cell bio proteins and enzymes

DNA polymerase

DNA polymerase

key enzyme in DNA replication

• all DNA polymerases add deoxyribonucleoside 5'-triphosphates to the 3' hydroxyl group of a primer strand.

DNA polymerase I

polymerase found in prokaryotes that has 5’ to 3’ exonuclease activity to remove RNA primers from DNA strand. it also acts as a DNA polymerase and fills in gaps between lagging strands

what is special about DNA pol I

its one protein that does 2 job in lagging strand of prokaryotes

DNA polymerase III

main synthesizing DNA polymerase in leading and lagging strands in prokaryotes

DNA polymerase α

relatively slow DNA polymerase that work with primase to make RNA primer in lagging strand of eukaryotes.

DNA polymerase ε

DNA polymerase that does synthesis in leading strand in eukaryotes

DNA polymerase δ

5’ to 3’ DNA polymerase that synthesizes DNA in eukaryotes lagging strand

• also fills in gap between Okazaki fragments

primase

RNA polymerase that is used in DNA replication to generate primers to initiate synthesis of Okazaki fragments

• RNA pol can generate polynucleotides de novo (from scratch) w/o pre-existing primer

DNA ligase

enzyme that joins DNA fragments together

RNase H

protein that is a 5’ to 3’ exonuclease used in lagging strands to remove RNA primers in eukaryotes

what are the processive DNA polymerases in both prokaryotes and eukaryotes?

• DNA pol III

• DNA pol δ

• DNA pol ε

helicase

enzyme that separated and stabilizes dsDNA into ssDNA - it catalyzes the unwinding of DNA

• needs ATP to break hydrogen bonds

• works with SSB

single stranded DNA binding proteins (SSB)

keep separated ssDNA strands apart till DNA polymerase can do its job

• works with helicase

sliding clamp protein

holds DNA pol in place so it can go faster (looks like a donut)

• naturally closed protein, requires help from other protein to open up and wrap around DNA

• known as PCNA in eukaryotes

clamp loading protein

uses ATP to open up the sliding clamp protein so its no longer in its closed form

• RFC in eukaryotes

topoisomerase (I & II)

enzyme that cuts supercoiled DNA strands, and once DNA unwinds (transient break) and no knots are present, enzyme joins strands back together

what is special about topoisomerase

its a type of nuclease and ligase

initiator

protein that recognizes origin of replication for DNA replication in prokaryotes and starts recruiting other protein such as primase and helicase

telomerase

enzyme that make telomeres through reverse transcriptase

• has its own RNA template

• part protein and part RNA

what mechanisms do processive DNA pol have to help ensure accurate DNA replications?

have proofreading activity that helps reduce error rate.

• exhibit 3’ to 5’ exonuclease activity

photolyase

light induced enzyme in plants that help repair thymine dimer

• not in humans

MutS

protein that recognizes mismatch in prokaryotes during mismatch repair

• work with MutL to do direct excision

MutH

protein that cleaves the strand with the mismatch adjacent to methyl group on parent strand

• in prokaryotes during mismatch replair

MutL

works with MutS to directly excisise strand of DNA with mismatch during mismatch repair

• in prokaryotes

MSH

mutS homolog - recognizes mismatch in eukaryotes

MLH

mutL homolog- excises nucleotides on DNA strand with the mismatch till it encounters a single stranded break

• part of mismatch repair in eukaryotes

DNA glycosylase

enzyme that removes nucleotide base U, leaving behind phosphate and sugar, creating an AP Site

• part of deamination base-excision repair

AP endonuclease

enzyme that cleaves DNA at at AP site

• part of deamination base-excision repair

deoxyribosephosphodiesterase

enzyme the breaks phosphodiester bonds

• part of deamination base-excision repair

exinuclease

complex of proteins that remove thymine dimer and additional nucleotides around it

• parts of nucleotides excision repair of thymine dimers in humans

Ku70-Ku80

proteins that recognize DSBs and recruit other proteins to fix it

• part of DSB repair by NHEJ

DNA-PKcs

DNA dependents protein kinase, add phosphates and changes activity of other proteins

• part of DSB repair by NHEJ

artemis

a nuclease that is part of DSB repair by NHEJ

Rad51

protein that help in repairing DNA DSB - recognizes overhangs and matching it to undamaged sister chromatid during G2 phase

• part of DSB repair by Homology-Directed Repair

Rag 1 & Rag 2

recombinase enzymes in antibodies that create more diversity by splicing certain pieces of DNA

• these enzymes recognize recombination signals (RS) which are contained within coding sequences (different V, D regions)

AID

activation induced deaminase - enzyme that deaminates cytosine into uracil which leads to base excision repair

• plays a key role in class switch recombination and somatic hypermutations

RNA polymerase

key enzyme in transcription - transcribes in 5’ to 3’ direction

describe RNA polymerase in bacteria

has 5 subunits: α (2 copies), β , β’ , ω, σ

describe the core polymerase in prokaryotes

includes the 4 subunits: α (2 copies), β , β’ , ω

• responsible for polymerase activity

describe the role of σ in transcription

it is a subunit that encounters the promoter sequences, forming a closed promoter complex and initiation transcriptions

• once transcription is initiated σ is released

what are the different RNA polymerase in eukaryotes

RNA I, RNA II, RNA III, mitochondrial RNA

RNA pol II

transcribes all protein coding genes and requires initiation fact that are not associated with the polymerase

• synthesizes mRNA, miRNA, lncRNA

what is RNA pol II recruited to promoter by?

general transcription factors - TFIID, TFIIB, TFIIF, TFIIE, TFIIH