Course Introduction
Advanced Biochemistry Exam Preparation Guide
Advanced Biochemistry delves into the molecular mechanisms that underpin cellular processes, emphasizing the structure, function, and regulation of biological macromolecules such as proteins, nucleic acids, carbohydrates, and lipids. This course explores advanced topics including enzyme kinetics, signal transduction pathways, metabolic regulation, and the application of modern analytical techniques in biochemical research. Students will also examine current developments in areas such as genomics, proteomics, and the molecular basis of disease, fostering a deeper understanding of the intricate chemical interactions essential for life.
Recommended Textbook
Principles of Biochemistry 5th Edition by Moran Horton
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Page 2
Chapter 1: Introduction to Biochemistry
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Q1) The study of the energy changes during metabolic reactions is called ________.
A)bioinformatics
B)metabodynamics
C)thermometrics
D)bioenergetics
E)biological heat dynamics
Answer: D
Q2) The mitotic spindles are formed from microtubule proteins.
A)True
B)False
Answer: True
Q3) Eukaryotes include plants,animals and bacteria.
A)True
B)False
Answer: False
Q4) Biochemists describing the molecular weight of a protein really mean the atomic weight in grams.
A)True
B)False
Answer: False
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Chapter 2: Water
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Q1) Oil and water do not form a solution due to ________.
A)the hydrophobic effect
B)the inability of oil to hydrogen bond with water
C)the nonpolarity of oil
D)All of the above.
E)A and C only.
Answer: D
Q2) Which of the following weak interactions is NOT an electrostatic interaction?
A)Hydrogen bonds.
B)Charge-charge interactions.
C)Hydrophobic interactions.
D)Van der Waals forces.
Answer: C
Q3) The buffering capacity of a weak acid and its conjugate base is strongest when the pH = pKa.
A)True
B)False
Answer: True
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4
Chapter 3: Amino Acids and the Primary Structures of Proteins
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Q1) Which technique is used less for protein purification and more for the determination of molecular weights?
A)Affinity chromatography.
B)SDS-PAGE.
C)Gel filtration.
D)Ion exchange chromatography.
Answer: B
Q2) The peptide bond is which of the following?
A)An amide bond.
B)An ester bond.
C)An ether bond.
D)An amine bond.
Answer: A
Q3) What is the purpose of SDS in SDS-PAGE?
A)To selectively bind the target protein.
B)To maintain buffer pH in the gel.
C)To cause the separation to be on the basis of molecular weight only.
D)To initiate polymerization of acrylamide to form a gel.
Answer: C
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Chapter 4: Proteins: Three-Dimensional Structure and Function
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Q1) Supersecondary structures that contain recognizable combinations of -helices, -strands and loops (e.g.the Greek Key)are called ________.
A)domains
B)folds
C)homologous regions
D)motifs
Q2) Which technique is commonly used to determine the three-dimensional conformation of a protein?
A)Isoelectric focusing.
B)The Edman degradation.
C)SDS-PAGE.
D)X-ray crystallography.
Q3) Which is not an example of an oligomeric protein?
A)Cytochrome c.
B)Potassium channel protein.
C)MS2 capsid protein.
D)Hemoglobin.
E)Bacterial photosynthetic reaction center.
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Chapter 5: Properties of Enzymes
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Q1) In a first order enzyme-catalyzed reaction,the velocity of the reaction is proportional to the ________,while in a zero order enzyme-catalyzed reaction,the velocity of the reaction is proportional to the ________.
A)amount of enzyme;concentration of substrate
B)concentration of substrate;amount of enzyme
C)concentration of substrate;speed of the reaction
D)speed of the reaction;concentration of substrate
Q2) In a multienzyme complex the process of directly transferring a product of one reaction to the next active site without allowing it to enter the bulk solvent is termed
A)a ping-pong reaction
B)metabolite channeling
C)the activity pathway
D)the sequential mode
Q3) The catalytic proficiency of an enzyme is the ________.
A)turnover number
B)Km/[E]
C)rate constant with the enzyme divided by the rate constant without the enzyme
D)rate constant with the enzyme times the rate constant without the enzyme
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Page 7
Chapter 6: Mechanisms of Enzymes
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Q1) A substrate changes the shape of an enzyme and that activates it.
A)induced fit
B)proximity effect
C)covalent catalysis
D)diffusion-controlled reaction
E)acid-base catalysis
Q2) Superoxide dismutase enzyme catalysis is faster than the rate of diffusion because it
A)is an acid-base catalyst.
B)is a two-step reaction.
C)has an electric field around the active site.
D)occurs in very high quantities in cells.
Q3) Nucleophiles are often anions or have unshared electrons.
A)True
B)False
Q4) In the modified "lock-and-key" theory of enzyme specificity,the key is still the enzyme while the lock is still the substrate.
A)True
B)False
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8
Chapter 7: Coenzymes and Vitamins
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Q1) Raw egg white contains a protein called avidin.What happens if you ingest raw egg whites?
A)Avidin helps to build muscle tissue.
B)Avidin is the main protein involved in Salmonella poisoning.
C)Avidin binds onto the coenzyme biotin and interferes with its absorption.
D)Avidin,also called intrinsic factor,helps transport cobalamin into the cells of the small intestine.
Q2) TPP is a(n)________ of yeast pyruvate decarboxylase.
A)cosubstrate
B)intrinsic factor
C)metalloenzyme
D)prosthetic group
Q3) What is the role of the magnesium ion in kinases that require the magnesium-ATP complex to donate phosphoryl groups?
A)Maintain the configuration of the holoenzyme.
B)Shield the charged phosphate groups of ATP.
C)Produce an electrophilic attack on the substrate.
D)Promote ionization of bound water.
E)Produce ionization of the substrate to be phosphorylated.
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Page 9
Chapter 8: Carbohydrates
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Q1) Which statement is false about the sugar units in DNA?
A)They are cyclic in DNA.
B)It is a deoxy form of ribose.
C)It is an epimer of glucose.
D)It has a D-configuration.
Q2) A monosaccharide whose anomeric carbon atom has a glycosidic bond to an alcohol,amine or thiol is a ________.
A)glycoside
B)glycoprotein
C)heteroglycan
D)glucoconjugate
Q3) Anomers can be interconverted ________.
A)by rotation about carbon-carbon bonds
B)via a linear intermediate
C)by an isotopic exchange reaction
D)None of the above.Anomers cannot be interconverted.
Q4) Steric strain is a major factor in determining the conformations of a monosaccharide that predominate in solution.
A)True
B)False
Page 10
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Chapter 9: Lipids and Membranes
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Sample Questions
Q1) Trans fatty acids have physical properties like those of
A)w-3 fatty acids.
B)cis-fatty acids.
C)unsaturated fatty acids.
D)saturated fatty acids.
Q2) Like bacteria,plants do not contain steroids.
A)True
B)False
Q3) Which is not involved in signal transduction?
A)Glycolytic pathway.
B)Receptor tyrosine kinases.
C)Adenylyl cyclase pathway.
D)Inositol-phospholipid pathway.
Q4) Lipids may be either hydrophobic or ________.
A)hydrophilic
B)amphoteric
C)inorganic
D)amphipathic
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11
Chapter 10: Introduction to Metabolism
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Q1) Although the CoA thioester is less stable than oxygen esters,it is stable in cells,resisting nonenzymatic hydrolysis at neutral pH values.
A)True
B)False
Q2) Enzymes that oxidize NADH can best be measured by the ________ .
A)increase in absorbance at 340 nm
B)decrease in absorbance at 340 nm
C)increase in absorbance at 250 nm
D)decrease in absorbance at 250 nm
Q3) Which statement is false about ATP?
A)Its concentration in a particular cell usually fluctuates very little.
B)The concentration of ATP in cells is generally much lower than that of AMP.
C)Its concentration is maintained in part by adenylate kinase.
D)The intracellular concentration of ATP varies among cell types.
Q4) The biochemical reactions that degrade molecules,such as nutrients,are called anabolic reactions.
A)True
B)False
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Page 12
Chapter 11: Glycolysis
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Q1) ATP is a cosubstrate of the enzyme PFK-1.In most species ATP is also an inhibitor of PFK-1 at higher concentrations.This seems to violate Le Chatelier's Principle.Which statement below would provide a suitable explanation?
A)PFK-1 must be phosphorylated by ATP in the active site and the phosphorylated PFK-1 must be the less active form.
B)There must be another cofactor interacting with ATP at high concentrations to achieve inhibition of PFK-1.
C)ATP actually activates the reverse of the reaction preceding the PFK-1 step in the pathway.It likely has no direct effect on PFK-1.
D)There are two sites on PFK-1 that bind ATP.One is the active site;the other is the regulatory site where inhibition occurs.
Q2) Which is among the possible fates of pyruvate after glycolysis?
A)Conversion to lactate.
B)Further reduction by the citric acid cycle.
C)Conversion to ethanol.
D)All of the above.
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Page 13
Chapter 12: Gluconeogenesis, the Pentose Phosphate
Pathway, and Glycogen Metabolism
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Q1) Glucose is stored as ________ in bacteria and animals.
A)glucagon
B)starch
C)glycogen
D)NADPH
Q2) Glycogenin is
A)a protein for attachment of primer glucose chains.
B)an enzyme that attaches glucose residues to a growing chain.
C)a pre-existing primer in glycogen synthesis.
D)A and B.
Q3) Fructose 2,6-bisphosphate is a modulator that can stimulate either glycolysis or gluconeogenesis,depending on cellular glucose concentrations.
A)True
B)False
Q4) Glucagon increases the transcription of the gene for phosphoenolpyruvate carboxykinase (PEPCK)in gluconeogenesis,while insulin decreases it.
A)True
B)False
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Chapter 13: The Citric Acid Cycle
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Q1) Each of the following leads to a biosynthetic pathway except A)a-ketoglutarate.
B)succinyl CoA.
C)oxaloacetate.
D)citrate.
E)None of the above.
Q2) What is the role of mitochondrial PEPCK?
A)It converts oxaloacetate to PEP,which can then be transported to the cytoplasm.
B)It aids in the transport of pyruvate across the inner mitochondrial membrane.
C)It converts oxaloacetate to malate,which feeds into the malate-aspartate shuttle.
D)It converts acetyl CoA to citrate,which can then be transported to the cytoplasm.
Q3) The succinate dehydrogenase complex catalyzes
A)the formation of a single hydrogen bond in the oxidation of succinate to fumarate.
B)the formation of a double bond in the oxidation of succinate to fumarate.
C)Both A and B.
D)None of the above.
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Chapter 14: Electron Transport and Atp Synthesis
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Q1) The reactions in complex II release very little free energy and do not contribute directly to the proton concentration gradient.
A)True
B)False
Q2) If an inhibitor disrupts the flow of protons from the matrix into the intermembrane space of mitochondria,no ATP will be formed.
A)True
B)False
Q3) Which is not a component of complex II?
A)Fe-S clusters.
B)FAD.
C)Heme.
D)Cytochrome b.
E)All of the above are components of complex II.
Q4) In bacteria,oxidative phosphorylation occurs in the mitochondrial membrane. A)True
B)False
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Chapter 15: Photosynthesis
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Q1) Rubisco has an active form during the day and an inactive form at night.
A)True
B)False
Q2) Chlorophyll molecules contain hydrophilic regions containing bonds for light-absorbing and hydrophobic regions anchoring them to membranes.
A)True
B)False
Q3) Calculate the energy of a photon with a wavelength of 700 nm.(h = 6.63 × 10-³ J s and c = 3.00 × 10 m s-¹)
A)2.8 × 10-² J
B)2.8 × 10-¹ J
C)1.3 × 10-²² J
D)3.6 × 10¹ J
Q4) Which enzyme is not part of the Calvin cycle?
A)Triose phosphate isomerase.
B)Rubisco.
C)Plastocyanin.
D)Transketolase.
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Chapter 16: Lipid Metabolism
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Q1) Which of the following is a true statement,concerning HMG-CoA reductase?
A)It is regulated by covalent modification of a serine in its active site.
B)It catalyzes the first committed step in cholesterol biosynthesis.
C)It causes the production of NADPH.
D)The product of the reaction it catalyzes is acetoacetyl CoA.
Q2) Which of the following is mismatched?
A)Bile salts - intestinal absorption of lipids.
B)B-estradiol - sex characteristics.
C)Cholesterol - membrane fluidity.
D)Squalene - lipid vitamin.
Q3) Which of the following is a true statement for fatty acid synthesis?
A)It occurs in the mitochondria.
B)The reducing power for synthesis is supplied by NAD+ and ubiquinone.
C)Both A and B.
D)None of the above.
Q4) Which of the following is not a stage of fatty acid synthesis?
A)Condensation of precursors.
B)Rearrangement.
C)Reduction.
D)Dehydration.
Page 18
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Chapter 17: Amino Acid Metabolism
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Q1) A Roundup Ready plant is one that has been genetically modified so that an enzyme (EPSP synthase)can no longer bind to the active ingredient (glyphosphate)which is a competitive inhibitor of A)shikimate (in the aromatic amino acid pathway).
B)tryptophan.
C)lysine.
D)phosphoenolpyruvate (PEP).
Q2) Phenylketonuria (PKU)is a disease caused by a defect in ________ formation.
A)phenylalanine
B) -ketoglutarate
C)tyrosine
D)urea
Q3) The catabolism of which amino acids can produce sulfuric acid?
A)cysteine and methionine
B)cysteine and serine
C)aspartate and glutamate
D)lysine and arginine
Q4) Nitric oxide functions as a neurotransmitter in the brain.
A)True
B)False
Page 19
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Chapter 18: Nucleotide Metabolism
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Q1) Substrates for reduction to form deoxyribonucleotides are
A)mononucleotides.
B)trinucleotides.
C)dinucleotides.
D)B and C.
E)All of the above.
Q2) Xanthine oxidase catalyzes the formation of ________.
A)xanthine
B)uric acid
C)hypoxanthine
D)xanthine and uric acid
E)All of the above
Q3) Which enzyme catalyzes the step in purine nucleotide biosynthesis that is the principal site of regulation for the pathway?
A)Adenylsuccinate lyase.
B)OPM decarboxylase.
C)IMP cyclohydrolase.
D)Glutamine-PRPP amidotransferase.
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20
Chapter 19: Nucleic Acids
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Q1) Which is not a difference between RNA and DNA?
A)The sugar ring of RNA is more oxidized than that in DNA.
B)RNA contains uracil;DNA usually does not.
C)RNA cannot form helices.
D)RNA is usually single-stranded;DNA is double-stranded.
Q2) ________ plays an important role in storing the energy needed for the unwinding of DNA during replication,recombination,repair and transcription.
A)A high percent of G:C base pairs
B)The charge on basic side chains of histone proteins
C)Negative supercoiling
D)Overwinding of the helix
Q3) What is the effect of incubating a mixture of RNA and DNA with 0.1 M NaOH?
A)RNA is hydrolyzed to nucleoside monophosphates.
B)DNA is hydrolyzed to nucleoside monophosphates.
C)Both RNA and DNA are hydrolyzed to nucleoside monophosphates.
D)No effect.RNA and DNA are resistant to base hydrolysis.
Q4) It is possible to synthesize DNA containing specific polynucleotide bases today.
A)True
B)False
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Chapter 20: DNA Replication, repair, and Recombination
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Q1) How many replisomes are required for one complete round of DNA replication in E.coli?
A)One
B)Two
C)Four
D)More than 4
Q2) The primosome is composed of polypeptides including primase which is
A)DNA polymerase III.
B)RNA dependent DNA polymerase.
C)DNA dependent RNA polymerase.
D)Parental DNA.
Q3) DNA polymerase III requires a(n)________ for synthesis of DNA to occur.
A)DNA template
B)RNA primer
C)free 3'-OH end of a DNA strand
D)All of the above
Q4) A short primer is added to the DNA polymerase reaction mix for Sanger DNA sequencing that has a 5' free hydroxyl to which new nucleotides can be added.
A)True
B)False
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Chapter 21: Transcription and RNA Processing
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Q1) The 70 subunit in E.coli RNA polymerase acts as a(n)________.
A)repressor
B)sliding clamp
C)helicase
D)initiation factor
Q2) What does it mean to say that the most common type of promoter in E.coli is bipartite?
A)The promoter region is divided into two parts which flank the sequence for the gene.
B)There are two separate regions of sequence similarity in the promoter.
C)The sequence of the promoter has dyad symmetry.
D)The promoter must bind two RNA polymerase holoenzymes to transcribe the gene.
Q3) Rho-dependent termination
A)is due to destabilization of the RNA-DNA hybrid.
B)is due to indirect contact between the transcription complex and rho as rho binds RNA.
C)may cause the RNA polymerase to bind to template DNA.
D)All of the above.
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Chapter 22: Protein Synthesis
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Q1) Different codons that specify the same amino acid are called ________ codons.
A)synonymous
B)repetitive
C)variable
D)multiplex
Q2) If there is more globin than heme present in a reticulocyte,globin synthesis is stopped by
A)the activation of HCI (heme-controlled inhibitor).
B)the inactivation of HCI.
C)increasing heme synthesis.
D)decreasing heme synthesis.
E)activating eIF-2.
Q3) The initiation codon ________.
A)specifies uracil
B)specifies methionine
C)binds a protein complex that starts translation
D)is part of the TATA box
Q4) The genes for rRNA tend to have very strong promoters.
A)True
B)False
Page 24
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