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medical sciences
biochemistry

Questions and Answers of Biochemistry

Why is it somewhat misleading to study biochemical pathways separately?
What is the Warburg effect? Why would cancer cells favor such inefficient metabolism?
To what extent can metabolic pathways be considered reversible? Why?
In eukaryotic cells, metabolic pathways occur in specific locations, such as the mitochondrion or the cytosol. What sort of transport processes are required as a result?
If suppose a chloride ion and a sodium ion are separated by a center-center distance of 5 Å. Is the interaction energy (the energy required to pull them inﬁnitely far apart) predicted to be larger
A 500-mL sample of a 0.100 M formate buﬀer, pH 3.75, is treated with 5 mL of 1.00 M KOH. What is the pH following this addition?
Describe the preparation of 2.00 L of 0.100 M glycine buﬀer, pH 9.0, from glycine and 1.00 M NaOH. What mass of glycine is required, and what volume of 1.00 NaOH is required? Te appropriate pKa of
Carbon dioxide is dissolved in blood (pH 7.4) to form a mixture of carbonic acid and bicarbonate. Neglecting free CO2, what fraction will be present as carbonic acid? Would you expect a signiﬁcant
What is the molecular basis for the observation that the overall charge on a protein becomes increasingly positive as pH drops and more negative as pH increases?
Te amino acid arginine ionizes according to the following scheme:(a) Calculate the isoelectric point of arginine. You can neglect contributions from form I. Why?(b) Calculate the average charge on
It is possible to make a buï¬€er that functions well near pH 7 using citric acid, which contains only carboxylate groups. Explain.Citric acid
A student is carrying out a biological preparation that requires 1 M NaCl to maintain an ionic strength of 1.0. Te student chooses to use 1.0 M ammonium sulfate instead. Why is this a serious error?
Histidine is an amino acid with three titratable groups: an - NH3+ group (pKa = 9.2), a -COOH group 1 (pKa = 1.8), and an imidazole (amine-like) group 1 (pKa = 6.0). Te titration curve for histidine
Te activity of an enzyme requires a glutamic acid to display its - COOH functional group in the protonated state. Suppose the pKa of the - COOH group is 4.07a. Will the enzyme be more active at pH
Draw two diﬀerent possible hydrogen-bonding interactions between two molecules of form amide (HCONH2). Clearly label the hydrogen-bond donor and acceptor atoms. Which of these two possible
What is the optimum pH to separate a mixture of lysine, arginine, and cysteine using electrophoresis? Draw the structures of the three amino acids in the protonation state that would predominate at
Suppose you have two genetic variants of a large protein that diﬀer only in that one contains a histidine (side chain pKa = 6.0) when the other has a valine (uncharged side chain).a. Which would be
The accompanying graph depicts the interaction energy between two water molecules situated so that their dipole moments are parallel and pointing in the same direction. Sketch an approximate curve
What is the pH of each of the following solutions?a. 0.35 M hydrochloric acib. 0.35 M acetic acidc. 0.035 M acetic acidd. Explain the diﬀerences in the pH values between the solutions in parts a-c.
a. Calculate the pH of a 1M NH4Cl solution. (see Figure 2.19).In Figure 2.19b. Calculate the pH of the solution that results following addition of 10 mL of 1 M NaOH to 40 mL of 1M NH4 Cl.c.
Te weak acid HA is 2% ionized (dissociated) in a 0.20 M solution.a. What is Ka for this acidb. What is the pH of this solution?
Calculate the pH values and draw the titration curve for the titration of 500 mL of 0.010 M acetic acid (pKa 4.76) with 0.010 M KOH.
What is the pH of the following buﬀer mixtures? a. 100 mL 1 M acetic acid plus 100 mL 0.5 M sodium acetate b. 250 mL 0.3 M phosphoric acid plus 250 mL 0.8 M KH2PO4
a. Suppose you wanted to make a buﬀer of exactly pH 7.00 using KH2PO4 and Na2HPO4. If the ﬁnal solution was 0.1 M in KH2PO4 , what concen-tration of Na2 HPO4 would you need b. Now assume you wish
Te process of a protein folding from an inactive unfolded structure to the active folded structure can be represented by the following equation:Te values of ˆ†Ho and ˆ†So for the folding of the
Suppose a reaction has ˆ†Ho and ˆ†So values independent of temperature (i.e., assume these values are constant over some range of temperature). Show from this, and equations given in this
Te following data give the ion product, Kw for water at various temperatures:To(C)Kw0 ....................... 1.14 Ã— 10-1o25 ....................... 1.00 Ã— 10-1430 .......................
The phosphate transfer potentials for glucose-1-phosphate and glucose-6-phosphate are 20.9 kJ / mol and 13.8 kJ / mol, respectively.a. What is the equilibrium constant for the reaction shown below at
Wheeler and Mathews (J. Biol. Chem . 287:31218-31222 (2012)) reported the NAD+ and NADH concentrations in yeast mitochondria as 20 mm and 0.3 mM, respectively. Consider the malate dehydrogenase
Undergoing moderate activity, an average person will generate about 350 kJ of heat per hour. Using the heat of combustion of palmitic acid (∆H = - 9977.6 kJ / mol) as an approximate value for fatty
The major difference between a protein molecule in its native state and in its denatured state lies in the number of conformations available. To a first approximation, the native, folded state can be
Suppose the concentration of glucose inside a cell is 0.1 mm and the cell is suspended in a glucose solution of 0.01 mm.a. What would be the free energy change involved in transporting 10-o mole of
For parts (a) and (b) of this problem, use the following standard reduction potentials, free energies, and nonequilibrium concentrations of reactants and products:ATP = 3.10 mMPi = 5. mM 5.90ADP =
Given the following reactions and their enthalpies:a. Devise a way to calculate ˆ†H for the reactionH2O(g) †’ 2H(g) + O(g)b. From this, estimate the H - O bond energy.
The decomposition of crystalline N2O5N2O5(s) → 2NO2(g) + 1/2 O2(g) is an example of a reaction that is thermodynamically favored even though it absorbs heat. At 25°C we have the following values
Te oxidation of glucose to CO2 and water is a major source of energy in aerobic organisms. It is a reaction favored mainly by a large negative en-thalpy change.a. At 37°C, what is the value for
The first reaction in glycolysis is the phosphorylation of glucose:This is a thermodynamically unfavorable process, with ˆ†Go€² = + 13.8 kJ/mol.a. In a liver cell at 37°C the concentrations of
In another key reaction in glycolysis, dihydroxyacetone phosphate (DHAP) is isomerized into glyceraldehyde-3-phosphate (GAP):Because ˆ†Go€² is positive, the equilibrium lies to the lef.a.
Assume that some protein molecule, in its folded native state, has one favored conformation. But when it is denatured, it becomes a "random coil," with many possible conformations.a. What must be the
It is observed that as temperature is increased, most protein molecules go from their deﬁned, folded state into a random-coil, denatured state that exposes more hydrophobic surface area than is
Predict the structure of a cruciform that could be formed from this oligonucleotide.
DNA from a newly discovered virus was puriﬁed, and UV light absorption was followed as the molecule was slowly heated. Te absorbance increase at the melting temperature was only 10%. What does this
Te gel electrophoresis pattern in Figure 4.23 was determined by soaking the gel in a solution of ethidium bromide (EtBr). This is a ﬂuorescent molecule with a planar structure:Te ﬂat molecule
DNA polymerase requires both a template, to be copied, and a primer, which provides a 3€² hydroxyl from which polymerase can extend. Yet this molecule supports DNA polymerase activity.
Draw the gel electrophoretic pattern that would be seen in dideoxy sequence analysis oî€ the DNA molecule in Problem 10.In Problem 10
Early gene-cloning experiments involved insertion at one restriction site in the vector; for example, the insert would have an EcoRI site at each end, and the vector would be opened at an RI site
pppApCpCpUpApGpApU-OH a. Using the straight-chain sugar convention shown on page 77, write the structure of the DNA strand that encoded this short stretch of RNA. b. Using the simplest convention for
Shown is a representation of a DNA molecule being transcribed?a. Identify every 3€² end and every 5€² end in the picture.b. Identify the template strand.c. Te non template strand
Base analysis of DNA from maize (corn) shows it to have 23 mole percent cytosine (moles per 100 moles total nucleotide), What are the percentages of the other three bases?
Using the pKa data in Table 4.1 and the Henderson-Hasselbalch equa-tion, calculate the approximate net charge on each of the four common ribonucleoside 5€² -monophosphates (rNMPs) at pH 3.8. If a
For some DNAs it is possible to separate the two strands, afer denaturation, in a CsCl gradient.a. What property of any DNA determines where it will band in a CsCl gradient?b. What kind of DNA might
Refer to Figure 4.15, which presents the Meselson-Stahl experiment. DNA molecules can be denatured by high pH, as well as by heat. Suppose that the CsCl gradient centrifugations were run at pH 12,
Using the data in Table 5.1, calculate the average amino acid residue weight in a protein of typical composition. This is a useful number to know for ap-proximate calculations.In Table 5.1
a. Write a possible sequence for an mRNA segment coding for apamine.b. Do you think apamine is synthesized in the form shown in Problem 11, or is it more likely a product of proteolytic cleavage of a
Suppose you had separated the A and B chains of insulin by disulfide reduction. What chromatographic method should make it possible to isolate pure A and B chains? Explain your choice of separation
Acetylating agents such as acetic anhydride react preferentially with primary amines, iodoacetate reacts preferentially with sulfhydryl groups (see Tools of Biochemistry 5B), and ATP-dependent
Consider the chemical modifications proposed in Problem 15. For each modification, consider:a. Would the chemical modification change the overall charge on the peptide at pH = 7?b. If so, is the pI
Sickle-cell disease is caused by a so-called point mutation in the human β -globin gene. A point mutation is the result of a single base substitution in the DNA encoding a gene. The sickle-cell
You have discovered a novel protein that has a pI = 5.5. To study the functional properties of this new protein, your research group has made a mutant that contains two amino acid changes-namely, a
You are a summer intern in a clinical hematology lab. The lab director gives you a sample of a patient's blood proteins and asks you to characterize the thrombin in the sample. She also tells you
Draw the structure of the peptide DTLH, showing the backbone and side-chain atoms. a. Draw a water molecule making a hydrogen bond to a side chain H-bond donor. b. Draw a water molecule making a
Suppose you performed two BLAST searches, one on the peptide sequence FIDPWE, and another on the sequence KRTIAAVNSPLLEVATY. Which search do you predict will give you alignments with "expect scores"
4. The melanocyte-stimulating peptide hormone a- melanotropin has the following sequence:Ser-Tyr-Ser-Met-Glu-His-Phe-Arg-Trp-Gly-Lys-Pro-Vala. Write the sequence using the one-letter abbreviations.b.
a. Sketch the titration curve you would expect for a -melanotropin (Problem 4). Assume the pKa s of the N- and C-termini are 7.9 and 3.8, respectively. For side chains, assume the pKa values given in
What peptides are expected to be produced when a-melanotropin (Problem 4) is cleaved bya. Trypsin, orb. Cyanogen bromide, orc. Thermolysin? (Refer to Table 5.3.)In Table 5.3
There is another melanocyte-stimulating hormone called β-melanotropin. Cleavage of β-melanotropin with trypsin produces the following peptides plus free aspartic acid. WGSPPK DSGPYK MEHFR If you
Given the following peptideSEPIMAPVEYPKa. Estimate the net charge at pH 7 and at pH 12. Assume the pKa values given in Table 5.1.In Table 5.1b. How many peptides would result if this peptide were
A mutant form of polypeptide hormone angiotensin II has the amino acid compositionThe following observations are made: €¢ Trypsin yields a dipeptide containing Asp and Arg, and a
Under physiological conditions, the protein hemerythrin exists as an octamer of eight chains of the kind shown in Problem 3. a. Name two symmetries possible for this molecule. b. Which do you think
Theoretical and experimental measurements show that in many cases, the contributions of ionic and hydrogen-bonding interactions to ΔH for protein folding are close to zero. Provide an explanation
The peptide hormone vasopressin is used in the regulation of saltwater balance in many vertebrates. Porcine (pig) vasopressin has the sequencea. Using the data in Figure 5.6 and Table 5.1, estimate
A protein gives, under conditions of buffer composition, pH, and temperature that are close to physiological conditions, a molecular weight by size exclusion measurements of 140,000 g/mol. When the
A protein gives a single band on SDS gel electrophoresis, as shown in lanes 1 and 2 below. There is little if any effect from adding Î² -mercaptoethanol (BME) to the sample; if anything,
It has been postulated that the normal (noninfectious) form of prion differs from the infectious form only in secondary/tertiary structure.a. How might you show that changes in secondary structure
Below are shown two views of the backbone representation of the Myc-Max complex binding to DNA (PDB ID: 1npk).Side view of Myc-Max bound to DNATop view of Myc-Max bound to DNA(looking down the DNA
Do you expect a Pro → Gly mutation in a surface-loop region of a globular protein to be stabilizing or destabilizing? Assume the mutant folds to a native-like conformation. Explain your answer in
Rank the following in terms of predicted rates: the nucleation of an α helix; the nucleation of α parallel β sheet; the nucleation of an anti parallel β sheet. Justify your predictions.
Polyglycine, a simple polypeptide, can form a helix with ( = -80°, ( = + 150o. From the Ramachandran plot, describe this helix with respect to handedness.
A schematic structure of the subunit of hemerythrin (an oxygen-binding protein from invertebrate animals) is shown to the right.a. It has been found that in some of the α-helical regions of
Give two reasons to explain why a proline residue in the middle of an α helix is predicted to be destabilizing to the helical structure.
Consider a small protein containing 101 amino acid residues. The protein will have 200 bonds about which rotation can occur. Assume that three orientations are possible about each of these bonds.a.
a. Based on a more conservative answer to Problem 6 (2.7 × 1092 conformations), estimate the conformational entropy change on folding a mole of this protein into a native structure with only one
a. A protein is found to be a tetramer of identical subunits. Name two symmetries possible for such a molecule. What kinds of interactions (isologous or heterologous) would stabilize each?b. Suppose
What physiological effect would you predict from a mutation that replaced with serine the cysteine in the constant part of the immunoglobulin light chain that is involved in disulfide-bond formation
Suppose you visit the Dalai Lama in Dharamsala, India (elevation 1460 m), and you begin to ponder the "big questions," such as, "What is the fractional saturation of the Dalai Lama's hemoglobin?"a.
Assume that a new oxygen-transport protein has been discovered in certain invertebrate animals. X-ray diffraction of the deoxy protein reveals that it has the dimeric structure shown here in panel
The mutation in hemoglobin at β82 Lys → Asp results in lowered O2-binding affinity compared to normal hemoglobin. β82 is one of the residues that lines the 2,3-BPG binding site. Based on the
A typical relaxed sarcomere is about 2.3 μm in length and contracts to about 2 μm in length. Within the sarcomere, the thin filaments are about 1 μm long and the thick filaments are about 1.5 μm
Each gram of mammalian skeletal muscle consumes ATP at a rate of about 1 Ã— 10-3 mol/min during contraction. To bridge the short interval between the moderate demand for ATP met by
A few hours after the death of an animal, the corpse will stiffen as a result of continued contraction of muscle tissue (this state is called rigor mortis). This phenomenon is the result of the loss
Certain antibodies have been shown to only bind to the folded structure of their target protein ligand, yet others will bind to both the folded and denatured states of the same protein ligand.
The following data describe the binding of oxygen to human myoglobin at 37°C.From these data, estimatea. P50 andb. The fraction saturation of myoglobin at 30 mm Hg, the partial pressure of O2 in
Measurements of oxygen binding by whole human blood, at 37°C, at pH 7.4, and in the presence of 40 mm Hg of CO2 and normal physiological levels of BPG (5 mmol/L of cells), give the following:a. From
Crocodile hemoglobin does not bind 2, 3-BPG. Instead, it binds bicarbonate ion, which is a strong negative allosteric effector. Why might crocodiles have a hemoglobin that is responsive to HCO3-
Suggest probable consequences of the following real or possible hemoglobin mutations.a. At β146 (HC3) His → Aspb. At β92 (F8) His → LeuIn each case, tell whether a single-nucleotide change is
Suppose each of the mutants listed in Problem 7 were electrophoresed in comparison with native hemoglobin (pI = 7.0) at pH 8.0.Which would move faster toward the anode than native protein, and which
In the experiments of Barrick et al., it was observed that replacement of histidine by a non covalently bonded imidazole not only reduced cooperativity but also increased the oxygen affinity of the
Show that the half-life for a first-order reaction is inversely proportional to the rate constant, and determine the constant of proportionality.
The catalytic efficiency of many enzymes depends on pH. Chymotrypsin shows a maximum value of kcat/KM at pH 8. Detailed analysis shows that k cat increases rapidly between pH 6 and 7 and remains
The following data describe the catalysis of cleavage of peptide bonds in small peptides by the enzyme elastase.The arrow indicates the peptide bond cleaved in each case.a. If a mixture of these

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