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The transcription of genes

The central dogma of molecular biology

transcription

translation

DNA
reversetranscription replication

RNA
replication

protein

Types of RNA
transcription

tRNA mRNA rRNA other types protein

translation

DNA

The transcription of genes: prokaryotes

Key proteins involved in the transcription of bacterial genes

RNA polymerase, core enzyme two subunits, one subunit, one subunit, [one subunit] sigma factor, RNA polymerase + sigma factor holoenzyme

synthesizes all 3 classes of RNA (mRNA, tRNA, rRNA)

Structure of eubacterial RNA polymerases

Transcription unit
A sequence of DNA transcribed into a single RNA, starting at the promoter and ending at the terminator

Promoter - region of DNA involved in binding of RNA polymerase to initiate transription

Functions of a promoter
The promoter determines:
Which strand will serve as a template. Transcription starting point. Strength of polymerase binding. Frequency of polymerase binding.

Four stages of transcription

2 3 template recognition initiation elongation termination 4

Template recognition

forming the closed promoter complex

Template recognition
RNA polymerase recognizes promoters based on consensus sequences consensus sequence an idealized sequence in which each position represents the base most often found when many actual sequences are compared

- 35 box

- 10 box

Transcription bubble

Contact points between the sigma factor and a typical prokaryotic promoter

HOOC

NH2

Initiation of transcription
formation of open complex initial synthesis loss of sigma factor promoter clearance

RNA polymerase moves like an inchworm during elongation

Back end moves 1 bp per nucleotide added to RNA

Front end moves several bp discontinuously

RNA synthesis

Termination of transcription
How does the RNA polymerase know when to stop? TERMINATORS - sequences at which
transcription stops and the complex dissociates Types (based on in vitro experiments):
intrinsic terminators - no proteins (factors) required rho-dependent - rho factor required

Intrinsic terminators: structural features

hairpin-forming (palindromic, inverse-repeat)

region a run of U residues

Intrinsic terminators: structural features

rho-dependent terminators
Principal feature: C-rich, G-poor sequence preceding actual termination site

Hot-pursuit model for rho-dependent termination

Coupling of transcription and translation in prokaryotes

The transcription of genes: eukaryotes

The generation of mature mRNAs involves the following major steps

Transcription Pre-mRNA processing Transport to the cytoplasm

1. transcription the eukaryotic RNA polymerases the transcription factors promoters and enhancers stages chromatin remodeling initiation of transcription elongation termination 2. pre-mRNA processing capping splicing polyadenylation 3. transport to the cytoplasm

Types of eukaryotic RNA polymerases

Type of Polymerase

Product

Location

RNA Polymerase I RNA Polymerase II RNA Polymerase III

pre-rRNA (except 5S) nucleolus pre-mRNA (hnRNA) tRNA, 5S rRNA, etc. nucleoplasm nucleoplasm

RNA pol II cannot initiate transcription by itself; requires auxilliary transcription factors to initiate transcription.
Transcription factor - any protein other than RNA Polymerase that is required for transcription may bind to RNA Polymerase may bind to another transcription factor may bind to cis-acting DNA sequences may bind to effectors

Transcription factors
Types of transcription factors:
(according to their importance to transcription initiation)

General factors -

required for initiating transcription at all promoters

Upstream factors - ubiquitous factors that increase the efficiency of transcription initiation; set of factors unique to each promoter Inducible factors - act in the same manner as an upstream factor but their synthesis is regulated in a temporal or spatial manner Basal transcription apparatus - RNA polymerase + general factors both needed to initiate transcription

Major types of DNA-binding domains (motifs found in the sequences)

zinc finger helix-turn-helix amphipathic helix-loop-helix leucine zippers

leucine zipper zinc finger

helix-turn-helix

Promoters vs. enhancers

Initiation of transcription
ordered sequence of assembly of initiation complex phosphorylation of the C-terminal domain (CTD) tail of RNA polymerase II (may be needed for promoter clearance)

Assembly of initiation complex

Elongation of transcript

phosphorylation of the CTD tail of RNA polymerase II

Termination and polyadenylation

CPSF

CPSF = cleavage and polyadenylation specificity factor

Pre-mRNA processing: capping

Caps may differ in number of methylations

Pre-mRNA processing: splicing

Spliceosomes consist of snRNPs

Conserved signals at intron-exon junctions

Translation of mRNA in the cytoplasm

Next meeting

Translation of mRNAs