Enzymes and Central Dogma

DNA Gyrase (Topoisomerase II)

Process: DNA supercoiling & replication

Function: introduces negative supercoils; relieves torsinal strain using ATP

DNA topoisomerase I

Process: DNA supercoiling

Primary Function: relaxes negative supercoils without ATP

Histone acetyltransferases (HATs)

Process: chromatin modification/transcription

Function: acetylated histone tails, loosening chromatin to promote transcription

DAM methylase

Process: DNA replication initiation

Function: methylates GATC sites to regulate replication timing

chromatin-modifying enzymes

Process: chromatin regulation

Function: adds or removes acetyl, methyl, or phosphate groups on histones.

DnaA protein

Process: replication initiation

Function: binds to DnaA boxes, bends DNA, and begins strand separation

DNA helicase (DnaB)

Process: replication elongation

Function: unwinds double-stranded DNA at replication fork using ATP

Primase

Process: replication elongation

Function: synthesizes short RNA primers for DNA polymerase binding

DNA polymerase III

Process replication elongation

Function: synthesizes new DNA strands (main bacterial polymerase)

DNA polymerase I

Process: Replication elongation

Function: removes RNA primers and replaces them with DNA

DNA ligase

Process: replication & cloning

Function: seals nicks between Okazaki fragments or joins DNA fragments

Tus protein

Process: replication termination

Function: Binds ter sequences to stop replication forks

Flap endonuclease

Process: replication elongation (eukaryotic)

Function: removes displaced RNA primers from lagging strand

Telomerase

Process: chromosome and maintenance

Function: extends 3’ ends using internal RNA template

RNA polymerase (bacterial)

Process: transcription

Function: synthesizes RNA from DNA template

sigma factor

Process: transcription

Function: guides RNA polymerase to bacterial promoter (-35/-10 regions)

rho factor 

Process: transcription termination

Function: binds RNA and terminates transcription (rho-dependent)

RNA polymerase I, II, III

Process: transcription (eukaryotic)

Function: Synthesizes rRNA, mRNA, & tRNA respectively

TFIIH

Process: transcription initiation

Function: acts as helicase and kinase; opens DNA and phosphorylates RNA Pol II

Spliceosome (snRNP complex)

Process: RNA processing 

Function: removes introns and joins exons in pre-mRNA

Poly(A) polymerase

Process: RNA processing

Function: adds adenine trail to 3’ end of mRNA

RNA methyltransferase

Process: RNA capping

Function: Adds 7-methylguanosine to 5’ cap of mRNA

Aminoacyl-tRNA synthetase

Process: Translation

Function: Charges tRNAs with correct amino acid (“second genetic code”) 

rRnA (peptidyl transferase activity)

Process: translation elongation

Function: Catalyzes peptide bond formation in ribosome

Release factors

Process: translation termination

Function: hydrolyze polypeptide-tRNA bond at stop codon.