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medical sciences
biochemistry

Questions and Answers of Biochemistry

Describe how the cells of the acquired-immunity system develop so that they do not recognize self-antigens but do recognize foreign antigens.
What part of the immune system has been linked to progression of cancer?
What determines the family in which a virus is categorized?
Explain the mode of action of the herpes viral RNAs and how they confound the immune system.
What characteristics are shown by cancer cells?
Why are the proteins called p53 and Ras studied so much these days?
How are viruses related to cancer?
What is virotherapy?
Why is it inaccurate to say, “Smoking causes cancer”?
Describe the difference between a tumor suppressor and an oncogene with respect to the actual causes of cancer.
Describe the relationships between Ras, Jun, and Fos.
Describe the nature of p53 reactivation as a cancer-fighting strategy.
Describe different techniques that might restore p53 to a cell lacking it.
Describe the positive and negative effects of the innate immune system on cancer cells.
Explain why some researchers believe science should focus its attention on the inflammation associated with cancer progression instead of looking for a cure.
What were the results of sequencing the human melanoma and lung cancer genomes?
How does HIV confound the human immune system?
Compare HIV, SARS, and the common flu in terms of transmissibility and lethalness.
How is the gp120 protein important to HIV and its ability to confound the immune system?
Why are some scientists reluctant to say that the Berlin Patient is cured?
If you were going to design a drug to fight a virus, what would be likely targets for the drug design?
Some viruses can undergo lysis or lysogeny even in the same host. What might be a reason for this? Under what conditions might the virus favor the one strategy over the other?
For the hydrolysis of ATP at 25°C∆ (298 K) and pH 7, ATP + H2O → ADP + Pi + H+, the standard free energy of hydrolysis (∆G°') is 230.5 kJ mol-1 (27.3 kcal mol-1), and the standard enthalpy
All the organophosphate compounds listed in Table 15.1 undergo hydrolysis reactions in the same way as ATP. The following equation illustrates the situation for
Why are ∆G°' values not rigorously applicable to biochemical systems?
Identify the molecules oxidized and reduced in the following reactions and write the half reactions. (a) CH3CH2CHO + NADH → CH3CH2CH2OH + NAD+ (b) Cu2+ (aq) + Fe2+ (aq) → Cu+ (aq) + Fe3+ (aq)
The following half reactions play important roles in metabolism. 1/2 O2 1 2H+ + 2e– → H2O NADH + H+ → NAD+ + 2H+ + 2e- Which of these two is a half reaction of oxidation? Which one is a half
Suggest a reason that catabolic pathways generally produce NADH and FADH2, whereas anabolic pathways generally use NADPH.
Does all the energy released by an exergonic reaction go into driving a coupled endergonic reaction? Give an example to support your answer.
Using information from Table 15.1, calculate the value of DG°' for the following reaction. Glucose- + -phosphate → Glucose-6-phosphate
The standard free-energy change for the reactionArginine + ATP → Phosphoarginine + ADPis 11.7 kJ mol21. From this information and that in Table 15.1, calculate the ∆G°' for the
What are the usual ionic forms of ATP and ADP in typical cells? Does this information have any bearing on the free-energy change for the conversion of ATP to ADP?
A very favorable reaction is the production of ATP and pyruvate from ADP and phosphoenolpyruvate. Given the standard free-energy change for this coupled reaction, why does the following reaction not
Explain why several biochemical pathways start by putting a coenzyme A onto the molecule that initiates the pathway.
Which of the following statements is (are) true about the modified standard state for biochemistry? For each, explain why or why not. (a) [H+] 5 1 3 10–7 M, not 1 M. (b) The concentration of any
Can the thermodynamic property DG° be used to predict the speed of a reaction in a living organism? Why or why not?
Define the following terms: polysaccharide, furanose, pyra-nose, aldose, ketose, glycosidic bond, oligosaccharide, glycoprotein.
Consider the structures of arabinose and ri-bose. Explain why nucleotide derivatives of arabinose, such as ara-C and ara-A, are effective metabolic poisons.
Convert the following Haworth projections to a Fischer projection. Name the monosaccharides you have drawn.
Convert each of the following chair conformations to an open-chain from and to a Fischer projection. Name the monosaccharides you have drawn.
Starting with a Fischer projection of d-fructose, write equations showing the formation of a-d-fructopyranose, a-d-fructofuranose, β-d-fructopyranose, and β-d-fructofuranose.
Starting with the open-chain form of d-ribose, write equations for the cyclization reactions that form the pyranose and the furanose forms.
Draw a Haworth projection for the disaccha-ride gentibiose, given the following information: (a) It is a dimer of glucose. (b) The glycosidic linkage is β(1 → 6). (c) The anomeric carbon not
Draw Haworth projection formulas for dimers of glucose with the following types of glycosidic linkages: (a) A β(1 → 4) linkage (both molecules of glucose in the β form) (b) An a,a(1 → 1)
Pectin, which occurs in plant cell walls, exists in nature as a polymer of D-galacturonic acid methylated at carbon 6 of the monomer. Draw a Haworth projection for a repeating disaccharide unit of
Suppose that a polymer of glucose with alternating a(1 → 4) and β(1 → 4) glycosidic linkages has just been discovered. Draw a Haworth projection for a repeating tetramer (two repeating dimers)
What is the benefit of fiber in the diet?
How would you expect the active site of a cel-lulase to differ from the active site of an enzyme that degrades starch?
Why is it advantageous that polysaccharides can have branched chains? How do they achieve this structural feature?
Why is the polysaccharide chitin a suitable material for the exoskeleton of invertebrates such as lobsters? What other sort of material can play a similar role?
Based on what you know about glycosidic bonds, propose a scheme for formation of covalent bonds between the carbohydrate and protein portions of glycoproteins.
Following are Fischer projections for a group of five-carbon sugars, all of which are aldopentoses. Identify the pairs that are enantiomers and the pairs that are epimers. (The sugars shown here are
Which reaction or reactions that we have met in this chapter require ATP? Which reaction or reactions produce ATP? List the enzymes that catalyze the reactions that require and that produce ATP.
Several of the enzymes of glycolysis fall into classes that we will see often in metabolism. What reaction types are catalyzed by each of the following: (a) Kinases (b) Isomerases (c) Aldolases (d)
Which reaction or reactions that we have met in this chapter require NADH? Which reaction or reactions require NAD+? List the enzymes that catalyze the reactions that require NADH and that require
What is the difference between an isomerase and a mutase?
Discuss the logic of the nature of the allosteric inhibitors and activators of glycolysis. Why would these molecules be used?
Many species have a third type of LDH sub-unit that is found predominantly in the testes. If this subunit, called C, were expressed in other tissues and could combine with the M and H subunits, how
The M and H subunits of lactate dehydrogenase have very similar sizes and shapes but differ in amino acid composition. If the only difference between the two were that the H subunit had a glutamic
The mechanism involved in the reaction catalyzed by phosphoglyceromutase is known to involve a phosphory-lated enzyme intermediate. If 3-phosphoglycerate is radioactively labeled with 32P, the
If lactic acid is the buildup product of strenuous muscle activity, why is sodium lactate often given to hospital patients intra-venously?
Using the Lewis electron-dot notation, show explicitly the transfer of electrons in the following redox reactions. (a) Pyruvate + NADH + H+ → Lactate + NAD+ (b) Acetaldehyde + NADH + H+ S Ethanol +
What is unique about TPP that makes it useful in decarboxylation reactions?
Beriberi is a disease caused by a deficiency of vitamin B1 (thiamine) in the diet. Thiamine is the precursor of thiamine pyrophosphate. In view of what you have learned in this chapter, why is it not
Cancer cells grow so rapidly that they have a higher rate of anaerobic metabolism than most body tissues, especially at the center of a tumor. Can you use drugs that poison the enzymes of anaerobic
What is the Warburg effect, and what does it have to do with the topics of this chapter?
Show how the estimate of 33% efficiency of energy use in anaerobic glycolysis is derived.
Show, by a series of equations, the energetics of phosphorylation of ADP by phosphoenolpyruvate.
Using Table 17.1, predict whether the following reaction is thermodynamically possible: Phosphoenolpyruvate + Pi + 2ADP → Pyruvate + 2ATP
Why would enzymes be found as isozymes?
What is the metabolic advantage of having both hexokinase and glucokinase to phosphorylate glucose?
What is the effect on gluconeogenesis and glycogen synthesis of(a) Increasing the level of ATP,(b) Decreasing the concentration of fructose-1,6-bisphosphate, and(c) Increasing the concentration of
Which steps of glycolysis are irreversible? What bearing does this observation have on the reactions in which gluconeogen-esis differs from glycolysis?
Which reaction or reactions discussed in this chapter require ATP? Which reaction or reactions produce ATP? List the enzymes that catalyze the reactions that require and that produce ATP.
Which reaction or reactions discussed in this chapter require ATP? Which reaction or reactions produce ATP? List the enzymes that catalyze the reactions that require and that produce ATP. Discuss.
How do glucokinase and hexokinase differ in function?
Why is it advantageous for two control mechanisms —allosteric control and covalent modification—to be involved in the metabolism of glycogen?
Explain how fructose-2,6-bisphosphate can play a role in more than one metabolic pathway.
How can the synthesis and breakdown of fructose-2,6-bisphosphate be controlled independently?
List three differences in structure or function between NADH and NADPH.
What is the connection between material in this chapter and hemolytic anemia?
List two ways in which glutathione functions in red blood cells.
Using the Lewis electron-dot notation, show explicitly the transfer of electrons in the following redox reaction.Glucose-6-phosphate + NADP+ →6-Phosphoglucono-d-lactone + NADPH + H+
Explain how the pentose phosphate pathway can respond to a cell’s need for ATP, NADPH, and ribose-5- phosphate.
How would it affect the reactions of the pen-tose phosphate pathway to have an epimerase and not an isomer-ase to catalyze the reshuffling reactions?
In metabolism, glucose-6-phosphate (G6P) can be used for glycogen synthesis or for glycolysis, among other fates. What does it cost, in terms of ATP equivalents, to store G6P as glycogen, rather than
Draw the structures of the activated carbon groups bound to thiamine pyrophosphate in three enzymes that contain this coenzyme.
What does it mean when an enzyme has the name synthase?
What is fluoroacetate? Why is it used?
What are the similarities and differences between the re-actions catalyzed by pyruvate dehydrogenase and α-ketoglutarate dehydrogenase?
How does substrate-level phosphorylation differ from phosphorylation linked to the electron transport chain?
What are the major differences between the oxidations in the citric acid cycle that use NAD+ as an electron acceptor and the one that uses FAD?
We have seen one of the four possible isomers of isocitrate, the one produced in the aconitase reaction. Draw the configurations of the other three.
Show, by Lewis electron-dot structures of the appropriate portions of the molecule, where electrons are lost in the following conversions: (a) Pyruvate to acetyl-CoA (b) Isocitrate to
How does an increase in the ADP/ATP ratio affect the activity of isocitrate dehydrogenase?
How does an increase in the NADH/NAD+ ratio affect the activity of pyruvate dehydrogenase?
Would you expect the citric acid cycle to be more or less active when a cell has a high ATP/ADP ratio and a high NADH/NAD+ ratio? Give the reason for your answer.
How could the expression “milking it for all it’s worth” relate to the citric acid cycle?
Using the information in Chapters 17–19, calculate the amount of ATP that can be produced from one molecule of lactose metabolized aerobically through glycolysis and the citric acid cycle.
Describe the various purposes of the citric acid cycle.

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