Final exam

Fill in the blanks: the concentration of ions won't be in equilibrium the concentration of ions will equalize yes no 1. For (a) - ______., because __________________. 2. For (b) - ______., because _________________ 3. For (c) - ______., because ________________.

1. no. the con of ions WON'T be 2. no. the con of ions WON'T 3. yes. the con of ions WILL

Briefly explain the shape of your curve. Check all that apply. 1) At pH = pKa expect 100% of maximal activity because the Asp will be 100% protonated. 2) The Asp must be protonated to act as a general acid catalyst; thus, activity will be higher when pH < pKa and lower when pH > pKa. 3) At pH = pKa expect 50% of maximal activity because the Asp will be 50% protonated. 4) At pH = pKa expect 100% of maximal activity because the Asp will be 100% deprotonated. 5) The Asp must be fully deprotonated to act as a general acid catalyst; thus, activity will be higher when pH < pKa and lower when pH > pKa.

2, 3

Assuming that the side chain cannot -bond to the oxyanion intermediate, by how much (in ) does appear to stabilize the transition state at 37 ?

20 kJ/mol

Enalaprilat is a competitive inhibitor of the angiotensin-converting enzyme (ACE), which cleaves the blood-pressure regulating peptide angiotensin I. ACE has a KM = 12 μM for angiotensin I, which is present in plasma at a concentration of 75 μM. When enalaprilat is present at 2.4 nM, the activity of ACE in plasma is 10% of its uninhibited activity. What is the value of KI for enalaprilat?

3.7 x 10^-11 M

In considering protein secondary structure which of the following is INCORRECT? A) The 310 helix is right-handed and often contains proline residues. B) The most common structures are the α helix and the β sheet. C) The β strands can be in either parallel or antiparallel configuration. D) A network of main-chain hydrogen bonds connect β strands in a β sheet. E) An α helix repeats after 18 residues and has 3.6 residues per turn.

A

What pH gradient would you choose for this experiment? a) A pH gradient between 2.0 to 7.0. b) A pH gradient between 7.0 to 10.0. c) A pH gradient between 8.0 to 12.0. d) A pH gradient between 2.0 to 5.0.

A

Where is the −S−S- bond (i.e., AB, BC, or AC)?

AC

What is the sequence of angiotensin II? Tyr Val Ile Asp Phe Met Arg Pro

Asp-Arg-Val-Tyr-Ile-Met-Pro-Phe

Protein folding is a thermodynamically favorable process under physiological conditions because: A) there is an increase in entropy associated with protein folding. B) of the large negative enthalpy change associated with many noncovalent interactions. C) there is a decrease in entropy of the solvent by burying hydrophobic groups within the molecule. D) no intermediate stage disulphide bonds form during the folding process. E) all of the above.

B

Which of the following is FALSE when considering the standard genetic code? A) There are 64 possible codons to represent 20 common amino acids. B) Each of the three stop codons can also encode rare modified amino acids. C) Apart from methionine, the only other amino acid with a single codon is tryptophan. D) Three separate codons encode translation stop signals. E) AUG serves as the translation start codon in most cases.

B

On the basis of these data, suggest what features of amino acid sequence dictate the specificity of proteolytic cleavage by elastase. Fill in the blanks: large small C-terminal N-terminal A hydrophobic residue seems to be favored at the position ________ to the site of bond cleavage. Elastase always requires a ________ residue (like Ala) to the ___________ side.

C-terminal small N-terminal

Calcium regulates muscle contraction by binding to: A) tropomyosin. B) actin. C) myosin. D) troponin T. E) troponin C.

E

Which of the following observations helps to explain the conformational changes that occur in hemoglobin upon binding to oxygen? A) The four heme groups are positioned close to the surface of the molecule. B) An αβ dimer rotates and slides with respect to the other dimer upon binding oxygen. C) Neither the heme nor the iron ion in the deoxy conformation is in a planar conformation. D) All of the above E) B and C

E

Which of the following statement is FALSE? A) An enzyme can increase a reaction rate by lowering the activation energy. B) The free energy barrier in a chemical reaction must be overcome in order for products to form. C) An increase in temperature can result in an increased reaction rate. D) Lowering the free energy of the transition state can increase a reaction rate. E) At a given temperature and time all molecules in a solution or a sample will have the same energy.

E

Would the chemical modification change the overall charge on the ATP-dependent kinases at pH=7? A) The positive charge on the peptide will be reduced. B) The positive charge on the peptide will be increased. C) The charge on the peptide will not change. D) The negative charge on the peptide will be reduced. E) The negative charge on the peptide will be increased.

E

Would the chemical modification change the overall charge on the iodoacetate at pH=7? A) The positive charge on the peptide will be increased. B) The negative charge on the peptide will be reduced. C) The charge on the peptide will not change. D) The positive charge on the peptide will be reduced. E) The negative charge on the peptide will be increased.

E

Which of the following modified amino acids is incorporated during translation rather than being modified post-translationally? Phosphoserine γ-carboxyglutamate N-ε-acetyllysine 4-hydroxyproline Selenocysteine

Selenocysteine

Which technique is able to investigate secondary structural features of proteins? A) Ultraviolet spectroscopy B) Circular dichroism C) Fluorescence spectroscopy D) Infrared spectroscopy E) All of the above

all of the above

Which of the following amino acids would most likely be found on the surface of a protein? Check all that apply. Valine Leucine Aspartic acid Phenylalanine Proline

aspartic acid and proline

Many proteins interact with DNA at physiological pH because: a) both proteins and DNA are at their isoelectric points at physiological pH and tend to aggregate. b) the negatively charged DNA is electrostatically attracted to positively charged regions on proteins. c) proteins are naturally attracted to DNA regardless of the pH. d) the positively charged DNA is electrostatically attracted to negatively charged regions on proteins. e) proteins and DNA interact using mainly hydrophobic interactions.

b

The cofactor NAD+ is: a) oxidized to NADH/H+ in dehydrogenase reactions. b) an oxidant. c) able to accept 2 electrons and 2 protons. d) covalently linked to enzymes in whose catalytic activity it assists. e) a reductant.

b

A second-order reaction: A) has a rate constant with units of (time)-1. B) only occurs in multistep processes. C) is characterized by two molecules coming together to form a product. D) is the rate-limiting step of a reaction. E) occurs when one substrate is converted into one product.

c

Briefly explain your choice. a) The best choice would be a buffer of H2PO4− and HPO42− because the pKa for this conjugate acid/base pair is greater than the target pH of 7.0. b) The best choice would be a buffer of H2PO4− and HPO42− because the pKa for this conjugate acid/base pair is lower than the target pH of 7.0. c) The best choice would be a buffer of H2PO4− and HPO42− because the pKa for this conjugate acid/base pair is close to the target pH of 7.0.

c

Enalapril is administered in pill form, but enalaprilat must be administered intravenously. Why do you suppose enalapril works as a pill, but enalaprilat does not? a) Enalaprilat has a larger size than enalapril and cannot cross membranes to get from the gut to circulation. b) Enalaprilat has a larger mass than enalapril and cannot cross membranes to get from the gut to circulation. c) Enalaprilat is too polar to cross membranes, whereas enalapril can cross membranes to get from the gut to circulation. d) Enalaprilat is not flexible enough to get into pores, whereas enalapril can cross membranes to get from the gut to circulation.

c

Which of the following is CORRECT when considering the tertiary structure of globular proteins? A) β sheets cannot be twisted or wrapped into barrel structures. B) The amino acid proline never occurs in a region where the polypeptide chain bends or turns. C) Hydrophobic residues are normally on the inside and hydrophilic residues are on the outside. D) All parts of the proteins can be classified as helix, β sheet or turns. E) None of the above.

c

Which of the following statements is FALSE? A) Hydrogen bonding to a histidine residue assists stabilization of the Fe2+ -O2 complex in both hemoglobin and myoglobin. B) Hemoglobin is a tetramer, each of which binds a heme group. C) The iron in both hemoglobin and myoglobin has two coordination sites that bind to oxygen. D) Myoglobin is a single polypeptide chain folded about a heme prosthetic group. E) In both hemoglobin and myoglobin, iron is chelated by a tetrapyrole ring system.

c

The protein that makes up about a third of the total protein mass in animals is: A) β-keratin. B) hemoglobin. C) α-keratin. D) myoglobin. E) collagen.

collagen

Which of the following is considered to be the smallest carbohydrate? Glucose Xylose Ribose Formaldehyde Dihydroxyacetone

dihydroxyacetone

Enzymes can accelerate reactions by: a) lowering the energy for activation. b) correctly positioning a metal ion for catalysis. c) promoting the removal or addition of protons. d) binding a substrate or substrates. e) all of the above.

e

The lock and key model of substrate binding and enzymatic catalysis explains: a) structural changes that occur on substrate binding. b) the release of product. c) formation of a transition state. d) the catalytic mechanism. e) substrate specificity.

e

Which conjugate pair is suited best to make this buffer? a) Formic acid HCOOH and formate ion HCOO− b) Acetic acid CH3COOH and acetate ion CH3COO− c) Lactic acid CH3CH(OH)COOH and lactate ion CH3CH(OH)COO− d) Phosphoric acid H3PO4 and dihydrogen phosphate ion H2PO4− e) Dihydrogen phosphate ion H2PO4− and monohydrogen phosphate ion HPO42− f) Monohydrogen phosphate ion HPO42− and phosphate ion PO43− g) Carbonic acid H2CO3 and bicarbonate ion HCO3− h) Bicarbonate ion HCO3− and carbonate ion CO32− i) Phenol C6H5OH and phenolate ion C6H5O− j) Ammonium ion +NH4 and ammonia NH3

e

Which of the following statements applies to metalloenzymes? a) Some metal ions assist in ATP binding. b) Amino acid residues in the enzyme are never covalently linked to the metal ion. c) The metal does not bind at the catalytic site. d) Many are oxido-reductases. e) A and D

e

Which of the following statements is FALSE? a) Entropy is a measure of disorder. b) Biological systems expend energy to overcome entropy. c) The entropy of a biological system can decrease. d) The entropy of an isolated system will tend to increase to a maximum value. e) Biological systems are highly ordered so entropy changes are not relevant.

e

A mutation causing an amino acid change in an enzyme that affects the turnover number kcat will always affect the KM as well. True False

false

At pH=0, the net charge on a polypeptide will be negative. True OR False

false

Both myoglobin and hemoglobin exhibit cooperative binding to oxygen. True OR False

false

Catalysts affect the thermodynamic f of a chemical reaction. True False

false

Coenzymes or cofactors are irreversibly changed during catalysis. True False

false

Conservative amino acid changes never affect stability or function of a protein. True OR False

false

Dideoxynucleotide sequence analysis is a template-directed method that makes use of chain terminators that stop DNA synthesis because they lack a 2'OH group. True False

false

Electrostatic catalysis proceeds via covalent bonding interactions. True False

false

If a mixture was prepared containing 1 M glucose-6-phosphate and 1×10−3M glucose-1-phosphate, what would be the thermodynamically favored direction for the reaction? The direct reaction is favored. The reverse reaction is favored.

reverse

The equilibrium constant for a first-order ________ reaction is equivalent to the ratio of the rate constant for the forward and reverse reactions.

reversible

Fill in the blanks: gel electrophoresis isoelectric focusing large small The single-charge difference would result in a ________ difference in mobility in a normal ______________ experiment (which separates chains based on size), but would make a detectable difference in pI.

small gel electrophoresis

The process of phosphorylating the glucose after it has been transported into the cell is considered a form of active transport-called "transport by modification"-even though is not bound by the transporter protein, nor is hydrolysis directly involved in the movement of glucose across the membrane. Which part of this process effectively stimulates glucose transporting inside the cell? (Hint: Consider Le Chatelier's principle). the phosphorylation reaction the transport reaction --------- Given = 4.7 ; = 0.15 ; = 6.1 , calculate the theoretical maximum concentration of inside a liver cell at 37 , = 7.2 when the glucose concentration outside the cell (i.e., is 5.0 : Express your answer to three significant figures and include the appropriate units.

the phosphorylation rxn 313 M

Covalent modification can either activate or inhibit enzymes. True False

true

If apamine does not react with iodoacetate, then how many disulfide bonds are present? One disulfide. Two disulfides. Three disulfides.

two disulfides

Fill in the blanks: terminal reversed same center (-) (+) 1. Make a mutant Lep that substitutes noncharged residues for the _______ charged side chains in the loop, and put _______ charged side chains in _________ positions. 2. If the inside-positive rule applies, the mutant ought to have the _________ orientation in the membrane.

(+) (+) terminal reversed

H+ transport from the outside of the IMM into the matrix drives this process. The inside the matrix is 8.2, and the outside is more acidic by 0.8 units. Assuming the IMM membrane potential is 168 (inside negative), calculate for the transport of 1 of across the IMM into the matrix at 37C : H+ (out) ----> H+ (in). --------- Write the overall reaction for ATP synthesis coupled to H+ transport. ---------- Assume three mol be translocated to synthesize one mol ATP as described in part B above. Given the following steady-state concentrations: = 2.70 and = 5.20 , the membrane potential = -168 (inside negative), and the values in part A, calculate the steady-state concentration of at 37 when = -11.7

-21.0 kJ/mol 3H+ (out) ----> 2H+ (in) 5.30 mM

Each gram of mammalian skeletal muscle consumes ATP at a rate of about 1×10−3mol/min during contraction. To bridge the short interval between the moderate demand for ATP met by aerobic metabolism and the high demand met by anaerobic ATP production, muscles carry a small reserve of the compound creatine phosphate which, due to its high phosphoryl group transfer potential (see the figure on the left), is capable of phosphorylating ADP very efficiently. The reaction is catalyzed by the enzyme creatine kinase: ----- Because the equilibrium lies well to the right, virtually all of the muscle ADP or AMP is converted to ATP as long as creatine phosphate is available. Concentrations of ATP and creatine phosphate in muscle are about 4 mM and 25 mM, respectively, and the density of muscle tissue can be taken to be about 1.2 g/cm3. How long could contraction continue using ATP alone? ***** If all creatine phosphate were converted into ATP and utilized as well, how long could contraction continue? ***** What do these answers tell you about the role of ATP in providing energy to cells? A) ATP must be no longer used in active muscle. B) Creatine phosphate must be continually produced in active muscle. C) Creatine phosphate must be no longer produced in active muscle. D) ATP must be constantly replenished from other sources. E) ATP must be no longer produced in active muscle. F) Creatine phosphate must be no longer used in active muscle.

0.2 s 1.25 s B

Under what circumstances would asymmetric cloning be desirable, with the inset having a different restriction site at each end? Check all that apply. 1) Cloning in a fixed direction prevents the vector from becoming ligated to itself and forming either a circle or an end-to-end aggregate. 2) Cloning in a fixed direction promotes the vector to become ligated to itself and form a double stranded ladder-type aggregate. 3) The orientation in one direction should be fixed because there is a desire to express a cloned gene driven from a promoter located near one end of the link between vector and insert. The 5' end of the sense strand would need to be located downstream from the promoter. 4) The orientation in one direction might be free because there is a desire to express a cloned gene driven from a promoter located near either one or another end of the link between vector and insert. The 3' end of the sense strand would need to be located downstream from the promoter.

1 and 3

The reagent periodate (IO4−) oxidatively cleaves the carbon-carbon bonds between two adjacent carbons carrying hydroxyl groups. Explain how periodate oxidation might be used to distinguish between methyl glycosides of glucose in the pyranose and furanose forms. Check all that apply. 1) Cleavage of the pyranose form will occur twice, producing formic acid. 2) Cleavage of the pyranose form will also occur twice (between C2 and C3 and between C5 and C6), but formaldehyde will be produced from C6. 3) Cleavage of the furanose form will occur only once (between C3 and C4), but neither formaldehyde nor formic acid will be produced. 4) Cleavage of the pyranose form will occur only once (between C3 and C4), but neither formaldehyde nor formic acid will be produced. 5) Cleavage of the furanose form will occur twice, producing formic acid. 6) Cleavage of the furanose form will also occur twice (between C2 and C3 and between C5 and C6), but formaldehyde will be produced from C6.

1 and 6

In some reactions, in which a protein molecule is binding to a specific site on DNA, a rate greater than that predicted by the diffusion limit is observed. Suggest an explanation. [Hint: The protein molecule can also bind weakly and nonspecifically to any DNA site.] Fill in the blanks using: 3-D 1-D enthalipically entropically If the protein can bind to a random location on the DNA and slide along until it finds the specific site, a more efficient _________ search replaces an _________ less favorable __________ search.

1-D entropically 3-D

If trypsin cleavage gave two peptides, then where is(are) the S−S bond(s)? 1. ______ - _______ 2. ______ - ________ Fill in the blanks with the following: Cys 1, Cys 3, Cys 11, Cys 15

1. Cys 1 - Cys 3 2. Cys 11 - Cys 15

The enzyme urease catalyzes the hydrolysis of urea to ammonia plus carbon dioxide. At 21 C the uncatalyzed reaction has an activation energy of about 125 kJ/mol , whereas in the presence of urease the activation energy is lowered to about 46 kJ/mol . By what factor does urease increase the velocity of the reaction?

1.1 x 10^14

Show that these data can be accounted for only if the erythrocyte membrane is a bilayer. The ratio of monolayer area to cell surface = ________

1.89

The phosphate transfer potentials for glucose-1-phosphate and glucose-6-phosphate are 20.9 kJ/mol and 13.8 kJ/mol, respectively. What is the equilibrium constant for the reaction shown below at 25 ∘C?

17.6

Linolenic acid has cis double bonds with the formula CH3CH2CH=CHCH2CH=CHCH2CH=CH(CH2)7COOH. Write out the abbreviated systematic numbering for this fatty acid. Enter the abbreviation for the fatty acid using systematic numbering. Type Delta if the Greek symbol is required.

18:3cdelta9,12,15

Which search do you predict will give you alignments with "expect scores" closer to one? Explain your reasoning. 1) The expect score for the longer sequence is more likely to be closer to one (i.e., the longer sequence consists of greater variety of amino acids). 2) The expect score for the shorter sequence is more likely to be closer to one (i.e., the shorter sequence is more likely to match many entries in the database).

2

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. Based on these assumptions, about how many random-coil conformations will be possible for this protein? ***** The estimate obtained in Part A is surely too large. Give one reason why. A) Not all of these conformations will be sterically possible. B) During folding protein does not pass into these conformation because of extra negative ΔHU→F values. C) Majority of these conformations has extra positive ΔSU→F.

2.7 x 10^95 A

The inhibitory effect of an uncompetitive inhibitor is greater at high [S] than at low [S]. Explain this observation. Check all that apply. 1) At [S] > KM the effect of the inhibitor on reducing Vmax is apparent because as [S] decreases, V approaches Vmax[S]/α′. 2) At [S] < KM the effect of the inhibitor is minimal because as [S] increases, V approaches Vmax/[S]KM. 3) At [S] < KM the effect of the inhibitor is minimal because as [S] decreases, V approaches Vmax[S]/KM. 4) At [S] > KM the effect of the inhibitor on reducing Vmax is apparent because as [S] increases, V approaches Vmax/α′.

3 and 4

In the former case, the binding epitope is composed of ______ (a _____ epitope). In the latter case, the binding epitope is composed of ______ (a ______ epitope). Fill in the blanks with the following terms: 1) discontinuous 2) continuous 3) a contiguous amino acid sequence 4) regions of the protein that are distant in primary sequence, but close in the folded structure

4, 1, 3, 2

Protein must have _____________, which cleavage at a critical Arg residue can relax, giving faster migration. Cleavage of disulfide bondes, after thrombin cleavage, ___________. The little effect of disulfide reduction means that _____________. Fill in the blanks. 1) separates two subunits 2) yields two fragments 3) the protein is a single chain 4) the protein consists of two subunits 5) an extended structure 6) a quaternary structure

5, 2, 3

The water content in the human body is approximately: 90%. 70%. 80%. 60%. 50%.

70%

Acetylating agents such as acetic anhydride react preferentially with primary amines, iodoacetate reacts preferentially with sulfhydryl groups, and ATP-dependent kinases preferentially add a phosphoryl group to side-chain hydroxyl or phenolic −OH groups. For each modification, consider. Would the chemical modification change the overall charge on the acetic anhydride at pH=7? A) The positive charge on the peptide will be reduced. B) The negative charge on the peptide will be increased. C) The negative charge on the peptide will be reduced. D) The charge on the peptide will not change. E) The positive charge on the peptide will be increased.

A

Consult the figure on the left and describe, in terms of the six-step model of muscle contraction, how a lack of ATP in sarcomeres would result in rigor mortis. A) Release of the myosin headpiece from the thin filament requires ATP binding. Until ATP binds, the myosin-actin cross-bridge will remain intact, thereby preventing extension of the sarcomeres. B) Lack of ATP in sarcomeres causes failure of the sodium-potassium pump and restricts actin-myosin cross-bridge building. This prevents relaxation of the muscles (no ATP to build cross-bridge between actin and myosin). C) The removal of excess lactic acid is very important for the proper functioning of muscles. Lack of ATP causes a decrease in intracellular pH because breakdown of lactic acid is arrested. This process results in a constant state of muscle contraction. D) After death, the protein structures in muscle contract and expel fluid from inside the cell into the intercellular spaces. Lack of ATP causes coagulation of muscle protein and water gets trapped within the tissue. It results in muscles being hard and stiff.

A

In the protein adenylate kinase, the C-terminal region has the sequence Val-Asp-Asp-Val-Phe-Ser-Gln-Val-Cys-Thr-His-Leu-Asp-Thr-Leu-Lys- The hydrophobic residues in this sequence are presented in boldface type. Suggest a possible reason for the periodicity in their spacing. A) Each residue that is hydrophobic lies on one side forming amphipathic α-helix. B) Active site of the adenylate kinase is formed by packed together hydrophobic residues. C) Hydrophobic residues give rise to a helical dipole moment and partial (-) charge of the C-terminus. D) Localization of hydrophobic residues on the one side of β-strand mediates the interactions with other one of the polypeptide chain.

A

The Ca2+ transporter in sarcomeres that keeps the [Ca2+]∼10−7M requires ATP to drive transport of Ca2+ ions across the membrane of the sarcoplasmic reticulum. How would a loss of this Ca2+ transport function result in the initiation of rigor mortis? A) Ca2+ will leak across the membrane from the side of high Ca2+ concentration (in the transverse tubule) to the side of lower Ca2+ concentration (inside the sarcomere). As [Ca2+] increases, it will bind TnC, thereby stimulating myosin binding to actin. B) Ca2+ will leak across the membrane from the side of low Ca2+ concentration (inside the sarcomere) to the side of higher Ca2+ concentration (in the transverse tubule). As [Ca2+] decreases, it will bind TnC, thereby preventing myosin binding to actin. C) Ca2+ will leak across the membrane from the side of high Ca2+ concentration (in the transverse tubule) to the side of lower Ca2+ concentration (inside the sarcomere). As [Ca2+] increases, it will bind TnC, thereby preventing myosin binding to actin. D) Ca2+ will leak across the membrane from the side of low Ca2+ concentration (inside the sarcomere) to the side of higher Ca2+ concentration (in the transverse tubule). As [Ca2+] decreases, it will bind TnC, thereby stimulating myosin binding to actin.

A

What qualitative effect would you expect each of the following to have on the P50 of hemoglobin? Dissociation into monomer polypeptide chains a) decrease in P50 b) increase in P50 c) no change in P50

A

What qualitative effect would you expect each of the following to have on the P50 of hemoglobin? Increase in pH from 7.2 to 7.4 a) decrease in P50 b) increase in P50 c) no change in P50

A

What would be the effect of a mutation that placed a proline residue at point A in the structure? A) This would break the helix near the binding sites and Fe2 could not be bound, and the mutant protein would be nonfunctional. B) This would break the helix near the Fe2 binding sites, and the mutant protein would change functions. C) This would break the helix and form hairpin structures, that would make the mutant protein nonfunctional.

A

Where do you predict the N- and C-termini are located for Max? A) The N-terminus is interacting with the DNA. The α-amino group of the N-terminus is positively charged and will interact favorably with the negative charge on the phosphodiester backbone of the DNA. B) The C-terminus is interacting with the DNA. The α-carboxyl group of the C-terminus has negative charge that help to relax the super coils of DNA. C) The N-terminus and the C-terminus are hidden in the protein core. Both free ends of the protein should be protected from the action of proteases by intramolecular interactions.

A

Which of the following statements about muscle contraction is TRUE? A) ATP hydrolysis causes a conformational change in the myosin head. B) ATP hydrolysis releases myosin from actin. C) ATP hydrolysis results in strong binding of myosin to actin. D) Muscle contraction occurs as ATP is hydrolyzed. E) ATP hydrolysis must occur before the actin-binding site closes.

A

Suggest the effects of each of the following mutations on the physiological role of chymotrypsinogen: R15S A) Activation of the molecule will be greatly reduced due to removal of the R that is binded in its active site. B) Automodification of π-chymotrypsin to α-chymotrypsin could be reduced, the effect on activation might be slight. C) If activation occurs, the N-terminal peptide will no longer be constrained by an SS bond and may be released. --------- C1S A) Activation of the molecule will be greatly reduced due to removal of the R that is binded in its active site. B) Automodification of π-chymotrypsin to α-chymotrypsin could be reduced, the effect on activation might be slight. C) If activation occurs, the N-terminal peptide will no longer be constrained by an SS bond and may be released. --------- T147S A) Activation of the molecule will be greatly reduced due to removal of the R that is binded in its active site. B) Automodification of π-chymotrypsin to α-chymotrypsin could be reduced, the effect on activation might be slight. C) If activation occurs, the N-terminal peptide will no longer be constrained by an SS bond and may be released.

A C B

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? Check all that apply. A) D2 symmetry with isologous interactions B) C2 symmetry with heterologous interactions C) C2 symmetry with isologous interactions D) C4 symmetry with isologous interactions E) D2 symmetry with heterologous interactions F) D4 symmetry with heterologous interactions

A and B

Applications of mass spectrometry include: A) determination of the mass of a protein. B) detection of post-translational modifications on proteins. C) determining the primary structure of proteins. D) A and B. E) A, B, and C.

A, B, and C

A biochemical reaction will proceed in the direction as written if: a) ΔH < 0. b) ΔG < 0. c) ΔG > 0. d) ΔG = zero. e) ΔH > 0.

B

At β146( HC3)His→Asp a) the effect is a decrease in oxygen affinity b) the effect is an increase in oxygen affinity c) the effect is the enhanced ability to ligate to the heme iron d) the effect is the disrupted ability to ligate to the heme iron

B

At β92( F8)His→Leu a) the effect is an increase in oxygen affinity b) the effect is the disrupted ability to ligate to the heme iron c) the effect is the enhanced ability to ligate to the heme iron d) the effect is a decrease in oxygen affinity

B

If so, is the pI of the modified peptide higher or lower than that of the untreated peptide? A) pI is higher in every case. B) pI is lower in every case.

B

If the circular DNA were nicked (had a single-stranded break) on one strand, what would be the effect on supercoiling? a) Supercoiling would remain the same. b) Supercoiling would disappear. c) Supercoiling would increase.

B

It has been found that in some of the α-helical regions of hemerythrin, about every third or fourth amino acid residue is a hydrophobic one. Suggest a structural reason for this finding. A) The hydrophobic residues share polar regions of the helix, forming a regular helical structure B) The four helices could be arranged so that to stabilize hydrophobic core. C) This order of residues stabilize turns and affects the angle of rotation of spiral turns.

B

Restriction endonucleases are useful in gene cloning because: a) they can both cut and rejoin DNA molecules. b) they can cut DNA at specific sequences. c) they all make cohesive ends when they cut DNA. d) they can join DNA molecules that have been cut at specific sequences. e) they all make 5' phosphate extensions and recessed 3' OH groups that can be rejoined by DNA ligase.

B

SDS gel electrophoresis can be used to determine: A) the overall charge on a polypeptide. B) the molecular mass of denatured protein subunits. C) whether subunits in a protein complex are identical or not. D) the molecular mass of a native protein complex. E) none of the above.

B

Schematic models of an IgG antibody molecule and an Fab fragment. a) versatility in the antigen binding b) loss of the antigen binding c) enhancement in the antigen binding d) antigen binding specificity

B

The effect of replacing the proximal histidine in hemoglobin with a glycine residue and adding a noncovalently bonded imidazole. Suggest an explanation. A) Unlike histidine imidazole binds to ATP forming a fairly stable complex. ATP binds to hemoglobin more strongly than does the ATP-imidazole complex. Imidazole, therefore, tends to increase oxygen affinity of hemoglobin by blocking the ATP-hemoglobin interaction. B) In native Hb, the binding of oxygen is actually hindered by the fact that pulling on helix F must move it against constraints within the molecule. In the imidazole replacement, there is no need to do the extra work of moving helix F. This difference shows up as a more favorable free energy for binding. C) Imidazole is significantly more acidic (lower pKa) than histidine. Thus, at the pH of blood, native hemoglobin is more acidic than the imidazole replacement. This lowering in pH causes the oxygen affinity of the hemoglobin to increase. D) In native hemoglobin, the initial binding of one O2 to a heme group promotes the binding of O2 to the other heme site on the molecule. In the imidazole replacement, the initial binding of one O2 to a heme group promotes the binding of two O2 to the other heme sites on the molecule. This effectively increase the oxygen affinity of the hemoglobin.

B

The ΔG o of a reaction: a) will change if the concentration of reactants and products are changed. b) can predict whether a reaction will be thermodynamically favorable under standard conditions. c) will change if the temperature of the reaction is changed. d) is not related to the equilibrium constant.

B

What qualitative effect would you expect each of the following to have on the P50 of hemoglobin? Increase in Pco2 from 20 to 40 mm Hg a) decrease in P50 b) increase in P50 c) no change in P50

B

Which of the following amino acid residues are often involved in proton transfers in enzyme-catalyzed reactions? a) Histidine, aspartate, lysine, and serine b) Histidine, aspartate, glutamate, arginine, and lysine c) Glutamine, asparagine, lysine, and tyrosine d) Serine, tyrosine, arginine, and cysteine e) Histidine, aspartate, serine, and cysteine

B

Which of the following is a feature of X-diffraction? a) Scattered radiation from repeating units in a structure will be weakened by interference. b) Scattered radiation from repeating units in a structure will be strengthened by interference. c) The wavelength of radiation used to generate diffraction patterns must be slightly longer than the spacings between the repeating units of the structure. d) Short spacings in repeating structures will result in short spacings in diffraction patterns. e) Radiation passing through a structure will be scattered only if the structure contains repeating units.

B

Which of the following statements BEST describes the Michaelis-Menton constant KM? A) It is a measure of enzyme efficiency. B) It is numerically equal to the substrate concentration required to reach half maximal velocity for an enzyme-catalyzed reaction. C) It has units of concentration. D) It is numerically equal to the affinity between the enzyme and its substrate. E) It is a measure of the rate of a catalytic process.

B

Which of the following statements about insulin is INCORRECT? A) The leader sequence is cleaved off after membrane transport. B) The disulphide bonds form after the final proteolytic cleavage to yield mature insulin. C) It is synthesized as a random coil single chain on membrane-bound ribosomes. D) In the active form it has two polypeptide chains joined by disulphide bonds. E) It is stored in the pancreas in an inactive form.

B

Which of the following statements about nucleic acid secondary structure is FALSE? a) The width of the major and minor grooves is more equal in the A-from of DNA than in the B-form. b) The A-form of DNA exists at high humidity, whereas the B-form exists at low humidity. c) Some nucleic acids can form a zig-zag structure or Z form. d) DNA can form cruciform structures at palindromic sequences. e) Triple helices and G-quadruplexes can form at specific sequences in DNA.

B

TPCK and TLCK are irreversible inhibitors of serine proteases. One of these inhibits trypsin and the other chymotrypsin. Which is which? A) TPCK inhibits trypsin, TLCK inhibits chymotrypsin. B) TLCK inhibits trypsin, TPCK inhibits chymotrypsin. ---------- Explain your reasoning. a) TPCK is an analog of Val and therefore a better inhibitor of chymotrypsin, whereas TLCK is an analog of Ala and therefore a better inhibitor of trypsin. b) TPCK is an analog of Lys and therefore a better inhibitor of chymotrypsin, whereas TLCK is an analog of Phe and therefore a better inhibitor of trypsin. c) TPCK is an analog of Phe and therefore a better inhibitor of chymotrypsin, whereas TLCK is an analog of Lys and therefore a better inhibitor of trypsin. d) TPCK is an analog of Ala and therefore a better inhibitor of chymotrypsin, whereas TLCK is an analog of Leu and therefore a better inhibitor of trypsin.

B C

Are the helices bound to the DNA likely to be amphiphilic? Explain. A) Yes, it is likely amphiphilic. DNA-binding helix has an affinity to specific DNA sites and has difficult change landscape for interactions with certain sequences of nucleic residues. B) Yes. DNA is uncharged charged, and protein sites that interact with DNA can have either positive or negative charge. Therefor the DNA-binding helix is likely nonpolar. C) No. DNA is charged and therefore polar, so the DNA-binding helix is likely to be composed of polar residues that interact with either the DNA or the solvent.

C

In each case, tell whether a single-nucleotide change is sufficient for the mutation. a) in the first case, a single base is not sufficient for the mutation. In the second case, a single base change could give rise to the mutation. b) In the first case, a single base change could give rise to the mutation. In the second case, a single base change is not sufficient for the mutation. c) In each case, a single base change could give rise to the mutation. d) In each case, a single base change is not sufficient for the mutation.

C

Rigor mortis is maximal at ∼12hrs after death, and by 72hrs is no longer observed. Propose an explanation for the disappearance of rigor mortis after 12hrs. A) Decomposition includes cleavage of actin and myosin by creatine kinase. B) Decomposition includes cleavage of actin and myosin by cellular lyases. C) Decomposition includes cleavage of actin and myosin by intracellular proteases. D) Decomposition includes cleavage of actin and myosin by phosphodiester isomerization.

C

The heavy chain of the muscle form of myosin: A) binds ATP near the C-termini. B) is a complex of 540 kDa. C) forms a coiled-coil structure with a globular head domain. D) contains the motor domain within the C-terminal region. E) has two covalently bound light chains.

C

Using the information in table, explain how a point mutation could change a codon for Glu to a codon for Val. A) A change of the G in the GAG codon for glutamate to a C would change the codon to GUC, which codes for valine. B) A change of the A in the GAA codon for glutamate to a U would change the codon to GAU, which codes for valine. C) A change of the A in the GAG codon for glutamate to a U would change the codon to GUG, which codes for valine.

C

What chromatographic method should make it possible to isolate pure A and B chains? A) Immobilized metal affinity chromatography. The strong interactions between a Ni2+, Zn2+, or Co2+ ion and histidine residues of B chain; thus, B chain will bind to the IMAC matrix. B) Size exclusion chromatography. The differences in size between A and B are big enough for SEC to be effective. C) Ion exchange chromatography. The A chain contains no basic residues in comparison with the B chain, so ion-exchange chromatography should work well.

C

Which of the following is NOT true of immunoglobulin molecules? A) Some are membrane bound. B) Proteolytic cleavage can generate fragments containing the antigen-binding site. C) Antigenic determinants reside only in the variable region of the light chains. D) They consist of four polypeptide chains held together by disulphide bridges. E) They have two identical heavy chains and two identical light chains.

C

Which of the following statements about α-keratins is FALSE? A) Individual molecules are α-helical. B) There is a strip of contiguous hydrophobic surface making a shallow spiral around the helix. C) Pairs of α-helices twist about each other in a coiled-coil structure held together entirely by hydrophobic interactions. D) They include a small globular regions covalently linked to the surface. E) They include a major class of protein that comprises hair, fingernails and animal skin.

C

Why might crocodiles have a hemoglobin that is responsive to HCO−3 instead of 2,3-BPG? Recall that crocodiles hold their prey underwater to kill them. A) As the crocodile stays underwater, its hemoglobin delivers most of the bound HCO−3 as a result of decreased binding of O2 to the R conformation. B) As the crocodile stays underwater, its hemoglobin delivers most of the bound HCO−3 as a result of increased binding of O2 to the T conformation. C) As the crocodile stays underwater, its hemoglobin delivers most of the bound O2 as a result of increased binding of HCO−3 to the T conformation. D) As the crocodile stays underwater, its hemoglobin delivers most of the bound O2 as a result of decreased binding of HCO−3 to the R conformation.

C

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. Chek all tha apply. A) Pro is nonpolar amino acid that destabilizes polar core of the protein. B) Pro is nonpolar amino acid that does not connect turns of the α-helix. C) Pro does not have the α−NH group that acts as a stabilizing H-bond donor in the middle of the helix. D) Pro is not able to adopt the ideal ϕ and ψ angles for an α -helix. E) Insertion of Pro gives an exceptional conformational rigidity to the protein chain chain.

C and D

Suppose a tetramer, like hemoglobin, consists of two each of two types of subunits, α and β. What is the highest symmetry now possible? C4 C1 D2 D4 C2

C2

Under physiological conditions, the protein hemerythrin exists as an octamer of eight chains of the kind shown in the figure below. Name two symmetries possible for this molecule. Check all that apply. D8 C8 D2 C2 C1 D4 ***** Which do you think is more likely? A) C8, because it increases the value of the free energy. B) D4, because it involves more subunit-subunit interactions. C) C8, because it increases the number of possible conformations. D) D4, because it forms more axes of symmetry. ***** For the more likely symmetry, what kinds of interactions (isologous, heterologous, or both) would you expect? Why? A) Both. There must be heterologous interactions about the 4-fold axis and isologous interactions about the twofold axes. B) Isologous interactions give rise to more complex quaternary structures of higher symmetry and lead to indefinite growth. C) Heterologous interactions set the angle and direction of attachment of oligomers that reduces the number of possible configurations and energy states.

C8 an D4 B A

A student is carrying out a biological preparation that requires 1 MNaCl to maintain an ionic strength of 1.0. The student chooses to use 1.0 M ammonium sulfate instead. Why is this a serious error? a) The ionic strength of 1.0 M ammonium sulfate is two times greater than the ionic strength of NaCl. b) The ionic strength of 1.0 M ammonium sulfate is three times lower than the ionic strength of NaCl. c) The ionic strength of 1.0 M ammonium sulfate is two times lower than the ionic strength of NaCl. d) The ionic strength of 1.0 M ammonium sulfate is three times greater than the ionic strength of NaCl.

D

Do you expect the pI for the sickle-cell β-globin to be higher or lower than the pI for wild-type β-globin? Explain. A) The pI of the sickle-cell globin will be higher than the wild-type globin because the mutation replaces an uncharged side chain with one that carries positive charge. B) The pI of the sickle-cell globin will be lower than the wild-type globin because the mutation replaces a positively charged side chain with one that carries negative charge. C) The pI of the sickle-cell globin will be lower than the wild-type globin because the mutation replaces an uncharged side chain with one that carries negative charge. D) The pI of the sickle-cell globin will be higher than the wild-type globin because the mutation replaces a negatively charged side chain with one that carries no charge.

D

Each of the following is a noncovalent interaction EXCEPT: a) the interaction between an amino and a carboxylate group. b) a van der Waals interaction. c) an interaction between NH3+ and a water molecule. d) a carbon-hydrogen bond. e) a hydrogen bond.

D

If this model is correct, what are the implications for structural -prediction schemes? A) Any protein has substantial number of conformations. Sorting of optional secondary/tertiary structures are not a reliable method. B) Prions are formed from normal proteins only under the influence of wrongly folded ones. This event cannot be predicted by existing methods. C) Environmental conditions greatly affect the protein folding. Investigation of unchangeable primary structure provides reliable data. D) More than one secondary/tertiary folding can be observed for the same sequence. Sequence alone cannot dictate folding, and sequence-based predictions must sometimes fail.

D

Polyglycine, a simple polypeptide, can form a helix with ϕ=−80∘ , ψ=+150∘. From the Ramachandran plot (see the figure on the left), describe this helix. Check all that apply. A) It could have α helix structure. B) It could have antiparallel β strands structure. C) It could have parallel β strands structure. D) It could have polypeptide II helix structure. E) It could have 310 helix structure.

D

Subtilisin is used in some laundry detergents to help remove protein-type stains. What unusual kind of stability does this suggest for subtilisin? a) The enzyme must be stable to very high pressures. b) The enzyme must be stable to the presence of hydrogen. c) The enzyme must be stable both to the presence of detergents and to high pressures. d) The enzyme must be stable both to the presence of detergents and to moderately high temperatures.

D

The four most abundant chemical elements in living systems are: a) carbon, nitrogen, oxygen and potassium. b) hydrogen, oxygen, sulfur and phosphorus. c) sodium, potassium, carbon and oxygen. d) hydrogen, carbon, nitrogen and oxygen. e) sodium, potassium, nitrogen and sulfur.

D

The most critical substance in stimulating muscle contraction is: A) troponin T. B) tropomyosin. C) ATP. D) Ca2+. E) troponin C.

D

What is the difference between a nucleoside triphosphate and a trinucleotide? a) A nucleoside triphosphate yields upon complete hydrolysis one nucleobase, three sugars, and at least two phosphates. A trinucleotide yields three nucleobases, one sugar, and three phosphates. b) A nucleoside triphosphate yields upon complete hydrolysis three nucleobases, three sugars, and at least two phosphates. A trinucleotide yields one base, one sugar, and three phosphates. c) A nucleoside triphosphate yields upon complete hydrolysis three nucleobases, one sugar, and three phosphates. A trinucleotide yields one base, three sugars, and at least two phosphates. d) A nucleoside triphosphate yields upon complete hydrolysis one nucleobase, one sugar, and three phosphates. A trinucleotide yields three bases, three sugars, and at least two phosphates.

D

Which of the following statements is FALSE? a) In biochemical processes, energy can neither be created or destroyed. b) Organisms are open systems as they can exchange both energy and materials with their environments. c) Energy can be transferred between a system and the surroundings. d) Organisms are open systems as they can create energy from their environments. e) In an open system energy can be converted from one form into another.

D

If you assume maximum sequence similarity between α-melanotropin and β-melanotropin, then what must the sequence of the latter be? (α-melanotropin-SerTyrSerMetGluHisPheArgTrpGlyLysProVal) Arrange in order: MEHFR, DSGPYK, WGSPPK

DSGPYK, MEHFR, WGSPPK

What is the role of Glu 270 and Arg 145 in catalysis? Fill in the blanks: GBC (general base catalyst) dipole-dipole carbamate ion-ion dipole-induced dipole GAC (general acid catalyst) carboxylate E270 acts as a _________ in step one and as a ___________ in step two. R145 provides specific ______ interactions with the C-terminal ______ of the substrate. This confers specificity for cleavage of the C-terminal residue from the peptide substrate.

GBC GAC ion-ion carboxylate

If a mixture of these three substrates was presented to elastase with the concentration of each peptide equal to 0.5 {\rm mm}, which would be digested most rapidly? Which most slowly? (Assume enzyme is present in excess.) Rank from most rapidly to most slowly. PAPA!F PAPA!G PAPA!A

PAPA!F PAPA!A PAPA!G

Synthesis of sugar polymers is enzyme catalyzed and requires activated monomers like ________ in lactose biosynthesis.

UDP-galactose

If negatively supercoiled DNA is titrated with EtBr, the electrophoretic mobility decreases at first, but then increases at higher EtBr concentrations. Explain. a) EtBr would decrease negative supercoiling until W=0 and electrophoretic mobility would reach a minimum. Continued addition would cause positive supercoiling and increase electrophoretic mobility. b) EtBr would decrease positive supercoiling until T=0 and electrophoretic mobility would reach a minimum. Continued addition would cause negative supercoiling and increase electrophoretic mobility. c) EtBr would decrease positive supercoiling until W=0 and electrophoretic mobility would reach a minimum. Continued addition would cause negative supercoiling and increase electrophoretic mobility. d) EtBr would decrease negative supercoiling until T=0 and electrophoretic mobility would reach a minimum. Continued addition would cause positive supercoiling and increase electrophoretic mobility.

a

Small ions in biological fluids: a) encourage strong electrostatic interactions between oppositely charged macroions at low ionic strengths. b) have no effect on the interactions between oppositely charged macroions. c) tend to cluster around macroions of the same charge. d) encourage strong electrostatic interactions between oppositely charged macroions at high ionic strengths. e) have large effects on pH.

a

The equilibrium constant of a reaction: a) is related to the change in free energy of the reaction. b) can change if the concentration of reactants and products are changed. c) cannot be used to determine whether a reaction will proceed in the direction as written under non-standard conditions. d) is the same as the mass action ratio when the reaction is displaced from equilibrium. e) is not related to the change in free energy of the reaction.

a

Which of the following is FALSE when considering van der Waals interactions? a) They are not important in determining the stability of three-dimensional structures of proteins. b) The total interaction energy is the sum of the attractive and repulsive forces. c) Van der Waals radii can determine molecular surfaces. d) Molecules that interact by van der Waals forces do not interpenetrate.

a

Which of the following is NOT a feature of substrate-level enzyme regulation? a) It is sufficient for regulation of most enzyme-catalyzed reactions. b) A high substrate concentration will speed up the rate of reaction. c) A high product concentration will slow the rate of reaction. d) The product can be a competitor. e) Sometimes products can be competitive or uncompetitive.

a

The difference between a nucleoside and a nucleotide is: a phosphodiester bond. methylated cytosine. the presence of uracil. a 2' H group. a phosphate group.

a phosphate group

Explain the shape of the curve in panel (b). Why does v0 increase initially, before decreasing at higher [succinate]? Check all that apply. a) As the [succinate] increases, succinate will bind to T-state ATCase and promote the T → R switch. This accounts for the decrease of v0 in plot (b). b) As the [succinate] increases, it blocks more active sites from binding the true substrate (Asp), and the turnover of Asp decreases (as shown in plot (b)). c) At low [succinate], succinate blocks more active sites from binding the true substrate (Asp). This accounts for the initial rise in v0 in plot (b). d) At low [succinate], succinate will bind to T-state ATCase and promote the T → R switch, thereby activating the ATCase. This accounts for the initial rise in v0 in plot (b).

b and d

Is the effect of the mutation what you would expect for a residue that makes up part of the oxyanion hole? How do the reported values of and support your answer? Check all that apply. a) kcat should be reduced due to the gain of enthalpic stabilization of the transition state. b) For a mutation of a residue that only interacts with the oxyanion intermediate, one would not expect Km to change significantly. c) The oxyanion is formed after S binds. d) For a mutation of a residue that only interacts with the oxyanion intermediate, one would expect Km to change significantly. e) The oxyanion is formed after S goes away. f) kcat should be reduced due to the loss of enthalpic stabilization of the transition state.

b c f

How might you show that changes in secondary structure occur? Check all that apply. a) with ultraviolet spectroscopy b) with circular dichroism spectropolarimetry c) with SDS gel electrophoresis d) with fourier transform infrared spectroscopy e) with nuclear magnetic resonance spectroscopy

b, d, e

Which of the following is TRUE of hydrophobic molecules? a) They have limited solubility in water. b) They self-associate by releasing some of the surrounding water molecules. c) Dissolving in water decreases the entropy of the mixture. d) Water forms a cage-like structure around them. e) All of the above

e

Which of the following is a feature of allosteric regulation of enzyme activity? a) Cooperativity in substrate binding. B) Allosteric enzymes often have multiple active sites. c) There is often a range of different effectors for a single enzyme. d) Ligand binding causes a conformation change in the enzyme. e) All of the above

e

Which of the following statements about inhibitors of enzyme-catalyzed reactions is TRUE? a) A competitive inhibitor binds irreversibly to the enzyme at the active site. b) An uncompetitive inhibitor will always bind at the active site. c) An uncompetitive inhibitor typically affects KM but not kcat. d) Reversible inhibitors bind to either free enzyme or the enzyme-substrate complex but not both. e) A competitive inhibitor does not affect Vmax.

e

Which of the following statements about the proposed mechanisms of action for hen egg white lysozyme does NOT support either model? a) A water molecule is deprotonated, which then attacks C1 of the substrate. b) The active site glutamic acid changes between being protonated and deprotonated. C) Glycosidic bond cleavage occurs by general acid/base catalysis. d) A covalent intermediate is formed between an active site aspartate and C1 of the substrate. e) The active site aspartic acid changes between being protonated and deprotonated.

e

A stopped-flow apparatus is used to measure rates of pre-steady state slow enzymatic reactions. True False

false

A thermodynamically unfavorable reaction can become favorable when coupled to a highly endergonic reaction. True False

false

Almost all irreversible enzyme inhibitors bind noncovalently to the enzyme. True False

false

Amino acids and simple organic compounds like carbon dioxide and hydrogen cyanide cannot be produced without the use of enzymes. True False

false

Amphipathic molecules are not able to interact via van der Waals forces. True False

false

Antibodies cannot be used to purify proteins because the antibody-antigen interaction is too strong. True OR False

false

F-actin is a polymer of G-actin monomers and exhibits symmetry. True OR False

false

Fetal hemoglobin has a higher affinity for oxygen than does maternal hemoglobin because it has a higher affinity for the allosteric regulator 2,3-bisphosphoglycerate. True OR False

false

Glycine cannot serve as a buffer because it has two ionizable groups. True False

false

Glycosaminoglycans are polysaccharides composed of repeating disaccharide units in which one of the sugars is always N-acetylgalactosamine. True False

false

Most proteins have blocked amino and carboxyl terminals. True OR False

false

Non-catalyzed biochemical reactions always occur at physiological useful timescales. True False

false

Oxidation-reduction reactions, which are the basis of many biochemical reactions and pathways, cannot take place in the absence of oxygen. True False

false

Protein folding is a random process, whereby a vast number of possible conformations are tested to find the desired most stable state. True OR False

false

Proteins cannot self-assemble into a functional conformation after they have been denatured. True OR False

false

The change in enthalpy (ΔH) for the complete oxidation of a fatty acid is different depending on whether it occurs via a biochemical pathway or combustion to CO2 and H2O. True False

false

The greatest conformational change in the neck piece of myosin occurs during ATP hydrolysis. True OR False

false

The interactions that stabilize multisubunit complexes are different to those that stabilize tertiary structure. True OR False

false

The principle component of a biological membrane is a triglyceride. True False

false

Tropocollagen is a double helix of two left-handed polypeptide chains. True OR False

false

Viral genomes cannot be used as vectors for making recombinant DNA molecules. True False

false

When referring to the amino acid sequences of proteins, sequence homology is the same as sequence similarity. True OR False

false

Which two are present in both waxes and sphingomyelin? Select all that apply. glycerol fatty acid phosphate long-chain alcohol carbohydrate

fatty acid long-chain alcohol

Which of the following is NOT classed as a lipid? Palmitic acid Cholesterol Phosphatidyl serine Glycerol Triacylglycerol

glycerol

Which two are present in both fats and phosphatidylcholine? Select all that apply. glycerol fatty acid phosphate long-chain alcohol carbohydrate

glycerol fatty acid

Elastase is closely related to chymotrypsin. Suggest two kinds of amino acid residues you might expect to find in or near the active site. Check all that apply. histidine valine alanine proline serine

his ser

What is the natural polysaccharide whose repeating structure can be symbolized by GlcUAβ(1→3)GlcNAc, with these units connected by β(1→4) links? N-Acetylgalactosamine Hyaluronic acid Keratan sulfate Chitin Heparin Chondroitin sulfate

hyaluronic acid

An amphipathic molecule provides the foundation for biological membranes because they have both ________ and ________ functional groups.

hydrophobic hydrophilic

Subtilisin does have a problem in that it becomes inactivated by oxidation of a methionine close to the active site. Suggest a way to make a better subtilisin. Fill in the blanks: Val hydrophobic hydrophilic Ser His Replace the methionine, by site-directed mutagenesis, with another residue. Because methionine is quite ___________, a ___________ replacement would seem appropriate. A single base change in the Met codon could yield Phe, Leu, Ile, or _______.

hydrophobic hydrophobic Val

Which would be better for separation: gel electrophoresis or isoelectric focusing? gel electrophoresis isoelectric focusing

isoelectric focusing

Given the helix formed by polyglycine, what can be inferred about its handedness? A) It is left-handed. B) It is right-handed.

left-handed

In a favorable reaction the free energy of the products is ________ than the free energy of the reactants.

less

Which are present in a ganglioside but not in a fat? Select all that apply. glycerol fatty acid phosphate long-chain alcohol carbohydrate

long-chain alcohol carbohydrate

Fill in the blanks with the following: His 57 gain loss N-terminus C-terminus Asp 102 Ser 195 The change in between 6 and 7 must involve _______ of a proton in the active site. The best candidate is _______. The increase in at higher must involve a change in the binding site. The group involved is probably the __________ at Ile 16, created by the cleavage that activates chymotrypsin.

loss His 57 N-terminus

Fill in the blanks: stronger weaker higher lower The dielectric constant, , is ________ in the enzyme active site than it is in water; thus, Coulomb,s law predicts a __________ interaction between the H-bond donor and acceptor.

lower stronger

Acetylating agents such as acetic anhydride react preferentially with primary amines, iodoacetate reacts preferentially with sulfhydryl groups, and ATP-dependent kinases preferentially add a phosphoryl group to side-chain hydroxyl or phenolic −OH groups. Which amino acid side chains, or main chain groups, in a polypeptide are most likely to be modified by treatment with: acetic anhydride Check all that apply. Glutamine Proline Asparagine Lysine Arginine N-terminal amine ***** iodoacetate Serine Cysteine Methionine Valine ****** kinase + ATP Check all that apply. Serine Glutamic Acid Tyrosine Aspartic Acid Threonine

lysine and n-terminal amine cysteine serine, tyrosine, threonine

Which myoglobin is more thermodynamically stable, the mutant or the wild-type? mutant myoglobin wild-type myoglobin

mutant myoglobin

The _______ charge on the ______ side chain can form salt bridges with the other ______ side chains in the BPG-binding pocket and stabilize the ____-state. In essence, the _____ side chain is mimicking the ______ charge on BPG. Fill in the blanks with the following: T positive (+)-charged Lys (−)-charged R negative Asp

negative, Asp, (+)-charged, T Asp, negative

Would you expect an "enzyme" designed to bind to its target substrate as tightly as it binds the reaction transition state to show a rate enhancement over the uncatalyzed reaction? yes no --------- In other words, would such a protein actually be a catalyst? yes no --------- Explain why not. A) because the activation energy would be identical for both the catalyzed and uncatalyzed reactions B) because the protein is a very strong inhibitor and it slows the reaction C) because the temperature would be identical for both the catalyzed and uncatalyzed reactions D) because the entropy would be identical for both the catalyzed and uncatalyzed reactions

no no A

Which of the following in biological compounds are sufficiently electronegative to serve as strong donors in a hydrogen bond? Hydrogen and carbon Hydrogen and oxygen Nitrogen and carbon Nitrogen and hydrogen Oxygen and nitrogen

oxygen and nitrogen

If EtBr was added to relaxed, closed circular DNA, would you expect positive or negative supercoiling to occur? positive supercoiling negative supercoiling --------- Explain. a) Ethidium bromide induces positive superhelical writhe because twist (T) becomes less positive. b) Ethidium bromide induces positive superhelical writhe because twist (T) becomes more positive. c) Ethidium bromide induces positive superhelical writhe because writhe (W) becomes nearly zero. d) Ethidium bromide induces positive superhelical writhe because twist (T) becomes nearly zero.

positive supercoiling A

Fill in the blanks: unsoluble hydrophilic steroid nonmediated peptide would pore-mediated soluble hydrophobic would not __________ hormones are generally ___________ and can cross the outer membrane bilayer by ___________ diffusion. ___________ hormones are generally water ___________ proteins/oligopeptides that ___________ easily cross the outer membrane of a cell.

steroid hydrophobic nonmediated peptide soluble would not

Nearly all proteins contain: phosphorus. cobalt. sulfur. selenium. none of the above.

sulfur

A Lineweaver-Burk plot can be used to determine KM using initial-rate data for an enzyme-catalyzed reaction. True False

true

A reaction with a large negative free energy of hydrolysis can be coupled to the synthesis of ATP from ADP and Pi. True False

true

An important observation that assisted in the elucidation of the secondary structure of DNA was that the mole percent adenine was almost always the same as the mole percent of thymine. True False

true

Comparison of globin sequences from many different species suggests that myoglobin and hemoglobin have evolved from a single myoglobin-like protein. True OR False

true

D-ribose can form a ring structure with either four or five carbons in the ring. True False

true

Feedback regulation of a metabolic pathway can either be activation or inhibition. True False

true

Fibroin is a β-sheet protein, with a high proportion of glycine. True OR False

true

In a general redox reaction, the reductant becomes oxidized and the oxidant becomes reduced. True False

true

In an enzyme-catalyzed reaction, the lifetime of the transition state is similar to the vibrational frequencies of covalent bonds. True False

true

In size exclusion chromatography, the smallest proteins are eluted last. True OR False

true

Life is an irreversible process, such that it never comes to equilibrium. True False

true

Many biochemical reactions that form biopolymers from monomeric units involve the removal of water. True False

true

Metal ions are often required for catalytic efficiency but they may not remain permanently bound to the protein or take part in the catalytic process. True False

true

Protein biosynthesis uses only L-amino acids. True OR False

true

Proteins have an asymmetrical tertiary structure, while multisubunit proteins can exhibit several types of symmetry. True OR False

true

Pyruvate carboxylase is an example of the ligase class of enzymes. True False

true

Serine proteases make use of covalent catalysis as well as electrostatic stability of the transition state to achieve rate enhancement. True False

true

Single-stranded RNA molecules can have extensive regions of intramolecular base pairing leading to defined secondary and tertiary structure. True False

true

The amino acid side chain residues in an α helix point outwards away from the center of the helix. True OR False

true

The average charge on an amino acid below its pI will be positive. True False

true

The concentration of Ca2+ in the myoplasm can increase as much as 10,000 fold in response to a motor nerve impulse. True OR False

true

The folded conformation of proteins can be stabilized by the binding of a metal ion or cofactor. True OR False

true

The immunoglobulin domain is a stable scaffold containing two antiparallel beta-sheets upon which to display hypervariable loops. True OR False

true

Water is both a hydrogen bond donor and acceptor. True False

true

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 in the figure below in panel (a) with a salt bridge between residues histidine 13 and aspartic acid 85. The two monomers interact by salt bridges between the C- and N-termini. The O2-binding site lies between the two iron atoms shown, which are rigidly linked to helices A and C (see panel (b)). In the deoxy form, the space between the iron atoms is too small to hold O2, and so the Fe atoms must be forced apart when O2 is bound. Answer the following questions, explaining your answer in each case in terms of the structure shown below. ***** Is this molecule likely to show cooperative oxygen binding? ***** Explain your answer. A) The linkage between subunits makes it easier for the hemoglobin to release oxygen bound to it. Release of oxygen facilitates binding of more oxygen. B) The linkage between subunits is such that forcing one pair of helices apart favors moving the other pair apart, making O2 binding easier in the second pair. C) The salt bridge is such that binding of a O2 molecule decreases affinity and hence makes binding of other O2 molecules less likely. D) The salt bridge makes it more difficult for the hemoglobin to release oxygen bound to it and makes binding of other O2 molecules less likely. ***** Is this molecule likely to exhibit a Bohr effect? ***** Explain your answer. A) Protonation of aspartic acid 85 creates additional salt bridges, making it more difficult for hemoglobin to bind oxygen. B) Protonation of histidine 13 creates additional salt bridges, making it more difficult for hemoglobin to bind oxygen. C) Deprotonation of histidine 13 destroys the salt bridge, allowing easier opening of the O2 binding site. D) Deprotonation of aspartic acid 85 destroys the salt bridge, allowing easier opening of the O2 binding site. Predict the likely effect of a mutation that replaced aspartic acid 85 by a lysine residue. ***** Check all that apply. 1) The whole structure would become unstable. 2) The molecule would exhibit higher cooperativity. 3) The molecule would exhibit lower O2 affinity. 4) The molecule would exhibit lesser cooperativity. 5) The molecule would exhibit higher O2 affinity. 6) The whole structure would become more stable.

yes, B, yes, C, 1,4,5