Biological Chemistry
Chapter Exam Questions
Course Introduction
Biological Chemistry explores the chemical principles and molecular mechanisms underlying biological systems. This course examines the structure and function of biomolecules such as proteins, nucleic acids, carbohydrates, and lipids, as well as the metabolic pathways and catalytic processes essential to life. Emphasis is placed on enzyme kinetics, regulation of metabolism, bioenergetics, and the molecular basis of genetic information flow. Integrating concepts from organic chemistry and cell biology, the course provides a foundational understanding of how chemical processes drive cellular activity and sustain living organisms.
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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Q1) Which of the following developed during the evolution of eukaryotic cells from prokaryotic cells?
A)DNA
B)the cell membrane
C)nuclear membranes
D)ribosomes
E)proteins
Answer: C
Q2) Which arrow points at an anhydride bond?
A)A
B)B
C)C
D)D
E)E
Answer: A
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) Phosphate (pK<sub>1</sub> = 2.15, pK<sub>2</sub> = 6.82, and pK<sub>3</sub> = 12.38)will be mostly in the HPO<sub>4</sub><sup>2-</sup> form at pH 7.2.At pH 5.82 it is mostly in the ______ form.
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: D
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Chapter 3: Nucleotides, Nucleic Acids, and Genetic Information
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Q1) Nucleic acids are composed of nucleotides that are linked by ______ linkages.
A)diploid
B)phosphodiester
C)probe
D)pyrimidine
E)introns
F)cloning
G)transformed
H)exons
I)ampicillin
J)autoradiography
K)chain-terminator
L)purine
M)ester
Answer: B
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Chapter 4: Amino Acids
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Q1) Zwitterions are
A)amino acids.
B)ionic molecules that are racemic.
C)ions that bear both negatively and positively charged groups.
D)side chain carboxylate anions.
E)delocalized ions.
Q2) What percentage of the 20 amino acids is considered to be nutritionally essential to lab animals?
A)0%
B)25%
C)50%
D)75%
E)100%
Q3) Glutamine is an amino acid (pK<sub>a</sub>s are 2.2, and 9.1).Draw the predominant structure of glutamine at pH 1.0.
Q4) Glutamic acid is an amino acid (pK<sub>a</sub>s are 2.1, 4.1 and 9.5).Calculate the isoelectric point of glutamic acid.
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Chapter 5: Proteins: Primary Structure
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Q1) A fast and common method for determining the protein concentration in column effluent is
A)tandem mass spectrometry.
B)salting in with ammonium sulfate.
C)drying a portion and weighing the solid.
D)measuring light absorption at 280 nm.
E)Edman degradation.
Q2) What can be done to increase the rate at which a protein of interest moves down an ion-exchange chromatography column?
A)reduce the ion concentration in the eluant
B)add a small amount of a non-ionic detergents to the eluant
C)change the pH of the eluant
D)add a protease inhibitor to the eluant
E)reduce the temperature of the eluant
Q3) The vast majority of polypeptides contain between ______ amino acid residues.
A)10 and 50
B)50 and 100
C)100 and 1000
D)1000 and 2000
E)2000 and 34,000
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Chapter 6: Proteins: Three-Dimensional Structure
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Q1) Evolutionary processes have
A)increased the stability of 4° structures.
B)decreased the number of subunits.
C)increased similarity amount 1° structures.
D)enhanced efficient folding pathways.
E)all of the above
Q2) The Protein Data Bank (PDB)is a database provides structural information about proteins that may be useful for which of the following?
I.A researcher studying the changes in protein fold associated with prions.
II.A researcher classifying structural elements by function.
III A researcher designing a compound to bind tightly to a particular region in the protein.
A)I only
B)II only
C)III only
D)I, II
E)I, II, II
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Chapter 7: Protein Function Part I: Myoglobin and Hemoglobin
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Q1) Hemerythrin and hemocyanin are:
A)human mutant hemoglobins with decreased oxygen affinity.
B)hemoglobin variants that are found in animals at high altitude.
C)synthetic derivatives of hemoglobin's heme group used in artificial blood substitutes.
D)oxygen transport proteins found in invertebrates.
E)tetrameric hemoglobin derivatives containing only \(\alpha\)-chains (\(\alpha\)<sub>4</sub> tetramers).
Q2) During the T to R conformational shift, Fe(II)drags the F-helix via a bond to the side chain of ________.
A)Leu F7
B)Leu F4
C)His F8
D)Leu FG3
E)Val FG5
Q3) It appears that the heme group in myoglobin binds the O<sub>2</sub>.What is the function of the polypeptide?
Q4) What is the primary physiological function of myoglobin in most mammals?
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Chapter 8: Carbohydrates
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Q1) Which of the following is an example of a heteropolysaccharide?
A)cellulose
B)chitin
C)starch
D)glycogen
E)hyaluronic acid
Q2) Chitin differs from cellulose due to
A)inversion of configuration at the anomeric carbon.
B)sulfonation of the C2 OH group.
C)a much greater prevalence of branching.
D)replacement of the C2 OH group by an acetamido group.
E)replacement of the C6 OH group by an amino group.
Q3) Which of the carbon atoms shown in the figure above represent the anomeric carbon?
A)A
B)B
C)C
D)D
E)E
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Chapter 9: Lipids and Biological Membranes
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Sample Questions
Q1) Adipocytes
A)are specialized cells for the synthesis of triglycerides.
B)are specialized cells for short term energy storage.
C)provide compartments for efficient membrane bilayer synthesis.
D)exist primarily in a thin layer surrounding major muscle groups as a rapid high energy source.
E)All of the above characterize adipocytes.
Q2) The protein that forms a transmembrane pore that allows growing polypeptides to pass through the RER membrane is called the ______.
A)signal recognition particle
B)signal peptide
C)docking protein
D)translocon
E)none of the above
Q3) Cholesterol
A)incorporation into the membrane results in increased rigidity.
B)functions as a precursor to cerebrosides.
C)is synthesized in two-carbon units.
D)is synthesized from steroid hormones.
E)all of the above
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Chapter 10: Membrane Transport
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Q1) D-Glucose and D-mannitol are similarly soluble, but D-glucose is transported through the erythrocyte membrane four times as rapidly as D-mannitol.What is the most likely explanation?
A)D-glucose undergoes simple diffusion more rapidly than mannitol because glucose is less polar.
B)D-glucose and D-mannitol enter the erythrocyte via an ion-gated channel.
C)D-glucose and D-mannitol are transported via a system that distinguishes the two sugars.
D)D-glucose flux through the membrane is linear whereas D-mannitol flux is described by a hyperbolic curve.
E)None of the above provides the explanation.
Q2) Which of the following is an example of nonmediated transport?
A)simple diffusion
B)facilitated diffusion
C)passive transport
D)active transport
E)all of the above
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Chapter 11: Enzyme Catalysis
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Q1) In trypsin the specificity for one substrate over another comes from
A)the negatively charged pocket.
B)the positively charge pocket.
C)the hydrophobic pocket.
D)the amino acid serine.
E)the amino acid histidine.
Q2) In affinity labeling, a technique used to study enzyme mechanisms, A)A compound designed to bind at the active site reacts with and therefore permits the identification of a nearby group.
B)A fluorescent group is attached to the substrate to identify the position of the active site.
C)Highly purified enzyme is obtained by affinity chromatography for mechanistic studies.
D)A radioactive isotope is incorporated into the substrate to identify the position of the active site.
E)Genetic modification of amino acid residues is used to alter the binding affinity of the active site.
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Chapter 12: Enzyme Kinetics, Inhibition and Control
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Q1) The Michaelis constant K<sub>M</sub> is defined as I.(k<sub>-1 </sub>+ k<sub>2</sub>)/k<sub>1</sub>
II.½ V<sub>max</sub>
III.[S] = [ES]
IV.[ES]/2
A)I
B)I, II
C)II
D)I, IV
E)II, IV
Q2) A compound that distorts the active site, rendering the enzyme catalytically inactive is called
A)a uncompetitive inhibitor
B)an allosteric effector
C)an inactivator
D)a competitive inhibitor
E)none of the above
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Chapter 13: Biochemical Signaling
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Q1) Phospholipase C cleaves PIP<sub>2</sub>, resulting in an increased cytosolic concentration of I.IP<sub>3</sub> (inositolpolyphosphate-3)
II.protein kinase C
III.cAMP <sub> </sub>IV.Ca<sup>2+</sup>
A)I only
B)II only
C)I, III
D)I, IV
E)IV only
Q2) Which of the following increases the affinity of SH2 binding to phosphor-tyrosine?
A)The absence of a Ser or Thr residue in the binding region.
B)The presence of an Arg residue deep in the binding pocket.
C)The presence of an Arg residue near the binding pocket entrance.
D)The absence of a Ser residue deep in the binding pocket.
E)None of the above.
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15
Chapter 14: Introduction to Metabolism
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Q1) ______ is the most reliable systems biology approach to assess gene expression.
A)genomics
B)transcriptomics
C)proteomics
D)metabolmics
E)none of the above
Q2) Negative feedback inhibition is one type of _______ metabolic control.
A)allosteric
B)hormonal
C)covalent modification
D)genetic
E)signal transduction
Q3) ATP contains ________ bonds.
A)one phosphoanhydride and two phosphoester
B)two phosphoester and one glycosidic
C)three phosphoanhydride
D)one amide and three phosphoanhydride
E)one phosphoester and two phosphoanhydride
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Chapter 15: Glycogen Metabolism and Gluconeogenesis
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Q1) Which enzyme below is NOT required for the synthesis of branched glycogen?
A)glycogen phosphorylase
B)glycogen synthase
C)branching enzyme
D)phosphoglucomutase
E)All are required for synthesis of glycogen.
Q2) The first step in the breakdown of glycogen is catalyzed by ______.
A)phosphorylase
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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Chapter 16: Glucose Catabolism
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Q1) Aerobic glycolysis produces a net yield of ______ ATP.
A)1
B)2
C)3
D)4
E)more than 4
Q2) The utilization of fructose in glycolysis in the liver
A)requires UDP-glucose.
B)requires one extra ATP.
C)uses GTP rather than ATP.
D)bypasses phosphofructokinase (PFK)regulation.
E)enters glycolysis as fructose bisphosphate (FBP).
Q3) In skeletal muscle cells, oxidation of NADH generated from anaerobic glycolysis occurs during which of the following reactions?
A) acetaldehyde ethanol
B) lactate pyruvate
C) phosphoenolpyruvate pyruvate
D) pyruvate lactate
E) glyceraldehyde-3-phosphate 1,3-bisphosphoglycerate
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Chapter 17: Citric Acid Cycle
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Q1) Which of the following steps of the citric acid cycle conserves the energy of a high energy thioester bond?
A)the reaction catalyzed by succinate dehydrogenase.
B)the reaction that produces oxalacetate.
C)the condensation reaction that produces citrate.
D)the reaction catalyzed by -ketoglutarate dehydrogenase.
E)the conversion of citrate to isocitrate.
Q2) Germinating plant seeds can convert acetyl-CoA (obtained from fatty acids stored as oils)into carbohydrates, whereas animals are incapable of converting fatty acids into glucose.This difference is due to the fact that:
A)animals have glycogen and don't need to make glucose from fatty acids.
B)plants use the glyoxylate cycle to convert two acetyl CoA to oxaloacetate, a precursor for gluconeogenesis.
C)plant seeds use photosynthesis to make sugar.
D)animals use the citric acid cycle selectively for energy production, whereas plants primarily use glycolysis.
E)B and D
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Chapter 18: Electron Transport and Oxidative
Phosphorylation
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Q1) Which of the following statements is(are)TRUE about oxidative phosphorylation?
I.Electron transport provides energy to pump protons into the intermembrane space.
II.An electrochemical gradient is formed across the inner mitochondrial membrane.
III.Potassium and sodium ions form an ionic gradient across the inner mitochondrial membrane.
IV.Complexes I, II, III, IV actively transport protons into the intermembrane space during electron transport.
A)I, II, III, IV
B)I, II, IV
C)II, III, IV
D)I, IV
E)II, IV
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,
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Chapter 19: Photosynthesis
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Q1) Which of the following is TRUE regarding the oxygen evolving complex (OEC)?
I.All states have high reduction potentials that exceed that of water.
II.The OEC is made up of magnesium atoms that bridge oxygen atoms together.
III.Current evidence indicates that the OEC cycles between five states in which the metal atoms exist in a variety of combinations of oxidation states.
IV.During the course of reaction, protons and electrons are abstracted from one water molecule yielding one O<sub>2</sub>.
A)I, II, III, IV
B)I, III
C)I, II
D)III only
E)III, IV
Q2) The photosynthetic electron transport system includes the transmembrane complexes PSI, PSII and A)PSIII.
B)cytochrome a<sub>3</sub>.
C)cytochrome b<sub>6</sub>f.
D)cytochrome c.
E)proton translocating ATP synthase
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Page 21
Chapter 20: Lipid Metabolism
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Q1) An enzyme that is inhibited by the statin group of drugs (e.g.Lipitor)is
A)phospholipase a2.
B)hormone sensitive lipase.
C)HMG CoA reductase.
D)desaturase.
E)glycerol kinase.
Q2) Which of the following statements about peroxisomes is FALSE?
A)(\(\beta\) oxidation in peroxisomes can shorten very long fatty acids.)
B)Mammalian peroxisomes can synthesize some lipids, including bile salts.
C)In plants, peroxisomes and glyoxysomes serve as the site of \(\beta\) oxidation.
D)Long chain fatty acids are transported into the peroxisome via a carnitine carrier protein where they are activated for oxidation.
E)(\(\beta\)oxidation in peroxisomes varies slightly from the mitochondrial process.)
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Chapter 21: Amino Acid Metabolism
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Q1) The majority of amino acids are deaminated by a ______ reaction.
A)reduction
B)transaminmation
C)condensation
D)transacetylation
E)oxidation
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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Chapter 22: Mammalian Fuel Metabolism: Integration and Regulation
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Q1) Which of the following metabolizes ketone bodies?
I.brain
II.liver
III.muscle
IV.adipose tissue
A)I, II, III, IV
B)I, II, III
C)I, III
D)II only
E)III only
Q2) Which of the following is FALSE relating to leptin?
A)Obese mice lacking leptin tend to overeat.
B)Leptin seems to function by different mechanisms in mice and humans.
C)Obesity in humans leads to a decrease in leptin production.
D)Obesity leads to leptin resistance.
E)none of the above
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Chapter 23: Nucleotide Metabolism
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Q1) Which of the following sequences for uric acid catabolism is correct for marine invertebrates?
A)uric acid \(\rarr\) allantoin\(\rarr\) allantoic acid\(\rarr\) urea\(\rarr\) NH<sub>4</sub><sup>+</sup>
B)uric acid \(\rarr\) allantoic acid\(\rarr\) urea\(\rarr\) NH<sub>4</sub><sup>+</sup>
C)uric acid \(\rarr\) allantoin\(\rarr\) urea\(\rarr\) NH<sub>4</sub><sup>+</sup>
D)uric acid \(\rarr\) allantoin\(\rarr\) allantoic acid\(\rarr\) urea
E)none of the above
Q2) Which of the following correctly describes the formation of CTP?
A)UTP + Glutamine + ATP + H<sub>2</sub>O \(\rarr\) Glutamate + ADP + P<sub>i</sub> + CTP
B)UMP + ATP + H<sub>2</sub>O + Glutamine \(\rarr\) CMP + Glutamate + ADP + P<sub>i</sub>
C)TTP + N<sup>5</sup>,N<sup>10</sup>-Methylenetetrahydrofolate \(\rarr\) CTP + Dihydrofolate
D)UMP + Glutamine \(\rarr\) Glutamate + CTP
E)CMP + Glutamine + ATP \(\rarr\) CTP + Glutamate + ADP + P<sub>i</sub>
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Chapter 24: Nucleic Acid Structure
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Q1) Which of the following is used to allow effective gel electrophoresis of DNAs > 100,000 base pairs?
A)hydroxyapatite treatment prior to gel loading
B)Northern blots
C)pulsed-field gel electrophoresis
D)Southern Blot
E)Western Blot
Q2) The chromosomes of some viruses and bacteria are ______ and often ______.
A)linear; single stranded
B)linear; supercoiled
C)circular; single stranded
D)circular; supercoiled
E)none of the above
Q3) Based on the information in this chapter, which of the following sequences would likely bind a repressor if double stranded?
A)5' TGAGCA3'
B)5' TGATCA3'
C)5' TACGTCA3'
D)All of the above would bind the repressor with equal efficiency
E)None of the above would bind would the repressor.
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Chapter 25: Dna Replication, Repair and Recombination
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Q1) Defects in the proteins ______, which associate with RAD-51, are correlated with several types of cancer.
A)BRCA1 and BRCA2
B)RecU and RecB
C)Pol \(\alpha\) and Pol \(\beta\)
D)DSB and NHEJ
E)RecA and RecUGA
Q2) When a section of DNA is damaged and polymerization cannot proceed, _____ repair can reconstitute the damaged replication fork.
A)mismatch
B)nucleotide excision
C)recombination
D)photoreactivation
E)base excision
Q3) Which of the following would result in increased processivity in E.coli?
A)(\(\beta\) (sliding)clamp)
B)primosome
C)helicase
D)Dna B
E)Dna G
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Chapter 26: Transcription and Rna Processing
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Q1) 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
Q2) Which of the following best describes the function of poly(A)tails for eukaryotic mRNAs?
A)They are required for accurate translation.
B)They have a protective role against degradation.
C)They signal transcription termination.
D)They function as splice sites.
E)No role has been observed for these features.
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Chapter 27: Translation
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Q1) Class I and Class II aminoacyl-tRNA synthetases differ in their I.structural motifs.
II.anticodon recognition.
III.site of aminoacylation.
IV.amino acid specificity.
A)I only
B)II, III
C)II, IV
D)II only
E)I, II, III, IV
Q2) Polypeptide synthesis
A)proceeds from the C-terminus to the N-terminus.
B)proceeds from the N-terminus to the C-terminus.
C)proceeds in both directions simultaneously.
D)proceeds in either direction once initiated.
E)proceeds randomly.
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Chapter 28: Regulation of Gene Expression
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Q1) The process of somatic recombination
I.results in antibody diversity.
II.involves selection of individual members of clustered gene sequences.
III.involves selection and recombination of specific exons on the F1F1F1S1 F1F1F10 and/or F1F1F1S1 F1F1F10 chain.
A)I, II, III
B)I, III
C)I, III
D)II, III
E)none of the above
Q2) Which of the following events are necessary for efficient expression of the lac operon?
I.The lac repressor must bind inducer and dissociate from the operator site.
II.CAP must bind cAMP.
III.CAP and the repressor must simultaneously bind to RNAP.
A)I, II, III
B)I, II
C)I, III
D)II, III
E)I only
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