Questions and Answers of Fundamentals Of Biochemistry

What thermodynamic force drives the transport of ADP and Pi into the mitochondrial matrix for ATP synthesis?
Nicotinamide nucleotide transhydrogenase (NNT) in the inner mitochondrial membrane catalyzes the reaction NADH + NADP+ → NAD+ + NADPH to generate the NADPH needed for certain reactions that help
Activated neutrophils and macrophages (types of white blood cells) fight invading bacteria by releasing superoxide. These cells contain an NADPH oxidase that catalyzes the reactionExplain why flux
The anti diabetes drug metformin inhibits 3-phosphoglycerol dehydrogenase. How would this affect ATP production by mitochondria?
During dietary restriction, amino acids may be used as metabolic fuels. In this process, glutamate is converted by glutamate dehydrogenase to α-ketoglutarate. α-Ketoglutarate binds to the β
Is the information in Problem 37 consistent with the hypothesis that dietary restriction can slow the aging process?Problem 37During dietary restriction, amino acids may be used as metabolic fuels.
(a) A simplistic interpretation of the Q cycle would predict that the proton pumping efficiency of cytochrome bc1 would be reduced by no more than 50% in the presence of saturating amounts of
Certain unscrupulous operators offer, for a fee, to freeze recently deceased individuals in liquid nitrogen until medical science can cure the disease from which they died. What is the biochemical
Glucose binds to glycogen phosphorylase and competitively inhibits the enzyme. What is the physiological advantage of this?
Phosphoglucokinase catalyzes the phosphorylation of the C6-OH group of G1P. Why is this enzyme important for the normal function of phosphoglucomutase?
Glucose-6-phosphatase is located inside the endoplasmic reticulum. Describe the probable symptoms of a defect in G6P transport across the endoplasmic reticulum membrane.
Comparisons of wolf and dog DNA reveal that dogs have 4 to 30 amylase genes, whereas wolves have only 2. Why might additional amylase genes have played a role in the domestication of wolves (the
Some archaebacteria produce an enzyme with two active sites: one catalyzes the dephosphorylation of fructose-1,6-bisphosphate, and one catalyzes the condensation of dihydroxyacetone phosphate and
Indicate the energy yield or cost, in ATP equivalents, for the following processes:(a) glycogen (3 residues) → 6 pyruvate(b) 3 glucose → 6 pyruvate(c) 6 pyruvate → 3 glucose
Predict the effect of a fructose-1,6-bisphosphatase deficiency on blood glucose levels(a) Before(b) After a 24-hour fast.
Explain why an individual with a fructose-1,6-bisphosphatase deficiency would have elevated levels of pyruvate in the blood.
The growth of new blood vessels, called angiogenesis, can be triggered by anoxia (lack of oxygen) and involves the rapid proliferation of endothelial cells, which form the vessel walls. These cells
In angiogenic endothelial cells, pyruvate is converted to lactate (generating 2 ATP per glucose) rather than being completely oxidized (which would generate ~32 ATP by oxidative phosphorylation).
The cells that line the mammalian intestine produce glycoproteins with O-linked oligosaccharides. Some of the glycoproteins remain anchored to the cell surface and some are released into the
A mature glycogen particle typically has 12 tiers of branches with 2 branches per tier and 13 residues per branch. How many glucose residues are in such a particle?
The Vmax of muscle glycogen phosphorylase is much larger than that of the liver enzyme. Discuss the functional significance of this phenomenon.
List four possible metabolic fates for pyruvate in a mammalian cell. Indicate the type of reaction that occurs. What additional reaction occurs in yeast?
Explain why metabolic acidosis may result from the accumulation of some citric acid cycle intermediates.
Photosynthetic organisms use elaborate machinery to incorporate carbon (as CO2) into glyceraldehyde-3-phosphate, which is used to synthesize glucose for later metabolism. However, one carbon is lost
Does the pyruvate-formate lyase reaction described in Problem 7 lead to the production of ATP, as pyruvate processing to acetyl-CoA does?Data from in Problem 7Photosynthetic organisms use elaborate
Some human brain cancer cells contain a mutated form of isocitrate dehydrogenase that has lost its normal activity and instead catalyzes the NADP+-dependent reduction of the carbonyl group of
The compound you identified in Problem 9 resembles glutamate and might therefore competitively inhibit glutamate transamination. How would this affect citric acid cycle activity?Data from in problem
Malonate competes with succinate in the succinate dehydrogenase reaction. Explain why increasing the oxaloacetate concentration can overcome malonate inhibition.
What citric acid cycle intermediates would accumulate in the presence of malonate?
What is the ΔG°′ value for the portion of the citric acid cycle that converts malate and acetyl-CoA to citrate?
Explain why a deficiency of pyruvate carboxylase leads to lactic acidosis.
How would a deficiency of pyruvate dehydrogenase activity affect blood pH?
The first organisms on earth may have been chemoautotrophs in which the citric acid cycle operated in reverse to “fix” atmospheric CO2 in organic compounds. Complete a catalytic cycle that
In germ-free mice, which harbor no intestinal bacteria, the O-linked oligosaccharides of intestinal glycoproteins tend to lack a terminal fucose residue.(a) What enzyme is not produced in normal
Bacterial glutamate synthetase consists of 12 identical subunits arranged in two stacked rings of six subunits. How would you describe this protein’s symmetry?
What types of rotational symmetry are possible for a protein with(a) Four or(b) Six identical subunits?
Explain why Pro residues can occupy the N-terminal turn of an α helix.
Which of the peptides in Problem 23 is least likely to form a β strand? 23. Which of the following polypeptides is most likely to form an a helix? (a) CRAGNRKIVLETY (b) SEDNFGAPKSILW (c)
Helices can be described by the notation nm, where n is the number of residues per helical turn and m is the number of atoms, including H, in the ring that is closed by the hydrogen bond.(a) What is
Describe how each of the amino acid modifications shown in Fig. 4-14 would affect the pI of a peptide containing that modified amino acid residue.Figure 4-14 -PO- CH NH-CH-CO O-Phosphoserine 2 N1 3
Classify the following proteins as α, β, or α/β:(a) Grb2 (Fig. 13-9)Figure 13-9(b) Plastocyanin (Fig. 19-19)Figure 19-19 SH3-C C N SH2 SH3-N
In some proteins, the side-chain carboxylate carbon of an N-terminal glutamate residue reacts with the free amino group to form a pentagonal lactam, a cyclic structure containing a C=O group. Draw
Experiments in mice suggest that pyroglutamylation increases the rate of aggregation of amyloid-β protein. Propose an explanation for this observation.
Proteins in solution are often denatured if the solution is shaken violently enough to cause foaming. Indicate the mechanism of this process.
Given enough time, will all denatured proteins spontaneously renature?
The GroEL/ES cycle diagrammed in Fig. 6-45 circulates only in the clockwise direction. Explain the basis for this irreversibility in terms of the sequence of structural and binding changes in the
Describe the intra-and intermolecular bonds or interactions that are broken or retained when collagen is heated to produce gelatin.
The coat protein of tomato bushy stunt virus consists of 180 chemically identical subunits, each of which is composed of ∼386 amino acid residues. The probability that a wrong amino acid residue
Not all heat shock proteins are chaperones; some are proteins that facilitate the degradation rather than the refolding of other proteins. Explain why the rate of protein degradation would increase
Explain why β sheets are less likely to form than α helices during the earliest stages of protein folding.
Hemoglobin S homozygotes who are severely anemic often have elevated levels of BPG in their erythrocytes. Is this a beneficial effect?
The force generated by a muscle fiber increases as the sarcomere shortens but decreases at very short sarcomere lengths. Explain this observation. Force (% max.) 100 75 50 25 0 1 2 3 Sarcomere length
Is myosin a fibrous protein or a globular protein? Explain.
Rigor mortis, the stiffening of muscles after death, is caused by depletion of cellular ATP. Describe the molecular basis of rigor.
Antibodies are well suited for recognizing extracellular substances from invading bacteria and viruses. However, the immune system must also be able to respond to intracellular infections. Explain
Give the approximate molecular masses of an immunoglobulin G molecule analyzed by(a) Gel filtration chromatography,(b) SDS-PAGE,(c) SDS-PAGE in the presence of 2-mercaptoethanol.
Many fish produce a tetrameric IgM. If each H chain has a mass of 70 kD, each light chain has a mass of 25 kD, and each J chain has a mass of 15 kD, what is the approximate mass of the IgM molecule?
Explain why the variation in VL and VH domains of immunoglobulins is largely confined to the hypervariable loops.
How many hypervariable loops are present in(a) IgG(b) IgM?
What is the likely range of the Hill constant for the hemoglobin described in Problem 23?Data from in Problem 23Some primitive animals have a hemoglobin that consists of two identical subunits.
An anemic individual, whose blood has only half the normal Hb content, may appear to be in good health. Yet a normal individual is incapacitated by exposure to sufficient carbon monoxide to occupy
Why do antibodies raised against a native protein sometimes fail to bind to the corresponding denatured protein?
How many stereoisomers are possible for(a) A ketopentose,(b) A ketohexose,(c) A ketoheptose?
Are(a) D-glucitol,(b) D-galactitol,(c) D-glycerol optically active?
Which of the following pairs of sugars are epimers of each other?(a) D-sorbose and D-psicose(b) D-sorbose and D-fructose(c) D-erythrose and D-arabinose
Which of the following pairs of sugars are epimers of each other?(a) D-fructose and L-fructose(b) D-arabinose and D-ribose(c) D-ribose and D-ribulose
Some bacteria produce thiosugars, which contain a C—S covalent bond, such as 2-deoxy-2-thio-β-D-glucose. Draw the structure of this sugar.
The metabolism of monosaccharides yields phosphorylated sugars such as β-D-fructose-6-phosphate. Draw its structure.
Identify the monosaccharides and their linkages in the following disaccharide. HOCH2 HO H OH H -O-CH2 H HO HO OH CHOH
The sucrose substitute tagatose is produced by hydrolyzing lactose and then chemically converting one of the two resulting aldoses to a ketose. Which residue of lactose gives rise to tagatose?
What type of sugar derivative is rhamnose?
How many reducing ends are in a molecule of glycogen that contains 10,000 residues with a branch every 10 residues?
Is amylose or amylopectin more likely to be a long-term storage polysaccharide in plants?
The core of pectin molecules is a polymer of α(1→4)-linked Dgalacturonate. Draw one of its residues.
Calculate the net charge of a chondroitin-4-sulfate molecule containing 100 disaccharide units.
Basic fibroblast growth factor binds to glycosaminoglycans in the extracellular matrix. Which amino acids would you expect to be abundant in this protein?
Draw the structure of the O-type oligosaccharide (the H antigen, described in Table 8-1). TABLE 8-1 Structures of the A, B, and H Antigenic Determinants in Erythrocytes H A B Antigen
In certain situations, a glycosyltransferase catalyzes the addition of a GlcNAc group to an arginine residue in a protein. Draw the structure of the modifi ed arginine side chain.
A protein that fails to fold properly in the endoplasmic reticulum may undergo O-mannosylation. Draw the structure of the resulting modified amino acid residue.
How many different disaccharides of D-glucopyranose are possible?
In addition to lactose, how many other heterodisaccharides can Dgalactose and D-glucose form?
Brown algae produce alginate, a polysaccharide containing β-Dmannuronate linked 1→4 to its C5 epimer α-L-guluronate. Draw the structure of an alginate disaccharide.
Human milk contains the oligosaccharide 2′-fucosyllactose (α-Lfucose-(1→2)-β-D-galactose-(1→4)-D-glucose), which may help protect the newborn from bacterial infections. Draw the structure of
The peptidoglycan cell walls of bacteria contain pores that allow the passage of substances with diameters less than 200 Å. Why is it important that the cell wall be porous rather than solid?
The enzyme β-amylase cleaves successive maltose units (maltose is an α(1→4)-linked glucose disaccharide) from the nonreducing end of α(1→4) glucans (polysaccharides containing only glucose
One demonstration of P.T. Barnum’s maxim that there’s a sucker born every minute is that new “reducing aids” regularly appear on the market. An eat-all-you-want nostrum, which was touted as a
Name this lipid. H3C(CH2)5CH ||| CH(CH)7 -0 CH -CH || -(CH2)12CH3 0 COO CH-O-P-0-CH-CH NH
Which of the glycerophospholipid head groups listed in Table 9-2 can form hydrogen bonds?Table 9-2 Name of X-OH Water Ethanolamine Choline Serine myo-Inositol Glycerol Phosphatidy Iglycerol HO R -H
Does trans-oleic acid have a higher or lower melting point than cis-oleic acid? Explain.
Which triacylglycerol yields more energy on oxidation: one containing three residues of linolenic acid or three residues of stearic acid?
Identify the hormone molecule shown here. What membrane lipid is it derived from? HO-P- 0- HN OH
Does the phosphatidylglycerol “head group” of cardiolipin project out of a lipid bilayer like other glycerophospholipid head groups?
Draw the structure of the fatty acid amide that forms when arachidonate is linked to ethanolamine.
Animals cannot synthesize linoleic acid (a precursor of arachidonic acid) and therefore must obtain this essential fatty acid from their diet. Explain why cultured animal cells can survive in the
Many bacterial fatty acids contain branches and even rings. What effect do these lipids have on membrane fluidity, compared to their straight-chain counterparts?
Why can’t triacylglycerols be significant components of lipid bilayers?
Why would a bilayer containing only gangliosides be unstable?
When bacteria growing at 20°C are warmed to 30°C, are they more likely to synthesize membrane lipids with(a) Saturated or unsaturated fatty acids,(b) Short-chain or long-chain fatty acids? Explain.
Do membranes of the Antarctic icefish have longer and/or more saturated fatty acids compared to tropical fish? Explain.
The distance between successive Cα atoms in a β sheet is ∼3.5 Å. Can a single 9-residue segment with a β conformation serve as the transmembrane portion of an integral membrane protein?

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