Course Introduction
Biological Chemistry
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Biological Chemistry explores the chemical principles underlying biological systems, focusing on the structure, function, and interactions of biomolecules such as proteins, nucleic acids, carbohydrates, and lipids. Students learn about enzymatic mechanisms, metabolic pathways, bioenergetics, and the regulatory processes that sustain life at the molecular level. Through a combination of theoretical concepts and practical laboratory techniques, the course provides insights into how chemical processes drive cellular functions and highlights the importance of chemistry in understanding and manipulating biological systems.
Recommended Textbook
Fundamentals of Biochemistry Life at the Molecular Level 5th Edition by Donald Voet
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Page 2
Chapter 1: Introduction to the Chemistry of Life
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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) The \(\Delta\)G° for the conversion of glucose 6-phosphate (G6P)to fructose 6-phosphate (F6P)is +1.7 kJ/mole.In a particular human cell the concentration G6P is 8.0 µM and the concentration F6P is 1.0 µM.Calculate the \(\Delta\)G of the reaction as it occurs in this cell at 37°C?
A) 37 kJ/mol
B) 3.7 kJ/mol
C)0 kJ/mol
D)+7.1 kJ/mol
E) 0.6 kJ/mol
Answer: B
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3
Chapter 2: Water
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Q1) The polarity of the O-H bond is caused by the ______ of oxygen relative to that of hydrogen.
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: I
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Chapter 3: Nucleotides, nucleic Acids, and Genetic Information
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Q1) Inside our cells,free nucleotides are almost always associated with ______. A)proteins
B)cholesterol
C)Cl<sup> </sup> counterions
D)fatty acids
E)Mg<sup>2+</sup> counterions
Answer: E
Q2) Small circular DNA molecules used to carry foreign DNA fragments are called
A)mRNAs
B)bacteriophage
C)clones
D)plasmids
E)nucleotides
Answer: D
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Chapter 4: Amino Acids
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Q1) When a peptide bond is formed,an ______ reacts with a carboxylate group.
A) glutamate
B) uncharged
C) deprotonated
D) three
E) amino group
F) two
G) C-terminus
H) lysine
I) racemic mixture
J) cysteine
K) zero
L) protonated
M) isoleucine
N) tryptophan
O) phenylalanine
P) N-terminus
Q2) 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) The endoprotease ______ cleaves polypeptides on the C-terminal side of certain bulky hydrophobic amino acid residues.
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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Q1) Which of the following contribute to the minimization of energy that occurs with protein folding?
A)orientating amino acid groups to maximize hydrogen bonding
B)folding hydrophobic groups towards the exterior of the protein
C)burying polar groups towards the interior of the protein
D)extensive cavity formation
E)all of the above
Q2) Which one of these characteristics is not true for the \(\alpha\) helix?
A)There are 3.6 amino acids per turn.
B)There is a requirement for glycine every third amino acid residue.
C)A hydrogen bond forms between the carbonyl oxygen of the nth amino acid residue and the - NH group of the (n + 4)th amino acid residue.
D)Proline is typically not found in the \(\alpha\) helix.
E)It is right-handed.
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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Chapter 7: Protein Function Part I: Myoglobin and Hemoglobin
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Q1) The Bohr effect refers to
A)the decrease in affinity of Hb for O<sub>2</sub> when the pH goes down
B)the decrease in affinity of Hb for O<sub>2</sub> when the pH goes up
C)the increase in the affinity of Hb for O<sub>2</sub> when the O<sub>2</sub> concentration goes up
D)the decrease in affinity of Hb for O<sub>2</sub> when the BPG concentration goes up
E)the decrease in affinity of Hb for O<sub>2</sub> when the BPG concentration goes down
Q2) Myoglobin is an oxygen binding protein in muscle.Describe in one sentence the overall structure of myoglobin.
Q3) IgG is the most common immunoglobulin in the circulatory system and in the extravascular fluid.It is composed of two light chains and two heavy chains.What is the approximate molecular mass of an IgG molecule?
A)23 kDa
B)75 kDa
C)150 kDa
D)360 kDa
E)950 kDa
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Chapter 8: Carbohydrates
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Sample Questions
Q1) Which two sugars shown in the figure above are epimers?
A)A and B
B)B and C
C)C and D
D)A and D
E)None of the above
Q2) Which of the following is a disaccharide?
A)amylose
B)saccharin
C)aspartame
D)amylopectin
E)none of the above
Q3) Cellulose is
A)a linear copolymer of glucose and galactose.
B)a branched polymer of glucose.
C)a linear polymer of glucose with (1\(\to\)4)linkages.
D)a linear polymer of glucose with (1\(\to\)4)linkages.
E)sometimes called starch.
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Chapter 9: Lipids and Biological Membranes
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Sample Questions
Q1) Rank the melting points of the following fatty acids from highest to lowest:
(1) cis-oleic(18:1)
(2) trans-oleic (18:1)
(3) linoleic (18:2)
(4) steraic (18:0)
(5) palmitic (16:0)
A)1 > 2 > 3 > 5 > 4
B)4 > 5 > 2 > 1 > 3
C)4 > 5 > 3 > 2 > 1
D)5 > 4 > 2 > 1 > 3
E)none of the above
Q2) The _________ model describes the cell membrane as an assortment of integral proteins suspended freely in a lipid bilayer.
A)FRAP
B)cellular fusion
C)transverse diffusion
D)lateral diffusion
E)fluid mosaic
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11
Chapter 10: Membrane Transport
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Q1) Drug resistance is frequently traced to (I)the MDR transporter.
(II)overexpression of P-glycoprotein.
(III)increased number of specific ABC transporters.
(IV)the evolution of selectivity filters.
A)I,II,III
B)II,III
C)I,III
D)III,IV
E)II,IV
Q2) Vanilomycin
A)is a cyclic polypeptide that functions as a K<sup>+</sup> carrier.
B)is a transmembrane polypeptide that transports K<sup>+</sup>.
C)is a cyclic polypeptide that functions as a Na<sup>+</sup> carrier.
D)is a transmembrane polypeptide that transports Na<sup>+</sup>.
E)is a \(\beta\)-barrel pore transporter that transfers K<sup>+</sup>.
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Chapter 11: Enzyme Catalysis
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Q1) Metal ion cofactors can coordinate to the substrate or stabilize electrostatic effects by enabling proper ______in the active site.
A) high
B) deprotonated
C) protonated
D) catalytic mechanism
E) covalent
F) rate-determining step
G) leaving group
H) formation of ES
I) amino acid
J) low
K) coenzymes
L) concerted acid-base
M) orientation
N) oxidation
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Chapter 12: Enzyme Kinetics, inhibition and Control
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Q1) A compound that distorts the active site,rendering the enzyme catalytically inactive is called
A)a uncompetitive inhibitor
B)an allosteric effector
C)an inactivator
D)a competitive inhibitor
E)none of the above
Q2) 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.
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Page 14
Chapter 13: Biochemical Signaling
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Q1) Isoproterenol functions as an agonist for receptors that bind hormones synthesized in the ___.
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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Q1) 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.
Q2) Which of the following is (are)true regarding vitamins? (I)They are essential organic molecules an organism is unable to synthesize. (II)Some water soluble vitamins mediate electron-transfer reactions. (III)In humans,the water soluble vitamins converted into organic coenzymes.
IV)In humans,the fat soluble vitamins mediate group transfer reactions.
A)I,II,III,IV
B)I,II,III
C)II,III,IV
D)I only
E)II,IV
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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) 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.
Q3) During glycolysis,the steps between glucose and formation of the triose phosphates collectively
A)consume two ATP and two NADH molecules.
B)consume two ATP molecules.
C)produce two ADP and two NADH molecules.
D)produce two ATP and two NAD<sup>+</sup> molecules.
E)consume two NAD<sup>+</sup> molecules.
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Chapter 16: Glycogen Metabolism and Gluconeogenesis
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Q1) 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.
Q2) Which of the following is true regarding the reaction shown below?
Pyruvate + HCO<sub>3</sub><sup> </sup> + ATP \(\to\) oxaloacetate + ADP + P<sub>i</sub>
(I)It requires the direct transport of oxaloacetate across the membrane.
(II)It utilizes the malate-aspartate shuttle in some species.
(III)It is essential for gluconeogenesis.
(IV)Its reactants require the function of enzymes which are only found in the cytosol.
A)I only
B)II,III
C)II,III,IV
D)III only
E)II,IV
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Page 18
Chapter 17: Citric Acid Cycle
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Q1) The reaction catalyzed by pyruvate carboxylase is an example of a(n)______ reaction because it replenishes the citric acid cycle intermediates that have been siphoned off for use in other reactions.
A)amphibolic B)amphipathic C)anaplerotic D)cataplerotic E)none of the above
Q2) 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"
Q3) Which reaction below produces GTP in the citric acid cycle?
A)"isocitrate \(\to\) \(\alpha\)-ketoglutarate"
B)"\(\alpha\)-ketoglutarate \(\to\) succinyl CoA"
C)"succinyl CoA \(\to\) succinate"
D)"fumarate \(\to\) malate"
E)"malate \(\to\) oxaloacetate"
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Chapter 18: Electron Transport and Oxidative
Phosphorylation
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Q1) Consider the following half-reactions: \(\varepsilon\)<sup>o</sup>' = -0.315 V NAD<sup>+</sup> + H<sup>+</sup> + 2 e<sup>-</sup> \(\leftrightarrow\) NADH \(\varepsilon\)<sup>o</sup>' = 0.815 V 1/2 O<sub>2</sub> + 2 H<sup>+ </sup>+ 2 e<sup>- </sup>\(\leftrightarrow\) H<sub>2</sub>O What is the \(\varepsilon\)<sup>o</sup>'for the following redox equation? O<sub>2</sub> + 2 NADH + 2 H<sup>+ </sup> \(\to\) 2 H<sub>2</sub>O + 2 NAD<sup>+</sup>
A)-1.130 V
B)-0.500 V
C)+0.500 V
D)+1.130 V
E)none of the above
Q2) The structure of ATP synthase changes in conformation as a result of
A)the rotation of the and subunits.
B)the rotation of the subunit.
C)the rotation of ATP.
D)the rotation of the \(\gamma\) subunit.
E)all of the above.
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Chapter 19: Photosynthesis
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Q1) Which of the following statements about the OEC is FALSE? (I)It is located at the lumenal surface of the D1 subunit (II)It has a low reduction potential in all states (III)It contains Mn<sub>4</sub>CaO<sub>4</sub> or Mn<sub>4</sub>CaO<sub>5</sub> (IV)Part of the cluster is liganded to the amino acids Asp and Glu
A)II,III
B)II only
C)III only
D)II,IV
E)Ii,III
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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Chapter 20: Lipid Metabolism
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Q1) 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
Q2) Knoop's experiments with fatty acids
A)involved the novel use of chemical labels to elucidate metabolic mechanisms.
B)demonstrated that fatty acids are broken down by two carbons at a time by oxidation at the carbon.
C)demonstrated a distinct difference in the mechanism of odd chain versus.even chain fatty acid oxidation.
D)A and B
E)A,B,and C
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Page 22
Chapter 21: Amino Acid Metabolism
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Q1) Which of the following is(are)advantages to the constant degradation and reformation of proteins?
A)Nutrients can be stored as proteins,which can be used during periods of metabolic need.
B)Damaged proteins are eliminated so they do not accumulate.
C)Metabolism can be efficiently regulated by the synthesis and degradation of enzymes.
D)All of the above are advantages.
E)None of the above is an advantage.
Q2) The aminotransferase reaction,in which an enzyme-PLP Schiff base forms, (I)is ATP dependent.
(II)results in formation of a hydroxylaldehyde.
(III)results in formation of an \(\alpha\)-ketoacid.
(IV)requires an active site lysine.
A)I,III,IV
B)I,IV
C)II,III
D)I,II,III
E)II,III,IV
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Page 23
Chapter 22: Mammalian Fuel Metabolism: Integration and Regulation
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Q1) Which of the following statements concerning the response of hepatocytes to insulin is FALSE?
A)Phosphorylase kinase is inactivated,decreasing glycogenolysis.
B)Glycogen synthase is activated.
C)Transcription of glucokinase increases.
D)Glucose uptake is increased in the liver.
E)The liver stores glucose as glycogen or triacylglycerols.
Q2) Which of the following are characteristics of metabolic syndrome?
(I)insulin resistance
(II)inflammation
(III)increased risk for type 1 diabetes.
(IV)hypersensitivity to insulin
A)I,II
B)I,II,III
C)I,II,III,IV
D)I,III
E)I only
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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) The amino group added to the C2 position on IMP to form GMP is derived from A)"aspartate"
B)"aspargine"
C)"glutamine"
D)"\(\alpha\)-ketoglutarate"
E)"arginine"
Q3) The first step in pyrimidine biosynthesis is the formation of A)carbamoyl phosphate.
B)carbamoyl aspartate.
C) -aminoisobutyrate.
D)dihydroorotate.
E)none of the above
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Chapter 24: Nucleic Acid Structure
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Q1) _________ topoisomerases that make double-strand breaks in DNA in a controlled fashion.
A) type I
B) ribocatalyzers
C) C2´-endo
D) repressors
E) ethidium
F) type II
G) C3´-endo
H) hybridized
I) interchanged
J) supercoiled
K) cooperative
L) non-cooperative
M) underwound
N) ribozymes
O) deuterium
P) zinc finger
Q) leucine zipper
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26
Chapter 25: DNA Replication, repair and Recombination
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Q1) Enzymes that undergo many rounds of polymerization catalysis before dissociating from the substrate are described as highly ______.
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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Page 27
Chapter 26: Transcription and Rna Processing
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Q1) 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.
Q2) Which of the following is correct regarding splicing?
A)CPSFs are products of RNA sequences designed to recognize the 3'OH at the splice site.
B)PABIII recognizes the A rich sequences at the 5' end of the splice site.
C)Lariats are the sequence recognized by the cleavage site.
D)smURFs are used to recognize the poly A tail and initiate slicing
E)snRNPs are the protein product of U rich RNAs that partially complement the 5' splice junction.
Q3) In eukaryotes,which of the following would decrease the rate of transcription?
A)mutation in the nucleotide sequences at 10 and 35
B)mutation in the nucleotide sequences at 10 and +5
C)mutation in the nucleotide sequences at 70 and 90
D)mutation at the \(\sigma\) binding site
E)all of the above
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Page 28
Chapter 27: Protein Synthesis
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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) Polypeptide synthesis
A)proceeds from the C-terminus to the N-terminus.
B)proceeds from the N-terminus to the C-terminus.
C)proceeds in both directions simultaneously.
D)proceeds in either direction once initiated.
E)proceeds randomly.
Q3) Codons that do not specify amino acids but signal the ribosome to terminate polypeptide chain elongation are termed A)frameshifts.
B)anticodon.
C)Stop codons.
D)suppressors.
E)terminators.
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Page 29
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) In prokaryotes,which of the following are effective at controlling gene expression relative to the concentration of a metabolite or catabolite?
(I)CAP or CRP
(II)long terminal repeats (LTRs)
(III)riboswitches
(IV)SWI/SNF
A)I,II,III,IV
B)I,II,III
C)I,III
D)II,IV
E)III,IV
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30