Aa 2pq
aa q2
A video explanation of the Hardy-Weinberg model can be viewed athttp://www.youtube.com/watch?v=4Kbruik_LOo (14:57).
Summary
• The Hardy-Weinberg theorem states that, if a population meets certain conditions, it will be in equilibrium.
• In an equilibrium population, allele and genotype frequencies do not change over time.
• The conditions that must be met are no mutation, no migration, very large population size, random mating, and no natural selection.
Explore More
Use this resource to answer the questions that follow.
• Hardy-Weinberg Equilibrium Model at anthro.palomar.edu/synthetic/synth_2.htm.
1. This resource states that evolution will not occur in a population if seven conditions are met. What are these seven conditions?
2. If there is no evolution, what happened to gene frequencies?
3. What are p and q?
4. How is p determined?
5. p + q = _____
6. p2 + 2pq + q2 = _____
Review
1. Describe a Hardy-Weinberg equilibrium population. What conditions must it meet to remain in equilibrium?
2. Assume that a population is in Hardy-Weinberg equilibrium for a particular gene with two alleles, A and a. The frequency of A is p, and the frequency of a is q. Because these are the only two alleles for this gene, p + q = 1.0. If the frequency of homozygous recessive individuals (aa) is 0.04, what is the value of q? What is the value of p?
3. Use the values of p and q from question 2 to calculate the frequency of the heterozygote genotype (Aa). | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/05%3A_Evolution/5.02%3A_Hardy-Weinberg_Theorem.txt |
How do we learn about the past?
We study the remains of things that existed many years ago. The Ruins of Pompeii have given archeologists, historians, and other scholars a tremendous amount of information about life two thousand years ago. This section discusses studying things that are many thousands of years older than these remains.
Earth in a Day
It’s hard to grasp the vast amounts of time since Earth formed and life first appeared on its surface. It may help to think of Earth’s history as a 24-hour day, as shown in Figure below. Humans would have appeared only during the last minute of that day. If we are such newcomers on planet Earth, how do we know about the vast period of time that went before us? How have we learned about the distant past?
History of Earth in a Day. In this model of Earth’s history, the planet formed at midnight. What time was it when the first prokaryotes evolved?
Learning About the Past
Much of what we know about the history of life on Earth is based on the fossil record. Detailed knowledge of modern organisms also helps us understand how life evolved.
The Fossil Record
Fossils are the preserved remains or traces of organisms that lived in the past. The soft parts of organisms almost always decompose quickly after death. On occasion, the hard parts—mainly bones, teeth, or shells—remain long enough to mineralize and form fossils. An example of a complete fossil skeleton is shown in Figure below. The fossil record is the record of life that unfolded over four billion years and pieced back together through the analysis of fossils.
Extinct Lion Fossil. This fossilized skeleton represents an extinct lion species. It is rare for fossils to be so complete and well preserved as this one.
To be preserved as fossils, remains must be covered quickly by sediments or preserved in some other way. For example, they may be frozen in glaciers or trapped in tree resin, like the frog in Figure below. Sometimes traces of organisms—such as footprints or burrows—are preserved (see the fossil footprints in Figure below). The conditions required for fossils to form rarely occur. Therefore, the chance of an organism being preserved as a fossil is very low. You can watch a video at the following link to see in more detail how fossils form:http://www.youtube.com/watch?v=A5i5Qrp6sJU.
The photo on the left shows an ancient frog trapped in hardened tree resin, or amber. The photo on the right shows the fossil footprints of a dinosaur.
In order for fossils to “tell” us the story of life, they must be dated. Then they can help scientists reconstruct how life changed over time. Fossils can be dated in two different ways: relative dating and absolute dating. Both are described below. You can also learn more about dating methods in the video at this link: http://www.youtube.com/watch?v=jM7vZ-9bBc0.
• Relative dating determines which of two fossils is older or younger than the other, but not their age in years. Relative dating is based on the positions of fossils in rock layers. Lower layers were laid down earlier, so they are assumed to contain older fossils. This is illustrated in Figure below.
• Absolute dating determines about how long ago a fossil organism lived. This gives the fossil an approximate age in years. Absolute dating is often based on the amount of carbon-14 or other radioactive element that remains in a fossil. You can learn more about carbon-14 dating by watching the animation at this link:http://www.absorblearning.com/media/attachment.action?quick=bo&att=832.
Relative Dating Using Rock Layers. Relative dating establishes which of two fossils is older than the other. It is based on the rock layers in which the fossils formed.
Molecular Clocks
Evidence from the fossil record can be combined with data from molecular clocks. A molecular clock uses DNA sequences (or the proteins they encode) to estimate relatedness among species. Molecular clocks estimate the time in geologic history when related species diverged from a common ancestor. Molecular clocks are based on the assumption that mutations accumulate through time at a steady average rate for a given region of DNA. Species that have accumulated greater differences in their DNA sequences are assumed to have diverged from their common ancestor in the more distant past. Molecular clocks based on different regions of DNA may be used together for more accuracy.
Consider the example in Table below. The table shows how similar the DNA of several animal species is to human DNA. Based on these data, which organism do you think shared the most recent common ancestor with humans?
Organism Similarity with Human DNA (percent)
Chimpanzee 98
Mouse 85
Chicken 60
Fruit Fly 44
Geologic Time Scale
Another tool for understanding the history of Earth and its life is the geologic time scale, shown in Figure below. The geologic time scale divides Earth’s history into divisions (such as eons, eras, and periods) that are based on major changes in geology, climate, and the evolution of life. It organizes Earth’s history and the evolution of life on the basis of important events instead of time alone. It also allows more focus to be placed on recent events, about which we know the most.
Geologic Time Scale. The geologic time scale divides Earth’s history into units that reflect major changes in Earth and its life forms. During which eon did Earth form? What is the present era?
Summary
• Much of what we know about the history of life on Earth is based on the fossil record.
• Molecular clocks are used to estimate how long it has been since two species diverged from a common ancestor.
• The geologic time scale is another important tool for understanding the history of life on Earth.
Explore More
Use the time slider in this resource to answer the questions that follow.
1. When did the Big Bang occur?
2. When did the sun ignite?
3. When did the Earth form? What was the form of this Earth?
4. What was lacking in the Earth's early atmosphere?
5. When did the first cells appear?
Review
1. What are fossils?
2. Describe how fossils form.
3. Distinguish relative dating from absolute dating.
4. This table shows DNA sequence comparisons for some hypothetical species. Based on the data, describe evolutionary relationships between Species A and the other four species. Explain your answer.
Species DNA Similarity with Species A
Species B 42%
Species C 85%
Species D 67%
Species E 91%
5. Describe the geologic time scale. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/05%3A_Evolution/5.03%3A_History_of_Life.txt |
What alien planet is represented by this picture?
Would it surprise you to learn that the picture represents Earth? After Earth first formed about 4.6 billion years ago, it may well have looked like this. Instead of rivers of water, rivers of molten rock flowed over its surface. Life as we know it could not have survived in such a place. How did this fiery hot planet become today’s Earth, covered with water and teeming with life? The long and incredible story of Earth’s history starts with this section.
How Earth Formed: We Are Made of Stardust!
We’ll start the story of life at the very beginning, when Earth and the rest of the solar system first formed. The solar system began as a rotating cloud of stardust. “Dust, rocks, and gas” may not sound inspiring, but this cloud contained the 92 elements which somehow combine to form every corner – living and nonliving – of Earth. Then the Big Bang (14 billion years ago) produced the atoms of hydrogen and helium. Elements as heavy as lithium followed the Big Bang within minutes. Stars such as red giants fused hydrogen and helium nuclei to form elements from carbon (the foundation of life) to calcium (now our bones and teeth). Supernova explosions formed and ejected heavier elements such as iron (for red blood cells). We are not just “dust.” We - and our world - are stardust!
How did this rotating cloud of stardust become our solar system? About 4.5 billion years ago, a nearby star exploded and sent a shock wave through the dust cloud, increasing its rate of spin. As a result, most of the mass became concentrated in the middle, forming the sun. Smaller concentrations of mass rotating around the center formed the planets, including Earth.
You can watch a video showing how Earth formed at this link:http://www.youtube.com/watch?v=-x8-KMR0nx8.
At first, Earth was molten and lacked an atmosphere and oceans. Gradually, the planet cooled and formed a solid crust. As the planet continued to cool, volcanoes released gases, which eventually formed an atmosphere. The early atmosphere contained ammonia, methane,water vapor, and carbon dioxide but only a trace of oxygen. As the atmosphere became denser, clouds formed and rain fell. Water from rain, and perhaps from comets and asteroidsthat struck Earth as well, eventually formed the oceans. The ancient atmosphere and oceans represented by the picture in Figure below would be toxic to today’s life, but they set the stage for life to begin.
Ancient Earth. This is how ancient Earth may have looked after its atmosphere and oceans formed.
Summary
• Earth formed about 4.5 to 4.6 billion years ago.
• At first, Earth was molten and lacked an atmosphere and oceans.
• Gradually, the atmosphere formed, followed by the oceans.
Explore More
Use the time slider in this resource to answer the questions that follow.
1. What does the Big Bang represent?
2. When did the sun ignite?
3. When did a molten Earth form?
4. How old are the oldest known rocks? Where were these rocks found?
5. Describe Earth's early atmosphere. What were the components of this atmosphere?
Review
1. Give an overview of how Earth formed.
2. How did Earth's atmosphere form?
3. How did Earth's oceans form?
4. Describe Earth's early atmosphere. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/05%3A_Evolution/5.04%3A_How_Earth_Formed.txt |
How do you make large molecules?
From smaller ones. The first organic molecules were probably very simple carbon-based molecules made of few atoms. These molecules then combined with other simple molecules to form more complex molecules. Over many years and probably trillions and trillions of chemical reactions, more complex molecules, and more stable molecules, formed.
The First Organic Molecules
All living things consist of organic molecules, centered around the element carbon. Therefore, it is likely that organic molecules evolved before cells, perhaps as long as 4 billion years ago. How did these building blocks of life first form?
Scientists think that lightning sparked chemical reactions in Earth’s early atmosphere. The early atmosphere contained gases such as ammonia, methane, water vapor, and carbon dioxide. Scientists hypothesize that this created a “soup” of organic molecules from inorganic chemicals.
In 1953, scientists Stanley Miller and Harold Urey used their imaginations to test this hypothesis. They created a simulation experiment to see if organic molecules could arise in this way (see Figure below). They used a mixture of gases to represent Earth’s early atmosphere. Then, they passed sparks through the gases to represent lightning. Within a week, several simple organic molecules had formed.
You can watch a dramatization of Miller and Urey’s experiment at this link:https://www.youtube.com/watch?v=NNijmxsKGbc.
Which Organic Molecule Came First?
Living things need organic molecules to store genetic information and to carry out the chemical work of cells. Modern organisms use DNA to store genetic information and proteins to catalyze chemical reactions. So, did DNA or proteins evolve first? This is like asking whether the chicken or the egg came first. DNA encodes proteins and proteins are needed to make DNA, so each type of organic molecule needs the other for its own existence. How could either of these two molecules have evolved before the other? Did some other organic molecule evolve first, instead of DNA or proteins?
RNA World Hypothesis
Some scientists speculate that RNA may have been the first organic molecule to evolve. In fact, they think that early life was based solely on RNA and that DNA and proteins evolved later. This is called the RNA world hypothesis. Why RNA? It can encode genetic instructions (like DNA), and some RNAs can carry out chemical reactions (like proteins). Therefore, it solves the chicken-and-egg problem of which of these two molecules came first. Other evidence also suggests that RNA may be the most ancient of the organic molecules. You can learn more about the RNA world hypothesis and the evidence for it at this link:http://www.youtube.com/watch?v=sAkgb3yNgqg.
Summary
• The first organic molecules formed about 4 billion years ago.
• This may have happened when lightning sparked chemical reactions in Earth’s early atmosphere.
• RNA may have been the first organic molecule to form as well as the basis of early life.
Explore More
Use the time slider in this resource to answer the questions that follow.
1. When did the element carbon first form?
2. When did the first elements appear in Earth's atmosphere and on its surface?
3. List 5 of these early chemicals.
4. When did the first organic molecules appear?
5. What were these first organic molecules? How did these organic molecules accumulate?
Review
1. Describe Miller and Urey’s experiment. What did it demonstrate?
2. State the RNA world hypothesis. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/05%3A_Evolution/5.05%3A_First_Organic_Molecules.txt |
How do you make complex cells?
You start with simple ones. The first cells were most likely primitive prokaryotic-like cells, even more simplistic than these E. coli bacteria. The first cells were probably no more than organic compounds, such as a simplistic RNA, surrounded by a membrane. Was it a phospholipid bilayer membrane? Probably not — it was likely a simplistic membrane able to separate the inside from the outside. Over time, as other organic compounds such as DNA and proteins developed, cells also evolved into more complex structures. Once a cell was able to be stable, reproduce itself, and pass its genetic information to the next generation, then there was life.
The First Cells
What was needed for the first cell? Some sort of membrane surrounding organic molecules? Probably.
How organic molecules such as RNA developed into cells is not known for certain. Scientists speculate that lipid membranes grew around the organic molecules. The membranes prevented the molecules from reacting with other molecules, so they did not form new compounds. In this way, the organic molecules persisted, and the first cells may have formed.Figure below shows a model of the hypothetical first cell. Were these first cells the first living organisms? Were they able to live and reproduce while passing their genetic information to the next generation? If so, then yes, these first cells could be considered the first living organisms.
Hypothetical First Cell. The earliest cells may have consisted of little more than RNA inside a lipid membrane.
LUCA
No doubt there were many early cells of this type. However, scientists think that only one early cell (or group of cells) eventually gave rise to all subsequent life on Earth. That one cell is called the Last Universal Common Ancestor (LUCA). It probably existed around 3.5 billion years ago. LUCA was one of the earliest prokaryotic cells. It would have lacked a nucleus and other membrane-bound organelles. To learn more about LUCA and universal common descent, you can watch the video at the following link: http://www.youtube.com/watch?v=G0UGpcea8Zg.
Photosynthesis and Cellular Respiration
The earliest cells were probably heterotrophs. Most likely they got their energy from other molecules in the organic “soup.” However, by about 3 billion years ago, a new way of obtaining energy evolved. This new way was photosynthesis. Through photosynthesis, organisms could use sunlight to make food from carbon dioxide and water. These organisms were the first autotrophs. They provided food for themselves and for other organisms that began to consume them.
After photosynthesis evolved, oxygen started to accumulate in the atmosphere. This has been dubbed the “oxygen catastrophe.” Why? Oxygen was toxic to most early cells because they had evolved in its absence. As a result, many of them died out. The few that survived evolved a new way to take advantage of the oxygen. This second major innovation wascellular respiration. It allowed cells to use oxygen to obtain more energy from organic molecules.
Summary
• The first cells consisted of little more than an organic molecule such as RNA inside a lipid membrane.
• One cell (or group of cells), called the last universal common ancestor (LUCA), gave rise to all subsequent life on Earth.
• Photosynthesis evolved by 3 billion years ago and released oxygen into the atmosphere.
• Cellular respiration evolved after that to make use of the oxygen.
Explore More
Use the time slider in this resource to answer the questions that follow.
1. When did the first cells appear? How did these cells develop?
2. Describe the first cells.
3. What was the role of RNA in the first cells?
4. When did photosynthesis begin? Discuss the significance of the evolution of photosynthesis.
Review
1. What was LUCA? What were its characteristics?
2. Which evolved first, autotrophs or heterotrophs? Why?
3. Why could cellular respiration evolve only after photosynthesis had evolved? | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/05%3A_Evolution/5.06%3A_First_Cells.txt |
Why can this fish live in these tentacles, but other fish cannot?
Anemones and Clown Fish have a well-known symbiotic relationship. In the ocean, the Clown Fish are protected from predator fish by the stinging tentacles of the anemone, and the anemone receives protection from polyp-eating fish, which the Clown Fish chases away. But what about symbiotic relationships at a much smaller scale? Is it possible for two single-celled organisms to have a symbiotic relationship? As you will find out, yes it is!
Evolution of Eukaryotes
Our own eukaryotic cells protect DNA in chromosomes with a nuclear membrane, make ATP with mitochondria, move with flagella (in the case of sperm cells), and feed on cells which make our food with chloroplasts. All multicellular organisms and the unicellular Protists share this cellular intricacy. Bacterial (prokaryotic) cells are orders of magnitude smaller and have none of this complexity. What quantum leap in evolution created this vast chasm of difference?
The first eukaryotic cells - cells with a nucleus an internal membrane-bound organelles - probably evolved about 2 billion years ago. This is explained by the endosymbiotic theory. As shown in the Figure below, endosymbiosis came about when large cells engulfed small cells. The small cells were not digested by the large cells. Instead, they lived within the large cells and evolved into organelles.
From Independent Cell to Organelle. The endosymbiotic theory explains how eukaryotic cells evolved.
The large and small cells formed a symbiotic relationship in which both cells benefited. Some of the small cells were able to break down the large cell’s wastes for energy. They supplied energy not only to themselves but also to the large cell. They became the mitochondria of eukaryotic cells. Other small cells were able to use sunlight to make food. They shared the food with the large cell. They became the chloroplasts of eukaryotic cells.
Mitochondria and Chloroplasts
What is the evidence for this evolutionary pathway? Biochemistry and electron microscopy provide convincing support. The mitochondria and chloroplasts within our eukaryotic cells share the following features with prokaryotic cells:
• Their organelle DNA is short and circular, and the DNA sequences do not match DNA sequences found in the nucleus.
• Molecules that make up organelle membranes resemble those in prokaryotic membranes – and differ from those in eukaryotic membranes.
• Ribosomes in these organelles are similar to those of bacterial ribosomes, and different from eukaryotic ribosomes.
• Reproduction is by binary fission, not by mitosis.
• Biochemical pathways and structures show closer relationships to prokaryotes.
• Two or more membranes surround these organelles.
The "host" cell membrane and biochemistry are more similar to those of Archaebacteria, so scientists believe eukaryotes descended more directly from that major group (Figure below). The timing of this dramatic evolutionary event (more likely a series of events) is not clear. The oldest fossil clearly related to modern eukaryotes is a red alga dating back to 1.2 billion years ago. However, many scientists place the appearance of eukaryotic cells at about 2 billion years. Some time within Proterozoic Eon, then, all three major groups of life – Bacteria, Archaea, and Eukaryotes – became well established.
What Does it all Mean?
Eukaryotic cells, made possible by endosymbiosis, were powerful and efficient. That power and efficiency gave them the potential to evolve new characteristics: multicellularity, cell specialization, and large size. They were the key to the spectacular diversity of animals, plants, and fungi that populate our world today. Nevertheless, as we close the history of early life, reflect once more on the remarkable but often unsung patterns and processes of early evolution. Often, as humans, we focus our attention on plants and animals, and ignore bacteria. Our human senses cannot directly perceive the unimaginable variety of single cells, the architecture of organic molecules, or the intricacy of biochemical pathways. Let your study of early evolution give you a new perspective – a window into the beauty and diversity of unseen worlds, now and throughout Earth’s history. In addition to the mitochondria that call your 100 trillion cells home, your body contains more bacterial cells than human cells. You, mitochondria, and your resident bacteria share common ancestry – a continuous history of the gift of life.
The three major domains of life had evolved by 1.5 billion years ago. Biochemical similarities show that eukaryotes share more recent common ancestors with the Archaea, but our organelles probably descended from bacteria by endosymbiosis.
Summary
• Eukaryotic cells probably evolved about 2 billion years ago. Their evolution is explained by endosymbiotic theory.
• Mitochondria and chloroplasts evolved from prokaryotic organisms.
• Eukaryotic cells would go on to evolve into the diversity of eukaryotes we know today.
Explore More
Use the time slider in this resource to answer the questions that follow.
1. When did cells begin to "swallow" other cells?
2. When did respiration develop?
3. The rapid rise in atmospheric oxygen favored which cells?
4. When did eukaryotic cells first form? What distinguished these cells from their predecessors?
Review
1. When did the first eukaryotic cells evolve?
2. Describe the endosymbiotic theory.
3. Discuss the evidence for the evolution of mitochondria and chloroplasts. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/05%3A_Evolution/5.07%3A_Evolution_of_Eukaryotes.txt |
What did early eukaryotic life look like?
Some looked like this. This is a fossil of an ammonite. Ammonites are excellent index fossils, and it is often possible to link the rock layer in which they are found to specific geological time periods.
Multicellular Life: Setting the Stage
Nearly 80% of Earth’s history passed before multicellular life evolved. Up until then, all organisms existed as single cells. Why did multicellular organisms evolve? What led up to this major step in the evolution of life? To put the evolution of multicellularity in context, let’s return to what was happening on planet Earth during this part of its history.
The Late Precambrian
The late Precambrian is the time from about 2 billion to half a billion years ago. During this long span of time, Earth experienced many dramatic geologic and climatic changes.
• Continents drifted. They collided to form a gigantic supercontinent and then broke up again and moved apart. Continental drift changed climates worldwide and caused intense volcanic activity. To see an animation of continental drift, go to this link:http://www.ucmp.berkeley.edu/geology/anim1.html.
• Carbon dioxide levels in the atmosphere rose and fell. This was due to volcanic activity and other factors. When the levels were high, they created a greenhouse effect. More heat was trapped on Earth’s surface, and the climate became warmer. When the levels were low, less heat was trapped and the planet cooled. Several times, cooling was severe enough to plunge Earth into an ice age. One ice age was so cold that snow and ice completely covered the planet. Earth during this ice age has been called snowball Earth(see Figure below).
Snowball Earth. During the late Precambrian, Earth grew so cold that it was covered with snow and ice. Earth during this ice age has been called snowball Earth.
Life During the Late Precambrian
The dramatic changes of the late Precambrian had a major impact on Earth’s life forms. Living things that could not adapt died out. They were replaced by organisms that evolved new adaptations. These adaptations included sexual reproduction, specialization of cells, and multicellularity.
• Sexual reproduction created much more variety among offspring. This increased the chances that at least some of them would survive when the environment changed. It also increased the speed at which evolution could occur.
• Some cells started to live together in colonies. In some colonies, cells started to specialize in doing different jobs. This made the cells more efficient as a colony than as individual cells.
• By 1 billion years ago, the first multicellular organisms had evolved. They may have developed from colonies of specialized cells. Their cells were so specialized they could no longer survive independently. However, together they were mighty. They formed an organism that was bigger, more efficient, and able to do much more than any single-celled organism ever could.
The Precambrian Extinction
At the close of the Precambrian 544 million years ago, a mass extinction occurred. In a mass extinction, many or even most species abruptly disappear from Earth. There have been fivemass extinctions in Earth’s history. Many scientists think we are currently going through a sixth mass extinction. What caused the Precambrian mass extinction? A combination of climatic and geologic events was probably responsible. No matter what the cause, the extinction paved the way for a burst of new life, called the Cambrian explosion, during the following Paleozoic Era.
Summary
• During the late Precambrian, continents drifted, carbon dioxide levels fluctuated, and climates changed. Many organisms could not survive the changes and died out.
• Other organisms evolved important new adaptations. These include sexual reproduction, cell specialization, and multicellularity.
• The Precambrian ended with a mass extinction, which paved the way for the Cambrian explosion.
Explore More
Use the time slider in this resource to answer the questions that follow.
1. Two billion years ago, what was the percentage of oxygen in the atmosphere?
2. When did multicellular organisms first appear?
3. When did photosynthesis begin on land?
4. When did sponges and fungi first evolve?
5. What was the time of the Snowball Earth? What caused the Earth to thaw?
Review
1. When was the late Precambrian?
2. Describe geologic and climatic changes that occurred during the late Precambrian.
3. What is a greenhouse effect?
4. What three significant evolutionary events occurred during the late Precambrian?
5. What is a mass extinction? | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/05%3A_Evolution/5.08%3A_Late_Precambrian_Period.txt |
What was early life like?
Prehistoric underwater life exploded with amazing new creatures during the Paleozoic Era. Evolution allowed life to take many diverse forms, eventually developing the necessary adaptations to move from the ocean onto land.
Life During the Paleozoic
The Paleozoic Era is literally the era of “old life.” It lasted from 544 to 245 million years ago and is divided into six periods. Major events in each period of the Paleozoic Era are described in Figure below. The era began with a spectacular burst of new life. This is called the Cambrian explosion. The era ended with the biggest mass extinction the world had ever seen. This is known as the Permian extinction. At the following link, you can watch a video about these and other events of the Paleozoic Era: http://www.youtube.com/watch?v=Bf2rrRmconU.
The Paleozoic Era includes the six periods described here.
The Paleozoic Era
The Cambrian Period: Following the Precambrian mass extinction, there was an explosion of new kinds of organisms in the Cambrian Period (544–505 million years ago). Many types of primitive animals called sponges evolved. Small ocean invertebrates called trilobites became abundant.
Two representatives of more than fifty modern animal phyla from the Cambrian explosion are reef-building sponges (left) and early arthropods known as trilobites (right). Both were abundant during the Cambrian and later became extinct; however, the phyla they represent persist to this day.
The Ordovician Period: During the next period, the Ordovician Period (505–440 million years ago), the oceans became filled with invertebrates of many types. Also during this period, the first fish evolved and plants colonized the land for the first time. But animals still remained in the water.
The Silurian Period: During the Silurian Period (440–410 million years ago), corals appeared in the oceans, and fish continued to evolve. On land, vascular plants appeared. With special tissues to circulate water and other materials, these plants could grow larger than the earlier nonvascular plants.
Cooksonia, a branching vascular plant with sporangia at the tips of each branch. Cooksonia fossils measure just centimeters in height and date from the Silurian period.
The Devonian Period: During the Devonian Period (410–360 million years ago), the first seed plants evolved. Seeds have a protective coat and stored food to help these plants survive. Seed plants eventually became the most common type of land plants. In the oceans, fish with lobe fins evolved. They could breathe air when they raised their heads above water. Breathing would be necessary for animals to eventually colonize the land.
On land, club mosses, horsetails, and ferns joined primitive seed plants and early trees to form the first forests.
The Carboniferous Period: Next, during the Carboniferous Period (360–290 million years ago), widespread forests of huge plants left massive deposits of carbon that eventually turned to coal. The first amphibians evolved to move out of the water and colonize land, but they had to return to the water to reproduce. Soon after amphibians arose, the first reptiles evolved. They were the first animals that could reproduce on dry land.
The Permian Period: During the Permian Period (290–245 million years ago), all the major land masses collided to form a supercontinent called Pangaea. Temperatures were extreme, and the climate was dry. Plants and animals evolved adaptations to dryness, such as waxy leaves or leathery skin to prevent water loss. The Permian Period ended with a mass extinction.
The supercontinent Pangaea encompassed all of today’s continents in a single land mass. This configuration limited shallow coastal areas which harbor marine species, and may have contributed to the dramatic event which ended the Permian - the most massive extinction ever recorded.
In the mass extinction that ended the Permian, the majority of species went extinct. Many hypotheses have been offered to explain why this mass extinction occurred. These include huge meteorites striking Earth and enormous volcanoes spewing ashes and gases into the atmosphere. Both could have darkened the skies with dust for many months. This, in turn, would have shut down photosynthesis and cooled the planet.
Despite the great loss of life, there was light at the end of the tunnel. The Permian extinction paved the way for another burst of new life at the start of the following Mesozoic Era. This included the evolution of the dinosaurs.
Summary
• The Paleozoic Era began with the Cambrian explosion. It ended with the Permian extinction.
• During the era, invertebrate animals diversified in the oceans. Plants, amphibians, and reptiles also moved to the land.
Explore More
Use the time slider in this resource to answer the questions that follow.
1. When did the Paleozoic Era begin?
2. The Paleozoic Era began with what event?
3. What animals formed during the Cambrian explosion?
4. What separates the Ordovician period from the Silurian period?
5. When did Cooksonia begin to evolve?
6. When did the first tree begin to evolve?
7. When did sharks first appear?
8. What may have caused the mass extinction at the end of the Permian period?
Review
1. What was the Cambrian explosion?
2. What was the Permian extinction?
3. List important evolutionary events that occurred during the Cambrian Period.
4. List important evolutionary events that occurred during the Ordovician Period.
5. List important evolutionary events that occurred during the Carboniferous Period.
6. Describe Pangaea. When did Pangaea form? | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/05%3A_Evolution/5.09%3A_Life_During_the_Paleozoic.txt |
What exactly is a dinosaur?
Two dinosaurs wade through shallow waters to get to the vegetation on this island. The Mesozoic Era is the age of dinosaurs. These animals grew so large they dominated the planet. Dinosaurs were so dominant that it took a catastrophic, environment-changing event for mammals to be able to take over.
Mesozoic Era: The Age of Dinosaurs
The Mesozoic Era is literally the era of “middle life.” It is also known as the age of dinosaurs. It lasted from 245 to 65 million years ago and is divided into the three periods described inFigure below. The Mesozoic began with the supercontinent Pangaea. Then, during the era, Pangaea broke up and the continents drifted apart. The movement of continents changed climates. It also caused tremendous volcanic activity.
Mass extinctions occurred at the end of the Triassic and Cretaceous Periods. The first extinction paved the way for a dinosaur takeover. In the second extinction, the dinosaurs finally disappeared. At the link below, you can watch a video about these and other exciting events during the age of dinosaurs. http://www.youtube.com/watch?v=watgb11LOHE
The Mesozoic Era consists of the three periods described here.
The Triassic Period: During the Triassic Period (245–200 million years ago), the first dinosaurs branched off from the reptiles and colonized the land, air, and water. Huge seedferns and conifers dominated the forests, and modern corals, fish, and insects evolved. The supercontinent Pangaea started to separate into Laurasia (today’s Northern Hemisphere continents) and Gondwanaland (today’s Southern Hemisphere continents). The Triassic Period ended with a mass extinction.
The Jurassic Period: The next period, the Jurassic Period (200–145 million years ago), began after the mass extinction that ended the Triassic Period. This mass extinction allowed dinosaurs to flourish in the Jurassic Period. This was the golden age of dinosaurs. Also during the Jurassic, the earliest birds evolved from reptile ancestors, and all the major groups of mammals evolved, though individual mammals were still small in size. Flowering plantsappeared for the first time, and new insects also evolved to pollinate the flowers. The continents continued to move apart, and volcanic activity was especially intense. The classic Steven Spielberg movie Jurassic Park realistically depicts some of the dinosaurs present during this period: http://www.youtube.com/watch?v=Bim7RtKXv90.
The Cretaceous Period: During the Cretaceous Period (145–65 million years ago), dinosaurs reached their peak in size and distribution. Tyrannosaurus Rex, weighed at least 7 tons. By the end of the Cretaceous, the continents were close to their present locations. Earth’s overall climate was warm; even the poles lacked ice. The period ended with the dramatic extinction of the dinosaurs.
What happened to the dinosaurs? Why did they go extinct at the end of the Cretaceous Period? Some scientists think a comet or asteroid may have collided with Earth, causing skies to darken, photosynthesis to shut down, and climates to change. A collision was probably at least a contributing factor. Without the dinosaurs, there were many opportunities for new organisms to exploit in the next era, the Cenozoic. Which living things do you think took over where the dinosaurs left off?
Summary
• The Mesozoic Era is the age of dinosaurs. They evolved from earlier reptiles to fill niches on land, in the water, and in the air.
• Mammals also evolved but were small in size.
• Flowering plants appeared for the first time.
• Dinosaurs went extinct at the end of the Mesozoic.
Explore More
Use the time slider in this resource to answer the questions that follow.
1. When did the Mesozoic Era begin?
2. What was the predominant type of animal during this time period?
3. When did placental mammals evolve? What were the first ones?
4. Describe the significant event that occurred at the end of the Mesozoic Era.
Review
1. Describe how the continents shifted during the Mesozoic Era.
2. Create a timeline of major evolutionary events during the Mesozoic Era.
3. Explain why scientists believe dinosaurs went extinct. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/05%3A_Evolution/5.10%3A_Mesozoic_Era_-_The_Age_of_Dinosaurs.txt |
What allowed mammals to outlast the dinosaurs?
With dinosaurs around, mammals could not thrive. It took a catastrophic event to rid the planet of dinosaurs. Luckily for mammals, the extinction of the dinosaurs left many opportunities for mammals to take over and flourish.
The Cenozoic Era: Age of Mammals
The Cenozoic Era literally means the era of “modern life.” It is also called the age of mammals. Mammals took advantage of the extinction of the dinosaurs. They flourished and soon became the dominant animals on Earth. You can learn more about the evolution of mammals during the Cenozoic at the link below. The Cenozoic began 65 million years ago and continues to the present. It may be divided into the two periods described in Figure below. http://www.youtube.com/watch?v=H0uTGkCWXwQ
One way of dividing the Cenozoic Era is into the two periods described here.
The Tertiary Period: During the Tertiary Period (65–1.8 million years ago), Earth’s climate was generally warm and humid. This allowed mammals to evolve further and fill virtually all niches vacated by the dinosaurs. Many mammals increased in size. Mammals called primatesevolved, including human ancestors. Modern rain forests and grasslands appeared, andflowering plants and insects were numerous and widespread.
The Quaternary Period: During the Quaternary Period (1.8 million years ago–present), Earth’s climate cooled, leading to a series of ice ages. Sea levels fell because so much water was frozen in glaciers. This created land bridges between continents, allowing land animals to move to new areas. Some mammals, like the woolly mammoths adapted to the cold by evolving very large size and thick fur. Other animals moved closer to the equator or went extinct, along with many plants.
The last ice age ended about 12,000 years ago. By that time, our own species, Homo sapiens, had evolved. After that, we were witnesses to the unfolding of life’s story. Although we don’t know all the details of the recent past, it is far less of a mystery than the billions of years that preceded it.
‘‘Walking With Cavemen’’ is an excellent depiction of the evolution of our species, from Lucy, the first upright ape, to her ancestors millions of years later. Seehttp://www.bbc.co.uk/sn/prehistoric_life/tv_radio/wwcavemen/ for additional information.
KQED: The Last Ice Age
Imagine a vast grassy ecosystem covered with herds of elephants, bison, and camels stretching as far as the eye can see. Africa? Maybe. But this also describes Northern California at the end of the last Ice Age. What happened to all this wildlife? Were they over-hunted and killed off? Did global warming destroy their populations? Scientists are not sure, but this relatively recent loss of life does raise many interesting questions. See Ice Age Bay Area at www.kqed.org/quest/television...-age-bay-area2 for additional information.
Summary
• The Cenozoic Era is the age of mammals. They evolved to fill virtually all the niches vacated by dinosaurs.
• The ice ages of the Quaternary Period of the Cenozoic led to many extinctions.
• The last ice age ended 12,000 years ago. By that time, Homo sapiens had evolved.
Explore More
Use the time slider in this resource to answer the questions that follow.
1. When did the Cenozoic Era begin? What animals are no longer present at the start of this era?
2. When did Antarctica's permanent ice cap begin to form?
3. What is the closest fossil to a human-chimp ancestor? How old is that fossil?
4. When were stone tools first used?
5. When did Homo sapiens evolve?
6. When did human migration begin? Where did it begin from?
Review
1. What explains why mammals were able to flourish during Cenozoic Era?
2. Create a timeline of major evolutionary events during the Cenozoic Era.
3. Discuss climate changes during the Tertiary and Quaternary Periods, and the effects of these changes on geology and vegetation.
5.12: Phylogenetic Classification
Can two different species be related?
Of course they can. For example, there are many different species of mammals, or of one type of mammal, such as mice. And they are all related. In other words, how close or how far apart did they separate from a common ancestor during evolution? Determining how different species are evolutionarily related can be a tremendous task.
Phylogenetic Classification
Linnaeus classified organisms based on obvious physical traits. Basically, organisms were grouped together if they looked alike. After Darwin published his theory of evolution in the 1800s, scientists looked for a way to classify organisms that showed phylogeny. Phylogeny is the evolutionary history of a group of related organisms. It is represented by a phylogenetic tree, like the one in Figure below.
Phylogenetic Tree. This phylogenetic tree shows how three hypothetical species are related to each other through common ancestors. Do you see why Species 1 and 2 are more closely related to each other than either is to Species 3?
One way of classifying organisms that shows phylogeny is by using the clade. A clade is a group of organisms that includes an ancestor and all of its descendants. Clades are based on cladistics. This is a method of comparing traits in related species to determine ancestor-descendant relationships. Clades are represented by cladograms, like the one in Figure below. This cladogram represents the mammal and reptile clades. The reptile clade includes birds. It shows that birds evolved from reptiles. Linnaeus classified mammals, reptiles, and birds in separate classes. This masks their evolutionary relationships.
This cladogram classifies mammals, reptiles, and birds in clades based on their evolutionary relationships.
Summary
• Phylogeny is the evolutionary history of group of related organisms. It is represented by a phylogenetic tree that shows how species are related to each other through common ancestors.
• A clade is a group of organisms that includes an ancestor and all of its descendants. It is a phylogenetic classification, based on evolutionary relationships.
Explore More
Use this resource to answer the questions that follow.
1. What is phylogenetic classification?
2. Describe the advantages of phylogenetic classification.
Review
1. What is a clade?
2. What is cladistics, and what is it used for?
3. Explain why reptiles and birds are placed in the same clade.
4. Dogs and wolves are more closely related to each other than either is to cats. Draw a phylogenetic tree to show these relationships. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/05%3A_Evolution/5.11%3A_Cenozoic_Era_-_The_Age_of_Mammals.txt |
What's that big red pouch?
The Frigate bird of the Galápagos Islands. This bird can be found throughout the tropical Atlantic down to the Galápagos Islands and Ecuador, but not in Europe or South America, so Darwin may never have come across one until he landed on the Galápagos. Such a unique creature was bound to make a naturalist such as Darwin wonder why. Why do they look the way they do? What's that big red pouch? What are the advantages?
Darwin’s Theory
The Englishman Charles Darwin is one of the most famous scientists who ever lived. His place in the history of science is well deserved. Darwin’s theory of evolution represents a giant leap in human understanding. It explains and unifies all of biology.
An overview of evolution can be seen at http://www.youtube.com/watch?v=GcjgWov7mTM(17:39).
As you view Introduction to Evolution and Natural Selection,focus on the following concepts:
1. the meaning of "evolution,"
2. the relationship between evolution and natural selection,
3. the relationship between natural selection and variation,
4. the evolution of the peppered moth.
Darwin’s theory of evolution actually contains two major ideas:
1. One idea is that evolution occurs. In other words, organisms change over time. Life on Earth has changed as descendants diverged from common ancestors in the past.
2. The other idea is that evolution occurs by natural selection. Natural selection is the process that results in living things with beneficial traits producing more offspring than others. This results in changes in the traits of living things over time.
In Darwin’s day, most people believed that all species were created at the same time and remained unchanged thereafter. They also believed that Earth was only about 6,000 years old. Therefore, Darwin’s ideas revolutionized biology. How did Darwin come up with these important ideas? It all started when he went on a voyage.
The Voyage of the Beagle
In 1831, when Darwin was just 22 years old, he set sail on a scientific expedition on a ship called the HMS Beagle. He was the naturalist on the voyage. As a naturalist, it was his job to observe and collect specimens of plants, animals, rocks, and fossils wherever the expedition went ashore. The route the ship took and the stops they made are shown in the Figure below. You can learn more about Darwin’s voyage at this link:www.aboutdarwin.com/voyage/voyage03.html.
Voyage of the Beagle. This map shows the route of Darwin’s 5-year voyage on the HMS Beagle. Each stop along the way is labeled. Darwin and the others on board eventually circled the globe.
Darwin was fascinated by nature, so he loved his job on the Beagle. He spent more than 3 years of the 5-year trip exploring nature on distant continents and islands. While he was away, a former teacher published Darwin’s accounts of his observations. By the time Darwin finally returned to England, he had become famous as a naturalist.
Darwin’s Observations
During the long voyage, Darwin made many observations that helped him form his theory of evolution. For example:
• He visited tropical rainforests and other new habitats where he saw many plants and animals he had never seen before (see Figure below). This impressed him with the great diversity of life.
• He experienced an earthquake that lifted the ocean floor 2.7 meters (9 feet) above sea level. He also found rocks containing fossil sea shells in mountains high above sea level. These observations suggested that continents and oceans had changed dramatically over time and continue to change in dramatic ways.
• He visited rock ledges that had clearly once been beaches that had gradually built up over time. This suggested that slow, steady processes also change Earth’s surface.
• He dug up fossils of gigantic extinct mammals, such as the ground sloth (see Figure below). This was hard evidence that organisms looked very different in the past. It suggested that living things—like Earth’s surface—change over time.
On his voyage, Darwin saw giant marine iguanas and blue-footed boobies. He also dug up the fossil skeleton of a giant ground sloth like the one shown here. From left: Giant Marine Iguana, Blue-Footed Boobies, and Fossil Skeleton of a Giant Ground Sloth
The Galápagos Islands
Darwin’s most important observations were made on the Galápagos Islands (see map in Figure below). This is a group of 16 small volcanic islands 966 kilometers (600 miles) off the west coast of Ecuador, South America.
Galápagos Islands. This map shows the location of the Galápagos Islands that Darwin visited on his voyage.
Individual Galápagos islands differ from one another in important ways. Some are rocky and dry. Others have better soil and more rainfall. Darwin noticed that the plants and animals on the different islands also differed. For example, the giant tortoises on one island had saddle-shaped shells, while those on another island had dome-shaped shells (see Figure below). People who lived on the islands could even tell the island a turtle came from by its shell. This started Darwin thinking about the origin of species. He wondered how each island came to have its own type of tortoise.
Galápagos Tortoises. Galápagos tortoises have differently shaped shells depending on which island they inhabit. Tortoises with saddle-shaped shells can reach up to eat plant leaves above their head. Tortoises with dome-shaped shells cannot reach up in this way. These two types of tortoises live on islands with different environments and food sources. How might this explain the differences in their shells?
The Farallon Islands – "California's Galapagos"
One of the most productive marine food webs on the planet is located on the Farallon Islands, just 28 miles off the San Francisco, California coast. These islands also host the largest seabird breeding colony in the continental United States, with over 300,000 breeding seabirds. The islands are known as the Galapagos of California. Why? Find out at http://science.kqed.org/quest/video/...ias-galapagos/ .
Summary
• Darwin’s theory of evolution by natural selection states that living things with beneficial traits produce more offspring than others do. This produces changes in the traits of living things over time.
• During his voyage on the Beagle, Darwin made many observations that helped him develop his theory of evolution.
• Darwin's most important observations were made on the Galápagos Islands.
Explore More
Use this resource to answer the questions that follow.
1. Describe Darwin's role on the Beagle.
2. Describe what Darwin encountered in the following places:
1. Salvador, Brazil,
2. Punta Alta, Argentina,
3. Chiloe Island, Chile,
4. Galapagos Islands,
5. Sydney, Australia.
Review
1. State the two main ideas in Darwin's theory.
2. What was Darwin's role on the Beagle?
3. Describe two observations Darwin made on his voyage on the Beagle that helped him develop his theory of evolution.
4. Why did Darwin’s observations of Galápagos tortoises cause him to wonder how species originate? | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/05%3A_Evolution/5.13%3A_Darwin%27s_Voyage_of_the_Beagle.txt |
How do structures like this form?
Cathedral Rock in Sedona, Arizona. Though Arizona was not on Darwin's itinerary, the work of others that saw and studied Earth's changing landscape influenced him. One geologist, Charles Lyell, proposed that gradual geological processes have shaped Earth’s surface, inferring that Earth must be far older than most people believed. How else could structures like those shown here develop? If in fact Earth was much older then just 6,000 years, Darwin believed there would have been plenty of time for evolution to occur.
Influences on Darwin
Science, like evolution, always builds on the past. Darwin didn’t develop his theory completely on his own. He was influenced by the ideas of earlier thinkers.
Earlier Thinkers Who Influenced Darwin
1. Jean Baptiste Lamarck (1744–1829) was an important French naturalist. He was one of the first scientists to propose that species change over time. However, Lamarck was wrong about how species change. His idea of the inheritance of acquired characteristics is incorrect. Traits an organism develops during its own life time cannot be passed on to offspring, as Lamarck believed.
2. Charles Lyell (1797–1875) was a well-known English geologist. Darwin took Lyell's book,Principles of Geology, with him on the Beagle. In the book, Lyell argued that gradual geological processes have gradually shaped Earth’s surface. From this, Lyell inferred that Earth must be far older than most people believed.
3. Thomas Malthus (1766–1834) was an English economist. He wrote an essay titled On Population. In the essay, Malthus argued that human populations grow faster than the resources they depend on. When populations become too large, famine and disease break out. In the end, this keeps populations in check by killing off the weakest members.
Artificial Selection
These weren’t the only influences on Darwin. He was also aware that humans could breed plants and animals to have useful traits. By selecting which animals were allowed to reproduce, they could change an organism’s traits. The pigeons in Figure below are good examples. Darwin called this type of change in organisms artificial selection. He used the word ‘‘artificial’’ to distinguish it from natural selection.
Artificial Selection in Pigeons. Pigeon hobbyists breed pigeons to have certain characteristics. Both of the pigeons in the bottom row were bred from the common rock pigeon.
Wallace’s Theory
Did you ever hear the saying that “great minds think alike?” It certainly applies to Charles Darwin and another English naturalist named Alfred Russel Wallace. Wallace lived at about the same time as Darwin. He also traveled to distant places to study nature. Wallace wasn’t as famous as Darwin. However, he developed basically the same theory of evolution. While working in distant lands, Wallace sent Darwin a paper he had written. In the paper, Wallace explained his evolutionary theory. This served to confirm what Darwin already thought.
Summary
• Darwin was influenced by other early thinkers, including Lamarck, Lyell, and Malthus.
• Darwin was also influenced by his knowledge of artificial selection.
• Wallace’s paper on evolution confirmed Darwin’s ideas.
Explore More
Use this resource to answer the questions that follow.
1. Briefly describe the influences on Darwin of the following individuals:
1. Comte de Buffon,
2. Erasmus Darwin,
3. Georges Cuvier,
4. James Hutton,
5. Thomas Malthus.
Review
1. What is the inheritance of acquired characteristics? What scientist developed this mistaken idea?
2. Who was Charles Lyell? How did he influence Darwin?
3. What is artificial selection? How does it work?
4. How did Alfred Russel Wallace influence Darwin? | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/05%3A_Evolution/5.14%3A_Influences_on_Darwin.txt |
How do new species form?
This is the only illustration in Charles Darwin's 1859 book On the Origin of Species, showing his ideas describing the divergence of species from common ancestors.
Darwin’s Theory of Evolution by Natural Selection
Darwin spent many years thinking about the work of Lamarck, Lyell, and Malthus, what he had seen on his voyage, and artificial selection. What did all this mean? How did it all fit together? It fits together in Darwin’s theory of evolution by natural selection. It’s easy to see how all of these influences helped shape Darwin’s ideas.
For a discussion of the underlying causes of natural selection and evolution seehttp://www.youtube.com/watch?v=DuArVnT1i-E (19:51).
Evolution of Darwin’s Theory
It took Darwin years to form his theory of evolution by natural selection. His reasoning went like this:
1. Like Lamarck, Darwin assumed that species can change over time. The fossils he found helped convince him of that.
2. From Lyell, Darwin saw that Earth and its life were very old. Thus, there had been enough time for evolution to produce the great diversity of life Darwin had observed.
3. From Malthus, Darwin knew that populations could grow faster than their resources. This “overproduction of offspring” led to a “struggle for existence,” in Darwin’s words.
4. From artificial selection, Darwin knew that some offspring have variations that occur by chance, and that can be inherited. In nature, offspring with certain variations might be more likely to survive the “struggle for existence” and reproduce. If so, they would pass their favorable variations to their offspring.
5. Darwin coined the term fitness to refer to an organism’s relative ability to survive and produce fertile offspring. Nature selects the variations that are most useful. Therefore, he called this type of selection natural selection.
6. Darwin knew artificial selection could change domestic species over time. He inferred that natural selection could also change species over time. In fact, he thought that if a species changed enough, it might evolve into a new species.
Wallace’s paper not only confirmed Darwin’s ideas. It also pushed him to finish his book, On the Origin of Species. Published in 1859, this book changed science forever. It clearly spelled out Darwin’s theory of evolution by natural selection and provided convincing arguments and evidence to support it.
Applying Darwin’s Theory
The following example applies Darwin’s theory. It explains how giraffes came to have such long necks (see Figure below).
• In the past, giraffes had short necks. But there was chance variation in neck length. Some giraffes had necks a little longer than the average.
• Then, as now, giraffes fed on tree leaves. Perhaps the environment changed, and leaves became scarcer. There would be more giraffes than the trees could support. Thus, there would be a “struggle for existence.”
• Giraffes with longer necks had an advantage. They could reach leaves other giraffes could not. Therefore, the long-necked giraffes were more likely to survive and reproduce. They had greater fitness.
• These giraffes passed the long-neck trait to their offspring. Each generation, the population contained more long-necked giraffes. Eventually, all giraffes had long necks.
Giraffes feed on leaves high in trees. Their long necks allow them to reach leaves that other ground animals cannot.
As this example shows, chance variations may help a species survive if the environment changes. Variation among species helps ensure that at least one will be able to survive environmental change.
A summary of Darwin's ideas are presented in the video ‘‘Natural Selection and the Owl Butterfly’’ : http://www.youtube.com/watch?v=dR_BFmDMRaI (13:29).
KQED: Chasing Beetles, Finding Darwin
It's been over 150 years since Charles Darwin published On the Origin of Species. Yet his ideas remain as central to scientific exploration as ever, and has been called the unifying concept of all biology. Is evolution continuing today? Of course it is.
QUEST follows researchers who are still unlocking the mysteries of evolution, including entomologist David Kavanaugh of the California Academy of Sciences, who predicted that a new beetle species would be found on the Trinity Alps of Northern California. See www.kqed.org/quest/television...inding-darwin2 for more information.
It's rare for a biologist to predict the discovery of a new species. For his prediction, Kavanaugh drew inspiration from Darwin's own 1862 prediction. When Darwin observed an orchid from Madagascar with a foot-long nectar, he predicted that a pollinator would be found with a tongue long enough to reach the nectar inside the orchid's very thin, elongated nectar ‘‘pouch’’, though he had never seen such a bird or insect. Darwin's prediction was based on his finding that all species are related to each other and that some of them evolve together, developing similar adaptations. Darwin's prediction came true in 1903, when a moth was discovered in Madagascar with a long, thin proboscis, which it uncurls to reach the nectar in the orchid's nectar. In the process of feeding from the orchid, the moth serves as its pollinator. The moth was given the scientific name Xanthopan morganii praedicta, in honor of Darwin’s prediction.
As you view Chasing Beetles, Finding Darwin, focus on the following concepts:
1. the relationship between studying beetles and evolution,
2. the development of new species,
3. the relationship between genetic make-up of an organism and evolution,
4. the role of beneficial mutations,
5. the role of ‘‘habitat islands’’,
6. the selection for certain traits among breeders, such as pigeon breeders,
7. the importance of identifying new species.
For an additional explanation of natural selection, see Darwin, Mice, and Picky Peacocksat https://www.youtube.com/watch?v=lvfNuz8B1jk.
Summary
• Darwin's book On the Origin of Species clearly spells out his theory.
• Darwin's book also provides evidence and logic to support that evolution occurs and that it occurs by natural selection.
Explore More
Explore More I
Use this resource to answer the questions that follow.
• Charles Darwin & Evolution at darwin200.christs.cam.ac.uk/p...php?page_id=d3.
1. What did Darwin mean by "common descent?"
2. What did Darwin mean by "gradualism?"
3. What is meant by "super fecundity?"
4. What did Darwin say would happen to individuals of the same species in an environment of scarce resources?
Explore More II
• Natural Selection
Review
1. Define fitness.
2. Apply Darwin’s theory of evolution by natural selection to a specific case. For example, explain how Galápagos tortoises could have evolved saddle-shaped shells.
3. Explain how the writings of Charles Lyell and Thomas Malthus helped Darwin develop his theory of evolution by natural selection.
4. Discuss the role artificial selection had on Darwin's theory. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/05%3A_Evolution/5.15%3A_Theory_of_Evolution_by_Natural_Selection.txt |
Would this be evidence of evolution?
Fossils, like this dinosaur fossil, provide evidence of species that lived in the past and have since gone extinct. In other words, these fossils are evidence of evolution.
Fossil Evidence
In his book On the Origin of Species, Darwin included evidence to show that evolution had taken place. He also made logical arguments to support his theory that evolution occurs by natural selection. Since Darwin’s time, much more evidence has been gathered. The evidence includes a huge number of fossils. It also includes more detailed knowledge of living things, right down to their DNA.
Fossils are a window into the past. They provide clear evidence that evolution has occurred. Scientists who find and study fossils are called paleontologists. How do they use fossils to understand the past? Consider the example of the horse, shown in the Figure below. The fossil record shows how the horse evolved.
Evolution of the horse. Fossil evidence, depicted by the skeletal fragments, demonstrates evolutionary milestones in this process. Notice the 57 million year evolution of the horse leg bones and teeth. Especially obvious is the transformation of the leg bones from having four distinct digits to that of today's horse.
The oldest horse fossils show what the earliest horses were like. They were about the size of a fox, and they had four long toes. Other evidence shows they lived in wooded marshlands, where they probably ate soft leaves. Through time, the climate became drier, and grasslands slowly replaced the marshes. Later fossils show that horses changed as well.
• They became taller, which would help them see predators while they fed in tall grasses.
• They evolved a single large toe that eventually became a hoof. This would help them run swiftly and escape predators.
• Their molars (back teeth) became longer and covered with cement. This would allow them to grind tough grasses and grass seeds without wearing out their teeth.
Similar fossil evidence demonstrates the evolution of the whale, moving from the land into the sea. An animation of this process can be viewed athttp://collections.tepapa.govt.nz/exhibitions/whales/Segment.aspx?irn=161.
"Does The Fossil Record Support Evolution?" This video can be seen at http://www.youtube.com/watch?v=QWVoXZPOCGk (9:20).
Summary
• Fossils provide a window into the past. They are evidence for evolution.
• Scientists who find and study fossils are called paleontologists.
Explore More
Explore More I
Use this resource to answer the questions that follow.
1. What is a fossil? Give an example.
2. What is the age of the earliest identified fossil?
3. How do fossils form?
Review
1. What is a fossil?
2. How do paleontologists learn about evolution?
3. Describe what fossils reveal about the evolution of the horse.
5.17: Living Species
Is this evidence of evolution?
Take a close look at this gorilla hand. The similarities to a human hand are remarkable. Comparing anatomy, and characterizing the similarities and differences, provides evidence of evolution.
Evidence from Living Species
Just as Darwin did many years ago, today’s scientists study living species to learn about evolution. They compare the anatomy, embryos, and DNA of modern organisms to understand how they evolved.
Comparative Anatomy
Comparative anatomy is the study of the similarities and differences in the structures of different species. Similar body parts may be homologies or analogies. Both provide evidence for evolution.
Homologous structures are structures that are similar in related organisms because they were inherited from a common ancestor. These structures may or may not have the same function in the descendants. Figure below shows the hands of several different mammals. They all have the same basic pattern of bones. They inherited this pattern from a common ancestor. However, their forelimbs now have different functions.
The forelimbs of all mammals have the same basic bone structure.
Analogous structures are structures that are similar in unrelated organisms. The structures are similar because they evolved to do the same job, not because they were inherited from a common ancestor. For example, the wings of bats and birds, shown in Figure below, look similar on the outside. They also have the same function. However, wings evolved independently in the two groups of animals. This is apparent when you compare the pattern of bones inside the wings.
Wings of bats and birds serve the same function. Look closely at the bones inside the wings. The differences show they developed from different ancestors.
Comparative Embryology
Comparative embryology is the study of the similarities and differences in the embryos of different species. Similarities in embryos are evidence of common ancestry. All vertebrate embryos, for example, have gill slits and tails. Most vertebrates, except for fish, lose their gill slits by adulthood. Some of them also lose their tail. In humans, the tail is reduced to the tail bone. Thus, similarities organisms share as embryos may be gone by adulthood. This is why it is valuable to compare organisms in the embryonic stage. Seehttp://www.pbs.org/wgbh/evolution/library/04/2/pdf/l_042_03.pdf for additional information and a comparative diagram of human, monkey, pig, chicken and salamander embryos.
Vestigial Structures
Structures like the human tail bone and whale pelvis are called vestigial structures. Evolution has reduced their size because the structures are no longer used. The human appendix is another example of a vestigial structure. It is a tiny remnant of a once-larger organ. In a distant ancestor, it was needed to digest food. It serves no purpose in humans today. Why do you think structures that are no longer used shrink in size? Why might a full-sized, unused structure reduce an organism’s fitness?
Comparing DNA
Darwin could compare only the anatomy and embryos of living things. Today, scientists can compare their DNA. Similar DNA sequences are the strongest evidence for evolution from a common ancestor. More similarities in the DNA sequence is evidence for a closer evolutionary relationship. Look at the cladogram in the Figure below. It shows how humans and apes are related based on their DNA sequences.
Evolution and molecules are discussed at http://www.youtube.com/watch?v=nvJFI3ChOUU(3:52).
Cladogram of Humans and Apes. This cladogram is based on DNA comparisons. It shows how humans are related to apes by descent from common ancestors.
Using various types of information to understand evolutionary relationships is discussed in the following videos: http://www.youtube.com/watch?v=aZc1t2Os6UU (3:38),http://www.youtube.com/watch?v=6IRz85QNjz0 (6:45), http://www.youtube.com/watch?v=JgyTVT3dqGY (10:51).
KQED: The Reverse Evolution Machine
In search of the common ancestor of all mammals, University of California Santa Cruz scientist David Haussler is pulling a complete reversal. Instead of studying fossils, he's comparing the genomes of living mammals to construct a map of our common ancestors' DNA. He also specializes in studying the DNA of extinct animals, asking how the DNA has changed over millions of years to create today's species. His technique, referred to as computational genomics, holds promise for providing a better picture of how life evolved. Seehttp://www.kqed.org/quest/televis...lution-machine for more information.
Summary
• Scientists compare the anatomy, embryos, and DNA of living things to understand how they evolved.
• Evidence for evolution is provided by homologous structures. These are structures shared by related organisms that were inherited from a common ancestor.
• Other evidence for evolution is provided by analogous structures. These are structures that unrelated organisms share because they evolved to do the same job.
• Comparing DNA sequences provided some of the strongest evidence of evolutionary relationships.
Explore More
Use this resource to answer the questions that follow.
1. Distinguish between homology and analogy.
2. How are tetrapod limbs similar to each other?
3. Give four examples of homologous tetrapod limbs.
4. Give an example of a homologous structure in insects.
5. What can happen to homologous structures of different species over time?
6. Why are tetrapod and octopus limbs not homologous?
Review
1. What are vestigial structures? Give an example.
2. Compare homologous and analogous structures.
3. Why do vertebrate embryos show similarities between organisms that do not appear in the adults?
4. Humans and apes have five fingers they can use to grasp objects. Do you think these are analogous or homologous structures? Explain.
5. What is the strongest evidence of evolution from a common ancestor? | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/05%3A_Evolution/5.16%3A_Fossils.txt |
Why would geography have anything to do with evolution?
Similar to "how did the chicken cross the road?" but on a much grander scale. How did the animal cross Europe and into Asia? Or Asia into America? How did anything get into Australia?
Evidence from Biogeography
Biogeography is the study of how and why plants and animals live where they do. It provides more evidence for evolution. Let’s consider the camel family as an example.
Biogeography of Camels: An Example
Today, the camel family includes different types of camels. They are shown in Figure below. All of today’s camels are descended from the same camel ancestors. These ancestors lived in North America about a million years ago.
Camel Migrations and Present-Day Variation. Members of the camel family now live in different parts of the world. They differ from one another in a number of traits. However, they share basic similarities. This is because they all evolved from a common ancestor. What differences and similarities do you see?
Early North American camels migrated to other places. Some went to East Asia. They crossed a land bridge during the last ice age. A few of them made it all the way to Africa. Others went to South America. They crossed the Isthmus of Panama. Once camels reached these different places, they evolved independently. They evolved adaptations that suited them for the particular environment where they lived. Through natural selection, descendants of the original camel ancestors evolved the diversity they have today.
Island Biogeography
The biogeography of islands yields some of the best evidence for evolution. Consider the birds called finches that Darwin studied on the Galápagos Islands (see Figure below). All of the finches probably descended from one bird that arrived on the islands from South America. Until the first bird arrived, there had never been birds on the islands. The first bird was a seed eater. It evolved into many finch species. Each species was adapted for a different type of food. This is an example of adaptive radiation. This is the process by which a single species evolves into many new species to fill available niches.
Galápagos finches differ in beak size and shape, depending on the type of food they eat.
Eyewitness to Evolution
In the 1970s, biologists Peter and Rosemary Grant went to the Galápagos Islands. They wanted to re-study Darwin’s finches. They spent more than 30 years on the project. Their efforts paid off. They were able to observe evolution by natural selection actually taking place.
While the Grants were on the Galápagos, a drought occurred. As a result, fewer seeds were available for finches to eat. Birds with smaller beaks could crack open and eat only the smaller seeds. Birds with bigger beaks could crack and eat seeds of all sizes. As a result, many of the small-beaked birds died in the drought. Birds with bigger beaks survived and reproduced (see Figure below). Within 2 years, the average beak size in the finch population increased. Evolution by natural selection had occurred.
Evolution of Beak Size in Galápagos Finches. The top graph shows the beak sizes of the entire finch population studied by the Grants in 1976. The bottom graph shows the beak sizes of the survivors in 1978. In just 2 years, beak size increased.
Summary
• Biogeography is the study of how and why plants and animals live where they do. It also provides evidence for evolution.
• On island chains, such as the Galápagos, one species may evolve into many new species to fill available niches. This is called adaptive radiation.
Explore More
Use this resource to answer the questions that follow.
1. What is biogeography? What scientist helped found the modern science of biogeography?
2. Where did Wallace collect much of his data?
3. What did Wallace study?
4. What was the proposal of Alfred Wegener?
5. What was Gondwanaland?
Review
1. Define biogeography.
2. Describe an example of island biogeography that provides evidence of evolution.
3. Describe the effects of the drought on the Galápagos Islands observed by the Grants. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/05%3A_Evolution/5.18%3A_Biogeography.txt |
Jeans vs. Genes. What's the difference?
Plenty. One you have for life, the other just lasts a few years. One is the basis for the passing of traits from one generation to the next. Some jeans you change frequently. But what happens when you change a gene's frequency? Essentially, evolution is a change in gene frequencies within a population.
Genes in Populations
Darwin knew that heritable variations are needed for evolution to occur. However, he knew nothing about Mendel’s laws of genetics. Mendel’s laws were rediscovered in the early 1900s. Only then could scientists fully understand the process of evolution. We now know that variations of traits are heritable. These variations are determined by different alleles. We also know that evolution is due to a change in alleles over time. How long a time? That depends on the scale of evolution.
• Microevolution occurs over a relatively short period of time within a population or species. The Grants observed this level of evolution in Darwin’s finches (see the "Biogeography" concept).
• Macroevolution occurs over geologic time above the level of the species. The fossil record reflects this level of evolution. It results from microevolution taking place over many generations.
Remember that individuals do not evolve. Their genes do not change over time. The unit of evolution is the population. A population consists of organisms of the same species that live in the same area. In terms of evolution, the population is assumed to be a relatively closed group. This means that most mating takes place within the population. The science that focuses on evolution within populations is population genetics. It is a combination of evolutionary theory and Mendelian genetics.
Gene Pool
The genetic makeup of an individual is the individual’s genotype. A population consists of many genotypes. Altogether, they make up the population’s gene pool. The gene poolconsists of all the genes of all the members of the population. For each gene, the gene pool includes all the different alleles for the gene that exist in the population. For a given gene, the population is characterized by the frequency of the different alleles in the gene pool.
Allele Frequencies
Allele frequency is how often an allele occurs in a gene pool relative to the other alleles for that gene. Look at the example in the Table below. The population in the table has 100 members. In a sexually reproducing species, each member of the population has two copies of each gene. Therefore, the total number of copies of each gene in the gene pool is 200. The gene in the example exists in the gene pool in two forms, alleles A and a. Knowing the genotypes of each population member, we can count the number of alleles of each type in the gene pool. The table shows how this is done.
Genotype Number of Individuals in the Population with that Genotype Number of Allele AContributed to the Gene Pool by that Genotype Number of Allele aContributed to the Gene Pool by that Genotype
AA 50 50 × 2 = 100 50 × 0 = 0
Aa 40 40 × 1 = 40 40 × 1 = 40
aa 10 10 × 0 = 0 10 × 2 = 20
Totals 100 140 60
Let the letter p stand for the frequency of allele A. Let the letter q stand for the frequency of allele a. We can calculate p and q as follows:
• p = number of A alleles/total number of alleles = 140/200 = 0.7
• q = number of a alleles/total number of alleles = 60/200 = 0.3
• Notice that p + q = 1.
Evolution occurs in a population when allele frequencies change over time. What causes allele frequencies to change? That question was answered by Godfrey Hardy and Wilhelm Weinberg in 1908 (see the Hardy-Weinberg Theorem concept).
Summary
• Microevolution occurs over a short period of time in a population or species.Macroevolution occurs over geologic time above the level of the species.
• The population is the unit of evolution.
• A population’s gene pool consists of all the genes of all the members of the population.
• For a given gene, the population is characterized by the frequency of different alleles in the gene pool.
Explore More
Use this resource to answer the questions that follow.
1. How is evolution defined in this resource?
2. How is macroevolution related to microevolution?
3. How are genetic changes introduced?
4. What is genetic drift?
Review
1. Compare microevolution to macroevolution.
2. Why are populations, rather than individuals, the units of evolution?
3. What is a gene pool?
4. Assume that a population of 50 individuals has the following numbers of genotypes for a gene with two alleles, B and b: BB = 30, Bb = 10, and bb = 10. Calculate the frequencies of the two alleles in the population’s gene pool. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/05%3A_Evolution/5.19%3A_Population_Genetics.txt |
How do a population's genes change?
Remember, without change, there cannot be evolution. Together, the forces that change a population's gene frequencies are the driving mechanisms behind evolution.
Forces of Evolution
The conditions for Hardy-Weinberg equilibrium are unlikely to be met in real populations. The Hardy-Weinberg theorem also describes populations in which allele frequencies are not changing. By definition, such populations are not evolving. How does the theorem help us understand evolution in the real world?
From the theorem, we can infer factors that cause allele frequencies to change. These factors are the "forces of evolution." There are four such forces: mutation, gene flow, genetic drift, and natural selection. Natural selection will be discussed in the "Natural Selection" concept.
Mutation
Mutation creates new genetic variation in a gene pool. It is how all new alleles first arise. In sexually reproducing species, the mutations that matter for evolution are those that occur in gametes. Only these mutations can be passed to offspring. For any given gene, the chance of a mutation occurring in a given gamete is very low. Thus, mutations alone do not have much effect on allele frequencies. However, mutations provide the genetic variation needed for other forces of evolution to act.
Gene Flow
Gene flow occurs when individuals move into or out of a population. If the rate of migration is high, this can have a significant effect on allele frequencies. The allele frequencies of both the population they leave and the population they enter may change.
During the Vietnam War in the 1960s and 1970s, many American servicemen had children with Vietnamese women. Most of the servicemen returned to the United States after the war. However, they left copies of their genes behind in their offspring. In this way, they changed the allele frequencies in the Vietnamese gene pool. Was the gene pool of the American population also affected? Why or why not?
Genetic Drift
Genetic drift is a random change in allele frequencies that occurs in a small population. When a small number of parents produce just a few offspring, allele frequencies in the offspring may differ, by chance, from allele frequencies in the parents.
This is like tossing a coin. If you toss a coin just a few times, you may, by chance, get more or less than the expected 50 percent heads or tails. In a small population, you may also, by chance, get different allele frequencies than expected in the next generation. In this way, allele frequencies may drift over time.
There are two special conditions under which genetic drift occurs. They are called bottleneck effect and founder effect.
1. Bottleneck effect occurs when a population suddenly gets much smaller. This might happen because of a natural disaster such as a forest fire. By chance, allele frequencies of the survivors may be different from those of the original population.
2. Founder effect occurs when a few individuals start, or found, a new population. By chance, allele frequencies of the founders may be different from allele frequencies of the population they left. An example is described in the Figure below.
Founder Effect in the Amish Population. The Amish population in the U.S. and Canada had a small number of founders. How has this affected the Amish gene pool?
Summary
• There are four forces of evolution: mutation, gene flow, genetic drift, and natural selection.
• Mutation creates new genetic variation in a gene pool.
• Gene flow and genetic drift alter allele frequencies in a gene pool.
Explore More
Use this resource to answer the questions that follow.
1. Define each of the following:
1. mutation,
2. gene flow,
3. genetic drift,
4. natural selection.
2. Which mechanism(s) is/are the source of variation within a population?
3. Which mechanism(s) is/are the most important influences on evolution?
Review
1. Identify the four forces of evolution.
2. Why is mutation needed for evolution to occur, even though it usually has little effect on allele frequencies?
3. What is founder effect? Give an example.
4. Explain why genetic drift is most likely to occur in a small population. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/05%3A_Evolution/5.20%3A_Forces_of_Evolution.txt |
What's fitness?
Does this type of fitness have anything to do with natural selection? Usually not. There are countless ways in which an organism can be more "fit," or better adapted to its habitat. And we probably do not know about most of these adaptations.
Natural Selection
Natural selection occurs when there are differences in fitness among members of a population. As a result, some individuals pass more genes to the next generation. This causesallele frequencies to change.
Sickle Cell and Natural Selection
The example of sickle-cell anemia is described in the Figure below and Table below. It shows how natural selection can keep a harmful allele in a gene pool. You can also watch a video about natural selection and sickle-cell anemia at this link:http://www.pbs.org/wgbh/evolution/library/01/2/l_012_02.html.
Sickle Cell and Natural Selection. Notice the normal-shaped red blood cell on the left, and the sickle-shaped cell on the right.
Genotype Phenotype Fitness
AA 100% normal hemoglobin Somewhat reduced fitness because of no resistance to malaria
AS Enough normal hemoglobin to prevent sickle-cell anemia Highest fitness because of resistance to malaria
SS 100% abnormal hemoglobin, causing sickle-cell anemia Greatly reduced fitness because of sickle-cell anemia
Here’s how natural selection can keep a harmful allele in a gene pool:
• The allele (S) for sickle-cell anemia is a harmful autosomal recessive. It is caused by a mutation in the normal allele (A) for hemoglobin (a protein on red blood cells).
• Malaria is a deadly tropical disease. It is common in Africa south of the Sahara, South and Southeast Asia and Northern Brazil.
• Heterozygotes (AS) with the sickle-cell allele are resistant to malaria. Therefore, they are more likely to survive and reproduce. This keeps the S allele in the gene pool.
• There are three alleles found in Africa. A fourth thought to have arisen independently is found in India and Saudi Arabia.
• The allele (S) for sickle-cell anemia found in African descended people in the Western Hemisphere is believed to have come from West Africa as a result of the slave trade.
The sickle-cell example shows that fitness depends on phenotypes. It also shows that fitness may depend on the environment. What do you think might happen if malaria was eliminated in a population with a relatively high frequency of the S allele? How might the fitness of the different genotypes change? How might this affect the frequency of the S allele?
Natural Selection and Polygenic Traits
Sickle-cell trait is controlled by a single gene. Natural selection for polygenic traits is more complex, unless you just look at phenotypes. Three ways that natural selection can affect phenotypes are shown in Figure below. You can also watch an animation comparing the three ways at the link below. bcs.whfreeman.com/thelifewire...hp23/2301s.swf.
1. Stabilizing selection occurs when phenotypes at both extremes of the phenotypic distribution are selected against. This narrows the range of variation. An example is human birth weight. Babies that are very large or very small at birth are less likely to survive. This keeps birth weight within a relatively narrow range.
2. Directional selection occurs when one of two extreme phenotypes is selected for. This shifts the distribution toward that extreme. This is the type of natural selection that the Grants observed in the beak size of Galápagos finches.
3. Disruptive selection occurs when phenotypes in the middle of the range are selected against. This results in two overlapping phenotypes, one at each end of the distribution. An example is sexual dimorphism. This refers to differences between the phenotypes of males and females of the same species. In humans, for example, males and females have different heights and body shapes.
Natural selection may affect the distribution of a polygenic trait. These graphs show three ways this can happen.
For a review of natural selection and genetic drift, and how they relate to evolution, see http://www.cultureunplugged.com/play/2533/Mechanisms-of-Evolution. Mutation, natural selection, genetic drift and gene flow are discussed at http://www.youtube.com/watch?v=RtIQvkQWTZY (8:45).
Summary
• Natural selection occurs when there are differences in fitness among members of a population.
• Natural selection for a polygenic trait changes the distribution of phenotypes. It may have a stabilizing, directional, or disruptive effect on the phenotype distribution.
Explore More
Explore More I
Use this resource to answer the questions that follow.
• 10 Examples of Natural Selection at www.discovery.com/tv-shows/cu...-selection.htm.
1. Describe natural selection in each of the following:
1. the peppered moth,
2. the Galapagos finches,
3. peacocks,
4. the deer mouse,
5. and humans.
Review
1. What is natural selection and what are its effects on allele frequencies?
2. Describe three types of natural selection for a polygenic trait.
3. How does the recessive sickle-cell allele stay in the gene pool? | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/05%3A_Evolution/5.21%3A_Natural_Selection.txt |
How can a river influence evolution?
Imagine a group of small organisms, such as mice, that become separated by a mighty river. This group has now become isolated, and formed two separate groups. The groups are obviously no longer able to breed together. Over many generations, each group will evolve separately, eventually forming two completely new species of mice.
Origin of Species
Macroevolution is evolution over geologic time above the level of the species. One of the main topics in macroevolution is how new species arise. The process by which a new species evolves is called speciation. How does speciation occur? How does one species evolve into two or more new species?
To understand how a new species forms, it’s important to review what a species is. A species is a group of organisms that can breed and produce fertile offspring together in nature. For a new species to arise, some members of a species must become reproductively isolated from the rest of the species. This means they can no longer interbreed with other members of the species. How does this happen? Usually they become geographically isolated first.
Allopatric Speciation
Assume that some members of a species become geographically separated from the rest of the species. If they remain separated long enough, they may evolve genetic differences. If the differences prevent them from interbreeding with members of the original species, they have evolved into a new species. Speciation that occurs in this way is called allopatric speciation. An example is described in the Figure below.
Allopatric Speciation in the Kaibab Squirrel. The Kaibab squirrel is in the process of becoming a new species.
Sympatric Speciation
Less often, a new species arises without geographic separation. This is called sympatric speciation. The following example shows one way this can occur.
1. Hawthorn flies lay eggs in hawthorn trees (see Figure below). The eggs hatch into larvae that feed on hawthorn fruits. Both the flies and trees are native to the U.S.
2. Apple trees were introduced to the U.S. and often grow near hawthorn trees. Some hawthorn flies started to lay eggs in nearby apple trees. When the eggs hatched, the larvae fed on apples.
3. Over time, the two fly populations—those that fed on hawthorn trees and those that preferred apple trees—evolved reproductive isolation. Now they are reproductively isolated because they breed at different times. Their breeding season matches the season when the apple or hawthorn fruits mature.
4. Because they rarely interbreed, the two populations of flies are evolving other genetic differences. They appear to be in the process of becoming separate species.
Sympatric Speciation in Hawthorn Flies. Hawthorn flies are diverging from one species into two. As this example shows, behaviors as well as physical traits may evolve and lead to speciation.
Isolating mechanisms are discussed in the following video http://www.youtube.com/watch?v=-e64TfKeAXU (2:57).
Summary
• New species arise in the process of speciation.
• Allopatric speciation occurs when some members of a species become geographically separated. They then evolve genetic differences. If the differences prevent them from interbreeding with the original species, a new species has evolved.
• Sympatric speciation occurs without geographic separation.
Explore More
Use this resource to answer the questions that follow.
• Speciation at evolution.berkeley.edu/evosit...eciation.shtml.
1. In terms of a gene pool, what is a species?
2. What is speciation?
3. Give three examples of events that may cause geographic isolation.
4. What can happen to a population by geographic isolation?
Review
1. Define speciation.
2. Describe how allopatric speciation occurs.
3. Why is sympatric speciation less likely to occur than allopatric speciation? | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/05%3A_Evolution/5.22%3A_Origin_of_Species.txt |
How can a predator, such as a wolf, influence evolution?
Wolves hunt caribou, chasing them down to capture them. The slower caribou are more likely to become lunch or dinner, leaving the faster individuals to reproduce. The resulting faster offspring will be even more difficult for the wolves to catch, and only the fastest wolves - or perhaps the wolves who are genetically capable of developing methods to hunt very fast prey - will get enough food to survive. This is coevolution in action.
Coevolution
Evolution occurs in response to a change in the environment. Environmental change often involves other species of organisms. In fact, species in symbiotic relationships tend to evolve together. This is called coevolution. As one species changes, the other species must also change in order to adapt.
Coevolution occurs in flowering plants and the species that pollinate them. The flower and bird in Figure below are a good example. They have evolved matching structures.
Results of Coevolution in a Flower and Its Pollinator. The very long mouth part of this hummingbird has coevolved with the tubular flower it pollinates. Only this species of bird can reach the nectar deep in the flower. What might happen to the flower if the bird species went extinct?
In coevolution, relationships may be positive for one species or both, or may be an evolutionary arms race between predator and prey. Flowering plants depend on insects for pollination, so have evolved colors, shapes, scents, and even food supplies that are attractive to certain insect species. Insects, in turn, have evolved mouthparts, senses, and flight patterns that allow them to respond to and benefit from specific floral “offerings,” shown in the Figure below.
Impressive proboscis and vivid colors! Hawk moths and the zinnias influence each other’s evolution, because the flower depends on the moth for pollination, and the moth feeds on the flower.
The endosymbiotic theory describes a special form of co-evolution: mitochondria and chloroplasts evolve within eukaryote cells, yet because these organelles have their own DNA sequence, different from that of the nucleus in the “host” cell, the organelle and host cell evolve in tandem – each influences the evolution of the other.
Explore More
Use this resource to answer the questions that follow.
• Coevolution and Pollination at biology.clc.uc.edu/courses/bi...oevolution.htm.
1. How does this resource define coevolution?
2. Describe the coevolutionary relationship between yucca moths and yucca plants, and between acacia ants and acacia trees.
3. What is a lichen?
4. Describe the relationship between many flowers and their pollinators.
Review
1. Define coevolution.
2. Apply the concepts of fitness and natural selection to explain the coevolution of insects and flowering plants.
5.24: Macroevolution
Fast or slow?
Which is better, the direct route or the scenic route? Each has its advantages, depending on the situation. And that describes evolution. It can be fast or slow, depending on the situation.
Timing of Macroevolution
Is evolution slow and steady? Or does it occur in fits and starts? It may depend on what else is going on, such as changes in climate and geologic conditions.
• When geologic and climatic conditions are stable, evolution may occur gradually. This is how Darwin thought evolution occurred. This model of the timing of evolution is called gradualism.
• When geologic and climatic conditions are changing, evolution may occur more quickly. Thus, long periods of little change may be interrupted by bursts of rapid change. This model of the timing of evolution is called punctuated equilibrium. It is better supported by the fossil record than is gradualism. This model suggests that niches left open by sudden geologic and climatic changes may be rapidly filled by bursts of evolution.
Two theories of evolutionary change - gradualism vs. punctuated equilibrium - are still debated. The former proposes continuous change, while the latter suggests that species remain constant for long periods of time and that change, when it occurs, is rapid.
Summary
• Darwin thought that evolution occurs gradually. This model of evolution is called gradualism.
• The fossil record better supports the model of punctuated equilibrium. In this model, long periods of little change are interrupted by bursts of rapid change.
Review
1. What is gradualism? When is it most likely to apply?
2. Describe the timing of evolutionary change according to the punctuated equilibrium model.
3. Which model of evolution would be predicted to follow the extinction of the dinosaurs? Why? | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/05%3A_Evolution/5.23%3A_Coevolution.txt |
What are these? Are these organisms plants, fungi, protists, or animals?
This colony of tube sponges resembles the pipes of a musical instrument. These sponges are actually animals, although they are the simplest animals on Earth. Sponges are frequently used as shelter for small crabs, shrimps, and other invertebrates.
Major Trends in Animal Evolution
The oldest animal fossils are about 630 million years old. By 500 million years ago, most modern phyla of animals had evolved. Figure below shows when some of the major events in animal evolution took place.
Partial Geologic Time Scale. This portion of the geologic time scale shows major events in animal evolution.
Animal Origins
Who were the ancestors of the earliest animals? They may have been marine protists that lived in colonies. Scientists think that cells of some protist colonies became specialized for different jobs. After a while, the specialized cells came to need each other for survival. Thus, the first multicellular animal evolved. Look at the cells in Figure below. One type of sponge cell, the choanocyte, looks a lot like the protist cell. How does this support the hypothesis that animals evolved from protists?
Choanoflagellate Protist and Choanocyte Cells in Sponges. Sponge choanocytes look a lot like choanoflagellate protists.
Evolution of Invertebrates
Many important animal adaptations evolved in invertebrates. Without these adaptations, vertebrates would not have been able to evolve. They include:
• Tissues, organs, and organ systems.
• A symmetrical body.
• A brain and sensory organs.
• A fluid-filled body cavity.
• A complete digestive system.
• A body divided into segments.
Moving from Water to Land
When you think of the first animals to colonize the land, you may think of amphibians. It’s true that ancestors of amphibians were the first vertebrates to move to land. However, the very first animals to go ashore were invertebrates, most likely arthropods.
The move to land required new adaptations. For example, animals needed a way to keep their body from drying out. They also needed a way to support their body on dry land without the buoyancy of water. One way early arthropods solved these problems was by evolving an exoskeleton. This is a non-bony skeleton that forms on the outside of the body. It supports the body and helps retain water. The ability to breath oxygen without gills was another necessary adaptation.
Evolution of Chordates
Another major step in animal evolution was the evolution of a notochord. A notochord is a rigid rod that runs the length of the body. It supports the body and gives it shape (see Figure below). It also provides a place for muscles to anchor, and counterbalances them when they contract. Animals with a notochord are called chordates. They also have a hollow nerve cord that runs along the top of the body. Gill slits and a tail are two other chordate features. Many modern chordates have some of these structures only as embryos.
This tunicate is a primitive, deep-sea chordate. It is using its notochord to support its head, while it waits to snatch up prey in its big mouth.
Evolution of Vertebrates
Vertebrates evolved from primitive chordates. This occurred about 550 million years ago. The earliest vertebrates may have been jawless fish, like the hagfish in Figure below. Vertebrates evolved a backbone to replace the notochord after the embryo stage. They also evolved a cranium, or bony skull, to enclose and protect the brain.
Hagfish are very simple vertebrates.
As early vertebrates evolved, they became more complex. Around 365 million years ago, they finally made the transition from water to land. The first vertebrates to live on land were amphibians. They evolved from lobe-finned fish. You can compare a lobe-finned fish and an amphibian in Figure below.
From Lobe-Finned Fish to Early Amphibian. Lobe-finned fish evolved into the earliest amphibians. A lobe-finned fish could breathe air for brief periods of time. It could also use its fins to walk on land for short distances. What similarities do you see between the lobe-finned fish and the amphibian?
Evolution of Amniotes
Amphibians were the first animals to have true lungs and limbs for life on land. However, they still had to return to water to reproduce. That’s because their eggs lacked a waterproof covering and would dry out on land. The first fully terrestrial vertebrates were amniotes.Amniotes are animals that produce eggs with internal membranes. The membranes let gases but not water pass through. Therefore, in an amniotic egg, an embryo can breathe without drying out. Amniotic eggs were the first eggs that could be laid on land.
The earliest amniotes evolved about 350 million years ago. They may have looked like the animal in Figure below. Within a few million years, two important amniote groups evolved: synapsids and sauropsids. Synapsids evolved into mammals. The sauropsids gave rise to reptiles, dinosaurs, and birds.
Early Amniote. The earliest amniotes probably looked something like this. They were reptile-like, but not actually reptiles. Reptiles evolved somewhat later.
Summary
• The earliest animals evolved from colonial protists more than 600 million years ago.
• Many important animal adaptations evolved in invertebrates, including tissues and a brain.
• The first animals to live on land were invertebrates.
• Amphibians were the first vertebrates to live on land.
• Amniotes were the first animals that could reproduce on land.
Review
1. List three traits that evolved in invertebrate animals.
2. Assume that a new species of animal has been discovered. It is an egg-laying animal that lives and reproduces on land. Explain what you know about its eggs without ever seeing them.
3. Relate similarities between choanoflagellates and choanocytes to animal origins.
4. What was important about the evolution of an exoskeleton? | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/05%3A_Evolution/5.25%3A_Animal_Evolution.txt |
Can a plant really grow in hardened lava?
It can if it is very hardy and tenacious. And that is how succession starts. It begins with a plant that must be able to grow on new land with minimal soil or nutrients.
Ecological Succession
Communities are not usually static. The numbers and types of species that live in them generally change over time. This is called ecological succession. Important cases of succession are primary and secondary succession.
Primary Succession
Primary succession occurs in an area that has never before been colonized. Generally, the area is nothing but bare rock. This type of environment may come about when
• lava flows from a volcano and hardens into rock.
• a glacier retreats and leaves behind bare rock.
• a landslide uncovers an area of bare rock.
The first species to colonize a disturbed area such as this are called pioneer species (see Figure below). They change the environment and pave the way for other species to come into the area. Pioneer species are likely to include bacteria and lichens that can live on bare rock. Along with wind and water, they help weather the rock and form soil. Once soil begins to form, plants can move in. At first, the plants include grasses and other species that can grow in thin, poor soil. As more plants grow and die, organic matter is added to the soil. This improves the soil and helps it hold water. The improved soil allows shrubs and trees to move into the area.
Primary Succession. New land from a volcanic eruption is slowly being colonized by a pioneer species.
Secondary Succession
Secondary succession occurs in a formerly inhabited area that was disturbed. The disturbance could be a fire, flood, or human action such as farming. This type of succession is faster because the soil is already in place. In this case, the pioneer species are plants such as grasses, birch trees, and fireweed. Organic matter from the pioneer species improves the soil. This lets other plants move into the area. An example of this type of succession is shown in Figure below.
Secondary Succession. Two months after a forest fire, new plants are already sprouting among the charred logs.
Climax Communities
Many early ecologists thought that a community always goes through the same series of stages during succession. They also assumed that succession always ends with a final stable stage. They called this stage the climax community. Today, most ecologists no longer hold these views. They believe that continued change is normal in most ecosystems. They think that most communities are disturbed too often to become climax communities.
Summary
• Ecological succession is the process in which a community changes through time.
• Primary succession occurs in an area that has never before been colonized.
• Secondary succession occurs in a formerly inhabited area that was disturbed.
Review
1. What is ecological succession?
2. Describe the main difference between primary and secondary succession.
3. Give two examples of habitats that will go through primary succession.
4. What is a climax community?
5. Summarize how ideas about ecological succession and climax communities have changed. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/06%3A_Ecology/6.01%3A_Succession.txt |
What lives in the forest?
Take a close look at this ecosystem. Obviously there are deer and many types of plants. But there are organisms that live there that cannot be seen in the picture. Many other animals, such as rabbits, mice, and countless insects. There are also bacteria and fungi. Add in the nonliving aspects of the area, such as the water, and you have an ecosystem.
The Ecosystem
Ecology is the study of how living things interact with each other and with their environment. It is a major branch of biology, but has areas of overlap with geography, geology, climatology, and other sciences. The study of ecology begins with two fundamental concepts in ecology: the ecosystem and their organisms.
Organisms are individual living things. Despite their tremendous diversity, all organisms have the same basic needs: energy and matter. These must be obtained from the environment. Therefore, organisms are not closed systems. They depend on and are influenced by their environment. The environment includes two types of factors: abiotic and biotic.
1. Abiotic factors are the nonliving aspects of the environment. They include factors such as sunlight, soil, temperature, and water.
2. Biotic factors are the living aspects of the environment. They consist of other organisms, including members of the same and different species.
An ecosystem is a unit of nature and the focus of study in ecology. It consists of all the biotic and abiotic factors in an area and their interactions. Ecosystems can vary in size. A lake could be considered an ecosystem. So could a dead log on a forest floor. Both the lake and log contain a variety of species that interact with each other and with abiotic factors. Another example of an ecosystem is pictured in Figure below.
A desert ecosystem. What are some of the biotic and abiotic factors in this desert ecosystem?
When it comes to energy, ecosystems are not closed. They need constant inputs of energy. Most ecosystems get energy from sunlight. A small minority get energy from chemical compounds. Unlike energy, matter is not constantly added to ecosystems. Instead, it is recycled. Water and elements such as carbon and nitrogen are used over and over again.
Niche
One of the most important concepts associated with the ecosystem is the niche. A niche refers to the role of a species in its ecosystem. It includes all the ways that the species interacts with the biotic and abiotic factors of the environment. Two important aspects of a species’ niche are the food it eats and how the food is obtained. Look at Figure below. It shows pictures of birds that occupy different niches. Each species eats a different type of food and obtains the food in a different way.
Bird Niches. Each of these species of birds has a beak that suits it for its niche. For example, the long slender beak of the nectarivore allows it to sip liquid nectar from flowers. The short sturdy beak of the granivore allows it to crush hard, tough grains.
Habitat
Another aspect of a species’ niche is its habitat. The habitat is the physical environment in which a species lives and to which it is adapted. A habitat’s features are determined mainly by abiotic factors such as temperature and rainfall. These factors also influence the traits of the organisms that live there.
Competitive Exclusion Principle
A given habitat may contain many different species, but each species must have a different niche. Two different species cannot occupy the same niche in the same place for very long. This is known as the competitive exclusion principle. If two species were to occupy the same niche, what do you think would happen? They would compete with one another for the same food and other resources in the environment. Eventually, one species would be likely to outcompete and replace the other.
Summary
• Ecology is the study of how living things interact with each other and with their environment.
• The environment includes abiotic (nonliving) and biotic (living) factors.
• An ecosystem consists of all the biotic and abiotic factors in an area and their interactions.
• A niche refers to the role of a species in its ecosystem.
• A habitat is the physical environment in which a species lives and to which it is adapted.
• Two different species cannot occupy the same niche in the same place for very long.
Review
1. Define ecology.
2. Define biotic and abiotic factors of the environment. Give an example of each.
3. How do ecologists define the term ecosystem? What makes up an ecosystem?
4. State the competitive exclusion principle.
5. Compare and contrast the ecosystem concepts of niche and habitat. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/06%3A_Ecology/6.02%3A_Ecosystems.txt |
What is happening inside each leaf and blade of grass?
Photosynthesis. Maybe the most important biochemical reaction of Earth. As sunlight shines down on this forest, the sunlight is being absorbed, and the energy from that sunlight is being transformed into chemical energy. That chemical energy is then distributed to all other living organisms in the ecosystem.
Flow of Energy
To survive, ecosystems need a constant influx of energy. Energy enters ecosystems in the form of sunlight or chemical compounds. Some organisms use this energy to make food. Other organisms get energy by eating the food.
Producers
Producers are organisms that produce food for themselves and other organisms. They use energy and simple inorganic molecules to make organic compounds. The stability of producers is vital to ecosystems because all organisms need organic molecules. Producers are also called autotrophs. There are two basic types of autotrophs: photoautotrophs and chemoautotrophs.
1. Photoautotrophs use energy from sunlight to make food by photosynthesis. They include plants, algae, and certain bacteria (see Figure below).
2. Chemoautotrophs use energy from chemical compounds to make food by chemosynthesis. They include some bacteria and also archaea. Archaea are microorganisms that resemble bacteria.
Different types of photoautotrophs are important in different ecosystems.
Consumers
Consumers are organisms that depend on other organisms for food. They take in organic molecules by essentially “eating” other living things. They include all animals and fungi. (Fungi don't really “eat”; they absorb nutrients from other organisms.) They also include many bacteria and even a few plants, such as the pitcher plant shown in Figure below. Consumers are also called heterotrophs. Heterotrophs are classified by what they eat:
• Herbivores consume producers such as plants or algae. They are a necessary link between producers and other consumers. Examples include deer, rabbits, and mice.
• Carnivores consume animals. Examples include lions, polar bears, hawks, frogs, salmon, and spiders. Carnivores that are unable to digest plants and must eat only animals are called obligate carnivores. Other carnivores can digest plants but do not commonly eat them.
• Omnivores consume both plants and animals. They include humans, pigs, brown bears, gulls, crows, and some species of fish.
Pitcher Plant. Virtually all plants are producers. This pitcher plant is an exception. It consumes insects. It traps them in a sticky substance in its “pitcher.” Then it secretes enzymes that break down the insects and release nutrients. Which type of consumer is a pitcher plant?
Decomposers
When organisms die, they leave behind energy and matter in their remains. Decomposersbreak down the remains and other wastes and release simple inorganic molecules back to the environment. Producers can then use the molecules to make new organic compounds. The stability of decomposers is essential to every ecosystem. Decomposers are classified by the type of organic matter they break down:
• Scavengers consume the soft tissues of dead animals. Examples of scavengers include vultures, raccoons, and blowflies.
• Detritivores consume detritus—the dead leaves, animal feces, and other organic debris that collects on the soil or at the bottom of a body of water. On land, detritivores include earthworms, millipedes, and dung beetles (see Figure below). In water, detritivores include “bottom feeders” such as sea cucumbers and catfish.
• Saprotrophs are the final step in decomposition. They feed on any remaining organic matter that is left after other decomposers do their work. Saprotrophs include fungi and single-celled protozoa. Fungi are the only organisms that can decompose wood.
Dung Beetle. This dung beetle is rolling a ball of feces to its nest to feed its young.
KQED: Banana Slugs: The Ultimate Recyclers
One of the most beloved and iconic native species within the old growth redwood forests of California is the Pacific Banana Slug. These slimy friends of the forest are the ultimate recyclers. Feeding on fallen leaves, mushrooms or even dead animals, they play a pivotal role in replenishing the soil. QUEST goes to Henry Cowell Redwoods State Park near Santa Cruz, California on a hunt to find Ariolimax dolichophallus, a bright yellow slug with a very big personality.
Summary
• Ecosystems require constant inputs of energy from sunlight or chemicals.
• Producers use energy and inorganic molecules to make food.
• Consumers take in food by eating producers or other living things.
• Decomposers break down dead organisms and other organic wastes and release inorganic molecules back to the environment.
Review
1. Identify three different types of consumers. Name an example of each type.
2. What are photoautotrophs? Give an example of one.
3. What can you infer about an ecosystem that depends on chemoautotrophs for food?
4. What is the role of decomposers?
5. What do scavengers do? Give an example of a scavenger. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/06%3A_Ecology/6.03%3A_Flow_of_Energy.txt |
Who eats whom?
Describing the flow of energy within an ecosystem essentially answers this question. To survive, one must eat. Why? To get energy. Food chains and webs describe the transfer of energy within an ecosystem, from one organism to another. In other words, they show who eats whom.
Food Chains and Food Webs
Food chains and food webs are diagrams that represent feeding relationships. Essentially, they show who eats whom. In this way, they model how energy and matter move through ecosystems.
Food Chains
A food chain represents a single pathway by which energy and matter flow through an ecosystem. An example is shown in Figure below. Food chains are generally simpler than what really happens in nature. Most organisms consume—and are consumed by—more than one species.
This food chain includes producers and consumers. How could you add decomposers to the food chain?
Food Webs
A food web represents multiple pathways through which energy and matter flow through an ecosystem. It includes many intersecting food chains. It demonstrates that most organisms eat, and are eaten, by more than one species. Examples are shown in Figures below and below.
Food Web. This food web consists of several different food chains. Which organisms are producers in all of the food chains included in the food web?
Examples of food webs.
Summary
• Food chains and food webs are diagrams that represent feeding relationships.
• Food chains and webs model how energy and matter move through ecosystems.
Review
1. What is a food chain?
2. Describe the role of decomposers in food webs.
3. Why is a food web more realistic than a food chain?
4. Draw a terrestrial food chain that includes four feeding levels.
6.05: Trophic Levels
Why are pyramids important in ecology?
The classic example of a pyramid is shown here. But the pyramid structure can also represent the decrease in a measured substance from the lowest level on up. In ecology, pyramids model the use of energy from the producers through the ecosystem.
Trophic Levels
The feeding positions in a food chain or web are called trophic levels. The different trophic levels are defined in the Table below. Examples are also given in the table. All food chains and webs have at least two or three trophic levels. Generally, there are a maximum of four trophic levels.
Trophic Level Where It Gets Food Example
1st Trophic Level: Producer Makes its own food Plants make food
2nd Trophic Level: Primary Consumer Consumes producers Mice eat plant seeds
3rd Trophic Level: Secondary Consumer Consumes primary consumers Snakes eat mice
4th Trophic Level: Tertiary Consumer Consumes secondary consumers Hawks eat snakes
Many consumers feed at more than one trophic level. Humans, for example, are primary consumers when they eat plants such as vegetables. They are secondary consumers when they eat cows. They are tertiary consumers when they eat salmon.
Trophic Levels and Energy
Energy is passed up a food chain or web from lower to higher trophic levels. However, generally only about 10 percent of the energy at one level is available to the next level. This is represented by the ecological pyramid in Figure below. What happens to the other 90 percent of energy? It is used for metabolic processes or given off to the environment as heat. This loss of energy explains why there are rarely more than four trophic levels in a food chain or web. Sometimes there may be a fifth trophic level, but usually there’s not enough energy left to support any additional levels.
Ecological Pyramid. This pyramid shows how energy and biomass decrease from lower to higher trophic levels. Assume that producers in this pyramid have 1,000,000 kilocalories of energy. How much energy is available to primary consumers?
Ecological pyramids can demonstrate the decrease in energy, biomass or numbers within an ecosystem.
Trophic Levels and Biomass
With less energy at higher trophic levels, there are usually fewer organisms as well. Organisms tend to be larger in size at higher trophic levels, but their smaller numbers result in less biomass. Biomass is the total mass of organisms at a trophic level. The decrease in biomass from lower to higher levels is also represented by Figure above.
Summary
• The different feeding positions in a food chain or web are called trophic levels.
• Generally, there are no more than four trophic levels because energy and biomass decrease from lower to higher levels.
Review
1. What is a trophic level?
2. What do energy pyramids depict?
3. Explain how energy limits the number of trophic levels in a food chain or web.
4. Draw a terrestrial food chain that includes four trophic levels. Identify the trophic level of each organism in the food chain. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/06%3A_Ecology/6.04%3A_Food_Chains_and_Food_Webs.txt |
Unlike energy, matter is not lost as it passes through an ecosystem. Instead, matter, including water, is recycled. This recycling involves specific interactions between the biotic and abiotic factors in an ecosystem. Chances are, the water you drank this morning has been around for millions of years, or more.
The Water Cycle
The chemical elements and water that are needed by organisms continuously recycle in ecosystems. They pass through biotic and abiotic components of the biosphere. That’s why their cycles are called biogeochemical cycles. For example, a chemical might move from organisms (bio) to the atmosphere or ocean (geo) and back to organisms again. Elements or water may be held for various periods of time in different parts of a cycle.
• Part of a cycle that holds an element or water for a short period of time is called an exchange pool. For example, the atmosphere is an exchange pool for water. It usually holds water (in the form of water vapor) for just a few days.
• Part of a cycle that holds an element or water for a long period of time is called a reservoir. The ocean is a reservoir for water. The deep ocean may hold water for thousands of years.
Water on Earth is billions of years old. However, individual water molecules keep moving through the water cycle. The water cycle is a global cycle. It takes place on, above, and below Earth’s surface, as shown in Figure below.
Like other biogeochemical cycles, there is no beginning or end to the water cycle. It just keeps repeating. During the water cycle, water occurs in three different states: gas (water vapor), liquid (water), and solid (ice). Many processes are involved as water changes state in the water cycle.
Evaporation, Sublimation, and Transpiration
Water changes to a gas by three different processes:
1. Evaporation occurs when water on the surface changes to water vapor. The sun heats the water and gives water molecules enough energy to escape into the atmosphere.
2. Sublimation occurs when ice and snow change directly to water vapor. This also happens because of heat from the sun.
3. Transpiration occurs when plants release water vapor through leaf pores called stomata (see Figure below).
Plant leaves have many tiny stomata. They release water vapor into the air.
Condensation and Precipitation
Rising air currents carry water vapor into the atmosphere. As the water vapor rises in the atmosphere, it cools and condenses. Condensation is the process in which water vapor changes to tiny droplets of liquid water. The water droplets may form clouds. If the droplets get big enough, they fall as precipitation—rain, snow, sleet, hail, or freezing rain. Most precipitation falls into the ocean. Eventually, this water evaporates again and repeats the water cycle. Some frozen precipitation becomes part of ice caps and glaciers. These masses of ice can store frozen water for hundreds of years or longer.
Groundwater and Runoff
Precipitation that falls on land may flow over the surface of the ground. This water is called runoff. It may eventually flow into a body of water. Some precipitation that falls on land may soak into the ground, becoming groundwater. Groundwater may seep out of the ground at a spring or into a body of water such as the ocean. Some groundwater may be taken up by plant roots. Some may flow deeper underground to an aquifer. This is an underground layer of rock that stores water, sometimes for thousands of years.
Summary
• Chemical elements and water are recycled through biogeochemical cycles. The cycles include both biotic and abiotic parts of ecosystems.
• The water cycle takes place on, above, and below Earth’s surface. In the cycle, water occurs as water vapor, liquid water, and ice. Many processes are involved as water changes state in the cycle.
• The atmosphere is an exchange pool for water. Ice masses, aquifers, and the deep ocean are water reservoirs.
Review
1. What is a biogeochemical cycle? Name an example.
2. Identify and define two processes by which water naturally changes from a solid or liquid to a gas.
3. Define exchange pool and reservoir, and identify an example of each in the water cycle.
4. Assume you are a molecule of water. Describe one way you could go through the water cycle, starting as water vapor in the atmosphere. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/06%3A_Ecology/6.06%3A_Water_Cycle.txt |
How could releasing this much pollution into the atmosphere not be a poor idea?
Burning of fossil fuels, such as oil, releases carbon into the atmosphere. This carbon must be cycled - removed from the atmosphere - back into living organisms, or it stays in the atmosphere. Increased carbon in the atmosphere contributes to the greenhouse effect on Earth.
The Carbon Cycle
Flowing water can slowly dissolve carbon in sedimentary rock. Most of this carbon ends up in the ocean. The deep ocean can store carbon for thousands of years or more. Sedimentary rock and the ocean are major reservoirs of stored carbon. Carbon is also stored for varying lengths of time in the atmosphere, in living organisms, and as fossil fuel deposits. These are all parts of the carbon cycle, which is shown in Figure below.
The Carbon Cycle. Carbon moves from one reservoir to another in the carbon cycle. What role do organisms play in this cycle?
Why is recycling carbon important? Recall that carbon is the cornerstone of organiccompounds, the compounds necessary for life. But do organisms make their own carbon? Do they have the genes that encode proteins necessary to make carbon? No. In fact, there are no such genes. Carbon must be recycled from other living organisms, from carbon in the atmosphere, and from carbon in other parts of the biosphere.
Carbon in the Atmosphere
Though carbon can be found in ocean water, rocks and sediment and other parts of thebiosphere, the atmosphere may be the most recognizable reservoir of carbon. Carbon occurs in various forms in different parts of the carbon cycle. Some of the different forms in which carbon appears are described in Table below. KEY: C = Carbon, O = Oxygen, H = Hydrogen
Form of Carbon Chemical Formula State Main Reservoir
Carbon Dioxide CO2 Gas Atmosphere
Carbonic Acid H2CO3 Liquid Ocean
Bicarbonate Ion HCO3 Liquid(dissolved ion) Ocean
Organic Compounds Examples: C6H12O6 (Glucose), CH4 (Methane) Solid Gas Biosphere Organic Sediments (Fossil Fuels)
Other Carbon Compounds Examples: CaCO3 (Calcium Carbonate), CaMg(CO3)2 (Calcium Magnesium Carbonate) Solid Solid Sedimentary Rock, Shells, Sedimentary Rock
Carbon in Carbon Dioxide
Carbon cycles quickly between organisms and the atmosphere. In the atmosphere, carbon exists primarily as carbon dioxide (CO2). Carbon dioxide cycles through the atmosphere by several different processes, including those listed below.
• Living organisms release carbon dioxide as a byproduct of cellular respiration.
• Photosynthesis removes carbon dioxide from the atmosphere and uses it to make organic compounds.
• Carbon dioxide is given off when dead organisms and other organic materials decompose.
• Burning organic material, such as fossil fuels, releases carbon dioxide.
• Carbon cycles far more slowly through geological processes such as sedimentation. Carbon may be stored in sedimentary rock for millions of years.
• When volcanoes erupt, they give off carbon dioxide that is stored in the mantle.
• Carbon dioxide is released when limestone is heated during the production of cement.
• Ocean water releases dissolved carbon dioxide into the atmosphere when water temperature rises.
• Carbon dioxide is also removed when ocean water cools and dissolves more carbon dioxide from the air.
Because of human activities, there is more carbon dioxide in the atmosphere today than in the past hundreds of thousands of years. Burning fossil fuels and has released great quantities of carbon dioxide into the atmosphere. Cutting forests and clearing land has also increased carbon dioxide into the atmosphere because these activities reduce the number of autotrophic organisms that use up carbon dioxide in photosynthesis. In addition, clearing often involves burning, which releases carbon dioxide that was previously stored in autotrophs.
Summary
• Carbon must be recycled through living organisms or it stays in the atmosphere.
• Carbon cycles quickly between organisms and the atmosphere.
• Due to human activities, there is more carbon dioxide in the atmosphere today than in the past hundreds of thousands of years.
Review
1. What is the role of the carbon cycle?
2. Why is cycling carbon important?
3. Describe a major method that carbon is cycled.
4. How have human activities increased atmospheric carbon dioxide levels?
6.08: Nitrogen Cycle
Alfalfa, clover, peas, beans, lentils, lupins, mesquite, carob, soy, and peanuts. What are these?
Legumes. Legume plants have the ability to fix atmospheric nitrogen, due to a mutualistic symbiotic relationship with bacteria found in root nodules of these plants.
The Nitrogen Cycle
Nitrogen makes up 78 percent of Earth’s atmosphere. It’s also an important part of living things. Nitrogen is found in proteins, nucleic acids, and chlorophyll. The nitrogen cycle moves nitrogen through the abiotic and biotic parts of ecosystems. Figure below shows how nitrogen cycles through a terrestrial ecosystem. Nitrogen passes through a similar cycle in aquatic ecosystems.
Nitrogen Cycle in a Terrestrial Ecosystem. Nitrogen cycles between the atmosphere and living things.
Even though nitrogen gas makes up most of Earth's atmosphere, plants cannot use this nitrogen gas to make organic compounds for themselves and other organisms. The two nitrogen atoms in a molecule of nitrogen gas are held together by a very stable triple bond. This bond must be broken for the nitrogen to be used. The nitrogen gas must be changed to a form called nitrates, which plants can absorb through their roots. The process of changing nitrogen gas to nitrates is called nitrogen fixation. It is carried out by nitrogen-fixing bacteria. The bacteria live in soil and roots of legumes, such as peas.
When plants and other organisms die, decomposers break down their remains. In the process, they release nitrogen in the form of ammonium ions. This process is calledammonification. Nitrifying bacteria change the ammonium ions into nitrites and nitrates. Some of the nitrates are used by plants. The process of converting ammonium ions to nitrites or nitrates is called nitrification. Still other bacteria, called denitrifying bacteria, convert some of the nitrates in soil back into nitrogen gas in a process called denitrification. The process is the opposite of nitrogen fixation. Denitrification returns nitrogen gas back to the atmosphere, where it can continue the nitrogen cycle.
Summary
• The nitrogen cycle moves nitrogen back and forth between the atmosphere and organisms.
• Bacteria change nitrogen gas from the atmosphere to nitrogen compounds that plants can absorb.
• Other bacteria change nitrogen compounds back to nitrogen gas, which re-enters the atmosphere.
Review
1. Why can't plants use nitrogen gas directly?
2. What is nitrogen fixation?
3. Explain why bacteria are essential parts of the nitrogen cycle.
4. What is ammonification? | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/06%3A_Ecology/6.07%3A_Carbon_Cycle.txt |
What do temperature, wind, and rain, have in common?
They are all part of climate, the statistical summary of temperature, humidity, atmospheric pressure, wind, rainfall, other meteorological measurements in a given region over long periods. In other words, is it dry or wet, hot or cold, or humid? And it is these abiotic factors that help determine the nature of a biome.
Terrestrial Biomes
If you look at the two pictures in Figure below, you will see very few similarities. The picture on the left shows a desert in Africa. The picture on the right shows a rainforest in Australia. The desert doesn’t have any visible plants, whereas the rainforest is densely packed with trees. What explains these differences?
Sahara Desert in northern Africa (left). Rainforest in northeastern Australia (right). Two very different biomes are pictured here. A biome is a group of similar ecosystems with the same general abiotic factors and primary producers. Both are found at roughly the same distance from the equator.
Terrestrial biomes include all the land areas on Earth where organisms live. The distinguishing features of terrestrial biomes are determined mainly by climate. Terrestrial biomes include tundras, temperate forests and grasslands, chaparral, temperate and tropical deserts, and tropical forests and grasslands.
Terrestrial Biomes and Climate
Climate is the average weather in an area over a long period of time. Weather refers to the conditions of the atmosphere from day to day. Climate is generally described in terms of temperature and moisture.
Temperature falls from the equator to the poles. Therefore, major temperature zones are based on latitude. They include tropical, temperate, and arctic zones (see Figure below). However, other factors besides latitude may also influence temperature. For example, land near the ocean may have cooler summers and warmer winters than land farther inland. This is because water gains and loses heat more slowly than does land, and the water temperature influences the temperature on the coast. Temperature also falls from lower to higher altitudes. That’s why tropical zone mountain tops may be capped with snow.
Temperature zones are based on latitude. What temperature zone do you live in?
In terms of moisture, climates can be classified as arid (dry), semi-arid, humid (wet), or semi-humid. The amount of moisture depends on both precipitation and evaporation. Precipitation increases moisture. Evaporation decreases moisture.
• The global pattern of precipitation is influenced by movements of air masses. For example, there is a global belt of dry air masses and low precipitation at about 30° N and 30° S latitude.
• Precipitation is also influenced by temperature. Warm air can hold more moisture than cold air, so tropical areas receive more rainfall than other parts of the world.
• Nearness to the ocean and mountain ranges may also influence the amount of precipitation an area receives. This is explained in Figure below.
• Evaporation of moisture is greatest where it is hot and sunny. Therefore, cold climates with low precipitation may not be as dry as warm climates with the same amount of precipitation.
• Moist air from the ocean rises up over the mountain range.
• As the air rises, it cools and its water vapor condenses. Precipitation falls on the windward side of the mountain range.
• The air is dry when it reaches the leeward side of the mountain range, so there is little precipitation there. This creates a “rain shadow.”
This diagram shows how precipitation is affected by the ocean and a mountain range.
Climate and Plant Growth
Plants are the major producers in terrestrial biomes. They have five basic needs: air, warmth, sunlight, water, and nutrients. How well these needs are met in a given location depends on the growing season and soil quality, both of which are determined mainly by climate.
• The growing season is the period of time each year when it is warm and wet enough for plants to grow. The growing season may last all year in a hot, wet climate but just a few months in a cooler or drier climate.
• Plants grow best in soil that contains plenty of nutrients and organic matter. Both are added to soil when plant litter and dead organisms decompose. Decomposition occurs too slowly in cold climates and too quickly in hot, wet climates for nutrients and organic matter to accumulate. Temperate climates usually have the best soil for plant growth.
Climate and Biodiversity
Because climate determines plant growth, it also influences the number and variety of other organisms in a terrestrial biome. Biodiversity generally increases from the poles to the equator. It is also usually greater in more humid climates. This is apparent from the desert and rainforest biomes pictured in Figure above.
Climate and Adaptations
Organisms evolve adaptations that help them survive in the climate of the biome where they live. For example, in biomes with arid climates, plants may have special tissues for storing water (see Figure below). The desert animals pictured in Figure below also have adaptations for a dry climate.
The aloe plant on the left stores water in its large, hollow leaves. The cactus plant on the right stores water in its stout, barrel-shaped stems.
The Gila monster’s fat tail is an adaptation to its dry climate. It serves as a storage depot for water. The kangaroo rat has very efficient kidneys. They produce concentrated urine, thus reducing the amount of water lost from the body.
In biomes with cold climates, plants may adapt by becoming dormant during the coldest part of the year. Dormancy is a state in which a plant slows down cellular activities and may shed its leaves. Animals also adapt to cold temperatures. One way is with insulation in the form of fur and fat. This is how the polar bears in Figure below stay warm.
Thick fur and a layer of blubber keep polar bears warm in their Arctic ecosystem. Why do you think their fur is white? Why might it be an adaptation in an Arctic biome?
Summary
• Terrestrial biomes are determined mainly by climate.
• Climate influences plant growth, biodiversity, and adaptations of land organisms.
Review
1. What is climate? How does it differ from weather?
2. What is a rain shadow?
3. What is a growing season? How does climate influence plant growth?
4. Describe the relationship between climate and biodiversity.
5. Compare the data for Seattle and Denver in Table below. Seattle is farther north than Denver. Why is Seattle warmer?
City, State Latitude (°N) Altitude (ft above sea level) Location (relative to ocean) Average Low Temperature in January (°F)
Seattle, Washington 48 429 Coastal 33
Denver, Colorado 41 5183 Interior 15 | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/06%3A_Ecology/6.09%3A_Climate_Effects_on_Biomes.txt |
Forest vs. desert. What explains these differences?
If you look at these two pictures, you will see very few similarities. The picture on the left shows a desert in Africa. The picture on the right shows a rainforest in Australia. The desert doesn’t have any visible plants, whereas the rainforest is densely packed with trees. Do they have different climates? Does one get more rain than the other?
Survey of Terrestrial Biomes
Terrestrial biomes are classified by the climate and their biodiversity, especially the types ofprimary producers. The world map in Figure below shows where 13 major terrestrial biomes are found.
Worldwide Distribution of Terrestrial Biomes. This map shows the locations of Earth’s major terrestrial biomes.
The following figures summarize the basic features of major terrestrial biomes. As you read about each biome, think about how its biodiversity and types of plants and animals relate to its climate. For example, why do you think there are no amphibians or reptiles in tundra biomes? (Hint: Amphibians and reptiles cannot maintain a constant body temperature. Instead, they have about the same temperature as their surroundings.)
Summary
• Terrestrial biomes include tundras, temperate forests and grasslands, chaparral, temperate and tropical deserts, and tropical forests and grasslands.
Review
1. Identify two types of tundra and where they are found.
2. What terrestrial biome has the highest biodiversity? the lowest?
3. In which biome are you most likely to find grasses, zebras, and lions?
4. If you were to design a well-adapted desert animal, what adaptations would you give it to help it survive in its desert biome?
6.11: Aquatic Biomes
Do aquatic ecosystems need sunlight?
Of course. The sunlight - in part - allows the diversity of life seen in this ecosystem. If the available sunlight was less, could this ecosystem still thrive? Maybe, but the ecosystem would probably be very different. Sunlight, of course, is necessary for photosynthesis, which brings energy into an ecosystem. So, the availability of that sunlight has a direct impact on the productivity and biodiversity of aquatic ecosystems.
Aquatic Biomes
Terrestrial organisms are generally limited by temperature and moisture. Therefore, terrestrial biomes are defined in terms of these abiotic factors. Most aquatic organisms do not have to deal with extremes of temperature or moisture. Instead, their main limiting factors are the availability of sunlight and the concentration of dissolved oxygen and nutrients in the water. These factors vary from place to place in a body of water and are used to define aquatic biomes.
Aquatic Biomes and Sunlight
In large bodies of standing water, including the ocean and lakes, the water can be divided into zones based on the amount of sunlight it receives:
1. The photic zone extends to a maximum depth of 200 meters (656 feet) below the surface of the water. This is where enough sunlight penetrates for photosynthesis to occur. Algae and other photosynthetic organisms can make food and support food webs.
2. The aphotic zone is water deeper than 200 meters. This is where too little sunlight penetrates for photosynthesis to occur. As a result, food must be made by chemosynthesis or else drift down from the water above.
These and other aquatic zones in the ocean are identified in Figure below.
The ocean is divided into many different zones, depending on distance from shore and depth of water.
Aquatic Biomes and Dissolved Substances
Water in lakes and the ocean also varies in the amount of dissolved oxygen and nutrients it contains:
1. Water near the surface of lakes and the ocean usually has more dissolved oxygen than does deeper water. This is because surface water absorbs oxygen from the air above it.
2. Water near shore generally has more dissolved nutrients than water farther from shore. This is because most nutrients enter the water from land. They are carried by runoff, streams, and rivers that empty into a body of water.
3. Water near the bottom of lakes and the ocean may contain more nutrients than water closer to the surface. When aquatic organisms die, they sink to the bottom. Decomposers near the bottom of the water break down the dead organisms and release their nutrients back into the water.
Marine Biomes
Anglerfish live in the ocean. Aquatic biomes in the ocean are called marine biomes. Organisms that live in marine biomes must be adapted to the salt in the water. For example, many have organs for excreting excess salt. Two ocean zones are particularly challenging to marine organisms: the intertidal zone and the deep ocean.
The intertidal zone is the narrow strip along the coastline that is covered by water at high tide and exposed to air at low tide (see Figure below). There are plenty of nutrients and sunlight in the intertidal zone. However, the water is constantly moving in and out, and the temperaturekeeps changing. These conditions require adaptations in the organisms that live there, such as the barnacles in Figure below.
These pictures show the intertidal zone of the Bay of Fundy, on the Atlantic coast in Maine. Can you identify the intertidal zone from the pictures?
Barnacles secrete a cement-like substance that anchors them to rocks in the intertidal zone.
Organisms that live deep in the ocean must be able to withstand extreme water pressure, very cold water, and complete darkness. However, even here, thriving communities of living things can be found. Organisms cluster around hydrothermal vents in the ocean floor. The vents release hot water containing chemicals that would be toxic to most other living things. The producers among them are single-celled chemoautotrophs. They make food using energy stored in the chemicals.
Monitoring Marine Protected Areas
Is overfishing an important issue? What would happen if fish populations dwindled? Marine Protected Areas are no-fishing zones that have recently been established up and down the California coast, in the hope of allowing fish to breed, grow large, and replenish state waters. Scientists monitor these areas to determine if this process is working.
Summary
• Aquatic biomes are determined mainly by sunlight and concentrations of dissolved oxygen and nutrients in the water.
• Marine biomes are found in the salt water of the ocean.
Review
1. How are aquatic biomes defined?
2. What is the photic zone of the ocean?
3. Where does food come from in the aphasic zone? | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/06%3A_Ecology/6.10%3A_Terrestrial_Biomes.txt |
What may be the most biologically diverse type of ecosystem?
These are wetland marshes in Delaware. Notice the abundance of vegetation mixed with the water. And of course, where there are plants, there are animals. Wetlands are considered the most biologically diverse of all ecosystems. Plant life found in wetlands includes mangrove, water lilies, cattails, black spruce, cypress, and many others. Animal life includes many different amphibians, reptiles, birds, insects, and mammals.
Freshwater Biomes
Freshwater biomes have water that contains little or no salt. They include standing and running freshwater biomes. Standing freshwater biomes include ponds and lakes. Lakes are generally bigger and deeper than ponds. Some of the water in lakes is in the aphotic zone, where there is too little sunlight for photosynthesis. Plankton and plants, such as the duckweed in Figure below, are the primary producers in standing freshwater biomes.
The pond on the left has a thick mat of duckweed plants. They cover the surface of the water and use sunlight for photosynthesis. The cattails on the right grow along a stream bed. They have tough, slender leaves that can withstand moving water.
Running freshwater biomes include streams and rivers. Rivers are usually larger than streams. Streams may start with runoff or water seeping out of a spring. The water runs downhill and joins other running water to become a stream. A stream may flow into a river that empties into a lake or the ocean. Running water is better able to dissolve oxygen and nutrients than standing water. However, the moving water is a challenge to many living things. Algae and plants, such as the cattails in Figure above, are the primary producers in running water biomes.
Wetlands
A wetland is an area that is saturated with water or covered by water for at least one season of the year. The water may be freshwater or salt water. Wetlands are extremely important biomes for several reasons:
• They store excess water from floods.
• They slow down runoff and help prevent erosion.
• They remove excess nutrients from runoff before it empties into rivers or lakes.
• They provide a unique habitat that certain communities of plants need to survive.
• They provide a safe, lush habitat for many species of animals, so they have high
biodiversity.
KQED: San Francisco Bay: A Unique Estuary
An estuary is a partly enclosed coastal body of water with one or more rivers or streams flowing into it, and with a free connection to the ocean. Estuaries can be thought of as the most biologically productive regions on Earth, with very high biodiversity. Estuaries are zones where land and sea come together, and where fresh and salt water meet.
The San Francisco Bay is one of the great estuaries of the world.
Summary
• Freshwater biomes include standing water and running water biomes.
• Wetlands are extremely important biomes. They may have freshwater or salt water.
Review
1. Describe a freshwater biome.
2. Define a wetland.
3. Why do wetlands have high biodiversity?
4. A developer wants to extend a golf course into a wetland. Outline environmental arguments you could make against this plan. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/06%3A_Ecology/6.12%3A_Freshwater_and_Wetlands_Biomes.txt |
What is this? Plant or animal?
It is actually the Yellow Christmas tree worm. These animals are colorful, and can be red, orange, yellow, blue, and white. The Christmas tree worm lives on tropical coral reefs throughout the world. The Christmas tree worm's plumes are used for feeding and respiration. These worms use their plumes to catch plankton and other small particles passing in the water. Cilia then pass the food to the worm's mouth.
Aquatic Organisms
Aquatic organisms generally fall into three broad groups: plankton, nekton, and benthos. They vary in how they move and where they live.
1. Plankton are tiny aquatic organisms that cannot move on their own. They live in the photic zone. They include phytoplankton and zooplankton. Phytoplankton are bacteria and algae that use sunlight to make food. Zooplankton are tiny animals that feed on phytoplankton.
2. Nekton are aquatic animals that can move on their own by “swimming” through the water. They may live in the photic or aphotic zone. They feed on plankton or other nekton. Examples of nekton include fish and shrimp.
3. Benthos are aquatic organisms that crawl in sediments at the bottom of a body of water. Many are decomposers. Benthos include sponges, clams, and anglerfish like the one inFigure below. How has this fish adapted to a life in the dark?
Anglerfish. This anglerfish lives between 1000 and 4000 meters below sea level. No sunlight penetrates to this depth. The rod-like structure on its face has a glow-in-the-dark tip. It is covered with microorganisms that give off their own light. The fish wiggles the structure like a worm to attract prey. In the darkness, only the rod-like worm is visible.
KQED: Studying Aquatic Animals
Oceans cover more than 70 percent of our planet, yet they are some of the least explored regions on Earth. Who better to unlock the mysteries of the ocean than marine animals themselves? Marine scientists have been tagging and tracking sharks, leatherback turtles, and other sea life to learn more about marine ecosystems. Through the Tagging of Pacific Predators program (TOPP), scientists hope to assess and explain the migration routes, ecosystems, and diversity of our oceans’ species.
Beginning in 2000, scientists from the National Oceanic and Atmospheric Administration, Stanford University, and the University of California, Santa Cruz combined to form TOPP. As part of TOPP, researchers attach satellite tags to elephant seals, white sharks, giant leatherback turtles, bluefin tuna, swordfish, and other marine animals. The tags collect information, such as how deep each animal dives, the levels of ambient light (to help determine an animal’s location), and interior and exterior body temperature. Some tags also collect information about the temperature, salinity, and depth of the water surrounding an animal to help scientists identify ocean currents. The tags send the data to a satellite, which in turn sends the data the scientists. They use this information to create maps of migration patterns and discover new information about different marine ecosystems. The information collected by TOPP offers rare insights into the lives of marine animals. Without TOPP, that information would otherwise remain unknown. With TOPP, scientists are developing a working knowledge of the particular migration routes animals take, as well as the locations of popular breeding grounds and the environmental dangers faced by different species. TOPP has shed light on how we can better protect the leatherback turtle and other endangered species.
Summary
• Aquatic organisms are either plankton, nekton, or benthos.
Review
1. Compare plankton, nekton, and benthos.
2. Give an example of plankton, nekton, and benthos.
3. What are phytoplankton and zooplankton? | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/06%3A_Ecology/6.13%3A_Aquatic_Organisms.txt |
What may be the most common way different species interact?
Biomes as different as deserts and wetlands share something very important. All biomes have populations of interacting species. Species interact in the same basic ways in all biomes. For example, all biomes have some species that prey on others for food.
Predation
Predation is a relationship in which members of one species (the predator) consume members of another species (the prey). The lionesses and zebra in Figure below are classic examples of predators and prey. In addition to the lionesses, there is another predator in this figure. Can you spot it? The other predator is the zebra. Like the lionesses, it consumes prey species, in this case species of grass. However, unlike the lionesses, the zebra does not kill its prey. Predator-prey relationships such as these account for most energy transfers in food chains and food webs.
Predators and Their Prey. These lionesses feed on the carcass of a zebra.
Predation and Population
A predator-prey relationship tends to keep the populations of both species in balance. This is shown by the graph in Figure below. As the prey population increases, there is more food for predators. So, after a slight lag, the predator population increases as well. As the number of predators increases, more prey are captured. As a result, the prey population starts to decrease. What happens to the predator population then?
Predator-Prey Population Dynamics. As the prey population increases, why does the predator population also increase?
In the predator-prey example, one factor limits the growth of the other factor. As the prey population deceases, the predator population is begins to decrease as well. The prey population is a limiting factor. A limiting factor limits the growth or development of an organism, population, or process.
Keystone Species
Some predator species are known as keystone species. A keystone species is one that plays an especially important role in its community. Major changes in the numbers of a keystone species affect the populations of many other species in the community. For example, some sea star species are keystone species in coral reef communities. The sea stars prey on mussels and sea urchins, which have no other natural predators. If sea stars were removed from a coral reef community, mussel and sea urchin populations would have explosive growth. This, in turn, would drive out most other species. In the end, the coral reef community would be destroyed.
Adaptations to Predation
Both predators and prey have adaptations to predation that evolve through natural selection. Predator adaptations help them capture prey. Prey adaptations help them avoid predators. A common adaptation in both predator and prey is camouflage. Several examples are shown in Figure below. Camouflage in prey helps them hide from predators. Camouflage in predators helps them sneak up on prey.
Camouflage in Predator and Prey Species. Can you see the crab in the photo on the left? It is camouflaged with the sand. The preying mantis in the middle photo looks just like the dead leaves in the background. Can you tell where one zebra ends and another one begins? This may confuse a predator and give the zebras a chance to run away.
Summary
• Predation is a relationship in which members of one species (the predator) consume members of another species (the prey).
• A predator-prey relationship keeps the populations of both species in balance.
Review
1. Describe the relationship between a predator population and the population of its prey.
2. What is a keystone species? Give an example.
3. What is a limiting factor?
4. What is the role of camouflage in prey and predator? | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/06%3A_Ecology/6.14%3A_Predation.txt |
Does there have to be a winner?
When animals compete? Yes. Animals, or other organisms, will compete when both want the same thing. One must "lose" so the winner can have the resource. But competition doesn't necessarily involve physical altercations.
Competition
Competition is a relationship between organisms that strive for the same resources in the same place. The resources might be food, water, or space. There are two different types of competition:
1. Intraspecific competition occurs between members of the same species. For example, two male birds of the same species might compete for mates in the same area. This type of competition is a basic factor in natural selection. It leads to the evolution of better adaptations within a species.
2. Interspecific competition occurs between members of different species. For example, predators of different species might compete for the same prey.
Interspecific Competition and Extinction
Interspecific competition often leads to extinction. The species that is less well adapted may get fewer of the resources that both species need. As a result, members of that species are less likely to survive, and the species may go extinct.
Interspecific Competition and Specialization
Instead of extinction, interspecific competition may lead to greater specialization. Specialization occurs when competing species evolve different adaptations. For example, they may evolve adaptations that allow them to use different food sources. Figure below describes an example.
Specialization lets different species of anole lizards live in the same area without competing.
Watch the beginning of the following video to learn more about competition.
Summary
• Competition is a relationship between organisms that strive for the same resources in the same place.
• Intraspecific competition occurs between members of the same species. It improves the species’ adaptations.
• Interspecific competition occurs between members of different species. It may lead to one species going extinct or both becoming more specialized.
Review
1. What is competition?
2. Describe the evolutionary effects of intraspecific and interspecific competition.
6.16: Symbiosis
Do interactions between species always result in harm?
A commensal shrimp sits on another sea organism, a sea slug. As a commensal shrimp, it neither brings a benefit nor has a negative effect on its host.
Symbiotic Relationships
Symbiosis is a close relationship between two species in which at least one species benefits. For the other species, the relationship may be positive, negative, or neutral. There are three basic types of symbiosis: mutualism, commensalism, and parasitism.
Mutualism
Mutualism is a symbiotic relationship in which both species benefit. An example of mutualism involves goby fish and shrimp (see Figure below). The nearly blind shrimp and the fish spend most of their time together. The shrimp maintains a burrow in the sand in which both the fish and shrimp live. When a predator comes near, the fish touches the shrimp with its tail as a warning. Then, both fish and shrimp retreat to the burrow until the predator is gone. From their relationship, the shrimp gets a warning of approaching danger. The fish gets a safe retreat and a place to lay its eggs.
The multicolored shrimp in the front and the green goby fish behind it have a mutualistic relationship.
Commensalism
Commensalism is a symbiotic relationship in which one species benefits while the other species is not affected. One species typically uses the other for a purpose other than food. For example, mites attach themselves to larger flying insects to get a “free ride.” Hermit crabs use the shells of dead snails for homes.
Parasitism
Parasitism is a symbiotic relationship in which one species (the parasite) benefits while the other species (the host) is harmed. Many species of animals are parasites, at least during some stage of their life. Most species are also hosts to one or more parasites.
Some parasites live on the surface of their host. Others live inside their host. They may enter the host through a break in the skin or in food or water. For example, roundworms are parasites of mammals, including humans, cats, and dogs (see Figure below). The worms produce huge numbers of eggs, which are passed in the host’s feces to the environment. Other individuals may be infected by swallowing the eggs in contaminated food or water.
Roundworms like this one might eventually fill a dog’s intestine unless it gets medical treatment.
Some parasites kill their host, but most do not. It’s easy to see why. If a parasite kills its host, the parasite is also likely to die. Instead, parasites usually cause relatively minor damage to their host.
Summary
• Symbiosis is a close relationship between two species in which at least one species benefits.
• Mutualism is a symbiotic relationship in which both species benefit.
• Commensalism is a symbiotic relationship in which one species benefits while the other species is not affected.
• Parasitism is a symbiotic relationship in which one species (the parasite) benefits while the other species (the host) is harmed.
Review
1. Define mutualism and commensalism.
2. Give examples of mutualism.
3. Explain why most parasites do not kill their host. Why is it in their own best interest to keep their host alive?
Roundworms like this one might eventually fill a dog’s intestine unless it gets medical treatment.
Some parasites kill their host, but most do not. It’s easy to see why. If a parasite kills its host, the parasite is also likely to die. Instead, parasites usually cause relatively minor damage to their host. | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/06%3A_Ecology/6.15%3A_Competition.txt |
Is this any way to live?
It is if you're a penguin. This population of penguins is made of all the individuals of the same species of penguins who live together. They seem to exist in a very crowded - or densely populated - environment, and in a random configuration.
Population Size, Density, and Distribution
Communities are made up of populations of different species. In biology, a population is a group of organisms of the same species that live in the same area. The population is the unit of natural selection and evolution. How large a population is and how fast it is growing are often used as measures of its health.
Population Size
Population size is the number of individuals in a population. For example, a population ofinsects might consist of 100 individual insects, or many more. Population size influences the chances of a species surviving or going extinct. Generally, very small populations are at greatest risk of extinction. However, the size of a population may be less important than its density.
Population Density
Population density is the average number of individuals in a population per unit of area or volume. For example, a population of 100 insects that live in an area of 100 square meters has a density of 1 insect per square meter. If the same population lives in an area of only 1 square meter, what is its density? Which population is more crowded? How might crowding affect the health of a population?
Population Distribution
Population density just represents the average number of individuals per unit of area or volume. Often, individuals in a population are not spread out evenly. Instead, they may live in clumps or some other pattern (see Figure below). The pattern may reflect characteristics of the species or its environment. Population distribution describes how the individuals are distributed, or spread throughout their habitat.
Patterns of Population Distribution. What factors influence the pattern of a population over space?
Summary
• Population size is the number of individuals in a population.
• Population density is the average number of individuals per unit of area or volume.
• The pattern of spacing of individuals in a population may be affected by the characteristics of a species or its environment.
Review
1. What is population density?
2. What are the differences between population density and distribution?
3. A population of 820 insects lives in a 1.2-acre area. They gather nectar from a population of 560 flowering plants. The plants live in a 0.2-acre area. Which population has greater density, the insects or the plants? Why?
4. What can you infer about a species that has a random pattern of distribution over space? A uniform pattern?
6.18: Population Structure
Young vs. old. Does it matter?
When it comes to populations, yes it does. The age structure (and the sex structure) of a population influences population growth. Can you explain why?
Population Structure
Population growth is the change in the size of the population over time. An important factor in population growth is age-sex structure. This is the number of individuals of each sex and age in the population. The age-sex structure influences population growth. This is because younger people are more likely to reproduce, while older people have higher rates of dying.
Population Pyramids
Age-sex structure is represented by a population pyramid. This is a bar graph, like the one Figure below. In this example, the bars become narrower from younger to older ages. Can you explain why?
A population pyramid represents the age-sex structure of a population. What does a large base represent?
Survivorship Curves
Another way to show how deaths affect populations is with survivorship curves. These are graphs that represent the number of individuals still alive at each age. Examples are shown inFigure below.
Survivorship curves reflect death rates at different ages.
The three types of curves shown in the figure actually represent different strategies species use to adapt to their environment:
• Type I: Parents produce relatively few offspring and provide them with a lot of care. As a result, most of the offspring survive to adulthood so they can reproduce. This pattern is typical of large animals, including humans.
• Type II: Parents produce moderate numbers of offspring and provide some parental care. Deaths occur more uniformly throughout life. This pattern occurs in some birds and many asexual species.
• Type III: Parents produce many offspring but provide them with little or no care. As a result, relatively few offspring survive to adulthood. This pattern is typical of plants, invertebrates, and many species of fish.
The Type I strategy occurs more often in stable environments. The Type III strategy is more likely in unstable environments. Can you explain why?
Summary
• The age-sex structure of a population is the number of individuals of each sex and age in the population.
• Age-sex structure influences population growth. It is represented by a population pyramid.
• The number of survivors at each age is plotted on a survivorship curve.
Review
1. How does the age-sex structure of a population influence growth?
2. Assume that a population pyramid has a very broad base. What does that tell you about the population it represents?
3. Compare and contrast Type I and Type III survivorship curves.
6.19: Population Growth
What would old luggage have to do with population growth?
Moving into an area, or immigration, is a key factor in the growth of populations. Shown above is actual vintage luggage left by some of the millions of immigrants who came through Ellis Island and into the United States.
Population Growth
Populations gain individuals through births and immigration. They lose individuals through deaths and emigration. These factors together determine how fast a population grows.
Population Growth Rate
Population growth rate (r) is how fast a population changes in size over time. A positive growth rate means a population is increasing. A negative growth rate means it is decreasing. The two main factors affecting population growth are the birth rate (b) and death rate (d). Population growth may also be affected by people coming into the population from somewhere else (immigration, i) or leaving the population for another area (emigration, e). The formula for population growth takes all these factors into account.
r = (b + i) - (d + e)
• r = population growth rate
• b = birth rate
• i = immigration rate
• d = death rate
• e = emigration rate
Dispersal
Other types of movements may also affect population size and growth. For example, many species have some means of dispersal. This refers to offspring moving away from their parents. This prevents the offspring from competing with the parents for resources such as light or water. For example, dandelion seeds have “parachutes.” They allow the wind to carry the seeds far from the parents (see Figure below).
Dandelion Seeds. These dandelion seeds may disperse far from the parent plant. Why might this be beneficial to both parents and offspring?
Migration
Migration is another type of movement that changes population size. Migration is the regular movement of individuals or populations each year during certain seasons. The purpose of migration usually is to find food, mates, or other resources. For example, many northern hemisphere birds migrate thousands of miles south each fall. They go to areas where the weather is warmer and more resources are available (see Figure below). Then they return north in the spring to nest. Some animals, such as elk, migrate vertically. They go up the sides of mountains in spring as snow melts. They go back down the mountain sides in fall as snow returns.
Swainson’s hawks migrate from North to South America and back again each year. This map shows where individual hawks have been identified during their migration.
Summary
• Population growth rate is how fast a population changes in size over time.
• Population growth is determined by rates of birth, death, immigration, and emigration.
Review
1. Define immigration and emigration.
2. What is migration? Give an example.
3. Write the formula for the population growth rate. Identify all the variables.
4. What is dispersal? State why dispersal of offspring away from their parents might be beneficial | textbooks/bio/Introductory_and_General_Biology/Introductory_Biology_(CK-12)/06%3A_Ecology/6.17%3A_Population_Size_Density_and_Distribution.txt |
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