Biochemistry for Life Sciences
Final Exam
Course Introduction
Biochemistry for Life Sciences explores the molecular foundations of living organisms, focusing on the structure, function, and interactions of biological macromolecules such as proteins, nucleic acids, carbohydrates, and lipids. The course provides a comprehensive understanding of metabolic pathways, enzyme mechanisms, and regulatory processes that drive cellular function. Emphasis is placed on the practical applications of biochemistry in medicine, genetics, biotechnology, and environmental science, preparing students with the foundational knowledge necessary for advanced studies and research in the life sciences.
Recommended Textbook
Biochemistry 4th Edition by Christopher K. Mathews
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Page 2
Chapter 1: The Scope of Biochemistry
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Q1) Which of the following organelles is found in plant cells, but not in animal cells
A)chloroplast
B)Golgi apparatus
C)mitochondrion
D)smooth endoplasmic reticulum
E)rough endoplasmic reticulum
Answer: A
Q2) Which of the following elements is considered a second tier biochemical element meaning that it is less abundant than first tier elements but still required for life in all organisms?
A)H
B)N
C)P
D)C
E)O
Answer: C
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3
Chapter 2: The Matrix of Life: Weak Interactions in an Aqueous Environment
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Q1) Which of the following represents the breaking of a noncovalent interaction?
A)hydrolysis of an ester
B)dissolving of salt crystals
C)ionization of water
D)decomposition of hydrogen peroxide
E)none of the above
Answer: B
Q2) Which of the following is the most likely noncovalent interaction observed between a carboxylic acid and an alcohol?
A)charge-charge interaction
B)charge-dipole interaction
C)dipole-dipole interaction
D)dipole-induced dipole interaction
E)formation of an ester bond
Answer: B
Q3) Imidazole is a commonly used buffer in biochemistry labs. With a pK<sub>a</sub> of 7.0, what would be the ratio of base to acid at pH 7.4?
Answer: 2.5 11ea7cd4_c4a8_33b6_a2ab_b9ca760947d7_TB2679_00
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Chapter 3: The Energetics of Life
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Q1) If acetyl phosphate is made from the combination of ATP and acetate, what is the \(\Delta\)G<sup>\(\circ\)</sup>'? How would this reaction proceed within a typical cell?
acetyl phosphate + H<sub>2</sub>O \(\rarr\) acetate + P<sub>i</sub> + H<sup>+</sup> \(\Delta\)G<sup>\(\circ\)</sup>'= -43.1 kJ/mol
ATP + H<sub>2</sub>O \(\rarr\)ADP + P<sub>i</sub> + H<sup>+</sup> \(\Delta\)G<sup>\(\circ\)</sup>' = -30.5 kJ/mol
Answer: \(\Delta\)G<sup>\(\circ\)</sup>'= +12.6 kJ/mol. If this reaction were to occur within a typical cell, the \(\Delta\)G for ATP hydrolysis is considerably more exergonic and is thus able to supply the necessary energy for the phosphorylation of acetate.
Q2) Which of the following best describes biochemical systems with respect to the first law of thermodynamics?
A)most biochemical systems operate at constant volume
B)most biochemical systems operate at constant temperature
C)most biochemical systems operate at constant pressure
D)most biochemical systems operate with a constant number of molecules
E)none of the above
Answer: C
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Chapter 4: Nucleic Acids
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Sample Questions
Q1) Which of the following, when paired with its complementary strand, would have the highest T<sub>m</sub>?
A)AAGTTCCAGT
B)GCAGCAGCAT
C)ATTACGAGCT
D)GCGAAATCAA
E)TGACCTTGAA
Q2) Which of the following is the most commonly observed nucleic acid form for storing of genomic information?
A)single-stranded DNA
B)double-stranded DNA
C)single-stranded RNA
D)double-stranded RNA
E)hybrid molecules of DNA and RNA
Q3) Show the typical hydrogen bonds that from when adenine pairs with its complimentary base.
Q4) Draw the structure of cytosine and thymine, then show the most common tautomer of each.
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Chapter 5: Introduction to Proteins: the Primary Level of
Protein Structure
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Sample Questions
Q1) Given the following peptide, what would be the overall charge at pH 5?
Met-Glu-Ser-Arg-His-Phe-Pro-Asn-Ala-Glu-Cys-Ala-Ser
A)+2
B)+1
C)0
D)-1
E)-2
Q2) Hydrolysis of a peptide bond produces:
A)an alcohol and an amine
B)an amine and a carboxylic acid
C)a carboxylic acid and an anhydride
D)an amide and a carboxylic acid
E)an alcohol and an amide
Q3) Which of the following amino acids is incorporated into proteins during ribosomal protein synthesis?
A)sarcosine
B)ornithine
C)4-hydroxyproline
D)phosphoserine
E)selenocysteine
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Chapter 6: The Three-Dimensional Structure of Proteins
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Q1) Which amino acid is often referred to as a "helix-breaker" due to its absence from \(\alpha\)-helices but is often found in structures such as \(\beta\)-turns?
A)Val
B)Met
C)Pro
D)Phe
E)Leu
Q2) Show the most likely interaction that would occur between a serine residue and a glutamine residue.
Q3) Which of the following is considered a dead-end complex (and therefore dangerous due to its resistance to proteolytic cleavage)in the protein-folding pathway?
A)disordered aggregate
B)molten globule state
C)prefibrillar species
D)amyloid fibril
E)unfolded protein
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8
Chapter 7: Protein Function and Evolution
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Sample Questions
Q1) Which of the following is responsible for the immense diversity of antibodies?
A)recombination of introns
B)recombination of exons
C)variable domain recombination
D)epitope recombination
E)none of the above
Q2) Which of the following is a homotropic effector of hemoglobin-oxygen binding?
A)O<sub>2</sub>
B)H<sup>+</sup>
C)CO<sub>2</sub>
D)Cl<sup>-</sup>
E)2,3-bisphosphoglycerate (2,3-BPG)
Q3) Which of the following mutations in the coding strand of DNA would be the most likely to cause a serious mutation?
A)AGA \(\rarr\) CGA
B)ATA \(\rarr\) TTA
C)GAA \(\rarr\) AAA
D)TAA \(\rarr\) TGA
E)ACT \(\rarr\) AGT
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Page 9
Chapter 8: Contractile Proteins and Molecular Motors
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Sample Questions
Q1) What is the 9 + 2 array seen in the axoneme?
A)2 central microtubules ringed by 9 microtubule doublets
B)2 central microtubule doublets ringed by 9 microtubules
C)9 central microtubules with 2 microtubules attached to each central microtubule
D)9 central microtubules with 2 microtubule doublets attached to each central microtubule
E)none of the above
Q2) Which portion of the myosin protein found in muscle is responsible for both ATP and actin binding?
A)heavy-chain coiled-coiled tails
B)heavy-chain stalk
C)heavy-chain globular head
D)essential light chain
E)regulatory light chain
Q3) Under typical conditions within a muscle cell, the \(\Delta\)G for hydrolysis of ATP is about -51 kJ/mol. If the energy required to move through one power stroke is 1.2 * 10<sup>-20</sup> J, what is the percent utilization of the energy from ATP hydrolysis?
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Page 10
Chapter 9: Carbohydrates: Sugars, Saccharides, Glycans
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Q1) Which of the following correctly identifies key elements present on the exterior of Gram-negative (GN)and Gram-positive (GP)bacteria?
A)GN: single lipid bilayer; GP: two lipid bilayers
B)GN: single peptidoglycan layer; GP: multiple peptidoglycan layers
C)GN: extensively crosslinked peptidoglycans; GP: uncrosslinked peptidoglycan
D)GN: contains both N-acetylmuramic acid and N-acetylglucosamine; GP: contains only N-acetylmuramic acid
E)none of the above
Q2) Antibiotic inhibition of cell wall synthesis can be facilitated by a number of agents. The crosslinking of peptidoglycan strands is inhibited by _________ while polymerization of the growing peptidoglycan is inhibited by __________.
A)penicillin; bacitracin
B)penicillin; vancomycin
C)vancomycin; bacitracin
D)vancomycin; penicillin
E)bacitracin; vancomycin
Q3) Show the interaction that would take place between the R-group of asparagine in a protein and the substituent on C-2 of an N-acetylglucosamine residue of a glycan.
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11
Chapter 10: Lipids, Membranes and Cellular Transport
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Q1) When fatty acids are added to an aqueous solution, they can either sit on top of the solution, forming a ________ or form spherical ________ throughout the solution.
A)monolayer; micelles
B)bilayer; micelles
C)monolayer; bilayer
D)bilayer; monolayer
E)micelle; bilayer
Q2) The transient association of lipid rafts is thought to play a significant role in which of the following?
A)cell signaling
B)bacterial entry into host cells
C)protein trafficking
D)membrane receptor dimerization
E)all of the above
Q3) Draw the following fatty acid: 18:3c\(\Delta\)9,12,15 as it would appear at physiological pH. With reference to the omega carbon, what type of fatty acid is this?
Draw the result if this fatty acid underwent partial hydrogenation to produce 18:1t\(\Delta\)11
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Chapter 11: Enzymes: Biological Catalysts
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Q1) An enzyme that catalyzes the intramolecular movement of a functional group from one carbon atom to another would be called a(n)____________.
A)isomerase
B)transferase
C)oxidoreductase
D)kinase
E)ligase
Q2) Both ATP and CTP are allosteric regulators of the enzyme aspartate transcarbamoylase. Which of the following correctly identifies the activities of these two regulators?
A)ATP: activator; CTP: activator
B)ATP: activator; CTP: inhibitor
C)ATP: inhibitor; CTP: activator
D)ATP: inhibitor; CTP: inhibitor
E)none of the above
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13
Chapter 12: Chemical Logic of Metabolism
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Q1) Which of the following functional groups is commonly the electrophile in nucleophilic acyl substitutions?
A)ester
B)hydroxide ion
C)amine
D)thiol
E)carboxylate
Q2) Which of the following would be considered a biosynthetic pathway?
A)glycolysis
B)glycogen synthesis
C)fatty acid \(\beta\)-oxidation
D)citric acid cycle
E)electron transport
Q3) Which of the following eukaryotic organisms is both autotrophic and heterotrophic?
A)yeast
B)humans
C)Venus fly trap
D)redwood trees
E)mushrooms
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Page 14
Chapter 13: Carbohydrate Metabolism: Glycolysis,
Gluconeogenesis, Glycogen Metabolism, and the Pentose
Phosphate Pathway
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Q1) The reaction catalyzed by triose phosphate isomerase is most similar in mechanism to which of the following glycolytic enzymes?
A)glucose-6-phosphate isomerase
B)fructose-1,6-bisphosphate aldolase
C)phosphoglycerate mutase
D)enolase
E)pyruvate kinase
Q2) What is the link between glutathione and the pentose phosphate pathway (PPP)?
A)during the oxidative phase, thiol groups on glucose-6-phosphate dehydrogenase become oxidized and must be reduced by glutathione
B)glutathione acts as an inhibitor of glucose-6-phosphate dehydrogenase
C)NADPH from the PPP is needed to keep glutathione in its reduced state
D)phosphopentose epimerase often produces free radicals that are quenched by glutathione
E)none of the above
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Page 15
Chapter 14: Citric Acid Cycle and Glyoxylate Cycle
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Q1) Which of the following molecules is correctly paired with the enzyme that can convert it to oxaloacetate to replenish the citric acid cycle when other intermediates are removed?
A)aspartate: aspartate deaminase
B)pyruvate: malic enzyme
C)phosphoenolpyruvate: PEP carboxylase
D)glutamate: glutamate transaminase
E)none of the above
Q2) Which of the following enzymes of the pyruvate dehydrogenase complex is responsible for the oxidation of the hydroxyethyl group from pyruvate decarboxylation to an acetyl group?
A)pyruvate dehydrogenase
B)dihydrolipoamide transacetylase
C)dihydrolipoamide dehydrogenase
D)pyruvate dehydrogenase kinase
E)pyruvate dehydrogenase phosphatase
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Chapter 15: Electron Transport, Oxidative Phosphorylation, and Oxygen Metabolism
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Q1) In the malate/aspartate shuttle, glutamate is converted to _________ in the mitochondria while aspartate is converted to ___________ in the cytosol.
A)oxaloacetate; malate
B)\(\alpha\)-ketoglutarate; oxaloacetate
C)oxaloacetate; glutamate
D)aspartate; \(\alpha\)-ketoglutarate
E)malate; oxaloacetate
Q2) What is the approximate P/O ratio if the source of electrons for the electron transport chain is FADH<sub>2</sub>?
A)1
B)1.5
C)2
D)2.5
E)3
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Chapter 16: Photosynthesis
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Q1) Which of the following carbohydrates is the most common molecule exported by photosynthetic cells for use in other parts of the plant?
A)amylose
B)amylopectin
C)glucose
D)sucrose
E)fructose
Q2) For every 12 molecules of 3-phosphoglycerate produced by rubisco, _____ are converted to hexoses while _____ are recycled to ribulose-1,5-bisphosphate.
A)2; 10
B)4; 8
C)6; 6
D)8; 4
E)10; 2
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18
Chapter 17: Lipid Metabolism I: Fatty Acids, Triacylglycerols, and Lipoproteins
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Q1) For the \(\beta\)-oxidation of a fatty acid with notation of 18:3c\(\Delta\)6,9,12, how many NADPH would be required and how many FADH<sub>2</sub> would be produced?
A)1 NADPH, 7 FADH<sub>2</sub>
B)1 NADPH, 8 FADH<sub>2</sub>
C)2 NADPH, 6 FADH<sub>2</sub>
D)2 NADPH, 7 FADH<sub>2</sub>
E)2 NADPH, 8 FADH<sub>2</sub>
Q2) Which of the following leads to the formation of atherosclerotic plaques?
A)non-specific interactions between LDL particles
B)oxidation of LDL particles resulting in cross linking with proteins
C)uptake of oxidized LDL particles by macrophages
D)excess uptake of LDL particles converting endothelial cells to foam cells
E)none of the above
Q3) If gadoleic acid (20:1c\(\Delta\)9)underwent complete mitochondrial oxidation to CO<sub>2</sub>, how many ATP could be produced assuming that all reduced electron carriers are re-oxidized by the mitochondrial electron transport chain?
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19
Chapter 18: Interorgan and Intracellular Coordination of Energy Metabolism in Vertebrates
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Q1) The transcription factor PGC-1\(\alpha\) is controlled by two forms of covalent modification. Which of the following correctly identifies a mechanism of control?
A)phosphorylation by AMPK inhibits PGC-1\(\alpha\)
B)dephosphorylation by AMPK activates PGC-1\(\alpha\)
C)acetylation by SIRT1 activates PGC-1\(\alpha\)
D)deacetylation by SIRT1 activates PGC-1\(\alpha\)
E)dephosphorylation by AMPK and deacetylation by SIRT1 activates PGC-1\(\alpha\)
Q2) Under starvation conditions, which of the following shows an increase in activity in the first few days, followed by a large decrease in activity after a week?
A)use of ketone bodies by the brain
B)lipolysis
C)glycolysis
D)muscle protein mobilization
E)none of the above
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Chapter 19: Lipid Metabolism Ii: Membrane Lipids, Steroids,
Isoprenoids, and Eicosanoids
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Q1) The synthesis of 1 molecule of cholesterol requires _____ molecules of isopentenyl pyrophosphate, with each molecule of isopentenyl pyrophosphate requiring _____ molecules of acetyl-CoA.
A)4; 2
B)5; 2
C)6; 2
D)5; 3
E)6; 3
Q2) Which of the following amino acids is critical for choline and phosphatidylcholine synthesis?
A)serine
B)\(\beta\)-alanine
C)homocysteine
D)methionine
E)homoserine
Q3) Show the reaction catalyzed by 3-hydroxy-3-methylglutrayl-CoA reductase.
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21
Chapter 20: Metabolism of Nitrogenous Compounds I:
Principles of Biosynthesis, Utilization, and Turnover
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Q1) Ubiquitin is added to _________ residues of the target protein by reaction with the terminal __________ group of ubiquitin.
A)lysine; carboxyl B)serine; carboxyl C)cysteine; carboxyl D)glutamate; amine
E)glutamine; amine
Q2) The reaction of ammonia with \(\alpha\)-ketoglutarate is catalyzed by _________ and requires _________ as a reactant.
A)glutamate synthetase; ATP
B)glutamate synthetase; NADH or NADPH
C)glutamate dehydrogenase; ATP
D)glutamate dehydrogenase; NADH or NADPH
E)none of the above
Q3) What would be the energy requirements of the urea cycle if both nitrogens of urea came from glutamine (assuming that any NADH made was re-oxidized via electron transport/oxidative phosphorylation)? Explain how this is possible.
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Page 22
Chapter 21: Metabolism of Nitogenous Compounds II: Amino
Acids, Porphyrins, and Neurotransmitters
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Q1) In the pathway for conversion of phenylalanine to fumarate and acetoacetate, there are two well-known enzyme defects that cause inheritable metabolic diseases. What are the names of these two diseases?
A)homocysteinuria and nonketotic hyperglycinemia
B)phenylketonuria and maple syrup urine disease
C)alkaptonuria and nonketotic hyperglycinemia
D)alkaptonuria and phenylketonuria
E)maple syrup urine disease and homocysteinuria
Q2) The route by which methionine is degraded provides for the synthesis of which amino acid?
A)serine
B)threonine
C)valine
D)isoleucine
E)cysteine
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Chapter 22: Nucleotide Metabolism
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Q1) The ten enzyme activities that convert PRPP to inosinic acid are part of a multienzyme complex known as the _________.
A)IMP synthetase complex
B)purine synthetase complex
C)purinosome
D)tetrahydrofolate synthase complex
E)none of the above
Q2) Which of the following shows the correct and complete flow of electrons for ribonucleotide reductase?
A)NADH\(\rarr\)FAD \(\rarr\)thioredoxin \(\rarr\) ribonucleotide reductase
B)NADPH \(\rarr\) glutathione \(\rarr\) glutaredoxin \(\rarr\) ribonucleotide reductase
C)NADPH \(\rarr\) thioredoxin \(\rarr\)cytochrome-b \(\rarr\) ribonucleotide reductase
D)FADH<sub>2</sub> \(\rarr\)glutathione \(\rarr\) glutaredoxin \(\rarr\)ribonucleotide reductase
E)none of the above
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Page 24
Chapter 23: Mechanisms of Signal Transduction
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Q1) The principle inhibitory neurotransmitter, __________, works by triggering an influx of ______ causing hyperpolarization of nerve cells.
A)\(\gamma\)-aminobutyric acid; K<sup>+</sup>
B)\(\gamma\)-aminobutyric acid; Cl<sup>-</sup>
C)serotonin; K<sup>+</sup>
D)serotonin; Cl<sup>-</sup>
E)none of the above
Q2) The enkephalins, along with \(\beta\)-endorphin, bind to the opioid receptor, so named because the opiate drugs such as __________ bind to it with high affinity
A)morphine
B)fluoxetine (Prozac)
C)phencyclidine
D)methyl phenidylacetate (Ritalin)
E)lysergic acid diethylamide (LSD)
Q3) Insulin activates glycogen synthase while glucagon inhibits glycogen synthase. Explain the intracellular mechanisms that are used to bring about this activity.
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Page 25
Chapter 24: Genes, Genomes and Chromosomes
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Q1) A typical size for a viral genome is ______ nucleotides per haploid genome while a typical size for a bacterial genome is ______ nucleotides per haploid genome.
A)2*10<sup>6</sup>; 4*10<sup>8</sup> B)8*10<sup>4</sup>; 5*10<sup>7</sup>
C)1*10<sup>3</sup>; 9*10<sup>4</sup> D)5*10<sup>4</sup>; 4*10<sup>6</sup> E)3*10<sup>4</sup>; 5*10<sup>9</sup>
Q2) For a restriction enzyme with a 6-base recognition site, what is the average number of base pairs between occurrences of the site?
A)1296 base pairs
B)4096 base pairs
C)46656 base pairs
D)16777216 base pairs
E)none of the above
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26
Chapter 25: DNA Replication
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Q1) Which of the following explains the result of type I topoisomerase activity on underwound DNA, considering that no energy (ATP)is used in the reaction?
A)the linking number is decreased by 1
B)the linking number is increased by 1
C)the linking number remains the same but the twist decreases by 1
D)the linking number remains the same but the twist increases by 1
E)none of the above
Q2) Which of the following is an 11-base consensus sequence that makes up the autonomously replicating sequence present in yeast DNA that is a requirement for the start of replication?
A)5'-GTGCGTGCGTG-3'
B)5'-CCTCCTGGTGG-3'
C)5'-AAGCGCGCGCC-3'
D)5'-GGTGGACCTCC-3'
E)5'-TTTTATATTTT-3'
Q3) For the following sequence, indicate the RNA primer that would be needed to start synthesis of the Okazaki fragment.
5'-A-A-C-T-A-G-A-C-C-A-G-A-3'
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Chapter 26: DNA Restructuring: Repair, Recombination, Rearrangement, Amplification
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Q1) Which of the following transposable elements is correctly defined?
A)insertion sequence: protein-encoding gene flanked by two insertion sequences
B)composite transposon: protein-encoding gene + transposase and resolvase genes flanked by two insertion sequences
C)class II transposon: protein-encoding gene + resolvase gene flanked by two insertion sequences
D)class III transposon: results from infection of a bacteriophage such as Mu
E)none of the above
Q2) In order for lysogeny to occur, the enzyme ______________ must insert the phage DNA into a specific site in the bacterial chromosome.
A)ligase
B)lysogenase
C)helicase
D)integrase
E)none of the above
Q3) Show the common base pair seen between 8-oxoguanine and adenine.
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Chapter 27: Information Readout: Transcription and
Post-Transcriptional Processing
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Q1) Draw a transcription bubble, clearly labeling the proteins and nucleic acids involved in the process.
Q2) What is the mechanism by which enhancers, despite the fact that they are often several kilobase pairs away from the promoter, activate transcription?
A)DNA unwinding
B)DNA looping
C)chromatin remodeling
D)DNA hairpin formation
E)none of the above
Q3) In vivo, which of the following transcription initiation factors is required for binding to a TATA box?
A)TFIID
B)TFIIE
C)TFIIF
D)TFIIH
E)TAF
Q4) Give the mRNA sequence that would result from the following sense strand:
Page 29
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Chapter 28: Information Decoding: Translation and Post-Translational
Protein Processing
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Q1) If a mutation in the template strand of DNA occurred in the following manner, which of the possible amino acid changes would occur? 5'-CAT-3' \(\rarr\) 5'-TAT-3'
A)methionine \(\rarr\) isoleucine
B)histidine \(\rarr\) tyrosine
C)methionine \(\rarr\) tyrosine
D)histidine\(\rarr\) isoleucine
E)none of the above
Q2) By saying that the genetic code is degenerate, what does this imply?
A)the code is different for bacteria than for eukaryotes
B)some codons can code for non-standard amino acids
C)most amino acids have more than one codon
D)there is more than one start codon
E)there is more than one stop codon
Q3) How many ATP equivalents are required to make a protein of 150 amino acids?
A)150
B)300
C)450
D)600
E)none of the above
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Chapter 29: Regulation of Gene Expression
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25 Verified Questions
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Sample Questions
Q1) Give the sequence and draw the first two residues of a morpholino oligo that would serve as an antisense RNA for the following mRNA sequence (you may use the letter A, C, G and U to denote the bases): 5'-CAUGUCC-3'
Q2) Show how glutamine interacts with an A-T base pair as seen in the cI and Cro repressors.
Q3) At the transcriptional level, how does tryptophan control the production of genes within the trp operon?
A)the trp repressor contains a high percentage of Trp residues and is thus only produced when Trp levels are high
B)without sufficient Trp, the production of the trp repressor is truncated, thus producing a protein that cannot bind to the operon, ultimately resulting in structural gene expression
C)high levels of Trp cause the repressor to be proteolytically digested
D)the trp repressor binds to the operon only when bound to Trp
E)none of the above
Q4) Design an antisense RNA that prevents the start of translation for any mRNA in an E. coli cell.
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