DNA Repair and Transcription Flashcards

Vocabulary flashcards for DNA Repair and Transcription

Hydrolysis (DNA Damage)

Loss of base from nucleotide leading to an abasic site.

Alkylation (DNA Damage)

Addition of alkyl groups to bases or phosphate backbone.

Deamination (DNA Damage)

Cytosine converted to Uracil or Adenine converted to Hypoxanthine.

UV Light (DNA Damage)

Causes pyrimidine dimers, blocking replication and transcription.

X-rays/Gamma Rays (DNA Damage)

Induces single- and double-strand breaks and generates ROS.

Intercalating Agents

Insert between base pairs, causing insertions/deletions and frameshift mutations.

Base Analogs

Mimic natural bases, leading to mispairing and transition mutations.

ROS (Reactive Oxygen Species)

Cause oxidative base damage, strand breaks, mutagenesis, and apoptosis.

Chemical Adducts

Large molecules covalently bound to DNA, distorting the helix.

Transition Mutation

Purine to Purine (A ↔ G) or Pyrimidine to Pyrimidine (C ↔ T).

Transversion Mutation

Purine to Pyrimidine (A/G ↔ C/T).

Tautomeric Shifts

Temporary proton shift in bases, leading to mispairing during replication.

Direct Repair

Reverses damage without replacing nucleotides.

Excision Repair

Excises damage and resynthesizes DNA.

Photoreactivation Repair

Carried out by DNA photolyase, uses blue light to cleave pyrimidine dimers.

Methyltransferases

Transfer methyl group from DNA to their own cysteine residue (suicide reaction).

Dioxygenases

Use Fe²⁺ and α-ketoglutarate to oxidatively demethylate.

UvrA/B

Detects bulky lesion in Nucleotide Excision Repair.

UvrC

Makes dual incision on damaged strand in Nucleotide Excision Repair.

UvrD

Helicase removes damaged fragment in Nucleotide Excision Repair.

DNA glycosylase

Removes damaged base, leaving an AP site in Base Excision Repair.

APE1 (AP endonuclease)

Cleaves backbone at AP site in Base Excision Repair.

Translesion Synthesis (TLS)

Bypasses replication-blocking lesions using specialized low-fidelity DNA polymerases.

MutS

Recognizes mismatch in Mismatch Repair.

MutL

Bridges MutS to MutH in Mismatch Repair.

MutH

Cleaves unmethylated (new) strand at GATC site in Mismatch Repair.

SOS Repair

Bacterial global response to severe DNA damage.

Promoter Region

Region where RNA polymerase binds to begin synthesizing RNA.

Elongation (Transcription)

Stage where RNA polymerase moves along the template adding ribonucleotides.

Termination (Transcription)

Stage where RNA polymerase stops transcription and releases the transcript.

Template Strand

DNA strand read by RNA polymerase (non-coding strand).

Coding Strand

DNA strand with the same sequence as RNA (sense strand).

DNA Template

Provides the sequence to be transcribed into RNA.

RNA Polymerase

Enzyme that catalyzes RNA synthesis.

Ribonucleotides (NTPs)

Building blocks (A, U, G, C) for RNA.

Sigma Factor

Helps RNA polymerase bind to the promoter in prokaryotes.

Promoter Sequence

DNA sequence that signals the start of transcription.

Prokaryotic RNA Polymerase

Composed of core enzyme (α₂ββ'ω) and sigma factor (σ).

Eukaryotic RNA Polymerase

Three main types: RNA polymerase I, II, and III.

α Subunits (RNA Polymerase)

Involved in enzyme assembly and interaction with transcription factors.

β Subunits (RNA Polymerase)

Catalytic site for RNA synthesis.

β' Subunit (RNA Polymerase)

Binds to the DNA template.

ω Subunit (RNA Polymerase)

Assists in enzyme assembly and stability.

Sigma Factor (RNA Polymerase)

Recognizes promoter sequences and initiates transcription.

Rifamycins

Block the elongation of the RNA chain by inhibiting transcription.

Promoter Element

-10 region (Pribnow box).

Promoter Element

-35 region.

Rho-Independent Termination

Formation of a GC-rich hairpin followed by a poly-U tail.

Rho-Dependent Termination

The Rho protein catches up to RNA polymerase and unwinds the RNA-DNA hybrid, releasing RNA.

Operon

Cluster of genes with related functions, regulated together.

Inducible Operon

Normally off, turned on in the presence of an inducer.

Repressible Operon

Normally on, turned off in the presence of a corepressor.

Negative Control (Operon)

The operon is regulated by a repressor protein.

Positive Control (Operon)

The operon is activated by an activator protein.

lacZ

Gene encoding β-galactosidase.

lacY

Gene encoding lactose permease.

lacA

Gene encoding thiogalactoside transacetylase.

Operator (lac operon)

Binding site for the lac repressor.

lacI

Gene encoding the lac repressor protein.

Allolactose

Product of lactose that inactivates the repressor.

Glucose

Bacteria prefer this as an energy source, leading to catabolite repression.

Tryptophan

Acts as the corepressor in the trp operon.

RNA Polymerase I

Transcribes rRNA genes (except 5S rRNA).

RNA Polymerase II

Transcribes mRNA and most non-coding RNAs.

RNA Polymerase III

Transcribes tRNA genes, 5S rRNA genes, and other small RNAs.

Sigma Factor (σ)

A detachable subunit that helps the polymerase recognize the promoter (prokaryotes).

C-terminal domain (CTD)

Plays a role in mRNA processing (eukaryotes).

Promoter (RNA Polymerase I)

Located upstream of the rRNA genes, recognized by core binding factor (CBF).

Promoter (RNA Polymerase II)

Typically contains a TATA box (-30 region) and initiator (Inr) sequences.

Promoter (RNA Polymerase III)

Contains A and B box sequences.

TFIIIA, TFIIIB, TFIIIC

Required for initiation (RNA Polymerase I).

General Transcription Factors (GTFs)

Requires general transcription factors (GTFs) to assemble the pre-initiation complex (PIC) and initiate transcription (RNA Polymerase II).

TFIIIA, TFIIIB, TFIIIC

Necessary for tRNA and 5S rRNA transcription initiation (RNA Polymerase III).

Termination (RNA Polymerase I)

Occurs via a torpedo mechanism or protein-dependent termination.

Termination (RNA Polymerase II)

After RNA cleavage at a specific site, the torpedo model is involved, where the Rat1 exonuclease degrades the remaining RNA to drive termination.

Termination (RNA Polymerase III)

Occurs through the formation of a hairpin loop and U-rich sequence.

Actinomycin D

Intercalates between the DNA bases, preventing the movement of RNA polymerase (transcriptional inhibitor).

Cordycepin

A nucleoside analog of adenosine, leading to chain termination during RNA synthesis (transcriptional inhibitor).