Biochemistry Laboratory
Question Bank
Course Introduction
Biochemistry Laboratory offers students hands-on experience with fundamental techniques used in the study of biological molecules and processes. Through a series of experiments, students learn to isolate, purify, analyze, and characterize proteins, nucleic acids, carbohydrates, and lipids. Emphasis is placed on experimental design, data collection, accurate record-keeping, and interpretation of results. The course introduces key tools such as spectrophotometry, electrophoresis, chromatography, and enzyme assays, while fostering critical thinking and problem-solving skills essential for laboratory research in biochemistry and related fields.
Recommended Textbook
Fundamentals of Biochemistry Life at the Molecular Level 5th Edition by Donald Voet
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2
Chapter 1: Introduction to the Chemistry of Life
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Sample Questions
Q1) The most abundant molecule in the human body is _____.
A) phylogenetic
B) negative
C) H<sub>2</sub>O
D) H°
E) H TS
F) halobacteria
G) open
H) entropy
I) flux
J) polymers
K) G°´
L) thermophiles
M) nitrogen
N) positive
Answer: C
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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Page 3
Chapter 2: Water
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Sample Questions
Q1) 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
Q2) The pK<sub>a</sub> of carbonic acid is 6.35.A solution is made by combining 50 mL 1.0 M carbonic acid,2.0 mL 5.0 M KOH and 448 mL pure water (assume the total volume is 500 mL).Calculate the pH of the resulting solution.
Answer: 50 × 10<sup> </sup><sup>3</sup> L × 1.0 mol/L carbonic acid = 50 × 10<sup> </sup><sup>3</sup> mol or 50 mmol carbonic acid.2 × 10<sup> </sup><sup>3</sup> × 5.0 mol/L KOH = 10 × 10<sup> </sup><sup>3</sup> mol or 10 mmol KOH.50 mmol carbonic acid + 10 mmol OH<sup> </sup> = 40 mmol carbonic acid and 10 mmol bicarbonate (and 10 mmol water).pH = pK<sub>a</sub> + log [A<sup> </sup>]/[HA] = 6.35 + log 10 mmol × (500 mL)<sup> </sup><sup> </sup><sup>1</sup>/40 mmol × (500 mL)<sup> </sup><sup> </sup><sup>1</sup> = 6.35 + log 10/40 = 6.35 - 0.60 = 5.75
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Page 4
Chapter 3: Nucleotides, nucleic Acids, and Genetic Information
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Sample Questions
Q1) Chargaff's rules state that:
A)The amount of guanine plus cytosine in mammalian genomes varies from about 39 to 46%.
B)DNA is always double stranded and RNA is always single stranded.
C)DNA contains two grooves,a major groove and a minor groove.
D)In DNA the number of adenine residues is identical to the number of thymine residues and the number of guanine residues is identical to the number of cytosine residues.
E)DNA contains two strands that run in opposite directions.
Answer: D
Q2) A genomic library
A)is a collection of protein structures from a specific organism.
B)is a collection of cloned DNA fragments representing all of an organism's DNA.
C)contains only protein-coding DNA sequences.
D)is best constructed from very short DNA fragments.
E)is built from mRNA by reverse transcription.
Answer: B
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5
Chapter 4: Amino Acids
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Sample Questions
Q1) Residues 1 and 2 in the peptide shown above are connected through a A)hydrogen bond.
B)an isopeptide bond.
C)an ester linkage.
D)disulfide bond.
E)a glycosidic bond.
Q2) What is the name of this molecule?
A)"GABA"
B)"thyroxine"
C)"\(\gamma\)-carboxyglutamate"
D)"glutathione"
E)"epinephrine"
Q3) The peptide AYDG has an N-terminal _________ residue.
A)glycine
B)glutamic acid
C)glutamine
D)aspartic acid
E)alanine
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.
Page 6
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Chapter 5: Proteins: Primary Structure
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Sample Questions
Q1) The endoprotease ______ cleaves polypeptides on the C-terminal side of certain bulky hydrophobic amino acid residues.
A) electrophoresis
B) hydrophobic interaction
C) enzyme-linked immunosorbent assay
D) three-dimensional shape
E) N-terminal amino acid
F) negative charge
G) nucleases
H) chromophore
I) foaming
J) high level expression
K) 2-mercaptoethanol
L) positive charge
M) cation exchange
N) pI
O) chymotrypsin
P) C-terminal amino acid
Q) Sodium dodecyl sulfate
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Chapter 6: Proteins: Three-Dimensional Structure
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Sample Questions
Q1) In most peptide groups the ______ conformation is not sterically favored.
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) Of the following,which amino acid is most likely to be found in position 1 or 4 on keratin?
A)Phe
B)Ala
C)Lys
D)Trp
E)Pro
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Chapter 7: Protein Function Part I: Myoglobin and Hemoglobin
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Sample Questions
Q1) Myoglobin is an oxygen binding protein in muscle.Describe in one sentence the overall structure of myoglobin.
Q2) Which of the following statements about actin is not true?
A)Actin is the most abundant cytoplasmic protein in many cell types.
B)Actin forms microfilaments in many cell types.
C)Actin plays an important role in endocytosis.
D)Actin is present only as monomers in nonmuscle cells.
E)Actin filaments are dynamic,they grow at one end and they lose subunits at the other end.
Q3) When the partial pressure of O<sub>2</sub> in venous blood is 30 torr,the saturation of myoglobin with O<sub>2</sub> is ______ while the saturation of hemoglobin with O<sub>2</sub> is ______.
A)0)55,0.91
B)0)91,0.55
C)2)8 torr,26 torr
D)0)91,0.97
E)none of the above
Q4) What is the primary physiological function of myoglobin in most mammals?
Page 9
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Chapter 8: Carbohydrates
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Sample Questions
Q1) Which of the following is the most abundant disaccharide?
A)lactose
B)cellulose
C) -amylose
D)maltose
E)sucrose
Q2) Which of these polysaccharides is a branched polymer?
A)chitin
B)amylose
C)cellulose
D)amylopectin
E)hyaluronic acid
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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Page 10
Chapter 9: Lipids and Biological Membranes
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Sample Questions
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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11
Chapter 10: Membrane Transport
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Sample Questions
Q1) KcsA is an example of a(n)_________.
A) Porins
B) gap junctions
C) symport
D) active
E) ion channel
F) secondary active
G) channel-forming
H) carrier ionophores
I) passive-mediated
J) uniport
K) simple diffusion
L) anti-ion transport
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>.
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Page 12
Chapter 11: Enzyme Catalysis
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Sample Questions
Q1) Glu 35 of lysozyme is found in a nonpolar environment.Which of the following is true?
A)Its pK is lower than the usual value in this environment.
B)Its pK is higher than the usual value in this environment.
C)Its pK would not change in this environment.
D)Its pK would depend on the sample buffer.
E)None of the above is correct.
Q2) An uncatalyzed reaction has a rate of 4.2 × 10<sup>-7</sup> sec<sup>-1</sup>.When an enzyme is added the rate is 3.2 × 10<sup>4</sup> sec<sup>-1</sup>.Calculate the rate enhancement caused by the enzyme.
A)3)2 × 10<sup>4</sup>
B)7)4 × 10<sup>-3</sup>
C)1)3 × 10<sup>-2</sup>
D)7)6 × 10<sup>10</sup>
E)The data are not appropriate for the calculation requested.
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Chapter 12: Enzyme Kinetics, inhibition and Control
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Sample Questions
Q1) At substrate concentrations much lower than the enzyme concentration,
A)the rate of reaction is expected to be inversely proportional to substrate concentration.
B)the rate of reaction is expected to be directly proportional to substrate concentration.
C)first order enzyme kinetics are not observed.
D)the K<sub>M</sub> is lower.
E)the rate of reaction is independent of substrate concentration.
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) Fourth-order reactions.
A)have three or more sequential rate determining steps.
B)require a 'Ping Pong' mechanism.
C)are best analyzed using Lineweaver-Burk plots.
D)exist only when enzymatically catalyzed.
E)none of the above.
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Page 14
Chapter 13: Biochemical Signaling
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Sample Questions
Q1) The insulin signaling pathway includes which of the following steps?
A)ligand-induced dimerization of the receptor and phosphorylation of IRS-1 and/or IRS-2 proteins
B)autophosphorylation and phosphorylation of IRS-1 and/or IRS-2 proteins
C)IRS-1-induced dimerization of the receptor,autophosphorylation,and phosphorylation of SH2 domains
D)autophosphorylation and dephosphorylation of IRS-1 and/or SH2 domains
E)none of the above
Q2) Which of the following are activated either directly or indirectly by a heterotrimeric G protein subunit?
(I)phospholipase C
(II)Herceptin ®
(III)calmodulin (CaM)sensitive kinase
(IV)MAPK
A)I,II,III,IV
B)I,II
C)I,III
D)II,III,IV
E)I,II,IV
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Page 15
Chapter 14: Introduction to Metabolism
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Sample Questions
Q1) Cells control or regulate the flux through metabolic pathways by means of (I)allosteric control of enzymes. (II)covalent modification of enzymes. (III)genetic control of the concentrations of enzymes.
(IV)genetic expression of allosteric effectors.
A)I,II,III,IV
B)II,III
C)I,II,IV
D)I,II,III
E)I,IV
Q2) 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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16
Chapter 15: Glucose Catabolism
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Sample Questions
Q1) 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
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) Glycolytic synthesis of ATP occurs via A)oxidation.
B)reduction.
C)substrate-level phosphorylation.
D)oxidative phosphorylation.
E)photophosphorylation.
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Chapter 16: Glycogen Metabolism and Gluconeogenesis
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Sample Questions
Q1) The glycogen debranching enzyme is required for
A)the transfer of 3-glucose units from one branch to another.
B)the transfer of phosphate from one position to another.
C)cleaving \(\alpha\)(1\(\to\)6)sugar linkages
D)A and C
E)A,B and C
Q2) A deficiency in the enzyme PEPCK (PEP carboxykinase)would
A)block function of the malate/aspartate shuttle.
B)block transfer of reducing equivalents across the membrane in the heart and liver.
C)inhibit formation of ATP via oxidative phosphorylation.
D)inhibit formation of NADH.
E)decrease flux through gluconeogenesis.
Q3) Muscle cells are not able to supply glucose for other tissues because
A)they lack the GLUT2 transporter.
B)they lack pyruvate carboxylase.
C)they lack glucose-6-phosphatase.
D)they lack the malate-aspartate shuttle.
E)they lack glycogen phosphorylase.
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Chapter 17: Citric Acid Cycle
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Q1) Which of the following is TRUE regarding the discovery of the citric acid cycle? (I)One of the first discoveries was the involvement of coenzyme A in the production of GTP.
(II)Krebs had knowledge of the sequence of reactions before he was able to demonstrate the link of the cycle to glucose metabolism. (III)The citric acid cycle was the first cyclic pathway discovered. (IV)Krebs demonstrated the involvement of the citric acid cycle in oxidation of amino acid and fatty acids.
A)I,II,III,IV
B)I,II,III
C)II,III
D)III,IV
E)II,IV
Q2) Which reaction below produces GTP in the citric acid cycle?
A)"isocitrate \(\to\) \(\alpha\)-ketoglutarate"
B)"\(\alpha\)-ketoglutarate \(\to\) succinyl CoA"
C)"succinyl CoA \(\to\) succinate"
D)"fumarate \(\to\) malate"
E)"malate \(\to\) oxaloacetate"
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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) 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) Electrons abstracted from water by ___ are relayed to ___ via formation of a
A)OEC;P680<sup>+</sup>;plastoquinone
B)PSII;cytochrome b<sub>6</sub>;plastoquinone
C)OEC;P680<sup>+</sup>;tyrosyl radical
D)OEC;cytochrome b<sub>6</sub>;tyrosyl radical
E)OEC;P960<sup>+</sup>;tyrosyl radical
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Page 21
Chapter 20: Lipid Metabolism
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Q1) Which of the following statements about apolipoproteins (with the possible exception of apoB-100)is TRUE?
(I)The apolipoproteins are water-soluble and loosely associate with the lipoproteins.
(II)The apolipoproteins contain helices with hydrophobic and hydrophilic groups on opposite sides of the helical cylinder.
(III)The apolipoproteins are synthesized in the intestinal tissues.
(IV)The apolipoproteins appear to float on the surface of phospholipids.
A)I only
B)I and II
C)III,IV
D)I,II,III
E)I,II,IV
Q2) Which of the following enzymes is NOT involved in the tricarboxylate transport system?
A)citrate synthase
B)ATP citrate lyase
C)malate dehydrogenase
D)malic enzyme
E)All are involved in the transport of acetyl-CoA into the cytosol
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Page 22
Chapter 21: Amino Acid Metabolism
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Q1) _____ catalyzes the synthesis of ____,a molecule that signals vasodilation,from the precursor _____
A)NOS;nitric oxide (NO);arginine
B)Nitrous oxidase;nitrous oxide;arginine
C)Arginate;nitric oxide (NO);citrulline
D)Citrulline dehydrogenase;nitrous oxide;citrulline
E)none of the above
Q2) Which of the following statements about maple syrup urine disease is FALSE?
(I)It is caused by a genetic deficiency in the enzyme BCKDH.
(II)The disease is fatal unless promptly treated.
(III)There is a buildup of the branched-chain \(\alpha\)-keto acids.
(IV)Patients with the disease excrete urine that smells like maple syrup.
A)I only
B)II only
C)I,III
D)III,IV
E)All of the statements are true.
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Page 23
Chapter 22: Mammalian Fuel Metabolism: Integration and Regulation
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Q1) Which of the following is part of the regulation of metabolism?
A)receptor tyrosine kinase
B)adenylate cyclase
C)phosphoinositide pathway
D)all of the above
E)none of the above
Q2) Which of the following is TRUE regarding pancreatic \(\beta\) cells?
A)Insulin is secreted by the \(\beta\) cells in response to the increase in \(\beta\) cell glucose receptor binding.
B)Glucagon is secreted by the \(\beta\) cells in response to the increase in \(\beta\) cell glucose receptor binding.
C)Insulin is secreted by the \(\beta\) cells in response to high glucose levels.
D)Insulin is secreted by the \(\beta\)cells in response to low glucose levels.
E)Glucagon is secreted by the \(\beta\) cells in response to high glucose levels.
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Chapter 23: Nucleotide Metabolism
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Q1) The symptoms of Lesch-Nyhan syndrome are caused by a deficiency of which of the following enzymes?
A)adenine phosphoribosyltransferase
B)HGPRT (hypoxanthine-guanine phosphoribosyltransferase)
C)adenosine deaminase
D)dihydrofolate reductase
E)xanthine oxidase
Q2) Recombinant forms of the enzyme urate oxidase are available for therapeutic purposes.Based on the information in this chapter,in which of the following conditions might this therapy be useful?
A)myoadenylate deaminase deficiency
B)severe combined immunodeficiency disease
C)gout
D)toxoplasmosis
E)folate deficiency
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Chapter 24: Nucleic Acid Structure
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Q1) Which of the following best describes the structure of a nucleosome?
A)approximately 150 bp of DNA wrapped around a set of two H2A/H2B and two H3/H4 dimers with H1 on the outside
B)approximately 15 bp of DNA wrapped around an octamer of H1 with H2A,B,H3 and H4 on the outside
C)approximately 150 bp of DNA wrapped around a tetramer of either H2A/H2B or H3/H4 with H1 on the outside
D)approximately 1500 bp of DNA wrapped around a tetramer of either H2A/H2B or H3/H4 with H1 on the outside
E)approximately 200 bp of DNA wrapped around a tetramer of H2A,H2B,H3,and H4 with H1 on the outside
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
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Chapter 25: DNA Replication, repair and Recombination
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Q1) Which of the following describes the usefulness of primase?
A)It removes RNA bases and replaces them with DNA bases.
B)It seals nicks.
C)It adds an RNA starter sequence which can be elongated.
D)It is only required on the leading strand.
E)It unwinds the DNA.
Q2) Which of the following statements about DNA methylation is TRUE?
(I)Methylation plays a role in genomic imprinting.
(II)Methylation can influence gene regulation.
(III)Methylation plays a role in restriction modification systems.
(IV)Methylation occurs in prokaryotic cells,but not eukaryotic cells.
A)I,II,III,IV
B)I,II,III
C)II,III
D)II,III,IV
E)II only
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Chapter 26: Transcription and Rna Processing
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Q1) The fact that some eukaryotic rRNAs are self-splicing indicates that
A)RNA structures are highly variable.
B)RNAs can contain modified bases.
C)eukaryotes have multiple RNA polymerases.
D)RNA can act as an enzyme or catalyst.
E)None of the above is correct.
Q2) Which of the following eukaryotic proteins are encoded by genes which have no known introns?
A)interferons
B)tropomyosin
C)SXL protein
D)all of the above
E)none of the above
Q3) Which of the following types of RNA undergo posttranscriptional modifications?
A)mRNA
B)rRNA
C)tRNA
D)all of the above
E)none of the above
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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) The Shine-Dalgarno sequence is
A)used to align ribosome subunits and initiation translation.
B)functions as a stop codon.
C)is used to align RNA polymerase.
D)is used during transcription termination.
E)all of the above
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Chapter 28: Regulation of Gene Expression
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Q1) Genes without a known function are called ______ genes.
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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