Molecular Bio

Fall25

Conserved Sequences

GU 5’ exon

A branchpoint

AG 3’ ss

snRNAs

form large ribonucleoprotein complexes

U1 Function

binds and bp 5’ss

U2 Function

binds and bp branchpoint and moves it ti 3’ss

U2AF

binds polpramidine tract and loads U2 onto branchpoint

triSNRP

activates spiceosome allos lariat formation via SN2

U5 stabilizes intermediates andmoves 5’ss to branchpoint, first bond broken and made

SR protein binding

bind to splicing enhancers to promote 

hnRNPs Binding

bind to splicing silencers to inhibitSR

SR protein location and interactions

on CTd of RNAPII, stabilize U1/2/2AF and recruit triSNRP

HNrnp Location and Interaction

block U1/2 recognition or U2AF binding

can spread along mRNA and loop out exons to promote skipping

GTP Hdrolsis

allows release of IFs and large subunit can bind to start elongation

elF4E

replaces cap binging complex, binds cap and recruits IF 

has helicas activit to remove hairpins what would inhibit trxl

elF4G

bridges cap and tail b binding polA tail and elF4E

elF2-GTP complex

recognize elF4 and loadat 5r’end of mRNA

if elF2 phosp0horlates can be used to reduce rate of translation initiation

tRNAs 

AA loaded via tRNA snthase, uses ATP to link AA , driving peptide bond formation in ribosome

one snthase per AA

IRP1

binds IRE in mRNA, onlt in low iron; stabilizes an prevents trxl

miRNAs

ctrl mRNA trxl

drosha

fragements pre-miRNAs for ctoplasm

dicer

cleaves pri-mRNA hp loop for 1 strand loading into RISC

RISC

blocks trxl b ribosomes if bp is imperfect

with miRNA binds 3’ UTR and block trxl

RNAi

siRNAs that target an mRNA for amplification into more siRNA, can be inherited over multiple generations

use to desttro viruses/ transposons or reduce levels of mRNA si

siRNAs

use bp to recognize targets

Primase

synthesizes RNA primer providing 3’OH next to ss NA for synthesis (near fork)

dNAPolI

removes RNA primer an fills gap left from primer

dNA Ligase

seals ssdNA nick left after primer removal an fills in b dNAPol (seals phosphodiester backbone)

HR

RPA- 3’ssdNA binding

Rad51- finds homologous dNA for sequence invading

Ligase- seals gap prod Hollida Junctions

Bridge Helix

seperates dNA strands

Rudder

guides dNA strands back together

Jaw

guides dNA into active site

TFIId

binds first in minor groove of TATA box for dNA melting

TFIIH

helicase - opens promotor for initiation

kinase - phosphorlates ctd for elongation initiation

Low Iron 5’ HP

IRP binds, inhibiting trxl

helicase activit unwinds hp

protein levels decrease

ferritin increases and stores iron

Low Iron 3’UTR

trxl proceeds

IRP stabilizes

increases mRNA and protein levels

High Iron

IRP cant bind hp

TfR brings in more iron

ferritin stores less iron

drosha Nuclease Activit

removes hp loop and creates fragments

drosha helicase activit

unwinds strands for ssdNA

IF1

prok trxl initiation

binds and blocks A site

IF2

prok trxl initiation

binds P site and GTP

IF3

prok trxl initiation

binds ribosome, loads mRNA on s subunit for Sd binding

eRF1

euk trxl termination

recognizes and binds stop codon on A site

allows learnign toward P site

Rli1-ATP

euk trxl termination

binds to promoter accomaation and increases peptive hlsis rate

Rli1/2 Prok

termination b recognizes stop codon

Ef-Tu GTP

masks AA to ensure accurac