12: Gene Transcription & RNA Modifications

First step in gene expression

Transcription

Gene

A DNA segment that makes a functional product (RNA or peptide)

Transcription

DNA → RNA copies

Structural gene

Protein encoding genes

Translation

mRNA → peptide

mRNA

Processed transcription product

Where does the info for proteins come from

DNA

Basic gene map of a bacterial gene

• Regulatory sequences

• Promoter region

• Coding region

• Terminator sequence

Basic bacterial transcript map

• 5’ ribosome binding site

• Start coon

• Stop codon

What binds to the promoter region to kickstart transcription

RNA polymerases and transcription factors (TFs)

What direction does RNA pol move

5’ → 3’

Where is the transcriptional start site in the promoter region

+1

In bacteria, where are the signal sequences for TFs and enzymes in the promoter region

-35 and -10

Consensus sequence

The most common variation of a highly conserved region of DNA

RNA pol structure in bacteria

5 subunits and a sigma factor

Purpose of sigma factor in RNA pol

Recognizes the -35 and-10 sequences, allowing for activation

Structure of the sigma factor

helix-turn-helix

Steps of transcription

• Initiation

• Elongation

• Termination

Steps of initiation in bacteria

• RNA pol binds to DNA

• Moves along until sigma factor recognizes the promoter sequence

• Sigma factor opens the dsDNA and dissociates

• Open complex begins moving down DNA 5’ → 3’

Elongation mechanism

NTPs enter open complex to form the DNA-RNA hybrid

What determines transcriptional direction

Promoter sequence

Types of termination in bacteria

Rho-dependent and rho-independent

Rho-dependent termination

rho-recognition site of DNA is transcribed, rho protein binds to mRNA, forming a stem loop structure in the RNA pol that causes it to dissociate

Rho-independent termination

Stem loop structure at the end followed by a uracil rich region serves as a binding site for NusA, which causes RNA pol to dissociate

Eukaryotic RNA pols

• I: rRNA genes, minus 5S rRNA

• II: protein genes and snRNA

• III: tRNA, microRNA, and 5S rRNA

What region of the RNA pol holds the growing mRNA in place

Rudder region

What cofactor is needed in eukaryotic RNA pols

Mg

Eukaryotic promoter region

TATA box

Basal transcription

Low transcription rate that happens due to minimal enzymatic and protein interactions

What helps regulate transcription above the basal rate

Regulatory elements that bind proteins upstream of the promoter region

Types of regulatory elements

Silencers and enhancers

Cis-acting elements

DNA sequences that affect transcription of the gene they are associated with

Trans-acting elements

Proteins that bind to cis-elements

The three components needed for eukaryotic basal transcription

• 5 general transcription factors

• Mediator complex

• RNA pol II

Euk general TFs

TFII D, B, F, H, and E

Pre-initiation complex

GTFs and RNA pol II

Types of euk termination

Allosteric and torpedo

General mechanism for euk termination

Poly-A signal is transcribed, then the mRNA is cleaved. Not much more is known