Intensive Cell bio test 2

DNA Repair

Mechanism that corrects DNA damage and mistakes occurring during replication.

Causes of DNA Damage

Spontaneous chemical changes, radiation, and exposure to damaging chemicals.

Consequences of Unrepaired DNA Damage

Mutations in codons, blocked DNA replication, and blocked transcription.

Deamination

Spontaneous removal of an amino group from a DNA base.

Cytosine Deamination

Chemical conversion of cytosine into uracil in DNA.

Thymine Dimer

Covalent linkage between adjacent thymine bases caused by UV light.

Cyclobutane Ring

Ring structure formed when two adjacent thymine bases become covalently linked.

Bulky DNA Adduct

Large chemical group attached to a DNA base, such as guanine, that distorts DNA structure.

Carcinogens

Cancer-causing substances that can chemically damage DNA.

Direct Reversal Repair

Repair mechanism that directly reverses DNA damage without removing nucleotides.

Photoreactivation

Light-dependent direct repair mechanism that reverses thymine dimers.

Photolyase

Enzyme that recognizes thymine dimers and uses light energy to break their cyclobutane ring.

Excision Repair

Repair mechanism that removes damaged DNA material and replaces it with newly synthesized DNA.

Base Excision Repair

Excision pathway that removes individual damaged bases, such as uracil produced by deamination.

DNA Glycosylase

Enzyme that recognizes and removes an incorrect or damaged nitrogenous base.

AP Site

Abasic site created when DNA glycosylase removes a damaged base but leaves the sugar-phosphate backbone.

AP Endonuclease

Enzyme that cuts the DNA backbone at an abasic site during base excision repair.

Deoxyribose Phosphodiesterase

Enzyme that removes the remaining sugar-phosphate material during base excision repair.

DNA Polymerase in Base Excision Repair

Enzyme that fills the gap with the correct complementary nucleotide.

DNA Ligase in Base Excision Repair

Enzyme that seals the repaired DNA backbone.

Nucleotide Excision Repair (NER)

Excision pathway that removes a stretch of nucleotides containing bulky DNA damage.

UvrABC Excinuclease

Bacterial enzyme complex that recognizes DNA damage and cuts the damaged strand on both sides of the lesion.

Helicase in Nucleotide Excision Repair

Enzyme that removes the damaged oligonucleotide after UvrABC cleavage.

Bacterial NER Oligonucleotide

Approximately 12–13 nucleotides removed around the damaged region.

DNA Polymerase I

Enzyme that fills the gap during nucleotide excision repair in E. coli.

Xeroderma Pigmentosum (XP)

Genetic disease that helped researchers identify genes involved in human nucleotide excision repair.

XPA–XPG

Seven proteins involved in recognizing DNA damage, cleavage, and removal during human nucleotide excision repair.

DNA Polymerase Delta

Polymerase that performs DNA synthesis during human nucleotide excision repair according to the lecture notes.

Mismatch Repair (MMR)

Repair pathway that corrects incorrectly paired bases missed during DNA replication proofreading.

DNA Methylation in Bacterial MMR

Addition of methyl groups to the parental DNA strand, allowing distinction from the newly synthesized strand.

MutS

Bacterial mismatch repair protein that recognizes incorrectly paired bases.

MutL

Bacterial mismatch repair protein that works with MutS to coordinate excision and repair.

MutH

Bacterial mismatch repair protein that identifies and cleaves the newly synthesized, unmethylated strand.

Parental DNA Strand

Methylated DNA strand used to identify the original sequence during bacterial mismatch repair.

Newly Synthesized DNA Strand

Initially unmethylated DNA strand targeted for correction during bacterial mismatch repair.

MSH

Human mismatch repair proteins corresponding to bacterial MutS; recognize mismatched bases.

MLH

Human mismatch repair proteins corresponding to bacterial MutL; coordinate mismatch repair.

Human Mismatch Repair

Uses MSH and MLH proteins rather than bacterial MutH.

Hereditary Colon Cancer

Can result from mutations in human mismatch repair genes such as MSH and MLH.

Single-Strand Breaks

Help identify the newly synthesized DNA strand during human mismatch repair.

DNA Polymerase Epsilon

Polymerase associated with leading-strand DNA synthesis in the lecture notes.

DNA Polymerase Proofreading

Mechanism in which DNA polymerase detects and removes incorrectly incorporated nucleotides.

DNA Replication Fidelity

Accuracy of DNA replication maintained through proofreading and DNA repair mechanisms.

Translesion Synthesis

Damage-tolerance process that allows DNA replication to continue past a damaged DNA template.

DNA Polymerase V

E. coli polymerase that bypasses DNA lesions so replication can continue.

DNA Polymerase III

Polymerase that resumes normal DNA synthesis after translesion bypass.

Translesion Synthesis vs. Excision Repair

Translesion synthesis bypasses damage; excision repair removes and replaces damaged DNA.

Double-Strand Break

Severe DNA damage involving breaks in both strands of the DNA molecule.

Causes of Double-Strand Breaks

Ionizing radiation, including X-rays and gamma rays.

Non-Homologous End Joining (NHEJ)

Repair pathway that directly rejoins broken DNA ends without requiring a homologous template.

NHEJ Advantage

Rapid repair of double-strand breaks without needing an undamaged DNA template.

NHEJ Disadvantage

Error-prone repair that can cause the loss of DNA bases during rejoining.

Homology-Directed Repair (HDR)

Repair pathway that uses an undamaged homologous DNA sequence as a template to repair a double-strand break.

Sister Chromatid

Identical DNA copy produced during replication that can provide a template for homology-directed repair.

BRCA2

Protein involved in hereditary breast cancer risk that recruits RAD51 during homology-directed repair.

RAD51

Protein that participates in repairing double-strand breaks through homologous recombination.

NHEJ vs. HDR

NHEJ directly rejoins broken ends and is error-prone; HDR copies information from an undamaged homologous template.

Site-Specific Recombination

Mechanism that rearranges DNA at specific recognition sequences.

Immunoglobulins

Antibodies composed of heavy and light polypeptide chains.

Antibody Diversity

Ability of the body to produce more than 10^11 different antibodies through immunoglobulin gene rearrangement.

B Lymphocytes (B Cells)

Cells that undergo immunoglobulin gene rearrangement and produce antibodies.

Light Chain

Shorter antibody polypeptide chain encoded by rearranged V, J, and C gene segments.

Heavy Chain

Longer antibody polypeptide chain encoded by rearranged V, D, J, and C gene segments.

V Region

Variable gene region containing multiple possible gene segments.

J Region

Joining gene region that connects with a selected V segment.

C Region

Constant gene region encoding the constant portion of an immunoglobulin chain.

D Region

Diversity gene segment found in heavy-chain genes but not light-chain genes.

V-J Recombination

Process that joins a selected variable segment to a selected joining segment.

VDJ Recombination

Process that joins variable, diversity, and joining segments in heavy-chain genes.

Intervening DNA

DNA between selected immunoglobulin gene segments that is removed during recombination.

RAG1 and RAG2

Proteins that recognize recombination sequences and participate in immunoglobulin DNA cleavage and joining.

Mature Light-Chain RNA

Contains the selected V, J, and C regions.

Mature Heavy-Chain RNA

Contains the selected V, D, J, and C regions.

Antibody Specificity

Depends on the combination of heavy and light chains.

Transcription

Process of synthesizing RNA using DNA as a template.

RNA Polymerase

Enzyme that synthesizes RNA in the 5′ to 3′ direction using a DNA template.

RNA Polymerase Primer Requirement

RNA polymerase can initiate RNA synthesis without a primer.

Transcriptional Regulation

Control of when, where, and how much RNA is produced.

Sigma Factor

Bacterial RNA polymerase component responsible for promoter recognition.

Promoter

DNA sequence where RNA polymerase binds to initiate transcription.

+1 Position

First nucleotide transcribed into RNA.

Upstream DNA

DNA located before the transcription start site, designated with negative numbers.

-10 Element

Bacterial promoter sequence rich in thymine and adenine that is recognized by sigma.

-35 Element

Bacterial promoter sequence recognized by sigma during transcription initiation.

Pribnow Box

Another name for the bacterial -10 promoter element.

Transcription Initiation

Stage in which RNA polymerase recognizes the promoter, unwinds DNA, and begins RNA synthesis.

DNA Unwinding

Separation of DNA strands to expose the template strand for transcription.

Phosphodiester Bond

Bond that connects nucleotides together in an RNA or DNA strand.

Sigma Detachment

Release of the sigma factor after transcription initiation as RNA polymerase transitions into elongation.

Transcription Elongation

Stage in which RNA polymerase moves along DNA and extends the RNA strand.

Transcription Termination

Process that stops RNA synthesis and releases the RNA transcript.

Stem-Loop Structure

RNA structure formed when complementary sequences within the same RNA molecule base-pair.

Bacterial Stem-Loop Termination

Formation of an RNA stem-loop that promotes dissociation of RNA from DNA and RNA polymerase.

Eukaryotic RNA Polymerase I

Enzyme that transcribes ribosomal RNA genes.

Eukaryotic RNA Polymerase II

Enzyme that transcribes protein-coding genes that produce mRNA.

Eukaryotic RNA Polymerase III

Enzyme that transcribes transfer RNA (tRNA) genes.

Eukaryotic Pre-Initiation Complex

Collection of general transcription factors and RNA polymerase assembled at a promoter before transcription begins.

General Transcription Factors

Proteins that assemble at promoters and help RNA polymerase initiate transcription.

TFIID

General transcription factor complex containing TBP and TAF proteins that recognizes core promoter elements.

TBP

TATA-binding protein; component of TFIID that recognizes the TATA box.