Lecture 9: Transcription Regulation and RNA processing

Question 1

If all cells in the body contain the genetic code for every protein, how are any cells unique?

Answer 1

A massive variety of regulators of gene expression are used. Such as transcription regulators that bind to specific DNA sequence. DNA sequences have less affinity on nucleosome (20x less at end of nucleosome, 200x less in middle).

Question 2

Which steps of gene expression take place inside the nucleus?

Answer 2

1. Transcriptional control
2. RNA processing control

Question 3

Which steps of gene expression take place outside the nucleus?

Answer 3

3. RNA transport and localization
4. RNA translation control
5. mRNA degradation control
6. Protein activity control

Question 4

How do nucleosomes affect transcription levels?

Answer 4

DNA sequences attached to nucleosomes have less affinity (20x end, 200x middle) for transcription factors, However, other transcription regulators can bind to other sections of DNA, disrupting nucleosome and allow binding of secondary transcription regulator.

Question 5

What is an operon?

Answer 5

A cluster of genes that encode for multiple proteins all controlled by a single promoter.

Question 6

What organisms do you find operons in?

Answer 6

Mostly found in prokaryotes but rarely in eukaryotes.

Question 7

Give two examples of an operon.

Answer 7

Lac operon, this operon in E. coli contains a group of genes designed to break down lactose for energy in the absence of other fuel sources.

Trp operon, this operon in E. coli contains a group of genes coding for a series of enzymes that result in tryptophan synthesis.

Question 8

How can trp operon gene expression be controlled?

Answer 8

Operon genes have repressor proteins that bind to the operator site on the operon. These proteins will only bind to the operator if tryptophan is present in high amounts, binding to the repressor and activating it. When bound to the operator, Polymerase cannot bind to the promoter region and the genes are not transcribed.

Question 9

What genes form lac operon?

Answer 9

• lacZ (beta-galactosidase)
• lacY (permease for lactose import)
• lacA (transacetylase)

Question 10

How is transcription regulated in the lac operon?

Answer 10

A combination of an activator CAP (Catabolite Activator Protein) and repressors function to only allow lactose to be used when under the right conditions:

• In the presence of glucose and lactose, neither lac repressor nor CAP are bound to the operon.
• In the presence of glucose but not lactose, a lac repressor protein will attach to the promoter.
• In the presence of neither lactose nor glucose, both the CAP and lac repressor attach to the operon.
• In the presence of only lactose, the repressor will detach from the operon and the CAP will bind just upstream of the promoter region, stimulating the attachment of RNA polymerase to the operon.

The lac repressor protein binds to ALLOLACTOSE, not lactose exactly.

Question 11

Some regulatory sequences are very distant from the genes they regulate. What is the name of these sequences?
What do they do?

Answer 11

Enhancer sequences.
They bind to enhancer proteins, which can affect gene transcription.

Question 12

How do enhancer proteins affect gene regulation?

Answer 12

They are distant to the promoters they affect. Therefore folding in the DNA strand facilitates the binding of this protein to a mediator complex which in turn binds to the general transcription factors. This whole complex increases the binding of RNA polymerase II, and enhances gene expression.

Question 13

What are the four ways transcription activators can alter chromatin structure to allow for transcription?

Answer 13

The chromatin remodeling complex can bind to the DNA sequence to allow for three methods of chromatin alteration:

• The chromatin remodeling complex alone can allow for nucleosome sliding, allowing for access to DNA sequence.
• Histone chaperones can allow for histone removal and access to DNA sequence.
• Histone chaperones can exchange histones and change the arrangement of DNA to allow for easier access to sequences.

Besides this, histone-modifying enzymes can alter the methylation and specific patterns of these changes can attract components of machinery.

Question 14

Describe the sequence of histone modifications and their effects on transcription initiation in the context of interferon promotion.

Question 15

What four ways can transcription activators act to influence transcription?

Answer 15

1. It can promote the binding of additional regulators to the site of transcription.
2. It can recruit RNA polymerase directly to the promoter.
3. It can bind to the activator sequence and this can release RNA polymerase from the promoter.
4. It can bind to activator sequence to release RNA polymerase from a pause.

Question 16

How effective is the combined binding of two activators?

Answer 16

It is greater than the sum of either one of the activators. For example is activator 1 and two induce 2 units of transcription each, the combined effect would be greater than 4 units, maybe as high as 100 units of transcription (it may be much higher).

Question 17

How can transcription regulator protein activation be controlled?

Question 18

How can eukaryotic repressor proteins function to inhibit gene transcription?

Question 19

What are master transcription regulators?

Question 20

How can transcription activators and repressors be modified in medicine?

Question 21

How can eukaryotic repressor proteins function to inhibit gene transcription?

Question 22

How can imprinting affect genetic inheritance patterns?

Question 23

What steps does RNA processing consist of?