Molecular Biology Exam 2

BI552

3'-->5' exonuclease

proofreading; removes incorrect basepair

Kf > Kr

proofreading; correct insertion

MutS

MMR; recognizes mispair, loads Mut L, binds Mut H

MutL

MMR; binds Mut S and Mut H

MutH

MMR; recognizes Dam sites and nicks the closest unmethylated strand

Nuclease (MMR)

MMR; digests from nick at mismatch pair

DNA Ligase (MMR)

MMR; seals nicks, synthesis continues

DNA glycosylase

BER: removes damaged base from its deoxyribose sugar

AP endonuclease

BER; nicks 5' side of AP site

dRpase

BER; nicks 3' side of AP site and removes deoxyribose sugar

DNAPI (BER)

BER; fills gap

DNA Ligase (BER)

BER; seals nick

Tag + AlkA/AlkB

DNA glycosylases that recognize N3meA and use O2 + alpha-ketoglutarate (H2O, CO2, succinate byproducts) to make an alcohol intermediate, and convert to adenine and formaldehyde

UrvA

NER; 2 units insert beside lesion

UrvB

NER; surrounds UrvA2 and lesion

UvrC

NER; nicks both sides of lesion and removes UvrA2

UvrD

NER; removes lesion and UvrC

DNAPI (NER)

NER; synthesizes DNA and removes UvrB

DNA Ligase (NER)

NER; seals nicks

Mfd

TCR; recognizes blocked RNAP and recruits NER

NusA (TC-TLS)

TC-TLS; recruits lesion bypass DNAP

Lesion Bypass DNAP

TC-TLS; inserts bases opposite lesion, allows DNAP to continue

RecBCD

recombination; initiation, B = nuclease nicks 3'-->5', C = unwinds ds-DNA and recognized Chi-site, D = motor 5'-->3'

RecF

recombination; initiation pathway, bindds ss/ds-DNA junctions

RecG

recombination; promotes branch migration, zips strands together

RecA

recombination; strand exchange, binds in minor groove of ds-DNA

RecQJ

recombination; enlarges ss-gap caused by lesion

RecOR

recombination; removes SSB and adds RecA to ss-DNA in gap

RuvC

recombination; nicks consensus sequences and resolves Holliday Junctions

Alpha Subunit

RNAP initiation; 2 copies

Beta + Beta' Subunits

RNAP initiation; active site

Sigma Subunit

RNAP initiation; recognizes -35 in ds-DNA, -10 in ss-DNA

Untranscribed Strand (open complex)

open complex; sigma subunit binds

Transcribed Strand (open complex)

open complex; inserts into Beta/Beta' active site

Stem Loop with U's

termination; causes duplex to break, leads to termination

Stem Loop without U's

termination; causes pausing, but straightens out and continues

Rho-Dependent Termination

termination; rho binds rut sites and triggers RNAP release causing termination

Monocistronic mRNA

translation; RBS, start, stop, trailer

Polycistronic A mRNA

translation; RBS, start, stop, RBS, start, stop

Polycistronic B mRNA

translation; RBS, start, stop/start, stop. encounters stop, frameshifts

2 Starts 1 Stop

translation; RBS, start 1, RBS, start 2, stop

1 Start 2 Stops

translation; RBS, start, stop 1, stop 2. often jumps over stop 1

50S subunit

ribosome structure; large subunit

30S subunit

ribosome structure; small subunit

E (ribosome structure)

tRNA exit cavity

P(ribosome structure)

peptide cavity

A (ribosome structure)

acceptor tRNA cavity

IF3

translation initiation; binds mRNA to 30S in E site

i-tRNA

translation initiation; enters 30S in P site

IF1 + IF2

translation initiation; bind i-tRNA in A site

50S (translation initiation)

translation initiation; binds mRNA

EF-P

translation/elongation; elongates mRNA and replaces IF3 in E site

Ribosome Complex

translates mRNA into protein, leaves IF1, IF2, and EF-p

EF-Tu GTP

elongation; brings in aa-tRNA into A site, GTP --> GDP when matched

EF-G GTP

elongation; translocation of tRNA and mRNA down the ribosome

Peptidyl Transfer

elongation; polypeptide is removed from the tRNA in the P site and transferred to the amino acid at the A site

30S Shifts

elongation; loss of tRNA in the P site

50S Shifts

elongation; translocation mRNA, loss of EF-G GDP