Biochemistry and Molecular Biology solutions

Question 1

Which of the following statements about photosynthesis is correct?

Your answer:

1. a) Carbohydrates are the source of electrons in photosynthesis.

Correct answer:

1. c) Water is the source of electrons in photosynthesis.

Feedback:

Photosynthesis occurs in chloroplasts. It is a biological process that recycles electrons from water using sunlight energy. Carbon dioxide and water are converted to carbohydrates and oxygen is produced. The latter has the fortunate side effect of providing an 'electron sink' to accept electrons from food oxidation by aerobic organisms in general. The light-dependent reactions of photosynthesis use solar energy to transfer electrons from water. This allows the production of reducing equivalents in the form of NADPH needed for the synthesis of carbohydrate from CO2 and water. It also permits the establishment of a proton gradient across the chloroplast membrane which drives ATP synthesis by the chemiosmotic mechanism. ATP is needed for carbohydrate synthesis by the Calvin cycle.
Page reference: Page 272

Question 2

Which of the following statements about thylakoids is not correct?

You did not answer the question.

Correct answer:

1. c) The thylakoid membranes contain the Calvin cycle enzymes.

Feedback:

Chloroplasts in green plants have a permeable outer membrane and an impermeable inner membrane that encloses the stroma which corresponds to the matrix in mitochondria. In addition there are interconnected membranous sacs called thylakoids. There are two photosystems named PSI and PSII, in order of their discovery but PSII occurs first in the photosynthetic process. These are connected by a complex called cytochrome bf. In the overall process electrons are extracted from water, liberating oxygen. The energy for this comes indirectly from light and transmitted by the three complexes to finally reduce NADP, ATP being generated on the way by the cytochrome bf complex. The products from these light-dependent reactions, NADPH and ATP are then used in the light-independent Calvin cycle to synthesise carbohydrates from CO2 and water.
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Question 3

Which of the following statements about the mechanism of the light-dependent reactions of photosynthesis is correct?

You did not answer the question.

Correct answer:

1. d) Ferredoxin-NADP reductase reduces NADP+ to NADPH.

Feedback:

The light-dependent reactions of photosynthesis occur on the thylakoid membrane. Chlorophyll molecules at the reaction centre of photosystem II (PSII) are activated causing the reduction of pheophytin which passes its electrons to cytochrome bf via plastoquinone. Cytochrome bf reduces plastocyanin while P700 from photosystem I causes the reduction of ferredoxin. Ferredoxin-NADP reductase then reduces NADP+ to NADPH + H+. Plastocyanin reduced via cytochrome bf replaces the missing electron in P700, and P680 returns to its ground state with an electron from water. This electron transfer in the thylakoid membrane leads to the translocation of protons to the thylakoid lumen producing a proton gradient that generates ATP by chemiosmosis (previously described in mitochondria). The ATP and NADPH generated in the light reactions are now used in the stroma for the Calvin cycle to synthesize carbohydrates.
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Question 4

Which of the following statements about cyclic photophosphorylation is correct?

You did not answer the question.

Correct answer:

1. c) Cyclic photophosphorylation occurs in the cytochrome bf complex and utilizes electrons from photosystem I.

Feedback:

In photosynthesis when all the available has NADP+ has been reduced, photoexcited electrons take a path that differs from the normal noncyclic photophosphorylation (from water to PS II, cytochrome bf complex, to PS I to NADP+). Ferredoxin transfers electrons back to the cytochrome bf complex leading to increased proton translocation and a greater potential for ATP synthesis.
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Question 5

Which of the following statements about the mechanism of the Calvin Cycle is correct?

You did not answer the question.

Correct answer:

1. d) The Calvin cycle is a metabolic pathway by which plants convert CO2 and water into carbohydrates.

Feedback:

CO2 is used by the enzyme ribulose-1:5-bisphosphate carboxylase (rubisco) to split ribulose-1:5-bisphosphate forming two molecules of 3-phosphoglycerate which are converted to fructose-1:6-bisphosphate essentially as occurs in gluconeogenesis except that NADPH is the reductant in this case and not NADH. Six molecules of ribulose-1:5-bisphosphate and six molecules of CO2 form twelve molecules of 3-phosphoglycerate. Ten of these twelve molecules of 3-phosphoglycerate are manipulated with the enzymes transketolase and transaldolase to six molecules of ribulose-1:5-bisphosphate (to supply rubisco). Two molecules of 3-phosphoglycerate are converted to fructose-1:6-bisphosphate using the ATP formed by photophosphorylation. The Calvin cycle reactions are not light-dependent and are known as 'dark reactions' which does not imply that they don't occur in the light when photosynthesis is active.
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Question 1

Which of the following statements about the role of the pentose phosphate pathway is correct?

Your answer:

1. a) The pentose phosphate pathway produces ribose-5-phosphate and NADPH.

Feedback:

The pentose phosphate pathway supplies ribose-5-phosphate for nucleotide and nucleic acid synthesis, and for synthesis of coenzymes such as NAD+, FAD and CoA. The pentose phosphate pathway also supplies NADPH for reductive biosyntheses such as fatty acid synthesis. It is also a route for excess pentose sugars to be brought into the mainstream of glucose metabolism pathways.
The pathway occurs in the cytoplasm of most cells and has two main parts. The first is the irreversible oxidation of glucose-6-phosphate to ribose-5-phosphate in which NADP+ is reduced to NADPH. The rate-limiting reaction here is catalyzed by glucose-6-phosphate dehydrogenase. The second part of the pentose phosphate pathway is the reversible nonoxidative reactions that interconvert sugars according to the cell's needs using the enzymes transketolase and transaldolase.
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Question 2

Which of the following statements about the oxidative section of the pentose phosphate pathway is correct?

You did not answer the question.

Correct answer:

1. d) The pathway supplies ribose-5-phosphate and NADPH in the quantities the cells require.

Feedback:

The pentose phosphate pathway supplies ribose-5-phosphate for nucleotide and nucleic acid synthesis, and for synthesis of coenzymes such as NAD+, FAD and CoA. The pathway also supplies NADPH for reductive biosyntheses. It is a route for excess pentose sugars to be brought into the mainstream of glucose metabolism.
The pathway has two main parts. One part is the irreversible oxidation of glucose-6-phosphate to ribose-5-phosphate while NADP+ is reduced to NADPH. The rate-limiting reaction here is catalyzed by glucose-6-phosphate dehydrogenase. This section of the pathway is controlled by the availability of NADP+. The second part of the pentose phosphate pathway is made up of nonoxidative reaction sequences that interconvert sugars according to the cell's needs. Excess ribose-5-phosphate is converted to glycolytic intermediates by a sequence of reversible reactions.
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Question 3

Which of the following statements about the nonoxidative section of the pentose phosphate pathway is correct?

You did not answer the question.

Correct answer:

1. d) Pentoses undergo isomerizations in the pentose phosphate pathway.

Feedback:

The oxidative section of the pentose phosphate pathway supplies ribose-5-phosphate for nucleotide and nucleic acid synthesis, ribose for coenzymes such as NAD and FAD, and NADPH for reductive biosyntheses. The nonoxidative section of the pathway is a route for excess pentose sugars to be brought into the mainstream of glucose metabolism. It is a mechanism by which sugars can be interconverted according to the cell's needs. The key reactions in this section are catalyzed by the enzymes transketolase and transaldolase. Transketolase transfers two-carbon units and transaldolase transfers three-carbon units from pentose sugar phosphates to other aldose sugars.
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Question 4

Which of the following statements about the use of the NADPH generated from the pentose phosphate pathway is not correct?

You did not answer the question.

Correct answer:

1. d) NADPH generated from the pentose phosphate pathway and cytoplasmic NADH are metabolically interchangeable.

Feedback:

There are multiple uses for the NADPH produced from the pentose phosphate pathway. It is required for reductive biosyntheses such as in fatty acid synthesis and for the regeneration of oxidised glutathione to its reduced state. Glutathione is involved in the glutathione peroxidase system for protection against peroxides. NADPH is also used in the cytochrome P450 monooxygenase system for drug metabolism and in the hydroxylation of steroids for cholesterol and steroid production.
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Question 5

Which of the following statements about the pentose phosphate pathway is not correct?

You did not answer the question.

Correct answer:

1. d) The pentose phosphate pathway relies on the availability of NADPH.

Feedback:

The pentose phosphate pathway produces ribose-5-phosphate for nucleotide and nucleic acid synthesis, and for coenzymes such as NAD and FAD. The pathway also supplies NADPH for reductive biosyntheses and it is a route for excess pentose sugars to be brought into the mainstream of glucose metabolism.
The pathway has two main parts. The first is the irreversible oxidation of glucose-6-phosphate to ribose-5-phosphate while NADP+ is reduced to NADPH and the rate-limiting reaction is catalyzed by glucose-6-phosphate dehydrogenase. Control of this part of the pathway is mainly by the availability of NADP+. The other part of the pentose phosphate pathway is made up of reversible nonoxidative reactions that interconvert sugars according to the cell's needs using the enzymes transketolase and transaldolase.
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Question 1

Which of the following statements about the regulation of a metabolic pathway is correct?

Your answer:

1. a) Most metabolic pathways are not regulated.

Correct answer:

1. d) Most metabolic pathways are regulated.

Feedback:

Living organisms, especially complex ones such as mammals, need to change their rates of metabolism according to physiological needs at the time. This means that the rates of metabolic pathways need to be changed in keeping with those needs. There are several methods for doing this. The amount of a given enzyme may change by regulation of its rate of synthesis and/or destruction or the catalytic activity of a given amount of enzyme may be changed. There are several methods of achieving the latter.
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Question 2

Which of the following correctly exhibits an example of metabolic control?

You did not answer the question.

Correct answer:

1. a) In cases where the direction of a metabolic pathway has to be reversed the pathway is controlled at an irreversible step.

Feedback:

As well as regulation of the rate of metabolic pathways their direction may need to be reversed. For example in gluconeogenesis much of the glycolytic pathway is reversed. Control of this can only occur at irreversible reactions where there are separate enzymes for the forward and backward directions. Regulation control of enzymes by changing the amount of a given enzyme is not instantaneous for it involves protein synthesis or destruction. However allosteric control is instantaneous. Regulatory enzymes are often the first irreversible one that commits a metabolite to that pathway. Most controlling mechanisms are reversible, but there are some irreversible ones such as the activation of trypsinogen to trypsin.
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Question 3

Which of the following statements about the mechanism of allosteric control of enzyme activity is correct?

You did not answer the question.

Correct answer:

1. b) Allosteric enzymes show a greater sensitivity to changes in substrate concentration than classical type enzymes with hyperbolic kinetics.

Feedback:

Allosteric enzymes are multi-subunit proteins which have allosteric sites ('allo' means other) separate from the active site to which bind allosteric modifiers (activators or inhibitors). These cause conformational changes in the enzyme, giving sigmoidal kinetics rather than the hyperbolic kinetics of classical enzymes. This affects the affinity of the enzyme for its substrate and hence the activity of the enzyme. An allosteric activator increases the affinity whereas an inhibitor decreases it. The sigmoid kinetics means that over a critical range, the enzyme is more sensitive to changes in substrate concentration than is the case for those with hyperbolic kinetics.
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Question 4

Which of the following statements about the control of enzyme activity by phosphorylation is correct?

You did not answer the question.

Correct answer:

1. d) Phosphorylation of an enzyme results in a conformational change.

Feedback:

Enzyme activity is often controlled by phosphorylation. Kinases transfer a phosphoryl group from ATP to specific -OH groups on the enzymes such as those belonging to a serine or threonine. The addition of the strongly charged phosphoryl group causes a conformational change in the protein. This alters the activity of the enzyme. The phosphorylation process is reversed by protein phosphatases. Although other forms of covalent modifications occur in cells, this is the most important. Phosphorylation usually occurs in cells in response to external signals.
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Question 5

Which of the following statements about the integration of fat and carbohydrate metabolism control in diabetes mellitus is correct?

You did not answer the question.

Correct answer:

1. c) Low insulinglucagon ratio activates lipolysis in adipocytes.

Feedback:

There are two types of diabetes mellitus: type 1, caused by the destruction of the insulin-producing cells of the pancreas, and type 2, where cells become insensitive to insulin. In uncontrolled type 1 diabetes mellitus the lack of insulin means the glucagon /insulin ratio is very high resulting in rapid release of fatty acids from adipose cells. These are metabolised in the liver where they are converted to ketone bodies, resulting in the condition known as ketoacidosis. Uptake of glucose into muscle and adipose cells is insulin dependent; the hormone is needed to recruit glucose transporters from a non-functional reserve site to the cell membrane. The result is that in type 1 where insulin is deficient in amount, glucose is not taken up into tissues causing hyperglycaemia (high blood glucose levels).
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Question 1

Which of the following statements about gluconeogenesis is correct?

Your answer:

1. a) Muscles have a large glycogen store which gives rise to blood glucose during prolonged starvation.

Correct answer:

1. d) Gluconeogenesis enables the liver to maintain blood glucose levels during starvation.

Feedback:

The liver maintains blood glucose levels by breaking down its glycogen stores to produce glucose for the blood but liver glycogen stores are exhausted after 24 hours of fasting. The brain and other cells such as red blood cells must have a constant supply of glucose to function normally. Unlike most other tissues these cells cannot use fatty acids. Fatty acids cannot penetrate the blood brain barrier; red blood cells lack mitochondria and cannot metabolise them. Gluconeogenesis is the production of glucose. It occurs in the liver in starvation. Glucose is released from glucose-6-phosphate by the enzyme glucose-6-phosphatase. Only liver and kidney have this enzyme though because of its small mass the latter is relatively insignificant in this respect. Amino acids released from muscle protein breakdown are the main source of carbon atoms for gluconeogenesis.
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Question 2

Which of the following statements about the use and synthesis of glucose in the body is correct?

You did not answer the question.

Correct answer:

1. d) The brain can use glucose for all its energy needs.

Feedback:

Glucose is essential for the brain, kidney medulla, red blood cells, retinal cells and any other cells without mitochondria. It cannot be made from acetyl-CoA, and can only be made from any molecule that can be converted to pyruvate. The brain needs a constant supply of glucose to function normally. Fatty acids are unable to be used as a fuel source by the brain since they cannot cross the blood-brain barrier (they are reversibly bound to albumin in the circulation). Ketone bodies can be used as a proportion (40%) of the brain's fuel source, but it still requires a continual supply of glucose. Cells without mitochondria cannot use ketone bodies as a fuel.
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Question 3

Which of the following statements about the process of gluconeogenesis is correct?

You did not answer the question.

Correct answer:

1. c) Glucose-6-phosphatase hydrolyses glucose-6-phosphate to release glucose into the blood.

Feedback:

Gluconeogenesis involves reversal of several glycolytic reactions but there are three reactions that need to be bypassed because of thermodynamic considerations which make them irreversible. These are; the phosphorylation of glucose to glucose-6-phosphate using ATP, the phosphorylation of fructose-6-phosphate to fructose-1:6-bisphosphate, again with ATP. The third is the conversion of phosphoenolpyruvate (PEP) to pyruvate using pyruvate kinase. This forms ATP. In gluconeogenesis, pyruvate is first converted to oxaloacetate by the ATP-dependent pyruvate carboxylase reaction. This is then converted to PEP by PEP carboxykinase using GTP. The PEP is converted to fructose-1:6-bisphosphate then hydrolysed by fructose-1:6-bisphosphatase. Glucose-6-phosphate is hydrolysed by glucose-6-phosphatase to release glucose into the blood.
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Question 4

Which of the following statements about the sources of pyruvate used by the liver for gluconeogenesis is correct?

You did not answer the question.

Correct answer:

1. d) The main source of glucose carbons for gluconeogenesis is alanine derived from breakdown of muscle proteins.

Feedback:

The main source of pyruvate used by the liver for gluconeogenesis is from the breakdown of muscle proteins promoted by the stress hormone cortisol. Several amino acids give rise to citric acid cycle acids and are converted to oxaloacetate. Pyruvate is converted to oxaloacetate by pyruvate carboxylase then to phosphoenolpyruvate by phosphoenolpyruvate carboxykinase. In muscles pyruvate accepts amino groups (from other amino acids), to form alanine which is released into the blood. In the liver it is converted back to pyruvate for gluconeogenesis.
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Question 5

Which of the following statements about the effect of ethanol metabolism on gluconeogenesis is correct?

You did not answer the question.

Correct answer:

1. d) The metabolism of ethanol by the liver increases the NADHNAD+ ratio reducing its ability to perform gluconeogenesis.

Feedback:

Ethanol is oxidised to acetaldehyde in the liver cytoplasm by alcohol dehydrogenase. This is oxidised to acetate by acetaldehyde dehydrogenase in the mitochondria. Two NADH molecules are produced in the liver cell from each ethanol molecule. Intake of large amounts of alcohol results in the cellular NADH/NAD+ ratio being increased. Several dehydrogenases such as lactate dehydrogenase can be inhibited by this so that the pyruvate/lactate equilibrium is disturbed resulting in reduced amounts of pyruvate available for gluconeogenesis. Excessive drinking often results in reduced food intake so that dietary sources of glucose diminish. This coupled with impaired gluconeogenesis can result in inadequate supply of glucose to the brain in extreme cases with dangerous consequences.
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Question 1

Which of the following statements about the metabolism of amino acids is correct?

Your answer:

1. a) Essential amino acids can be formed from other amino acids supplied in the diet.

Correct answer:

1. d) Essential amino acids cannot be formed from other amino acids but must be supplied in the diet.

Feedback:

Humans have lost the ability to synthesise ten amino acids, so these must be supplied in the diet. They are known as essential amino acids. Humans have no method of storing amino acids. After immediate needs are met, surplus amino acids are oxidised or converted to glycogen or fat and their amino group nitrogen is excreted as urea.
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Question 2

Which of the following statements about the role of glutamate dehydrogenase is correct?

You did not answer the question.

Correct answer:

1. d) Glutamate dehydrogenase oxidatively deaminates glutamate producing ?-ketoglutarate.

Feedback:

Most amino acids are deaminated by a process known as deamination. Their amino groups are transferred by transaminases to α-ketoglutarate forming glutamate. Glutamate dehydrogenase plays a central role in amino acid deamination. Using either NAD+ or NADP+ as coenzyme (which is unusual) it removes two hydrogen atoms from the glutamate so formed, producing an α-ketoglutarate ammonia Schiff base. This spontaneously hydrolyses to give α-ketoglutarate and ammonia. The carbon skeletons of the deaminated amino acids are metabolized to acetyl-CoA or intermediates of the citric acid cycle depending on the particular amino acid they were derived from.
α-ketoglutarate can be a source of energy since it can enter the citric acid cycle and lead to increased ATP production. Accordingly, glutamate dehydrogenase is allosterically inhibited by ATP and GTP, high levels of which indicate a high energy charge, and activated by ADP and GDP.
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Question 3

Which of the following statements about transamination reactions is correct?

You did not answer the question.

Correct answer:

1. d) Transamination reactions require pyridoxal-5-phophate.

Feedback:

Most amino acids are deaminated in a two step process in which their amino groups are transferred to α-ketoglutarate by transaminases (amino transferases) forming glutamate. The latter is then deaminated by glutamate dehydrogenase. Transaminases have pyridoxal phosphate as a cofactor tightly bound to their active site. It acts as an intermediary in the transfer of amino groups. It accepts the amino group from the donor amino acid transiently forming pyridoxamine phosphate. The amino group is then transferred to the acceptor α-keto acid, reforming pyridoxal phosphate.
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Question 4

Which of the following statements about the urea cycle is correct?

You did not answer the question.

Correct answer:

1. d) Arginine is hydrolysed to urea and ornithine in the urea cycle.

Feedback:

Urea is the major excreted form of amino acid nitrogen. One of the urea nitrogens is supplied as free ammonia from the oxidative deamination of glutamate by glutamate dehydrogenase. The hydrolysis of two ATP molecules is used to incorporate this ammonia and carbon dioxide into carbamoyl phosphate. Carbamoyl phosphate condenses with ornithine to form citrulline. This is transported out of the mitochondrial matrix to the cytosol and condenses with aspartate. Another ATP is used to form argininosuccinate which is lysed to fumarate and arginine. Arginase cleaves this to urea and ornithine is regenerated and transported back to the mitochondrion.
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Question 5

Which of the following statements about aminolevulinate synthase (ALA synthase) is correct?

You did not answer the question.

Correct answer:

1. c) ALA synthase catalyses the rate-limiting reaction in haem synthesis.

Feedback:

The haem biosynthesis pathway begins with glycine and succinyl-CoA forming aminolevulinic (ALA) acid using aminolevulinate synthase (ALA synthase) in the mitochondrial matrix. This is the committed step in porphyrin synthesis. Two molecules of ALA condense to form porphobilinogen finally producing haem via protoporphyrin synthesis. When drugs such as barbiturates are administered to a patient the synthesis of hepatic cytochrome P450 required for their metabolism, is increased. The synthesis of ALA synthase is also increased in response to the demand for haem. Individuals with acute intermittent porphyria cannot handle the increased supply of ALA due to a deficiency in an enzyme of the biosynthetic pathway. This results in the preceding metabolites ALA and porphobilinogen accumulating. The symptoms of the disease are associated with this.
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