Regulation Of Gene Expeession In Eukaryotes

Question 1

Why regulate gene expression?

Answer 1

1. Control the types and quantities of proteins (gene products) produced
2. Respond to the environment by turning on or off specific genes or groups of genes
3. Turn genes on or off in the correct sequence during development

Question 2

What are the 6 main steps involved in the regulation of gene expression in eukaryotes?

Answer 2

1. Transcriptional control
2. mRNA processing
3. mRNA transport
4. mRNA stability
5. Ribosomal secretion
6. Protein stability

Question 3

Control of differential gene transcription involves:

Answer 3

1. Cis-regulatory sequence of DNA (promoter and enhancer sequences
2. Transcription factors (=trans-acting factors)- nuclear proteins that bind to promoter or enhancer sequences of genes and stimulate/ inhibit transcription
3. Changes of chromatin conformation-
   - Gene methylation
   - Histine acetylation

Question 4

Define epigenetics

Answer 4

A change in the expression of a gene that changes the phenotype without permanently changing the gene itself. Typically involving changes in chromatin structure

Question 5

Describe epigenetics

Answer 5

Turning off expression without changing the code

Gene activity can be modulated in a manner that doesn’t involve changes in the DNA code and these changes can persist through one or more generations. These are called epigenetics effetcs

Question 6

What are some examples of epigenetics?

Answer 6

Chromatin modifications

DNA methylation: can lead to parent-of-origin effects(imprinting which is not covered here)

Question 7

What are the types of chromatin?

Answer 7

Euchromatin-are loose because they’re transcribed

Heterochromatin- dense packing if DNA, which makes it less accessible

Question 8

What is nucleosome structure?

Answer 8

Positively charged histone proteins bind with each other along with DNA to form a structure called the nucleosome

The nucleosome core is composed of two molecules each of H2A, H2B, H3, and H4 histone proteins

Question 9

What are nucleosomes connected by?

Answer 9

Linker DNA of variable length and H1 histone

Question 10

How is the 30 Nm fiber formed from beads on a string?

Answer 10

Nucleosome can associate with each other via interactions between H1 to form a more compact structure that has been termed, due to size, the 30nm fiber

Question 11

What are the two types of chromatin?

Answer 11

These are based on chromosome staining properties

Euchromatin-decondensed and transcriptionally active

Heterochromatin- condensed and transcriptionally inactive

Question 12

What is the order of condensation of chromatin?

Answer 12

1. DNA double helix-2nm
2. Beads on a string- 11nm
3. Chromatin fiber of packed nucleosomes- 30nm
4. Extended section of chromosomes- 300nm
5. Condensed section of chromosomes- 700 Nm
6. Metaphase chromosomes

Question 13

Give examples of histone modification that alter interaction of the DNA and the histone tails

Answer 13

Modifications include:

• (de)acetylation
• methylation
• phosphorylation
• ubiquitination (protein is destroyed in the proteosome “meat grinder”)

Question 14

What enzymes are responsible for acetylation and deacetylation?

Answer 14

Acetylation by HATs(histone Acetyl transferase)

Deacetylation by HDACs (histone deacetylase)

Question 15

Deacetylation is linked to…

Answer 15

Methylation of cytosine

Question 16

Explain DNA methylation

Answer 16

DNA methylation involves the modification of the DNA base cytosine to 5-methyl-cytosine

DNA methyltransferase enzyme

Flag for silencing mechanism

Question 17

Explain methylation inheritance and transcriptional repression

Answer 17

Dnmt3-performs de novo methylation of DNA at cytosine

MeCP2- recruited to methylated cytosines (CpG islands)

HDAC 1 or 2- and other enzymes bind to MeCP2

Deacetylase activity (HDAC) on the acetylated lysine residues of the his robes leading to tightly packed chromatin

At DNA replication the full methylation pattern is restored. First, MeCP2 in an altered confirmation will recognize hemi-methylated DNA. This altered conformation of MeCP2 will recruit Dnmt1 which is also called the maintenance methyltransferase because it maintains the original methylation pattern

After DNA replication, there is conformational change of MeCP2. Again, HDAC 1 or 2 and other enzymes bind to MeCP2

Transcriptional repression is restored

Question 18

What are the enzymes involved in methylation inheritance and transcriptional repression?

Answer 18

Transcriptional repression and chromatin integrity
Dnmt3: DNA methyltransferase (de novo)

MeCP2: methyl CpG binding protein

Dnmt1: maintenance

Question 19

What kind of chromatin does transcription factor bind to?

Answer 19

Euchromatin is transcriptionally active, able to bind transcription factors and RNA polymerase

Question 20

What is the function of basal machinery?

Answer 20

Maintains low level of of transcription

Modulation requires more players

Question 21

What is the function of enhancer?

Answer 21

Retains function even when reversed or moved far from gene whose transcription it influences

Question 22

Where is the promoter?

Answer 22

Is close to a gene’s initiation site

Question 23

Regulation of gene transcription in eukaryotes involves the interaction of…

Answer 23

• Basal transcriptional machinery located at the genes promoter
• trans-acting proteins bound to did-regulatory elements

Question 24

Describe Cis-acting elements

Answer 24

• contain short consensus sequences.
• not fixed in location but usually within 200 bp upstream of the transcription start site
• a single element is Usually sufficient to confer a regulatory response
• can be located in a promoter or an enhancer
• a specific protein binds to the element and the presence of that protein is regulated

Question 25

Describe trans acting elements

Answer 25

- proteins that bind to the cis-acting sequences to control gene expression - Also called activator proteins and silencer proteins - Bind to promoter, enhancer, and silencer DNA in specific ways - Interact with other proteins to activate and increase transcription as much as 100-fold above basal levels - Or repress transcription in the case of silencers of repressors

Question 26

What are the common structural types of transcription factors?(dimer types)

Answer 26

1. Zinc finger 2. Helix-turn-helix 3. Leucine zipper

Question 27

Folding of DNA can result in interactions between...

Answer 27

Enhancer or repressor proteins Bound to distant cis-elements and the basal transcriptional machinery Multiple sets of gene regulatory proteins can work together to influence transcription initiation

Question 28

Different genes provide the same cisxregulatiry sequences...

Answer 28

This provides spatial and temporal coordination of gene regulation 1. Stage specific expression during embryonic development 2. Tissue specific expression 3. Response to external stimuli: hypoxia, hormonal, stress, heat

Question 29

Why are there 2 proline residues in HIF-a?

Answer 29

For hydroxylation by prolyl hydroxylase in normal oxygen environment Ubiquitin ligase senders ligase, proteosome degrades HIF-a

Question 30

What happens to HIF-a in low oxygen environments?

Answer 30

Low oxygen environment causes HIF- 1a stabilization and transport nucleus where it binds to Hypoxia response element While interacting with basal transcription machinery Erythropoiesis, angiogenesis and anaerobic metabolism is stimulated

Question 31

Explain glucocorticoid response element

Answer 31

Glucocorticoid-steroid hormone In the absence of glucocorticoid, the GR is maintained predominantly in the cytoplasm as part of an inactive multi protein complex When glucocorticoid binds to GR, the receptor undergoes a change in conformation dissociates from regulatory heat shock proteins, and is hyperphosphorylated and moves to the nucleus In the nucleus, hormone-activated GR regulates transcription. The GR binds as a homodimer directly to DNA sequences located in the promoter regions of glucocorticoid responsive genes. Binding to these sequences, known as glucocorticoid response elements Leads to transcriptional induction or repression of target genes

Question 32

What are the types of glucocorticoid receptors?

Answer 32

These response elements are palindromic There are positive GREs(trans activation ) and negative(transrepression) GREs