BIOS 430: Molecular Biology Study Guide for Final Exam

Flashcards covering DNA repair mechanisms, transcription, and translation processes in prokaryotes and eukaryotes.

Hydrolysis

Loss of base from nucleotide, leading to an abasic (AP) site.

Alkylation

Addition of alkyl groups to bases or the phosphate backbone, leading to mispairing or strand breaks.

Deamination

Conversion of cytosine to uracil or adenine to hypoxanthine, causing transition mutations.

UV Light Damage

Causes pyrimidine dimers, which interfere with replication and transcription.

X-rays Damage

Induces single- and double-strand breaks and generates reactive oxygen species, leading to base damage.

Intercalating Agents

Molecules that insert between base pairs, causing insertions or deletions and resulting in frameshift mutations.

Base Analogs

Molecules that mimic natural bases, leading to mispairing and transition mutations.

Reactive Oxygen Species (ROS)

Cause oxidative base damage and lead to mutagenesis and strand breaks.

Chemical Adducts

Large molecules that covalently bind to DNA, distorting the helix and blocking replication.

Transition Mutations

Mutations that involve purine to purine or pyrimidine to pyrimidine substitutions.

Transversion Mutations

Mutations that involve purine to pyrimidine or vice versa substitutions.

Tautomeric Shifts

Temporary shifts in the proton position of bases that lead to mispairing during replication.

Direct Repair

Repair mechanism that reverses damage without replacing nucleotides, such as photoreactivation.

Excision Repair

Repair mechanism that excises damaged DNA and resynthesizes; includes BER and NER.

Translesion Synthesis (TLS)

Repair process that bypasses replication-blocking lesions with specialized low-fidelity DNA polymerases.

Mismatch Repair (MMR)

Corrects replication errors by recognizing mismatches and excising the erroneous DNA segment.

SOS Response

Bacterial response to severe DNA damage that induces multiple repair genes and leads to error-prone repair.

Base Excision Repair (BER)

Repair pathway that removes and replaces damaged bases in DNA.

Nucleotide Excision Repair (NER)

Repairs bulky lesions and helix-distorting damage in DNA.

UvrABC Nuclease

Nuclease involved in NER that detects and excises bulky lesions.

DNA Polymerase I

Fills in the gap during repair processes like NER and BER.

DNA Ligase

Seals nicks in the DNA strand after repair.

Photolyase

Enzyme that performs photoreactivation repair of UV-induced damage.

UvrD

Helicase that removes damaged DNA fragments during nucleotide excision repair.

MutS

Protein that recognizes mismatched bases during mismatch repair.

MutL

Protein that bridges MutS to MutH during mismatch repair.

MutH

Enzyme that cleaves the unmethylated strand at GATC sites during mismatch repair.

Negative Control Operons

Operons regulated by repressor proteins that inhibit transcription.

Positive Control Operons

Operons activated by activator proteins that enhance transcription.

Inducible Operon

Operon that is usually off and turned on in response to an inducer.

Repressible Operon

Operon that is usually on and turned off in the presence of a corepressor.

Silencers

Sequences that bind repressor proteins to inhibit transcription.

Enhancers

Sequences that bind activator proteins to enhance transcription.

Sigma Factor

Protein that aids RNA polymerase binding to the promoter in prokaryotes.

TATA Box

DNA sequence that functions as a promoter in eukaryotic transcription.

Rho-Independent Termination

Termination mechanism that relies on hairpin formation followed by a poly-U tail.

Rho-Dependent Termination

Termination mechanism involving the Rho protein catching up to RNA polymerase.

Eukaryotic RNA Polymerase I

Enzyme responsible for transcribing rRNA genes.

Eukaryotic RNA Polymerase II

Enzyme that transcribes mRNA and most non-coding RNAs.

Eukaryotic RNA Polymerase III

Enzyme that transcribes tRNA genes and 5S rRNA.

Nuclear RNA Processing

Includes capping, polyadenylation, and splicing of eukaryotic hnRNA.

Capping

Modification adding a 5' cap to mRNA to protect it from degradation.

Polyadenylation

Addition of a poly-A tail to the 3' end of mRNA to increase stability.

Spliceosome

Molecular complex responsible for splicing introns out of pre-mRNA.

mRNA Stability

Determined by the presence and length of the poly-A tail.

Heat-Shock Proteins

Proteins that assist in proper protein folding during stress.

Ubiquitination

Post-translational modification marking proteins for degradation by the proteasome.

Proteasome

Cellular complex responsible for degrading ubiquitinated proteins.

Chaperonins

Proteins that facilitate the proper folding of other proteins.

Ribosome Recycling Factor

Initiates the disassembly of the ribosome after translation termination.