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medical sciences
biochemistry

Biochemistry Concepts and Connections 1st edition Dean R. Appling, Spencer J. Anthony Cahill, Christopher K. Mathews - Solutions

Brieï¬‚y describe the mechanism(s) of these two types of photophosphorylation that explain all of these results.
Assume a pH gradient of 4.0 units across a thylakoid membrane, with the lumen more acidic than the stroma.(a) What is the standard free energy change per mol of protons associated with this gradient at 25o C? (b) What is the longest wavelength of light that could provide enough energy per photon to
Suppose a brief pulse of 14CO2 is taken up by a green plant. (a) Trace the 14C label through the steps leading to fructose-1, 6-bisphosphate synthesis, showing which carbon atoms in each com-pound should carry the label during the first cycle. (b) Will all molecules of fructose-1, 6-bisphosphate
The flux of solar energy reaching the Earth's surface is approximately 7 J / cm2. Assume that all of this energy is used by a green leaf (10 cm in area), with the maximal efficiency of 35%. How many moles of hexose could the leaf theoretically generate in an hour? Use 600 nm for an average
Suppose a researcher is carrying out studies in which she adds a non-physiological electron donor to a suspension of chloroplasts. Illumination of the chloroplasts yields oxidation of the donor. How could she tell whether photosystem I, II, or both are involved?
Calculate the ATP yield from oxidation of palmitic acid, taking into account the energy needed to activate the fatty acid and transport it into mitochondria. Do the same for stearic acid, linoleic acid, and oleic acid.
As low carbohydrate diets have had a dramatic popularity increase in the past decade, arguments have been made that glucose can be made from odd-chain fatty acids. Based on the metabolism of such molecules, what quantity of a C-19 fatty acid would be required to produce 1g of glucose? Considering
The following both link carbohydrate metabolism with lipid biosynthesis: (a) How many molecules of glucose are required to provide the carbon for the synthesis of one molecule of palmitate? (b) How many molecules of glucose are required if all of the glucose first proceeds through the pentose
Glucagon secretion causes inhibition of intracellular acetyl-CoA carboxylase activity by several mechanisms. Name all you can think of.
Identify and briefly discuss each mechanism ensuring against simultaneous fatty acid synthesis and oxidation in the same cell.
Describe the probable effect in adipocytes of insulin-stimulated uptake of glucose into these cells.
Phosphatidylserine (PS) is considered to be an intermediate in the biosynthesis of phosphatidylethanolamine (PE) in E. coli, yet PS is not found in appreciable amounts among E. coli membrane phospholipids. Because PS must be present in the membrane to serve as an intermediate, how might you explain
If palmitic acid is subjected to complete combustion in a bomb calorimeter, one can calculate a standard free energy of combustion of 9788 kJ/mol. From the ATP yield of palmitate oxidation, what is the metabolic efficiency of the biological oxidation, in terms of kilojoules saved as ATP per
Write a balanced equation for the synthesis of sn -1- stearoyl -2- oleoylglycerophosphorylserine, starting with glycerol, the fatty acids involved, and serine.
Which step in lipid metabolism would you expect to be affected by 3, 4- dihydroxybutyl-1-phosphonic acid (shown here)? Explain your answer.
Briefly describe how cyclic AMP controls phospholipid synthesis.
In the experiment shown below, fibroblasts obtained from a normal subject (closed symbols) or from a patient homozygous for familial hypercholester-olemia (FH Homozygote) (open symbols) were grown in monolayer cultures. At time zero, the medium was replaced with fresh medium depleted of
In addition to the pathway described in Figure 16.31, eukaryotes can also synthesize phosphatidylcholine and phosphatidylethanolamine, starting with free choline or ethanolamine, respectively. In this salvage pathway, the phosphodiester linkage in the glycerophospholipid is formed by activating the
During constant flight, hummingbirds expend about 2.9 kJ / hr, relying on fat oxidation as an energy source. (a) Calculate the gms of fat necessary to sustain a 20-hr nonstop flight. (b) If the birds relied on carbohydrate for this energy, how much additional weight would they have to start the
Write a balanced equation for the complete metabolic oxidation of each of the following. Include O2, ADP, and Pi as reactants and ATP, CO2, and H2O as products. (a) Stearic acid (b) Oleic acid (c) Palmitic acid (d) Linoleic acid
Calculate the number of ATPs generated from the metabolic oxidation of the four carbons of acetoacetyl-CoA to CO2. Now consider the homolog derived from oxidation of an odd-numbered carbon chain, namely propionoacetyl-CoA. Calculate the net ATP yield from oxidation of the five carbons of this
Under conditions where ketone bodies are being produced in the liver, how many ATPs can be produced from a molecule of palmitic acid if all resulting molecules of acetyl-CoA are converted into β-hydroxybutyrate?
Mammals cannot undergo net synthesis of carbohydrate from acetyl-CoA, but the carbons of acetyl-CoA can be incorporated into glucose and amino acids. Present pathways by which this could come about.
(a) Brieﬂy describes the relationship between intracellular malonyl-CoA levels in the liver and the control of ketogenesis. (b) Describe how the action of hexokinase IV helps the liver to buﬀer the level of blood glucose.
AMPK and mTOR can both be considered intracellular signal integrators. Explain this deﬁnition.
Marathon runners preparing for a race engage in "carb loading" to maximize their carbohydrate reserves. This involves eating large quantities of starchy foods. Why is starch preferable to candy or sugar-rich foods?
Supposing that an average human consumes energy at the rate of 1500 kcal/day at rest and that long-distance running consumes energy at 10 times that rate, how long would the glycogen reserves last during a marathon run?
Proteolysis increases during the early phases of fasting, but later it decreases as the body adapts to using alternative energy sources. Given that feedback control mechanisms have not been described for intracellular proteases, how might you explain these apparent changes in protease activity?
Shortly after a typical meal, your blood glucose will rise from its fasting level of 4.4 mM to 6.6 mM. (a) How many grams of glucose does this increase represent? (An average adult male weighing 70 kg has a blood volume of about 5 L.)(b) Estimate the change in velocity for the liver hexokinase
Glucose has been found to react non-enzymatically with hemoglobin, through Schiﬀ base formation between C-1 of glucose and the amino termini of the b chains. How might this ﬁnding be applied in monitoring diabetic patients?
Ketone bodies are exported from liver for use by other tissues. Because many tissues can synthesize ketone bodies, what enzymatic property of liver might contribute to its special ability to export these compounds?
Explain the basis for the following statement: As a coenzyme, pyridoxal phosphate is covalently bound to enzymes with which it functions, yet during catalysis the coenzyme is not covalently bound.
Suppose that you wanted to determine the metabolic half-life of glutamine synthetase in HeLa cells (a line of human tumor cells) growing in tissue culture. Describe how this could be done experimentally.
Folic acid is synthesized in bacteria as dihydrofolate, in a pathway starting from guanosine triphosphate. In this pathway, C-8 is lost as formate. From the structural similarities between guanine and pterin, predict which carbon and nitrogen atoms of GTP are the precursors to N-1, C-2, C-4, N-5,
Which folate structure (from the list below)(a) Is the substrate for the enzyme that is inhibited by methotrexate and trimethoprim?(b) Has the most highly oxidized one-carbon substituent?(c) Is used in the conversion of serine to glycine?(d) Transfers its one-carbon substituent to a B 12 coenzyme?
In bacteria much of the putrescine is synthesized, not from ornithine but from arginine, which decarboxylates to yield agmatine. Formulate a plausible pathway from arginine to putrescine, using this intermediate.
The mitochondrial form of carbamoyl phosphate synthetase is allosterically activated by N-acetylglutamate. Briefly describe a rationale for this effect.
Psilocybin is a hallucinogenic compound found in some mushrooms. Present a straight forward pathway for its biosynthesis from one of the aromatic amino acids.
One can identify phenylketonurics and PKU carriers (heterozygotes) by means of a phenylalanine tolerance test. One injects a large dose of phenylalanine into the bloodstream and measures its clearance from the blood by measuring serum phenylalanine levels at regular intervals. Sketch curves showing
(a) Formaldehyde reacts non enzymatically with tetrahydrofolate to generate 5,10-methylenetetrahydrofolate. [14C] Formaldehyde can be used to prepare serine labeled in the β-carbon. What else would be needed? (b) [14C] Serine, prepared as described above, is useful for many things, but you would
The following diagram shows the biosynthesis of B12 coenzymes, starting with the vitamin. DMB is dimethylbenzimidazole.(a) What one additional substrate or cofactor is required by enzyme B? (b) Genetic deficiency in animals of enzyme C would result in excessive urinary excretion of what
If oxidation of acetyl-CoA yields 10 ATPs per mole through the citric acid cycle, how many ATPs will be derived from the complete metabolic oxidation of 1 mole of alanine in a mammal? Would the corresponding energy yield in a fish be higher or lower? Why? How much energy would be derived from the
Proline betaine is a putative osmoprotectant in plants and bacteria, helping to prevent dehydration of cells.Propose a plausible pathway for biosynthesis of this compound.
The structure shown below is an intermediate in the synthesis of which biogenic amine? Use arrows to show how the next intermediate in this reaction is formed, and draw the structure of that intermediate.
Methyl-labeled [14C] methionine at a specific activity of 2.0 millicuries per millimole was injected into rats. Six hours later the rats were killed. Phosphatidylcholine was isolated from the liver and found to have a specific activity of 1.5 millicuries per millimole. Calculate the proportions of
Using the principles described in the text regarding pyridoxal phosphate mechanisms, propose a mechanism for the reaction catalyzed by serine hydroxymethyltransferase.
Use numbers 1 to 5 to identify each carbon atom in the product of this reaction. What coenzyme is involved?
The precise mechanism of ammonia toxicity to the brain is not known. Speculate on a possible mechanism, based on possible effects of ammonia on levels of key intermediates in energy generation.
Mutants of Neurospora crassa that lack carbamoyl phosphate synthetase I (CPS I) require arginine in the medium in order to grow, whereas mutants that lack carbamoyl-phosphate synthetase II (CPS II) require a pyrimidine, such as uracil. A priori, one would expect the active CPS II in the arginine
Indicate whether each of the following statements is true or false, and briefly explain your answer.(a) In general, the metabolic oxidation of protein in mammals is less efficient, in terms of energy conserved, than the metabolic oxidation of carbohydrate or fat. (b) Given that the nitrogen of
Write a series of balanced equations and a summary equation for the reactions of the glucosealanine cycle.
Consider the following questions about glutamate dehydrogenase. (a) The reaction as shown on page 569 has NH3 as a reactant, instead of NH4+, which is far more abundant at physiological pH. Why is NH3 preferred? (b) Glutamate dehydrogenase has a KM for ammonia (NH3) of ∼ 1 mM. However, at
As stated in the text, bacteriophages have been discovered with the following base substitutions in their DNA: (a) dUMP completely substituting for dTMP (b) 5-hydroxymethyl-dUMP completely substituting for dTMP (c) 5-methyl-dCMP completely substituting for dCMPFor any one of these cases,
6-Diazo-5-oxonorleucine (DON) irreversibly inhibits glutamine-dependent amidotransferases.(a) Which intermediate or intermediates in purine nucleotide biosynthesis would you expect to accumulate in DON-treated cells?(b) Which participants in pyrimidine synthesis?(c) Speculate on the mechanism by
Consider either the purinosome or a multifunctional protein such as the CAD protein, and propose one or two experiments to determine whether the enzyme "channels" substrates through a multistep reaction sequence.
Write balanced equations for the three known reactions that transfer an amino group to a substrate by condensation with aspartate to give an inter-mediate that then undergoes an α, β-elimination to give the product plus fumarate.
CTP synthetase catalyzes the glutamine-dependent conversion of UTP to CTP. The enzyme is allosterically inhibited by the product, CTP. Mammalian cells defective in this allosteric inhibition are found to have a complex phenotype: They require thymidine in the growth medium, they have unbalanced
The purino some contains enzymes that convert the serine hydroxymethyl group to the formyl group of 10-formyltetrahydrofolate. Write a balanced equation for each reaction in this conversion.
Sulfonamide drugs like sulfanilamide inhibit tetrahydrofolate biosynthesis. What intermediate or intermediates in purine synthesis would you expect to accumulate in sulfanilamide-treated bacteria? Suppose that a cultured mammalian cell line was treated with sulfanilamide? What intermediates might
The text describes a form of gout that results from HGPRT deficiency. Pro-pose one or two additional enzyme abnormalities that might similarly lead to hyperuricemia.
CTP synthetase is allosterically activated by GTP. What function might this play in the cell?
As stated in the text, adenosine deaminase deficiency can be treated by injection of the stabilized enzyme. Why might this treatment be effective, while injection of the missing enzyme is ineffective in other conditions, such as HGPRT deficiency or a deficiency of one of the mitochondrial
Consider the large number of therapeutically effective nucleoside analogs. Why do you suppose that these drugs are administered as nucleosides, rather than as nucleotides, which would be more readily converted to the active form of the drug?
In the pyrimidine degradative pathway, all pyrimidines undergo conversion to uracil, which undergoes an NADPH-dependent reduction. Show plausible reactions leading from cytidine, cytosine, and uridine to uracil, and write a plausible structure for the product of uracil reduction (dihydrouracil).
The text states that in E. coli ribo-nucleotide reductase Tyrosine-122 was identified as the source of the catalytically essential free radical. Describe experimental evidence that would support this conclusion.
Cell cultures can be synchronized, or brought into the same phase of the cell cycle, by various means. For example, adding thymidine to a cell culture causes all cells to become arrested early in S phase. What is the mechanism by which thymidine treatment blocks DNA replication?
Predict the effects of the following compounds on intracellular nucleoside triphosphate levels. For each answer, plot percent initial nucleotide level as a function of time after administration of the agent, for each of the four nucleotides (semi-quantitatively). Consider not only the primary
Radioactive uracil can be used to label all of the pyrimidine residues in DNA. Using either names or structures, present pathways for the conversion of uracil to dTTP and to dCTP for each reaction, show the involvement of cofactors, and identify sites of allosteric regulation.
Similarly, hypoxanthine (HX) can be used to label purine residues. As in Problem 4, write reactions showing the conversion of hypoxanthine to dATP and dGTP.
Leukemia is a neoplastic (cancerous) proliferation of white blood cells. Clinicians are currently testing deoxycoformycin, an adenosine deaminase inhibitor, as a possible antileukemic agent. Why might one expect this therapy to be effective?
The text states that a side effect of 5-fluorouracil therapy is its incorporation into RNA. Show pathways by which 5-fluorouracil could be converted both to FdUMP and to an immediate RNA precursor
A classic way to isolate thymidylate synthase negative mutants of bacteria is to treat a growing culture with thymidine and trimethoprim. Most of the cells are killed, and the survivors are greatly enriched in thymidylate synthase-negative mutants. (a) What phenotype would allow you to identify
As stated in Chapter 23, mammalian cells can become resistant to the lethal action of methotrexate by the selective survival of cells containing increases in dihydrofolate reductase gene copy number so that intracellular levels of the enzyme become very high. What other biochemical or genetic
Caﬀeine is an inhibitor of cyclic AMP phosphodiesterase. How would drinking several cups of coﬀee aﬀect muscle function? How might it aﬀect lipid metabolism?
Describe two features of insulin signaling that aﬀect glucose utilization. A b -adrenergic response can be modulated through the actions of a receptor kinase and arrestin, because phosphorylation by the kinase desensitizes the receptor. How might signaling by a tyrosine receptor kinase, such as
Suppose that a G protein undergoes a mutation that allows the exchange of bound GTP for GDP to occur in the absence of G protein binding to a receptor. How might this mutation aﬀect signaling involving a GPCR? Which subunit of the G protein is most likely aﬀected by the mutation?
Studies on cAMP actions in cultured cells usually involve adding to the cell culture not cAMP, but dibutyryl cAMP (see structure). Why is this structural modiï¬cation necessary? How could you test the premise that di-Bu-cAMP has the same biochemical eï¬€ects as cAMP?
Bisphenol A is widely used as a building block in polymer synthesis and is found in the polycarbonate hard plastics of reusable drink containers, DVDs, cell phones, and other consumer goods. Bisphenol A is reported to have estrogenic activity, and its widespread occurrence in our environment is a
Mutations that inactivate p53 have a recessive phenotype, whereas mutations aﬀecting Ras are dominant. Explain the diﬀerence.
GTP g S is a nonhydrolyzable analog of GTP. Suppose this compound were added to a cell-free system containing active components of an adrenergic signaling system. What consequences would you expect? What would be the eï¬€ects on cAMP levels?
Suppose that you had a monoclonal antibody that recognized phosphotyrosine. How would you expect that antibody to aﬀect insulin signaling?
List two or three factors that make it advantageous for peptide hormones to be synthesized as inactive prohormones that are activated by proteolytic cleavage
Describe a mechanism by which a steroid hormone might act to increase intracellular levels of cyclic AMP.
Signaling molecules interact with cells through speciﬁc macromolecular receptors. For each of the four receptors identiﬁed below, list all characteris-tics, by number, which accurately describe that receptor. (a) An adrenergic receptor ________ (b) A steroid receptor ____________ (c) Te LDL
Upon activation by a receptor, a G protein exchanges bound GDP for GTP, rather than phosphorylating GDP that is already bound. Similarly, the α subunit-GTP complex has a slow GTPase activity that hydrolyzes bound GTP, rather than exchanging it for GDP. Describe experimental evidence that would be
Answer each question in about one sentence:(a) What is the biochemical basis for the action of Viagra?(b) What is the biochemical basis for the action of Prozac?(c) Oral administration of S-adenosylmethionine has been reported to be eﬀective in treating depression. Suggest a possible explanation.
Lithium ion inhibits the synthesis of inositol trisphosphate by inhibiting a reaction in the breakdown of inositol trisphosphate. Explain this apparent paradox.
Suppose that you measured binding to the isolated EGF receptor of EGF at various concentrations. Would you expect the binding curve to be hyper-bolic? Explain your answer.
Te exponential nature of PCR allows spectacular increases in the abundance of a DNA sequence being ampliﬁed. Consider a 10-kbp DNA sequence in a genome of 1010 base pairs. What fraction of the genome is rep-resented by this sequence? That is, what is the fractional abundance of this sequence in
Suppose that you wished to determine the number of pseudogenes related to a particular gene in an organism whose complete genome had not yet been sequenced. How might you do this experimentally?
Some viruses, such as SV40, contain closed circular DNAs carrying nucleosomes. If the SV40 viral chromosome is treated with topoisomerase, and the histone is then removed, it is still supercoiled. If histones are removed before topoisomerase treatment, however, the DNA is relaxed. Explain.
Histone genes are unusual among eukaryotic genes because they do not have introns, and histone mRNAs do not have poly (A) tails (see Chapter 24). Moreover, in almost all eukaryotes, histone genes are arranged in multiple tandem domains, each domain carrying one copy of each of the ﬁve histone
Consider the l bacteriophage DNA molecule as shown in Figure 21.15. Total digestion with the two restriction endonucleases used does not allow unambiguous placement of restriction sites, as shown in the map. Describe restriction patterns-either from partial digestion or from digestion with both Bam
RFLPs can include sequence changes created by single-base change, single-base insertion, single-base deletion, or tetranucleotide repeat, as shown in Figure 21.21. For each polymorphism, show a speciï¬c sequence change that would alter the restriction fragmentation pattern at that
Why do you suppose that forensic DNA analysis relies principally on short tandem repeats (repeat polymorphisms), rather than single- nucleotide polymorphisms, such as that described on page 669 and in Figure 21.21
DNA methylation is considered an epigenetic phenomenon because the pattern of methylation can be inherited. Brieﬂy discuss the question of whether histone modiﬁcations in chromatin represent an epigenetic phenomenon.
DNA renaturation curves occasionally show three distinct phases of renaturation. In this graph, DNA renaturation is plotted against "C0t" (initial concentration times time of renaturation-essentially a measure of relative renaturation time). See Figure 21.4.(a) Identify each part of this plot that
The following diagram shows one-half of a restriction site.(a) Draw the other half.(b) Use heavy arrows (†‘†“) to identify type II cleavage sites that would yield blunt-ended duplex DNA products. (c) Use light arrows (†‘†“) to identify type II cleavage sites
pBR322 DNA (4.36 kb; see Figure 4A.3) was cleaved with Hind III nuclease and ligated to a Hind III digest of human mitochondrial DNA. One recombinant plasmid DNA was analyzed by gel electrophoresis of restriction cleavage fragments, with the following results: lane A = Eco RI-treated recombinant,
A small DNA molecule was cleaved with several diﬀerent restriction nucleases, and the size of each fragment was determined by gel electrophoresis. The following data were obtained. Enzyme Fragment Size (kb) Eco RI ................................. 1.3, 1.3 Hpa II

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