Question 1

HIV reverse transcriptase — Identify the function it explicitly lacks (consider template use, directionality, and primer requirement)

Accepted Answer

Introduction: HIV reverse transcriptase is a hallmark enzyme of retroviruses that converts viral RNA into DNA. This question tests detailed conceptual understanding of which activities the enzyme has and, critically, which activity it does not possess, because that absence explains HIV’s high mutation rate. Given Data / Assumptions: The enzyme uses viral RNA as a template to synthesize DNA. Reverse transcriptase works with a primer (typically a host tRNA). Polymerization occurs in the 5' to 3' direction like other DNA polymerases. Proofreading activity would mean 3' to 5' exonuclease activity that removes misincorporated nucleotides. Concept / Approach: Reverse transcriptase has two main catalytic functions: RNA dependent DNA polymerase and RNase H (degrades RNA in RNA–DNA hybrids). It lacks the canonical 3' to 5' exonuclease proofreading found in many high-fidelity DNA polymerases. This deficiency leads to frequent replication errors and rapid viral evolution. Step-by-Step Solution: Confirm template usage: the enzyme synthesizes cDNA from RNA → true.Confirm directionality: nucleotide addition occurs 5' to 3' → true.Confirm primer requirement: a preexisting 3'-OH (from tRNA or DNA primer) is necessary → true.Assess proofreading: lacks 3' to 5' exonuclease activity → therefore, this is the function it does not have. Verification / Alternative check: Error rates measured for reverse transcriptase are much higher than for replicative DNA polymerases, consistent with no 3' to 5' proofreading. Antiretroviral drugs like nucleoside reverse transcriptase inhibitors exploit the enzyme’s active site chemistry and primer dependence but do not confer proofreading. Why Other Options Are Wrong: Uses RNA as a template: correct; fundamental to reverse transcription. Has 5' to 3' polymerase activity: correct; all DNA synthesis proceeds 5' to 3'. Requires a primer: correct; the enzyme cannot initiate de novo synthesis. Can synthesize cDNA from RNA: restates its core function. Common Pitfalls: Assuming all polymerases proofread. Many specialized polymerases, especially reverse transcriptases, sacrifice fidelity for function, accelerating viral diversity. Final Answer: Has 3' to 5' exonuclease proofreading activity.

Question 2

Restriction enzymes — After EcoRI cleaves DNA at its recognition site, which ends are generated on the products?

Accepted Answer

Introduction: Understanding the chemistry of restriction endonuclease cleavage is essential for cloning. EcoRI is a classic type II enzyme that generates sticky ends. This question checks your knowledge of the terminal groups produced during the cut. Given Data / Assumptions: EcoRI recognizes a palindromic 6 bp site and makes staggered cuts. Phosphodiester bond cleavage leaves characteristic 5' and 3' termini. Sticky ends facilitate ligation into vectors with compatible overhangs. Concept / Approach: EcoRI cleaves to produce 5'-overhangs. For each break, the scissile phosphate remains attached to the 5' terminus, leaving a 5'-phosphate and a complementary 3'-hydroxyl on the opposing end. Across both strands, products present two 5'-phosphate ends and two 3'-OH ends poised for ligation by DNA ligase. Step-by-Step Solution: Recognize cleavage pattern: staggered cut with 5' overhangs.Assign chemical groups: cleavage yields 5'-phosphate and 3'-OH terminals.Account for both strands: two of each type across the duplex break.Therefore, the correct description is two 3'-OH ends and two 5'-phosphate ends. Verification / Alternative check: Ligation requires a 5'-phosphate and a 3'-OH. EcoRI-cut fragments can be directly ligated without additional phosphorylation because the necessary termini are already present. Why Other Options Are Wrong: Single 3'-OH and single 5'-phosphate: undercounts ends formed across both strands. 3'-phosphate ends: typical type II enzymes leave 5'-phosphate, not 3'-phosphate. Blunt ends: EcoRI makes sticky 5' overhangs, not blunt ends. One 3'-OH and two 5'-phosphate: mismatched stoichiometry. Common Pitfalls: Confusing the nature of sticky vs blunt ends and which terminus bears the phosphate after type II restriction enzyme cleavage. Final Answer: Two 3'-OH ends and two 5'-phosphate ends.

Question 3

Protein–nucleic acid interactions — Which amino acids most commonly engage the DNA/RNA phosphate backbone via electrostatic attraction?

Accepted Answer

Introduction: Phosphate groups on nucleic acids are negatively charged. Proteins use basic side chains to contact this backbone and stabilize complexes. This question asks which residues most typically make those interactions. Given Data / Assumptions: DNA and RNA backbones are rich in negatively charged phosphates. Electrostatics guide initial association in many complexes. Side chain chemistry determines interaction preferences. Concept / Approach: Lysine (ε-amino) and arginine (guanidinium) are positively charged at physiological pH. Their long, flexible side chains form strong ionic and hydrogen bond contacts with phosphate oxygens, explaining their enrichment at nucleic acid binding interfaces. Step-by-Step Solution: Identify charge complementarity: negative phosphate ↔ positive side chains.Compare side-chain properties: Lys and Arg are basic; Ile, Val, Leu, Ala are hydrophobic; Cys and Met are sulfur-containing but not strongly basic.Therefore, Lys and Arg are the best matches for phosphate backbone binding. Verification / Alternative check: Sequence logos and structural analyses of DNA binding domains (e.g., helix–turn–helix, zinc fingers) show overrepresentation of Lys/Arg facing the backbone. Why Other Options Are Wrong: Ile/Val and Leu/Ala: nonpolar; prefer hydrophobic cores rather than anionic phosphate contact. Cys/Met: can coordinate metals or form disulfides (Cys) but are not typically used for phosphate neutralization. Phe/Trp: aromatic and hydrophobic; may stack with bases but not primarily backbone contacts. Common Pitfalls: Confusing base-stacking or base-specific contacts with backbone neutralization; the latter is mainly the role of basic residues. Final Answer: Lys and Arg.

Question 4

Type II restriction endonucleases — How do they recognize and bind their DNA sites?

Accepted Answer

Introduction: Type II restriction endonucleases are essential tools for DNA manipulation. Their high specificity arises from precise DNA recognition and binding strategies. This question reviews the key features of that recognition. Given Data / Assumptions: Type II enzymes cut within or near their recognition sites. Recognition often involves symmetric sequences. Binding includes both base-specific and backbone contacts. Concept / Approach: Most type II enzymes recognize short palindromic sequences and achieve specificity through networks of hydrogen bonds with base edges in the major or minor groove. At the same time, non-sequence-specific interactions with the sugar–phosphate backbone stabilize the complex and aid docking and catalysis. Step-by-Step Solution: Sequence pattern: many sites are palindromic, reflecting dimeric enzyme symmetry.Specificity mechanism: hydrogen bonds read base identity.Stabilization: additional ionic/backbone contacts position DNA for cleavage.Therefore, the most complete answer is 'All of the above'. Verification / Alternative check: Crystal structures (e.g., EcoRI–DNA) show direct H-bonding to bases plus contacts to the phosphate backbone, and palindromic recognition consistent with dimer binding. Why Other Options Are Wrong: Picking any single feature alone is incomplete; enzymes typically use all listed strategies. Nonpalindromic, AT-only tracts: not a general rule for type II enzymes. Common Pitfalls: Assuming specificity derives only from base contacts; backbone interactions and DNA bending also contribute significantly to catalysis. Final Answer: All of the above.

Question 5

DNA end joining — The enzyme that seals nicks and joins DNA fragments is called what?

Accepted Answer

Introduction: DNA manipulation often requires sealing phosphodiester backbone breaks. The canonical enzyme used in cloning and in vivo repair is being asked for here. Given Data / Assumptions: Nick sealing requires a 5'-phosphate and a 3'-OH. ATP (or NAD+ in some ligases) provides energy for ligation. Enzyme must catalyze phosphodiester bond formation. Concept / Approach: DNA ligases form a ligase–AMP intermediate and transfer AMP to the 5'-phosphate, activating the end for nucleophilic attack by the 3'-OH, thus sealing the nick. In cloning, T4 DNA ligase is standard; cells have their own ligases for replication and repair. Step-by-Step Solution: Identify function: join DNA ends by creating a phosphodiester bond.Match to enzyme class: ligases catalyze bond formation with energy input.Exclude look-alikes: reverse transcriptase copies RNA to DNA; phosphorylase removes/attaches phosphates differently; topoisomerase alters supercoiling.Thus, the correct enzyme name is DNA ligase. Verification / Alternative check: Standard cloning protocols rely on T4 DNA ligase to join cohesive or blunt ends, confirming the role and nomenclature. Why Other Options Are Wrong: Joinase: not a standard enzyme name. DNA phosphorylase: different catalytic role. Reverse transcriptase: polymerase activity, not ligation. Topoisomerase: cuts/reseals transiently to manage topology, not intended for permanent ligation of separate fragments. Common Pitfalls: Assuming any enzyme that touches DNA can join fragments; only ligases perform the final sealing step in cloning. Final Answer: Ligase.

Question 6

DNA synthesis polarity — All known DNA polymerases add dNTPs in which direction relative to the growing strand, and only to what type of primer end?

Accepted Answer

Introduction: Directionality is a fundamental rule of DNA synthesis. This question checks whether you know the universal polarity of DNA polymerases and the primer requirement that underlies replication and repair mechanisms. Given Data / Assumptions: DNA polymerases cannot start synthesis de novo. They extend from a primer with a free 3'-OH group. Nucleotide addition chemistry is conserved across life. Concept / Approach: Nucleotidyl transfer adds the alpha phosphate of an incoming dNTP to the 3'-OH of the primer, releasing pyrophosphate. This reaction can only proceed 5' to 3' along the newly synthesized strand, explaining leading and lagging strand asymmetry and the need for RNA primers in replication. Step-by-Step Solution: Identify the nucleophile: the primer 3'-OH attacks the dNTP alpha phosphate.Infer direction: growth proceeds by adding to the 3' end → synthesis is 5' to 3'.Primer requirement: a preexisting 3'-OH is mandatory; polymerases cannot start without it.Therefore, the correct statement is 5' to 3' synthesis onto a 3'-OH primer end. Verification / Alternative check: Okazaki fragment formation and replication fork architecture directly reflect this polarity: primase provides RNA primers; DNA polymerase extends 5' to 3' only. Why Other Options Are Wrong: 3' to 5' synthesis: not supported by known polymerase chemistry. Any end or no primer: contradicts the requirement for a 3'-OH primer. Organism dependent polarity: not observed; polarity is universal. Common Pitfalls: Confusing the reading of the template (3' to 5') with the direction of synthesis (5' to 3'). Final Answer: 5' to 3' direction, onto a preformed 3'-OH primer end.

Question 7

Base-specific contacts — Which amino acid side chains commonly hydrogen-bond directly to DNA/RNA bases?

Accepted Answer

Introduction: While basic residues often contact the phosphate backbone, base readout in the grooves relies on side chains capable of forming directional hydrogen bonds. This question focuses on amino acids frequently used for base-specific recognition. Given Data / Assumptions: DNA bases present hydrogen bond donors/acceptors in grooves. Protein side chains differ in polarity and H-bonding capacity. Specificity requires complementary H-bond patterns. Concept / Approach: Asparagine and glutamine possess amide side chains that can both donate and accept hydrogen bonds, making them ideal for precise base recognition. They are common in helix–turn–helix and other DNA binding motifs for reading base identity in the major groove. Other polar residues (e.g., Arg) also contact bases, but among the listed choices, Asn and Gln best represent base-specific hydrogen bonding pairs. Step-by-Step Solution: Identify required chemistry: side chains must have donor and acceptor capability.Evaluate options: Asn/Gln fit; Cys/Met are less polar; Lys is mainly protonated and backbone oriented; Ile/Val are hydrophobic; Gly/Pro lack suitable side chains for base H-bonding.Therefore, Asn and Gln are correct. Verification / Alternative check: Structural databases show frequent Asn/Gln–base contacts in transcription factor–DNA complexes; mutation of these residues often alters sequence specificity. Why Other Options Are Wrong: Cys/Met: limited polar H-bonding; roles include metal binding or hydrophobic packing. Lys/Leu: Lys interacts strongly with phosphates; Leu is hydrophobic. Ile/Val: hydrophobic; poor H-bond donors/acceptors. Gly/Pro: minimal or constrained side chains. Common Pitfalls: Assuming any polar residue will give specificity; geometry and dual donor/acceptor capacity are important for accurate base readout. Final Answer: Asn and Gln.

Protein and Nucleic Acid Interactions Questions