Biochemistry for Pre-Medical Students
Exam Preparation Guide
Course Introduction
This course provides an in-depth exploration of the fundamental principles of biochemistry with a focus on their relevance to human health and medicine. Topics include the structure and function of biomolecules, enzyme kinetics, metabolism, molecular genetics, and the biochemical basis of disease. Students will develop a foundational understanding of biochemical processes at the cellular and molecular levels, emphasizing their implications for physiological functions and clinical applications. The course is designed to equip pre-medical students with the essential biochemical knowledge needed for advanced study in medical and health-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) Halophiles and thermophiles are
A)early versions of eukaryotic cells.
B)highly evolved organisms that thrive in their specific environments.
C)relatively inefficient and unevolved organisms.
D)more complex than eukaryotes.
E)extremely slow growing.
Answer: B
Q2) An endergonic reaction with a ______ \(\Delta\)H and a ______ \(\Delta\)S can be changed into an exergonic reaction by decreasing the temperature.
A)positive, positive
B)positive, negative
C)negative, positive
D)negative, negative
Answer: D
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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3
Chapter 2: Water
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Sample Questions
Q1) Which of the following statements about water is not true?
A)It has a high dielectric constant.
B)It dissolves salts and polar substances.
C)It can form two hydrogen bonds per water molecule.
D)It packs in a hexagonal (honeycomb)shaped lattice when the temperature falls below 0°C.
E)In the liquid state it is only 15% less hydrogen bonded than in the solid state at 0°C.
Answer: C
Q2) A solution is made by mixing 1.0 mL of 1.0 M acetic acid (pK = 4.76, K<sub>a</sub> = 1.74 x 10<sup>-5</sup> )with one 999 mL of pure water.Calculate the pH of the resulting solution (assume the total volume is 1.0 L).
A)10.1
E)1.32
Answer: D
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Page 4
Chapter 3: Nucleotides, Nucleic Acids, and Genetic Information
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Q1) Alterations in genetic information cannot be caused by A)mistakes made during replication
B)faulty recombination.
C)transposition of genes.
D)mistakes made during translation.
E)all of the above
Answer: D
Q2) DNA polymerase from Thermus aquaticus is used in PCR because A)it is a soluble protein.
B)the genes from Thermus aquaticus are readily distinguished from those of 'normal' organisms.
C)the enzyme is readily deactivated by heat, effectively halting the reaction.
D)it is stable at high temperatures.
E)it is not infectious.
Answer: D
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Chapter 4: Amino Acids
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Q1) Which of the following amino acids does not have an ionizable side chain?
A)Asp
B)Cys
C)Lys
D)His
E)Asn
Q2) Ribosomes use L amino acids to synthesize proteins.These amino acids are called "L" because
A)they are chiral.
B)they turn polarized light to the left.
C)they have a configuration of groups around the C<sub>\(\alpha\)</sub> that can be related to the configuration of groups around the asymmetric carbon in L-glyceraldehyde.
D)they are all (S)-amino acids.
E)they are all (R)-amino acids.
Q3) 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.
Q4) Glutamic acid is an amino acid (pK<sub>a</sub>s are 2.1, 4.1 and 9.5).Calculate the isoelectric point of glutamic acid.
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Chapter 5: Proteins: Primary Structure
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Q1) In ______ chromatography, a protein mixture must be applied to the column at a low pH so that the proteins will have a net positive charge and bind to the column.
A)electrophoresis
B)hydrophobic interaction
C)enzyme-linked immunosorbent assay
D)three-dimensional shape
E)N-terminal amino acid
F)negative charge
G)nucleases
H)chromophore
I)foaming
J)high level expression
K)2-mercaptoethanol
L)positive charge
M)cation exchange
N)pI
O)chymotrypsin
P)C-terminal amino acid
Q)Sodium dodecyl sulfate
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Chapter 6: Proteins: Three-Dimensional Structure
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Sample Questions
Q1) In the absence of ascorbic acid, prolyl oxidase is unable to oxidize proline residues in collagen to hydroxyproline, resulting in:
A)lathyrism
B)prion diseases
C)amyloid formation
D)scurvy
E)allysine
Q2) Which of the following occurs first when folding a disordered polypeptide chain into a stable protein formation?
A)formation of a low energy state
B)association of ordered subunits
C)aggregation of hydrophobic regions in the protein
D)tertiary structure refinement
E)formation of a low entropy state
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8
Chapter 7: Protein Function Part I: Myoglobin and Hemoglobin
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Q1) Hemoglobin S, the variant responsible for the misshapen red blood cells characteristic of the disease sickle-cell anemia, is potentially advantageous to heterozygotes because it confers some level of resistance to the disease _________.
A)rickets
B)AIDS
C)cyanosis
D)polycythemia
E)malaria
Q2) BPG stands for A)biphenylglycine.
B)boronylphenylglutamate.
C)bisphosphoglycerate.
D)bisphenylglycerol.
E)betapropylglutamine.
Q3) What is the primary physiological function of myoglobin in most mammals?
Q4) Myoglobin is an oxygen binding protein in muscle.Describe in one sentence the overall structure of myoglobin.
Q5) It appears that the heme group in myoglobin binds the O<sub>2</sub>.What is the function of the polypeptide?
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Chapter 8: Carbohydrates
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Q1) The disaccharide commonly found in dairy products is ______.
A)eight
B)deoxy
C)peptidoglycan
D)axial
E)anomers
F)two
G)lactose
H)glyceraldehyde
I)amylopectin
J)epimers
K)sixteen
L)glycogen
M)equatorial
N)chitin
O)hyaluronic acid
P)amylose
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Page 10
Chapter 9: Lipids and Biological Membranes
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Q1) I-cell disease results in psychomotor retardation, skeletal deformities and death.Which of the following is true regarding this disease?
A)The disease results in inclusion of glycosaminoglycans and glycolipids due the absence of an essential carbohydrate marker that directs the lysosomal hydrolases to the lysosome.
B)The disease results in inclusion of glycolipids due mutations in the lysosomal hydrolases that render them inactive.
C)The disease results in increased expression of SNARE proteins that result in vesicle fusion and exchange of glycosaminoglycans.
D)The disease results from the lack of KDEL sequences which would normally signal their return to the ER following Golgi processing.
E)All of the above are true.
Q2) Which of the following lipid types is the least polar?
A)triacylglycerols
B)glycerophospholipids
C)sphingolipids
D)gangliosides
E)glycolipids
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Chapter 10: Membrane Transport
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Q1) An example of nonmediated transport is ______.
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) The rapid transport of K<sup>+</sup> ions by the KcsA ion channel moves up to ____ ions per ______.
A)10<sup>6</sup>; minute
B)10<sup>1</sup>; second
C)10<sup>23</sup>; minute
D)10<sup>8</sup>; second
E)10<sup>8</sup>; hour
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Page 12
Chapter 11: Enzyme Catalysis
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Sample Questions
Q1) The imidazole side chain of histidine can function as either a general acid catalyst or a general base catalyst because
I.the imidazole group has a pK<sub>a</sub> in the physiological pH range.
II.in the physiological pH range, the nitrogen in the ring can be easily protonated/deprotonated.
III.one guanidino group is protonated, and the other is deprotonated at physiological pH.
IV.the imidazole group is a strong reducing agent at physiological pH.
A)I, II
B)I
C)II, IV
D)II, III
E)IV
Q2) Proximity effects
A)result from active site specificity.
B)result from substrate channeling.
C)result in increased effective concentration of substrate.
D)lower the energy of activation.
E)All of the above of the above are correct.
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Chapter 12: Enzyme Kinetics, Inhibition and Control
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Q1) The Michaelis constant K<sub>M</sub> is defined as I.(k<sub>-1 </sub>+ k<sub>2</sub>)/k<sub>1</sub>
II.½ V<sub>max</sub>
III.[S] = [ES]
IV.[ES]/2
A)I
B)I, II
C)II
D)I, IV
E)II, IV
Q2) The catalytic efficiency of an enzyme can never exceed A)k<sub>2</sub>.
B)k<sub>1</sub>.
C)k<sub>-1</sub>.
D)k<sub>-1 </sub>+ k<sub>2</sub>.
E)(k<sub>-1 </sub>+ k<sub>2</sub>)/k<sub>1</sub>.
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14
Chapter 13: Biochemical Signaling
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Q1) The ____ signaling pathway undergoes autophosphorylation resulting in kinase activation.
A)receptors
B)phosphoinositide
C)rhodopsin
D)calmodulin
E)insulin
F)hypothalamus
G)cortisol
H)adrenal cortex
I)cyclic AMP
J)RasGAP
K)islets of Langerhans
L)adenylate cyclase (AC)
M)receptor tyrosine kinase (RTK)
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Page 15
Chapter 14: Introduction to Metabolism
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Sample Questions
Q1) Consider the following metabolic reaction: 3-Phosphoglycerate \(\rarr\) 2-Phosphoglycerate \(\Delta\)G°' = +4.40 kJ/mol
What is the \(\Delta\)G for this reaction when the concentration of 2-phosphoglycerate is 0.290 mM and the concentration of 3-phosphoglycerate is 2.90 mM at 37°C?
A)+10.3 kJ/mol
B)-1.53 kJ/mol
C)-1.30 kJ/mol
D)-5.93 kJ/mol
E)-4.40 kJ/mol
Q2) In the catabolic pathway major nutrients are _________ broken down resulting in the synthesis of __________ .
A)exergonically; ADP
B)endergonically; ADP
C)exergonically; ATP
D)endergonically; NADP<sup>+</sup>
E)endergonically; ATP
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Chapter 15: Glycogen Metabolism and Gluconeogenesis
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Q1) What molecules correspond to correspond to X and Y in the following gluconeogenic reaction? Fructose-1,6-bisphosphotase + X \(\rarr\) Fructose-6-phosphate + Y
A)X = NADH + H<sup>+</sup> , Y = NAD<sup>+</sup>
B)X = ATP ,Y = ADP + P<sub>i</sub>
C)X = NAD<sup>+</sup> , Y = NADH + H<sup>+</sup>
D)X = GTP ,Y = GTP + Pi
E)X = H<sub>2</sub>O , Y = Pi
Q2) Individuals with McArdle's disease lack the ____ in the ____,
A)debranching enzyme; liver
B)phosphoglucomutase; liver
C)glycogen phosphorylase; muscle
D)phosphoglucomutase; muscle
E)glycogen phosphorylase; liver
Q3) 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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Chapter 16: Glucose Catabolism
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Q1) The reaction catalyzed by the enzyme aldolase has a \(\Delta\)G' +23 kJ/mol.In muscle cells, the reaction proceeds in this same, forward direction.How can this occur?
A)This \(\Delta\)G' means it is thermodynamically favored.
B)The enzyme changes the G of the reaction in cells to something favorable.
C)The concentration of reactant(s)must be significantly greater than product(s)in cells.
D)The concentration of product(s)must be significantly greater than reactant(s)in cells.
E)none of the above
Q2) 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.
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18
Chapter 17: Citric Acid Cycle
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Sample Questions
Q1) ______ catalyzes a substrate-level phosphorylation reaction within the citric acid cycle.
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 of the following organisms does not utilize the glyxolate cycle?
A)trees
B)bacteria
C)fungi
D)mammals
E)All of the above utilize the glyxolate cycle when necessary.
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Page 19
Chapter 18: Electron Transport and Oxidative
Phosphorylation
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Q1) An animal with the UCP-1 protein would I.generate excess heat.
II.have lower energy levels.
III.generate ATP efficiently via oxidative phosphorylation.
A)I
B)I, II
C)I, II, III
D)I, III
E)II, III
Q2) One method used by newborn mammals to generate heat is referred to as nonshivering thermogenesis.This method utilizes a protein channel called ________ which is present in high levels inside the mitochondria of _____tissue.
A)thermogenin; muscle
B)UCP-1; muscle
C)thermogenin; brown adipose
D)UCP-1; white adipose
E)UCP-2; brown adipose
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Page 20
Chapter 19: Photosynthesis
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Q1) The light reactions of photosynthesis occur in the _____ membrane of the chloroplast.
A)photosynthetic reaction center
B)tyrosyl radical
C)thylakoid
D)H O
E)CF CF
F)Z-scheme
G)NADPH
H)plastoquinone
I)H+
J)RuBP carboxylase
K)CO
L)2 OH
M)O
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Chapter 20: Lipid Metabolism
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Q1) The molecules acetoacetate, acetone, and d-\(\beta\)-hydroxybutyrate are metabolic fuels termed ________.
A)HDL
B)propionyl-CoA
C)LDL
D)Dihydroxyacetone phosphate
E)malonyl-CoA
F)ACP
G)chylomicrons
H)phosphopantetheine
I)flavin
J)albumin
K)ketone bodies
L)cholesterol
Q2) An enzyme that is inhibited by the statin group of drugs (e.g.Lipitor)is
A)phospholipase a2.
B)hormone sensitive lipase.
C)HMG CoA reductase.
D)desaturase.
E)glycerol kinase.
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Page 22
Chapter 21: Amino Acid Metabolism
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Q1) The total cost of nitrogen reduction is ____ and ___ transferred electrons.
A)8 ATP; 4
B)12 ATP; 8
C)12 ATP; 6
D)16 ATP; 8
E)16 ATP; 6
Q2) Which of the following reaction sequences could result in glucose synthesis?
A)fumarate \(\rarr\) arginine \(\rarr\) urea
B)fumarate \(\rarr\) malate \(\rarr\) oxaloacetate
C)citrulline \(\rarr\) urea \(\rarr\)aspartate
D)urea \(\rarr\) arginine \(\rarr\) ornithine
E)none of the above
Q3) Which of the following is required for synthesis of tryptophan?
A)serine
B)phosphoenolpyruvate
C)erythrose-4-phosphate
D)all of the above
E)none of the above
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Chapter 22: Mammalian Fuel Metabolism: Integration and Regulation
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Q1) The interorgan pathway that allows transport of nitrogen from muscle to the liver utilizes ____ as an amino group acceptor in the transamination reaction generating
A)acetyl-CoA; alanine
B)acetyl-CoA; glutamine
C)pyruvate; glutamine
D)pyruvate; glutamate
E)pyruvate; alanine
Q2) Glucose uptake
A)in the liver is mediated by GLUT4.
B)in the muscle is increased in response to insulin due to increased expression of GLUT4.
C)in the brain is adjusted relative to the concentration of glucose.
D)A and B
E)A, B, C
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24
Chapter 23: Nucleotide Metabolism
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Q1) Recombinant forms of the enzyme urate oxidase are available for therapeutic purposes.Based on the information in this chapter, in which of the following conditions might this therapy be useful?
A)myoadenylate deaminase deficiency
B)severe combined immunodeficiency disease
C)gout
D)toxoplasmosis
E)folate deficiency
Q2) Glycine contributes to the ring at position _____.
A)A
B)B
C)C
D)D
E)E
Q3) The proposed mechanism of the Class I RNR involves
A)electron transfer directly from substrate to tyrosine 122.
B)electron transfer from substrate to various cysteine residues.
C)an exposed tyrosine which accepts an electron from the ribosyl radical.
D)electron donation to external reducing agents.
E)none of the above
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Chapter 24: Nucleic Acid Structure
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Q1) Which of the following materials would be useful for a researcher seeking to purify chromosomal DNA of lysed E.coli cells from cellular proteins and RNA?
A)ethidium bromide
B)hydroxyapatite
C)acridine orange
D)proflavin
E)DNA gyrase
Q2) Hammerhead ribozyme
A)contains a catalytic core with a Fe<sup>2+</sup> at its center.
B)utilizes hydrogen bonding to position itself favorably for nucleophilic attack.
C)enhances the rate of cleavage of itself by a factor of five.
D)A and C
E)B and C
Q3) During which of the following processes are RNA DNA hybrids observed?
A)transcription, both eukaryotic and prokaryotic
B)translation, both eukaryotic and prokaryotic
C)replication, both eukaryotic and prokaryotic
D)transcription, prokaryotic only
E)replication, prokaryotic only
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Page 26
Chapter 25: Dna Replication, Repair and Recombination
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Q1) In yeast, DNA replication begins at sequences known as ______.
A)SSB
B)Tus
C)primosome
D)ARS
E)ATS
F)primer
G)transposons
H)nick translation
I)photolyase
J)processive
K)G-loops
L)G-quartets
M)accurate
N)lagging strand synthesis
O)MCM
P)abortive
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Chapter 26: Transcription and Rna Processing
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Q1) Which of the following statements best describes the role of F1F1F1S1 F1F1F10 factors in bacterial gene expression?
A)(F1F1F1S1 F1F1F10 factors determine which RNA polymerase is used during transcription.
B)(F1F1F1S1 F1F1F10 factors mediate the excision of intronic sequences.
C)(F1F1F1S1 F1F1F10 factors can be used to express certain genes necessary based on cell type.
D)(F1F1F1S1 F1F1F10 factors bind to the TATA box and initiate 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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Chapter 27: Translation
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Q1) The steps required for peptide elongation at the ribosome are, respectively,
A)initiation, elongation and termination.
B)decoding, transpeptidation, and translocation.
C)initiation, elongation, and release.
D)aa-tRNA binding, GTP-peptidation, and translocation.
E)none of the above
Q2) The site on the ribosome complex which binds the new incoming amino acid- tRNA is called the
A)P site.
B)A site.
C)E site.
D)50 S site.
E)30 S site.
Q3) The Shine-Dalgarno sequence is
A)used to align ribosome subunits and initiation translation.
B)functions as a stop codon.
C)is used to align RNA polymerase.
D)is used during transcription termination.
E)all of the above
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29
Chapter 28: Regulation of Gene Expression
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Q1) How many nucleotide pairs does a bacterial genome typically contain?
A)10<sup>3</sup> - 10<sup>4</sup>
B)10<sup>5</sup> - 10<sup>6</sup>
C)10<sup>6</sup> - 10<sup>7</sup>
D)10<sup>8</sup> - 10<sup>9</sup>
E)none of the above
Q2) Human cancers are often caused by a mutation in ___, which generally functions to restrain uncontrolled cell proliferation.
A)the cyclin gene
B)the p53 gene
C)a high mobility group (HMG)gene
D)an activator region
E)a silencer region
Q3) The p53 protein functions as a ___ arresting the cell cycle in the ___ phase.
A)cyclin; G<sub>2</sub>
B)tumor suppressor; G<sub>2</sub>
C)cyclin; G<sub>o</sub>
D)tumor suppressor; G<sub>o</sub>
E)tumor suppressor; S
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Page 30