Genetics exam 3

DNA Gyrase/Topoisomerase II

DNA supercoiling and replication

Introduces negative supercoils; relieves torsional strain using ATP

DNA Topoisomerase I

DNA supercoiling

Relaxes negative supercoiling without ATP

Dam methylase (DNA adenine methyltransferase)

DNA Replication Initiation

methylates GATC sites to regulate replication timing

Histone Acetyltransferase (HATs)

chromatin modification/transcription

acetylate histone tails, loosening chromatin to promote transcription

chromatin-modifying enzymes

chromatin regulation

add or remove acetyl, methyl, or phosphate groups on histones

DnaA protein

replication initiation

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

DNA Helicase (DnaB)

Replication elongation

unwinds double-stranded DNA at replication fork using ATP

Primase

Replication elongation

synthesizes short RNA primers for DNA polymerase binding

DNA Pol III

Replication elongation

synthesizes new DNA strand (main bacterial polymerase)

DNA Pol I

Replication Elongation

Removes RNA primers and replaces them with DNA

DNA Ligase

Replication and cloning

seals nicks between okazaki fragments or joins DNA fragments

Tus Protein

replication termination

binds ter sequences to stop replication forks

Flap endonuclease

replication elongation

removes displaced RNA Primers form lagging strand

telomerase

chromosome and maintenance

extends 3’ ends using internal RNA template

RNA polymerase (Bacterial)

transcription

synthesizes RNA from DNA template

sigma factor

transcription initiation

guides RNA polymerase to bacterial promotor (-35/-10 regions)

rho factor

transcription termination

binds RNA and terminates transcription (rho-dependent)

RNA polymerase I, II, III

Transcription (eukaryotic)

synthesizes rRNA, mRNA, and tRNA respectively

TFIIH

transcription initiation

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

splisosome (snRNP complex)

RNA Processing

removes introns and joins exons in pre-mRNA

poly(A) polymerase

RNA Processing

adds adenine tail to 3’ end of mRNA

RNA methyltransferase

RNA capping

adds 7-methylguanosine to 5’ cap of mRNA

aminoacetyl-tRNA synthease

Translation

charges tRNA with correct amino acids (“second genetic code”)

rRNA (peptidyl transferase activity)

translation elongation

catalyzes peptide bond formation in ribosome

release factor (RF)

Translation Termination

Hydrolyze polypeptide-tRNA bonds at stop codons

DAM (DNA adenine methyltransferase) (p)

Initiates replication at OriC via methylation at GATC sites

Anticodon (p/e)

Matches with mRNA codon

RNA Pol III (e)

primarily catalyzes RNA synthesis of tRNA

Hydrogen (p/e)

type of bond found in secondary protein structures

DNA Pol III (p)

synthesizing DNA in prokaryotes

Shine Delgarno

5'- AGGAGG -3' sequence that lies upstream of the start codon

RNA Pol II (e)

Catalyzes RNA synthesis of protein coding genes in eukaryotes

GC-rich hairpin

initiates rho-independent termination

Wobble (p/e)

When tRNA accepts a mismatch in the third position of the codon-anticodon

TATA box(e)

Site where transcription factors and RNA polymerase II initially bind, found upstream of the promoter

TFIID (e)

Binds the TATA box and recruits other proteins like it in order to initiate transcription

phosphodiester (p/e)

Bond formed between nucleotides of a growing DNA/RNA molecule

AUG (p/e)

Start Codon

RNA Pol (p)

Catalyzes RNA synthesis in prokaryotes

G4 Motif (e)

G-rich sequence that promotes replication

UAA(p/e), UAG, UGA

Stop Codon

Stop Codon(p/e)

Causes the addition of a water molecule instead of an amino acid which releases the polypeptide

codon(p/e)

A sequence of three nucleotides found in mRNA

Peptide (p/e)

BOND FORMED BETWEEN AMINO ACIDS DURING PROTEIN ELONGATION

Rut (p)

where rho binds

leading (p/e)

Strand that undergo continuous replication

Activators (e)

TRANS-ACTING ELEMENTS THAT UP REGULATION TRANSCRIPTION

Replisome (p/e)

COMPLEX THAT INCLUDES A PRIMOSOME AND TWO DNA POLYMERASES

Lagging (p/e)

strand that produces okazaki fragments

Tus(p)

a protein that binds to the ter sequence to stop helicase

ARS (Autonomously Replicating Sequence)(e)

origin of replication in eukaryotes

NFR (nucleosome free region)(e)

Regions with no nucleosomes

DNA Pol Delta (E)

specific to lagging strand synthesis in eukaryotes

Telomerase (E)

Adds DNA overhangs on 3’ ends of chromosomes

Sigma factor (p)

part of the holoenzyme, recognizes -35 sequence

terminator (p/e)

Sequence found at the end of the gene that stops transcription

Okzaki (p/e)

small fragments of DNA on the lagging strand

OriC (p)

origin of replication in E. Colo

DnaA (p)

binds DNA to break H-bonds at AT-rich regions

Ter (p)

Termination sequence found at the opposite end of OriC

amino (p/e)

Functional group at the N-terminus

NusA (p)

protein increases pausing of RNA polymerase during transcription termination when rho is absent

primosome (p/e)

Helicase and primase complex

A-site (p/e)

codon recognition that occurs here in the robosome

DNA Pol epsilon (e)

specific to leading strand synthesis in eukaryotes

mediators (e)

A GROUP OF PROTEINS THAT INCREASE THE RATE OF TRANSCRIPTION BY ACTING AS A BRING BETWEEN ENHANCER/ ACTIVATOR ELEMENTS AND THE DNA POL II/GTFS

RNA Pol I (E)

catalyzes RNA synthesis of ribosomal RNA (rRNA)

prokaryotic ribosome (p)

composed of a 30s and 50s subunit

Gyrase (p)

Alleviates positive supercoiling

Acceptor stem (p/e)

within the tRNA, binds to the correct amino acid

-10 region (p)

SITE WITHIN THE PROMOTOR WHERE THE HOLOENZYME IS ABLE TO INITIATE THE CREATION OF AN OPEN COMPLEX

+1 site (p)

specific site within the promotor where transcription begins

20 (p/e)

Number of amino acids

SSB (p/e)

Single Stranded Binding Protein

proteins that hold strands of DNA apart during replication

enhancer (e)

CIS-ACTING ELEMENTS FOUND UPSTREAM OF THE PROMOTER SEQUENCE

p-site (p/e)

peptidyl transfer occurs here in the ribosome

DNA Pol alpha

mimics primase but in eukaryotes

Eukaryotic ribosome

composed of 40s and 50s subunits

tRNA (p/e)

carries amino acid to be added

rho (p)

ENZYME THAT DISOCIATES NEWLY SYNTHESIZED MRNA AND RNA POLYMERASE FROM THE DNA MOLECULE

promotor (p/e)

INCLUDES THE -35, -10, AND +1 REGIONS

primase (p)

SYNTHESIZES RNA PRIMER IN PROKARYOTES

RNA Pol I(p)

replaces RNA primer with DNA in prokaryotes

carboxylic acid (p/e)

function group at the c-terminus

ligase (p/e)

links okazaki fragments together

helicase (p/e)

unwinds DNA

TFIIH (e)

BINDS THE TATA BOX WITH OTHER PROTEINS LIKE ITSELF. THIS PROTIEN HAS HELICASE ACTIVITY AND IS RESPONSIBLE FOR CREATING AN OPEN COMPLEX DURING TRANSCRIPTION