Etiket Arşivleri: BIOL0280

BIOL0280 Third Midterm Examination 2013

Biological amines are generated by decarboxylation of amino acids . 2. [2 points] The hormones epinephrine and norepinephrine are derived biosynthetically from: A) arginine. B) histidine. C) isoleucine. D) tryptophan. E) tyrosine. Circle the correct answer 3. [4 points] Draw the structure of UMP in the space provided below. Your answer must be completely correct to receive credit. 4. [2 points] Ribonucleotide reductase is a key enzyme in nucleotide biosynthesis. In one sentence, describe its biochemical function. Ribonucleotide reductase converts ribonucleotides to deoxyribonucleotides.

Explain the function of the two regulatory sites of ribonucleotide reductase, The primary regulatory site controls overall enzymatic activity and the substrate specificity site controls relative enzymatic activity i.e., which substrates are preferentially reduced. and list molecules that bind to each of these two regulatory sites. Primary site: ATP and dATP Specificity site: ATP, dATP, dGTP, dTTP 6. [2 points] The difference between a ribonucleotide and a deoxyribonucleotide is: A) a deoxyribonucleotide has an —H instead of an —OH at C-2. B) a deoxyribonucleotide has α configuration at C-1; a ribonucleotide has β configuration. C) a ribonucleotide has an extra —OH at C-4. D) a ribonucleotide has more structural flexibility than deoxyribonucleotide. E) a ribonucleotide is a pyranose, deoxyribonucleotide is a furanose. Circle the correct answer 7. [2 points] Which of the following are possible base compositions for double-stranded DNA? %A %G %C %T %U A) 5 45 45 5 0 B) 20 20 20 20 20 C) 35 15 35 15 0 D) All of the above. E) None of the above. Circle the correct answer.

In the Watson-Crick model of DNA structure (now called B-form DNA): A) a purine in one strand always hydrogen bonds with a purine in the other strand. B) A–T pairs share three hydrogen bonds. C) G–C pairs share two hydrogen bonds. D) the 5 ‘ ends of both strands are at one end of the helix. E) the bases occupy the interior of the helix. Circle the correct answer. 9. [2 points] Nucleosomes: A) are important features of chromosome organization in bacteria. B) contain proteins that are rich in acidic amino acids. C) are composed of protein and RNA. D) bind DNA in the form of a solenoidal supercoil. E) occur in chromatin at irregular intervals along the DNA molecule. Circle the correct answer. 10. [6 points] Calculate values for the following topological properties of a closed-circular DNA molecule containing 2,000 base pairs (for simplicity, assume there are 10 base pairs per turn in the relaxed DNA). (a) What is the linking number (Lk) when the DNA is 200 relaxed? (b) What is the linking number (Lk) when the DNA has 198 been underwound by 2 turns? (c) Will the DNA in (b) adopt positive or negative negative supercoils? 11. [2 points] When a DNA molecule is described as replicating bidirectionally, that means that it has two: A) chains. B) independently replicating segment. C) origins. D) replication forks. E) termination points. Circle the correct answer.

Briefly describe the biochemical role of the following enzymes in DNA replication in E. coli: (a) DNA helicase unwinds double-stranded DNA during replication (b) Primase synthesizes RNA primers (c) the 3 ‘ → 5′ exonuclease activity of DNA polymerase proofreads newly synthesized DNA by removing mismatched nucleotides (d) the 5′ → 3’ exonuclease activity of DNA polymerase I removes RNA primers 13. [6 points] In the space below, draw the product of the deamination reaction for the base shown on the left: deamination Name the bases: Cytosine Uracil Which repair pathway is most likely to repair this lesion? The base excision repair pathway

Below, an RNA molecule is being transcribed from a strand of DNA. (a) Label the 5′ and 3′ ends of the RNA molecule. (b) Label the 5′ and 3′ ends of the DNA template strand. (c) Using an arrow, indicate the direction of synthesis. 3´ 5´ 3´ 5´ 15. [5 points] For each of the following statements, indicate with a P if the statement applies only to prokaryotes, an E if the statement applies only to eukaryotes, and a B if the statement applies to both eukaryotes and prokaryotes. _B_ RNA polymerase initiates transcription de novo, with no requirement for a primer. _ E_ Promotor sequences have little intrinsic affinity for RNA polymerase. _P_ A single RNA polymerase transcribes genes that encode mRNAs, tRNAs, and rRNA. _P_ Sigma (σ) subunit detaches from RNA polymerase after transcription has initiated. _ E_ At the 5′ end of the mature mRNA there is a cap consisting of a guanosine joined to the 5′-terminal nucleotide through a 5 ‘ to 5 ‘ triphosphate group. 16. [2 points] A branched (“lariat”) structure is formed during: A) attachment of a 5’ cap to mRNA. B) attachment of poly(A) tails to mRNA. C) processing of preribosomal RNA. D) splicing of all classes of introns. E) splicing of group II introns. Circle the correct answer. 17. [2 points] Splicing of introns in nuclear mRNA primary transcripts requires: A) a guanine nucleoside or nucleotide. B) endoribonucleases. C) polynucleotide phosphorylase. D) RNA polymerase II. E) small nuclear RNAs (snRNAs). Circle the correct answer.

The template strand of a segment of double-stranded DNA contains the sequence: (5ʹ)CTT TGA TAA GGA TAG CCC TTC(3ʹ) (a) What is the base sequence of the mRNA that can be transcribed from this strand? Be certain to label all 5 ʹ and 3 ʹ ends in your answer. (5ʹ)GAA GGG CUA UCC UUA UCA AAG(3ʹ) (b) What amino acid sequence could be coded by the mRNA base sequence in (a), using only the first reading frame starting at the 5 ‘ end? (You may refer to the genetic code on the last page of the exam.) Glu-Gly-Leu-Ser-Leu-Ser-Lys (c) Suppose the other (complementary) strand is used as a template for transcription. What is the amino acid sequence of the resulting peptide, again starting from the 5’ end and using only the first reading frame? The codons translate to Leu-Stop-Stop. No peptide would be produced because of the stop codons. 19. [7 points] Match the factor or enzyme at the left with the stage(s) of protein synthesis at which it acts. If a factor or enzyme participates in two stages of protein synthesis, indicate both of them. A) RF C Amino acid activation B) EF-G D, E Initiation C) aminoacyl-tRNA B Elongation D) Shine-Dalgarno sequence E) IF-3 A, B, E Termination 20. [2 points] Approximately how many high-energy phosphate bonds must be consumed to incorporate one amino acid into a protein? (I.e., per peptide bond.) A) 0 B) 1 C) 2 D) 4 E) 8 Circle the correct answer.

In one or two sentences, define the following terms with respect to regulation of transcription: (a) Constitutive Refers to constant, unregulated transcription (b) Induction Refers to increased transcription through activation or positive regulation (c) Repression Refers to decreased transcription through negative regulation (d) Repressor Acts to impede access of RNA polymerase to promoters. (e) Co-activator Mediates interactions between RNA polymerase and transactivators. Does not bind DNA directly. 22. [4 points] In prokaryotes such as E. coli, many operons that encode enzymes involved in amino acid biosynthesis begin with a sequence coding for a leader peptide. This peptide has no known enzymatic function and is rich in the amino acid that is synthesized by the enzymes coded for in the operon. What is the function of this leader peptide? The leader peptide is integral to the regulatory mechanism called transcription attenuation. In prokaryotes, transcription and translation are closely coupled. The ability to translate the leader peptide signals that the relevant amino acid is readily available in the cell and that transcription of the operon is undesirable at this time. Translation through the leader peptide (when the amino acid is abundant) allows the formation of a hairpin attenuator structure downstream in the nascent RNA chain. This attenuator acts as a transcription terminator, causing dissociation of the RNA polymerase. When the relevant amino acid is in short supply, the ribosome stalls trying to synthesize the leader peptide. A different secondary structure forms in the nascent RNA, preventing formation of the terminator and allowing continued transcription of the operon.

Certain restriction enzymes produce cohesive (sticky) ends. This means that they: A) cut both DNA strands at the same base pair. B) cut in regions of high GC content, leaving ends that can form more hydrogen bonds than ends of high AT content. C) make a staggered double-strand cut, leaving ends with a few nucleotides of single- stranded DNA protruding. D) make ends that can anneal to cohesive ends generated by any other restriction enzyme. E) stick tightly to the ends of the DNA they have cut. Circle the correct answer. 24. [3 points] Match each vector with the appropriate method used for its introduction into host cells: (a) Electroporation b Plasmid (b) Transformation c Bacteriophage λ (c) Infection a BAC (Bacterial Artificial Chromosome) 25. [3 points] In order to amplify Gene X shown below using PCR, to what region and strand would the two oligonucleotide primers anneal? A) Region A and B of the top strand. B) Region A of both strands. C) Region A of the top strand and region B of the bottom strand. D) Region A of the bottom strand and region B of the top strand. E) None of the above. Circle the correct answer and draw the primers on the diagram.

A plasmid that encodes resistance to ampicillin and tetracycline is digested with the restriction endonuclease PstI, which cuts the plasmid at a single site in the ampicillin- resistance gene. The cut plasmid DNA is then ligated with a PstI digest of human DNA and introduced into E. coli cells. (a) What antibiotic would you put in an agar plate to ensure that the cells of a bacterial colony contain the plasmid? tetracycline (b) What will the antibiotic-resistance phenotypes be of the bacteria growing on the plate? R S (In your answer, use tet to refer to tetracycline resistance, tet to refer to tetracycline R S sensitivity, amp to refer to ampicillin resistance and amp to refer to ampicillin sensitivity.) R R tet amp R S tet amp (c) Which phenotype will indicate the presence of plasmids that contain human DNA fragments? Provide a brief explanation. R S tet amp This phenotype indicates that the gene for ampicillin resistance has been interrupted by the insertion of a human DNA fragment.

BIOL0280 Third Midterm Examination 2012

δ-Aminolevulinic acid is formed from succinyl-CoA and __________ and is an intermediate in the biosynthesis of _________.

A) acetyl-CoA; long chain fatty acids

B) glycine; heme

C) serine; heme

D) serine; sphingosine

E) α-ketoglutarate; glutamate and proline

Circle the correct answer

BIOL0280 First Midterm Examination 2014

Given that pK = 2; pK = 9; pK = 11, Draw the ionization states and calculate the pI of 1 2 R lysine . Write the PI on the line below 3points for correct ionization state structures, 1 point for correct pI PI=9+11/2=10 pI = 10 3 points for drawing and 1 point for PI 2. [4 points] Draw the structure of Tyr-Ser-Asp in the ionic form that predominates at pH 7. Draw all atoms (including hydrogens) as well as any charges necessary. O O O H H H N CH C N CH C N CH C O 3 CH2 CH2 CH2 OH C O O OH 2 points for correct structure (side chains and amide bond linkages), 1 point for putting correct amino acids at the n terminus and c terminus, 1 point for getting the ionization states correct including all side chains and the n and c terminus

The amino acid substitution of Val for Glu in Hemoglobin S results in aggregation of the protein because of ___________ interactions between molecules. A) covalent B) disulfide C) hydrogen bonding D) hydrophobic E) ionic Circle the correct answer. 4. [2 points] In the sequencing of peptides by tandem mass spectrometry, peptide molecules are fragmented into smaller molecules to determine the amino acid sequence of the peptide. The types of bonds broken to generate MSMS tandem mass spectra are A) carbon-carbon bonds within the amino acid side chains B) disulfide bonds C) amide bonds D) bonds between alpha carbons and amino groups in the polypeptide backbone E) bonds between alpha carbons and carbonyl groups in the polypeptide backbone Circle the correct answer. 5. [2 points] A B C D E Leu-Ala-Phe Tyr-Lys-Met Asp-Pro-Glu Gly-Pro-Arg Asp-Trp-Tyr Which one of the above tripeptides: __C__(a) is most negatively charged at pH 7? __A__(b) contains the largest number of nonpolar R groups? 6. [2 points] An α helix would be destabilized most by: A) interactions between neighboring Asp and Arg residues. B) interactions between two adjacent hydrophobic Val residues. C) the presence of an Arg residue near the carboxyl terminus of the α helix. D) the presence of two Lys residues near the amino terminus of the α helix. E) the presence of a Glu residue near the amino terminus of the α helix. Circle the correct answer. 7. [2 points] The major reason that antiparallel β-stranded protein structures are more stable than parallel β-stranded structures is that the latter: A) are in a slightly less extended configuration than antiparallel strands. B) do not have as many disulfide crosslinks between adjacent strands. C) do not stack in sheets as well as antiparallel strands. D) have fewer lateral hydrogen bonds than antiparallel strands. E) have weaker hydrogen bonds laterally between adjacent strands. Circle the correct answer.

Experiments on denaturation and renaturation in the enzyme ribonuclease (RNase) by Dr. Anfinsen have shown that: A) folding of denatured RNase into the native, active conformation, requires the input of energy in the form of heat. B) native ribonuclease does not have a unique secondary and tertiary structure. C) the completely unfolded enzyme, with all —S—S— bonds broken, is still enzymatically active. D) the enzyme, dissolved in water, is thermodynamically stable relative to the mixture of amino acids whose residues are contained in RNase. E) the primary sequence of RNase is sufficient to determine its specific secondary and tertiary structure. Circle the correct answer. 9. [2 points] Which one phrase best describes the hydrogen bonds in a β sheet? A) they occur mainly near the amino and carboxyl termini of the strands. B) they are perpendicular to the plane of the sheet. C) they occur mainly between atoms of the R groups. D) they occur only between some of the amino acids of each strand. E) they occur mainly between atoms of adjacent strands in a sheet. Circle the correct answer. 10. [6 points] Supply the missing words in each of the following 3 sentences. Choose from increase, decrease, or remain unchanged. Increasing the concentration of HCO3– in a solution of hemoglobin (without changing the pH) causes the affinity for O to _____decrease_. 2 Increasing the pH of a solution of hemoglobin causes the affinity for O to _______ increase __. 2 Removing 2,3 BPG from a solution of adult hemoglobin causes the affinity for O to _ increase _. 2 14. [4 points] Name two examples of proteins with atypical protein structures discussed in lecture 2 and explain briefly the key characteristics of these atypical protein structures . 2 points for naming them. Myosin, keratin or collagen 2 points for explaining the concept of coiled-coils. 1 point for either of the following concepts: – myosin and keratin contain two right-handed helices twisted in a left-handed superhelix – amphiphilic helices – collagen contains three left-handed helices in a right-handed superhelix – rope-like structures -3.5 residues per turn myosin keratin -collagen contains Gly at center of triple helix -collagen contains Pro hydroxyproline

Enzymes catalyze the rapid formation of product by: A) shifting the position of the equilibrium between substrate and product in favor of product. o B) lowering ΔG´ of the reaction. C) raising the free energy of the substrate. D) raising ΔG‡ E) none of the above. Circle the correct answer. 13. [5 points] Write out the simple chemical reaction that describes the mechanism for enzyme action used as a model by Michaelis and Menten. Indicate the rate constants for all steps in this reaction. List the assumptions used by Michaelis and Menten to derive a rate equation for this reaction. Finally write down the Michaelis Menten equation. The chemical reaction (with rate constants) is: 2 points k k k 1 2 3 E + S ES EP E + P k-1 k-2 k-3 Assumptions: One assumption is that significant product has not accumulated, so that the rate of the reaction depends exclusively on the breakdown of ES and is not influenced by the reverse reaction; that is, k-2 can be ignored and V = k [ES]. This condition is possible only if early reaction times are 0 2 measured; the velocity, therefore, is an initial velocity. A second assumption is that the rate of ES formation equals the rate of ES breakdown; in other words, the reaction is at a steady state. A third assumption is [S] >> [E ], so that total [S], which equals free substrate and enzyme-bound substrate, t is essentially equal to [S]. 2 points for assumptions (1 each) Michaelis Menten equation: V =V [S]/(K +[S]) 0 max m 1 point 11. [4 points] In lecture 3 we discussed the T and R states describing the quaternary structure of hemoglobin. Describe briefly the two principal models for the cooperative binding of ligands to proteins such as hemoglobin with multiple ligand binding sites. Be sure to name both models and provide an explanation of the differences between the two. Ans: In the concerted model, binding of a ligand to one site on one subunit results in an allosteric effect that converts all of the remaining subunits to the high-affinity conformation. As a result, all of the subunits are either in the low- or high-affinity conformation. In the sequential model, each subunit is changed individually to the high affinity conformation. As a result, there are many possible combinations of low- and high-affinity subunits.

An enzyme follows Michaelis-Menten kinetics. Indicate (with an “x”) which of the kinetic parameters at the left would be altered by the following factors. Give only one answer for each. K V Neither Both Factor m max X competitive inhibitor X noncompetitive inhibitor 16. [2 points] Which amino acids in chymotrypsin are found in the active site and are participants in substrate cleavage? A) his, ser, asp B) his, ser, glu C) asp, lys D) lys, arg E) his, ser, arg Circle the correct answer. 17. [2 points] How is specificity determined by chymotrypsin? A) interaction of the substrate with the oxyanion hole B) binding of the N-terminus amino acid at the active site C) covalent binding of a his residue to the substrate D) conformational change upon binding of substrate E) binding of the proper amino acid into a deep pocket on the enzyme Circle the correct answer. 18. [2 points] In the following oligopeptide, indicate by drawing vertical line(s) where chymotrypsin would hydrolyze peptide bond(s). (You cannot receive credit if your vertical line(s) is/are drawn through a letter) : D—A—V—T—W–|-C—L—A—F–|-T—K—S—G 19. [2 points] Catalytic antibodies are most likely to be active if they are made by using an antigen that: A) resembles the substrate. B) is composed of an equimolar mixture of substrate and product. C) resembles the enzyme-substrate complex. D) resembles a transition state intermediate. E) is an allosteric modulator. Circle the correct answer. 20. [4 points] The Michaelis-Menten constant, Km, is actually a summary of three rate constants. Write down the equation to calculate Km based on these rate constants. Describe a method to determine Km graphically indicating precisely how K is measured. m K = (k + k )/k m 2 –1 1 K can be determined graphically on a plot of V vs. [S] by finding the [S] at which V = 1/2 m 0 0 V . More conveniently, on a double-reciprocal plot, the x-axis intercept = –1/ K . max m 2 points for Km equation, 2 points for Km from V vs. S plot, or 2 points for double reciprocal plot x intercept of -1/Km

How is chymotrypsinogen converted to chymotrypsin? A) A protein kinase-catalyzed phosphorylation converts chymotrypsinogen to chymotrypsin. B) An increase in Ca2+ concentration promotes the conversion. C) Proteolysis of chymotrypsinogen forms chymotrypsin. D) Chymotrypsinogen dimers bind an allosteric modulator, cAMP, causing dissociation into active chymotrypsin monomers. E) Two inactive chymotrypsinogen dimers pair to form an active chymotrypsin tetramer. Circle the correct answer. 22. [2 points] The enzyme ATCase is regulated by CTP, which binds to the T-state of ATCase. CTP is a: A) heterotropic positive allosteric regulator. B) heterotropic negative allosteric regulator. C) cofactor. D) competitive inhibitor. E) homotropic negative allosteric regulator. Circle the correct answer. 23. [2 points] Circle the fatty acid in each pair that has the lower melting temperature. A) 18:1Δ9 18:2Δ 9,12 B) 16:0 18:0 24. [2 points] Vitamin A (retinol), vitamin K (phylloquinone), testosterone, and cortisol are all members of a single family of lipids. Draw the structure of the basic building block that is used to assemble all of these molecules. 25. [4 points] The bacterium E. coli can grow at 20 °C or at 40 °C. At which growth temperature would you expect the membrane phospholipids to have a lower ratio of unsaturated to saturated fatty acids, and why? At 40 °C, the membranes of E. coli will contain a lower ratio of unsaturated to saturated fatty acids than at 20 °C. The cell regulates fatty acid composition to achieve the same fluidity in its membranes, regardless of growth temperature. Saturated fatty acids counterbalance the fluidizing effect of high temperature by providing additional hydrophobic interactions.

Glucose transport through intestinal epithelial cells involves two types of transporters. Glucose is first transported into the intestinal epithelial cell by _________ and then it is transported out by _________. A) secondary active transport / primary active transport B) facilitated diffusion / secondary active transport C) primary active transport / secondary active transport D) secondary active transport / facilitated diffusion E) secondary active transport / secondary active transport Circle the correct answer. + + 27. [2 points] In one catalytic cycle, the Na /K ATPase transporter transports: + + A) 2 Na out, 3 K in, and converts 1 ATP to ADP + P . i + + B) 3 Na out, 2 K in, and converts 1 ATP to ADP + P . i + + C) 3 Na in, 2 K out, and converts 1 ATP to ADP + P . i + + D) 1 Na out, 1 K in, and converts 1 ATP to ADP + P . i + + E) 2 Na out, 3 K in, and converts 1 ADP + P to ATP. i Circle the correct answer. 28. [2 points] Which one of the following chemical modifications (I-IV) would result in the conversion of D-fructofuranose from a reducing carbohydrate to a non-reducing carbohydrate? I CH3 A) II H C O 3 IV B) I O a HO a OH e O f C) IV H C 2 b b H OH e OH D) III H H c d H C f E) None of the above OH H 2 OH Circle the correct answer. H III CH3 c II O d O CH3 H 29. [2 points] Label each of the following as an aldose, a ketose, or neither. H H H H H H C OH O C H C OH HO C H C O C O H C OH HO C H H C OH H C OH H C OH HO C H HO C H C O H C H H H H H H (a) (b) (c) (d) (e) ___Ketose__ __Aldose___ __neither__ ___aldose_

Indicate in the blanks provided the match between the molecules and their biological roles. (a) peptidoglycan ____d____ homopolysaccharide of glucose in animals (b) starch ____b____ homopolysaccharide of glucose in plants (c) chitin ____c____ exoskeleton of lobsters (d) glycogen ____a____ structural component of bacterial cell walls 33. [3 points] Indicate the oxidation state of each carbon in the fructose molecule shown below: Oxidation State C1 _____5______ C2 _____2______ C3 _____4______ C4 _____4______ C5 _____4______ C6 _____5______ 31. [2 points] What factor contributes most significantly to the thermodynamic stability of the monosaccharide glucose relative to other monosaccharide six carbon D-aldoses? Most thermodynamically stable form of glucose is the form with all non-hydrogen substituents in the equatorial position. No other 6 carbon D-aldose is fully equatorial 32. [4 points] (a) Describe one biological advantage of storing glucose units in branched polymers (glycogen, amylopectin) rather than in linear polymers. The enzymes that act on these polymers to mobilize glucose for metabolism act only on their nonreducing ends. With extensive branching, there are more such ends for enzymatic attack than would be present in the same quantity of glucose stored in a linear polymer. In effect, branched polymers increase the substrate concentration for these enzymes. (b) What is the biological advantage to an organism that stores its carbohydrate reserves as starch or glycogen rather than as an equivalent amount of free glucose? The polymers are essentially insoluble and contribute little to the osmolarity of the cell, thereby avoiding the influx of water that would occur with the glucose in solution. They also make the uptake of glucose energetically more feasible than it would be with free glucose in the cell. Full credit for recognition of concentration difference or full credit for concept of less reducing ends

Standard reduction potentials are tabulated as: Oxidized form → Reduced form + electrons. A) True B) False Catabolic pathways diverge, anabolic pathways converge. A) True B) False Circle the correct answer. 36. [2 points] One molecule of NADH is produced per glucose in the conversion of glucose to lactate A) True B) False Circle the correct answer. Triose phosphate isomerase decreases ΔG for the step in glycolysis catalyzed by aldolase through rapid removal of dihydroxyacetone phosphate. A) True B) False Circle the correct answer 37. [2 points] The pentose phosphate pathway can alternatively be called the pentose phosphate cycle because _______ is a net product of the pathway that can be recycled. A) phosphate B) NADP+ C) carbon dioxide D) ribose 5-phosphate E) UDP-glucose Circle the correct answer. 38. [2 points] The conversion of pyruvate to ethanol also causes the ______. A) Oxidation of NADH B) Production of ADP C) Release of CO 2 D) Generation of an ion gradient across mitochondrial membranes E) Both A and C Circle the correct answer. 39. [2 points] ATP is both a substrate and a negative effector (inhibitor) for the allosteric, glycolytic enzyme phosphofructokinase (PFK). Which of the following answers best explains this observation? A) ATP has equal affinity for the active site and the regulatory (allosteric) site of PFK B) ATP only binds the regulatory site of PFK at low concentrations C) ATP only binds the regulatory site of PFK at high concentrations D) ATP and AMP are both negative effectors of PFK Circle the correct answer.

BIOL0280 First Midterm Examination 2013

Is the molecule shown D- or L-alanine? D-alanine 2. [2 points] What kind of reaction is peptide bond formation (eg. redox, cleavage, hydrolysis, etc)? a condensation reaction 3. [2 points] In a highly basic solution, pH = 13, the dominant form of glycine is: A) NH —CH —COOH. 2 2 – B) NH —CH —COO . 2 2 + – C) NH —CH —COO . 2 3 D) NH +—CH —COOH. 3 2 + – E) NH —CH —COO . 3 2 Circle the correct answer. 4. [6 points] Draw the structure of Met–Leu-Arg in the ionic form that predominates at pH 7. Draw all atoms (including hydrogens) as well as any charges as necessary. O O O H H H N CH C N CH C N CH C O 3 CH2 CH2 CH2 CH2 CH CH2 H C CH S 3 3 CH2 CH3 NH C NH2+ NH2 5. [2 points] Why are peptide bonds planar? The partial double bond character makes the peptide bond planar.

Which of the following refers to particularly stable arrangements of amino acid residues in a protein that give rise to recurring patterns? A) Primary structure B) Secondary structure C) Tertiary structure D) Quaternary structure E) None of the above Circle the correct answer. 7. [2 points] A D-amino acid would interrupt an α helix made of L-amino acids. Another naturally occurring hindrance to the formation of an α helix is the presence of: A) a negatively charged Asp residue. B) two Ala residues side by side. C) a nonpolar residue near the carboxyl terminus. D) a positively charged Lys residue. E) a negatively charged Glu residue. Circle the correct answer. 8. [2 points] Which two amino acids are most commonly found in β-turns? Pro and Gly 9. [4 points] What types of amino acids are typically found in the interior of a water-soluble globular protein and why are these amino acids located in the interior? Hydrophobic amino acid residues cluster away from the surface in globular proteins, so much of the protein’s interior is a tightly packed combination of hydrocarbon and aromatic ring R groups with very few water molecules. 10. [2 points] List two (or more) ways to denature proteins High or low pH, detergents, temperature, chaotropic agents 11. [2 points] In a mixture of the five proteins listed below, which should elute first in size- exclusion (gel- filtration) chromatography? A) cytochrome c M = 13,000 r B) immunoglobulin G M = 145,000 r C) ribonuclease A M = 13,700 r D) RNA polymerase M = 450,000 r E) serum albumin M = 68,500 r Circle the correct answer.

In one sentence, define the term ‘ligand’ A ligand is a molecule that is bound reversibly by a protein. 13. [2 points] In the binding of oxygen to myoglobin, the relationship between the concentration of oxygen and the fraction of binding sites occupied can best be described as: A) linear with a negative slope. B) hyperbolic. C) linear with a positive slope. D) random. E) sigmoidal. Circle the correct answer. 14. [2 points] Carbon monoxide (CO) is toxic to humans because: A) it binds to myoglobin and causes it to denature. B) it is rapidly converted to toxic CO . 2 C) it binds to the globin portion of hemoglobin and prevents the binding of O . 2 D) it binds to the Fe in hemoglobin and prevents the binding of O . 2 E) it binds to the heme portion of hemoglobin and causes heme to unbind from hemoglobin. Circle the correct answer. 15. [2 points] Which of the following is not correct concerning 2,3-bisphosphoglycerate (BPG)? A) It binds at a distance from the heme groups of hemoglobin. B) It binds with lower affinity to fetal hemoglobin than to adult hemoglobin. C) It increases the affinity of hemoglobin for oxygen. D) It is an allosteric modulator. E) It is normally found associated with the hemoglobin extracted from red blood cells. Circle the correct answer. 16. [2 points] Which one of the following statements is true of enzyme catalysts? A) Their catalytic activity is independent of pH. B) They are generally equally active on D and L isomers of a given substrate. C) They can increase the equilibrium constant for a given reaction by a thousand-fold or more. D) They can increase the reaction rate for a given reaction by a thousand-fold or more. E) To be effective, they must be present at the same concentration as their substrate. Circle the correct answer.

In one or two sentences, describe the lock-and-key and the transition state model as proposed by Emil Fischer and Linus Pauling, respectively. Lock-and-key: Enzymes are structurally complementary to their substrates Transition state model: Enzyme active sites are complementary not to the substrate but to the transition state conformation. 2 points each. 18. [2 points] Michaelis and Menten assumed that the overall reaction for an enzyme- catalyzed reaction could be written as k k 1 2 E + S ES E + P k-1 Using this reaction, the rate of breakdown of the enzyme-substrate complex can be described by the expression: A) k ([E ] – [ES]). 1 t B) k ([E ] – [ES])[S]. 1 t C) k [ES]. 2 D) k [ES] + k [ES]. -1 2 E) k-1 [ES]. Circle the correct answer. 19. [2 points] The following data were obtained in a study of an enzyme known to follow Michaelis-Menten kinetics: V Substrate added 0 (mmol/min) (mmol/L) ————————————— 217 0.8 325 2 433 4 488 6 647 1,000 ————————————— The K for this enzyme is approximately: m A) 1 mM. B) 1,000 mM. C) 2 mM. D) 4 mM. E) 6 mM. Circle the correct answer.

The double-reciprocal transformation of the Michaelis-Menten equation, also called the Lineweaver-Burk plot, is given by 1/V = K /( V [S]) + 1/V . 0 m max max To determine K from a double-reciprocal plot, you would: m A) multiply the reciprocal of the x-axis intercept by -1. B) multiply the reciprocal of the y-axis intercept by -1. C) take the reciprocal of the x-axis intercept. D) take the reciprocal of the y-axis intercept. E) take the x-axis intercept where V = 1/2 V . 0 max Circle the correct answer. 21. [2 points] The number of substrate molecules converted to product in a given unit of time by a single enzyme molecule at saturation is referred to as the: A) dissociation constant. B) half-saturation constant. C) maximum velocity. D) Michaelis-Menten number. E) turnover number. Circle the correct answer. 22. [2 points] Which three amino acids (residues) form the catalytic triad of chymotrypsin? Ser, His, Asp 23. [4 points] Describe the functional contribution of the hydrophobic pocket for the enzymatic reaction catalyzed by chymotrypsin. The hydrophobic pocket accommodates aromatic residues (F, Y, W) and defines substrate binding and enzymatic specificity. 24. [2 points] Indicate with numbers the correct order of steps in the chymotrypsin reaction mechanism (must be all correct to receive credit): ____6_____ release of product 2 ____3_____ release of product 1 ____2_____ ester formation ____5_____ ester hydrolysis ____ 1_____ substrate binding ____4_____ water deprotonation

Enzyme X exhibits maximum activity at pH = 6.9. X shows a fairly sharp decrease in its activity when the pH goes much lower than 6.4. One likely interpretation of this pH activity is that: A) a Glu residue on the enzyme is involved in the reaction. B) a His residue on the enzyme is involved in the reaction. C) the enzyme has a metallic cofactor. D) the enzyme is found in gastric secretions. E) the reaction relies on specific acid-base catalysis. Circle the correct answer. 26. [2 points] A good transition-state analog: A) binds covalently to the enzyme. B) binds to the enzyme more tightly than the substrate. C) binds very weakly to the enzyme. D) is too unstable to isolate. E) must be almost identical to the substrate. Circle the correct answer. 27. [2 points] What is the effect of a double bond on fatty acid structure? Most double bonds in fatty acids are in the cis configuration. This results in a rigid bend in the hydrocarbon chain. 28. [4 points] What is the (molecular) difference between triglycerides and phosphoglycerides and what are their most common functions in cells? Triglycerides: glycerol esterified with three fatty acids Phosphoglycerides: 3-phosphoglycerate esterified with two fatty acids Triglycerides: storage, phosphoglycerides: membrane components 29. [2 points] Which of these is a general feature of the lipid bilayer in all biological membranes? A) Individual lipid molecules in one face (monolayer) of the bilayer readily diffuse (flip-flop) to the other monolayer. B) Polar, but uncharged, compounds readily diffuse across the bilayer. C) Individual lipid molecules are free to diffuse laterally in the surface of the bilayer. D) The bilayer is stabilized by covalent bonds between neighboring phospholipid molecules. E) The polar head groups face inward toward the inside of the bilayer. Circle the correct answer.

In one sentence, define integral membrane proteins. Integral membrane proteins are tightly associated (and span) the membrane and can only be removed by disrupting hydrophobic interactions with detergents or organic solvents. 31. [2 points] Movement of water across membranes is facilitated by proteins called: A) annexins. B) aquaporins. C) hydropermeases. D) selectins. E) transportins. Circle the correct answer. 32. [2 points] Glucose transport into erythrocytes (not into intestinal epithelial cells) is an example of A) primary active transport B) secondary active transport C) facilitated symport D) facilitated uniport E) none of the above Circle the correct answer. 33. [2 points] The molecule shown to the right is a(n) A) aldopentose B) ketopentose C) aldohexose D) ketohexose E) aldotetrose Circle the correct answer. 34. [2 points] When two carbohydrates are epimers: A) they differ only in the configuration around one chiral carbon atom. B) they differ only in the configuration of the anomeric carbon. C) one is a pyranose, the other a furanose. D) one is an aldose, the other a ketose. E) they differ only in the number of carbon atoms. Circle the correct answer.

Which of the following pairs is interconverted in the process of mutarotation? A) α-D-glucose and β-D-fructose B) α-D-glucose and β-D-galactose C) α-D-glucose and β-D-glucosamine D) α-D-glucose and β-D-glucose E) α-D-glucose and β-L-glucose Circle the correct answer. 36. [4 points] a) Explain how it is possible that a polysaccharide molecule, such as glycogen, may have only one reducing end, and yet have many nonreducing ends. The molecule is branched, with each branch ending in a nonreducing end. 2 points for the word branched b) Explain how homopolysaccharides of glucose can have either helical or planar structures. Helical confirmation results from α1-4 linkages between the glucose monomers and planar structures result from β1-4 linkages between the glucose monomers. Hydrogen bonding stabilizes these structures 2 points for discussion of α/β linkages or 1 point for discussion of H bonds 37. [2 points] Penicillin and related drugs inhibit the enzyme ; A) β-lactamase B) transpeptidase C) chymotrypsin D) lysozyme E) hexokinase Circle the correct answer. 38. [2 points] All of the following contribute to the large, negative, free-energy change upon hydrolysis of ATP except: A) electrostatic repulsion in the reactant. B) low activation energy of forward reaction. C) stabilization of products by extra resonance forms. D) stabilization of products by ionization. Circle the correct answer.

Biological oxidation-reduction reactions always involve: A) direct participation of oxygen. B) formation of water. C) transfer of electron(s). D) mitochondria. E) transfer of proton(s). Circle the correct answer. 40. [2 points] The first five reactions of glycolysis (the preparatory phase) transform each glucose molecule that enters into: A) One molecule of fructose-1,6-bisphosphate B) One molecule of dihydroxyacetone phosphate and one molecule of glyceraldehyde-3- phosphate C) Two molecules of glyceraldehyde-3-phosphate D) Two molecules of pyruvate E) Two molecules of dihydroxyacetone phosphate Circle the correct answer. 41. [2 points] Transfer of a high-energy phosphoryl group to ADP, resulting in ATP, occurs when: A) 1,3-bisphosphoglycerate → 3-phosphoglycerate B) phosphoenolpyruvate (PEP) → 2-phosphoglycerate C) 3-phosphoglycerate → 2-phosphoglycerate D) Both A and B E) Both A and C Circle the correct answer. 42. [2 points] The main function of the pentose phosphate pathway is to: A) give the cell an alternative pathway should glycolysis fail. B) supply pentoses and NADPH. C) make use of pyruvate produced in glycolysis. D) supply ATP. E) supply NADH. Circle the correct answer. 43. [2 points] During strenuous exercise, the NADH formed in the glyceraldehyde 3- + phosphate dehydrogenase reaction in skeletal muscle must be reoxidized to NAD if glycolysis is to continue. The most important reaction involved in the reoxidation of NADH is: A) dihydroxyacetone phosphate → glycerol 3-phosphate B) glucose 6-phosphate → fructose 6-phosphate C) pyruvate → lactate D) isocitrate → α-ketoglutarate E) oxaloacetate → malate Circle the correct answer.

BIOL0280 First Midterm Examination 2012

Draw the structure of Ala–Glu-Gly in the ionic form that predominates at pH 7. Draw all atoms (including hydrogens) as well as any charges as necessary. O O O H H H N CH C N CH C N CH C O 3 CH3 CH2 H CH2 C O O 2. [2 points] Titration of isoleucine by a strong base, for example NaOH, reveals two pK ’s. The titration reaction occurring at pK (pK = 2.4) is: 1 1 − − A) —COOH + OH → —COO + H O. 2 + − B) —COOH + —NH2 → —COO + —NH2 . + − C) —COO + —NH → —COOH + —NH . 2 2 + − D) —NH + OH → —NH + H O. 3 2 2 − − E) —NH + OH → —NH + H O. 2 2 Circle the correct answer. 3. [4 points] Pauling and Corey showed that in small peptides, six atoms associated with the peptide bond all lie in a plane. Draw a dipeptide of two amino acids in trans linkage (side-chains must be shown as —R), and indicate which six atoms are part of the planar structure of the peptide bond.

An octapeptide composed of four repeating alanylglycyl units has: A) one free amino group on an glycyl residue. B) one free amino group on an glycyl residue and one free carboxyl group on a alanyl residue. C) one free amino group on a alanyl residue and one free carboxyl group on an glycyl residue. D) two free amino and two free carboxyl groups. E) two free carboxyl groups, both on glycyl residues. Circle the correct answer. 5. [2 points] The diagram to the right illustrates: A) the polypeptide chain of an alpha-helix B) two polypeptides of a beta-pleated sheet running in a parallel fashion C) two polypeptides of a beta-pleated sheet running in an antiparallel fashion D) a flexible coil segment of a polypeptide E) two polypeptides of a coiled coil Circle the correct answer. 6. [2 points] A sequence of amino acids in a certain part of protein is -S-G-P-G-. The sequence is most probably part of a(n): A) random coil B) parallel beta sheet C) beta turn D) alpha helix E) antiparallel beta sheet Circle the correct answer. 7. [2 points] Roughly how many amino acids are there in one turn of an α helix? A) 1 B) 2.8 C) 3.6 D) 4.2 E) 10 Circle the correct answer. 8. [4 points] Describe (succinctly) the experimental design of the experiment conducted by Dr. Anfinsen that led to the conclusion: “The primary sequence of a protein determines its three-dimensional shape and thus its function.” 2 points for the word “denatured” 1 point for concept of fold back into native configuration 1 point for concept of native configuration has enzymatic activity

In hemoglobin, the transition from R state to T state (high to low affinity) is triggered by: A) Fe2+ binding. B) heme binding. C) oxygen binding D) subunit dissociation. E) 2,3 BPG binding Circle the correct answer. 10. [2 points] Which of the following statements about allosteric control of enzymatic activity is false ? A) Allosteric effectors give rise to sigmoidal V vs. [S points] kinetic plots. 0 B) Allosteric proteins are generally but not always composed of several subunits. C) An effector may either inhibit or activate an enzyme. D) Binding of the effector changes the conformation of the enzyme molecule. E) Heterotropic allosteric effectors compete with substrate for binding sites. Circle the correct answer. 11. [2 points] When oxygen binds to a heme-containing protein, the two open coordination bonds of Fe2+ are occupied by: A) one O molecule and one amino acid atom. 2 B) one O molecule and one heme atom. 2 C) two O atoms. D) two O molecules. 2 Circle the correct answer. 12. [2 points] The following values were determined for alcohol dehydrogenase in the absence and in the presence of acetaldehyde, an inhibitor: K (mM) V (micromoles/min) m max In the absence of acetaldehyde 0.10 750 In the presence of acetaldehyde 0.10 500 Acetaldehyde is a(n) __________________ inhibitor. A) competitive B) noncompetitive C) uncompetitive D) mixed E) irreversible Circle the correct answer. 13. [2 points] The proximal histidine residue in myoglobin coordinates Fe2+ and acts to (choose one): A) prevent oxidation of the heme Fe2+ B) lower the relative affinity for CO C) assist in the binding of O 2 D) prevent binding of N 2 E) decrease Θ Circle the correct answer.

The steady state assumption, as applied to enzyme kinetics, implies: A) K = K . m D B) the enzyme is regulated. C) the ES complex is formed and broken down at equivalent rates. D) the K is equivalent to the cellular substrate concentration. m E) the maximum velocity occurs when the enzyme is saturated. Circle the correct answer. 15. [6 points] (No calculators allowed on this question) An enzyme catalyzes the reaction A → B. The initial rate of the reaction was measured as a function of the concentration of A. The following data were obtained: [A], micromolar V , nmoles/min 0 0.05 0.08 0.1 0.16 0.5 0.79 1 1.6 5 7.3 10 13 50 40 100 53 5,000 79 10,000 80 20,000 80 A) What is the K of the enzyme for the substrate A (expressed as a number and explain how you m determined it to get credit for the answer)? K =[S] when V =1/2 * Vmax or 50 micromolar m 0 B) What is the value of V when [A] = 43 (Setup but do not solve the calculation)? 0 V =Vmax [S]/(K +[S])=80 * 43 / (50+43) or 37 nmoles/min 0 m The above data was plotted as 1/ V vs. 1/[A] , and a straight line was obtained. 0 C) What is the value of the x-intercept of the line (expressed as a fraction)? -1 -1 x intercept: -1/km=-1/50 micromolar or -0.02 micromolar

An enzyme catalyzes a reaction at a velocity of 10 µmol/min when all enzyme active sites -5 are occupied with substrate. The K for this substrate is 1 × 10 M. Assuming that Michaelis- m Menten kinetics are followed, what will the reaction velocity be when the concentration of S is (a) 1 -5 × 10 M . (a)= 5 umol/min 17. [2 points] One of the enzymes involved in glycolysis, aldolase, requires Zn2+ for catalysis. Under conditions of zinc deficiency, when the enzyme may lack zinc, it would be referred to as the: A) apoenzyme. B) coenzyme. C) holoenzyme. D) prosthetic group. E) substrate. Circle the correct answer. 18. [2 points] The scheme S → T → U → V → W → X → Y represents a hypothetical pathway for the metabolic synthesis of compound Y. The pathway is regulated by feedback inhibition. Assuming S → T is the rate-limiting step, indicate where the inhibition is most likely to occur and what the most likely inhibitor is. Draw an arrow at where the inhibition occurs and circle the likely inhibitor: S → T → U → V → W → X → Y 19. [4 points] a) What is the effect of increased concentration of CO2 on the binding of oxygen to hemoglobin? [2 points] The affinity decreases with increasing CO2. (b) Briefly describe the mechanism of this effect. At higher [CO2], CO2 reacts with the n terminus of the polypeptide (1point), which alters charge-charge interactions between the subunits(1 point), which stabilizes the low affinity conformation of the protein subunits.

Provide the correct answers below in the spaces given A) In the active site of chymotrypsin, a ___His[1 points]_____ residue increases the nucleophilicity of a nearby ____Ser[1 points]______ residue, which makes a covalent bond to the substrate. B) A hydrophobic pocket provides_________ substrate specificity [2 points]________ C) The oxyanion hole provides________ transition state stabilization[2 points]____________ 21. [2 points] Which of the following contains an ether-linked alkyl group? A) Oleoyl oleate B) Triacylglycerol C) Phosphatidyl serine D) Platelet-activating factor E) Sphingomyelin Circle the correct answer. 22. [2 points] An example of a glycerophospholipid that is involved in cell signaling is: A) cholesterol. B) triacylglycerol. C) phosphatidylinositol. D) testosterone. E) vitamin A (retinol). Circle the correct answer. 23. [2 points] Which of these statements about facilitated diffusion across a membrane is true? A) A specific membrane protein lowers the activation energy for movement of the solute through the membrane. B) It can increase the size of a transmembrane concentration gradient of the diffusing solute . C) It is impeded by the solubility of the transported solute in the nonpolar interior of the lipid bilayer. D) It is responsible for the transport of gases such as CO across biological membranes. 2 E) It requires the highly exergonic hydrolysis of ATP. . Circle the correct answer. 24. [4 points] Explain how a biochemist might discover that a certain enzyme is allosterically regulated in the absence of a crystal structure. The enzyme would show kinetics that do not fit the Michaelis-Menten equation; the plot of V0 vs. [S] would be sigmoidal, not hyperbolic and the plot of 1/v vs 1/[S] would be nonlinear. The 0 enzyme kinetics would be affected by molecules other than the substrate(s). 4 points for sigmoidal v vs. [S points] plot or nonlinear 1/v vs 1/[s] plot 4 points for enzyme kinetics affected by molecules other than substrate for a max of 4 points

Which of the sugars shown in the figure are L sugars? A) A and B B) B and C C) C and D D) A and D E) None of the above Circle the correct answer. 26. [2 points] Which sugar is the enantiomer of sugar A? A) B B) C C) D D) B and D E) none of the above Circle the correct answer. 27. [2 points] Which two sugars shown in the figure are epimers? A) A and B B) B and C C) C and D D) A and D E) None of the above Circle the correct answer. 28. [2 points] Which of the following monosaccharides is not an aldose? A) erythrose B) fructose C) glucose D) glyceraldehyde E) ribose Circle the correct answer. 29. [4 points] Show the basic structure of all glycerophospholipids. Indicate the charge on the molecule if any at pH 7. All glycerophospholipids have two fatty acids in ester linkage with C-1 and C-2 of glycerol; often the fatty acid at C-1 is saturated, and that at C-2 is unsaturated. C-3 of glycerol is joined to an alcohol-containing head group through a phosphodiester linkage, which is negatively charged at neutral pH.

The fluidity of the lipid side chains in the interior of a bilayer is generally increased by: A) a decrease in temperature. B) an increase in fatty acyl chain length. C) an increase in the percentage of phosphatidyl ethanolamine D) a decrease in the number of unsaturated fatty acids. E) an increase in the number of double bonds in fatty acids. Circle the correct answer. 31. [2 points] Which of following is an anomeric pair? A) D-glucose and D-fructose B) D-glucose and L-fructose C) D-glucose and L-glucose D) α-D-glucose and β-D-glucose Ε) α-D-glucose and β-L-glucose Circle the correct answer. 32. [2 points] Indicate whether the following two statements are true or false (True / False) 2 protons are transferred in every redox reaction (True / False) Standard reduction potentials, E’ º, are relative to that of oxygen 33. [2 points] Redox reactions require an electron _____donor____________ and an electron _______acceptor_________ Answer can be inverted and still be correct 34. [3 points] Explain how homopolysaccharides of glucose can have either helical or planar structures. Helical confirmation results from alpha1-4 linkages (1.5 pts) between the glucose monomers and planar structures result from beta1-4 (1.5 pts) linkages between the glucose monomers. Hydrogen bonding stabilizes these structures

Once inside a cell, glucose is rapidly phosphorylated to glucose-6-phosphate. What is the main purpose of this phosphorylation? A) to form a low-energy compound B) to activate PFK-1 C) to trap glucose inside the cell D) to prevent mutarotation Circle the correct answer. 36. [2 points] Hamsters love to run on exercise wheels. Prolonged running at a high rate of speed requires ATP. Could a hamster with a defective gene for the enzyme lactate dehydrogenase meet the extra ATP demand for prolonged, fast wheel-running by maintaining a high rate of glycolysis? Why or why not? A) No, not enough NAD+ can be regenerated for glycolysis to continue at a high rate. B) No, the defective gene will cause a rapid decline in pH in the muscles used for running. C) Yes, the defective gene has no effect on the glycolytic pathway. D) Yes, the enzyme alcohol dehydrogenase will supply the needed NAD+ if the lactose dehydrogenase cannot. Circle the correct answer. 37. [2 points] Indicate whether the following statement is true or false (True/False) In the preparatory phase of glycolysis, a glucose molecule is converted to two pentose phosphate molecules, at the expense of (driven by) the hydrolysis of two ATP molecules. 38. [2 points] Indicate whether the following statements are true or false by circling T or F for each question. T / F Phosphofructokinase 1 requires ATP as a substrate. T / F Phosphofructokinase 1 is allosterically activated by AMP. 39. [2 points] The ultimate electron acceptor in the fermentation of glucose to ethanol is: A) acetaldehyde. B) acetate. C) ethanol. + D) NAD . E) pyruvate. Circle the correct answer.