Biochemistry for Life Sciences
Final Exam
Course Introduction
Biochemistry for Life Sciences explores the molecular foundations of living organisms, focusing on the chemical structures and processes that underlie biological function. This course covers the properties of biomolecules such as proteins, nucleic acids, lipids, and carbohydrates, as well as fundamental metabolic pathways, enzyme function, and regulation. Emphasis is placed on the integration of biochemical principles to understand cellular processes, signaling mechanisms, and the molecular basis of health and disease, providing a solid foundation for advanced study in the life sciences and related fields.
Recommended Textbook
Fundamentals of Biochemistry Life at the Molecular Level 4th Edition by Donald Voet
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Page 2
Chapter 1: Introduction to the Chemistry of Life
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Q1) A reaction with a ______ \(\Delta\)H and a ______ \(\Delta\)S, will never be spontaneous.
A)positive, positive
B)positive, negative
C)negative, positive
D)negative, negative
E)none of the above
Answer: B
Q2) Phylogeny is
A)the science of biological classification based on gross morphology.
B)the science of biological classification based on the evolutionary relationships between organisms.
C)the science of biological classification based on reproductive strategies.
D)the branch of science that studies phyllopods.
E)none 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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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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Sample Questions
Q1) Transfer RNA molecules are involved in A)transcription.
B)translation.
C)replication.
D)reverse transcription.
E)posttranslational processing.
Answer: B
Q2) What group is attached to the pyrimidine ring in thymine and is not present in uracil?
A)ribose
B)-CH<sub>3</sub>
C)(<sub>-</sub>NH<sub>2</sub>)
D)deoxyribose
E)none of the above
Answer: B
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Page 5
Chapter 4: Amino Acids
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Q1) At a pH below its pK<sub>a</sub>, the \(\varepsilon\)-amino group of lysine 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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Page 6
Chapter 5: Proteins: Primary Structure
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Q1) The peptide Leu Cys Arg Ser Gln Met is subjected to Edman degradation.In the first cycle the peptide first reacts with phenylisothiocyanate under basic conditions.The product of this reaction is incubated with anhydrous trifluoroacetic acid and subsequently with an aqueous acid.What are the products generated in the first cycle.
A)PTH Leu, PTH Cys, PTH Arg, PTH Ser, PTH Gln, and PTH Met
B)PTH Leu Cys Arg Ser Gln Met
C)PTH Met and Leu Cys Arg Ser Gln Met
D)PTH Leu Cys and PTH Arg Ser Gln Met
E)PTH Leu and Cys Arg Ser Gln Met
Q2) The acronym HPLC stands for
A)hydrophobic protein liquid chromatography.
B)high performance liquid chromatography.
C)hydrophilic partition liquid chromatography.
D)high priced liquid chromatography.
E)hydrostatic process liquid chromatography.
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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Page 7
Chapter 6: Proteins: Three-Dimensional Structure
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Q1) The low pH found in the gut can enhance the digestibility of dietary protein by causing ___.
A)amide hydrolysis
B)protein denaturation
C)disulfide reduction
D)prion formation
E)cysteine oxidation
Q2) Examine the three sequences below for collagen-like proteins and their melting temperatures (Tm).(Note: Flp = fluoroproline; Hyp = hydroxyproline)Based on this data, what is the most important feature in determining the strength of the collagen protein?
1) -Pro-Hyp-Gly-Pro-Hyp-Gly-Pro-Hyp-Gly- Tm=60<sup>o</sup>C
2) -Pro-Flp-Gly-Pro-Flp-Gly-Pro-Flp-Gly- Tm=78<sup>o</sup>C
3) -Gly-Pro-Thr-Gly-Pro-Thr-Gly-Pro-Thr- Tm=30<sup>o</sup>C
A)hydrogen bonding
B)inductive effect
C)electrostatic effect
D)electrostatic and Inductive effect are equal
E)hydrogen bonding and inductive effect are equal
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Chapter 7: Protein Function Part I: Myoglobin and Hemoglobin
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Q1) 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
Q2) What is the primary physiological function of myoglobin in most mammals?
Q3) IgG is one of five classes of antibodies that can be produced by our immune system.IgGs have a molecular mass of approximately 150 kDa, what is their subunit composition?
A)2 light chains and 2 heavy chains
B)2 light chains, 2 heavy chains, and a J chain
C)4 light chains, 4 heavy chains, and a J chain
D)6 light chains, 6 heavy chains, and a J chain
E)10 light chains, 10 heavy chains , and a J chain.
Q4) Myoglobin is an oxygen binding protein in muscle.Describe in one sentence the overall structure of myoglobin.
Page 9
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Chapter 8: Carbohydrates
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Sample Questions
Q1) The configuration around which carbon atom shown in the figure above determines whether this is a D or an L sugar?
A)A
B)B
C)C
D)D
E)E
Q2) A saccharide that has free aldehyde group is called a(n)_____________.
A)ketose
B)nonreducing sugar
C)reducing sugar
D)aldohexose
E)alditol
Q3) Uronic acids
A)are aldoses where the aldehyde is oxidized to a carboxylic acid.
B)are aldoses where the 1° alcohol is oxidized to a carboxylic acid.
C)can be found in the pyranose or furanose forms.
D)A and C are both correct.
E)B and C are both correct.
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Page 10
Chapter 9: Lipids and Biological Membranes
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Q1) Which of the following is comprised primarily of fatty acids and other single tailed amphiphiles?
A)lipid bilayers
B)two-dimensional membranes
C)liposomes
D)micelles
E)solvent-filled vesicles
Q2) Coated vesicles are used to ensure that the enclosed protein maintains its proper orientation.Clathrin is one type of protein used to coat vesicles.Which of the following is true regarding clathrin vesicles?
A)They transport proteins between successive components of the Golgi compartments.
B)They transport transmembrane proteins and GPI-linked proteins from the Golgi to the plasma membrane.
C)They transport proteins from the ER to the Golgi.
D)They form a rigid complex capable of protecting protein structure and orientation as it is passed from hydrophobic to hydrophilic environments.
E)None of the above.
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Chapter 10: Membrane Transport
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Q1) In the body hydrogen ions produced from the reaction of carbonic anhydrase are transported into the lumen of the stomach via an ATP utilizing proton pump.The removal of hydrogen ions drives formation of bicarbonate ions and a concentration gradient is formed.Bicarbonate is transported out at the same time that chloride ions are transferred in.Based on this information, which of the following is FALSE?
A)The pump driving the driving the hydrogen ions into the lumen must undergo a conformational change.
B)The pump driving bicarbonate out and chloride in must be an antiport system.
C)The pump driving bicarbonate out and chloride in must require ATP directly.
D)The bicarbonate-chloride pump requires ATP indirectly.
E)The bicarbonate-chloride pump must require activity of the proton pump.
Q2) Which statement does not describe the transport of ions by valinomycin?
A)Mutations in the peptide sequence may alter ability to transport through the membrane.
B)Transport may be active or passive.
C)The active site binds K<sup>+</sup> with greater affinity than Na<sup>+</sup>
D)Transport results in equilibration of a concentration gradient across membranes.
E)All of the above do describe transport by valinomycin.
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Page 12
Chapter 11: Enzyme Catalysis
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Q1) Since proteins are limited in their abilities to catalyze oxidation-reduction reactions, enzymes often employ ______ to assist with catalysis.
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) In ______, the inhibitor binds to a site involved in both substrate binding and catalysis.
A)isozymes
B)[A]
C)the rate constant
D)Ping Pong
E)bimolecular
F)ES complex
G)random ordered
H)competitive inhibition
I)unimolecular
J)[A]²
K)Competitive inhibition
L)phosphorylation
M)small KS
N)large KS
O)uncompetitive inhibition
P)[B]
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Page 14
Chapter 13: Biochemical Signaling
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Q1) Ras is an example of
I.a protein anchoted by prenylation.
II.a heterotrimeric G protein.
III.a kinase activated protein.
IV.a GTP dependent protein.
A)I, II, III, IV
B)I, III, IV
C)I, III
D)II, III, IV
E)IV only
Q2) Which of the following functions as a regulatory protein by dephosphorylating activated enzymes?
A)receptor tyrosine kinase
B)phosphoprotein phosphatase
C)heterotrimeric G protein phosphorylase
D)guanine nucleotide exchange factor
E)Sos protein
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Chapter 14: Introduction to Metabolism
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Q1) Consider the following metabolic reaction important in muscle and nerve cells: ATP + creatine \(\rightleftarrows\) phosphocreatine + ADP \(\Delta\)G°' = +12.6 kJ/mol
Under intracellular conditions, the \(\Delta\)G for the reaction, which is catalyzed by the enzyme creatine kinase, is ~0 kJ/mol.From this information we can conclude that
A)creatine kinase catalysis would not be necessary under intracellular conditions.
B)ATP has a greater phosphoryl group transfer potential compared to phosphocreatine.
C)at equilibrium, most intracellular creatine is phosphorylated.
D)the reaction operates close to equilibrium in cells.
E)None of the above is a correct conclusion.
Q2) The conversion of triacylglycerides into fatty acids for the purpose of energy generation is an example of which of the following?
A)heterotropism
B)anaerobism
C)catabolism
D)anabolism
E)glycolysis
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Chapter 15: Glycogen Metabolism and Gluconeogenesis
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Q1) 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
Q2) 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\(\rarr\)6)sugar linkages
D)A and C
E)A, B and C
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17
Chapter 16: Glucose Catabolism
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Q1) Which is the net equation for aerobic glycolysis?
A)Glucose + 2 ATP 2 lactate + 2 ADP + 2 Pi
B)Glucose + 2 ADP + 2 Pi + 2 NAD+ 2 pyruvate + 2 ATP + 2 NADH + + 2 H<sub>2</sub>O 4 H+
C)Glucose + 2 ADP + 2 Pi 2 lactate + 4 ATP + 4 H+
D)Glucose + 2 ATP + 2 NAD+ 2 pyruvate + 4 ATP + 4 NADH + 4 H+
E)Glucose + 2 ADP + 2 Pi + 2 NAD+ 2 lactate + 4 ATP + 2 NADH + 4 H+
Q2) Phosphofructokinase is allosterically _____ by high concentrations of _____.
I.activated; ATP
II.inhibited; ATP
III.inhibited; fructose-2,6-bisphosphate
IV.activated; fructose -2,6-bisphosphate
A)I, III
B)II, III
C)II, IV
D)I, IV
E)none of the above
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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 utilizes intermediates of the citric acid cycle?
I.gluconeogenesis
II.amino acid biosynthesis
III.fatty acid oxidation
IV.glycolysis
A)I only
B)II only
C)I, II, III
D)I, II
E)I, IV
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Page 19
Chapter 18: Electron Transport and Oxidative
Phosphorylation
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Q1) The inner mitochondrial membrane divides the mitochondrion into the inner membrane space and the ______.
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) A houseplant has been mutated so that its chlorophyll is more efficient at fluorescence than normal.What will be the likely result?
A)Both forms of the light reactions will improve and the plant will better tolerate low light conditions.
B)Z-scheme photosynthesis will be favored over cyclic photophosphorylation, making additional illumination at long wavelengths necessary.
C)Cyclic photophosphorylation will be favored over Z-scheme, making additional illumination at short wavelengths necessary.
D) Both forms of the light reaction will be impaired and the plant will be less tolerant to low light conditions.
E)none of the above
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) LDL taken up by the liver is
A)broken down into fatty acids and amino acids.
B)taken up by the ER and used to control synthesis of HMG CoA reductase and LDL receptor synthesis.
C)converted into clathrin and recycled.
D)irreversibly bound to LDL receptors.
E)excreted in a clathrin coated vesicle.
Q2) The activity of lipases is controlled in part by a process known as ____ which functions effectively due to the ____ where lipases are active.
A)interfacial activation; lipid-water interface
B)lipase activation; lipid-water interface
C)lipase activation; bile salt-water interface
D)micelle activation; water-salt interface
E)none of the above
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22
Chapter 21: Amino Acid Metabolism
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Q1) Infants who cannot properly degrade bilirubin develop ______.
A)ribosomes
B)jaundice
C)channeling
D)26S proteasome
E)glutamine synthetase
F)alanine
G)glutamate
H)vitamin B6
I)anammox
J)glutamine transferase
K)THF
L)autotroph
M)vitamin D
N)lysosomes
O)diazotrophs
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Page 23
Chapter 22: Mammalian Fuel Metabolism: Integration and Regulation
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Q1) Which of the following occurs during starvation?
I.The kidney generates approximately half the glucose required for the body.
II.The brain utilizes ketone bodies as a fuel source.
III.The adipose tissue releases fatty acids.
IV.Gluconeogenesis occurs in the liver.
A)I, II, III, IV
B)I, II, III
C)I, II
D)II, III
E)II, III, IV
Q2) The glucose transporter in muscle cells is
A)insulin.
B)glucagon.
C)GLUT2.
D)GLUT4.
E)none of the above
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Chapter 23: Nucleotide Metabolism
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Q1) A final common product from both purine degradation and pyrimidine degradation is
A)uric acid.
B)aspartate.
C)ribose-1-phosphate.
D)ribose-5-phosphate.
E)malonyl-CoA.
Q2) 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
Q3) The amino group added to the C6 position of IMP to form AMP is derived from A)aspartate.
B)asparagine.
C)glutamine.
D)(\(\alpha\)-ketoglutarate.)
E)arginine.
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Chapter 24: Nucleic Acid Structure
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Q1) 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.
Q2) The sugar pucker is___ in the ___form.
A)C2'-endo; A-DNA
B)C3'-endo; B-DNA
C)C2'-endo for pyrimidines and C3'-endo for purines: Z-DNA
D)C2'-endo for purines and C3'-endo for pyrimidines: B-DNA
E)C2'-endo for purines and C3'-endo for pyrimidines: A-DNA
Q3) Which of the following prokaryotic enzymes can introduce negative supercoils?
A)topoismerase IA
B)topoismerase III
C)DNA gyrase
D)all of the above
E)none of the above
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Page 26
Chapter 25: Dna Replication, Repair and Recombination
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Q1) Which of the following activities does E.coli DNA polymerase III contain?
I.5' 3' polymerase
II.5' 3' exonuclease
III.3' 5' exonuclease
A)I only
B)I, II
C)II only
D)I, III
E)I, II, III
Q2) The DNA sequence shown below is copied by the Klenow fragment.Which of the following would most likely result? 5' TGCGTGCACTCGA 3'
A)identical
B)5' TGCGT 3'
C)5' TGCAGTGACGCT 3'
D)cannot predict
E)none of the above
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Chapter 26: Transcription and Rna Processing
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Q1) Which of the following is required for correct translation in eukaryote initiation?
A)poly(A)tail.
B)5' cap consisting of 7-methylguanosine.
C)intron excision.
D)alternative splicing.
E)exon skipping.
Q2) In which of the following types of eukaryotics RNAs are introns completely removed most of the time, although exceptions can occur?
I.mRNA
II.rRNA
III.tRNA
A)I, II
B)I, III
C)II, III
D)I, II, III
E)none of the above
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Chapter 27: Translation
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Q1) Insertions or deletions of one or two nucleotides can cause
A)frameshift mutations.
B)degenerate mutations.
C)synonymous mutations.
D)wobble codons.
E)transpeptidation.
Q2) During translation, the reaction catalyzed by peptidyl transferase is coupled to which of the following?
A)ATP ADP + P<sub>i</sub>
B)ATP AMP + PP<sub>i</sub>
C)GTP GDP + P<sub>i</sub>
D)GTP GMP + PP<sub>i</sub>
E)Release of the tRNA in the P site
Q3) The signal recognition particle (SRP)is a _____, and its function is to ______.
A)DNA:protein complex, transport proteins into the eukaryotic nucleus
B)multisubunit protein, modify proteins
C)ribosome complex, catalyze posttranslational modification
D)ribonucleoprotein, bind the N-terminal end of growing polypeptides for membrane translocation
E)none of the above
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Chapter 28: Regulation of Gene Expression
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Q1) 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
Q2) In humans, approximately ______ of the genome encodes proteins.
A)0.4%
B)1.4%
C)14%
D)24%
E)44%
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