the genetic code and transcription

mRNA

RNA that is translated into protein

rRNA

an integral part of the ribosome

tRNA

serves as intermediaries, brining amino acids to the ribosome

which types of RNA function in translation?

rRNA and tRNA

Proflavin

a mutagen that induces insertion or deletion of single nucleotides

degenerate code

a particular amino acid can be specified by more than one triplet

non overflapping code

reading frame advances three nucleotides at a time

How is transcription different than DNA replication?

1. only one strand is copied

2. U instead of T

How does transcription begin?

RNA polymerase binds to a promoter sequence, triggering local unwinding of the double helix

which enzyme initiates synthesis of RNA

RNA polymerase

Describe the bacteria transcription start site

almost always a purine and usually an adenine

name the essential sequences in a typical bacterial promoter

1. start site

2. -10 seq or pribnow box (TATAAT)

3. -35 sequence (TTGACA)

in bacteria what binds the -35 and -10 sequences?

row

in bacteria what binds the upstream element

alpha subunits

many termination sequences contain

short GC rich sequence followed by several Us

Termination of RNA synthesis

RNA polymerase copies the termination signal causing the GC region in the RNA tp form a hairpin loop pulling the RNA molecule away from the DNA, breaking the A-U bonds and releasing the RNA

name 6 differences between EUK transcription and PROK

1. 3 RNA polymerases

2. more varied promoters

3. transcription factors

4. protein protein interactions play and important role

5. RNA cleavage more important

6. RNA processing

core promoter

the smallest set of DNA sequences that initiates transcription

name the four sequences involved in core promoter function of RNA polymerase 2

1. initiator

2. TATA box

3. TFIIB recognition element (BRE)

4. downstream promoter element (DPE)

initiator sequence

surrounds start site

TATA box

a consensus sequence of TATA followed by two to three A’s, is located about 25 nucleotides upstream of the start point

BRE (TFIIB. recognition element) location

slightly upstream of TATA box

DPE location

about 30 nucleotides downstream from the start point

for RNA polymerase II, where is the start site?

mid promoter

TATA driven promoters always contain

TATA box and Inr

TATA driven promoters may or may not contain

BRE

TATA driven promoters do not contain

DPE sequence

DPE driven promoters always contain

DPE seq and Inr

DPE driven promoters dont contain

TATA box or BRE

RNA polymerase III usues promoters that are located where?

downstream of the start point

tRNA has which boxes?

box A/B

rRNA has which boxes?

box A/C

Core promoters are capable of driving only a____level of transcription

basal (low)

proximal control elements

Those within 100–200 nucleotides of the start point

distal/enhancer elements

farther than 200 nucleotides from start

general transcription factor

always required for RNA polymerase binding to promoters

General Transcription Factors Are Involved in the Transcription of ____

all nuclear genes

in EUK which TF binds first?

TFIID

where does the preinitiation complex for?

on the promoter

What is essential for Initiation at a RNA Polymerase II Promoter?

TFIID

TFIID function in Initiation at a RNA Polymerase II Promoter

recognizes and binds DNA because of its TATAbinding protein (TBP) subunit, followed by other TFs, leading to recruitment of RNA polymerase II

2 functions of TFIIH in Initiation at a RNA Polymerase II Promoter

1. helicase (local unwinding)

2. kinase (Phosphorylation of the Cterminal domain (CTD) of RNA Polymerase II)

function of both of TFIIH’s enzymatic activites in Initiation at a RNA Polymerase II Promoter

Both promote the release of RNA Polymerase II from the initiation complex and the beginning of transcription

RNA pol III termination signal

a short run of Us with no protein factors needed for recognition

RNA pol II termination signal

transcripts are cleaved at a specific site before transcription ceases ; The cleavage site is 10–35 nucleotides downstream of a AAUAAA sequence in the RNA

tRNA secondary structure

most containing four hairpin loops; but some have a fifth region called a variable loop; cloverleaf structure and are synthesized as pre-tRNAs, followed by processing

hnRNA

a mixture of mRNA molecules and their precursors, pre-mRNA

how are pre-mRNAs processed?

by removal of sequences and addition of 5′ caps and 3′ tails

what acts as a platform for protein complexes involved in processing in RNA polymerase II?

C terminal domain

5’ cap

is a guanosine that is methylated at position 7 of the purine ring

how is the 5’ cap bound to RNA?

5-5 linkage

2 functions of 5’ cap

1. stabilizes by protecting against nuclease attack

2. plays a role in positioning the RNA on the ribosome for initiation of translation

poly A tail

ranges from 50 to 250 nucleotides long

what adds the Poly A tail?

poly A polymerase

poly adenylation signal

AAUAAA, is located just upstream of the polyadenylation site, and a GU- or U-rich element is located downstream of it

3 functions of the poly A tail

1. protect against nuclease attack

2. required for export of the transcript to the cytoplasm

3. may also help ribosomes recognize and bind mRNAs

the 5′ end of an intron typically starts with ___ and terminates with ___ at the 3′ end

GU; AG

Intron removal is catalyzed by large molecular complexes called___

spliceosomes

spliceosomes consist of…

consisting of five types of RNA and many proteins

Spliceosomes assemble on transcripts from a group of smaller RNA-protein complexes called ___

snRNPs (small nuclear ribonuclearprotein complexes)

snRNPs (small nuclear ribonuclearprotein complexes)

each containing one or two snRNA molecules (small nuclear RNA)

how are spliceosomes assembled?

by sequential binding of snRNPs to pre-mRNA

first step of spliceosome assembly

the binding of a snRNP called U1, which contains an RNA that can base-pair with the 5′ splice site

second step of spliceosome assembly

A second snRNP called U2 binds to the branch-point sequence

last step of spliceosome assembly before lariat formation

a group of snRNPs (U4/U6 and U5) brings the ends of the intron together to form a mature spliceosome and pre-mRNA is cleaved at the 5′ splice site, which is joined to an adenine residue located at the branch-point sequence

what is the name of the structure resultinf from the last step of spliceosome assembly?

lariat

step of spliceosome asssembly followinf lariat formation

the 3′ splice site is cleaved, and the two ends of the exon are joined together; an exon junction complex (EJC) is deposited near the boundary of each newly formed exon-exon junction

mRNA half life

the time required for 50% of the molecules to degrade

when do most RNA processing events occur?

cotranscriptionally

what is responsible for RNA processing

The long C-terminal domain (CTD) of RNA polymerase; Many repeats of a seven-amino-acid sequence on the CTD bind enzymes needed for capping, splicing, and cleavage/polyadenlylation