Lecture 4

Question 1

What are the six steps of gene expression control?

Answer 1

1. transcriptional control
2. RNA processing control
3. RNA transport and localizing control
4. translation control
5. mRNA degradation control
6. protein activity control

Question 2

Explain how the tryptophan repressor in bacteria works

Answer 2

There are 5 genes that encode enzymes that are necessary to create tryptophan in E coli. These genes are arranged in an operon. Under normal circumstances, there is a repressor bound to the operater within the promotor region. (This is that so E Coli won’t waste energy). If the level of tryptophan gets too low, RNA poly will bund to promoter and trascribe the genes to make tryptophan. If the level of tryptophan is too high, the repressor prevents the RNA polymerase from binding… THIS IS NEGATIVE CONTROL

Question 3

Explain the two different mechanism for negative regulation (transcriptional activators)

Answer 3

Negative control means that under normal conditions, the operon is repressed or shut off.

1. Ligand binds to remove the repressor from the DNA (addition of the ligand switches gene on by removing the repressor protein) aka inducing ligand
2. Removal of ligand switches gene on by removing repressor protein (inhibitory ligand)

Question 4

Explain the two different mechanism for positive regulation of transcriptional activation

Answer 4

Under positive control, the operon is normally on. You can turn the operon off via two ways

1. Turn off a gene by adding a ligand which removes the activator protein (inhibitory ligand)
2. Turn off gene by removing a ligand, which removes the activator protein (inducing ligand)

Question 5

Explain the overview of the lac operon.

Answer 5

The lac operon is a set of genes that codes beta galactosidase which can turn lactose and galactose into glucose. Expression of this operon never fully shuts down.

Question 6

What happens during the lac operon during the following scenarios:

1. presence of glucose and lactose
2. presence of glucose but NO lactose
3. NO glucose or lactose
4. presence of lactose but no glucose

Answer 6

Think of the figure.

1. Presence of glucose and lactose: OPERON OFF
2. Glucose but no lactose, repressor binds
3. no glucose or lactose: cAMP binds to CAP in absence of glucose but because there is no lactose either, the repressor is still bound… OPERON OFF
4. Presence of lactose, no glucose… the repressor falls off, cAMP bound to CAP, operon is on.

NOTE: operon is only turned on in the presence of only lactose

Question 7

What does DNA looping help with?

Answer 7

DNA looping stabilizes protein-DNA interactions. The lac repressor is a tetramer protein, and it can simultaneously bind two operators. Folds DNA into a loop to work on both operators

Question 8

What are the differences in gene trascription control in eukaryotes vs prokaryotes?

Answer 8

1. Euckaryotic RNA Poly II requires five general transcription factors, where as prokaryotic poly only needs the one sigma subunit
2. Eukaryotic cells do not have operons, have to regulate each gene individually
3. Eukaryotic genes can by controlled by several different regulatory proteins whereas prokaryotic genes are only controlled by one or a few
4. Eukaryotes need a mediator (24 subunit complex) that serves as an intermediary between gene regulatory proteins and RNA poly
5. Packaging of eukaryotic DNA into chromatin provides many opportunities for transcriptional regulation not available to bacteria.

Question 9

Explain the structure of the following: helix turn helix, homeodomain, and zinc finger

Answer 9

Helix turn helix, homeodomain and zinc fingers are all gene regulatory proteins

Helix turn helix has two helices

homeodomain has three helixes

zinc finger has zinc and alpha helices and beta sheets

Question 10

DNA methylation can be ______.

Genomic imprinting can be based on ______.

Answer 10

DNA methylation can be inherited

Genomic imprinting can be based on DNA methylation

Question 11

Name four epigenetic mechanisms that can be inherited.

Answer 11

1. Histone modification
2. Activated Positive Feedback Loop
3. DNA Methylation
4. Protein Aggregated State

Question 12

Name five post transcriptional controls

Answer 12

1. Riboswitch
2. Alternative Splicing
3. RNA editing
4. snRNAs regulating gene expression
5. RNA interference

Question 13

What is a Riboswitch?

Answer 13

Riboswitch is short sequence of RNA that can change its conformation or bind small molecules, it binds directly to RNA poly

Question 14

What is RNA editing?

Answer 14

Where you can change the nucleotides on RNA after transcription and therefore change the message

Question 15

Explain small noncoding RNAs and RNAi

Answer 15

If there is an extensive match, small noncoding mRNAS will cause RAPID mRNA degradation

With RNAi, there is not as extensive of a match and translation is reduced

Question 16

Name the five post transcriptional controls that we learned about

Answer 16

1. Riboswitch
2. Alternative Splicing
3. RNA editing
4. small noncoding RNAs
5. RNA interference/ RNAi