Questions and Answers of Biochemistry Concepts And Connections

Write a pathway leading from glucose to lactose in mammary gland, and write a balanced equation for the overall pathway. ATP “Kinase" ADP Glucose B HK ATP
Because of the position of arsenic in the periodic table, arsenate (AsO43-) is chemically similar to inorganic phosphate and is used by phosphate-requiring enzymes as an alternative substrate.
As early as the 1930s, it was known that frog muscles could still contract when glycolysis was inhibited. Where did the ATP come from to drive these contractions?
Enolase has a strict requirement for two Mg2+ ions in its active site. Propose a role for these ions in the catalytic mechanism of the enzyme.
How many ATP equivalents are consumed in the conversion of each of the following to a glucosyl residue in glycogen? (a) Dihydroxyacetone phosphate (b) Fructose-1,6-bisphosphate (c) Pyruvate (d)
Avidin is a protein that binds extremely tightly to biotin, so avidin is a potent inhibitor of biotin-requiring enzyme reactions. Consider glucose biosynthesis from each of the following substrates
Predict the effect of each of the following mutants on the rate of glycolysis in liver cells (increase, decrease, no change): (a) Loss of the allosteric site for ATP in PFK-1 (b) Loss of the
Glycogen synthesis and breakdown are regulated primarily at the hormonal level. However, important nonhormonal mechanisms also control the rates of synthesis and mobilization. Describe these
Although most enzymes are quite specific, they can catalyze side reactions with compounds that are structurally similar to their physiological substrates, but usually at much slower rates. For
Why does it make good metabolic sense for phosphoenolpyruvate carboxykinase, rather than pyruvate carboxylase, to be the primary target for regulating gluconeogenesis at the level of control of
Many of the mechanisms involved in the regulation of glycogen metabolism involve covalent modification of enzymes. In particular, reversible phosphorylation/dephosphorylation plays a central
Consider the fate of pyruvate labeled with 14C in each of the following positions: carbon 1 (carboxyl), carbon 2 (carbonyl), and carbon 3 (methyl). Predict the fate of each labeled carbon during one
Considering the evidence that led Krebs to propose a cyclic pathway for oxidation of pyruvate, discuss the type of experimental evidence that might have led to realization of the cyclic nature of the
Which carbon or carbons of glucose, if metabolized via glycolysis and the citric acid cycle, would be most rapidly lost as CO2?
Given what you know about the function of the glyoxylate cycle and the regulation of the citric acid cycle, propose control mechanisms that might regulate the glyoxylate cycle.
Write a balanced equation for the conversion in the glyoxylate cycle of two acetyl units, as acetyl-CoA, to oxaloacetate.
Referring to Table 14.1 for E′0 values, calculate ∆G°′ for oxidation of malate by malate dehydrogenase.Table 14.1 TABLE 14.1 Standard reduction potentials of interest in
Construct a table that lists all of the metabolic reactions from Chapters 12 and 13 that form or break C—C bonds. Arrange them according to whether the C—C bond is a or b to a carbonyl. Which
Isocitrate lyase cleaves the 6-carbon isocitrate to glyoxylate and succinate. Draw a plausible mechanism for this reaction.
Given the roles of NAD+/NADH in dehydrogenation reactions and NADPH/NADP+ in reductions, as discussed in Chapter 11 (Section 11.4), would you expect the intracellular ratio of NAD+ to NADH to be high
From E°′ values in Table 14.1, calculate the equilibrium constant for the glutathione peroxidase reaction at 37 °C.Table 14.1 TABLE 14.1 Standard reduction potentials of interest in
Inflammatory stimuli cause macrophages to undergo dramatic metabolic reprogramming, including a switch from oxidative phosphorylation to aerobic glycolysis. Cordes et al. (J. Biol. Chem.
If you were to determine the P/O ratio for oxidation of a-ketoglutarate, you would probably include some malonate in your reaction system. Why? Under these conditions, what P/O ratio would you expect
In the early days of “mitochondriology,” P/O ratios were determined from measurements of volume of O2 taken up by respiring mitochondria and chemical assays for disappearance of inorganic
Referring to Figure 14.16, predict the P/O ratio for oxidation of ascorbate by isolated mitochondria.Figure 14.16, B-Hydroxybutyrate NAD+ FMN Coupling site Complex I Rotenone and
Years ago there was interest in using uncouplers such as dinitrophenol as weight control agents. Presumably, fat could be oxidized without concomitant ATP synthesis for re-formation of fat or
The antibiotic valinomycin (see Section 10.4) is an ionophore that forms a specific complex with potassium ion. Because the complex is lipophilic and can diffuse into the membrane, valinomycin brings
In cyclic photophosphorylation, it is estimated that two electrons must be passed through the cycle to pump enough protons to generate one ATP. Assuming that the ∆G for hydrolysis of ATP under
The substance dichlorophenyldimethylurea (DCMU) is an herbicide that inhibits photosynthesis by blocking electron transfer between plastoquinones in photosystem II. (a) Would you expect DCMU to
Suppose ribulose-5-phosphate, labeled with 14C in carbon 1, is used as the substrate in carbon reactions. In which carbon of 3PG will the label appear?
The following data, presented by G. Bowes and W. L. Ogre in J. Biol. Chem. (1972) 247:2171–2176, describe the relative rates of incorporation of CO2 by Rubisco under N2 and under pure O2. Decide
It is believed that the ratio of cyclic photophosphorylation to noncyclic photophosphorylation changes in response to metabolic demands. In each of the following situations, would you expect the
Daniel Arnon and coworkers carried out experiments with intact, saltwashed chloroplasts to study photophosphorylation. When the chloroplasts were illuminated in the presence of ADP + Pi , ATP was
If algae are exposed to 14CO2 for a brief period while illuminated, the labeled carbon is initially found almost entirely in the carboxyl group of 3-phosphoglycerate. However, if illumination is
Macías-Rubalcava et al., in J. Photochem. Photobiol. (2017) B 166:35–43, investigated the mechanism of action of several compounds that might serve as new herbicides. One of these new compounds
β-hydroxybutyrate dehydrogenase catalyzes the last step in ketogenesis, the reduction of acetoacetate to b-hydroxybutyrate. (a) Write a balanced equation for this reaction. (b) Calculate the
Calculate the number of ATPs generated by the complete metabolic oxidation of tripalmitin (tripalmitoylglycerol). Hydrolysis of the triacylglycerol occurs at the cell surface. Consider the energy
2-Bromopalmitoyl-CoA inhibits the oxidation of palmitoyl-CoA by isolated mitochondria but has no effect on the oxidation of palmitoylcarnitine. What is the most likely site of inhibition by
When the identical subunits of chicken liver fatty acid synthase are dissociated in vitro, all of the activities can be detected in the separated subunits except for the b-ketoacyl synthase reaction
How many tritium atoms (3H) are incorporated into palmitate when fatty acid synthesis is carried out in vitro with the following labeled substrate? 010 -OOC-C³H₂-C-S-COA
A dialyzed pigeon liver extract will catalyze the conversion of acetyl-CoA to palmitate and CoASH if supplied with Mg2+, NADPH, ATP, HCO3-, and citrate. (a) If H14CO3– is supplied, what compounds
What would be the effect on fatty acid synthesis of an increase in intramitochondrial oxaloacetate level? Briefly explain your answer.
Discuss the metabolic rationale for phosphorylation of acetyl-CoA carboxylase by AMP-activated protein kinase (AMPK) and cyclic AMP–dependent protein kinase (PKA).
What would you expect to happen to levels of mevalonate in human plasma if an individual were to go from a meat-containing diet to a vegetarian diet?
If mevalonate labeled with 14C in the carboxyl carbon were administered to rats, which carbons of cholesterol would become labeled?
Identify a pathway for utilization of the four carbons of acetoacetate in cholesterol biosynthesis. Carry your pathway as far as the rate-determining reaction in cholesterol biosynthesis.
Thyroid-stimulating hormone (TSH) has been shown to stimulate cholesterol synthesis in liver. Zhang et al, in J. Lipid Res. (2105) 56, 963–971 investigated the mechanism of this effect by treating
Explain why a deficiency of steroid 21-hydroxylase leads to excessive production of sex steroids (androgens and estrogens).
On your way to class this morning, you stop at your favorite coffeehouse and grab a caffé mocha and a blueberry scone. The caffé mocha contains 260 Calories and the scone contains 460
What proportion of the total energy consumption supports brain function in an average resting human? What proportion in a human running in a marathon?
Adipose tissue cannot resynthesize triacylglycerols from glycerol released during lipolysis (fat breakdown). Why not? Describe the metabolic route that is used to generate a glycerol compound for
The action of glucagon on liver cells leads to inhibition of pyruvate kinase. What is the most probable mechanism for this effect?
Pancreatic b cells secrete insulin in response to increased blood glucose. This process requires the catabolism of glucose to pyruvate via glycolysis, producing ATP. which initiates the exocytosis of
Identify the most likely additional substrates, products, and coenzymes for each reaction in the following imaginary pathway.
Lysine degradation requires removal of two amino groups. Removal of its e-amino group gives a-aminoadipic semialdehyde. This product is then degraded to acetoacetate by the same chemical strategy
Although proteins differ in nitrogen content because of differences in their amino acid compositions, the N content of protein in a typical Western diet averages 16% (w/w). Using this average value,
Proline betaine is a putative osmoprotectant in plants and bacteria, helping to prevent dehydration of cells. + Coo "N CH3 CH3
A clinical test sometimes used to diagnose folate deficiency or B12 deficiency is a histidine tolerance test, where one injects a large dose of histidine into the bloodstream and then carries out a
Most bacterial mutants that require isoleucine for growth also require valine. Why? Which enzyme or reaction would be defective in a mutant requiring only isoleucine (not valine) for growth?
Propose a mechanism for the TPP-dependent step in isoleucine biosynthesis (see Figure 18.20). Draw the predicted product of this reaction.Figure 18.20. Isoleucine Threonine Serine-threonine
Why is phenylketonuria resulting from dihydropteridine reductase deficiency a more serious disorder than PKU resulting from phenylalanine hydroxylase deficiency?
Identify each reaction catalyzed by (a) A nucleotidase; (b) A phosphorylase; (c) A phosphoribosyltransferase. Guanine A B GMP E F LL D C Guanosine
Adenine phosphoribosyltransferase converts adenine to AMP. If you were to determine whether a similar reaction converts adenine directly to dAMP, what metabolite would you need to find in cells at
The text states that ATP is synthesized primarily by energy metabolism, whereas other nucleoside triphosphates are formed from the action of nucleoside diphosphate kinase. What additional pathway
Oxidation of DNA bases is mutagenic. An oxidized form of guanine, 8-oxoguanine, can base-pair with adenine, leading to errors in DNA replication. A gene called mutT acts to minimize the tendency of
Gemcitabine is a deoxycytidine analog used in treating pancreatic and ovarian cancer. The drug requires metabolic activation after uptake into cells. Speculate on the pathway for activation and the
The paper cited in References by Franzolin et al. (2013) presents evidence that dNTP pool sizes are controlled not only at the level of dNTP synthesis (RNR), but also at the level of dNTP breakdown,
Write a balanced equation for the hydrolysis of cGMP, catalyzed by cGMP phosphodiesterase. Would you expect an inhibitor of this enzyme to potentiate or antagonize the action of Viagra? Explain.
In early studies of adrenergic signaling, it was thought that the epinephrine receptor and adenylate cyclase were one and the same protein. What kind of evidence would prove otherwise?
Pertussis toxin ADP ribosylates the a subunit of Gi . How would you expect this toxin to affect blood pressure?
Explain the effectiveness of Gleevec in treating chronic myelogenous leukemia.
Of the restriction enzymes listed in Table 21.3, which enzymes generate flush, or blunt-ended, fragments? Of those that recognize offset sites and generate staggered cuts, which of these cuts cannot
How did analysis of the mechanism of chymotrypsin action help lead to understanding of the action of the paralytic action of the nerve poison Sarin? -P. F Sarin
Herceptin is an antibody that is used to treat certain forms of breast cancer by binding to a class of estrogen receptors. What is the basis for its effectiveness in treating certain forms of breast
Refer to Figure 19.22 (page 632), which describes the base modifications of bacteriophage T4 DNA, and briefly describe some issues that must be dealt with in preparing a restriction map of T4
Huntington’s disease is a hereditary central nervous system disorder characterized by tandem repeats of the sequence 5′-CAG-3′ in the gene that encodes a protein called huntingtin. The disease
The restriction endonuclease NotI recognizes the octanucleotide sequence GCGGCCGC. Calculate the expected number of NotI cleavage sites in the bacteriophage λ genome, a linear DNA duplex 48.5 kbp in
A major difficulty in preparing vaccines against viral diseases is the rapidity with which the virus mutates to vaccine resistance. What is the likely mechanism for this hypermutability? Would you
Bacteriophage T4 mutants defective in genetic recombination usually show defective DNA replication as well. What specific defect might you expect to see? Describe a plausible explanation for this
Before about 1960 it wasn’t clear whether both replicating DNA strands were extended in the same fork. Did the Cairns experiment (Figure 22.1) shed light on this question? Why or why not?Figure
Homologous recombination in E. coli forms heteroduplex regions of DNA containing mismatched bases. Why are these mismatches not eliminated by the mismatch repair system?
Analysis of p53 gene mutations in human tumors shows that a large proportion of these mutations involve GC → AT transitions originating at sites of DNA methylation. Propose a model to explain
Write a balanced equation for the hydrolytic deamination of a DNA 5-methylcytosine residue.
A mammalian cell line was cultured for many generations in the presence of methotrexate, whose concentration in the culture medium was steadily increased. After maximum resistance to methotrexate had
Consider the two processes involved in repairing double-strand DNA breaks. Which process—homologous recombination or NHEJ—is more likely to restore the original gene sequences and why?
Introns in protein-coding genes of some eukaryotes are rarely shorter than 65 nucleotides long. What might be a rationale for this limitation?
Heparin is a polyanionic polysaccharide that blocks initiation by RNA polymerase by virtue of its binding to double-stranded DNA. But heparin inhibits only when added before the onset of
Is RNA polymerase saturated with substrates in vivo? Describe experiments that might indicate whether RNA polymerase is operating at Vmax with respect to its nucleotide substrates.
Briefly explain why RNA-seq gives more information about the transcriptome than does microarray analysis. Read Tools of Biochemistry 24A before answering this question.
Why does it make biological sense for RNA synthesis in vivo to be less accurate than DNA synthesis?
The antibacterial protein colicin E3 is an effective inhibitor of protein synthesis in bacteria. This protein is a nuclease, specifically attacking a phosphodiester bond near the 3′ end of the 16S
The earliest work on the genetic code established UUU, CCC, and AAA as the codons for Phe, Pro, and Lys, respectively. Can you think of a reason why polyG was not used as a translation template in
Ribosomal proteins have high pI values. Why is this advantageous for ribosome stability?
The 5′ sequence for the mRNA for E. coli ribosomal L10 protein is shown below. Identify the Shine–Dalgarno sequence and the initiator codon. 5′¬CUACCAGGAGCAAAGCUAAUGGCUUUA¬3′
Chaperones are generally thought to facilitate protein folding. What additional functions do mitochondrial chaperones perform?
A nonsense mutation is a substitution mutation that creates a chain-terminating codon in the mRNA corresponding to the mutant gene. Identify three substitution mutations that could change a
A nonsense codon can be suppressed. Suppression is a mutation at an unlinked site that restores wild-type function at the mutant site without changing the original mutation. Suppression of nonsense
Is attenuation likely to be involved in eukaryotic gene regulation? Briefly explain your answer.
A lac operon containing one mutation was cloned into a plasmid, which was introduced by transformation into a bacterium containing a wild-type lac operon. The three genes of the chromosomal operon
What condition must be fulfilled in order for histone modification to be considered an epigenetic phenomenon? Does DNA methylation meet that criterion? Explain.

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