Lecture 4: Transcription (DNA to mRNA)

What are regulatory DNA sequences

Stretches of non-coding DNA vital for RNA transcription which lie upstream of the coding region

Define exon

Sections of mRNA that code for amino acids and are translated into proteins

Define introns

Sections of mRNA that don’t code for amino acids in protein product which are removed in post processing

What are the 3 stages of mRNA transcription

Initiation

Elongation

Termination

What section of the gene does RNA polymerase II bind to

Promotor region

What recognises the start site in a prokaryote

Sigma factor

What is a TATA box

Sequence of T and A nucleotides in the promotor region where general transcription factors bind

What is TFII

The transcription factor that recruits RNA polymerase II

What is the process where RNA is polymerised from DNA template

Elongation

Does RNA polymerase require a primer

NO

What are topoisomerases

Prevents build up of tension caused by supercoiling by creating controlled breaks in the DNA

What is the pre-initiation complex (PIC)

Large protein assembly that assembles on the DNA promotor to correctly position the RNA polymerase II for transcription initiation

Where is termination signal on the gene

Downstream of the stop codon

What is the termination signal

Terminates transcription

How does the RNA displace from the DNA

RNA folds into a hairpin

What are the 3 ways of processing an mRNA transcript

1. Capping

2. Polyadenylation

3. Splicing

What is the mRNA cap

Modified guanine nucleotide with a 5’-5’ phosphodiester bond (triphosphate bridge) with a methyl group added

What does the cap act as

Recognition site for ribosomes on mRNA

What is the polyA tail

Long stretch of A nucleotides on 3’ end added 1 at a time

What is the function of the polyA tail

Protects the reactive mRNA from degradation and play a role in exporting mRNA from nucleus to cytoplasm

When is the mRNA cleaved

After the polyA signal in the 3’ untranslated region

What is a Spliceosome

A complex of proteins and small nuclear ribonucleoprotein (snRNP)

What does this catalyse

The intron removal (mRNA splicing)

What is ribonucleoprotein

A complex of protein and RNA

What is snRNA

Small nuclear RNA

• Small RNA that recognise splice sites and catalyse splicing reaction

What is alternative splicing

A process that allows a single gene/ polypeptide to produce multiple proteins by joining different combinations of its exons

What are cis-regulatory elements

DNA sequences around the protein coding regions that control when and how much mRNA is transcribed

What site does the transcription factor bind to

Enhancer region (upstream of 5’ gene)

The presence of what affects the probability that the protein initiation complex forms (PIC)

Transcriptional activators

What are the 2 ways that cis-regulatory elements can activate/inhibit transcription

Synergistically and/ or antagonistically (the sum of inhibitory and promotory added to see whether PIC forms)

What protein complex links activator transcription factors with the pre- initiation complex

Mediator protein complex

What else is used as complex regulation of gene transcription

Co-factors for transcription factors and chromatin modifiers

What is the function of chromatin modifiers

Facilitate access to DNA by transcription factors adding/removing modifications from histones

What is the nucleosome

Wound sections of DNA with histone protein cores packed into chromatin fibres

What is the electrostatic interaction between histones and DNA

The DNA backbone is negatively charged due to phosphate groups

The histones contain positively charged residues

What makes nucleosomes dynamic

The chromatin remodelling factors slide along DNA strand, exchanging histone octamers/subunits

This removes the core histones and alter the structure of the nucleosome

What are the 2 ways histone tails can be modifies

Methylation

Acetylation

What is the action of methylation

The chromatin condenses to become more tightly packed and the transcription is repressed

What is the action of acetylation

The chromatin decondenses (opens up) and transcription activated so edges are expressed

How does histone acetylation affect gene expression?

It increases gene expression as it loosens chromatin structure by reducing the affinity of the nucleosome tails

Also recruits proteins that drive the transcription of genes

How does histone methylation affect gene expression

It decreases gene expression as chromatin structure tightens by increasing affinity of nucleosome tails

Also recruits proteins that suppress transcription

Also attract proteins that pack DNA into heterochromatin