Biological Chemistry
Practice Exam
Course Introduction
Biological Chemistry explores the chemical principles and processes underlying biological systems, bridging the disciplines of chemistry and biology. This course covers the structure, function, and interactions of biomolecules such as proteins, nucleic acids, lipids, and carbohydrates. Students will examine enzyme mechanisms, metabolic pathways, bioenergetics, and the chemical basis of genetic information flow. Emphasis is placed on understanding how molecular structure dictates function and how chemical transformations drive cellular processes, providing foundational knowledge for advanced studies in biochemistry, molecular biology, and related fields.
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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Q1) Calculate the \(\Delta\)G for a reaction with \(\Delta\)H = 20.kJ/mol and \(\Delta\)S =20.J/K mol,that is carried out at 27°C.
A)14 J/mol
B)140 J/mol
C)1400 J/mol
D)14,000 J/mol
E)none of the above
Answer: D
Q2) The bulk of aerobic metabolism in eukaryotic cells takes place in
A)the endoplasmic reticulum.
B)the nucleus.
C)the mitochondria.
D)peroxisomes.
E)the Golgi apparatus.
Answer: C
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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Q1) The insolubility of nonpolar molecules in water is due to the large ______,which is the result of water molecules forming an ordered network surrounding nonpolar molecules.
A) hydrogen bond
B) rotational
C) H<sub>3</sub>PO<sub>4</sub>
D) H<sub>2</sub>PO<sub>4</sub><sup> </sup>
E) HPO<sub>4</sub> <sup>2 </sup>
F) disordered
G) positive entropy
H) negative entropy
I) higher electronegativity
J) insoluble
K) tetrahedral arrangement
L) acid
M) base
N) only partially ionized
Answer: H
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Page 4
Chapter 3: Nucleotides, nucleic Acids, and Genetic Information
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Q1) A genomic library
A)is a collection of protein structures from a specific organism.
B)is a collection of cloned DNA fragments representing all of an organism's DNA.
C)contains only protein-coding DNA sequences.
D)is best constructed from very short DNA fragments.
E)is built from mRNA by reverse transcription.
Answer: B
Q2) Which of the following molecules does not contain an energy rich phosphoanhydride bond?
A)ADP
B)GDP
C)AMP
D)CDP
E)all of the above
Answer: C
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Page 5
Chapter 4: Amino Acids
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Q1) 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.
Q2) The peptide AYDG has an N-terminal _________ residue.
A)glycine
B)glutamic acid
C)glutamine
D)aspartic acid
E)alanine
Q3) All amino acids derived from proteins have the same stereochemical conformation as.
A)L-glyceraldehyde.
B)(R)-alanine.
C)D-glucose.
D)(S)-cysteine.
E)glycine.
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Chapter 5: Proteins: Primary Structure
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Q1) SDS-PAGE separates proteins primarily due to differences in A)isoelectric point.
B)mass.
C)polarity.
D)solubility.
E)amino acid sequence.
Q2) The positive charge on proteins in electrospray ionization mass spectrometry is the result of
A)protons fired at the gas-phase protein molecules.
B)protonated side chains of Asp and Glu residues.
C)protonated side chains of Arg and Lys residues.
D)a high pH.
E)electrons fired at the gas-phase protein molecules.
Q3) Which of the following amino acids would be first to elute at pH 8.0 from an anion-exchange column?
A)lysine
B)alanine
C)glutamic acid
D)asparagine
E)glycine
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Chapter 6: Proteins: Three-Dimensional Structure
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Q1) Which of the following statements is true regarding collagen?
A)The inability to hydroxylate proline results in the inability to synthesize collagen.
B)The helical structure is ideal for intertwining 3 filaments.
C)Hydrogen bonds between the OH groups of Hyp residues stabilize the helix.
D)The requirement for glycine every 3rd amino acid is essential for the triplet helix formation.
E)On average,there is one proline for every hydroxyproline.
Q2) Noncovalent interactions account for the strength of which of the following structural proteins?
A)"\(\alpha\) keratin"
B)"collagen"
C)"pleated collagen"
D)"A and B"
E)"B and C"
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8
Chapter 7: Protein Function Part I: Myoglobin and Hemoglobin
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Q1) The value of n,the Hill constant (coefficient),for hemoglobin is about ______ as great as the value for myoglobin.
A)half
B)twice
C)three times
D)five times
E)ten times
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) Mammals and other animals have a circulatory system because diffusion is to slow to supply the tissues with oxygen in animals that are larger than 2 millimeter.Explain in one sentence why these circulatory systems contain hemoglobin or other oxygen binding proteins?
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Chapter 8: Carbohydrates
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Q1) Which of these polysaccharides is a branched polymer?
A)chitin
B)amylose
C)cellulose
D)amylopectin
E)hyaluronic acid
Q2) We encounter a great variety of sugars in living organisms.
a.Draw a Haworth projection of an aldohexose in the pyranose form (include all atoms).
b.Draw the Haworth projection of the anomer of the aldose you drew in "a" above.
c.Draw a circle around the carbon that determines whether this sugar is a D or an L sugar.
d.How many chiral carbon atoms are present in each of the structures drawn in "a" and b" above?
e.How many stereoisomers exist for these pyranoses?
Q3) We encounter a great variety of sugars in living organisms.
a.Are most carbohydrates in living organisms D or L?
b.Draw a Fischer projection of the smallest aldose (include all atoms).
c.What is the name of this molecule?
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Page 10
Chapter 9: Lipids and Biological Membranes
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Q1) Which of the following statements describes integral membrane proteins?
(I)They protect the contents of the cell from chaotropic agents such as urea.
(II)They are easily dissociated from the membrane by changes in pH or high salt concentration.
(III)They are held tightly in place by hydrophobic effects between the membrane and hydrophobic amino acids.
A)I,II,III
B)I,III
C)I
D)II
E)III
Q2) While fatty acids are most often formed by the condensation of __-carbon units,isoprenoids are assembled from __-carbon units.
A)5,3
B)4,2
C)2,3
D)2,5
E)3,4
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Page 11
Chapter 10: Membrane Transport
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Q1) A pore that simultaneously transports two different molecules in different directions is called
A)a symport.
B)a uniport .
C)a gap junction.
D)an equilibrium channel.
E)an antiport.
Q2) Which statement does not describe the transport of ions by valinomycin?
A)Mutations in the peptide sequence may alter ability to transport through the membrane.
B)Transport may be active or passive.
C)The active site binds K<sup>+</sup> with greater affinity than Na<sup>+</sup>
D)Transport results in equilibration of a concentration gradient across membranes.
E)All of the above do describe transport by valinomycin.
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Chapter 11: Enzyme Catalysis
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Q1) Research scientists are trying to clone a gene.In order to accomplish this task they join two pieces of DNA.Which class of the enzymes below might accomplish this task?
A)oxidoreductase
B)ligase
C)hydrolase
D)isomerase
E)lyase
Q2) Why can histidine NOT act as a base in the lysosome (an organelle where the pH is close to 4.5)?
A)Histidine has a positive charge at pH 4.5.
B)Histidine has a side chain pK close to 6.
C)Histidine would be protonated at pH 4.5.
D)All of the above are correct.
E)None of the above is correct.
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Chapter 12: Enzyme Kinetics, inhibition and Control
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Q1) The breakdown of dopamine is catalyzed by the enzyme monoamine oxidase (MAO).What is the final concentration of product if the starting dopamine concentration is 0.050 M and the reaction runs for 5 seconds.(Assume the rate constant for the reaction is 0.249 s<sup> 1</sup>. )
A)0)050 M
B)0)014 M
C)0)018 M
D)1)2 M
E)0)025 M
Q2) Which of the following is correct in regards to the diagram above?
A)X=A,Y=B,Z=P
B)X=B,Y=A,Z=Q
C)X=E,Y=A,Z=E
D)X=E,Y=B,Z=Q
E)X=E,Y=B,Z=P
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Chapter 13: Biochemical Signaling
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Q1) Autoinhibition in the SH2 and SH3 domains
A)occurs when a SH2 phospho-Tyr forms a salt bridge with an Arg on SH3.
B)occurs when a SH2 phospho-Tyr binds a Pro segment on the SH3 domain,therefore blocking the active site and burying the required Tyr.
C)occurs when a salt bride forms between the active site phosphor-Tyr on SH3 and the Glu on the activation loop.
D)occurs when the salt bridge between Glu and Arg is broken.
E)None of the above is correct.
Q2) Which of the following statements concerning the action of G proteins on adenylate cyclase is true?
(I)G proteins always serve to activate adenylate cyclase.
(II)G proteins always serve to inhibit adenylate cyclase.
(III)Some G proteins activate adenylate cyclase,while others inhibit it.
(IV)G proteins do not act on adenylate cyclase at all.
A)I only
B)II,III
C)I,III
D)II only
E)III only
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Chapter 14: Introduction to Metabolism
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Q1) ATP contains ________ bonds.
A)one phosphoanhydride and two phosphoester
B)two phosphoester and one glycosidic
C)three phosphoanhydride
D)one amide and three phosphoanhydride
E)one phosphoester and two phosphoanhydride
Q2) Negative feedback inhibition is one type of _______ metabolic control.
A)allosteric
B)hormonal
C)covalent modification
D)genetic
E)signal transduction
Q3) The conversion of triacylglycerides into fatty acids for the purpose of energy generation is an example of which of the following?
A)heterotropism
B)anaerobism
C)catabolism
D)anabolism
E)glycolysis
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Page 16
Chapter 15: Glucose Catabolism
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Q1) 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
Q2) Glycolytic synthesis of ATP occurs via A)oxidation.
B)reduction.
C)substrate-level phosphorylation.
D)oxidative phosphorylation.
E)photophosphorylation.
Q3) Glucose is converted to ______ in skeletal muscle under anaerobic conditions.
A)lactate
B)acetyaldehyde
C)fructose
D)glycogen
E)acetyl-CoA
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Chapter 16: Glycogen Metabolism and Gluconeogenesis
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Q1) The first step in the breakdown of glycogen is catalyzed by ______.
A) phosphorylase a
B) gluconeogenesis
C) glucagon
D) glucose-6-phosphatase
E) cAMP
F) biotin
G) insulin
H) glycogenolysis
I) liver
J) glucose-1-phosphate
K) dolichol
L) muscle
Q2) Which of the following enzymes catalyzes the conversion of glucose-1-phosphate to glucose-6-phosphate?
A)glucose-1-isomerase
B)glucokinase
C)glucose-1-phosphatase
D)phosphoglucomutase
E)glycogen phosphorylase
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Page 18
Chapter 17: Citric Acid Cycle
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Q1) Which of the following can be said about the isocitrate product of aconitase?
A)The product always has the R configuration.
B)The product always has the S configuration.
C)The product is not chiral.
D)The product can exist in either the R or S configuration in eukaryotes.
E)If the product is in the R configuration it has by passed the cis-aconitate intermediate.
Q2) Which of the following would decrease activity of the citric acid cycle overall?
(I)high concentration of NADH
(II)high concentration of Ca<sup>2+</sup>
(III)high concentration of ATP
(IV)high concentration of citrate
A)I only
B)I,II,III,IV
C)I,III
D)I,III,IV
E)I,IV
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Chapter 18: Electron Transport and Oxidative Phosphorylation
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Q1) The rate of oxidative phosphorylation (I)is regulated by the availability of ADP and P<sub>i</sub>. (II)is reduced when the ratio of [NADH]/[NAD<sup>+</sup>] is high. (III)increases with a higher concentration of reduced cytochrome c (IV)is regulated by activity of the ADP-ATP translocator.
A)I,II,IV
B)III,IV
C)II,III
D)I,III,IV
E)II,IV
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) Light-harvesting antennas gather photons and pass the energy to the ______ .
A) photosynthetic reaction center
B) tyrosyl radical
C) thylakoid
D) H<sub>2</sub>O
E) CF<sub>1</sub>CF<sub>0</sub>
F) Z-scheme
G) NADPH
H) plastoquinone
I) H<sup>+</sup>
J) RuBP carboxylase
K) CO<sub>2</sub>
L) 2 OH<sup> </sup>
M) O<sub>2</sub>
Q2) Which of the following is the site of ATP synthesis in chloroplasts?
A)smooth outer membrane
B)inner membrane space
C)stroma
D)thylakoid membrane
E)thylakoid compartment
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Page 21
Chapter 20: Lipid Metabolism
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Q1) Two phosphatidylglycerol molecules condense to form the molecule ______,and glycerol is eliminated as the side product.
A)phosphatidic acid
B)cardiolipin
C)plasmalogen
D)sphingomyelin
E)squalene
Q2) Which of the following compounds are required to make sphingosine?
(I)palmitoyl-CoA
(II)serine
(III)acetyl-CoA
(IV)isoprene
(V)arachidonic acid
A)I,II
B)I,III
C)II,IV
D)IV,V
E)II,V
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Chapter 21: Amino Acid Metabolism
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Q1) The neurotransmitters,dopamine,epinephrine,and norepinephrine are synthesized from the amino acid
A)tryptophan
B)tyrosine
C)glutamate
D)aspartate
E)lysine
Q2) Which of the following require a cyclic carbohydrate precursor for synthesis? (I)histidine
(II)alanine
(III)arginine
(IV)tyrosine
A)I,II
B)II only
C)I,III
D)I ,IV
E)II,IV
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Page 23
Chapter 22: Mammalian Fuel Metabolism: Integration and Regulation
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Q1) Phospholipase C cleaves PIP<sub>2</sub>,generating
A)IP<sub>3</sub> and DAG (inositol-1,4,5-trisphosphate and 1,2-diacylglycerol).
B)cAMP and PP<sub>i</sub>.
C)cAMP and DAG (1,2-diacylglycerol).
D)IP<sub>3</sub> and PP<sub>i</sub>.
E)IP<sub>3</sub> and P<sub>i</sub>.
Q2) Activation of AMPK activity is
A)accomplished by AMP induced conformational changes facilitating phosphorylation.
B)accomplished by ATP induced conformational change facilitating phosphorylation.
C)inhibited by high levels of AMP due to conformational changes burying the phosphorylation site.
D)increased by high levels of ATP due to conformational changes burying the phosphorylation site.
E)none of the above
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Chapter 23: Nucleotide Metabolism
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Q1) Acyclovir is a derivative of which of the following?
A)a pyrimidine
B)a purine
C)malonic semialdehyde
D)dihydrofolate
E)thioredoxin
Q2) Rank the additions to the rings in order of formation.
A)C,B,A,F,D,E
B)C,E,D,C,F,A,B
C)A,C ,D ,E ,F ,B
D)D,F,A,C,B,E
E)C,F,A,C,B ,E ,D
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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25
Chapter 24: Nucleic Acid Structure
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Q1) Heat-denatured DNA exhibits ______ UV absorbance,which is called the ______.
A)increased;hyperchromic effect
B)decreased;hyperchromic effect
C)increased;hypochromic effect
D)decreased;hypochromic effect
E)identical;renaturation effect
Q2) Indirect readout refers to
(I)a protein's ability to form hydrogen bonds through a network of water molecules. (II)the 5' to 3' sequence on the opposite strand of a DNA helix.
(III)a protein's ability to recognize a specific DNA sequence by its backbone conformation and flexibility.
(IV)the protein's ability to make hydrogen bonds with nonesterified phosphate oxygens
A)I,III,IV
B)II,IV
C)III,IV
D)I,III
E)I,IV
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Chapter 25: DNA Replication, repair and Recombination
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Q1) The process whereby nucleotides are removed from the 5' end of one DNA segment while nucleotides are added to the 3' end of the immediately preceding DNA segment is called ______.
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) What function is accomplished by snoRNAs?
A)spicing site recognition
B)capping of the mRNA
C)methylation of tRNAs
D)methylation of rRNA
E)splicosome catalytic site recognition
Q2) The phosphorylation of the CTD of RNA polymerase II is important for which phase of transcription?
A)initial binding of the promoter
B)conversion from the pre-initiation (closed)complex to the initiation (open)complex
C)progression from initiation to elongation
D)termination of transcription
E)none of the above
Q3) In eukaryotes all three RNA polymerases recognize
A)the promoter sequence bound by \(\sigma\) factor.
B)a single promoter sequence named TF II D.
C)class I promoters.
D)promoters with TATA boxes.
E)none of the above.
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Chapter 27: Protein Synthesis
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Q1) Which of the following is NOT a feature of tRNA structure?
A)acceptor or amino acid stem
B)D arm
C)anticodon loop
D)3' terminal phosphate arm
E)variable arm
Q2) 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
Q3) Which of the following is a ribonucleoprotein required for the delivery of membrane and secretory proteins to the endoplasmic reticulum?
A)protein-conducting channel (PCC)
B)small ubiquitin-related modifier (SUMO)
C)trigger factor
D)calnexin
E)signal recognition particles (SRP)
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Page 29
Chapter 28: Regulation of Gene Expression
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Q1) Hormone response elements
(I)are DNA segments that contain repeated sequences separated by several bases. (II)bind members of the nuclear receptor superfamily of proteins. (III)are highly conserved sequences found in prokaryotic and eukaryotic cells.
A)I,II,III
B)I,II
C)II,III
D)I,III
E)II only
Q2) Gene regulation by the JAK-STAT pathway relays signals initiated by
A)phosphorylated cytokines binding to hormone response elements.
B)steroids binding to steroid receptors inducing phosphorylation of tyrosine.
C)methylation of the SH2 domain.
D)bromodomain recruitment of coactivators.
E)ligand binding induced dimerization of cytokine receptor.
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