Molecular Biology Review Questions
Course Introduction
Molecular Biology is an in-depth exploration of the molecular mechanisms that govern the processes of life. This course examines the structure and function of nucleic acids and proteins, emphasizing the molecular basis of gene expression, replication, transcription, translation, and regulation. Students will gain insight into techniques such as cloning, PCR, gel electrophoresis, sequencing, and CRISPR gene editing. The course integrates both theoretical concepts and practical applications, highlighting how molecular biology advances research in genetics, medicine, and biotechnology.
Recommended Textbook
Organic Chemistry With Biological Applications 2nd Edition by John E. McMurry
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Chapter 1: Structure and Bonding
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Sample Questions
Q1) Instructions: Consider the two structures below to answer the following question.
CH<sub>3</sub>CH<sub>2</sub>OH CH<sub>3</sub>OCH<sub>3</sub>
Refer to instructions.Which of the following correctly describes the structure of these compounds?
A)All carbon atoms are sp<sup>3</sup> hybridized.
B)All of the bonds are sigma bonds.
C)Each oxygen atom has two nonbonding pairs of electrons.
D)The bond angle around each oxygen atom is ideally about 109.5<sup>\(\circ\)</sup>.
E)All of these
Answer: E
Q2) Instructions: Write valid Lewis (electron-dot)structures for each formula below.Show all electrons as dots and show all nonbonding electrons.
Write:
CH<sub>3</sub>CH<sub>2</sub>OH ethanol
Answer: 11ea7ca1_4b4f_0561_9d3f_35bab2410b8c_TB4938_00
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Chapter 2: Polar Covalent Bonds: Acids and Bases
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Sample Questions
Q1) Refer to instructions.The strongest Brønsted-Lowry base in the equation is indicated by letter _____. A)A
Answer: C
Q2) Refer to instructions.Indole can function as a Brønsted-Lowry acid in the presence of strong bases.Formulate a reaction,using a generic base (:B<sup>-</sup>),showing electron flow with arrows,that demonstrates this reactivity of indole.
Answer: 11ea7ca1_4b34_0341_9d3f_f787c2e12e2e_TB4938_00
Q3) Refer to instructions.Using the curved arrow formalism,show the flow of electrons for this reaction.
Answer: 11ea7ca1_4b34_033f_9d3f_cd711d6f2f17_TB4938_00
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Chapter 3: Organic Compounds: Alkanes and Their
Stereochemistry
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Sample Questions
Q1) One of the functional group classifications is characterized by the presence of an sp<sup>2</sup> hybridized carbon atom.This functional group could be:
A)alkyl halide
B)sulfide
C)alcohol
D)aldehyde
E)alkyne
Answer: D
Q2) The most stable conformation of an alkane occurs when
A)carbon-carbon bonds are staggered and bulky groups are gauche.
B)carbon-carbon bonds are staggered and bulky groups are anti.
C)carbon-carbon bonds are eclipsed and bulky groups are gauche.
D)carbon-carbon bonds are eclipsed and bulky groups are anti.
Answer: B
Q3) Refer to instructions.Draw a Newman projection of the anti conformation of 1,2-dichloroethane.
Answer: 11ea7ca1_4b29_2d1c_9d3f_3fc448576ec5_TB4938_00
Q4) Draw the structure of a five carbon ketone containing one tertiary carbon atom.
Answer: 11ea7ca1_4b29_060a_9d3f_9d00f5d6707c_TB4938_00
Page 5
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Chapter 4: Organic Compounds: Cycloalkanes and Their
Stereochemistry
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Sample Questions
Q1) Which of the following cycloalkanes has the most ring strain?
A)cyclopropane
B)cyclobutane
C)cyclopentane
D)cyclohexane
Q2) Substitution of which of the following groups on a cycloalkane would result in the greatest amount of steric strain?
A)bromo
B)ethyl
C)isopropyl
D)hydroxyl
Q3) In cycloheptane,which of the following factors contributes the least to the stability of the ring conformation?
A)torsional strain
B)angle strain
C)steric strain
D)all of these contribute to an approximately equal degree
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Chapter 5: Stereochemistry at Tetrahedral Centers
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Q1) (-)-cholesterol
A)does not have a chiral center.
B)is dextrorotatory.
C)rotates the plane of polarized light counterclockwise.
D)does not rotate polarized light.
Q2) Which of the following has a plane of symmetry?
A)boot
B)laboratory beaker
C)hammer
D)both b and c
E)none of these
Q3) Refer to instructions.The configuration of this carbon atom is _____.
Q4) Refer to instructions.The configuration of this carbon atom is _____.
Q5) Rank the following substituent groups from highest to lowest priority according to the sequencing rules.
CO<sub>2</sub>CH<sub>3</sub> CO<sub>2</sub>H OH Cl
Q6) Refer to instructions.Does streptimidone have a meso stereoisomer? Explain.
Q7) Refer to instructions.Assign R or S configuration to each chirality center indicated in streptimidone.
Page 7
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Chapter 6: An Overview of Organic Reactions
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Sample Questions
Q1) Refer to instructions.The forward and reverse reactions are classified,respectively,as:
A)addition,elimination
B)elimination,substitution
C)elimination,addition
D)elimination,rearrangement
E)substitution,addition
Q2) Refer to instructions.Add curved arrows to indicate electron flow in the first step.
Q3) Refer to instructions.Label the nucleophile,Nu,and the electrophile,E<sup>+</sup>,in the blanks provided under the structures.
Q4) In an organic reaction,which of the following is most likely to function as only a nucleophile?
A)BF<sub>3</sub>
B)(CH<sub>3</sub>)<sub>2</sub>CH<sub>2</sub>NH<sub>2</sub> C)Fe<sup>2+</sup>
D)CH<sub>3</sub>CH<sub>2</sub>S<sup>-</sup>
E)both a and c
Q5) Identify and predict: mustard gas
Cl-CH<sub>2</sub>CH<sub>2</sub>-S-CH<sub>2</sub>CH<sub>2</sub>-Cl
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Chapter 7: Alkenes and Alkynes
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Sample Questions
Q1) Which of the following substituents has the highest priority according to the Cahn-Ingold-Prelog system?
A)-COOH
B)-CHO
C)-CH<sub>2</sub>OH
D)-CH<sub>3</sub>
Q2) A compound with the following molecular formula contains two double bonds.What is the correct subscript for H in the formula?
C<sub>10</sub>H<sub>?</sub>ClN<sub>2</sub>O
A)19
B)22
C)18
D)20
E)21
Q3) Refer to instructions.Calculate the degree of unsaturation for Dieldrin.
Q4) Draw:
(3E)-3,7-dimethylocta-1,3,6-triene
Q5) Refer to instructions. Draw the cis and trans isomers of pent-2-ene and label them.
Q6) Refer to instructions.How many double bonds does dieldrin have?
Page 9
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Chapter 8: Reactions of Alkenes and Alkynes
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Sample Questions
Q1) What type of reaction mechanism accounts for the reaction of an alkyne with HBr to give an alkyl bromide?
A)nucleophilic addition
B)electrophilic addition
C)radical addition
D)elimination
Q2) Refer to instructions.Write the complete reaction mechanism for the first step of this reaction sequence.Show all electron flow with arrows and show all intermediate structures.
Q3) Refer to instructions. The reaction mixture would contain a majority of which isomeric product?
Q4) Which set of reagents is used for the Markovnikov addition of water to an alkene without rearrangement?
A)BH<sub>3</sub>,THF followed by H<sub>2</sub>O<sub>2</sub>,NaOH
B)H<sub>2</sub>O,H<sub>2</sub>SO<sub>4</sub>
C)Hg(O<sub>2</sub>CCH<sub>3</sub>)<sub>2</sub>,H<sub>2</sub>O followed by NaBH<sub>4</sub>,NaOH
D)none of these
Q5) Refer to instructions.Which product is the Markovnikov product?
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Chapter 9: Aromatic Compounds
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Q1) Which of the following is a correct statement regarding electrophilic aromatic substitution?
A)The carbocation intermediate will lose a proton to regain aromaticity,usually from a position other than the site of electrophilic attack.
B)Formation of the carbocation intermediate has a high activation barrier due to loss of aromaticity.
C)The carbocation intermediate has several resonance structures and is negatively charged.
D)Re-formation of the aromatic ring has a low activation barrier and therefore occurs slowly.
E)Many suitable electrophiles are unreactive and can be stored for long periods of time prior to use.
Q2) Which of the following undergoes the most rapid acylation upon treatment with acetyl chloride and AlCl<sub>3</sub>?
A)benzene
B)toluene
C)chlorobenzene
D)1,4-dichlorobenzene
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Chapter 10: Structure Determination: Mass
Spectrometry,infrared Spectroscopy,and Ultraviolet Spectroscopy
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Sample Questions
Q1) Refer to instructions.Propose structures for fragment ions at m/z = 57,43,and 29.
Q2) Examining the infrared spectrum of a compound allows us to:
A)determine the types of functional groups present in the compound
B)determine the carbon-hydrogen framework of the compound
C)determine the molecular weight of the compound
D)determine the nature of the conjugated pi electron system in the compound
Q3) Which of the following bonds undergoes stretching at the highest frequency?
A)O-H
B)C-H
C)C=O
D)CºC
Q4) The amount of energy in infrared light corresponds to:
A)the amount of energy needed to promote one electron from a bonding to an antibonding molecular orbital
B)the amount of energy needed to fragment a molecule
C)the amount of energy needed to strip a molecule of one electron to generate a cation radical
Page 12
D)the amount of energy needed to increase certain molecular motions,such as bond vibrations,in organic molecules
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Chapter 11: Structure Determination: Nuclear Magnetic
Resonance Spectroscopy
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Sample Questions
Q1) Which of the following combinations of peaks appears in the <sup>1</sup>H NMR spectrum of diethyl ether,CH<sub>3</sub>CH<sub>2</sub>OCH<sub>2</sub>CH<sub>3</sub>?
A)a triplet and a doublet
B)a quartet and a sextet
C)two singlets
D)a triplet and a quartet
Q2) Refer to instructions.What is the ratio of peak areas upon integration of the spectrum for A,B,and C respectively?
A)3:1:3:3
B)1:1:6
C)1:2:6
D)3:1:6
Q3) How many signals appear in the broadband-decoupled <sup>13</sup>C NMR spectrum of 1,3-dibromobenzene?
A)1
B)2
C)3
D)4
Q4) Refer to instructions.Propose a structure for this compound.
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Chapter 12: Organohalides: Nucleophilic Substitutions and Eliminations
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Q1) Which of the following statements about an S<sub>N</sub>1 reaction is true?
A)the reaction occurs in one-step
B)there is no effect on reaction rate by nucleophile
C)primary alkyl halides react faster than secondary alkyl halides
D)the reaction proceeds with inversion of stereochemistry
E)the reaction is favored by aprotic solvents
Q2) Refer to instructions.Compound C is the:
A)S<sub>N</sub>2 product
B)S<sub>N</sub>1 product
C)E2 product
D)E1 product
Q3) Refer to instructions.The mechanism for this reaction is:
A)S<sub>N</sub>2
B)E2
C)S<sub>N</sub>1
D)E1
Q4) Refer to instructions.Draw a Newman projection of the reactive conformation of the starting material.
Page 14
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Chapter 13: Alcohols,phenols,and Thiols: Ethers and Sulfides
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Sample Questions
Q1) Refer to instructions.Mechanistically,the Williamson ether synthesis outlined above is:
A)an E1 process
B)an S<sub>N</sub>1 process
C)an E2 process
D)an S<sub>N</sub>2 process
Q2) Which of the following is probably the least useful in IR characterization of a compound?
A)phenol: 3500 cm<sup>-1</sup>
B)alcohol: 3500 cm<sup>-1</sup>
C)phenol: 1500-1600 cm<sup>-1</sup>
D)ether: 1050-1150 cm<sup>-1</sup>
E)all of these are about equally useful
Q3) Refer to instructions.The conversion of an alcohol into an alkyl chloride by reaction with SOCl<sub>2</sub> is an example of:
A)an E1 process
B)an S<sub>N</sub>1 process
C)an E2 process
D)an S<sub>N</sub>2 process
Q4) Refer to instructions.Provide the IUPAC name for the product alcohol.
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Chapter 14: Aldehydes and Ketones: Nucleophilic Addition
Reactions
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Sample Questions
Q1) Refer to instructions.This reaction is called a(n)_____ reaction.
A)conjugate addition.
B)electrophilic addition.
C)direct addition
D)1,2-addition.
Q2) Refer to instructions.Calculate the degree of unsaturation for this compound.
Q3) Refer to instructions.The electrophile,the nucleophile and the catalyst in this reaction are indicated by letters _____,_____,and _____,respectively.
A)A
B)B
C)C
D)D
Q4) Refer to instructions.What functional group is indicated by the IR data?
Q5) Many nucleophilic addition reactions of aldehydes and ketones are catalyzed by acid or base.Bases catalyze hydration by:
A)making the carbonyl group more electrophilic
B)shifting the equilibrium of the reaction
C)making the carbonyl group less electrophilic
D)converting the water to hydroxide ion,a much better nucleophile
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Chapter 15: Carboxylic Acids and Nitriles
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Sample Questions
Q1) Refer to instructions.This compound is known to contain both a -C=O group and an -OH group.Based on this spectrum,this compound would be classified as:
A)aromatic carboxylic acid
B)aliphatic carboxylic acid
C)carbonyl containing an alcohol functional group
D)either a or b
Q2) Which of the following is the correct order of decreasing acid strength (more acidic > less acidic)?
A)FCH<sub>2</sub>COOH > CH<sub>3</sub>COOH > F<sub>2</sub>CHCOOH
B)FCH<sub>2</sub>COOH > CH<sub>3</sub>COOH > CH<sub>3</sub>OH
C)CH<sub>3</sub>CH<sub>2</sub>OH > ClCH<sub>2</sub>COOH > BrCH<sub>2</sub>COOH
D)CH<sub>3</sub>COOH > ClCH<sub>2</sub>COOH > CH<sub>3</sub>OH
Q3) Draw the structure of (Z)-4-methylhex-3-enoic acid.
Q4) Refer to instructions.This reaction can be described as a _____ process.
A)carbonylation
B)carboxylation
C)carbaniolation
D)cationation
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Chapter 16: Carboxylic Acid Derivatives: Nucleophilic Acyl
Substitution Reactions
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Sample Questions
Q1) Refer to instructions.Compound C functions as _____ in this reaction.
A)a base scavenger
B)a solvent
C)a catalyst
D)a neutralizer
Q2) Of the following,which represents a possible direct conversion of the reactant to product shown?
A)ester to acid chloride
B)thioester to acid anhydride
C)ester to amide
D)acid anhydride to acid chloride
Q3) Refer to instructions.This reaction is an example of:
A)an intermolecular nucleophilic acyl substitution reaction
B)an intramolecular nucleophilic acyl substitution reaction
C)an intermolecular S<sub>N</sub>2 reaction
D)an intramolecular S<sub>N</sub>2 reaction
Q4) Refer to instructions.Write the complete stepwise mechanism for this reaction.Show intermediate structures and all electron flow with arrows.
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Chapter 17: Carbonyl Alpha-Substitution and Condensation Reactions
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Sample Questions
Q1) Which of the following would form an enol on treatment with an acid?
A)4-chlorobenzaldehye
B)2,2,-dimethylbutanal
C)2,2,4,4-tetrachlorohexan-3-one
D)none of these
Q2) Which of the following is common to both tautomers and resonance forms of a compound?
A)have the same molecular formula
B)differ only in the position of electrons
C)rapidly interconvertible
D)differ in connectivity of atoms
E)all of these describe both tautomers and resonance forms
Q3) The common feature of a-substitution and condensation reactions of carbonyl groups:
A)involve two carbonyl partners
B)involve the formation of an enol or enolate ion
C)involve a nucleophile
D)produce a new carbon to carbon bond
E)all of these describe both types of reactions
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Q4) How would you prepare 3-phenylpropanoic acid using a malonic ester synthesis?
Chapter 18: Amines and Heterocycles
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Q1) Refer to instructions.Based on the pK<sub>a</sub>s for their corresponding ammonium ions,which arylamine above is the strongest base?
Q2) The pK<sub>a</sub> of the 4-methoxyanilinium ion is 5.34.What is the pK<sub>b</sub> for 4-methoxyaniline?
Q3) The pK<sub>a</sub> of aniline is 6.15.What percent exists in the neutral and protonated forms in a 0.00100 M solution of aniline at pH 5.75?
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Chapter 19: Biomolecules: Amino Acids,peptides,and
Proteins
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Q1) An enzyme classified as a ligase would be associated with a reaction than involves the:
A)introduction of a double bond.
B)loss of water.
C)loss of carbon dioxide.
D)transfer of an amino group.
E)hydrolysis of an ester.
Q2) Which of the following reagents can be used to cleave a tert-butoxycarbonyl (Boc)protecting group from a peptide?
A)H<sub>2</sub>/Pd
B)CF<sub>3</sub>CO<sub>2</sub>H
C)Na<sub>2</sub>CO<sub>3</sub>,H<sub>2</sub>O
D)LiAlH<sub>4</sub>
Q3) Refer to instructions.What fragments would result if dynorphin were cleaved by chymotropsin?
Q4) To what structural feature does the term "tertiary structure" refer?
A)the sequence of amino acids in proteins
B)the overall folding pattern of proteins
C)the aggregation of polypeptides
D)the conformation of local regions of polypeptides
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Chapter 20: Amino Acid Metabolism
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Q1) 3-Phosphoglycerate contains the carbon skeleton used to make A)serine
B)cysteine
C)glycine
D)all of these
Q2) All of the following are metabolic intermediates of a-amino acid carbon skeletons except:
A)pyridoxine
B)a-ketoglutarate
C)oxaloacetate
D)succinyl-CoA
E)fumarate
Q3) The key functional group in the PLP-dependent transamination of an a-amino acid is an activated A)amine
B)imine
C)amide
D)enamine
Q4) Many biological reactions are endergonic.Explain how it is possible that these reactions occur spontaneously.
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Chapter 21: Biomolecules: Carbohydrates
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Q1) Refer to instructions._____ a dextrorotary hexose and ______ a levorototary tetrose.
Q2) Refer to instructions.Which anomer is the LEAST stable? Q or Z
Q3) Refer to instructions.Sorbose is ____________________.
Q4) Refer to instructions.Classify ribose by carbonyl type and number of carbons.
Q5) Refer to instructions.Assign R or S configuration to each chirality center in sorbose.
Q6) Refer to instructions._____ oxidizes to an optically inactive aldaric acid. A)a
Q7) Refer to instructions.Place a triangle around the anomeric carbon in compound Q.
Q8) Draw the Fisher projection of L-mannose.
Q9) Refer to instructions.Erythrulose is ____________________.
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Chapter 22: Carbohydrate Metabolism
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Q1) Gluconeogenesis differs from glycolysis because
A)it does not produce ATP
B)different enzymes are involved
C)biotin is required for gluconeogenesis and not for glycolysis
D)all of these
Q2) Glyceraldehyde-3-phosphate reacts with the SH group of a cysteine residue (abbreviated (Enz-SH))of a dehydrogenase to produce a hemithioaectal intermediate.Draw its structure.
Q3) The following reactions all occur during oxidative decarboxylation of pyruvate,except:
A)Removal of CO<sub>2</sub>.
B)Oxidation of an acetate group.
C)Addition of Coenzyme A to a 2-carbon fragment.
D)Reduction of NAD<sup>+</sup>
E)All of these reactions take place during oxidative decarboxylation.
Q4) When acetyl-CoA reacts with oxaloacetate to form citrate
A)a new carbon-carbon bond is formed
B)an oxidative decarboxylation reaction takes place
C)a dehydration reaction takes place
D)a rearrangement takes place
Page 24
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Chapter 23: Biomolecules: Lipids and Their Metabolism
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Q1) Which of the following is not true about cholesterol?
A)a steroid
B)a precursor for other steroids
C)produced from lanosterol
D)geometry allows for ring-flips
E)all of these are true
Q2) Cell membranes,which form an effective barrier to the passage of ions and other components into and out of the cell,are:
A)fatty acid esters
B)tricacylglycerols
C)lipid bilayers
D)micelles
Q3) When soaps disperse in water,the long hydrocarbon tails cluster together in a hydrophobic ball,while the ionic heads on the surface of the cluster stick out into the water.These spherical clusters are called:
A)fatty acid esters
B)triacylglycerols
C)lipid bilayers
D)micelles
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Chapter 24: Biomolecules: Nucleic Acids and Their Metabolism
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Q1) What mRNA sequence is complementary to the following DNA base sequence? (5')TAAGGCGATA (3')
Q2) How many hydrogen bonds are present in a G-C base pair and an A-T base pair,respectively?
A)1,2
B)2,2
C)2,3
D)3,2
E)3,3
Q3) What is the anticodon sequence in tRNA that corresponds the following segment of mRNA? (5')CUU-AGC-UGG-CCC(3')
Q4) Which of the following characterizes the polymerase chain reaction (PCR)?
A)produces multiple copies of DNA segments
B)requires small amount of the source DNA
C)the key to the process is a thermally stable enzyme
D)involves temperature cycling
E)all of these
Page 26
Q5) Describe,in general terms,the steps involved in the automated synthesis of the DNA sequence GCT.
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