Regulation of gene expression

Question 1

What are transcription regulators + function?

Answer 1

Group of proteins that recognise a specific sequence of bases on the DNA (5-10bp) that are often called cis-regulatory sequences, because they are on the same chromosome as the gene they control.

The Transcription regulators bind and determine which genes are to be transcribed and at what rate.

Question 2

How do transcription regulators bind?

Answer 2

Makes a series of contacts with the DNA, hydrogen bonds, ionic bonds and hydrophobic interactions. Often interact with structural motifs in the major groove

Question 3

Why is transcription regulation simpler in bacteria?

Answer 3

DNA in plasmids, no histone association, no chromosomes

Question 4

What is an operon? vs eukaryotes

Answer 4

Cluster of genes controlled by a single promoter, found mainly in bacteria. Genes in eukaryotes are often transcribed and regulated individually

Question 5

Explain tryptophan regulation

Answer 5

Tryptophan repressor transcription regulator binds to cis-regulatory sequence, blocking the promoter, preventing RNA polymerase from binding, stopping transcription

Question 6

How do transcription activators work?

Answer 6

Bind to poorly functioning promoter- improving the way the RNA polymerase binds.

Question 7

How many transcription factors does eukaryotic RNA polymerase require to work?

Answer 7

5

Question 8

Gene control region definition

Answer 8

The whole expanse of DNA involved in regulating and initiating transcription of a eukaryotic gene.

Question 9

Promoter definition

Answer 9

Where general transcription factors and polymerases assemble

Question 10

What is a cis-regulatory sequence?

Answer 10

Where transcription regulators bind and control the rate of assembly processes at the promoter.

Question 11

What are general transcription factors + function?

Answer 11

Proteins that recognise specific promoters and recruit the correct RNA polymerases. Bind to core promoter upstream of gene.

Question 12

Another broad class of multisubunit proteins

Answer 12

Coactivators and co repressors

Question 13

How do they assemble on DNA?

Answer 13

Do not recognise specific sequences themselves however they are brought to the sequences due to transcription regulators. The appropriate combination of coactivators or co repressors and cis-regulatory sequences can crystallise the assembly of the complex on DNA

Question 14

Co activator various functions

Answer 14

Involved in activating transcription

• bind to general transcription factors accelerating their assembly on a promotor
• form mediator complex that serves a s a bridge between DNA bound transcription activators,RNA polymerase and the general transcription factors

Question 15

Another name for co-activators

Answer 15

enhancers

Question 16

Transcription activator functions

Answer 16

• alter chromatin through covalent histone modifications
• nucleosome remodeling
• nucleosome removal
• histone replacement
• move from facultative heterochromatin to euchromatin, so can be assessed by general transcription factors
• promotes binding of additional regulators
• release RNA polymerase from promotors

Question 17

How is RNA polymerase released from promoters?

Answer 17

• activator removes nucleosome block
• communicates with RNA polymerase, through coactivator, to signal it to move ahead
• activator loads elongation factors onto more DNA, allowing RNA polymerase to move onto a new promoter

Question 18

Transcriptional synergy definition

Answer 18

Exhibited by transcription activators, where their overall transcription rate is much higher than the sub of their transcription rates alone.

Question 19

6 ways transcription repressors can work

Answer 19

• competitive DNA binding with activators
• masking the activation surface
• direct interaction with general transcription factors
• recruitment of chromatin remodelling complexes to condense the chromatin
• recruitment of histone deacetylases
• recruit histone methyl transferase which attaches methyl groups to histones, maintaining the chromatin in the silent form

Question 20

How do transcription repressors typically act?

Answer 20

Bring co-repressors to DNA

Question 21

Insulator DNA sequence function

Answer 21

prevents cis regulatory sequences activating inappropriate genes. Form loops of chromatin, holding the gene and its control region in close proximity to prevent control spilling over into different genes.

Question 22

Explain DNA looping

Answer 22

Allows a protein bound at a distance activator or repressor site to come into contact with the RNA polymerase

Question 23

What is the TATA box?

Answer 23

Found in the core promoter region of the DNA. Binding site for TATA binding protein and other transcription factors .

Question 24

Features of General Transcription Factors

Answer 24

• Have at least one DNA-binding domain
• Can be activated by ligand binding, phosphorylation or coactivators/corepressors
• Contain an activation domain, for regulators to bind
• bind to TATA

Question 25

Examples of cis-regulatory sequences

Answer 25

Enhancer region, silencer region and insulator region

Question 26

Difference between enhancer and promoter region

Answer 26

Enhancer increases the rate of transcription, promoter initiates transcription

Promoter must be close to the gene that is being transcribed whereas the enhancer does not.

Question 27

Which chromatin can be added by transcription factors?

Answer 27

Euchromatin, loosely wrapped DNA regions containing active genes

Question 28

How can chromatin be manipulated to silence transcription?

Answer 28

• Increase deactylation, more charges on histones, more attracted to DNA, more condensed chromatin- proteins cannot bind
• increase methylation of DNA bases cytosine and adenine, proteins cannot bind

Question 29

Where is the site of epigenetic modifications on histones?

Answer 29

N- terminal Histone tail

Question 30

Enzymes involved in methylation and acetylation

Answer 30

DNA methyltransferase - adds methyl groups
Demethylases- removes methyl groups

Acetyltransferases- transfer acetyl group from CoA
Histone deacetylase- removes acetyl group