AP Biology Chapter 9

What are autotrophs?

The autotrophs, such as plants and algae, are called the producers of the food chain because of their ability to produce their food with no need to consume another organism. Examples are: Herbivores, omnivores, and carnivores.

State the most likely hypothetical order of evolution of anaerobic respiration, aerobic respiration, and photosynthesis. Provide two pieces of evidence to support the hypothesis.

1. Anaerobic respiration 2.photosynthesis 3.aerobic respiration The most ancient type of respiration is glycolysis (anaerobic). Since there was little to no oxygen present when the first eukaryotic cells evolved through endosymbiosis, they could only undergo anaerobic respiration or something similar to fermentation. This was not a problem, however, since those first cells were unicellular. Producing only 2 ATP at a time was enough to keep the single cell running. The oldest known fossils of bacteria date back 3.5 billion years when appreciable quantities of oxygen were not accumulated in the atmosphere -- so therefore since glycolysis does not require Oxygen, it is thought to be the first catabolic pathway to have evolved. As multicellular eukaryotic organisms began to appear on Earth, the larger and more complex organisms needed to produce more energy-- aerobic respiration processes developed. Through natural selection, organisms with more mitochondria that could undergo aerobic respiration survived and reproduced, passing on these favorable adaptations to their offspring. The more ancient versions could no longer keep up with the demand for ATP in the more complex organism and went extinct. All of the oxygen in the atmosphere (needed for aerobic respiration) had to be produced by photosynthesis so aerobic respiration could occur, therefore photosynthesis had to evolve before oxidative phosphorylation in aerobic respiration.

What does this conversion do to the pyruvate molecules?

Each pyruvate molecule loses one carbon atom with the release of carbon dioxide. During the breakdown of pyruvate, electrons are transferred to NAD+ to produce NADH, which will be used by the cell to produce ATP. This reaction involves NAD+ removing two hydrogen molecules and two electrons from pyruvic acid. The result is acetyl coenzyme A, NADH, H+ and CO2. These products go into the citric acid cycle to produce more CO2 and ATP. The NADH produced will be used by the cell to produce ATP.

Why do we use glucose as the model?

Glucose is one of the most important molecules for producing energy and it is the fuel that cells most often use. Glucose provides quick energy for cells. Fat has more energy than glucose, but it requires some chemical conversions before we can get it into the process of cellular respiration, so it takes longer to use. Glucose, on the other hand, is stored as glycogen, or long chains of glucose inside muscle.

Why aren't protons able to diffuse through the inner mitochondrial membrane?

There is an electrochemical gradient across membrane and the positively charged protons don't easily diffuse across nonpolar sections. They must be pumped via a large protein complex that pumps protons across the inner membrane.

Explain the effect of ATP on phosphofructokinase, and the overall effect it has on cellular respiration and the system; logic of each effect:

PFK is allosterically inhibited by high levels of ATP. ATP concentration build up indicates an excess of energy and does have an allosteric modulation site on PFK where it decreases the affinity of PFK for its substrate. So PFK regulates to decrease the production of ATP.

Explain the effect of AMP on phosphofructokinase, and the overall effect it has on cellular respiration and the system; logic of each effect:

AMP stands for adenosine monophosphate. AMP may be produced by combining two molecules of ADP during ATP synthesis. It may also be formed by the hydrolysis of one inorganic phosphate of ADP, or by the hydrolysis of ATP into AMP and pyrophosphate. PFK is allosterically inhibited by high levels of ATP but AMP reverses the inhibitory action of ATP. Therefore, the activity of the enzyme increases when the cellular ATP/AMP ratio is lowered. Glycolysis is thus stimulated when energy charge falls.

Why are pyruvate converted into acetyl-CoA prior to entering the Kreb's cycle?

Acetyl-CoA consists of an acetyl group attached to a coenzyme A molecule. Coenzyme A is a large molecule that contains a molecule of ADP with two side chain groups stemming from its phosphate arms. Acetyl groups attach to the end of these side chains. In this way, the coenzyme A acts as a carrier of acetyl groups. When Acetyl CoA is broken down by water, large amounts of energy are released, which will drive the citric acid cycle. Acetyl-CoA is the starting product and is the fuel for the citric acid cycle. The conversion of pyruvate to acetyl coenzyme A is known as the oxidative decarboxylation of pyruvic acid. Pyruvate oxidation is a key connector that links glycolysis to the rest of cellular respiration. The citric acid cycle is also known as the Kreb's cycle.

How much more energy is produced by aerobic cellular respiration than by anaerobic cellular respiration?

Aerobic -- 36-38 ATP/glucose Anaerobic 2 ATP/glucose Anaerobic respiration -organisms can only break a 6-carbon glucose into two 3-carbon pyruvate molecules. Glycolysis releases only enough energy to produce 2 ATPs per molecule of glucose. In anaerobic respiration, this is where ATP production stops. This anaerobic process does occur very quickly though. For example, it lets your muscles get the energy they need for short bursts of intense activity. Aerobic respiration produces ATP more slowly. It breaks glucose all the way down to CO2, producing up to 38 ATPs per molecule of glucose. Aerobic respiration consistently produces at least 15 times as much ATP as anaerobic respiration. This vast increase in energy production probably explains why aerobic organisms have come to dominate life on earth. It may also explain how organisms were able to increase in size, adding multicellularity and great diversity.

Why do anaerobic cellular systems use fermentation?

Anaerobic systems use fermentation because it does not require oxygen -- which they don't have. Fermentation is a way of harvesting chemical energy without using either oxygen or any electron transport chain (without cellular respiration). Glycolysis can happen without oxygen -- fermentation is an expansion of glycolysis that allows continuous generation of ATP by the substrate level phosphorylation of glycolysis. It is a method used to recycle NAD+. In glycolysis with each breakdown of glucose, 2pyruvate, 2 NADH, and 2 ATP are formed. If all the NAD+ is used up to make NADH though, there's no way to get it back and reuse it so the process must continue to lactate or ethanol+CO2, which turns the NADH to NAD+.

Compare the electron transport chain of the mitochondrion with the electron transport chain of the chloroplast.

Chloroplasts and mitochondria generate ATP by the same basic mechanism: chemiosmosis. An electron transport chain assembled in a membrane pumps protons across the membrane as electrons are passed through a series of carriers that are progressively more electronegative. Electron transport chains transform redox energy to a proton-motive force, potential energy stored in the form of an H+ gradient across a membrane. Built into the same membrane is an ATP synthase complex that couples the diffusion of hydrogen ions down their gradient to the phosphorylation of ADP. The ATP synthase complexes of the two organelles are also very much alike. There is a difference between the organization of mitochondria and that of chloroplasts. The inner membrane of the chloroplast is not folded into cristae and does not contain electron-transport chains. Instead, the electron-transport chains, photosynthetic light-capturing systems, and ATP synthase are all contained in the thylakoid membrane, a third distinct membrane that forms a set of flattened disclike sacs, the thylakoids. The lumen of each thylakoid is thought to be connected with the lumen of other thylakoids, creating a third internal compartment called the thylakoid space, which is separated by the thylakoid membrane from the stroma that surrounds it. Some of the electron carriers, including the iron-containing proteins called cytochromes, are very similar in chloroplasts and mitochondria. Comparison of chemiosmosis in mitochondria and chloroplasts. In both kinds of organelles, electron transport chains pump protons (H+) across a membrane from a region of low H+ concentration (light brown in the diagram below) to one of high H+ concentration (darker brown). The protons then diffuse back across the membrane through ATP synthase, driving the synthesis of ATP. The diagram identifies the regions of high and low H+ concentration in the two organelles.

Name 3 differences between the electron transport chain of the mitochondrion with the electron transport chain of the chloroplast.

Differences between oxidative phosphorylation in mitochondria and photophosphorylation in chloroplasts. In mitochondria, the high-energy electrons dropped down the transport chain are extracted from food molecules (which are thus oxidized). --Chloroplasts' energy is derived from sunlight which energizes an electron in the green organic pigment chlorophyll. This enables the electron to move along an electron-transport chain in the thylakoid membrane in much the same way that an electron moves along the respiratory chain in mitochondria. The chlorophyll obtains its electrons from water (H2O), producing O2 as a by-product. In other words, mitochondria transfer chemical energy from food molecules to ATP, whereas chloroplasts transform light energy into chemical energy. The spatial organization of chemiosmosis also differs in chloroplasts and mitochondria The inner membrane of the mitochondrion pumps protons from the mitochondrial matrix out to the intermembrane space, which then serves as a reservoir of hydrogen ions that powers the ATP synthase. The thylakoid membrane of the chloroplast pumps protons from the stroma into the thylakoid space, which functions as the H+ reservoir. The thylakoid membrane makes ATP as the hydrogen ions diffuse from the thylakoid space back to the stroma through ATP synthase complexes, whose catalytic knobs are on the stroma side of the membrane. Thus, ATP forms in the stroma, where it is used to help drive sugar synthesis during the Calvin cycle. The inner membrane of the mitochondrion pumps protons (H+) from the matrix into the intermembrane space (higher concentration of H+). ATP is made on the matrix side of the membrane as hydrogen ions diffuse through ATP synthase complexes. In chloroplasts, the thylakoid membrane pumps protons from the stroma into the thylakoid compartment. As the hydrogen ions leak back across the membrane through the ATP synthase, phosphorylation of ADP occurs on the stroma side of the membrane.

Is glucose the only molecule that can be catabolized during cellular respiration?

Glucose is the main molecule to undergo cellular respiration (by glycolysis and then kreb's cycle) to give ATP. Other molecules include the products of the glycolysis and kreb's cycle especially acetyl-coenzyme A (acetyl CoA). Fatty acids are broken down to acetyl CoA which can then enter the kreb's cycle and give ATP. Proteins can be broken down into amino acids and transaminated to give products that can enter into the kreb's cycle to give energy. Even lactic acid (product of anaerobic respiration) can be converted back to glucose (via cori's cycle) which can then enter glycolysis to give energy.

Why is it thought that glycolysis is the first catabolic pathway to have evolved in the metabolism of all cellular systems?

Glycolysis produces much less ATP than does oxidative phosphorylation. Glycolysis takes place in the cytosol, does not involve oxygen, and is present in most organisms. It is found in prokaryotic cells but not in eukaryotic cells. Glycolysis is the first step that breaks down glucose and MUST be done before any further metabolic pathways can break down the glycolysis products. Glycolysis occurs in the cytoplasm which mean it would have been able to be used before the bacteria that formed the mitochondria invade the cell that gave rise to all eukaryotes, indicating it must have been a very fundamental early pathway. Glycolysis does not require any of the membrane-bound organelles of the eukaryotic cell which evolved approximately 1 billion years after the prokaryotic cells. Before there was oxygen in the earth's atmosphere, there was only anaerobic processes - So they must have developed first. The primary method for anaerobic bacteria is glycolysis because it provides energy without oxygen. Aerobic processes require a huge number of specific proteins, whereas glycolysis has a minimal number of proteins involved. The oldest known fossils of bacteria date back 3.5 billion years when appreciable quantities of oxygen were not accumulated in the atmosphere -- so therefore since glycolysis does not require Oxygen and is thought to be the first catabolic pathway to have evolved.

What are heterotrophs?

Heterotrophs are also called 'other feeders,' and because they need to consume energy to sustain themselves, they are also known as 'consumers.' They must make use of food that comes from other organisms in the form of fats, carbohydrates and proteins.

Why do mammalian muscle cells perform lactic acid fermentation(instead of, say ethanol fermentation)

Human muscle cells make ATP by lactic acid fermentation because alcohol fermentation produces ethanol that is a toxin and would kill the cells or have to be detoxified in the liver. During strenuous exercise, when sugar catabolism outpaces the muscle's supply of oxygen from the blood, cells switch to fermentation to keep a supply of ATP by recycling NAD+ using pyruvate to lactate. It was once thought that lactate build up in the muscle caused fatigue and pain, but new research suggests that is increased levels of K+ instead. Lactate is thought to enhance muscle performance.

How is the structure of the inner mitochondrial membrane related to its function in oxidative phosphorylation?

Inner Membrane picture described -- Oxidative phosphorylation: electron transport and ATP synthesis. Three large protein complexes are fixed in the membrane (colored orange) and two mobile electron carriers (colored black). Electrons are donated from NADH to NADH dehydrogenase, a large protein complex that pumps protons across the inner membrane. Then, electrons are transported to the cytochrome b-c complex via the small, mobile molecule coenzyme Q (Q); the cytochrome b-c complex also pumps protons across the inner membrane. These electrons are delivered to the last protein complex, cytochrome oxidase, by the mobile protein cytochrome c (cyt c). Cytochrome oxidase donates the electrons to oxygen, and water is formed. Cytochrome oxidase also pumps protons across the membrane. The hydrogen concentration is much greater in the intermembrane space than in the matrix, thus generating an electrochemical proton gradient. This gradient drives protons back across the inner membrane through the ATP synthase (shown in gray) that catalyzes the synthesis of ATP from ADP and inorganic phosphate.

What are the most likely prokaryotic ancestors of modern day mitochondria and chloroplasts? How was this determined?

Mitochondria and chloroplasts evolved from endosymbiotic associations between an ancestral host cell and smaller prokaryotic partners. In the case of chloroplasts, the symbiont was a photosynthetic cyanobacterium. The DNA in the chloroplast is very similar to photosynthetic bacteria called cyanobacteria. For mitochondria, most likely it was ana-proteobacterium. The DNA in the mitochondria is most like that of the bacteria that causes typhus which is an ana-probacterium.

Name three electron acceptors in cellular respiration and explain how they fulfill their roles

NAD+ , FAD and Oxygen are all electron acceptors. NAD+ can accept a pair of electrons and a hydrogen ion to become NADH. NADH then gives electrons to FMN in the first step of the electron transport chain. FAD can accept a pair of electrons and two hydrogen ions to become FADH2. FADH2 is involved in the first step of Complex II in the electron transport chain. Oxygen is the "terminal electron acceptor" in the electron transport chain. Oxygen's purpose is to be the final electron acceptor of the electron transport chain. It has a high affinity for electrons so it readily accepts the electrons that come out the end of the electron transport chain. Each oxygen atom also picks up a pair of hydrogen ions from aqueous solution and forms water.

What products of the prior phases of cellular respiration are used in the electron transport chain? How are they used?

NADH and FADH2 shuttle high-energy electrons extracted from food during glycolysis and the citric acid cycle to the electron transport chain. The electron transport chain is an energy converter that uses the exergonic flow of electrons from NADH and FADH2 to pump H+ across the membrane. The H+ gradient drives ATP synthesis by the ATP synthase protein complex. The ATP synthases are the only sites that provide a route through the membrane for H+. The energy stored in an H+ gradient across a membrane couples with the redox reaction of the electron transport chain to ATP synthesis= chemiosmosis.

In cellular respiration, what is oxidized and what is reduced?

NADH is oxidized to NAD+ and NAD+ is reduced to NADH. Pyruvate is oxidized to Acetyl CoA. Glucose is oxidized to CO2 and oxygen is reduced to H2O in the cellular respiration.

Where in the mitochondria does oxidative phosphorylation occur?

Oxidative phosphorylation (electron transport chain coupled with chemiosmosis) occurs in the Inner mitochondrial membrane. A mitochondrion has two membranes: an inner membrane and an outer membrane. The space surrounded by the inner membrane is termed the matrix, and invaginations of the inner membrane are termed cristae. The space between the inner and outer membrane is termed the intermembrane space.

Why is oxygen needed for oxidative phosphorylation?

Oxygen's purpose is to be the final electron acceptor of the electron transport chain. It has a high affinity for electrons so it readily accepts the electrons that come out the end of the electron transport chain. O2 accepts four electrons and then forms two water molecules.

Explain the effect of citrate on phosphofructokinase, and the overall effect it has on cellular respiration and the system; logic of each effect:

PFK is allosterically inhibited by citrate, and ATP. Citrate is a metabolite of the citric acid cycle. Citrate builds up when the Krebs Cycle enzymes approach their maximum potential. So when the Krebs cycle is producing maximum amounts of ATP and has the most energy -- citrate levels are high and slow down the process using the PFK regulatory enzyme.

What is phosphofructokinase?

Phosphofructokinase (PFK) is one of the most important regulatory enzymes of glycolysis. It is an allosteric enzyme made of 4 subunits and controlled by many activators and inhibitors. PFK-1 catalyzes the conversion of fructose 6-phosphate and ATP to fructose 1,6-bisphosphate and ADP in glycolysis. Because phosphofructokinase (PFK) catalyzes the ATP-dependent phosphorylation to convert fructose-6-phosphate into fructose 1,6-bisphosphate and ADP, it is one of the key regulatory and rate limiting steps of glycolysis. PFK is able to regulate glycolysis through allosteric inhibition, and in this way, the cell can increase or decrease the rate of glycolysis in response to the cell's energy requirements.

What is the relationship between photosynthesis and aerobic cellular respiration?

Photosynthesis removes CO2 from the atmosphere, and cellular respiration puts it back in the atmosphere. Photosynthesis releases O2 into the atmosphere that cellular respiration uses to release energy from food and it releases CO2 back into the atmosphere.

Oxygen is not used in the Kreb's cycle, so why must the Kreb's cycle occur in aerobic cellular respiration.

The Krebs cycle does not directly require oxygen but it can only take place when oxygen is present because it relies on by-products from the electron transport chain, which requires oxygen. The Krebs cycle takes place in the mitochondrial matrix, the innermost compartment of the mitochondria. The activity of the Krebs cycle is closely linked to the availability of oxygen although none of the steps in the pathway directly use oxygen. Oxygen is required for the electron transport chain to function which recycles NADH back to NAD+ and FADH2 back to FADH providing NAD+ and ADH required by enzymes in the Krebs cycle. If the oxygen supply to a muscle cell or a yeast cell is low NAD+ and FADH levels fall, the Krebs cycle cannot proceed forward, and the cell must resort to fermentation (anaerobic) to continue making ATP. The Krebs cycle is therefore an aerobic process.

Compare and contrast the metabolism of glucose with the metabolism of complex carbohydrates, proteins, and fats. Explain where each molecule (or component of the molecule) enters the aerobic cellular respiration pathway, and order each in terms of the amount of energy they produce for the cell.

The amount of energy you'll get from carbohydrate, protein and fat is measured in calories per gram. Energy provided = 4 calories/ gram of carbohydrate or protein, 9 calories/gram of fat. Fats have the most energy and proteins have the same amount of energy as carbohydrates. The body is designed to use carbohydrates as its primary fuel because carbohydrates are burned immediately. Excess energy gained from fat is stored in the body for future use. Carbohydrates are more readily digested than lipids and release their energy more rapidly. Monosaccharides and disaccharides are water soluble and easier to transport to and from storage sites than lipids. Too much stored fat can lead to obesity and other health problems. Carbohydrates are stored as glycogen in animals while lipids are stored as fats (in plants carbohydrates are stored as cellulose and lipids as oils). Complex carbohydrates are long, complex chains of sugar; take longer to break down; provide energy source for a longer time. Proteins are large organic compounds made of amino acids arranged in a linear chain. 8 of the amino acids contained in proteins are necessary in the human body to survive. The body needs protein to maintain and replace tissues and to function and grow. Protein is not usually used for energy. However, if the body is not getting enough calories from other nutrients or from the fat stored in the body, protein is used for energy. Because proteins are complex molecules, the body takes longer to break them down. As a result, they are a much slower and longer-lasting source of energy than carbohydrates.

Explain how the movement of electrons through the electron transport chain is used.

The events of the electron transport chain involve NADH and FADH, which act as electron transporters as they flow through the inner membrane space. In complex I, electrons removed from glucose by NAD+, during glycolysis and the citric acid cycle, are transferred to NADH to the first molecule in the electron transport chain (FMN). FMN is reduced to its oxidized form as it passes electrons to an iron sulfur protein FeS. The FeS passes electrons to ubiquinone (Q, CoQ or Coenzyme Q). Ubiquinone is the only member of the electron transport chain that is not a protein -- it is a small hydrophobic molecule. Most of the remaining electron carriers between CoQ and Oxygen are proteins called cytochromes. They have a heme group that accepts and donates electrons --The last cytochrome passes its electrons to Oxygen. Oxygen is very electronegative and picks up a pair of H+ atoms forming water. Another source of electrons is FADH, which is oxidized providing still more electrons for the chain. It is through complex II. It has a lower energy level than NADH and provides about ⅓ less energy than NADH. The movement of electrons through complexes I-IV causes protons (hydrogen atoms) to be pumped out of the intermembrane space into the cell cytosol. As a result, a net negative charge (from the electrons) builds up in the matrix space while a net positive charge (from the proton pumping) builds up in the intermembrane space. This differential electrical charge establishes an electrochemical gradient. It is this gradient that drives ATP synthesis in oxidative phosphorylation.

Why do hydrogen atoms accompany electrons as they are transferred in biological systems?

The hydrogen ions (protons) are there as a result of the reactions occurring in an aqueous (water) solution. The water, H2O, ionizes to form H+ and OH- in solution. Both pH and concentration of other ions such as K+, Na+, and Cl- also affect the balance. NAD+ is an electron shuttle. It has a "plus" form, and then, once it picks up two electrons and a hydrogen from glucose (organic food), it is reduced and called NADH. One proton (H) is released and one proton (H) is added to NAD+ along with 2 electrons. This molecule will pick up electrons at several steps and deliver them to the electron transport chain. Many biologically important oxidation and reduction reactions involve the removal or the addition of hydrogen atoms (protons plus electrons) rather than the transfer of isolated electrons. Protons are soluble in aqueous solutions (as H3O+), but electrons are not and must be transferred directly from one atom or molecule to another. Cellular respiration uses an electron transport chain to break the fall of electrons to oxygen in several energy releasing steps. An electron transport chain consists of a number of molecules, mostly proteins, built into the inner membrane of mitochondria of eukaryotic cells and the plasma membrane of aerobically respiring prokaryotes.

Why does oxidative phosphorylation occur in the inner membrane of the mitochondria?

The inner membrane is highly impermeable, only allowing water, carbon dioxide, and oxygen to freely cross it. The proteins that mediate the processes of oxidative phosphorylation, including electron transport and ATP synthesis, are embedded within the inner membrane. Because only specific molecules are allowed to cross the inner mitochondrial membrane, an imbalance, or gradient, can develop between one side of the membrane versus the other. Molecules that cannot freely pass through the inner membrane must be specifically transported in order to cross. The mitochondria uses gradients to produce ATP in oxidative phosphorylation. At several sites during electron transport from NADH to O2, protons from the mitochondrial matrix are transported uphill across the inner mitochondrial membrane and a proton concentration gradient forms across it. Because the outer membrane is freely permeable to protons, the pH of the mitochondrial matrix is higher so the proton concentration is lower than that of the cytosol and intermembrane space. An electric potential across the inner membrane also results from the uphill pumping of positively charged protons outward from the matrix. Energy released during the oxidation of NADH or FADH2 is stored both as an electric potential and a proton concentration gradient across the inner membrane. The movement of protons back across the inner membrane, driven by this force, is coupled to the synthesis of ATP (energy)from ADP. Oxidative phosphorylation depends on generation of an electrochemical proton gradient across the inner membrane, with electron transport, proton pumping, and ATP formation occurring simultaneously.

2 types of Heterotroph

There are two different types: Photoheterotroph, Chemoheterotroph.

How do heterotrophs capture free energy?

They cannot produce their own food through solar energy and must feed off another life form. In the food chain, heterotrophs represent the consumers.

What would happen anaerobic cellular systems didn't use fermentation?

Without fermentation (in anaerobic conditions), glycolysis would soon deplete the cells supply of NAD+ by reducing it all to NADH. The system would shut itself down for lack of an oxidizing agent (NAD+) -- it would run out because there would be no process to recycle it.

Can a cell produce enough ATP to persist by using glycolysis alone? Why or why not?

Yes -- a single cell can exist on 2 ATP but No for an organism, glycolysis only makes 2 ATP and 2 NADH but it continues to feed the Citric Acid Cycle with it NADH and Acetyl CoA and that cycle makes 2 more and 6 NADH and 2 FADH2 -- Then it drops off electrons to power(chemiosmosis/proton-motive force) Oxidative phosphorylation: more ATP synthesis in the electron transport and chemiosmosis (about 32-34 ATP produced). All total cellular respiration accounts for about 36-38 ATP per glucose. Glycolysis alone has no way to recycle NADH to NAD+ and so the cell would eventually die due to no more components of glycolysis.

chemoheterotroph

are unable to utilize carbon dioxide to form their own organic compounds.

photoheterotroph

feed themselves in two ways: they make food using light, and they consume food molecules (or organisms) from their environment.