Transcriptional Regulation

Question 1

Describe transcriptional regulation?

Answer 1

Gene expression beings at the promoter; a sequence of DNA adjacent to the gene where transcription factors bind and RNA polymerase is recruited to initiate transcription

Question 2

What are the two types of regulatory proteins may bind DNA?

Answer 2

Repressor proteins and activator proteins

Question 3

Explain regulation of gene expression in prokaryotes

Answer 3

Core promoter elements variants recognised and bound by specific sigma factors; strong promoters conform to the consensus sequence and initiate transcription frequently

Question 4

What are the 3 proteins involved in the uptake and metabolism of lactose?

Answer 4

beta-galactoside permease ( carrier protein that moves sugar into the cell); beta-galactosidase (an enzyme that hydrolyses lactose); beta-galactoside transacetylase (transfers acetyl groups to certain b-galactosides)

Question 5

What are the two ways to regulate a metabolic pathway?

Answer 5

allosteric regulation of enzyme-catalysed reactions allows rapid fine-tuning or regulation of gene expression

Question 6

What is an operon?

Answer 6

It is a cluster of genes with a single promoter and transcribed together in a single mRNA, within a prokaryote

Question 7

What does an operon consist of?

Answer 7

A promoter; two or more structural genes; an operators (short stretch of DNA between promoter and structural genes)

Question 8

What are the 3 ways transcription is regulated in prokaryotes?

Answer 8

An inducible operon regulated by a repressor protein (default is off); a repressible operon regulated by a repressor protein (default is on); an operon regulated by an activator protein (default is off)

Question 9

What do inducible operons control?

Answer 9

Catabolic pathways

Question 10

What do repressor systems control?

Answer 10

Anabolic pathways

Question 11

If an operon is regulated by an activator protein, what happens?

Answer 11

It increases transcription through positive control

Question 12

Name the 10 points of regulation of gene expression in Eukaryotes

Answer 12

Must be regulated to ensure proper timing of protein production; can occur at multiple points; remodelling of chromatin for transcription; transcriptional regulation; pre-mRNA splicing; transport of the mRNA; mRNA stability; translational control at the ribosome; post-translational modification of proteins; protein degradation

Question 13

What is chromatin remodelling?

Answer 13

It is the alteration of chromatin structure

Question 14

What charge is the amino acid tail on histones at its N terminus?

Answer 14

Positively charged

Question 15

How are histone acetyltransferases able to change the charge of their tails?

Answer 15

By adding acetyl groups to lysine residues

Question 16

What does changing the charge of the tails do?

Answer 16

It opens up nucleosomes; increases DNA accessibility; facilitates transcription factor binding and recruitment of chromatin remodelers; activates transcription

Question 17

What are the possible mechanisms for increased local access?

Answer 17

Nucleosome sliding; nucleosome displacement; partial histone displacement; replacement of octamer subunit with histone variants

Question 18

What are the two kinds of chromatins that are visible during interphase?

Answer 18

Euchromatin and heterochromatin

Question 19

What does euchromatin do?

Answer 19

It actively transcribes genes

Question 20

What is heterochromatin?

Answer 20

It contains genes that are not transcribed

Question 21

What determines the levels of transcription (promoter strength)?

Answer 21

The efficiency of binding of GTFs to the core promoter DNA sequences

Question 22

Describe regulation of transcription in eukaryotes.

Answer 22

General transcription factors binding the core promoter to recruit RNA polymerase.
Transcriptional activator or repressor proteins bind to the DNA regulatory elements.
General transcriptional factors binding the core DNA promoter (starting with TFIID) to recruit RNA polymerase.

Question 23

What is the tata-box?

Answer 23

It is a DNA sequence that indicates where a genetic sequence can be read and decoded and is a type of promoter sequence, which specifies to other molecules where transcription begins.

Question 24

What helps repress or enhance the transcription levels?

Answer 24

Transcriptional activator and repressor proteins

Question 25

What are the four DNA binding domains?

Answer 25

Helix-turn-helix Leucine zipper Zinc finger Helix-loop-helix

Question 26

What does the activation/repression domain do?

Answer 26

It interacts with target proteins

Question 27

What is DBD?

Answer 27

DNA binding domains

Question 28

What are the 3 things DBD must have?

Answer 28

Must fit into major or minor groove Must have amino acids that can protect into interior of double helix Must have amino acids that can bond with interior bases (recognition helix)

Question 29

What is cooperative binding?

Answer 29

The arrangement of transcription factor binding sites that twp different transcription factors can interact, stabilising each other's binding to the DNA

Question 30

How can gene expression be regulated in prokaryotes?

Answer 30

``` Downregulation of transcription Hydrolysis of mRNA Prevent mRNA translation at the ribosome Degrade protein after its made Inhibit the function of protein Kinase can phosphorylate protein to alter functionality ```

Question 31

Describe transcriptional regulation in prokaryotes

Answer 31

Gene expression begins at the promoter. sequence of DNA adjacent to the gene where transcription factors bind and RNA polymerase is recruited to initiate transcription. A repressor protein can bind to DNA and competes with RNA polymerase so the sigma factor cannot bind, blocking transcription.

Question 32

What are core promoters bound by?

Answer 32

Specific sigma factors

Question 33

What is the Holo-RNA polymerase?

Answer 33

It is a form of eukaryotic RNA polymerase II that is recruited to the promoters of protein-coding genes in living cells.

Question 34

What 3 proteins are involved in the uptake and metabolism of lactose in prokaryotes?

Answer 34

beta-galactoside permease (carrier protein that moves sugar into cell) beta-galactosidase (an enzyme that hydrolyses lactose) beta-galactoside transacetylase (transfers acetyl groups to certain B-galactosides)

Question 35

What are the three ways to control operon transcription?

Answer 35

An inducible operon regulated by a repressor protein A repressibe operon regulated by a repressor protein An operon regulated by an activator protein

Question 36

Describe what happens when an inducible operon is regulated by a repressor protein

Answer 36

A repressor protein encoded by gene X prevents the transcription by binding to the operator. RNA polymerase cannot bind to the promoter, blocking transcription. An inducer can inactivate the repressor to allow the RNA polymerase to transcribe.

Question 37

Key points for the regulation of gene expression in eukaryotes.

Answer 37

Transcription - transcriptional regulation, pre-mRNA splicing, transport of the mRNA from the nucleus to the cytoplasm Translation - protein degradation, post-translational modification, translational control, mRNA stability

Question 38

How is 2m of DNA packaged into the nucleus?

Answer 38

Wrapped around histone octamer twice and histone H1 further compacts this into tighter fibres

Question 39

What is covalent modification?

Answer 39

Each histone has a positively charged amino tail at its N terminus. Histone acetyltransferases can change the tails charge by adding acetyl groups to lysine residues. This opens up the nucleosome and increases DNA accessibilty.

Question 40

What are the mechanisms to increase access to DNA?

Answer 40

Nucleosome sliding; nucleosome displacement; partial histone displacement; replacement of octmer subunits with histone variants