Chapter 15 - Gene Regulation in Eukaryotes

Question 1

Contrast the ground state of gene expression in bacteria vs eukaryotes

Answer 1

• Bacteria ground state of gene expression is ON
  vs.
• Eukaryotes is OFF

Question 2

What are the 2 main types of transcription factors?

Answer 2

1. General Transcription Factors (GTFs)
2. Regulatory Transcription Factors

Question 3

Describe transcription factors (general overview)

Answer 3

proteins that influence the ability of RNA polymerase to transcribe a given gene

Question 4

General Transcription Factors -

Answer 4

• Required for the binding of the RNA pol to the core promoter and its progression to the elongation stage
• necessary for basal transcription

Question 5

Regulatory transcription factors -

Answer 5

• Serve to regulate the rate of transcription of target genes
• influence the ability of RNA pol to begin transcription of a particular gene
• helps increase or decrease rates

Question 6

RTFs can be what 2 things?

Answer 6

1. Activators that bind to enhancers and increase transcription
   or
2. Repressors that inhibit transcription

Question 7

Allosteric effector does what?

Answer 7

• Helps it bind or cause the repressor to fall off

Question 8

What 3 things can activators and repressors be modulated by?

Answer 8

1. Binding of small effector molecules
2. protein-protein interactions
3. covalent modifications (phosphorylation aka change the shape)

Question 9

Chromatin-Remodeling complexes do what? where are they only found?

Answer 9

1. alter the positions and compositions of nucleosomes
2. only in eukaryotes

Question 10

Why are chromatin-remodeling complexes important?

Answer 10

removes histones, makes space, so the mRNA can actually bind.
- more loosely = more expression
- if under stress or infected by a viruses, need immediate defense so histone octamers can be fully removed

Question 11

HATS stands for

Answer 11

Histone acetyltransferases

Question 12

What does HATs do?

Answer 12

1.has neutral charges
2. located on the histone tail and increases gene expression, DNA moves more flowly here

Question 13

HDACs stands for

Answer 13

Histone deacetylases

Question 14

What does HDACs do?

Answer 14

• Less gene expression
• tight
• taking it off

Question 15

What is DNA methylation? (3)

Answer 15

• the covalent attachment of methyl groups
• carried out by DNA methyltransferase
• usually inhibits eukaryotic gene transcription

Question 16

Why does methylation of DNA inhibit transcription?

Answer 16

adding (+) charges causes tighter configuration of DNA which means less gene expression

Question 17

Where are CpG islands found?

Answer 17

In vertebrates and plants near their promoters

Question 18

What do CpG islands do?

Answer 18

1. In Housekeeping genes - they are unmethylated and genes tend to be expressed in most cell types
2. In Tissue-specific genes - expression may be silenced by the methylation of CpG islands (only when needed)

Question 19

What are housekeeping genes?

Answer 19

basic homeostasis genes that you would want to be on all the time
- need genes to be there to make ATP, TCA cycle, make amino acids etc.

Question 20

Basal Factors are what type of factors and describe them

Answer 20

1. General transcription factors
2. essential for transcription but by themselves cannot turn on transcription

Question 21

Coactivators

Answer 21

link basal factors with activators
- could be a protein or an allosteric small molecule

Question 22

Activators are what type of factor? Describe.

Answer 22

Regulatory transcription factor that binds to enhancer sequences (sequences that are away from the promoter)

Question 23

Enhancer sequences are found in what?

Answer 23

Eukaryotes

Question 24

Repressor is what type of factor? describe

Answer 24

Regulatory transcription factor that bind to silencer sequences
- a physical protein that moves around

Question 25

What is the goal of the Galactose-utilization pathway?

Answer 25

to use glucose

Question 26

Describe galactose utilization pathway:

Answer 26

when glucose is low, need to find a way to bring in galactose

Question 27

What are the genes/proteins that are needed to import galactose and convert galactose into glucose? (3)

Answer 27

1. GAL3 2. GAL4 3. GAL80

Question 28

who is the key regulator in the galactose utilization pathway(GAL)?

Answer 28

GAL4

Question 29

If Upstream activator sequences (UAS) are deleted then?

Answer 29

genes are silent

Question 30

Describe Gal4 protein:

Answer 30

Two domains 1. activation domain that is required for regulatory activity (the actual gene expression) 2. DNA binding domain that associates with UAS

Question 31

What protein inhibits and what protein promotes?

Answer 31

Inhibits/prevents = GAL80 Promotes = GAL3 (inducer + sensor) - can cause allosteric change and release GAL80 from GAL4

Question 32

Transferrin is

Answer 32

a protein that carries iron through the bloodstream

Question 33

Ferritin is

Answer 33

where excess iron is stored

Question 34

what influences the two mRNAS that encode ferritin and transferrin receptors?

Answer 34

an RNA-binding protein known as the Iron regulatory protein (IRP)

Question 35

What does the IRP bind to?

Answer 35

the regulatory element called iron response element (IRE)

Question 36

IRE in ferritin mRNA is in

Answer 36

5' UTR

Question 37

IRE in transferrin receptor mRNA is in

Answer 37

3' UTR

Question 38

If iron is low then?

Answer 38

no ferritin is needed because there is no excess of iron so don't want to store it away

Question 39

If iron is high then?

Answer 39

want the ferritin so excess iron could be stored