DNA Replication, Repair, and Transcription Review Flashcards

These questions cover key concepts across DNA replication, repair, transcription, chromatin, and cell cycle as presented in the notes.

What is the difference between the leading and lagging strands during DNA replication?

Leading strand is synthesized continuously toward the replication fork; lagging strand is synthesized discontinuously away from the fork as short Okazaki fragments.

Which enzymes relieve torsional strain ahead of the replication fork?

Topoisomerase I and Topoisomerase II.

What is the role of single-strand binding proteins (SSBs) in DNA replication?

SSBs bind exposed single-stranded DNA to prevent reannealing and stabilize the unwound strands.

Which enzyme synthesizes RNA primers for DNA replication?

Primase (an RNA polymerase) lays down short RNA primers.

What enzyme seals nicks between Okazaki fragments on the lagging strand?

DNA ligase.

Name two endogenous and two exogenous sources of DNA damage discussed in the notes.

Endogenous: reactive oxygen species (ROS); other metabolic byproducts. Exogenous: ultraviolet (UV) light; methylating agents.

Outline base excision repair (BER) steps.

DNA glycosylase removes the damaged base creating an AP site; AP endonuclease cuts the backbone; DNA polymerase β fills the gap; DNA ligase seals.

Outline nucleotide excision repair (NER) steps.

XP-C/other factors recognize bulky lesions, recruit TFIIH to unwind DNA; XP-G/X-PF endonucleases cut on both sides of the lesion; gap filled by DNA polymerase δ/ε; ligase seals.

Which repair pathway removes a damaged base without removing the entire nucleotide?

Base Excision Repair (BER).

Which repair pathway fixes replication errors that escape proofreading?

Mismatch Repair (MMR).

Which repair pathway uses a sister chromatid as a template to repair double-strand breaks?

Homologous Recombination (HR).

Which repair pathway joins DNA ends without a template and is error-prone?

Nonhomologous End Joining (NHEJ).

List the common types of mutations: silent, missense, nonsense, frameshift, splice site.

Silent: no amino acid change; Missense: amino acid change; Nonsense: stop codon; Frameshift: insertion/deletion not multiple of 3; Splice-site: affects splicing.

What are the major regulatory elements involved in gene expression regulation?

Promoter, enhancer, silencer, and TATA box.

What is transcription? Which enzyme synthesizes RNA? Where does transcription occur in eukaryotes?

Transcription is RNA synthesis from a DNA template; RNA polymerase synthesizes RNA; occurs in the nucleus (and mitochondria) of eukaryotes.

During transcription, which DNA strand serves as the template (antisense) strand?

The antisense (template) strand; the coding strand has the same sequence as the RNA (with U for T).

In which direction is RNA synthesized?

5' to 3' direction by RNA polymerase.

Which promoter element is commonly found in eukaryotic promoters?

TATA box.

Which transcription factor is essential for RNA polymerase II binding in eukaryotes?

TFIID.

What is the function of the 5′ cap on eukaryotic mRNA?

Protects mRNA from degradation and aids translation initiation.

Which enzyme adds the 5′ cap to mRNA?

Guanylyltransferase (cap-addition enzyme).

What is the function of the poly-A tail in mRNA?

Stabilizes mRNA, aids in nuclear export, and enhances translation.

Which enzyme adds the poly-A tail to mRNA?

Poly-A polymerase.

What is the role of small nuclear ribonucleoproteins (snRNPs) in mRNA processing?

They form the spliceosome to remove introns from pre-mRNA.

What is alternative splicing?

Generating multiple mRNA transcripts from a single gene by splicing exons in different combinations.

Name the major classes of RNA and their general roles.

mRNA (template for protein), tRNA (adaptor for amino acids), rRNA (ribosome components), snoRNA, snRNA, miRNA/siRNA.

Describe chromatin structure: core histones, linker histone, nucleosome, euchromatin vs heterochromatin.

DNA wraps around a histone octamer (H2A/H2B/H3/H4) to form a nucleosome; H1 is the linker histone; euchromatin is transcriptionally active, heterochromatin is condensed and often inactive.

What is Chargaff’s rule?

% Purines = % Pyrimidines; A = T and G = C in DNA.

What are telomeres and what does telomerase do?

Telomeres are repetitive TTAGGG sequences at chromosome ends; telomerase (TERC RNA component plus TERT protein) extends telomeres to prevent shortening.

What initiates DNA replication in bacteria vs. eukaryotes?

Bacteria: ori with DnaA recruitment of DnaB helicase; SSBs stabilize. Eukaryotes: ORC at ori recruits MCM helicase; RPA stabilizes ssDNA.

What are the three main cell cycle checkpoints?

G1 checkpoint (G1/S), G2 checkpoint (G2/M), and the Metaphase/Spindle Assembly checkpoint.

How is the G1/S transition regulated by p53 and p21?

DNA damage elevates p53, which activates p21, a CDK inhibitor that halts G1/S and S-phase progression.

What happens during M phase to trigger chromosome separation?

APC/C activation leads to destruction of cyclin B and securin degradation; cohesin is cleaved by separase, enabling anaphase.

What is the proofreading activity of DNA polymerases?

3′→5′ exonuclease activity removes misincorporated nucleotides during replication.

Which enzyme removes RNA primers in prokaryotic DNA replication?

DNA polymerase I removes RNA primers and fills in with DNA.

Which enzyme removes RNA primers in eukaryotic DNA replication?

RNase H removes RNA primers; DNA polymerase δ fills the gaps.

Which enzyme joins Okazaki fragments on the lagging strand?

DNA ligase.

Which enzyme unwinds the DNA double helix at the replication fork?

Helicase.

What structure protects chromosome ends from degradation and fusion?

Telomeres.

Which enzyme is responsible for maintaining telomere length?

Telomerase (TERC RNA template + TERT protein).

What is the difference between prokaryotic and eukaryotic origin of replication?

Prokaryotes: single origin per chromosome; eukaryotes: multiple origins per chromosome.

What is the primary form of DNA repair for bulky, helix-distorting lesions like thymine dimers?

Nucleotide Excision Repair (NER).

Which DNA repair pathway uses a sister chromatid as a template and is accurate?

Homologous Recombination (HR).