Biochemical Techniques
Exam Materials
Course Introduction
Biochemical Techniques introduces students to the fundamental laboratory methods used to analyze and manipulate biomolecules. The course covers principles and practical applications of techniques such as spectrophotometry, chromatography, electrophoresis, centrifugation, and enzyme assays. Special emphasis is placed on the design and interpretation of experiments, data analysis, and troubleshooting common problems encountered during laboratory work. Students gain hands-on experience in isolating, purifying, and characterizing proteins, nucleic acids, and other biological macromolecules, laying the groundwork for further study and research in biochemistry, molecular biology, and related fields.
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) An increase in disorder in the system
A)is required for a process to be spontaneous.
B)results in a decrease in entropy.
C)is characteristic of a system increasing in enthalpy.
D)results in the factor T\(\Delta\)S being positive .
E)is found in every exergonic process.
Answer: D
Q2) In 1953, Urey and Miller carried out an experiment in which they subjected a mixture of H<sub>2</sub>O, CH<sub>4</sub>, NH<sub>3</sub>, and H<sub>2</sub> to electrical discharges.Which of the following were among the products?
A)proteins
B)amino acids
C)nucleic acids
D)ribosomes
E)all of the above
Answer: B
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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Page 3
Chapter 2: Water
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Sample Questions
Q1) 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
Q2) The strongest noncovalent interactions are
A)ionic interactions.
B)hydrogen bonds.
C)dipole-dipole interactions.
D)London dispersion forces.
E)van der Waals forces.
Answer: A
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Page 4
Chapter 3: Nucleotides, Nucleic Acids, and Genetic Information
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Q1) After hybridization, the fragment of interest can be detected by ______.
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: J
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Chapter 4: Amino Acids
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Q1) Typically, modified amino acids, those with side chain modifications that are present in proteins
A)are synthesized due to genetic mutations.
B)are assembled by specialized bacterial enzymes.
C)are formed by modification of standard side chain residues after the protein is synthesized.
D)are toxic.
E)are racemic.
Q2) Which of the following amino acids has a sulfur atom in its side chain?
A)Asn
B)Ser
C)Phe
D)Met
E)Tyr
Q3) Which of the amino acids represented below has two chiral centers?
A)Ala
B)Leu
C)Ile
D)Pro
E)Asn
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Chapter 5: Proteins: Primary Structure
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Sample Questions
Q1) You are purifying a nuclease by affinity chromatography.To determine which fractions contain the protein of interest, you test samples of all fractions for their ability to break down DNA.This is an example of A)a binding assay.
B)a biological assay.
C)an enzyme assay.
D)an immunological assay.
E)none of the above
Q2) Proteins are often constructed from multiple segments of 40-200 amino acid residues, commonly called A)pseudogenes.
B)hypervariable residues.
C)protolytic fragments.
D)domains. E)subunits.
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) A historical experiment exploring denaturation upon - mercaptoethanol reduction of disulfide bonds and spontaneous renaturation upon dialysis to remove themercaptoethanol was carried out using the protein ______.This experiment demonstrated the importance of disulfide bonds and amino acid sequence in folding of proteins.
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
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8
Chapter 7: Protein Function Part I: Myoglobin and Hemoglobin
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Sample Questions
Q1) Which statement about actin is not true?
A)There are two actin genes, one for F-actin and one for G-actin.
B)Monomeric G-actin polymerizes to form F-actin.
C)Actin filaments are polar (the ends can be distinguished).
D)Actin can bind ATP.
E)Actin is a common protein in nonmuscle cells.
Q2) Max Perutz's investigation of the structure of hemoglobin primarily utilized_____.
A)X-ray crystallography
B)NMR spectroscopy
C)genomics
D)mass spectrometry
E)genetic engineering
Q3) The energy needed to drive muscle contraction comes from ATP hydrolysis that is carried out by
A)G-actin.
B)F-actin.
C)myosin heads.
D)myosin tails.
E)tropomyosin.
Page 9
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Chapter 8: Carbohydrates
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Sample Questions
Q1) At equilibrium in solution, D-glucose consists of a mixture of its anomers.Which statement most accurately describes this solution?
A)The solution consists of approximately equal amounts of the \(\alpha\)- and \(\beta\)-anomers.
B)The straight-chain form is present in high concentration.
C)The \(\alpha\)-anomer is more stable and is slightly preferred over the \(\beta\)-anomer.
D)The \(\beta\)-anomer predominates over the \(\alpha\)-anomer by a ratio of approximately 2:1.
E)None of the answers above is correct.
Q2) 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
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10
Chapter 9: Lipids and Biological Membranes
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Sample Questions
Q1) 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.
Q2) Unsaturated fatty acids:
A)are commonly found in plants and animals
B)usually contain a double bond with cis stereochemistry
C)sometimes contain multiple double bonds
D)have lower melting points than the analogous saturated fatty acids
E)all of the above
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Chapter 10: Membrane Transport
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Q1) KcsA is an example of a ______ ionophore.
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) 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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Page 12
Chapter 11: Enzyme Catalysis
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Sample Questions
Q1) On a transition state diagram for a one-step very spontaneous reaction a large peak (high \(\Delta\) G<sup> </sup>)would imply a ______ rate for the reaction.
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) K<sub>M</sub> is
A)a measure of the catalytic efficiency of the enzyme.
B)equal to half of V<sub>max</sub>
C)the rate constant for the reaction ES \(\rightarrow\) E + P.
D)the [S] that half-saturates the enzyme.
E)a ratio of substrate concentration relative to catalytic power.
Q2) A Lineweaver-Burk plot is also referred to as
I.a sigmoidal plot.
II.a linear plot.
III.a Michaelis-Menten plot.
IV.a double reciprocal plot.
A)II
B)II, III
C)IV
D)II, IV
E)III, IV
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Chapter 13: Biochemical Signaling
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Sample Questions
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) Which of the following hormones functions by binding to receptors that function directly as transcription factors?
A)steroids
B)insulin
C)epinephrine
D)glucagon
E)somatostatin
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Chapter 14: Introduction to Metabolism
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Sample Questions
Q1) The term "Nutrition" involves which of the following components?
I.food intake
II.metabolic utilization of food
III.the intake requirement of oxygen
IV.the control of metabolic flux
A)I only
B)II only
C)I, II
D)I, II, III
E)I, II, III, IV
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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Page 16
Chapter 15: Glycogen Metabolism and Gluconeogenesis
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Q1) In glycogen synthesis, the intermediate between glucose-1-phosphate and glycogen is
A)UDP-glucose .
B)UDP-glycogen.
C)glucose-1,6-bisphosphate.
D)glucose-6-phosphate.
E)glucose.
Q2) 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
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17
Chapter 16: Glucose Catabolism
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Sample Questions
Q1) Which enzyme is involved in substrate level phosphorylation in glycolysis?
A)Hexokinase
B)Pyruvate kinase
C)Glyceraldehyde-3phosphate dehydrogenase
D)Aldolase
E)None of the above.
Q2) 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.
Q3) Glycolytic synthesis of ATP occurs via A)oxidation.
B)reduction.
C)substrate-level phosphorylation.
D)oxidative phosphorylation.
E)photophosphorylation.
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Page 18
Chapter 17: Citric Acid Cycle
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Sample Questions
Q1) A membrane-bound enzyme of the citric acid cycle that catalyzes an oxidation reaction is ______.
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) Which reaction below produces GTP in the citric acid cycle?
A)isocitrate \(\rarr\)\(\alpha\)-ketoglutarate
B)(\(\alpha\)-ketoglutarate \(\rarr\)succinyl CoA)
C)succinyl CoA \(\rarr\) succinate
D)fumarate \(\rarr\) malate
E)malate \(\rarr\) oxaloacetate
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Page 19
Chapter 18: Electron Transport and Oxidative Phosphorylation
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Q1) The rate of oxidative phosphorylation
I.is regulated by the availability of ADP and P<sub>i</sub>.
II.is reduced when the ratio of [NADH]/[NAD<sup>+</sup>] is high.
III.increases with a higher concentration of reduced cytochrome c IV.is regulated by activity of the ADP-ATP translocator.
A)I, II, IV
B)I, III, IV
C)II, III
D)I, III, IV
E)II, IV
Q2) Which conformation of the active sites in ATP synthase allows binding of substrates?
A)L state
B)O state
C)T state
D)C state
E)A and B
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Page 20
Chapter 19: Photosynthesis
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Q1) In the dark reactions of photosynthesis, glyceraldehyde-3-phosphate is converted to dihydroxyacetone phosphate by___.
A)phosphoglucoisomerase
B)triose phosphate isomerase
C)glyceraldehyde-3-phosphate dehydrogenase
D)phosphotriose epimerase
E)phosphoglycerate kinase
Q2) Which of the following is TRUE regarding the difference between chlorophyll structures and heme?
A)Chlorophyll structures contain copper rather than iron.
B)Chlorophyll structures typically have five rings while heme typically has four.
C)Chlorophyll often has fewer R groups attached to the ring system that heme.
D)Chlorophyll metal atoms coordinate to the nitrogen atoms from the ring where as heme iron atoms coordinate to carbon atoms.
E)all of the above
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Chapter 20: Lipid Metabolism
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Q1) Pain and inflammation are triggered by ___ which are synthesized by an enzyme inhibited by ____.
A)cardiolipins; aspirin
B)prostaglandins; aspirin
C)analgesics; statins
D)prostaglandins; COX-1
E)cyclooxygen; NSAIDS
Q2) Two phosphatidylglycerol molecules condense to form the molecule ______, and glycerol is eliminated as the side product.
A)phosphatidic acid
B)cardiolipin
C)plasmalogen
D)sphingomyelin
E)squalene
Q3) Which of the following components would be condensed to form acetoacetate?
A)acetyl CoA and acetyl-CoA
B)HMG-CoA and acyl-CoA
C)acetone and betahydroxybutyrate
D)malonyl-CoA and acyl-CoA
E)DHAP and glycerol-3-phosphate
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Chapter 21: Amino Acid Metabolism
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Q1) A number of compounds, including neurotransmitters, are synthesized from amino acids via decarboxylations.The enzymes catalyzing these steps usually use _______ as a cofactor.
A)pyridoxal-5 -phosphate
B)thiamine pyrophosphate
C)biotin
D)cobalt containing compounds [vitamin B<sub>12</sub>]
E)tetrahydrofolate
Q2) The amino acids Ala, Cys, Gly, Ser, and Thr are all degraded to the metabolic intermediate ___ and are considered ____.
A)acetyl-CoA; glucogenic
B)acetyl-CoA; ketogenic
C)pyruvate; glucogenic
D)pyruvate; ketogenic
E)acetoacetate; ketogenic
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Chapter 22: Mammalian Fuel Metabolism: Integration and Regulation
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Q1) The ______ stores very little glycogen and therefore requires a steady supply of glucose from the blood.
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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Page 24
Chapter 23: Nucleotide Metabolism
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Q1) The precursor to AMP and GMP is ______.
A)fumarate
B)NADPH
C)salvage
D)uric acid
E)oxidation
F)XMP
G)iron
H)allopurinol
I)IMP
J)Oxidation
K)therapeutic
L)suicide
M)molybdenum
N)FADH
O)Malonyl-CoA
P)reduction
Q)antifolate
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Page 25
Chapter 24: Nucleic Acid Structure
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Q1) ________, an ion that intercalates into double-stranded DNA, is often used for staining gels.
A)type I
B)ribocatalyzers
C)C2'-endo
D)repressors
E)ethidium
F)type II
G)C3'-endo
H)hybridized
I)interchanged
J)supercoiled
K)cooperative
L)non-cooperative
M)underwound
N)ribozymes
O)deuterium
P)zinc finger
Q)leucine zipper
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Chapter 25: Dna Replication, Repair and Recombination
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Q1) Which of the following are TRUE about transposons?
I.They are normal components of plasmids.
II.They often carry genes for antibiotic resistance.
III.They insert at a target sequence that is a repetitive unit of about 200 bp.
A)I, II, III
B)I, II
C)II, III
D)II only
E)III only
Q2) 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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Chapter 26: Transcription and Rna Processing
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Q1) The phosphorylation of the CTD of RNA polymerase II is important for which phase of transcription?
A)initial binding of the promoter
B)conversion from the pre-initiation (closed)complex to the initiation (open)complex
C)progression from initiation to elongation
D)termination of transcription
E)none of the above
Q2) The precursors of most eukaryotic rRNAs are synthesized by I.RNA polymerase I.
II.RNA polymerase II.
III.RNA polymerase III.
A)I or III
B)I or II
C)I only
D)II only
E)III only
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28
Chapter 27: Translation
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Q1) Which of following describes proofreading for the addition of amino acids (AAs)to the growing peptide?
A)An RNA component of the ribosome ensures that the correct AA is associated with the A site before addition occurs.
B)An RNA component of the ribosome ensures that the correct AA has been added, but before the peptidyl-tRNA is shifted to the P site.
C)The EF-Tu GTP complex ensures that the correct AA is associated with the A site before addition occurs.
D)EF-G ensures that the correct AA has been added, but before the peptidyl-tRNA is shifted to the P -site.
E)No proofreading of this process occurs.
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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29
Chapter 28: Regulation of Gene Expression
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Q1) An organism's metabolic complexity and morphology are not always consistent with the amount of its genetic material.This inconsistency is called
A)genomic degeneracy.
B)the C-value paradox.
C)nucleotide polymorphism.
D)chromatin reorganization.
E)Prader-Willi syndrome.
Q2) Which of the following is TRUE regarding eukaryotic mRNAs?
I.They uniformly stable.
II.The poly (A)tail appears to partially Moderate the rate of degradation.
III.The 5' cap appears to partially Moderate the rate of degradation.
IV.They have decay times ranging from 10-30 minutes.
A)I, II
B)II, III
C)II, IV
D)III, IV
E)II only
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Page 30