bio41 test 2 proteins + RNAs

DNA polymerase III (SPECIFIC)

Primary player in DNA replication; catalyzes condensation reaction between the 3’ nucleotide of the growing strand and the 5’ phosphate of the new nucleotide.

Exonuclease

Checks sequence and removes incorrect nucleotide during DNA replication.

Sliding (beta) clamp

Keeps DNA polymerase on the DNA during replication.

DNA helicase

Breaks hydrogen bonds between helices so DNA strands can separate.

SSB

Single-strand binding protein; protects DNA from repair molecules during Okazaki fragment construction on the lagging strand.

Primase

Creates the RNA primer so DNA polymerase can extend the strand and build Okazaki fragments.

DNA polymerase I

Removes the RNA primer on Okazaki fragments and replaces it with DNA.

Topoisomerase

Nicks DNA to relieve coiling tension during replication.

Telomerase

Builds back telomere repeated sequences on the ends of chromosomes.

TFIIH

General transcription factor that opens the transcription bubble using ATP hydrolysis and phosphorylates RNA polymerase II tail to initiate transcription.

RNA polymerase II

Synthesizes RNA 5’ to 3’ from template DNA, maintains no primer or proofreading, and reads template DNA in the 3’ to 5’ direction.

TFIID

TBP subunit binds to TATA box, causing a distortion that recruits other transcription factors to form the transcription initiation complex.

TFIIB

Helps to form the RNA polymerase II pre-initiation and TATA-TBP complexes.

TBP

TATA-binding protein; subunit of TFIID.

TFIIF

Helps RNA polymerase II form the pre-initiation complex and prevents it from interacting with DNA outside the promoter.

TFIIE

Helps recruit TFIIH for the RNA polymerase II pre-initiation complex.

Elongation factors

Help transcription by wedging between DNA and histones to allow access to RNA polymerase II and transcription factors.

RNA polymerase (prokaryotic)

Synthesizes RNA strand from template DNA; reads and moves 3’ to 5’ to build RNA 5’ to 3’.

Sigma factor

Binds to -35 and -10 sequences to recruit and orient RNA polymerase during prokaryotic transcription.

Nuclear pore complexes

Control which mRNA molecules exit the nucleus to regulate translation based on proteins that bind to processed RNA.

Aminoacyl-tRNA synthetase

Recognizes the anticodon loop of tRNA and uses ATP to create a covalent bond (between the carboxyl group of the amino acid and the 3' hydroxyl group of the terminal ribose of the tRNA molecule) linking tRNA with its corresponding amino acid

Release factor

Binds to the A site on the ribosome to terminate translation.

Small nuclear ribonucleoprotein (snRNP)

Form a spliceosome with snRNAs that complements splice sites for RNA splicing.

mRNA

Messenger RNA; protein-encoding RNA that has been spliced, has a poly A tail, and a 5’ cap.

tRNA

Transfer RNA; adaptor that brings amino acids to ribosomes during translation, with an anticodon on one end and amino acid on other; made by aminoacyl-tRNA synthetase

rRNA

Ribosomal RNA; structural and catalytic core of the ribosome.

snRNA

Small nuclear RNA; part of spliceosome with about 200 nucleotides.

miRNA

Micro RNA; noncoding RNA that base pairs with specific mRNA to regulate its stability and translation; can form complex w RISC to degrade target mRNAs

siRNA

Small (22 bp) interfering RNA; produced by Dicer (which breaks double-stranded RNA during RNA interference); exogenous; in complex w RISC (takes single strand to destroy complementary RNA) or RITS (binds to strands as they emerge from RNA pol and promotes heterochromatin formation on DNA)

lncRNA

Long noncoding RNA; involved in regulation and structural roles in the cell; scaffolding