Course Introduction
Advanced Biochemistry
Pre-Test Questions
Advanced Biochemistry delves into the molecular mechanisms underlying biological processes, emphasizing the structure and function of proteins, nucleic acids, lipids, and carbohydrates. The course explores enzyme kinetics and regulation, metabolic pathways and their integration, signal transduction, and advanced topics such as protein folding, molecular recognition, and cellular energetics. Through analysis of current research and experimental techniques, students develop an in-depth understanding of the central dogma of molecular biology and its relevance to health, disease, and biotechnology.
Recommended Textbook
Biochemistry 4th Edition by Christopher K. Mathews
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29 Chapters
705 Verified Questions
705 Flashcards
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Page 2
Chapter 1: The Scope of Biochemistry
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Sample Questions
Q1) Of the following biomolecules,which is found only in a monomeric form as opposed to a polymeric form?
A)amino acids
B)carbohydrates
C)lipids
D)nucleotides
E)none of the above
Answer: C
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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Page 3
Chapter 2: The Matrix of Life: Weak Interactions in an Aqueous Environment
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Sample Questions
Q1) What happens to DNA when placed into an aqueous solution at physiological pH?
A)individual DNA molecules attract each other due to presence of positive and negative charges
B)individual DNA molecules repel each other due to presence of negative charges
C)individual DNA molecules repel each other due to presence of positive charges
D)DNA molecules bind to negatively charged proteins
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 11ea8a11_436e_4b29_8b44_234f570e4c48_TB4872_00
Page 4
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Chapter 3: The Energetics of Life
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Sample Questions
Q1) The highly exergonic nature of ATP hydrolysis is explained by which of the following?
A)the resulting orthophosphate is stabilized by resonance
B)electrostatic repulsion occurs between phosphate groups and the adenine base of ATP
C)the resulting product undergoes tautomerization to the keto form of ADP
D)the bond that is hydrolyzed is considered an ester of phosphoric acid,making it highly unstable
E)all of the above
Answer: A
Q2) Which of the following correctly relates the relative entropies?
A)sodium chloride crystals > sodium chloride dissolved in water
B)carbon dioxide in air > dry ice
C)carbon in a molecule of glucose > carbon in carbon dioxide gas
D)a solution of ATP > the same solution with ATP converted to ADP and P<sub>i</sub>
E)ice made from pure water > ice made from salt water
Answer: B
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Chapter 4: Nucleic Acids
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Sample Questions
Q1) Which of the following is correctly paired with the type of tautomerization(s)that occurs?
A)adenine: keto-enol
B)cytosine: amino-imino and keto-enol
C)guanine: amino-imino
D)thymine: keto-enol
E)none of the above
Q2) In a circular DNA molecule of 126 bp with 10.5 bp/turn,which of the following represents an unstrained circle? (L = linking number,T = twist and W = writhe)
A)L = 12,T = 12,W = 0
B)L = 11,T = 11,W = 0
C)L = 11,T = 12,W = -1
D)L = 12,T = 11,W = +1
E)L = 11,T = 10,W = 0
Q3) Draw the structure of cytosine and thymine,then show the most common tautomer of each.
Q4) Draw the two forms of a phosphodiester bond that can occur under physiological pH.If the pK<sub>a</sub> for this conversion is 6.2,what form predominates in the lysosome where the pH is about 5?
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Chapter 5: Introduction to Proteins: the Primary Level of
Protein Structure
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Q1) 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
Q2) Which of the following amino acids is derived from another amino acid by the addition of an amine group?
A)lysine
B)asparagine
C)arginine
D)histidine
E)none of the above
Q3) Draw each of the structures of aspartic acid that predominate at pH 1,3,7,and 11.
Q4) What is the pI for the following peptide: Ala-Glu-Val-Asp-Lys-Leu
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Chapter 6: The Three-Dimensional Structure of Proteins
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Q1) Which of the following statements regarding structural proteins is true?
A)silk fibroin is made from a repeat of three amino acids where each third amino acid is Gly
B)\(\alpha\)-keratin is composed of peptides that contain mostly \(\alpha\)-helical structure with the exception of short sequences where the peptide folds back on itself
C)collagen has its own helical structure where three individual peptides are wound around each other in a left-handed helix
D)generally speaking,structural proteins are soluble in water
E)none of the above
Q2) If a peptide was composed entirely of \(\alpha\)-helical structure and found to contain an integer number of complete turns,which of the following would be a possible number of amino acid residues in the peptide?
A)12
B)20
C)32
D)36
E)60
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Chapter 7: Protein Function and Evolution
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Sample Questions
Q1) Which of the following occurs when hemoglobin switches from the T (deoxy)state to the R (oxy)state?
A)the heme group goes from a slightly puckered conformation to a flat conformation
B)the ferrous ion is pulled into the plane of the heme group
C)the F8 (proximal)histidine rotates about 8S1U1P1\(\circ\)S1S1P0 to better align with the ferrous ion
D)movement of the F8 histidine causes a shift in the F helix,thus weakening interactions with other subunits
E)all of the above
Q2) Changes in hemoglobin's oxygen affinity are primarily the result of changes in the _________ structure of the protein.
A)primary
B)secondary
C)tertiary
D)quaternary
E)all of the above
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9
Chapter 8: Contractile Proteins and Molecular Motors
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Q1) Which of the following correctly describes the organization that gives rise to muscle?
A)myofibril \(\to\)sarcomere \(\to\)myofiber \(\to\) muscle
B)sarcomere \(\to\) myofiber \(\to\) myofibril \(\to\) muscle
C)myofibril \(\to\) myofiber \(\to\) sarcomere \(\to\) muscle
D)sarcomere \(\to\) myofibril \(\to\) myofiber \(\to\) muscle
E)myofiber \(\to\) myofibril \(\to\) sarcomere \(\to\) muscle
Q2) Which protein of the thin filament is responsible for calcium binding?
A)tropomyosin
B)troponin C
C)troponin T
D)calmodulin
E)actin
Q3) Which of the following only occurs when ATP (not ADP)is bound to the myosin head?
A)actin is released from its binding site on myosin
B)weak binding of myosin head to actin
C)strong binding of myosin head to actin
D)power stroke of muscle contraction
E)none of the above
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Chapter 9: Carbohydrates: Sugars,saccharides,glycans
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Q1) 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.
Q2) The reaction of a cyclic monosaccharide with an alcohol converts a(n)_________ into a(n)________.
A)acetal;hemiacetal
B)hemiacetal;acetal
C)acetal;ether
D)hemiacetal;ether
E)alcohol;ether
Q3) Which of the following explains the importance of sucrose as a disaccharide?
A)the glycosidic bond is much more stable than a typical glycosidic bond
B)the presence of two glucose residues provides a readily available glucose source
C)\(\beta\)-glycosidic bonds are much more stable than \(\alpha\)-glycosidic bonds
D)since both anomeric carbons are involved in the glycosidic bond,oxidation is limited E)none of the above
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11
Chapter 10: Lipids,membranes and Cellular Transport
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Sample Questions
Q1) Which of the following is used to drive glucose uptake by intestinal epithelial cells?
A)potassium gradient across the blood vessel/epithelial cell membrane
B)potassium gradient across the intestinal lumen/epithelial cell membrane
C)sodium gradient across the blood vessel/epithelial cell membrane
D)sodium gradient across the intestinal lumen/epithelial cell membrane
E)none of the above
Q2) Which of the following does not specifically cause a membrane to be more rigid or fluid,but rather causes the T<sub>m</sub> to occur over a greater range?
A)increasing the content of unsaturated fatty acids
B)raising the temperature
C)increasing the cholesterol content
D)decreasing the phosphatidylcholine content while increasing the phosphatidylethanolamine content
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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12
Chapter 11: Enzymes: Biological Catalysts
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Sample Questions
Q1) An enzymatic reaction has a V<sub>max</sub> of 100 \(\mu\)M/min.At a substrate concentration of 5 \(\mu\)M,the velocity is 25 \(\mu\)M/min.What is the K<sub>M</sub> for the reaction?
A)5 \(\mu\)M
B)10 \(\mu\)M
C)15 \(\mu\)M
D)20 \(\mu\)M
E)none of the above
Q2) Which of the following cofactors is used during the activation and transfer of carbon dioxide?
A)nicotinamide adenine dinucleotide (NAD)
B)thiamine pyrophosphate
C)biotin
D)coenzyme A
E)tetrahydrofolate
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13
Chapter 12: Chemical Logic of Metabolism
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Q1) Which of the following statements regarding the general concepts of metabolism is true?
A)once glucose is converted to pyruvate,there is no way to convert pyruvate back to glucose
B)when triacylglycerols are used as fuel,only the fatty acids can be metabolized,the glycerol is a waste product
C)amino acids serve as substrates for many pathways including glycolysis and the citric acid cycle
D)the citric acid cycle is generally considered an anabolic pathway while gluconeogenesis is generally considered a catabolic pathway
E)none of the above
Q2) 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
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14
Chapter
13: Carbohydrate Metabolism: Glycolysis, gluconeogenesis, glycogen Metabolism, and the Pentose
Phosphate Pathway
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Q1) During aerobic glycolysis,pyruvate is most likely oxidized to ________ while in anaerobic glycolysis,pyruvate is converted to _________.
A)acetaldehyde;ethanol
B)acetyl CoA;glyceraldehyde
C)acetyl CoA;lactate
D)acetaldehyde;lactate
E)none of the above
Q2) With respect to carbons 1 and 2 of the intermediate in the conversion of glucose-6-phosphate to fructose-6-phosphate,which of the following would best describe this intermediate?
A)vicinal diol
B)enediol
C)aldehyde
D)ketone
E)enol
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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) Arsenic poisoning by either arsenite or organic arsenical agents work by binding to dithiol compounds such as _________ meaning that in addition to inactivation of pyruvate dehydrogenase,the citric acid cycle enzyme _________ would be inactivated.
A)cysteine;aconitase
B)coenzyme A;\(\alpha\)-ketoglutarate dehydrogenase
C)coenzyme A;citrate synthase
D)thiamine pyrophosphate;isocitrate dehydrogenase
E)lipoic acid;\(\alpha\)-ketoglutarate dehydrogenase
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Page 16
Chapter 15: Electron Transport, oxidative Phosphorylation, and Oxygen Metabolism
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Q1) Rotation of the ____ subunit causes the _____ subunit to change from tight conformation where ATP is produced to open conformation where ATP is released.
A)\(\gamma\);\(\alpha\)
B)\(\gamma\);\(\beta\)\(\gamma\)
C)\(\delta\);\(\alpha\)
D)\(\delta\);\(\beta\)
E)\(\varepsilon\);\(\beta\)
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) In the mechanism of Rubisco,what role does the Mg<sup>2+</sup> play?
A)neutralizes negative charges of active site Asp and Glu,enabling ionization of CO<sub>2</sub>
B)activates water molecule that hydrates the carboxy-\(\beta\)-keto intermediate C)complexes with the phosphate on C-1 to hold ribulose-1,5-bisphosphate in the active site
D)repels the product,3-phosphoglycerate,allowing it to leave the active site more rapidly E)none of the above
Q2) When photorespiration occurs and phosphoglycolate must be salvaged,which of the following occurs during the salvage reactions?
A)NADP<sup>+</sup> is used in the oxidation of glycolate to glyoxylate
B)NADPH is used in the reduction of hydroxypyruvate to glycerate
C)carbon is lost in the form of CO<sub>2</sub>
D)ATP is made during the conversion of phosphoglycolate to glycolate
E)none of the above
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Chapter 17: Lipid Metabolism I: Fatty
Acids,triacylglycerols,and Lipoproteins
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Q1) Low levels of oxaloacetate with high levels of \(\beta\)-oxidation cause the production of what metabolites,particularly within the liver?
A)acetate and ethanol
B)acetoacetate and \(\beta\)-hydroxybutyrate
C)3-hydroxy-3-methyglutaryl-CoA and propionyl-CoA
D)D-methylmalonyl-CoA and L-methylmalonyl-CoA
E)all of the above
Q2) Individuals with diets high in coconut oil consume large amounts of lauric (12:0).What are the \(\beta\)-oxidation products of lauric acid?
A)6 acetyl-CoA,6 NADH,6 FADH<sub>2</sub>,1 ATP used for activation
B)6 acetyl-CoA,5 NADH,5 FADH<sub>2</sub>,1 ATP used for activation
C)6 acetyl-CoA,6 NADH,6 FADH<sub>2</sub>,2 ATP used for activation
D)6 acetyl-CoA,5 NADH,5 FADH<sub>2</sub>,2 ATP used for activation
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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Page 19
Chapter 18: Interorgan and Intracellular Coordination of Energy Metabolism in Vertebrates
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Q1) Which of the following pathways is activated in response to phosphorylation of key enzymes by AMPK?
A)glycogenolysis in the heart
B)glycolysis in the heart
C)gluconeogenesis in the liver
D)fatty acid synthesis in the liver
E)triacylglycerol synthesis in the liver
Q2) For each of the following liver enzymes,indicate what happens to the enzyme (i.e. ,phosphorylated/dephosphorylated )when the cell is under the influence of glucagon.Indicate whether the enzyme is activated or inhibited and how that contributes to the overall role of glucagon.
PFK-2:
Pyruvate kinase:
Fruc-1,6-BPase:
Glycogen phosphorylase:
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Chapter 19: Lipid Metabolism Ii: Membrane Lipids, steroids, isoprenoids,
and Eicosanoids
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Q1) Which of the following is accomplished in one enzyme catalyzed reaction?
A)progesterone to androstenedione
B)17-hydroxyprogesterone to cortisol
C)progesterone to aldosterone
D)androstenedione to testosterone
E)androstenedione to estradiol
Q2) The enzyme PGH synthase contains two different functionalities,a __________ that uses two molecules of oxygen as substrates and __________ which performs a 2 electron reduction.
A)cyclooxygenase;peroxidase
B)cyclooxygenase;reductase
C)dioxygenase;peroxidase
D)dioxygenase;reductase
E)lipoxygenase;peroxidase
Q3) Show the reaction catalyzed by 3-hydroxy-3-methylglutrayl-CoA reductase.
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Chapter 20: Metabolism of Nitrogenous Compounds I: Principles
of Biosynthesis, utilization, and Turnover
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Q1) Which of the following correctly explains the covalent modification used to control glutamine synthetase?
A)uridylylation activates,deuridylylation inhibits
B)uridylylation inhibits,deuridylylation activates
C)adenylation activates,deadenylation inhibits
D)adenylation inhibits,deadenylation activates
E)phosphorylation inhibits,dephosphorylation activates
Q2) Which of the following is an essential amino acid for humans?
A)alanine
B)serine
C)tyrosine
D)cysteine
E)histidine
Q3) What is a PEST sequence in a protein?
A)a sequence where phosphorylation occurs at every serine and tyrosine
B)a sequence that confers resistance to cathepsin-mediated proteolysis
C)a sequence of phenylalanine-glutamate-serine-threonine that is found in many proteins with half lives less than 2 hours
D)a sequence that causes ubiquitination of the protein followed by degradation
E)none of the above
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Chapter 21: Metabolism of Nitogenous Compounds Ii:
Amino Acids, porphyrins, and Neurotransmitters
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Q1) 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
Q2) Threonine is converted into acetyl-CoA and pyruvate while proline is converted into \(\alpha\)-ketoglutarate.Classify each of these amino acids.
A)threonine is ketogenic,proline is ketogenic
B)threonine is ketogenic and glucogenic,proline is ketogenic
C)threonine is ketogenic,proline is glucogenic
D)threonine is ketogenic and glucogenic,proline is glucogenic
E)none of the above
Q3) Which of the following molecules uses chorismate as a precursor?
A)p-aminobenzoic acid
B)coenzyme Q
C)phenylalanine
D)tryptophan
E)all of the above
Page 23
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Chapter 22: Nucleotide Metabolism
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Q1) Which of the following best explains the enzyme(s)involved in ribonucleotide reduction?
A)there is 1 enzyme for each of the 4 different nucleotides
B)1 enzyme for pyrimidine nucleotides and 1 for purine nucleotides
C)1 enzyme for pyrimidine nucleotides,1 for ADP and 1 for GDP
D)1 enzyme for purine nucleotides,1 for CDP and 1 for UDP
E)1 enzyme for all 4 nucleotides
Q2) Which of the following correctly describes the activity or regulation of E coli ribonucleotide reductase?
A)the overall activity of the enzyme is controlled by ATP and dATP
B)the specificity of the enzyme is controlled by all four dNTPs
C)a tyrosine free radical participates in the reaction
D)the reduction is not a result of simple hydride transfer
E)all of the above
Q3) Which of the following coenzymes contains an adenylate group?
A)cobalamin
B)tetrahydrofolate
C)thiamine pyrophosphate
D)pyridoxal phosphate
E)coenzyme A
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Chapter 23: Mechanisms of Signal Transduction
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Q1) The complex of zinc and cysteine residues seen in the structure of steroid hormone receptors is referred to as a(an)______________ structural motif.
A)zinc loop
B)zinc helix
C)antiparallel zinc sheet
D)zinc finger
E)zinc turn
Q2) When a nerve cell terminates at a muscle cell,the action potential causes opening of _____ channels that results in muscle contraction.
A)Na<sup>+</sup>
B)K<sup>+</sup>
C)Ca<sup>2+</sup>
D)Cl<sup>-</sup>
E)none of the above
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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Chapter 24: Genes,genomes and Chromosomes
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Q1) What technique is used to amplify portions of DNA,usually about 500 base pairs in size?
A)DNA sequencing
B)polymerase chain reaction
C)cloning
D)restriction digestion
E)electrophoresis
Q2) The combination of histone proteins with DNA gives rise to what structure?
A)cohesins
B)telomeres
C)centromeres
D)nuclear scaffold
E)nucleosomes
Q3) A linear DNA molecule was treated with PstI and gave two fragments with sizes of 2150 and 3420 base pairs.The same DNA was treated with BamHI and gave three fragments of 1250,1930 and 2390 base pairs.Finally,the DNA was treated with both enzymes at the same time and gave fragments of 900,1250,1490 and 1930 base pairs.Provide a map of the DNA molecule clearly indicating the restriction sites.
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Chapter 25: Dna Replication
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Q1) 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'
Q2) What is an Okazaki fragment?
A)a small section of DNA bound to the leading strand
B)a small section of DNA bound to the lagging strand
C)a small section of RNA and DNA bound to the leading strand
D)a small section of RNA and DNA bound to the lagging strand
E)none of the above
Q3) In DNA synthesis,the _____________ strand is synthesized in a __________ fashion.
A)template;discontinuous
B)template;continuous
C)leading;discontinuous
D)lagging;discontinuous
E)none of the above
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Chapter 26: Dna Restructuring:
Repair,recombination,rearrangement,amplification
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Q1) Which of the following coenzymes forms the photochemical reaction center of DNA photolyase?
A)NADH
B)thiamine pyrophosphate
C)biotin
D)FADH<sup>-</sup>
E)5-methyltetrahydrofolate
Q2) Methylation of guanine to produce O<sup>6</sup>-methylguanine (mG)results in what change to DNA?
A)mG frequently pairs with thymine resulting in a GC \(\to\) AT mutation
B)mG loses its methoxy group resulting in hydrogen bonding with adenine and a bulge in the double helix
C)mG is prone to deamination and eventually,depurination
D)repair of mG adducts uses a radical mechanism that has the potential to further damage adjacent bases,particularly thymine
E)none of the above
Q3) Show the common base pair seen between 8-oxoguanine and adenine.
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Page 28
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) Rapid transcription of ribosomal RNA is thought to occur as a result of what unique feature in the DNA that encodes these genes?
A)high A-T content
B)highly repetitive sequence
C)multiple promoter sites that allow high affinity with RNA polymerase
D)presence of hairpin structures in the DNA
E)absence of nucleosomes
Q3) Which subunit of E.coli RNA polymerase is responsible for DNA binding?
A)\(\alpha\)
B)\(\beta\)
C)\(\beta\)'
D) \(\sigma\)
E)\(\omega\)
Q4) The figure below shows a newly transcribed mRNA still associated with the template DNA.Draw the stem-loop structure that often forms during termination.
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Chapter 28: Information Decoding: Translation and Post-Translational
Protein Processing
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27 Verified Questions
27 Flashcards
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Sample Questions
Q1) Which of the following is an intermediate in the reaction catalyzed by aminoacyl-tRNA synthetase?
A)pyrophosphorylated 3' hydroxyl on the tRNA
B)aminoacyl phosphate
C)aminoacyl pyrophosphate
D)aminoacyl adenylate
E)none of the above
Q2) In prokaryotes,mRNA is ____________.In eukaryotes,mRNA is _____________.
A)equally monocistronic and polycistronic;mostly monocistronic
B)equally monocistronic and polycistronic;mostly polycistronic
C)mostly monocistronic;equally monocistronic and polycistronic
D)mostly polycistronic;equally monocistronic and polycistronic
E)mostly polycistronic;mostly monocistronic
Q3) What enzyme attaches the correct amino acid to its tRNA?
A)aminoacyl-tRNA synthase
B)aminoacyl-tRNA synthetase
C)aminoacyl-tRNA transferase
D)aminoacyl-tRNA ligase
E)none of the above
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Chapter 29: Regulation of Gene Expression
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24 Verified Questions
24 Flashcards
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Sample Questions
Q1) DNA methylation in eukaryotes plays a role in ____________.
A)methyl-directed mismatch repair
B)protection of restriction sites
C)chromatin remodeling
D)cancerous cell growth
E)gene silencing
Q2) What elements are contained within the promoter of the lactose operon?
A)operator and CRP site
B)operator and repressor
C)CRP site and repressor
D)operator,CRP site and repressor
E)none of the above
Q3) DNA damage that requires RecA to bind to a DNA gap activates proteolysis of _____,which then activates the transcription of genes within the SOS regulon.
A)cI
B)Cro
C)LexA
D)uvrA
E)uvrB
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