Course Introduction
Advanced Biochemistry Exam Preparation Guide
Advanced Biochemistry builds upon foundational biochemical principles to explore the molecular mechanisms underpinning biological processes at a deeper level. This course covers topics such as enzyme kinetics and regulation, advanced metabolic pathways, protein and nucleic acid structure and function, and the integration of cellular signaling networks. Emphasis is placed on the latest research techniques, including molecular modeling, spectroscopic analysis, and omics technologies. Students will critically analyze primary literature, engage in experimental design, and develop a deeper understanding of the molecular basis of health and disease.
Recommended Textbook
Fundamentals of Biochemistry Life at the Molecular Level 4th Edition by Donald Voet
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Chapter 1: Introduction to the Chemistry of Life
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Sample Questions
Q1) Phosphoglucomutase catalyses the reaction in which a phosphate group is transferred from the 1 carbon of glucose to the 6 carbon of glucose (G1P \(\rightleftarrows\) G6P).A student at SDSU incubates a 0.2 M solution of glucose-1-phosphate overnight with a small amount of the enzyme.At equilibrium the concentration of glucose 1-phosphate is 9.0 × 10<sup> </sup><sup>3</sup> M and the concentration of glucose 6-phosphate is 19.1 × 10<sup> </sup><sup>2</sup> M. Calculate the equilibrium constant (K<sub>eq</sub>)and the standard state free energy ( G°')for this reaction at 25°C.
Answer: The equilibrium constant K<sub>eq</sub> = [G6P]eq/[G1P]eq = 19.1 × 10<sup> </sup><sup>2</sup> M/ 9.0 × 10<sup> </sup><sup>3</sup> M = 21.
\(\Delta\)G° = RTlnK<sub>eq</sub> = 8.3145 × 298 J/mol × ln 21.2 = 7,600 J/mol.
Q2) 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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Chapter 2: Water
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Q1) Octane molecules dispersed in water tend to aggregate because that allows water molecules to be more ______.
A)hydrogen bond
B)rotational
C)H PO
D)H PO
E)HPO 2
F)disordered
G)positive entropy
H)negative entropy
I)higher electronegativity
J)insoluble
K)tetrahedral arrangement
L)acid
M)base
N)only partially ionized
Answer: F
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Chapter 3: Nucleotides, Nucleic Acids, and Genetic Information
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Q1) Gel electrophoresis generally separates nucleic acids on the basis of A)shape.
B)sequence.
C)size.
D)charge-density.
E)none of the above
Answer: C
Q2) RNA occurs primarily as single stranded molecules that can give rise to _______ structures.
A)diploid
B)stem-loop
C)parallel
D)tautomeric
E)haploid
Answer: B
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Chapter 4: Amino Acids
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Q1) What is the name of the N-terminal amino acid in the peptide shown above?
A)cysteine
B)methionine
C)valine
D)alanine
E)tryptophan
Q2) The pK<sub>1</sub>, pK<sub>2</sub>, and pK<sub>R</sub> for the amino acid lysine are 2.2, 9.1, and 10.5, respectively.At pH 1.0, lysine would be charged predominantly as follows:
A)(\(\alpha\)-carboxylate 0, \(\alpha\)-amino 1, \(\varepsilon\)-amino 1, net charge 2)
B)(\(\alpha\)-carboxylate 1, \(\alpha\)-amino +1, \(\varepsilon\)-amino +1, net charge +1)
C)(\(\alpha\)-carboxylate +1, \(\alpha\)-amino +2, \(\varepsilon\)-amino +2, net charge +5)
D)(\(\alpha\)-carboxylate 0, \(\alpha\)-amino +1, \(\varepsilon\)-amino +1, net charge +2)
E)(\(\alpha\)-carboxylate +2, \(\alpha\)-amino +1, \(\varepsilon\)-amino +1, net charge +4)
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Chapter 5: Proteins: Primary Structure
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Q1) We are able to purify proteins because they differ from each other in various physical or chemical properties.List 5 physicochemical properties of proteins that can be used as basis for their separation.Give a method of separation based on each of these properties (match the method with the property).
Q2) You are trying to separate five proteins, which are listed below, by gel filtration chromatography.Which of the proteins will elute first from the column?
A)cytochrome c (12 kDa)
B)RNA polymerase (99 kDa)
C)glutamine synthetase (621 kDa)
D)interferon-\(\gamma\) (34 kDa)
E)hemoglobin (62 kDa)
Q3) Which statement about insulin is correct?
A)Insulin is composed of two polypeptides, the A chain and the B chain.
B)Insulin contains an intrachain disulfide bond.
C)Insulin contains interchain disulfide bonds.
D)The A chain and the B chain of insulin are encoded by a single gene.
E)All of the above are correct.
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Chapter 6: Proteins: Three-Dimensional Structure
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Q1) Which of the following is true regarding crystalline proteins?
A)Many crystallized enzyme proteins remain catalytically active.
B)The diffractive pattern observed during X-ray exposure to the crystal can be used to calculate the electron density map of the crystalline protein.
C)The larger region indicating electron density with in the electron density map, the more accurate the structure determination.
D)A and B are true.
E)A, B, and C are true.
Q2) Which of the following changes would not alter the functional characteristics of keratin?
A)Increasing the number of residues per turn to 4.1 while maintaining the same amino acid sequence.
B)Substitution of a hydrophilic amino acid for a hydrophobic amino acid at position a and d of the 7-residue pseudorepeat.
C)Decreasing the number of cysteine amino acids within each protofilament.
D)Changing the environment surrounding the protein to one that is more reductive.
E)All of the above would alter the functional characteristics of keratin.
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Page 8
Chapter 7: Protein Function Part I: Myoglobin and Hemoglobin
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Q1) Myoglobin's primary physiological role is to facilitate oxygen ________.
A)storage
B)metabolism
C)binding
D)reduction
E)diffusion
Q2) During muscle contraction
A)myosin pulls actin filaments toward the M disk.
B)myosin pushes actin filaments toward the Z disk.
C)actin pulls myosin toward the Z disk.
D)actin pushes myosin toward the M disk.
E)All of the answers above are correct.
Q3) Which statement about myosin is not true?
A)Myosin is a heterohexamer.
B)Myosin contains two globular heads.
C)Myosin contains six different polypeptides
D)Myosin aggregates to form thick filaments
E)All of the answers above are true of myosin.
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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Q1) Which polysaccharide is found in a helically coiled conformation?
A)chitin
B) -amylose
C)cellulose
D)lignin
E)none of the above
Q2) Which two sugars shown in the figure above are epimers?
A)A and B
B)B and C
C)C and D
D)A and D
E)None of the above
Q3) How many stereoisomers are possible for an aldopentose such as ribose?
A)2
B)4
C)8
D)16
E)32
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Chapter 9: Lipids and Biological Membranes
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Q1) Which of the following amino acids from an integral membrane protein would likely contact the membrane?
A)Asn
B)Gln
C)Glu
D)Ala
E)Asp
Q2) Lipid bilayers with high concentrations of gangliosides are rare.Which of the following explanations is correct?
A)The hydrophobic tails on gangliosides form a conical shape rather than a cylindrical shape making close packing difficult.
B)Gangliosides contain large headgroups making close packing difficult.
C)Gangliosides contain trans fatty acids resulting in a bent hydrophobic tail making close packing difficult.
D)All of the above are correct.
E)None of the above is correct.
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Chapter 10: Membrane Transport
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Q1) The concentration of cytosolic Ca<sup>2+</sup> is _________ the extracellular concentration of Ca<sup>2+</sup>.
A)dependent upon B)equal to C)4 orders of magnitude greater than D)2 order of magnitude greater than E)much less than
Q2) Which of the following is evidence for aquaporins?
A)Kidney cells are otherwise incapable of maintaining a gradient.
B)Kidney cell transport of water molecules can be inhibited by mercuric ions.
C)Water, a polar substance, cannot cross the hydrophobic membrane without mediation.
D)Rapid rates of water transport require mediation.
E)Studies measuring flux of water molecules in the kidney yielded only linear plots of flux vs.[H<sub>2</sub>O] despite the large excess in water.
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12
Chapter 11: Enzyme Catalysis
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Q1) Large rate enhancement in enzyme catalysis may occur when binding the substrate via _________ attachment.
A)high
B)deprotonated
C)protonated
D)catalytic mechanism
E)covalent
F)rate-determining step
G)leaving group
H)formation of ES
I)amino acid
J)low
K)coenzymes
L)concerted acid-base
M)orientation
N)oxidation
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Chapter 12: Enzyme Kinetics, Inhibition and Control
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Q1) Enzyme activity in cells is controlled by which of the following?
I.covalent modifications
II.modulation of expression levels
III.feedback inhibition
IV.allosteric effectors
A)I
B)II
C)III
D)III, IV
E)I, II, III, IV
Q2) An enzyme is near maximum efficiency when A)its turnover number is near V<sub>max</sub>.
B)k<sub>cat</sub>/K<sub>M</sub> is near 10<sup>8</sup> M<sup>-1</sup>s<sup>-1</sup>.
C)k<sub>1</sub> << k<sub>-1</sub>.
D)k<sub>cat</sub>/K<sub>M</sub> is equal to k<sub>cat</sub>.
E)K<sub>M</sub> is large when k<sub>2</sub> exceeds k<sub>1</sub>.
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Page 14
Chapter 13: Biochemical Signaling
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Q1) A release of _____ would result in the stimulation of the liver to synthesize glycogen.
A)receptors
B)phosphoinositide
C)rhodopsin
D)calmodulin
E)insulin
F)hypothalamus
G)cortisol
H)adrenal cortex
I)cyclic AMP
J)RasGAP
K)islets of Langerhans
L)adenylate cyclase (AC)
M)receptor tyrosine kinase (RTK)
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Page 15
Chapter 14: Introduction to Metabolism
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Q1) Acetyl-CoA contains a ____ bond which often provides the energy required for substrate-level phosphorylation.
A)phosphoester
B)phosphoanhydride
C)phosphothioester
D)ester
E)thioester
Q2) Negative feedback inhibition is one type of _______ metabolic control.
A)allosteric
B)hormonal
C)covalent modification
D)genetic
E)signal transduction
Q3) In eukaryotes, glycolysis typically occurs in the A)mitochondrion.
B)cytosol.
C)lysosome.
D)rough endoplasmic reticulum.
E)smooth endoplasmic reticulum.
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Page 16
Chapter 15: Glycogen Metabolism and Gluconeogenesis
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Q1) Which of the following best describes the role of fructose-2,6-bisphosphate (FBP)in liver cells?
A)It is an intermediate in glycolysis.
B)It is an intermediate in gluconeogenesis.
C)It is an intermediate in both glycolysis and gluconeogenesis.
D)FBP is a potent allosteric activator of phosphofructokinase and an inhibitor of fructose bisphosphatase.
E)FBP is a potent allosteric activator of fructose bisphosphatase and an inhibitor of phosphofructokinase.
Q2) Which of the following overall sequences is correct with regard to gluconeogenesis?
A)Oxaloacetate \(\rarr\) PEP \(\rarr\) G6P \(\rarr\) Glucose
B)Pyruvate \(\rarr\) FBP \(\rarr\) PEP \(\rarr\) Glucose
C)Lactate \(\rarr\) PEP \(\rarr\) Pyruvate \(\rarr\) G6P
D)Oxaloacetate \(\rarr\) F6P \(\rarr\) FBP \(\rarr\) Glucose
E)F6P \(\rarr\) FBP \(\rarr\) Glucose \(\rarr\) G6P
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Chapter 16: Glucose Catabolism
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Q1) A genetic deficiency of a single transferase enzyme required for sugar group exchange causes the medical condition known as _____ which results in failure to thrive, mental retardation, and potential liver damage.
A)fructose-1,6-bisphosphatase
B)pentose phosphate
C)pyruvate decarboxylase
D)hypoglycemia
E)phosphofructokinase
F)NADP+
G)thiamine pyrophosphate
H)ATP
I)galactosemia
J)NAD+
K)fluoride ion
L)pyruvate
M)glucogenic
N)FAD
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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) Cyanide (CN<sup>-</sup>)
I.inhibition can be restored by addition of succinate.
II.inhibition can be restored by addition of cytochrome c.
III.inhibits electron transport which stops consumption of oxygen.
IV.blocks transfer of electrons from CoQ to Complex III.
A)I, III, IV
B)I, III
C)II, III, IV
D)I only
E)III only
Q2) Phosphate (P<sub>i</sub>)is transported into the mitochondria from the cytosol by a phosphate carrier which is driven by the A)hydrolysis of ATP.
B)simultaneous transport of H<sup>+</sup> into the mitochondrion.
C)simultaneous transport of ADP into the mitochondrion.
D)simultaneous transport of H<sup>+</sup> out of the mitochondrion.
E)simultaneous transport of ATP out of the mitochondrion.
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Page 20
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> \(\rarr\) Q<sub>B</sub> \(\rarr\)Chl \(\rarr\)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) Which of the following is the site of ATP synthesis in chloroplasts?
A)smooth outer membrane
B)inner membrane space
C)stroma
D)thylakoid membrane
E)thylakoid compartment
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Chapter 20: Lipid Metabolism
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Q1) Fatty acid synthesis requires both acetyl-CoA and ________ as initiator molecules.
A)HDL
B)propionyl-CoA
C)LDL
D)Dihydroxyacetone phosphate
E)malonyl-CoA
F)ACP
G)chylomicrons
H)phosphopantetheine
I)flavin
J)albumin
K)ketone bodies
L)cholesterol
Q2) Which of the following is the starting metabolite in ketone body biosynthesis?
A)acetyl CoA
B)malonyl CoA
C)propionlyl CoA
D)acetyl CoA and propionyl CoA
E)acetyl CoA and malonyl CoA
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Chapter 21: Amino Acid Metabolism
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Q1) Proteins targeted for destruction via the ubiquitin pathway include
I.proteins with a destabilizing N-end rule component.
II.proteins with a PEST sequence.
III.proteins that contain the RING finger E3 component named E3a.
IV.protein with polyubiquitin proteins.
A)I only
B)II only
C)I, II, III
D)I, II, IV
E)II, IV
Q2) Which of the following is(are)advantages to the constant degradation and reformation of proteins?
A)Nutrients can be stored as proteins, which can be used during periods of metabolic need.
B)Damaged proteins are eliminated so they do not accumulate.
C)Metabolism can be efficiently regulated by the synthesis and degradation of enzymes.
D)All of the above are advantages.
E)None of the above is an advantage.
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Page 23
Chapter 22: Mammalian Fuel Metabolism: Integration and Regulation
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Q1) Which of the following reactions is catalyzed by adenylate cyclase?
A)ATP \(\rarr\) cAMP + PP<sub>i</sub>
B)cAMP \(\rarr\) AMP
C)ATP \(\rarr\) cATP
D)ADP \(\rarr\) cAMP + P<sub>i</sub>
E)AMP \(\rarr\) cAMP
Q2) Which of the following proteins stimulates the appetite?
A)leptin
B)ghrelin
C)adiponectin
D)insulin
E)( PYYS1U1B13-36S1U1B0)
Q3) The common products of fuel metabolism in mammals are
A)oxaloacetate and acetyl- CoA.
B)pyruvate and acetyl-CoA.
C)ATP and acetyl-CoA.
D)pyruvate and glucose.
E)none of the above
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Chapter 23: Nucleotide Metabolism
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Q1) The synthesis of 5-phosphoribosylamine from PRPP is I.inhibited allosterically by ATP and GTP.
II.activated by PRPP via feed forward activation.
III.controlled by cAMP dependent phosphorylation.
A)I, II, III,
B)I, II
C)II, III
D)II only
E)III only
Q2) The disease gout is characterized by high levels of ____, which forms crystal deposits in joints and is treated by inhibition of _______.
A)uric acid; urate oxidase
B)uric acid; xanthine oxidase
C)urea; urate oxidase
D)xanthine; xanthine oxidase
E)none of the above
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25
Chapter 24: Nucleic Acid Structure
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Q1) Indirect readout refers to
I.a protein's ability to form hydrogen bonds through a network of water molecules.
II.the 5F1F1F1S1 F1F1F10 to 3F1F1F1S1 F1F1F10 sequence on the opposite strand of a DNA helix.
III.a protein's ability to recognize a specific DNA sequence by its backbone conformation and flexibility.
IV.the protein's ability to make hydrogen bonds with nonesterified phosphate oxygens
A)I, III, IV
B)II, IV
C)III, IV
D)I, III
E)I, IV
Q2) Which of the following would NOT result in the relaxation of supercoiled DNA?
A)heating the DNA to induce denaturation
B)nicking one strand
C)treatment with pancreatic DNaseI
D)treatment with type II topoisomerase
E)treatment with type I topoisomerase
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Chapter 25: Dna Replication, Repair and Recombination
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Q1) Pol I is proteolytically cleaved to yield the ____, which lacks 5'\(\rarr\)3' exonuclease activity.
A)Klenow fragment
B)Klentaq1 polymerase
C)Okazaki fragment
D)ligase
E)primase
Q2) E.coli DNA repair enzymes act on the sequence.Which of the following will result?
A)The underlined A will be changed to a C.
B)The underlined G will be changed to a T.
C)The underlined A will be methylated.
D)The underlined G will be methylated.
E)More than one of the above is correct
Q3) In most organisms, replication proceeds in a ______ manner from the ______.
A)discontinuous; leading strand
B)unidirectional; chromosome ends
C)bidirectional; replication origin
D)bidirectional; chromosome ends
E)discontinuous; chromosome ends
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Page 27
Chapter 26: Transcription and Rna Processing
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Q1) Which of the following describes the cap nucleotide linkage on a eukaryotic mRNA?
I.5' 5' linkage
II.5' 3' linkage
III.3' 5' linkage
IV.3' 3' linkage
A)I or II
B)I or III
C)I only
D)II only
E)II or IV
Q2) Which of the following statements best describes the role of F1F1F1S1 F1F1F10 factors in bacterial gene expression?
A)(F1F1F1S1 F1F1F10 factors determine which RNA polymerase is used during transcription.
B)(F1F1F1S1 F1F1F10 factors mediate the excision of intronic sequences.
C)(F1F1F1S1 F1F1F10 factors can be used to express certain genes necessary based on cell type.
D)(F1F1F1S1 F1F1F10 factors bind to the TATA box and initiate transcription.
E)none of the above
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Chapter 27: Translation
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Q1) The triplet code allows many amino acids to be specified by more than one codon.Such a code is said to be
A)replicative.
B)synonymous.
C)duplicative.
D)universal.
E)degenerate.
Q2) Which of the following best describes the wobble hypothesis?
I.The degree of variance in base pairing is greater at the 5' end of the anticodon, thus accounting for more than one codon.
II.The degree of variance in base pairing is greater at the 3' end of the anticodon, thus accounting for more than one codon
III.Non-Watson-Crick base pairing is sometimes allowed in the last position of the anticodon-codon pairing.
A)I only
B)II only
C)I and III
D)II and III
E)III only
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29
Chapter 28: Regulation of Gene Expression
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Q1) In bacteria, riboflavin can inhibit its own synthesis by binding to an mRNA element termed a ______.
A)globin
B)M phase
C)G 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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Page 30