Advanced Biochemistry
Pre-Test Questions
Course Introduction
Advanced Biochemistry explores the chemical processes and molecular mechanisms that govern living systems at an in-depth level. This course delves into topics such as protein structure and function, enzyme kinetics and regulation, metabolic pathways, bioenergetics, and signal transduction. Students will analyze molecular interactions, regulatory networks, and experimental methodologies used in modern biochemical research. Emphasis is placed on applying theoretical concepts to real-world biological problems and interpreting current scientific literature. Through lectures, case studies, and laboratory experiments, learners will build a comprehensive understanding of how biochemical principles underlie cellular and physiological processes.
Recommended Textbook Fundamentals of Biochemistry Life at the Molecular Level 5th Edition by Donald Voet
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Chapter 1: Introduction to the Chemistry of Life
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Sample Questions
Q1) Which cellular compartment or organelle is involved in the synthesis of proteins and lipids?
A)endoplasmic reticulum
B)lysosomes
C)peroxisomes
D)vacuoles
E)all of the above
Answer: A
Q2) Living organisms
A)are closed systems.
B)maintain a steady state.
C)exist outside the laws of thermodynamics.
D)are all of the above
E)are none of the above
Answer: B
Q3) Carbohydrates,proteins,nucleotides,and nucleic acids are important groups of molecules found in living organisms.Which 6 elements do living organisms need to build these molecules?
Answer: C,H,O,N,S,P
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Page 3
Chapter 2: Water
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Sample Questions
Q1) Physical properties that depend on the amounts of various species,rather than the identities of those species,are called
A)osmotic properties.
B)hydrophobic properties.
C)London dispersion forces.
D)aggregate properties.
E)colligative properties.
Answer: E
Q2) Hydrogen bonds within liquid water
A)are attractions between protons and oxygen nuclei.
B)are attractions between two hydrogen atoms.
C)are attractions between protons<sup> </sup>and hydroxide ions.
D)are ion-induced dipole attractions.
E)are dipole-dipole attractions.
Answer: E
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Chapter 3: Nucleotides, nucleic Acids, and Genetic Information
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Sample Questions
Q1) Small circular DNA molecules used to carry foreign DNA fragments are called
A)mRNAs
B)bacteriophage
C)clones
D)plasmids
E)nucleotides
Answer: D
Q2) Which of the following DNA sequences (in which N is any nucleic acid residue)is palindromic?
A)ANAGCTT
B)AANGCTT
C)AAGNCTT
D)AAGCNTT
E)AAGCTNT
Answer: C
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5
Chapter 4: Amino Acids
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Sample Questions
Q1) The pK<sub>1</sub>,pK<sub>2</sub>,and pK<sub>R</sub> for the amino acid glutamate are 2.1,9.5,and 4.1,respectively.At pH 11.0,glutamate would be charged predominantly as follows:
A)"\(\alpha\)-carboxylate +1,\(\alpha\)-amino 0,\(\gamma\)-carboxylate +1,net charge +2"
B)"\(\alpha\)-carboxylate 1,\(\alpha\)-amino +1,\(\gamma\)-carboxylate 1,net charge 1"
C)"\(\alpha\)-carboxylate 0,\(\alpha\)-amino 0,\(\gamma\)-carboxylate 0,net charge 0"
D)"\(\alpha\)-carboxylate +1,\(\alpha\)-amino 1,\(\gamma\)-carboxylate +1,net charge +1"
E)"\(\alpha\)-carboxylate 1,\(\alpha\)-amino 0,\(\gamma\)-carboxylate 1,net charge 2"
Q2) An amide bond between a side-chain carboxylate and an \(\alpha\)-amino group is also called a(n)
A)disulfide bond.
B)anhydride bond.
C)ester bond.
D)isopeptide bond.
E)glycosidic bond.
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Page 6
Chapter 5: Proteins: Primary Structure
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Sample Questions
Q1) Which physical characteristic is not commonly used in protein separation?
A)solubility
B)stereochemistry
C)size
D)charge
E)polarity
Q2) ___________ is an example of a very slowly evolving protein.
A)Histone H4
B)Hemoglobin
C)Cytochrome c
D)Fibrinopeptides
E)none of the above
Q3) Proteins can vary in size from approximately 40 to 34,000 amino acids.
a.Why is there a lower limit to the size of proteins?
b.Why is there an upper limit to the size of polypeptides?
Q4) A variety of chromatographic techniques are available for protein purification.
a.Explain briefly the principle of hydrophobic interaction chromatography.
b.Name three changes that can be made to the eluant that can be used to speed up elution of the protein of interest from a hydrophobic interaction chromatography column.
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Chapter 6: Proteins: Three-Dimensional Structure
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Sample Questions
Q1) Proteins can denature due to a change in A)pH.
B)temperature.
C)ionic strength.
D)all of the above
E)none of the above
Q2) A helix has hydrogen bonds between the carbonyl group from residue "n" and the amino group of residue "n+6," which of the following is TRUE?
A)It has 3.6 residues per turn.
B)It is a random coil,not a helix.
C)It is an helix.
D)It has more residues per turn than an helix.
E)It has fewer residues per turn than an helix.
Q3) In general molecular chaperone proteins function by
A)mediating disulfide bond formation
B)synthesizing new proteins when one is misfolded.
C)preventing premature folding by binding hydrophobic regions of the protein.
D)enhancing salt bridge formation.
E)none of the above
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Page 8
Chapter 7: Protein Function Part I: Myoglobin and Hemoglobin
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Sample Questions
Q1) Which of the statements about muscle contraction is not true?
A)During muscle contraction the sarcomere becomes shorter.
B)During muscle contraction the I band becomes shorter.
C)During muscle contraction the H zone becomes shorter.
D)During muscle contraction the A band becomes shorter
E)During muscle contraction the distance between the Z disk and the M disk becomes shorter.
Q2) The oxygen binding by hemocyanins is mediated by
A)an iron ion
B)a pair of iron ions
C)a heme group
D)a copper atom
E)a pair of copper atoms
Q3) What are the main bonds or forces that stabilize the dimer formed by two myosin heavy chains?
A)hydrophobic interactions
B)hydrogen-bonds
C)ionic interactions
D)disulfide bonds
E)isopeptide bonds
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Chapter 8: Carbohydrates
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Sample Questions
Q1) A saccharide that has free aldehyde group is called a(n)_____________.
A)ketose
B)nonreducing sugar
C)reducing sugar
D)aldohexose
E)alditol
Q2) How many stereoisomers are possible for a ketopentose such as ribulose?
A)2
B)4
C)8
D)16
E)32
Q3) Which of these polysaccharides is a branched polymer?
A)chitin
B)amylose
C)cellulose
D)amylopectin
E)hyaluronic acid
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Chapter 9: Lipids and Biological Membranes
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Sample Questions
Q1) Cold blooded animals modulate the fatty acid composition of their membranes as a function of temperature in order to
A)adjust the membrane thickness and increase thermal insulation.
B)maximize available fatty acids for metabolic use.
C)ensure consistent membrane fluidity.
D)compensate for decreasing cholesterol solubility.
E)all of the above
Q2) Adipocytes
A)are specialized cells for the synthesis of triglycerides.
B)are specialized cells for short term energy storage.
C)provide compartments for efficient membrane bilayer synthesis.
D)exist primarily in a thin layer surrounding major muscle groups as a rapid high energy source.
E)All of the above characterize adipocytes.
Q3) 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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Sample Questions
Q1) D-glucose is added to cells and the rate of glucose transport is plotted against D-glucose concentration.In the presence of the D-galactose derivative 6-O-benzyl-D-galactose,the curve is shifted to the right,indicating that D-glucose and the D-galactose derivative both compete for a place in the binding site.Which of the following is true?
A)The D-galactose derivative occupies some of the available binding sites.
B)Given the same concentration of glucose available,the number of binding sites with D-glucose present would decrease.
C)Given the same concentration of glucose,the rate of D-glucose flux would remain the same with the D-galactose derivative added.
D)Presumably a higher concentration of D-glucose would be required in order to maintain the same rate of D-glucose flux as before the D-galactose derivative was added.
E)All of the above are true.
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Chapter 11: Enzyme Catalysis
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Sample Questions
Q1) Which one of the following is correct?
(I)All enzymes are highly specific for the reactions they catalyze.
(II)Prosthetic groups are loosely associated with the polypeptide chain of an enzyme.
(III)If an enzyme-catalyzed reaction requires a group with a low pK to be deprotonated and a group with a higher pK to be protonated,the pH vs.rate curve will have a peak in the middle of the two pK values.
(IV)When comparing types of catalysis,the proximity effect provides the largest rate enhancement.
A)I,II,III,IV
B)I,III
C)I
D)III
E)IV
Q2) Curved arrows are conventionally used to illustrate the movement of A)electron pairs.
B)single electrons.
C)protons.
D)anions.
E)All of the above use this convention.
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Page 13
Chapter 12: Enzyme Kinetics, inhibition and Control
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Sample Questions
Q1) Find the initial velocity for an enzymatic reaction when V<sub>max</sub> = 6.5 × 10<sup>-5</sup> mol sec<sup>-1</sup>,[S] = 3.0 × 10<sup>-3</sup> M,K<sub>M</sub> = 4.5 × 10<sup>-3</sup> M and the enzyme concentration at time zero is 1.5 × 10<sup>-2</sup> \(\mu\)M.
A)3)9 × 10<sup>-5</sup> mol sec<sup>-1</sup>
B)2)6 × 10<sup>-5</sup> mol sec<sup>-1</sup>
C)1)4 × 10<sup>-2</sup> mol sec<sup>-1</sup>
D)8)7 × 10<sup>-3</sup> mol sec<sup>-1</sup>
E)Not enough information is given to make this calculation.
Q2) Based on the figure in the question above (question 54),which of the following expressions would correctly define K<sub>M</sub>?
A)A= K<sub>M</sub>
B)K<sub>M</sub> = A/2
C)B = K<sub>M</sub>
D)C = - K<sub>M</sub>
E)D= 1/ K<sub>M</sub>
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14
Chapter 13: Biochemical Signaling
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Sample Questions
Q1) Sildenafil (Viagra®)
A)inhibits activity of a phosphoprotein phosphatase.
B)increases the relative concentration of cGMP.
C)increases the relative concentration of nitric oxide in the blood.
D)A,B,and C
E)A and B
Q2) The \(\alpha\) cells of the islets of Langerhans secrete _____ in response to ____ glucose levels in the liver.
A)insulin;low
B)insulin;elevated
C)glucagon;low
D)glucagon;elevated
E)somatostatin;elevated
Q3) Which of the following activities would lead to a decrease in the level of IP<sub>3</sub> in the cytosol?
A)increased activity of inositol polyphosphate 5-phosphatase
B)increased activity of phospholipase C
C)increased activation of protein kinase C
D)increased Ca<sup>2+</sup><sup> </sup>concentration
E)all of the above
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Chapter 14: Introduction to Metabolism
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Sample Questions
Q1) The vitamin ______ is one of the components of coenzyme A,which is involved in
A)pantothenic acid;carboxylation
B)pantothenic acid;acyl transfer
C)cobalamin;acyl transfer
D)riboflavin;carboxylation
E)niacin;electron transfer
Q2) Organisms that can grow in either the presence or absence of oxygen are classified as
A)obligate aerobes
B)facultative anaerobes
C)autotrophs
D)heterotrophs
E)obligate anaerobes
Q3) The terminal electron acceptor in an aerobic organisms is
A)CO<sub>2</sub>.
B)NAD<sup>+</sup>.
C)FAD.
D)O<sub>2</sub>.
E)H<sub>2</sub>O.
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Chapter 15: Glucose Catabolism
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Sample Questions
Q1) In which reaction above is ATP required?
A)I,II
B)II only
C)III only
D)IV,V
E)None of the reactions I-V requires ATP.
Q2) The metabolism of mannose requires _____ to produce ____ for entry into the glycolytic pathway.
A)hexokinase;glucose-6-phosphate
B)hexokinase;fructose-6-phosphate
C)phosphomannose isomerase;glucose-6-phosphate
D)phosphomannose isomerase;fructose-6-phosphate
E)phosphofructokinase;bisphosphoglycerate
Q3) Of the reaction types listed below,which type of reaction is NOT used in glycolysis?
A)oxidation
B)phosphorylation
C)dehydration
D)isomerization
E)All are used in glycolysis.
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Chapter 16: Glycogen Metabolism and Gluconeogenesis
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Q1) Increased levels of epinephrine in the blood will (I)activate adenylate cyclase in liver and muscle cells. (II)stimulate glycogen synthesis. (III)inhibit glycolysis in the muscle cell. (IV)stimulate gluconeogenesis in the muscle cell.
A)I only
B)I,II
C)I,II,III
D)II only
E)I,II,III,IV
Q2) In glycogen synthesis,the intermediate between glucose-1-phosphate and glycogen is
A)UDP-glucose .
B)UDP-glycogen.
C)glucose-1,6-bisphosphate.
D)glucose-6-phosphate.
E)glucose.
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18
Chapter 17: Citric Acid Cycle
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Q1) Which of the following steps of the citric acid cycle conserves the energy of a high energy thioester bond?
A)the reaction catalyzed by succinate dehydrogenase.
B)the reaction that produces oxalacetate.
C)the condensation reaction that produces citrate.
D)the reaction catalyzed by -ketoglutarate dehydrogenase.
E)the conversion of citrate to isocitrate.
Q2) During the oxidation of isocitrate,_____ is decarboxylated to form \(\alpha\)-ketoglutarate.
A)hydroxyethyl-TPP
B)carboxybiotin
C)oxalosuccinate
D)succinyl-phosphate
E)none of the above
Q3) Which of the following enzymes of the citric acid cycle is inhibited by ATP?
A)"citrate synthase"
B)"isocitrate dehydrogenase"
C)"\(\alpha\)-ketoglutarate dehydrogenase"
D)"succinyl-CoA synthetase"
E)"A and B"
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Chapter 18: Electron Transport and Oxidative
Phosphorylation
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Q1) Rotenone and amytal (I)inhibition can be restored by addition of succinate (II)inhibition can be restored by addition of cytochrome c. (III)blocks consumption of oxygen. (IV)blocks transfer of electrons from CoQ to Complex III.
A)I,II,III,IV
B)I,II,III
C)II,III,IV
D)III only
E)IV only
Q2) 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
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Chapter 19: Photosynthesis
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Q1) Synthesis of starch requires (I)ATP
(II)glucose-1-phosphate (III)ADP-glucose phosphatase
(IV)ADP-glucose
A)I,II,III
B)II,III,IV
C)I,III,IV
D)I,II,IV
E)II,III
Q2) Electron transfer in PbRC is approximately ____ efficient. A)25%.
B)50%.
C)75%.
D)96%.
E)100%.
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21
Chapter 20: Lipid Metabolism
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Q1) Which of the following drugs acts by acetylating a serine residue preventing adequate enzyme activity?
A)ibuprofen
B)acetaminophen
C)Vioxx®
D)aspirin
E)Celebrex®
Q2) Which of the following diets would most likely promote the formation of ketone bodies?
A)high simple carbohydrates,low fat
B)high complex carbohydrates,high fructose
C)high fat,high protein,low carbohydrate
D)low fat,high protein,high complex carbohydrates
E)high fructose;high whole grain carbohydrates
Q3) 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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Chapter 21: Amino Acid Metabolism
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Q1) Organisms known as _____ can fix nitrogen into metabolically useful molecules.
A) ribosomes
B) jaundice
C) channeling
D) 26S proteasome
E) glutamine synthetase
F) alanine
G) glutamate
H) vitamin B<sub>6</sub>
I) anammox
J) glutamine transferase
K) THF
L) autotroph
M) vitamin D
N) lysosomes
O) diazotrophs
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Page 23
Chapter 22: Mammalian Fuel Metabolism: Integration and Regulation
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Q1) ______ and other waste products from the blood are excreted by the kidney.
A) -adrenergic receptor
B) -adrenergic receptor
C) Cori cycle
D) urea cycle
E) leptin
F) phosphatase
G) liver
H) hormones
I) acetyl CoA
J) ketone bodies
K) urea
L) kidney
M) brain
N) pancreas
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Chapter 23: Nucleotide Metabolism
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Q1) The symptoms of Lesch-Nyhan syndrome are caused by a deficiency of which of the following enzymes?
A)adenine phosphoribosyltransferase
B)HGPRT (hypoxanthine-guanine phosphoribosyltransferase)
C)adenosine deaminase
D)dihydrofolate reductase
E)xanthine oxidase
Q2) The end products of pyrimidine catabolism are
A)"uric acid and glyoxylic acid."
B)"uric acid and allantoin."
C)"\(\beta\)-alanineand \(\beta\)-aminoisobutyrate."
D)"\(\beta\)-alanine and \(\alpha\)-ketoglutarate."
E)"none of the above"
Q3) Orotate is synthesized from
A)glycine and carbamoyl phosphate.
B)arginine and carbamoyl phosphate.
C)aspartate and carbamoyl phosphate.
D)aspartate and glutamine.
E)asparagine and glutamine.
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Chapter 24: Nucleic Acid Structure
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Q1) Which of the following scientists is now accredited with generating the X-ray diffraction photograph that played a pivotal role in the discovery of the structure of B-DNA?
A)James Watson
B)Francis Crick
C)Maurice Wilkins
D)Rosalind Franklin
E)all of the above
Q2) E.coli topoisomerase III
(I)contains a hole capable of holding duplex DNA that is lined with negatively charged residues.
(II)binds the sugar-phosphate backbone such that base recognition is possible.
(III)functions by nucleophilic attack on the binding phosphate group.
A)I,II
B)II,III
C)I,III
D)I only
E)II only
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Page 26
Chapter 25: DNA Replication, repair and Recombination
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Q1) Deamination of cytosine leads to the formation of A)thymine.
B)5-methylcytosine. C)uracil.
D)5-bromouracil.
E)5-methyluracil.
Q2) Which of the following enzymes catalyze the creation of AP sites for base excision repair?
A)exonuclease
B)endonuclease
C)ligase
D)glycosylase
E)methylase
Q3) Which of the following would result in single stranded DNA?
A)Klenow fragment
B)Klentaq I
C)DnaB
D)DnaG
E)pol III
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Chapter 26: Transcription and Rna Processing
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Q1) Eukaryotic RNA molecules are altered by removal of intervening sequences called
A) Rho ( )
B) introns
C) sigma ( )
D) sense
E) operons
F) structural
G) Pribnow
H) promoters
I) antisense
J) exons
K) nucleolus
L) TATA
M) Sense
N) AAAA (poly A)
O) Ribosome
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Chapter 27: Protein Synthesis
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Q1) A silent mutation occurs when a nucleotide mutation results in the identical amino acid in place upon completion of translation.If the original sequence is as follows,which example below represents a silent mutation?
GUACAAGCAUGAAGUUUGGUAAGCG
A)GUGCAAGCAUGAAGUUUGGUAAGCG
B)GUACAAGCAUGAAAUUUGGUAAGCG
C)GUACAAGCAUGAAGUUGGGUAAGCG
D)GUACAGGCAUGAAGUUUGGUAAGCG
E)GUACAAGCAUGAAGUUUGGUAACCG
Q2) Insertions or deletions of one or two nucleotides can cause
A)frameshift mutations.
B)degenerate mutations.
C)synonymous mutations.
D)wobble codons.
E)transpeptidation.
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Chapter 28: Regulation of Gene Expression
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Q1) What type of mutation causes conditions such as Huntington's disease and Fragile X syndrome?
A)an excess of trinucleotide repeats in a protein-coding gene
B)a mutation in the p53 tumor suppressor
C)a mutation in a cyclin-dependent protein kinase
D)a mutation in the retinoblastoma gene
E)a mutation in caspase-activated DNase
Q2) How many nucleotide pairs does a mammalian genome typically contain?
A)10<sup>5</sup> - 10<sup>6</sup>
B)10<sup>6</sup> - 10<sup>7</sup>
C)10<sup>8</sup> - 10<sup>9</sup>
D)10<sup>9</sup> - 10<sup>10</sup>
E)none of the above
Q3) Which of the following would likely result in the formation of RNAi?
A)injection of antisense RNA from a human into human cells
B)injection of sense RNA into C.elegans
C)injection of antisense RNA from yeast into a human
D)all of the above
E)none of the above
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