Advanced Biochemistry
Exam Answer Key
Course Introduction
Advanced Biochemistry delves into the intricate molecular mechanisms that govern biological processes, building upon foundational biochemical principles. The course covers in-depth topics such as enzyme kinetics and regulation, metabolic pathway integration, advanced techniques in protein and nucleic acid analysis, signal transduction, and the biochemistry of complex biomolecules. Emphasis is placed on current research methods, experimental design, and the critical evaluation of scientific literature, preparing students for research or professional practice in the biochemical and biomedical sciences.
Recommended Textbook
Fundamentals of Biochemistry Life at the Molecular Level 5th Edition by Donald Voet
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Chapter 1: Introduction to the Chemistry of Life
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Sample Questions
Q1) Change in enthalpy (\(\Delta\)H)is best defined as
A)the sum of heat absorbed and work done.
B)the heat transferred at constant pressure.
C)the pressure change at constant temperature.
D)the measure of disorder in a system.
E)none of the above
Answer: B
Q2) The bulk of aerobic metabolism in eukaryotic cells takes place in A)the endoplasmic reticulum.
B)the nucleus.
C)the mitochondria.
D)peroxisomes.
E)the Golgi apparatus.
Answer: C
Q3) Explain in one or two sentences why scientists believe that all living organisms are related (that they have all evolved from a common ancestor)?
Answer: Biochemically,all living organisms are very similar.
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3
Chapter 2: Water
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Q1) Which of the following statements about water is not true?
A)The electron-rich oxygen atom of one water molecule can interact with the electron-poor proton on another water molecule to form a hydrogen bond.
B)Liquid water is only 15% less hydrogen bonded than ice.
C)Water is a nonpolar molecule that with a bent molecular geometry.
D)Water can form highly ordered,cage-like,structures around nonpolar molecules.
E)Water is a key player in the energetics of hydrophobic interactions.
Answer: C
Q2) The pH of a 0.1 M solution of sodium acetate would be
A)basic,because of the acetate ion reacts with water to form acetic acid and OH<sup>-</sup>.
B)acidic,because the acetate ion is acidic.
C)acidic,because the acetate ion forms acetic acid.
D)neutral,because salts are neither acidic nor basic.
E)basic,because the Na<sup>+</sup> ionizes and combines with OH<sup>-</sup>.
Answer: A
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Page 4
Chapter 3: Nucleotides, nucleic Acids, and Genetic Information
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Q1) Which of the following statements about nucleotides is false?
A)Nucleotides mediate transport of energy within the cell.
B)Nucleotides are involved in oxidation-reduction reactions.
C)Nucleotides store genetic information.
D)Nucleotides are involved in biosynthetic reactions.
E)none of the above
Answer: C
Q2) Genomic DNA is ______,resulting in the production of _________.
A)transcribed;mRNA
B)translated;tRNA
C)transcribed;protein
D)translated;protein
E)translated;rRNA
Answer: A
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Chapter 4: Amino Acids
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Sample Questions
Q1) Which amino acid does not have a primary \(\alpha\)-amino group?
A)glutamine
B)arginine
C)lysine
D)proline
E)glutamate
Q2) Which of the following amino acids has an uncharged polar side chain at pH 7.0?
A)Arg
B)Thr
C)Glu
D)Pro
E)Ile
Q3) Ribosomes use L amino acids to synthesize proteins.These amino acids are called "L" because
A)they are chiral.
B)they turn polarized light to the left.
C)they are all (S)-amino acids.
D)they are all (R)-amino acids.
E)none of the above
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Chapter 5: Proteins: Primary Structure
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Q1) A technique that can be used to separate proteins based primarily on the presence of non-polar residues on their surface is called
A)ion-exchange chromatography.
B)gel filtration chromatography.
C)affinity chromatography.
D)gel electrophoresis.
E)hydrophobic interaction chromatography.
Q2) Since there are 20 standard amino acids,the number of possible linear polypeptides of length N can be expressed as:
A)n × 20
B)20<sup>n</sup>
C)20 × 10<sup>n</sup>
D)n<sup>20</sup>
E)n × 10<sup>20</sup>
Q3) A variety of chromatographic techniques are available for protein purification.
a.Explain briefly the principle of hydrophobic interaction chromatography.
b.Name three changes that can be made to the eluant that can be used to speed up elution of the protein of interest from a hydrophobic interaction chromatography column.
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Chapter 6: Proteins: Three-Dimensional Structure
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Q1) Which one of these characteristics is not true for the \(\alpha\) helix?
A)There are 3.6 amino acids per turn.
B)There is a requirement for glycine every third amino acid residue.
C)A hydrogen bond forms between the carbonyl oxygen of the nth amino acid residue and the - NH group of the (n + 4)th amino acid residue.
D)Proline is typically not found in the \(\alpha\) helix.
E)It is right-handed.
Q2) Which of the following contribute to the minimization of energy that occurs with protein folding?
A)orientating amino acid groups to maximize hydrogen bonding
B)folding hydrophobic groups towards the exterior of the protein
C)burying polar groups towards the interior of the protein
D)extensive cavity formation
E)all of the above
Q3) When considering fibrous proteins,which of the following statements is TRUE?
A)Noncovalent interactions contribute to the strength of all of these proteins.
B)All of them consist of \(\alpha\) helix structure.
C)All of them require vitamin C.
D)Decrease in amounts of any of them cause scurvy.
E)All of these are true of fibrous proteins.
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Chapter 7: Protein Function Part I: Myoglobin and Hemoglobin
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Q1) The reaction of carbonic anhydrase catalyzes
A)the formation of carbamates with the concomitant release of protons.
B)the hydration of bicarbonate,resulting in the formation of carbonic acid.
C)the reduction of carbon dioxide with the concomitant consumption of protons.
D)the hydration of carbon dioxide,forming bicarbonate and protons.
E)the hydrolysis of carbamates with the concomitant consumption of protons.
Q2) Myoglobin and a single chain of hemoglobin have similar ______ structures.
A)primary
B)secondary
C)tertiary
D)quaternary
E)none of the above
Q3) Which statement about actin is correct?
A)Actin is expressed only in muscle.
B)Actin is expressed at low levels in most cells.
C)No known function has been described for actin in nonmuscle cells.
D)Nonmuscle cells only contain G actin.
E)Actin is the most abundant cytoplasmic protein in many cell types.
Q4) It appears that the heme group in myoglobin binds the O<sub>2</sub>.What is the function of the polypeptide?
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Chapter 8: Carbohydrates
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Sample Questions
Q1) Which structures shown in the figure above represent possible structures of glucose?
A)A
B)A and B
C)A and C
D)A,B,and C
E)None of the above
Q2) We encounter a great variety of sugars in living organisms.
a.Are most carbohydrates in living organisms D or L?
b.Draw a Fischer projection of the smallest aldose (include all atoms).
c.What is the name of this molecule?
Q3) Which of the following sequences represents a recognition site for N-linked glycosylation where X is any amino acid except Pro?
A)Gln-X-Ser
B)His-X-Ser
C)Arg-X-Ser
D)Asn-X-Ser
E)Asp-X-Ser
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Chapter 9: Lipids and Biological Membranes
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Q1) Proteins which are passed from one Golgi compartment to the next in a successive fashion do so via a mechanism called____.
A)maturation
B)cisternal progression
C)retrograde transport
D)anterograde transport
E)medialgrade transport
Q2) Which of the following processes presented in this chapter is (are)readily reversible with the help of enzymes known as thioesterases?
A)myristoylation
B)glycosylphosphotidylinositalation
C)palmitoylation
D)all of the above
E)none of the above
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11
Chapter 10: Membrane Transport
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Q1) Which of the following is not an example of a passive-mediated transporter?
A)aquaporins
B)the Kv ion channel
C)GLUT1
D)lactose permease
E)none of the above
Q2) Vanilomycin
A)is a cyclic polypeptide that functions as a K<sup>+</sup> carrier.
B)is a transmembrane polypeptide that transports K<sup>+</sup>.
C)is a cyclic polypeptide that functions as a Na<sup>+</sup> carrier.
D)is a transmembrane polypeptide that transports Na<sup>+</sup>.
E)is a \(\beta\)-barrel pore transporter that transfers K<sup>+</sup>.
Q3) The greater the magnitude of the concentration gradient:
A)the more rapid the rate of diffusion.
B)the more likely mediated transport is required.
C)the easier it is to reverse the flux.
D)the higher number of ATPs required to diffuse.
E)All of the above are true.
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Chapter 11: Enzyme Catalysis
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Sample Questions
Q1) Curved arrows are conventionally used to illustrate the movement of A)electron pairs.
B)single electrons.
C)protons.
D)anions.
E)All of the above use this convention.
Q2) Which of the following is TRUE regarding cofactors?
A)Coenzymes are often separate from the enzyme and do not need recharged.
B)Metal ions must be covalently attached to function as a cofactor.
C)Cofactor is a broad term used for all enzyme "helpers".
D)Prosthetic groups can dissociate readily and be regenerated for use in another enzyme.
E)An apoenzyme implies that a cofactor is present.
Q3) Which of the following amino acid residues would provide a side chain capable of increasing the hydrophobicity of a binding site?
A)histidine
B)lysine
C)isoleucine
D)arginine
E)serine
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Chapter 12: Enzyme Kinetics, inhibition and Control
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Q1) The catalytic efficiency of an enzyme can never exceed A)k<sub>2</sub>.
B)k<sub>1</sub>.
C)k<sub>-1</sub>.
D)k<sub>-1 </sub>+ k<sub>2</sub>.
E)(k<sub>-1 </sub>+ k<sub>2</sub>)/k<sub>1</sub>.
Q2) When [S] = K<sub>M</sub>,\(v\)<sub>0 </sub>= (_____)× (V<sub>max</sub>).
A)[S]
B)0.75
C)0.5
D)K<sub>M</sub>
E)k<sub>cat</sub>
Q3) [S] = K<sub>M</sub> for a simple enzymatic reaction.When [S] is doubled the initial velocity is
A)2 V<sub>max</sub>
B)equal to V<sub>max</sub>
C)(1/3)V<sub>max</sub>
D)0)5 V<sub>max</sub>
E)2 K<sub>M</sub>/[S]
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Chapter 13: Biochemical Signaling
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Q1) Which of the following functions as a regulatory protein by dephosphorylating activated enzymes?
A)receptor tyrosine kinase
B)phosphoprotein phosphatase
C)heterotrimeric G protein phosphorylase
D)guanine nucleotide exchange factor
E)Sos protein
Q2) Anthrax toxin functions by altering levels of cAMP.The toxin also contains an edema factor,which requires the activity of calmodulin (CaM)for proper function.Based on this information,which of the following can you conclude?
A)The toxin alters cAMP dependent cell signaling.
B)Calcium levels affect the function of the edema factor.
C)Unlike other toxins,the anthrax toxin does not function by altering biochemical signaling.
D)A and B
E)A and C
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15
Chapter 14: Introduction to Metabolism
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Q1) Consider the following metabolic reaction: 3-Phosphoglycerate \(\to\)2-Phosphoglycerate \(\Delta\)G°' = +4.40 kJ/mol
What is the \(\Delta\)G for this reaction when the concentration of 2-phosphoglycerate is 0.290 mM and the concentration of 3-phosphoglycerate is 2.90 mM at 37°C?
A)+10.3 kJ/mol
B)-1.53 kJ/mol
C)-1.30 kJ/mol
D)-5.93 kJ/mol
E)-4.40 kJ/mol
Q2) In redox half-reactions,a more positive standard reduction potential means
(I)the oxidized form has a higher affinity for electrons. (II)the oxidized form has a lower affinity for electrons. (III)the reduced form has a higher affinity for electrons. (IV)the greater the tendency for the oxidized form to accept electrons.
A)I only
B)II only
C)II,III
D)I,IV
E)II,IV
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Chapter 15: Glucose Catabolism
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Q1) The enzymes that catalyze glycolysis are located in the A)endoplasmic reticulum.
B)mitochondrial matrix.
C)cytosol.
D)inner mitochondrial membrane.
E)outer mitochondrial membrane.
Q2) Which of the following metabolic conversions is considered to be the major control point of glycolysis?
A)fructose-1,6-bisphosphate \(\to\) dihydroxyacetone phosphate + glyceraldehyde-3-phosphate
B)glucose \(\to\) glucose-6-phosphate
C)2-phosphoglyerate \(\to\) phosphoenolpyruvate
D)fructose-6-phosphate \(\to\) fructose-1,6-bisphosphate
E)phosphoenolpyruvate \(\to\) pyruvate
Q3) ATP
A)inhibits activity of phosphofructokinase (PFK)allosterically.
B)activates activity of phosphofructokinase (PFK)allosterically.
C)inhibits activity of phosphofructokinase (PFK)hormonally.
D)activates activity of phosphofructokinase (PFK)hormonally.
E)does not alter phosphofructokinase (PFK)activity.
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Chapter 16: Glycogen Metabolism and Gluconeogenesis
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Q1) Which of the following will NOT activate glycogen phosphorylase in the liver?
A)epinephrine
B)glucagon
C)eating a high carbohydrate meal
D)cAMP
E)All of the above will activate glycogen phosphorylase.
Q2) The membrane-bound polyisoprenol involved in the synthesis of N-linked glycoproteins is called ______.
A) phosphorylase a
B) gluconeogenesis
C) glucagon
D) glucose-6-phosphatase
E) cAMP
F) biotin
G) insulin
H) glycogenolysis
I) liver
J) glucose-1-phosphate
K) dolichol
L) muscle
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Page 18
Chapter 17: Citric Acid Cycle
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Q1) The compound ______ is a structural analog and competitive inhibitor of the enzyme succinate dehydrogenase.
A) oxaloacetate
B) malate synthase
C) malate
D) malonate
E) Krebs
F) aconitase
G) succinyl-CoA synthetase
H) -ketoglutarate
I) carbon dioxide
J) malate dehydrogenase
K) isocitrate
L) succinate dehydrogenase
Q2) One turn of the citric acid cycle generates
A)2 FADH<sub>2</sub>,3 ATP,1 NADH
B)1 NAD+,2FADH<sub>2</sub>,1 ATP
C)1 GTP,3 NADH,1 FADH<sub>2</sub>
D)1 FAD,2 ATP,3 NADH
E)1 FADH<sub>2</sub>,1GTP,2 NADH
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Page 19
Chapter 18: Electron Transport and Oxidative
Phosphorylation
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Q1) Molecules that prevent oxidative damage by the superoxide radical possess ______ properties.
A) shuttle
B) matrix
C) respiration
D) copper
E) heme
F) tunnel
G) plasma membrane
H) coenzyme Q
I) cytosol
J) antioxidant
K) wire
L) proton pump
Q2) All of the following inhibit electron transport EXCEPT
A)oxaloacetate
B)rotenone
C)anitimycin A
D)cyanide
E)All of the above inhibit electron transport,
Page 20
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Chapter 19: Photosynthesis
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Q1) Light activation of P680 results in which of the following?
(I)electron transfer as follows: Q<sub>A</sub> \(\to\) Q<sub>B</sub> \(\to\) Chl \(\to\) Pheo
(II)electron transfer from PSI directly back to the Pheo -Q<sub>A</sub> complex (III)reduction of S<sub>4</sub> of the OEC to S<sub>1</sub> of the OEC (IV)reduction of cytochrome b<sub>6</sub>f
A)I,III,IV
B)I,II
C)II,III
D)I only
E)IV only
Q2) The groups that initially absorb light in the Rps.viridis photosynthetic reaction center are observed to be arranged with ______,and are called the ______.
A)twofold symmetry,special pair
B)anti-parallel symmetry,RHC
C)trifold symmetry,tri-harvest center
D)shared menaquinone prosthetic groups,shared pair
E)none of the above
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Chapter 20: Lipid Metabolism
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Q1) In which location listed below does the following reaction take place?
HMG-CoA acetoacetate + Acetyl-CoA
A)cytosol of cardiomyocytes
B)mitochondria of cardiomyocytes
C)cytosol of liver cells
D)mitochondria of liver cells
E)all of the above
Q2) Which of the following diets would most likely promote the formation of ketone bodies?
A)high simple carbohydrates,low fat
B)high complex carbohydrates,high fructose
C)high fat,high protein,low carbohydrate
D)low fat,high protein,high complex carbohydrates
E)high fructose;high whole grain carbohydrates
Q3) PGH<sub>2</sub> is synthesized from ______ and triggers pain and ________.
A)cardiolipins;foam cell development
B)steroids;fever
C)salicylic acid;foam cell development
D)NSAIDS;COX-1
E)arachidonate;inflammation
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Chapter 21: Amino Acid Metabolism
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Q1) What species are combined to produce carbamoyl phosphate?
A)NH<sub>3</sub>
,PO<sub>4</sub><sup>3</sup><sup> </sup>,HCO<sub>3</sub><sup> </sup>
B)NH<sub>4</sub><sup>+</sup>,PO<sub>4</sub><sup>3</sup><sup> </sup>,Ac-CoA,rel
easing CoA-SH
C)glycine & inorganic phosphate,releasing CO<sub>2</sub>
D)acetate & NH<sub>4</sub><sup>+</sup>,releasing CO<sub>2</sub>
E)alanine & inorganic phosphate,releasing acetate
Q2) The majority of amino acids are deaminated by a ______ reaction.
A)transaminmation
B)reduction
C)condensation
D)transacetylation
E)oxidation
Q3) The metabolite chorismate
A)allosterically enhances production of aromatic amino acids.
B)is an important intermediate in the production of Trp,Tyr,and Phe.
C)is a derivative of glucose.
D)A and B
E)B and C
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Chapter 22: Mammalian Fuel Metabolism: Integration and Regulation
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Q1) At low glucose concentrations ( 5mM),the majority of glucose produced by liver cells is due to the action of A)glucokinase.
B)hexokinase.
C)glucose-6-phosphatase.
D)AMP-dependent protein kinase (AMPK).
E)AMP-responsive tyrosine kinase.
Q2) Animals lack the ability to produce glucose from ______.
A)other sugars
B)fatty acids
C)pyruvate
D)amino acids
E)starches
Q3) The glucose transporter in muscle cells is A)insulin.
B)glucagon.
C)GLUT2.
D)GLUT4.
E)none of the above
Page 24
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Chapter 23: Nucleotide Metabolism
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Q1) The amino group added to the C2 position on IMP to form GMP is derived from
A)"aspartate"
B)"aspargine"
C)"glutamine"
D)"\(\alpha\)-ketoglutarate"
E)"arginine"
Q2) The proposed mechanism of the Class I RNR involves
A)electron transfer directly from substrate to tyrosine 122.
B)electron transfer from substrate to various cysteine residues.
C)an exposed tyrosine which accepts an electron from the ribosyl radical.
D)electron donation to external reducing agents.
E)none of the above
Q3) John Buchanan began the elucidation of the synthesis of purine nucleotides by studying _______ excreted by pigeons fed isotopically labeled compounds.
A)"xanthine"
B)"hypoxanthine"
C)"uric acid"
D)"\(\beta\)-alanine"
E)"\(\beta\)-aminoisobutyrate"
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Page 25
Chapter 24: Nucleic Acid Structure
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Q1) Which of the following materials would be useful for a researcher seeking to purify chromosomal DNA of lysed E.coli cells from cellular proteins and RNA?
A)ethidium bromide
B)hydroxyapatite
C)acridine orange
D)proflavin
E)DNA gyrase
Q2) In B-DNA
A)the width of the base pair varies depending on the bases involved.
B)the base planes are rotated approximately 90<sup>°</sup> from the axis of the helix.
C)the sugar pucker must be variable depending on the base attached.
D)the helix twist is approximately 10<sup>°</sup> per base pair.
E)all of the above
Q3) Which of the following prokaryotic enzymes can introduce negative supercoils?
A)topoismerase IA
B)topoismerase III
C)DNA gyrase
D)all of the above
E)none of the above
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Page 26
Chapter 25: DNA Replication, repair and Recombination
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Q1) The process whereby nucleotides are removed from the 5' end of one DNA segment while nucleotides are added to the 3' end of the immediately preceding DNA segment is called ______.
A) SSB
B) Tus
C) primosome
D) ARS
E) ATS
F) primer
G) transposons
H) nick translation
I) photolyase
J) processive
K) G-loops
L) G-quartets
M) accurate
N) lagging strand synthesis
O) MCM
P) abortive
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Chapter 26: Transcription and Rna Processing
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Q1) The term rRNA refers to ______ RNA.
A)ribosomal
B)retroviral
C)recombinant
D)rho factor
Q2) In which of the following types of eukaryotics RNAs are introns completely removed most of the time,although exceptions can occur?
(I)mRNA
(II)rRNA
(III)tRNA
A)I,II
B)I,III
C)II,III
D)I,II,III
E)none of the above
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28
Chapter 27: Protein Synthesis
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Q1) The fidelity of amino acid attachment to a tRNA is enhanced by the ______ ability of the corresponding aaRS.
A) AUG
B) sense
C) release factors
D) noninitiator
E) hairpin
F) preproteins
G) genetic code
H) penicillin
I) proproteins
J) proofreading
K) UUA
L) synonyms
M) nucleotide cypher
N) streptomycin
O) nonsense
P) revising
Q) cloverleaf
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Chapter 28: Regulation of Gene Expression
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Q1) To induce expression of the lac operon,_______ can be added to the cell medium.
A) globin
B) M phase
C) G<sub>0</sub> phase
D) necrosis
E) euchromatin
F) S phase
G) riboswitch
H) histone
I) insulators
J) heterochromatin
K) Mediator
L) 1,6-allolactose
M) apoptosis
N) orphan
O) galactose
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