Transcription

lower

as genomes get larger, (lower/higher) rates of mutation are tolerable

A←>G C←>T

substitution mutation possibilities for transitions

purine←>pyrimidine

substitution mutation possibilities for transversions

base excision repair

single DNA strand repair, involves exonuclease activity, replaces 1-10 nts, used to repair abnormal bases in DNA like covalently modified bases, oxidative damage, and deamination/depuration

nucleotide excision repair

single DNA strand repair, thymine cross linking complex chews up region, used for bulky adduct and cross linking lesions caused by UV photoproducts that cause major structural changes

mismatch repair

single DNA strand repair, involves mismatch recognition and excision by MutL and chewing up by Exo1, used to fix base mismatches and short deletions/insertions

homologous recombination

double strand repair, uses template strand to resynthesizes broken/mutated strand

proto oncogene

genes stimulate cell growth, division, and survival, gain of function mutations in these promote cancer

tumor suppressor genes

genes help prevent unrestrained cellular growth and promote DNA repair and cell cycle checkpoint, loss of function mutations promote cancer

slower, higher

compared to DNAP, RNAP is (slower/faster) and has a (higher/lower) error rate

RNAP I

eukaryotic RNAP makes rRNA, located in nucleolus

RNAP III

eukaryotic RNAP makes tRNA, located in nucleoplasm

coding/sense/+

transcribed mRNA will be identical to this DNA strand

TFIIH

RNAP II transcription factor helicase subunit required for transcription initiation

promoters

present in eukaryotes, DNA sequences that direct the transcription machinery to the transcription start site (TSS)

enhancers

present in eukaryotes, DNA sequences bind activators/repressors to regulate transcription

TFIID

RNAP II transcription factor, contains TATA binding protein (TBP) that bends DNA sharply to facilitate melting

TBP

contained within RNAP II TFIID, bends DNA sharply to facilitate melting

ATP hydrolysis

required for melting DNA to get a transcription bubble to synthesize mRNA

TFIIK

for RNAP II, kinase subunit of TFIIH, phosphorylates RNAP II C term domain

Ser5

phosphorylation at RNAP II CTD associated with promoter escape

Ser2

phosphorylation at RNAP II CTD associated with elongation and RNA processing

TFIIK

kinase phosphorylates RNAP II CTD Ser5

P-TEFb

kinase phosphorylates RNAP II CTD Ser2

7-methylguanosine cap

added in a stepwise manner by RNAP II to create 5’ cap protecting mRNA from degradation and assisting in ribosome binding

poly A tail

template DNA sequence “tells” RNAP II to terminate transcription creating this at the end, protects mRNA from degradation and aids in export of mature mRNA

AAUAAA

conserved signal/nt sequence in mRNA known as the polyadenylation signal indicates transcription termination

repressors

bound by enhancer sequences, promote chromatin condensation

activators

bound by enhancer sequences, promote chromatin decondensation and bind to the mediator complex to promote transcription initiation

mediator

transcription regulation, complex interacts with transcription initiation factors at the promoter, bound by activators

cytosine methylation

specific nt chromatin modification is a repressive modification to transcription carried out by DNMTs

TETs

enzyme capable of reversing DNA methylation in chromatin modification

DNMTs

methyltransferase performs DNA methylation modification of chromatin

DNA methylation

-ive regulator/modifier for transcription

histone acetylation

+ive regulator/modifier for transcription/activates transcription

exon

sequence in a gene that is transcribed and remains in mature mRNA that is translated to protein

intron

sequence in a gene that is transcribed but removed from mRNA before translation

group one

class of self splicing introns, requires free guanosine

5’ splice site

location where free guanosine attacks the phosphodiester bond in group 1 self splicing introns