LS7A: Cell and Molecular Biology (Sections 7.3-7.7 + 8.1-8.3)

Describe the fermentation pathway of ethanol fermentation, which occurs in plants and fungi.

During ethanol fermentation, pyruvate releases carbon dioxide to form acetaldehyde, and electrons from NADH are transferred to acetaldehyde to produce ethanol and NAD+ Overall reaction: Glucose + 2 ADP + 2 Pi → 2 ethanol + 2CO2 + 2 ATP + 2H2O

Describe the fermentation pathway of lactic acid fermentation, which occurs in animals and bacteria.

During lactic acid fermentation, electrons from NADH are transferred to pyruvate to produce lactic acid and NAD+ Overall reaction: Glucose + 2 ADP + 2 Pi → 2 lactic acid + 2 ATP + 2H2O

Glycogen provides a source of glucose 6-phosphate to feed glycolysis when the level of blood glucose is low. Explain how glycogen is a source of glucose 6-phosphate for the process of glycolysis.

Glucose molecules located at the end of glycogen chains can be cleaved one by one, and they are released in the form of glucose 1-phosphate. Glucose 1-phosphate is then converted into glucose 6-phosphate, an intermediate in glycolysis. One glucose molecule cleaved off a glycogen chain produces three and not two molecules of ATP by glycolysis because the ATP-consuming step 1 of glycolysis is bypassed.

Carbohydrates that are consumed by animals are broken down into simple sugars and circulate in the blood. The level of glucose in the blood is tightly regulated. When the blood glucose level is high, as it is after a meal, glucose molecules that are not consumed by glycolysis are linked together to form glycogen in liver and muscle. What is function of glycogen in the muscle? In the liver?

Glycogen stored in muscle is used to provide ATP for muscle contraction. By contrast, the liver does not store glycogen primarily for its own use, but is a central glycogen storehouse for the whole body, able to release glucose into the bloodstream when it is needed elsewhere.

What is the net production of molecules in the citric acid cycle? (Hint: Don't forget that the cycle begins with two molecules of acetyl-CoA)

Overall, two molecules of acetyl-CoA produced from a single molecule of glucose yield two molecules of ATP, six molecules of NADH, and two molecules of FADH2 in the citric acid cycle.

Animals breathe in air that contains more oxygen than the air they breathe out. Where is oxygen consumed?

Oxygen is consumed in cellular respiration. Oxygen is the final electron acceptor in the electron transport chain and is converted to water.

If every triose phosphate molecule produced by the Calvin cycle were exported from the chloroplast, this molecule could not be regenerated and the Calvin cycle would grind to a halt. In fact, most of the triose phosphate molecules must be used to regenerate this molecule. What molecule is this?

RuBP.

The carbohydrates in your diet are digested to produce a variety of sugars. Distinguish between disaccharides and monosaccharides, and give examples of each. How are disaccharides converted into monosaccharides?

Some of these are disaccharides (maltose=barley, lactose=milk, and sucrose=candy) with two sugar units; others are monosaccharides (fructose=apple, mannose=apple, and galactose=milk) with a single sugar unit. The disaccharides are hydrolyzed into monosaccharides, which are transported into cells.

If you want to produce carbohydrates containing the heavy oxygen (18O) isotope, should you water your plants with H218O or inject C18O2 into the air?

You should label the oxygen in CO2 (that is, inject C18O2) because the entire CO2 molecule is used in synthesizing carbohydrates, whereas H2O donates only the electron needed for the reduction step of the Calvin cycle. The extraction of electrons from water releases O2 as a by-product.

Complete the following phrase: The citric acid cycle results in the complete oxidation of_______________________.

the acetyl group of acetyl-CoA.

Where does pyruvate oxidation occur in eukaryotes? Where does pyruvate travel to after it is created during glycolysis?

the mitochondria Pyruvate travels to the mitochondrial matrix, where it is converted into acetyl-CoA.

At the end of the citric acid cycle, but before the subsequent steps of cellular respiration, which molecules contain the energy held in the original glucose molecule?

At the end of the citric acid cycle, the energy in the original glucose molecule is held in ATP, NADH, and FADH2.

Excess glucose can be stored in cells and then mobilized—that is, broken down—when necessary. Glucose can be stored in two major forms. What are those two major forms, and in what types of organisms?

glycogen in animals starch in plants

Like all components of the Calvin cycle, NADPH can move freely within the stroma of the chloroplast. Although NADPH is a powerful reducing agent, energy and electrons are transferred from NADPH only under the catalysis of a specific enzyme, thus providing a high degree of control over the fate of these electrons. In the Calvin cycle, the reduction of 3-PGA involves two steps. What are those two steps?

(1) ATP donates a phosphate group to 3-PGA, and (2) NADPH transfers two electrons plus one proton (H+) to the phosphorylated compound, which releases one phosphate group (Pi). Because two molecules of 3-PGA are formed each time rubisco catalyzes the incorporation of one molecule of CO2, two ATP and two NADPH are required for each molecule of CO2 incorporated by rubisco. NADPH provides most of the energy incorporated in the bonds of the carbohydrate molecules produced by the Calvin cycle. Nevertheless, ATP plays an essential role in preparing 3-PGA for the addition of energy and electrons from NADPH.

The Calvin cycle consists of 15 chemical reactions that synthesize carbohydrates from CO2. These reactions can be grouped into three main steps. What are those three steps?

1) carboxylation, in which incoming CO2 is added to a 5-carbon molecule (RuBP), which is catalyzed by the enzyme rubisco; (2) reduction, in which energy and electrons are transferred to the compounds formed in step 1 (More specifically, NADPH transfers two electrons and one proton; inorganic phosphate is released); (2.1) Carbohydrates exit as 3-carbon compounds; and (3) regeneration of the 5-carbon molecule needed for carboxylation (In this multistep process, 3-carbon compounds are reorganized and combined to produce RuBP). CALVIN CYCLE: CO2-->Carboxylation-->3-Phosphoglycerate (3-PGA)-->Reduction--->Triose phosphate-->Regeneration--->Ribulose-1,5-biphosphate (RuBP)-->RESTART.

What reactions are the sources of carbon dioxide released during cellular respiration and therefore the sources of the carbon dioxide that we exhale when we breathe?

1.) Pyruvate oxidation 2.) The citric acid cycle

Complete the following sentence: When the photosynthetic electron transport chain is operating at full capacity, the concentration of protons in the lumen can be more than _______ times greater than their concentration in the stroma (equivalent to a difference of 3 pH units). This accumulation of protons on one side of the thylakoid membrane can then be used to power the synthesis of ATP by oxidative phosphorylation.

1000

Fatty acids are a useful and efficient source of energy (except for the brain and RBCs). The oxidation of fatty acids produces a large amount of ATP. Whereas glycolysis yields just 2 molecules of ATP, and the complete oxidation of a glucose molecule produces about 32 molecules of ATP, how much ATP is produced by the complete oxidation of palmitic acid, a type of fatty acid containing 16 carbons?

106 molecules of ATP.

Complete the following sentence: Approximately _____ molecules of ATP are produced for each NADH that donates electrons to the chain and _____ molecules of ATP for each FADH2. Therefore, overall, the complete oxidation of glucose yields about ______ molecules of ATP from glycolysis, pyruvate oxidation, the citric acid cycle, and oxidative phosphorylation.

2.5...........1.5............32.

After the reduction of 3-PGA through energy transfers, these molecules are formed. These molecules are the true products of the Calvin cycle and they are the principal form in which carbohydrates are exported from the chloroplast during photosynthesis. Larger sugars, such as glucose and sucrose, are assembled from these molecules in the cytoplasm. What are these molecules?

3-carbon carbohydrate molecules known as triose phosphates.

What are the two components of the proton gradient?

A chemical gradient due to the difference in concentration and an electrical gradient due to the difference in charge between the two sides of the membrane. To reflect the dual contribution of the concentration gradient and the electrical gradient, the proton gradient is also called an electrochemical gradient.

In 1961, Peter Mitchell proposed a hypothesis to explain how the energy stored in the proton electrochemical gradient is used to synthesize ATP. According to Mitchell's hypothesis, the gradient of protons provides a source of potential energy that is converted into chemical energy stored in ATP. First, for the potential energy of the proton gradient to be released, there must be an opening in the membrane for the protons to flow through. Mitchell suggested that protons in the intermembrane space diffuse down their electrical and concentration gradients through a transmembrane protein channel into the mitochondrial matrix. Second, the movement of protons through the enzyme must be coupled with the synthesis of ATP. This coupling is made possible by...?

ATP synthase a remarkable enzyme composed of two distinct subunits called F0 and F1.

Of the 15 chemical reactions that make up the Calvin cycle, 12 occur in the last step, the regeneration of RuBP. A large number of reactions is needed to rearrange the carbon atoms from five 3-carbon triose phosphate molecules into three 5-carbon RuBP molecules. This molecule is required for the regeneration of RuBP, raising the Calvin cycle's total energy requirements to two molecules of NADPH and three molecules of this molecule for each molecule of CO2 incorporated by rubisco.

ATP.

Cellular respiration is one of several features that heterotrophic organisms like ourselves share with photosynthetic organisms. In mitochondria, carbohydrates are broken down to generate ATP. Why do cells that have chloroplasts also contain mitochondria?

Although photosynthetic organisms are correctly described as autotrophs because they can form carbohydrates from CO2, they also require a constant supply of ATP to meet each cell's energy requirements. Although ATP is produced within chloroplasts, only carbohydrates (and not ATP) are exported from chloroplasts to the cytosol.

How do antenna chlorophylls differ from reaction center chlorophylls?

Antenna chlorophyll molecules transfer absorbed energy from one antenna chlorophyll molecule to another, and ultimately to the reaction center. Reaction center chlorophylls transfer electrons to an electron acceptor, resulting in the oxidation of reaction center chlorophyll molecules.

Generally describe the structure of glycogen in animals, and starch in plants.

Both these molecules are large branched polymers of glucose. Glycogen is a large, branched chain of glucose molecules attached to a central protein. It can be made up of thousands of glucose molecules. Starch is a large, branched chain of glucose molecules found in plants such as potatoes, wheat, and corn. It is stored in granules inside cells.

Complete the following sentence: Mitchell's hypothesis for the synthesis of ATP via a proton gradient is called______________.

Chemiosmotic hypothesis.

What are photosystems, and how are they formed?

Chlorophyll molecules are bound by their tail region to integral membrane proteins in the thylakoid membrane. These protein-pigment complexes, referred to as photosystems, are the functional and structural units that absorb light energy and use it to drive electron transport.

Electrons also must be transported between the four complexes in the electron transport chain. Explain how coenzyme Q (CoQ) and cytochrome c aid in this process.

Coenzyme Q (CoQ), also called ubiquinone, accepts electrons from both complexes I and II. In this reaction, two electrons and two protons are transferred to CoQ from the mitochondrial matrix, forming CoQH2. Once CoQH2 is formed, it diffuses in the inner membrane to complex III. In complex III, electrons are transferred from CoQH2 to cytochrome c and protons are released into the intermembrane space. When it accepts an electron, cytochrome c is reduced, diffuses in the intermembrane space, and passes the electron to complex IV.

Explain how electrons make their entry into the electron transport chain. What is their general path along this chain?

Electrons enter the electron transport chain at either complex I or II. Electrons donated by NADH enter through complex I, and electrons donated by FADH2 enter through complex II. (Complex II is the same enzyme that catalyzes step 6 in the citric acid cycle.) These electrons are transported through either complex I or II to complex III and then through complex IV.

When are fermentation pathways necessary? For what organisms are these pathways necessary?

Fermentation pathways are important for anaerobic organisms that live without oxygen, as well as some organisms such as yeast that favor fermentation over oxidative phosphorylation, even in the presence of oxygen. It is also sometimes used in aerobic organisms when oxygen cannot be delivered fast enough to meet the cell's metabolic needs, as in exercising muscle.

Explain how pyruvate is converted into acteyl-CoA in pyruvate oxidation.

First, part of the pyruvate molecule is oxidized and splits off to form carbon dioxide, the most oxidized (and therefore the least energetic) form of carbon. The electrons lost in this process are donated to NAD+, which is reduced to NADH. The remaining part of the pyruvate molecule—an acetyl group (COCH3)—still contains a large amount of potential energy that can be harnessed. It is transferred to coenzyme A (CoA), a molecule that carries the acetyl group to the next set of reactions.

What are the functions of the two distinct subunits that are F0 and F1 of the enzyme, ATP synthase?

Fo forms the channel in the inner mitochondrial membrane through which protons flow; F1 is the catalytic unit that synthesizes ATP. Proton flow through the channel (Fo) makes it possible for the enzyme (F1) to synthesize ATP.

When visible light is absorbed by a chlorophyll molecule, one of its electrons is elevated to a higher energy state. Compare and contrast how the absorbed light energy is released for chlorophyll molecules that have been extracted from chloroplasts in the laboratory and those that are within an intact chloroplast.

For chlorophyll molecules that have been extracted from chloroplasts in the laboratory, this absorbed light energy is rapidly released, allowing the electron to return to its initial "ground" energy state. Most of the energy (>95%) is converted into heat; a small amount is reemitted as light (fluorescence). By contrast, for chlorophyll molecules within an intact chloroplast, energy can be transferred to an adjacent chlorophyll molecule instead of being lost as heat. When this happens, the energy released as an excited electron returns to its ground state raises the energy level of an electron in an adjacent chlorophyll molecule. This mode of energy transfer is extremely efficient (that is, very little energy is lost as heat), allowing energy initially absorbed from sunlight to be transferred from one chlorophyll molecule to another and then on to another.

Complete the following sentence: For every _______ triose phosphate molecules that are produced, only ______ can be withdrawn from the Calvin cycle.

six....one

Because the overall energy trajectory has an up-down-up configuration resembling a "Z," the photosynthetic electron transport chain is sometimes referred to as the Z scheme. How did it get this name?

If you follow the flow of electrons from water through both photosystems and on to NADP+, you can see a large increase in energy as the electrons pass through each of the two photosystems. You can also see that at every other step along the photosynthetic electron transport chain there is a small decrease in energy. This decrease in energy indicates that these are exergonic reactions and thus explains why electrons move in one "direction" through the series of redox reactions that make up the photosynthetic electron transport chain. To run these reactions in the opposite direction would require an input of energy. The use of water as an electron donor requires input of light energy at two places in the photosynthetic electron transport chain.

So far, we have considered only how the photosynthetic electron transport chain leads to the formation of NADPH. However, we know that the Calvin cycle also requires ATP. How is ATP synthesized in the process of photosynthesis?

In chloroplasts, as in mitochondria, ATP is synthesized by ATP synthase, a transmembrane protein powered by a proton gradient. In chloroplasts, the ATP synthase is oriented such that the synthesis of ATP is the result of the movement of protons from the thylakoid lumen to the stroma.

Where do the electrons used to reduce CO2 come from in photosynthesis?

In photosynthesis carried out by plants and many algae, the ultimate electron donor is water. The oxidation of water results in the production of electrons, protons, and O2. Thus, oxygen is formed in photosynthesis as a by-product of water's role as a source of electrons.

To use sunlight to power the Calvin cycle, the cell must be able to use light energy to produce both NADPH and ATP. Briefly describe without detail how this happens in photosyntheis. (Hint: These molecules must first absorb the sunlight and electrons have to flow through this mechanism in order to produce NADPH an ATP)

In photosynthesis, light energy absorbed by pigment molecules drives the flow of electrons through the photosynthetic electron transport chain. The movement of electrons through the photosynthetic electron chain leads to the formation of both NADPH and ATP.

In photosynthesis, how does the proton pump build up an electrochemical gradient?

In photosynthesis, the proton pump involves: (1) the transport of two electrons and two protons, by the diffusion of plastoquinone, from the stroma side of photosystem II to the lumen side of the cytochrome-b6 f complex and (2) the transfer of electrons within the cytochrome-b6 f complex to a different molecule of plastoquinone, which results in additional protons being picked up from the stroma and subsequently released into the lumen.

What is the overall equation for photosynthesis?

Overall, then, the equation for photosynthesis leading to the synthesis of glucose (C6H12O6) can be described as follows: 6CO2+6H2O-->C6H12O6+O2

Electron transport chains play a key role in both photosynthesis and respiration. In both cases, electrons move within and between large protein complexes embedded in specialized membranes. Where is the photosynthetic electron transport chain located in photosynthetic bacteria? In eukaryotic cells?

In photosynthetic bacteria, the photosynthetic electron transport chain is located in membranes within the cytoplasm or, in some cases, directly in the plasma membrane. In eukaryotic cells, photosynthesis takes place in chloroplasts. In the center of the chloroplast is the highly folded thylakoid membrane. The photosynthetic electron transport chain is located in the thylakoid membrane.

What happens in the first step of the carbon cycle? What enzyme catalyzes this first step?

In the first step of the Calvin cycle, CO2 is added to a 5-carbon sugar called ribulose 1,5-bisphosphate (RuBP). This step is catalyzed by the enzyme ribulose bisphosphate carboxylase oxygenase, or rubisco for short. An enzyme that adds CO2 to another molecule is called a carboxylase, explaining part of rubisco's long name.

Where does the citric acid cycle take place? How many reactions compose the cycle? Why is it called a cycle?

In the mitochondrial matrix. 8 total reactions. The starting molecule, oxaloacetate, is regenerated at the end.

Recall that during glycolysis, glucose is oxidized to form pyruvate, and NAD+ is reduced to form NADH. For glycolysis to continue, NADH must be oxidized to NAD+. If that did not happen, glycolysis would grind to a halt. How is NAD+ regenerated both in the presence and absence of oxygen?

In the presence of oxygen, NAD+ is regenerated when NADH donates its electrons to the electron transport chain. In the absence of oxygen during fermentation, NADH is oxidized to NAD+ when pyruvate or a derivative of pyruvate is reduced.

Photosynthetic organisms have evolved adaptations that allow them to tolerate a wide range of environmental conditions. What are these organisms, and under what conditions do they carry out photosynthesis?

In very dry regions, a combination of photosynthetic bacteria and unicellular algae forms an easily disturbed layer on the surface of the soil known as desert crust. Photosynthetic bacteria are also found in the hot springs of Yellowstone National Park at temperatures up to 75˚C. At the other extreme, unicellular algae can grow on the surfaces of glaciers, causing the surface of the snow to appear red.

In the absence of oxygen, how can pyruvate be broken down?

It can be broken down by fermentation, which does not rely on oxygen or any other electron acceptor. Fermentation is accomplished through a wide variety of metabolic pathways that extract energy from fuel molecules such as glucose.

The movement of electrons through membrane-embedded protein complexes is coupled with the pumping of protons from the mitochondrial matrix into the intermembrane space. The consequence is a proton gradient, a difference in proton concentration across the inner membrane. Why does this proton gradient result? Can't the protons just move down their concentration gradient?

Like all membranes, the inner mitochondrial membrane is selectively permeable: Protons cannot passively diffuse across this membrane, and the movement of other molecules is controlled by transporters and channels.

The reactants in photosynthesis are water and carbon dioxide. Both contain oxygen, so it is unclear which one is the source of the oxygen that is produced in the reaction. Does the oxygen released by photosynthesis come from H2O or CO2?

Most of the oxygen in the atmosphere is 16O, a stable isotope containing 8 protons and 8 neutrons. A small amount (0.2%) is 18O, a stable isotope with 8 protons and 10 neutrons. The relative abundance of molecules containing 16O versus 18O can be measured using a mass spectrometer. H2O and CO2 containing a high percentage of 18O can be used to determine whether the oxygen produced in photosynthesis comes from water or carbon dioxide. Conclusion: The percentage of 18O increases only when water contains 18O, but not when carbon dioxide contains 18O. This finding indicates that the oxygen produced in photosynthesis comes from water, not carbon dioxide.

The complete oxidation of glucose during the first three stages of cellular respiration results in the production of two kinds of reduced electron carriers. What are these carriers?

NADH and FADH2.

Complete the following sentence: Electrons donated by _______ and ______ are transported along a series of four large protein complexes that form the electron transport chain (complexes I to IV). Where are these large protein complexes found?

NADH and FADH2. These membrane proteins are embedded in the mitochondrial inner membrane. The inner mitochondrial membrane contains one of the highest concentrations of proteins found in eukaryotic membranes.

The Calvin cycle does not use sunlight directly. For this reason, this pathway is sometimes referred to as the light-independent or even the "dark" reactions of photosynthesis. However, this pathway cannot operate without the energy input provided by a steady supply of these two molecules. What are they? How are they supplied?

NADPH and ATP. Both are supplied by the photosynthetic electron transport chain, in which light is captured and transformed into chemical energy. In addition, several Calvin cycle enzymes are regulated by cofactors that must be activated by the photosynthetic electron transport chain. Thus, in a photosynthetic cell, the Calvin cycle occurs only in the light.

The Calvin cycle requires both ATP and NADPH. Which of these molecules provides the major input of energy needed to synthesize carbohydrates?

NADPH supplies the major input of energy that is used to synthesize carbohydrates in the Calvin cycle.

____________is formed when electrons are passed from photosystem I to a membrane-associated protein called ferredoxin (Fd). The enzyme ferredoxin-NADP+ reductase then catalyzes the formation of ___________ by transferring two electrons from two molecules of reduced ferredoxin to NADP+ as well as a proton from the surrounding solution.

NADPH.......NADPH NADP+ + 2e− + H+ → NADPH

Is rubisco responsible for the increase in the amount of energy stored within the newly formed bonds of carbohydrates? If not, then what is needed for this energy increase to take place?

No! Rubisco is only responsible for the addition of the carbon atoms needed for the formation of carbohydrates. For this energy increase to take place, the carbon compounds formed by rubisco must be reduced. Nicotinamide adenine dinucleotide phosphate (NADPH) is the reducing agent used in the Calvin cycle. NADPH transfers the electrons that allow carbohydrates to be synthesized from CO2.

Before rubisco can act as a carboxylase, RuBP and CO2 must diffuse into its active site. How does the enzyme rubisco help in catalyzing this step once CO2 and RuBP diffuse into its active site? What are the products of this catalysis?

Once the active site is occupied, the addition of CO2 to RuBP proceeds spontaneously in the sense that no addition of energy is required. The product is a 6-carbon compound that immediately breaks into two molecules of 3-phosphoglycerate (3-PGA). These 3-carbon molecules are the first stable products of the Calvin cycle.

When oxygen is present, this molecule is converted to acetyl-CoA, which then enters the citric acid cycle, resulting in the production of ATP and reduced electron carriers to fuel the electron transport chain, as we saw. When oxygen is not present, however, this molecule is metabolized along a number of different pathways. What is this molecule?

One of the major forks in the metabolic road occurs at pyruvate, the end product of glycolysis.

Why are two photosystems needed if H2O is used as an electron donor?

One photosystem is needed to pull electrons from water, and a second photosystem is needed to raise the energy of these electrons enough that they can reduce NADP+.

Where does photosynthesis take place? Under what optimal conditions?

Photosynthesis takes place almost everywhere sunlight is available to serve as a source of energy. In the ocean, photosynthesis occurs in the surface layer extending to about 100 m deep, called the photic zone, through which enough sunlight penetrates to enable photosynthesis. On land, photosynthesis occurs most readily in environments that are both moist and warm. Tropical rain forests have high photosynthetic productivity, as do grasslands and forests in the temperate zone.

For the two photosystems to work together to move electrons from water to NADPH, they must have distinct chemical properties. What is the need for two photosystems, and what function do they serve respectively?

Photosystem II supplies electrons to the beginning of the electron transport chain. When photosystem II loses an electron (that is, when it is itself oxidized), it is able to pull electrons from water. In contrast, photosystem I energizes electrons with a second input of light energy so they can be used to reduce NADP+. The key point here is that photosystem I when oxidized is not a sufficiently strong oxidant to split water, whereas photosystem II is not a strong enough reductant to form NADPH.

Pigments are molecules that absorb some wavelengths of visible light. Why do pigments, such as chlorophyll, look colored?

Pigments look colored because they reflect light enriched in the wavelengths that they do not absorb. Chlorophyll is the major photosynthetic pigment; it appears green because it is poor at absorbing green wavelengths.

Proteins, like fatty acids, are a source of chemical energy that can be broken down, if necessary, to power the cell. What are these generally broken down into, and how do they ultimately power the cell?

Proteins are typically first broken down to amino acids, some of which can then enter glycolysis and others the citric acid cycle.

Explain how the F0 and F1 subunits of ATP synthase convert potential energy from the proton gradient into chemical energy of ATP.

Proton flow through the Fo channel causes it to rotate, converting the energy of the proton gradient into mechanical rotational energy, a form of kinetic energy. The rotation of the Fo subunit leads to rotation of the F1 subunit in the mitochondrial matrix. The rotation of the F1 subunit in turn causes conformational changes that allow it to catalyze the synthesis of ATP from ADP and Pi. In this way, mechanical rotational energy is converted into the chemical energy of ATP.

Glycolysis occurs in almost all living organisms, but it does not generate very much energy in the form of ATP. The end product, pyruvate, still contains a good deal of chemical potential energy in its bonds. If oxygen is present, what happens to pyruvate?

Pyruvate can be further oxidized to release more energy, first to acetyl-CoA and then even further in the series of reactions in the citric acid cycle.

What happens in the very first reaction of the citric acid cycle? What happens in the very last reaction of the cycle?

The 2-carbon acetyl group of acetyl-CoA is transferred to a 4-carbon molecule of oxaloacetate to form the 6-carbon molecule citric acid or tricarboxylic acid. The molecule of citric acid is then oxidized in a series of reactions. The last reaction of the cycle regenerates a molecule of oxaloacetate, joining to a new acetyl group and allowing the cycle to continue.

The citric acid cycle is the stage in cellular respiration in which fuel molecules are completely oxidized. It supplies electrons to the electron transport chain, leading to the production of much more energy in the form of ATP than is obtained by glycolysis alone. How are these molecules oxidized in a general overview sense?

The acetyl group of acetyl-CoA is completely oxidized to carbon dioxide and the chemical energy is transferred to ATP by substrate-level phosphorylation and to the reduced electron carriers NADH and FADH2.

Explain why organisms that produce ATP by fermentation must consume a large quantity of fuel molecules to power the cell?

The breakdown of a molecule of glucose by fermentation yields only two molecules of ATP. The energetic gain is relatively small compared with the total yield of aerobic respiration because the end products, lactic acid and ethanol, are not fully oxidized and still contain a large amount of chemical energy in their bonds.

Based on the structure of the pigment chlorophyll, why is chlorophyll so efficient at absorbing visible light?

The chlorophyll molecule consists of a large, light-absorbing "head" containing a magnesium atom at its center and a long hydrocarbon "tail". The large number of alternating single and double bonds in the head region explains why chlorophyll is so efficient at absorbing visible light.

Why do photosystems contain accessory pigments? What is an example of one?

The most notable are the orange-yellow carotenoids, which can absorb light from regions of the visible spectrum that are poorly absorbed by chlorophyll. Carotenoids play an important role in protecting the photosynthetic electron transport chain from damage. Thus, the presence of these accessory pigments allows photosynthetic cells to absorb a broader range of visible light than would be possible with just chlorophyll alone.

What series of reactions constitutes the photosynthetic electron transport chain?

The oxidation of water is linked with the reduction of CO2 through a series of redox reactions in which electrons are passed from one compound to another.

The energy in the electron carriers is released in a series of redox reactions that occur as electrons pass through a chain of protein complexes in the inner mitochondrial membrane to the final electron acceptor, oxygen, which is reduced to water. The energy released by these redox reactions is not converted directly into the chemical energy of ATP, however. What then drives the synthesis of ATP?

The passage of electrons is coupled to the transfer of protons (H+) across the inner mitochondrial membrane, creating a concentration and charge gradient. This electrochemical gradient provides a source of potential energy that is then used to drive the synthesis of ATP.

Briefly give a general overview of the process of photosynthesis.

The process begins with the absorption of sunlight by protein-pigment complexes. The absorbed sunlight provides the energy that drives electrons through the photosynthetic electron transport chain. In turn, the movement of electrons through this transport chain is used to produce ATP and NADPH. And finally, ATP and NADPH are the energy sources needed to synthesize carbohydrates using CO2 in a process called the Calvin cycle.

In many ways, water is an ideal source of electrons for photo-synthesis. Water is so abundant within cells that it is always available to serve as an electron donor in photosynthesis. In addition, O2, the by-product of pulling electrons from water, diffuses readily away rather than accumulates. However, from an energy perspective, water is a challenging electron donor: It takes a great deal of energy to pull electrons from water. The amount of energy that a single photosystem can capture from sunlight is not enough both to pull an electron from water and produce an electron donor capable of reducing NADP+. How is this dilemma dealt with?

The solution is to use two photosystems arranged in series. The energy supplied by the first photosystem allows electrons to be pulled from water, and the energy supplied by the second photosystem step allows electrons to be transferred to NADP+.

The inner and outer mitochondrial membranes are not close to each other in all areas because the inner membrane has folds that project inward. These membranes define two spaces. What is the intermembrane space? What is the mitochondrial matrix?

The space between the inner and outer membranes=intermembrane space The space enclosed by the inner membrane=mitochondrial matrix

What are the major protein complexes of the photosynthetic electron transport chain? What function do each of them serve?

The two photosystems as well as the cytochrome-b6 f complex (cyt), through which electrons pass between photosystem II and photosystem I. Small, relatively mobile compounds convey electrons between these protein complexes. Plastoquinone (Pq), a lipid-soluble compound similar in structure to coenzyme Q, carries electrons from photosystem II to the cytochrome-b6 f complex by diffusing through the membrane, while plastocyanin (Pc), a water-soluble protein, carries electrons from the cytochrome-b6 f complex to photosystem I by diffusing through the thylakoid lumen.

In both fermentation pathways, NADH is oxidized to NAD+. However, NADH and NAD+ do not appear in the overall chemical equations. What is the reason for this?

There is no net production or loss of either molecule. NAD+ molecules that are reduced during glycolysis are oxidized when lactic acid or ethanol is formed.

The Calvin cycle is capable of producing more carbohydrates than the cell needs or, in a multicellular organism, more than the cell is able to export. If carbohydrates accumulated in the cell, what would happen to the cell? How does the cell deal with excess carbohydrates?

They would cause water to enter the cell by osmosis, perhaps damaging the cell (lysis/swelling). Excess carbohydrates are converted to starch, a storage form of carbohydrates. Because starch molecules are not soluble, they provide a means of carbohydrate storage that does not lead to osmosis. The formation of starch during the day provides photosynthetic cells with a source of carbohydrates that they can use during the night.

The hydrolysis of some disaccharides produces glucose molecules that directly enter glycolysis. What happens to other monosaccharides?

They, too, enter glycolysis, although not as glucose. Instead, they are converted into intermediates of glycolysis that come later in the pathway. For example, fructose is produced by the hydrolysis of sucrose (table sugar) and receives a phosphate group to form either fructose 6-phosphate or fructose 1-phosphate. In the liver, fructose 1-phosphate is cleaved and converted into glyceraldehyde 3-phosphate, which enters glycolysis at reaction 6.

Carbohydrates are synthesized from CO2 molecules during photosynthesis, yet they have more energy stored in their chemical bonds than is contained in the bonds of CO2 molecules. Therefore, to build carbohydrates using CO2 requires an input of energy. Where does this energy come from? How does energy from this source become incorporated into chemical bonds?

This energy comes from sunlight. The synthesis of carbohydrates from CO2 and water is a reduction-oxidation, or redox, reaction. Reduction reactions are reactions in which a molecule acquires electrons and gains energy, whereas oxidation reactions are reactions in which a molecule loses electrons and releases energy. During photosynthesis, CO2 molecules are reduced to form higher-energy carbohydrate molecules. This requires both an input of energy from ATP and the transfer of electrons from an electron donor. In photosynthesis, energy from sunlight is used to produce ATP and electron donor molecules capable of reducing CO2.

Following a meal, the small intestine very quickly absorbs triacylglycerols, which are then transported by the bloodstream and either consumed or stored in fat (adipose) tissue. Triacylglycerols are broken down inside cells to glycerol and fatty acids. Then, the fatty acids themselves are shortened by a series of reactions that sequentially remove two carbon units from their ends. What is the name of these series of reactions? What are the end products? Does it directly produce ATP?

This process is called β-(beta-)oxidation. It does not produce ATP, but releases a large number of NADH and FADH2 molecules that provide electrons for the synthesis of ATP by oxidative phosphorylation. In addition, the end product of the reaction is acetyl-CoA, which feeds the citric acid cycle and leads to the production of an even larger quantity of reduced electron carriers.

Butter, oils, ice cream, and the like all contain lipids and are high in calories, which are units of energy. We can also infer that lipids are a good source of energy from their chemical structure. Recall a type of fat called triacyleglycerol. What is its composition/structure? Does this molecule have a lot of potential energy? If so, for what reason?

Three fatty acid molecules bound to a glycerol backbone. These fatty acid molecules are rich in carbon-carbon and carbon-hydrogen bonds, which carry chemical potential energy.

Explain how a proton gradient is a source of potential energy. What is the significance of that potential energy?

Through the actions of the electron transport chain, protons have a high concentration in the intermembrane space and a low concentration in the mitochondrial matrix. As a result, there is a tendency for protons to diffuse back to the mitochondrial matrix, driven by a difference in concentration and charge on the two sides of the membrane. This movement, however, is blocked by the membrane, so the gradient stores potential energy. That energy can be harnessed if a pathway is opened through the membrane because the resulting movement of the protons through the membrane can be used to perform work (synthesize ATP).

Bread making involves ethanol fermentation and typically uses yeast, sugar, flour, and water. Why are yeast and sugar used?

Yeast cells are eukaryotes. In bread making, yeast can use sugar as a food source for ethanol fermentation. The carbon dioxide produced in the process causes the bread to rise. The ethanol is removed in the baking process.

Describe the structure of the chloroplast. Where does carbohydrate synthesis take place in the chloroplast?

Thylakoid membranes form structures that resemble flattened sacs, and these sacs are grouped into structures called grana (singular, granum) that look like stacks of interlinked pancakes. Grana are connected to one another by membrane bridges in such a way that the thylakoid membrane encloses a single interconnected compartment called the lumen The region surrounding the thylakoid membrane is called the stroma. Carbohydrate synthesis takes place in the stroma, whereas sunlight is captured and transformed into chemical energy by the photosynthetic electron transport chain in the thylakoid membrane.

What are some examples of photosynthetic organisms? Is it common among prokaryotes and eukaryotes?

Trees, grasses, and shrubs are all examples of photosynthetic organisms. However, photosynthesis occurs among prokaryotic as well as eukaryotic organisms, on land as well as in the sea. Approximately 60% of global photosynthesis is carried out by terrestrial organisms, with the remaining 40% taking place in the ocean. The majority of photosynthetic organisms in marine environments are unicellular. About half of oceanic photosynthesis is carried out by single-celled marine eukaryotes, while the other half is carried out by photosynthetic bacteria.

How do protons accumulate in the thylakoid lumen?

Two features of the photosynthetic electron transport chain are responsible for the buildup of protons in the thylakoid lumen. First, the oxidation of water releases protons and O2 into the lumen. Second, the cytochrome-b6 f complex, the protein complex situated between photosystem II and photosystem I, and plastoquinone together function as a proton pump that is functionally and evolutionarily related to proton pumping in the electron transport chain of cellular respiration.

A single molecule of glucose forms two molecules of pyruvate during glycolysis. How many molecuels of carbon dioxide, NADH, and acteyl-CoA are produced from a single starting glucose molecule?

Two molecules of carbon dioxide, two molecules of NADH, and two molecules of acetyl-CoA are produced from a single starting glucose molecule in this stage of cellular respiration. Acetyl-CoA is the substrate of the first step in the citric acid cycle.

Uncoupling agents are proteins spanning the inner mitochondrial membrane that allow protons to pass through the membrane and bypass the channel of ATP synthase. Describe the consequences to the proton gradient and ATP production.

Uncoupling agents decrease the proton gradient and therefore decrease levels of ATP. The energy of the proton gradient is not used for oxidative phosphorylation, but instead is dissipated as heat. Uncoupling agents are found naturally in certain tissues, such as fat, for heat generation. They can also act as poisons.

The sun, like all stars, produces a broad spectrum of electromagnetic radiation ranging from gamma rays to radio waves. Each point along the electromagnetic spectrum has a different energy level and a corresponding wavelength. What is the portion of the spectrum that can be seen by the human eye?

Visible light is the portion of the electromagnetic spectrum apparent to our eyes, and it includes the range of wavelengths used in photosynthesis. The wavelengths of visible light range from 400 nm to 700 nm. Approximately 40% of the sun's energy that reaches Earth's surface is in this range.

Complete the following sentence: ____________ donates electrons to one end of the photosynthetic electron transport chain, whereas _________ accepts electrons at the other end. The enzyme that pulls electrons from water, releasing both H+ and O2, is located on the lumen side of photosystem II.

Water......NADP+

Summarize the entire process of cellular respiration as briefly as possible.

We began with glucose and noted that it holds chemical potential energy in its covalent bonds. This energy is released in a series of reactions and captured in chemical form. Some of these reactions generate ATP directly by substrate-level phosphorylation. Others are redox reactions that transfer energy to the electron carriers NADH and FADH2. These electron carriers donate electrons to the electron transport chain, which uses the energy stored in the electron carriers to pump protons across the inner membrane of the mitochondria. In other words, the energy of the reduced electron carriers is transformed into energy stored in a proton electrochemical gradient. ATP synthase then converts the energy of the proton gradient to rotational energy, which drives the synthesis of ATP. The cell now has a form of energy that it can use in many ways to perform work.

Describe the configuration of the reaction center chlorophylls.

When excited, the reaction center transfers an electron to an adjacent molecule that acts as an electron acceptor. When the transfer takes place, the reaction center becomes oxidized and the adjacent electron-acceptor molecule is reduced. The result is the conversion of light energy into a chemical form. This electron transfer initiates a light-driven chain of redox reactions that leads ultimately to the formation of NADPH. Once the reaction center has lost an electron, it can no longer absorb light or contribute additional electrons. Thus, for the photosynthetic electron transport chain to continue, another electron must be delivered to take the place of the one that has entered the transport chain. These replacement electrons ultimately come from water.

One of the reactions of the citric acid cycle is a substrate-level phosphorylation reaction that generates a molecule of GTP. This is the only substrate-level phosphorylation in the citric acid cycle. GTP can transfer its terminal phosphate to_______________.

a molecule of ADP to form ATP.

Complete the following sentence: Most of the chlorophyll molecules in the thylakoid membrane function as an ____________: Energy is transferred between chlorophyll molecules until it is finally transferred to a specially configured pair of chlorophyll molecules known as the reaction center.

antenna.

Since the first reaction creates a molecule with six carbons and the last reaction regenerates a 4-carbon molecule, two carbons are eliminated during the cycle. These carbons are released as__________________.

carbon dioxide.

Complete the following sentence: Within each protein complex of the electron transport chain, electrons are passed from electron __________ to electron ______________. Each donor and acceptor is a redox couple, consisting of an oxidized and a reduced form of a molecule. The electron transport chain contains many of these redox couples.

electron donor to electron acceptor.

Complete the following sentence: These electron transfer steps are each associated with the release of energy as electrons are passed from the reduced electron carriers NADH and FADH2 to the final electron acceptor, oxygen. Some of this energy is used to reduce the next carrier in the chain, but in complexes I, III, and IV, some of it is used to pump protons (H+) across the inner mitochondrial membrane, from the _____________ to the ____________________. Thus, the transfer of electrons through complexes I, III, and IV is coupled with the pumping of protons. The result is an accumulation of protons in the __________________.

mitochondrial matrix........intermembrane space.......intermembrane space

When oxygen accepts electrons at the end of the electron transport chain, it forms water by the following reaction: O2 + 4e- + 4H+ → 2H2O Does oxygen get oxidized or reduced? What complex protein catalyzes this reaction?

oxygen is reduced. Complex IV.

Complete the following sentence: The _________________________ is where light energy is converted into chemical energy as a result of the excited electron's transfer to an adjacent molecule. This division of labor among chlorophyll molecules was discovered in the 1940s in a series of experiments by the American biophysicists Robert Emerson and William Arnold, who showed that only a small fraction of chlorophyll molecules are directly involved in electron transport. We now know that several hundred antenna chlorophyll molecules transfer energy to each reaction center. The antenna chlorophylls allow the photosynthetic electron transport chain to operate efficiently. Without the antennae to gather light energy, reaction centers would sit idle much of the time, even in bright sunlight.

reaction center

The oxidation reactions that produce carbon dioxide are coupled with the reduction of the electron carrier NAD+ to NADH. In this way, energy released in the oxidation reactions is transferred to NADH. More reduced electron carriers (NADH and FADH2) are produced in two additional redox reactions. Per turn of the cycle, how many reduced electron carriers are produced? What is the significance of these electron carriers?

three molecules of NADH and one molecule of FADH2 per turn of the cycle. These electron carriers donate electrons to the electron transport chain, which leads to the production of ATP by oxidative phosphorylation.