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fundamentals of biochemistry
Questions and Answers of
Fundamentals Of Biochemistry
Are the following lipid samples likely to correspond to the inner or outer leaflet of a eukaryotic plasma membrane?(a) 20% phosphatidylcholine, 15% phosphatidylserine, 65% other lipids.(b) 35%
In order to consume and dispose of dying cells, macrophages (amoebalike white blood cells) recognize phosphatidylserine (PS) on the outer surface of the target cell. Why is PS a useful marker of a
Lipids known as sulfatides occur in cells of the central nervous system. To which class of lipid does the sulfatide shown below belong? How does it differ from a typical member of that class?
E. coli outer membranes include a component known as Lipid A, shown here. Identify its saccharide and fatty acid constituents. HO HO HO NH HO - 0 - NH 0- HO HO
In some autoimmune diseases, an individual develops antibodies that recognize cell constituents such as DNA and phospholipids. Some of the antibodies react with both DNA and phospholipids. What is
Archaebacteria and Eubacteria produce different types of membrane lipids. How does the archaeal lipid shown here differ from phosphatidylglycerol? HO HO
Most hormones, such as peptide hormones, exert their effects by binding to cell-surface receptors. However, steroid hormones do so by binding to cytosolic receptors. How is this possible?
Shigella bacteria cause severe diarrhea by altering the metabolism of intestinal cells. Explain why a Shigella enzyme that cleaves polypeptide backbones next to N-terminal Gly residues could alter
The inner membranes of mitochondria are rich in cardiolipin; when the organelle is damaged, cardiolipin appears in the outer membrane, where it is recognized by a cytosolic protein. Why does the
Describe the labeling pattern of glycophorin A when a membrane- impermeable protein-labeling reagent is added to(a) A preparation of solubilized erythrocyte proteins;(b) Intact erythrocyte ghosts;(c)
Identify a 20-residue segment that could form a transmembrane α helix in this protein sequence (from the mosquito protein Orco).FRYVNGPVLIRKLYSWWNLIMILLQYFAIMGNLVMNTGDVNELTANTITT
Macropinocytosis is a variation of endocytosis in which cells take up large amounts of extracellular fluid, which accumulates in intracellular vesicles. The drug vacquinol stimulates macropinocytosis
Explain why the action of phospholipase A2 on membrane lipids could affect the lipid bilayer changes that occur during endocytosis or exocytosis.
The symmetries of oligomeric integral proteins are constrained by the requirement that their subunits must all have the same orientation with respect to the plane of the membrane. What symmetries can
Rank the rate of transmembrane diffusion of the following compounds: 0 CH,CNH, A. Acetamide O CHgCH,CH,CNH, B. Butyramide O || HN-C-NH C. Urea
(a) Individuals with a certain one of the ABO blood types are said to be “universal donors,” whereas those with another type are said to be “universal recipients.” What are these blood types?
Indicate whether the following compounds are likely to cross a membrane by nonmediated or mediated transport:(a) Ethanol,(b) Glycine,(c) Cholesterol,(d) ATP.
The smallest β-barrel protein contains only eight β strands. Explain why porins, which are also β barrels, usually contain at least 16 or 18 strands.
Which amino acids would you expect to be particularly abundant at the entrance of a porin that is specific for phosphate ions?
If a reaction has a ΔG°′ value of at least −30.5 kJ · mol−1, sufficient to drive the synthesis of ATP (ΔG°′ = 30.5 kJ ·mol−1), can it still drive the synthesis of ATP in vivo when its
E. coli cells transport xylose across the cell membrane via a symport system that uses the free energy of a proton gradient. The intracellular pH is higher than the extracellular pH.(a) Is xylose
What happens to K+ transport by valinomycin when the membrane is cooled below its transition temperature?
Most animals have neurons that respond to unfavorable environmental conditions by sending pain signals to the brain. For example, elevated [CO2] triggers an influx of Na+ that opens voltage-gated Na+
Scorpion toxin triggers an action potential in pain-sensing neurons in animals by binding to a specific receptor. The toxin also acts to delay the inactivation of the neurons’ voltage-gated Na+
Choose the best description of an enzyme:(a) It allows a chemical reaction to proceed extremely fast.(b) It increases the rate at which a chemical reaction approaches equilibrium relative to its
Which type of enzyme catalyzes the following reactions? (a) COO H-C-CH3 NH (b) COO- T C=O + H+ CH3 HC-C-H NH H COO C=0+0=C=0 1 CH3
Which type of enzyme catalyzes the following reactions? (a) COO (b) CONADH + H+ CH3 COO COO HO-C-H + NAD* COO H-C(CH)2 C + ATP + NH+ NH H-C-(CH)2 C NH3 CH3 NH + ADP + Pi
Approximately how much does staphylococcal nuclease decrease the activation free energy ΔG‡ of its reaction (the hydrolysis of a phosphodiester bond) at 25°C?
Calculate the rate enhancement that could be accomplished by an enzyme forming one low-barrier hydrogen bond with its transition state at 25°C. Rate 40 Temperature (C) 20
Studies at different pH’s show that an enzyme has two catalytically important residues whose pKs are ∼4 and ∼10. Chemical modification experiments indicate that a Glu and a Lys residue are
Explain why RNase A cannot catalyze the hydrolysis of DNA.
Predict the effect of mutating Asp 102 of trypsin to Asn(a) On substrate binding(b) On catalysis.
Lysozyme residues Asp 101 and Arg 114 are required for efficient catalysis, although they are located at some distance from the active site Glu 35 and Asp 52. Substituting Ala for either Asp 101 or
Predict the effect on lysozyme’s activity of mutating Glu 35 to Asp and Asp 52 to Glu.
Under certain conditions, peptide bond formation rather than peptide bond hydrolysis is thermodynamically favorable. Would you expect chymotrypsin to catalyze peptide bond formation? Explain.
Identify the enzymes in Table 12-1 whose catalytic efficiencies are near the diffusion-controlled limit.Table 12-1 Enzyme Acetylcholinesterase Carbonic anhydrase Catalase Chymotrypsin Fumarase Urease
Hemophiliacs who lack factor IX are sometimes given infusions of factor VII to restore normal blood clotting activity. Explain.
The hypothetical elementary reaction 2A → B + C has a rate constant of 10−6 M−1 ∙ s−1. What is the reaction velocity when the concentration of A is 10 mM?
If there is 10 μmol of the radioactive isotope 32P (half-life 14 days) at t = 0, how much 32P will remain at(a) 7 days(b) 14 days(c) 21 days,(d) 70 days?
The KM for the reaction of chymotrypsin with N-acetyl valine ethyl ester is 8.8 × 10−2 M, and the KM for the reaction of chymotrypsin with N-acetyl tyrosine ethyl ester is 6.6 × 10−4 M.(a)
In a bisubstrate reaction, a small amount of the first product P is isotopically labeled (P*) and added to the enzyme and the first substrate A. No B or Q is present. Will A (= P—X) become
Molecule A is the substrate for enzyme X. Which is more likely to be a competitive inhibitor of enzyme X: molecule B or molecule C? Explain. cao HC-C-COO A HC-C-CH3 B HC-C-0- -NO
In a bisubstrate reaction, a small amount of the first product P is isotopically labeled (P*) and added to the enzyme and the first substrate A. No B or Q is present. Will A (= P—X) become
How would diisopropylphosphofluoridate affect the apparent KM and Vmax of a sample of chymotrypsin?
Estimate KI for a competitive inhibitor when [I] = 5 mM gives an apparent value of KM that is three times the KM for the uninhibited reaction.
Is it necessary to know [E]T to determine(a) KM,(b) Vmax(c) kcat?
Enzyme X and enzyme Y catalyze the same reaction and exhibit the νo versus [S] curves shown below. Which enzyme is more efficient at low [S]? Which is more efficient at high [S]? Vo [S] Enzyme X
You are attempting to determine KM by measuring the reaction velocity at different substrate concentrations, but you do not realize that the substrate tends to precipitate under the experimental
Sphingosine-1-phosphate (S1P) is important for cell survival. The synthesis of S1P from sphingosine and ATP is catalyzed by the enzyme sphingosine kinase. An understanding of the kinetics of the
For an enzyme-catalyzed reaction, the presence of 5 nM of a reversible inhibitor yields a Vmax value that is 80% of the value in the absence of the inhibitor. The KM value is unchanged.(a) What type
Ethanol in the body is oxidized to acetaldehyde (CH3CHO) by liver alcohol dehydrogenase (LADH). Other alcohols are also oxidized by LADH. For example, methanol CH3OH), which is mildly intoxicating,
Why are uncompetitive and mixed inhibitors generally considered to be more effective in vivo than competitive inhibitors?
Would the pancreatic hormone somatostatin require a receptor on the surface of or in the cytosol of a target cell?
The anabolic steroid methandrostenolone is shown here.(a) How does it differ structurally from testosterone?(b) Why might such drugs be administered to burn victims? H3C H3C H3C
Retinoic acid is a hormone that mediates immune system function. Would retinoic acid require a receptor on the surface of a target cell?
What biochemical changes are required to convert tyrosine to(a) Norepinephrine(b) Epinephrine?
Some bacterial signaling systems involve kinases that transfer a phosphoryl group to a His side chain. Draw the phospho-His side chain.
Why might a compound resembling ADP function as an inhibitor of a protein kinase?
A growth factor that acts through a receptor tyrosine kinase stimulates cell division. Predict the effect of a viral protein that inhibits the corresponding protein tyrosine phosphatase.
How does the presence of the poorly hydrolyzable GTP analog GTPγS (in which an O atom on the terminal phosphate is replaced by an S atom) affect cAMP production by adenylate cyclase?
One of the toxins produced by Bacillus anthracis (the cause of anthrax) is known as EF, or edema factor (edema is the abnormal buildup of extracellular fluid). EF, which enters mammalian host cells,
Another B. anthracis toxin is lethal factor, LF, a protease that cleaves members of the MAPK kinase family so that they cannot bind to their downstream MAPK targets in white blood cells. Explain how
Diacylglycerol is a substrate for the enzyme diacylglycerol kinase. What is the product of this reaction?
Predict the effect on cell growth of an Sos mutation that decreased its affinity for Ras.
Phosphatidylethanolamine and PIP2 containing identical fatty acyl residues can be hydrolyzed with the same efficiency by a certain phospholipase C. Will the hydrolysis products of the two lipids have
The white blood cells known as T lymphocytes respond to antigens that bind specifically to the T cell receptor, which consists of an antigen-binding αβ transmembrane protein as well as a set of
The diagnosis of some lymphomas (blood cell cancers) includes cytogenetic analysis, which involves examining a patient’s cells for chromosomal abnormalities. Chromosomes are visible by light
Explain why a heterotrophic organism may require vitamins, whereas an autotroph does not.
Rank the following compounds in order of increasing oxidation state. OH HC-CH-CHOH A -OOC-CH-COO- B HCCH,CH3 HC-CH=CH HC-C-COO- C D E
A strain of bacteria isolated from an alkaline lake with a high concentration of arsenic is able to incorporate As into biological molecules. What class of molecules is most likely to contain As as
In the partial reactions shown below, is the reactant undergoing oxidation or reduction? (a) COO- CH C=0 T COO (b) COO CH CH-OH 1 COO COO T CH T CH-OH T COO COO T CH || CH 1 COO
Explain why cadmium and mercury are toxic to most organisms.
Use the data in Table 2-4 to estimate the net charge of an ATP molecule in vivo.Table 2-4 Acid Oxalic acid HPO4 Formic acid Succinic acid Oxalate Acetic acid Succinate 2-(N-Morpholino)ethanesulfonic
Choose the best definition for a near-equilibrium reaction:(a) Always operates with a favorable free energy change.(b) Has a free energy change near zero.(c) Is usually a control point in a metabolic
Assuming 100% efficiency of energy conservation, how many moles of ATP can be synthesized under standard conditions by the complete oxidation of 1 mol of glucose?
The reaction for “activation” of a fatty acid (RCOO−),
Assuming 100% efficiency of energy conservation, how many moles of ATP can be synthesized under standard conditions by the complete oxidation of 1 mol of palmitate?
Biochemists studying cellular activity can quantify RNA sequences by converting them to DNA sequences that can be amplified via PCR, and they can quantify proteins by engineering the corresponding
Researchers have noted that different patients respond differently to the cholesterol-lowering statin drugs. They have attempted to link the adverse side effects of drugs to genetic variations such
Does the magnitude of the free energy change for ATP hydrolysis increase or decrease as the pH increases from 5 to 6?
A certain metabolic pathway can be diagrammed aswhere A, B, C, and D are the intermediates, and X, Y, and Z are the enzymes that catalyze the reactions. The physiological free energy changes for the
Some proteins contain internal thioesters, which form when a Cys side chain condenses with a Gln side chain a few residues away. Draw this structure.
The thioester described in Problem 29 reacts readily with compounds with the formula ROH or RNH2. Draw the resulting ester and amide reaction products.Problem 29Some proteins contain internal
The reversible reaction shown here is part of the Calvin cycle, a pathway in photosynthetic organisms. Which glycolytic reaction does this reaction resemble and what type of enzyme catalyzes it?
In a mixture of NAD+, NADH, ubiquinone, and ubiquinol, which compound will be oxidized? Which will be reduced?
Why is it possible for the ΔG values in Table 15-1 to differ from the ΔG°′ values?
Step 4 of the pentose phosphate pathway converts ribulose-5- hosphate to ribose-5-phosphate. Which glycolytic reaction does this reaction resemble and what type of enzyme catalyzes it?
Identify the intermediate in the phosphoglucomutase reaction.
Although it is not the primary flux-control point for glycolysis, pyruvate kinase is subject to allosteric regulation. What is the metabolic importance of regulating flux through the pyruvate kinase
Tumor cells, which tend to grow rapidly, typically express high levels of the glycolytic enzymes. Explain the advantage of high glycolytic flux for these cells.
The pyruvate kinase isozyme in cancerous cells has low activity compared to the isozymes in other tissues. What effect would this have on the cells and how does it promote tumor growth?
Compare the ATP yield of three glucose molecules that enter glycolysis and are converted to pyruvate with that of three glucose molecules that proceed through the pentose phosphate pathway such that
If G6P is labeled at its C2 position, where will the label appear in the products of the pentose phosphate pathway?
Describe the lengths of the products of the transketolase reaction when the two substrates are both five-carbon sugars.
You combine 0.2 g of yeast, 0.2 g of sucrose and 10 mL of water, place the mixture inside an uninflated balloon, then tie off the opening of the balloon.(a) Explain what you would observe over the
Nerve cells require a source of free energy to transport vesicles containing neurotransmitters along the length of the axon, where mitochondria are scarce. Explain why it makes sense that
A proposed pathway for ascorbic acid (vitamin C) biosynthesis in plants takes the form D-glucose-6-phosphate D-fructose-6-phosphate D-mannose-6-phosphate D-mannose-1-phosphate 6 GDP-D-mannose
Explain why some tissues continue to produce CO2 in the presence of high concentrations of fluoride ion, which inhibits glycolysis.
For enzymes a–e in Problem 35, identify their closest counterparts.Problem 35A proposed pathway for ascorbic acid (vitamin C) biosynthesis in plants takes the form D-glucose-6-phosphate
The diameter of the KcsA K+ channel is ∼6 Å. Why can’t H2O (diameter 2.75 Å) pass through this channel?
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