BIO Exam 4

What do general transcription factors do

They help RNA polymerase II bind to the core promoter

Required for transcription to happen

Form the basal transcription apparatus

Where do general transcription factors bind

Core promoter (ex. TATA box)

What is an example of a general transcription factor

TFIID - binds to the TATA box

What do regulatory transcription factors do

Control the rate of transcription

Can increase (activators) or decrease (repressors) transcription

Without them transcription can happen but at a low level (not required for transcription)

Where do regulatory transcription factors bind

Enhancers (increase transcription)

Silencers (decrease transcription)

Regulatory promoter

Describe how a regulatory transcription factor binds to an enhancer

A regulatory transcription factor binds to a specific DNA sequence called regulatory elements within an enhancer. The enhancer may be far from the promoter so the DNA looping brings the bound transcription factor closer. The transcription factor recruits coactivators and the basal transcription machinery which will increase the rate of transcription

What are 3 ways that the function of a regulatory transcription factor can be modulated

Binding of a small effector molecule

Protein-protein interactions

Covalent modification

What does binding of a small effector molecule do

a small molecule like a hormone binds the transcription factor which changes the shape (conformation)

what’s the effect of binding of a small effector molecule

can activate or deactivate the transcription factors

changes the ability to bind to DNA or recruit proteins

What does protein-protein interaction do

the transcription factor interacts with other proteins

what’s the effect of protein-protein interactions

can enhance or inhibit its activity (helps recruit corepressors and coactivators)

What does covalent modification do

chemical groups added to the transcription factors (ex. phosphorylation and acetylation)

what’s the effect of covalent modification

changes the stability, activity, and ability to bind to DNA

How do chromatin remodeling complexes alter nucleosomes

by changing how DNA is wrapped around nucleosomes to control access to genes

What do chromatin remodeling complexes do

Reposition nucleosome (exposes or hides promoter region)

Remove nucleosomes from DNA ( makes DNA more accessible)

Replace standard histones with variant histones (alters chromatin structure and gene activity)

what’s a nucleosome

DNA wrapped around histone proteins

what are histone variants

alternative version of a standard histone protein that has a slightly different amino acid sequence and can be

How do histone variants affect transcription

Some make DNA looser which it makes it easier for transcription factors to bind → increase transcription

Some make DNA tighter which makes it hard to access → decrease transcription

Where can the histone variant be used

active genes, centromeres, DNA repair sites

gives chromatin specific functions

how do histone variant influence gene expression

by changing nucleosome properties they affect TF binding and RNA polymerase access

ultimately controls whether genes are off or on