Chemical Biology Study Guide
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Course Introduction
Chemical Biology explores the interdisciplinary field at the interface of chemistry and biology, focusing on how chemical techniques and molecules are used to study, manipulate, and understand biological systems. The course covers foundational principles such as molecular recognition, enzyme mechanisms, and the design of small molecules to probe or alter biological processes. Students will examine topics including chemical genetics, biomolecular labeling, drug discovery, and the development of chemical tools to investigate cellular pathways. Emphasis is placed on real-world applications and cutting-edge research, equipping students with skills to analyze and solve biological problems using chemical approaches.
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) Which of the following is a similarity between all prokaryotes and all eukaryotes?
A)Both contain DNA in a nucleus.
B)Both contain some of the same membrane bound cell organelles (like mitochondria,Golgi complexes,etc).
C)Both have a cytoskeleton.
D)All of the above are similarities between prokaryotes and eukaryotes.
E)None of the above is a similarity between prokaryotes and eukaryotes.
Answer: E
Q2) For a reaction with \(\Delta\)H = 23 kJ/mol and \(\Delta\)S =22 J/K mol,at 2°C,the reaction is:
A)spontaneous
B)nonspontaneous
C)at equilibrium
D)impossible to determine reactivity
E)none of the above
Answer: B
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Chapter 2: Water
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Q1) Methanol can act both as a H-bond donor and as a H-bond acceptor.What is the maximal number of H-bonds a single molecule of methanol can form with surrounding water molecules.
A)1
B)2
C)3
D)4
E)5
Answer: C
Q2) Covalent C C and C H bonds have bond strengths that are approximately ____ times higher than those of H-bonds.
A)2
B)5
C)10
D)20
E)100
Answer: D
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Chapter 3: Nucleotides, nucleic Acids, and Genetic Information
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Q1) Which of the following DNA sequences is considered palindromic?
A)AAGCTT
B)GAACTT
C)GAACAA
D)AAGCAA
E)AAGTTC
Answer: A
Q2) 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
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Chapter 4: Amino Acids
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Sample Questions
Q1) At a pH above its pK<sub>a</sub>,the phenol group of tyrosine is ______.
A) glutamate
B) uncharged
C) deprotonated
D) three
E) amino group
F) two
G) C-terminus
H) lysine
I) racemic mixture
J) cysteine
K) zero
L) protonated
M) isoleucine
N) tryptophan
O) phenylalanine
P) N-terminus
Q2) 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.
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Chapter 5: Proteins: Primary Structure
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Q1) Natural proteins most commonly contain linear polypeptides between 100 and 1000 residues in length.One of the reasons polypeptides outside this range may be disfavored is that
A)larger polypeptides would likely be insoluble.
B)smaller polypeptides do not form stable folded structures.
C)smaller polypeptides typically assemble into prion-like aggregates.
D)amide linkages are not strong enough to keep larger polypeptides intact.
E)ribosomes are unable to synthesize larger polypeptides.
Q2) The quantitation of proteins due to their absorbance at ~280 nm (UV region)is due to the large absorbtivity of the ________ amino acids.
A)anionic
B)dansylated
C)cleaved
D)polar
E)aromatic
Q3) 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).
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Chapter 6: Proteins: Three-Dimensional Structure
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Q1) The _____________ of an amino acid can be used to predict whether an amino acid side chain folds towards the inside or outside of a globular protein.
A) tertiary structure
B) keratin
C) molecular chaperones
D) hydropathy
E) cis
F) trans
G) sterically forbidden conformation
H) regular secondary structure
I) collagen
J) peptide bond
K) ribonuclease A (RNase A)
L) alpha
Q2) A chaperonin
A)helps fold some proteins in their lowest energy state.
B)is required for all proteins to fold properly.
C)mediates the unfolding of proteins.
D)is required for protein denaturation.
E)counteracts the laws of thermodynamics.
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Chapter 7: Protein Function Part I: Myoglobin and Hemoglobin
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Q1) Humoral immunity refers to that part of the immune response that is mediated by A)T lymphocytes.
B)antibodies.
C)antigens.
D)the thymus.
E)the skin.
Q2) Muscle contraction is directly caused by
A)structural changes in actin.
B)structural changes in myosin.
C)thick and thin filaments sliding past each other.
D)structural changes in the Z disk.
E)None of the above is correct.
Q3) Fab fragments can be generated by
A)reduction of IgG molecules.
B)oxidation of IgG molecules.
C)limited digestion of IgG molecules with papain.
D)combining two light chains.
E)combining two heavy chains.
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 of the following polysaccharides cannot be digested by mammalian salivary,gastric,or pancreatic enzymes?
A)cellulose
B)amylopectin
C)amylose
D)glycogen
E)starch
Q2) Which statement about N-linked glycosylation is correct?
A)N-linked oligosaccharides are attached to proteins one sugar at the time in the endoplasmic reticulum.
B)N-linked sugars are attached to proteins as a 14 residue oligosaccharide during translation in the endoplasmic reticulum.
C)N-linked sugars are attached to proteins as a 14 residue oligosaccharide during translation in the cytoplasm.
D)N-linked sugars are attached to proteins as a 14 residue oligosaccharide after translation in the Golgi apparatus.
E)N-linked oligosaccharides are attached to proteins one sugar at the time in the Golgi apparatus.
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Chapter 9: Lipids and Biological Membranes
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Q1) A steroid-derived hormone that must be activated by hydroxylation,______ regulates Ca<sup>2+</sup> metabolism.
A) amphiphiles
B) vitamin D
C) arachidonic acid
D) phosphatidylethanolamine
E) sterol
F) gangliosides
G) phosphatidylcholine
H) glycerophospholipids
I) sphingomyelins
J) cholesterol
K) triacylglycerols
L) plasmalogen
M) nonpolar
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Chapter 10: Membrane Transport
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Q1) Which of the following compounds would cross a biological membrane most readily by nonmediated diffusion?
A)water
B)acetone
C)hexane
D)acetic acid
E)methanol
Q2) When the cardiac glycoside,digitoxin,is used for heart failure,the effects include: (I)inhibition of phosphate hydrolysis from E<sub>2</sub> of the (Na<sup>+</sup>-K<sup>+</sup>)-ATPase pump (II)activation of the (Na<sup>+</sup>-K<sup>+</sup>)-ATPase pump (III)increase in intracellular Na<sup>+</sup> concentration (IV)increase in Ca<sup>2+</sup> concentration in the sarcoplasmic reticulum
A)I,II,III,IV
B)I,III,IV
C)II,III,IV
D)II,III
E)I,III
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Chapter 11: Enzyme Catalysis
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Q1) If you add enzyme to a solution containing only the product(s)of a reaction,would you expect any substrate to form?
A)It depends on the time interval and temperature of reaction.
B)It depends on the concentration of products added.
C)It depends on the energy difference between E + P and the transition state.
D)All of the above may determine if product forms.
E)None of the above determines if product forms.
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) Acid-base catalysis may be accomplished by:
A)active site specificity
B)charge delocalization
C)buffer effects
D)induced strain
E)conformational change
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Chapter 12: Enzyme Kinetics, inhibition and Control
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Q1) 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>.
Q2) Allosteric activators
A)bind via covalent attachment.
B)stabilize conformations with higher K<sub>s</sub>.
C)stabilize conformations with higher substrate affinity.
D)all of the above
E)none of the above.
Q3) In order for an enzymatic reaction obeying the Michaelis-Menten equation to reach 3/4 of its maximum velocity,
A)[S] would need to be equal to K<sub>M</sub>
B)[S] would need to be ½ K<sub>M</sub>
C)[S] would need to be 3K<sub>M</sub>
D)[S] would need to be ¾ K<sub>M</sub>
E)not enough information is given to make this calculation
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Chapter 13: Biochemical Signaling
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Q1) Which of the following generalizations explains how anabolic steroids can affect muscle growth?
A)Anabolic steroids increase the level of testosterone,a hormone predominately found in males.
B)Anabolic steroids easily pass through the membrane and bind steroid receptors which migrate to the nucleus and function as a transcription factor.
C)Anabolic steroids are water soluble and can transport to the muscle tissue readily.
D)Anabolic steroids alter the phosphoinositide pathway,thereby increasing levels of calcium in the cytosol and subsequently increase the strength of muscle contraction.
E)None of the above is correct.
Q2) The \(\alpha\) cells of the islets of Langerhans secrete _____ in response to ____ glucose levels in the liver.
A)insulin;low
B)insulin;elevated
C)glucagon;low
D)glucagon;elevated
E)somatostatin;elevated
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Chapter 14: Introduction to Metabolism
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Q1) The K<sub>eq</sub> is 0.503 at 25°C for the following reaction.What is the \(\Delta\)G°' for this reaction?
D-Glucose-6-phosphate \(\to\) D-Fructose-6-phosphate \(\Delta\)G°'= ?
A)-2.87 × 10<sup>3</sup> J/mol
B)+1.70 kJ/mol
C)+143 J/mol
D)The \(\Delta\)G°' cannot be determined with the given information.
E)The \(\Delta\)G°' can be determined with the given information but the correct answer is not shown.
Q2) Which of the following is (are)true regarding vitamins?
(I)They are essential organic molecules an organism is unable to synthesize.
(II)Some water soluble vitamins mediate electron-transfer reactions.
(III)In humans,the water soluble vitamins converted into organic coenzymes.
IV)In humans,the fat soluble vitamins mediate group transfer reactions.
A)I,II,III,IV
B)I,II,III
C)II,III,IV
D)I only
E)II,IV
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Chapter 15: Glucose Catabolism
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Q1) Which of the following best describes the control exhibited by phosphofructokinase (PFK)?
A)It is allosterically inhibited by ATP and citrate.
B)It is allosterically activated by F2,6P.
C)It is allosterically activated by ATP and citrate.
D)Both A and B are correct.
E)Both B and C are correct.
Q2) In alcoholic fermentation,acetaldehyde is produced by A)the decarboxylation of pyruvate.
B)the carboxylation of pyruvate.
C)the decarboxylation of lactate.
D)the carboxylation of lactate.
E)none of the above
Q3) Aerobic glycolysis produces a net yield of ______ ATP.
A)1
B)2
C)3
D)4
E)more than 4
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Chapter 16: Glycogen Metabolism and Gluconeogenesis
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Q1) Patient "G" has a glycogen storage disease which results in decreased muscle glycogen levels.Muscle biopsies indicate poor glycogen structure in the muscle.Which of the following enzymes might be related to the cause?
A)muscle debranching enzyme
B)muscle glycogen phosphorylase
C)liver debranching enzyme
D)muscle glycogen synthase
E)liver glycogen synthase
Q2) 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.
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Chapter 17: Citric Acid Cycle
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Q1) Which of the following statements correctly and most accurately describes the function of FAD in the pyruvate dehydrogenase enzyme complex?
A)NADH passes electrons to FAD to form FADH<sub>2</sub>.
B)Lipoamide passes electrons through FADH2,which almost instantly passes them to NAD thus forming NADH.
C)FADH<sub>2</sub> donates electrons to lipoamide thus regenerating FAD.
D)Lipoamide oxidizes NADH to NAD by passing electrons to FAD.
E)NAD accepts electrons directly from lipoamide,which has gained them via oxidation of FADH<sub>2</sub>.
Q2) Which of the following organisms does not utilize the glyxolate cycle?
A)trees
B)bacteria
C)fungi
D)mammals
E)All of the above utilize the glyxolate cycle when necessary.
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Chapter 18: Electron Transport and Oxidative
Phosphorylation
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Q1) Which statement concerning Complex II of the electron transport chain is FALSE?
(I)This complex oxidizes FADH<sub>2</sub> and reduces coenzyme Q.
(II)This complex includes the covalently bound enzyme succinate dehydrogenase.
(III)This complex pumps protons from the matrix to the intermembrane space.
IV)This complex also oxidizes succinate to fumarate in the citric acid cycle.
A)I,II
B)II only
C)II,III
D)III only
E)IV only
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) ______ carries electrons between PSII and PSI.
A) photosynthetic reaction center
B) tyrosyl radical
C) thylakoid
D) H<sub>2</sub>O
E) CF<sub>1</sub>CF<sub>0</sub>
F) Z-scheme
G) NADPH
H) plastoquinone
I) H<sup>+</sup>
J) RuBP carboxylase
K) CO<sub>2</sub>
L) 2 OH<sup> </sup>
M) O<sub>2</sub>
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) Which of the following drugs acts by acetylating a serine residue preventing adequate enzyme activity?
A)ibuprofen
B)acetaminophen
C)Vioxx®
D)aspirin
E)Celebrex®
Q2) Which of the following is the source of the two carbon fragments in fatty acids biosynthesis?
A)acetyl CoA
B)malonyl CoA
C)palmitic acid
D)propionyl CoA
E)ceramides
Q3) 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.
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Chapter 21: Amino Acid Metabolism
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Q1) The synthesis of which of the following uses an aminotransferase in the first step of the synthesis?
A)glutamine
B)proline
C)serine
D)valine
E)all of the above
Q2) Which of the following statements about tryptophan synthase is FALSE?
A)Indole can pass between active sites via a channel in the enzyme.
B)Tryptophan synthase catalyzes two distinct reaction steps to form tryptophan.
C)The enzyme is a tetramer of four identical subunits.
D)The enzyme has two states,an "open" and "closed",to ensure that bound indole is not lost to solvent.
E)The indole group is produced following release of glyceraldehyde-3-phosphate from the indole-glycerol-3-phosphate.
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Chapter 22: Mammalian Fuel Metabolism: Integration and Regulation
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Q1) Mice lacking the protein ______ are genetically obese.
A) -adrenergic receptor
B) -adrenergic receptor
C) Cori cycle
D) urea cycle
E) leptin
F) phosphatase
G) liver
H) hormones
I) acetyl CoA
J) ketone bodies
K) urea
L) kidney
M) brain
N) pancreas
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Chapter 23: Nucleotide Metabolism
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Q1) The last step in purine degradation (I)generates hydrogen peroxide as a byproduct. (II)utilizes molecular oxygen. (III)is inhibited by methotrexate. (IV)requires NAD<sup>+</sup>.
A)I,II,III,IV
B)I,II,IV
C)II,IV
D)I,III,IV
E)I,II
Q2) Which of the following reactions is NOT catalyzed by nucleoside diphosphate kinase?
A)GDP + ATP \(\to\) GTP + ADP
B)UDP + ATP \(\to\) UTP + ADP
C)CDP + ATP \(\to\) CTP + ADP
D)dGDP + ATP \(\to\) dGTP + ADP
E)It catalyzes all the above.
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Chapter 24: Nucleic Acid Structure
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Q1) Which of the following statements about zinc fingers is FALSE?
A)Zinc fingers contain Cys and His residues.
B)Zinc is tetrahedrally coordinated as part of a small compact protein domain.
C)More than one finger can be found in a protein;as many as 60 have been observed.
D)Zinc fingers are the predominant DNA-binding motif of restriction enzymes.
E)A zinc finger recognizes specific sequences of DNA via its N-terminal helices.
Q2) Which the following sequences of DNA is most likely to form Z-DNA in vitro?
A)5'-ATATATATATATATATATAT-3'
3'-TATATATATATATATATATA-5'
B)5'-AAAAAAAAAAAAAAAAAAAA-3'
3'-TTTTTTTTTTTTTTTTTTTT-5'
C)5'-GCGCGCGCGCGCCGCGCGCG-3'
3'-CGCGCGCGCGCGCGCGCGCG-5'
D)5'-GGGGGGGGGGGGGGGGGGGG-3'
3'-CCCCCCCCCCCCCCCCCCCC-5'
E)5'-GATCGATCGATCGATCGATC-3'
3'-CTAGCTAGCTAGCTAGCTAG-5'
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Chapter 25: DNA Replication, repair and Recombination
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Q1) Termination of replication fork movement in E.coli involves the binding of the ______ protein at a Ter site.
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 processing of pre-rRNAs includes ______.
(I)nucleolytic cleavage.
(II)snoRNA-assisted methylation.
(III)snRNP-assisted methylation.
A)I,II
B)I,III
C)II,III
D)I,II,III
E)III only
Q2) Which of the following if TRUE regarding prokaryotic DNA polymerase?
(I)Abortive initiation is common.
(II)RNA polymerase processivity increases with the clamp.
(III)The error rate is 1 in 10<sup>6</sup>.
(IV)Initiation of transcription begins at the 10 position.
A)I,II,III
B)I only
C)III only
D)III,IV
E)II,III,IV
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Chapter 27: Protein Synthesis
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Q1) 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
Q2) Which linkage best describes the covalent bond between an amino acid (AA)and its cognate tRNA?
A)amino group of AA linked to 5' -OH of tRNA
B)amino group of AA linked to 5' phosphate of tRNA
C)carboxyl group of AA linked to 3' -OH of tRNA
D)carboxyl group of AA linked to 3' phosphate of tRNA
E)none of the above
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Chapter 28: Regulation of Gene Expression
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Q1) A database of _____ is being compiled to examine possible genetic links to the susceptibility to disease or infection..
A)CpG islands
B)ORFs
C)SNPs
D)LINEs
E)SINEs
Q2) In humans,approximately ______ of the genome encodes proteins.
A)0)4%
B)1)4%
C)14%
D)24%
E)44%
Q3) RNA interference is a mechanism of posttranscriptional RNA-dependent A)chromatin-remodeling.
B)gene silencing.
C)histone methylation.
D)coactivation.
E)apoptosis.
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Page 30