Control of Gene Expression 1: Transcriptional Controls

Question 1

Different cells contain the same genes but express different what?

Answer 1

sets of protein; gene expression is different in different cells

Question 2

What is an example of a “housekeeping protein”?

Answer 2

glucose metabolism

Question 3

Hemoglobin is an example of what type of protein?

Answer 3

specifically limited protein

Question 4

True or false?

Typical human cells express 30-60% of its 25,000 genes but level of gene expression varies

Answer 4

true

Question 5

Alternative splicing (dystrophin gene) and post translational modification are other factors that occur when?

Answer 5

after transcription

Question 6

What two things does gene regulation require?

Answer 6

1. short stretches of DNA of defined sequence -recognition sites for DNA binding proteins
2. gene regulatory proteins - transcription factors

Question 7

True or False?

Recognition sequences can only be proximal to first exon

Answer 7

false; can be proximal or distal to first exon

Question 8

In regards to DNA motif recognition, regulatory proteins associate with what?

Answer 8

major groove in DNA - presents a specific face for each of the specific base pairs

Question 9

True or false?

The surface of the protein is extensively complementary to the surface of the DNA region to which it binds

Answer 9

true

Question 10

A series of contacts between the regulatory protein and DNA is made which involves how many possible configurations?

Answer 10

4 configurations of base pairs

Question 11

A typical gene regulatory protein-DNA interaction ivolves how many interactions?

Answer 11

10-20

Question 12

The parts of a DNA transcription factor can be modular. What are some of these modules?

Answer 12

DNA binding module, dimerization module, activation module, regulatory module

Question 13

What is the simplest, most common DNA binding motif?

Answer 13

helix-turn-helix

Question 14

Describe the structure of the helix-turn-helix domain

Answer 14

two alpha helices are connected by short chain of amino acids that make the “turn” at a fixed angle

Question 15

The longer helix in the helix-turn-helix domain is what type of module?

Answer 15

recognition module - DNA binding module that fits into major groove

Question 16

This DNA binding motif binds to the major groove of DNA and includes a Zn atom and when the amino acid sequence is drawn out, the structure looks like a finger.

Answer 16

Zinc finger domain

Question 17

Are Zn Finger domains found in tandem clusters? If so, why?

Answer 17

yes; stabilizes interaction with DNA and provides multiple contact points

Question 18

This motif has a dimerization domain, activation domain and DNA binding domain and has a two alpha helical structure with leucine side arms.

Answer 18

Leucine zipper motif

Question 19

Where do interactions occur in the leucine zipper motif?

Answer 19

between hydrophobic amino acid (leucine) side chains

Question 20

In the leucine zipper motif there is a leucine residue every __ amino acids down one side of the alpha helix in the dimerization domain

Answer 20

7

note: this forms zipper structure

Question 21

In the leucine zipper motif, which domain does the activation domain overlap?

Answer 21

dimer domain

Question 22

Describe the structure of the helix-loop-helix domain

Answer 22

consists of a short alpha chain connected by a loop to a second longer alpha chain

Question 23

True or false?

the helix-loop-helix domain can only occur as a homodimer.

Answer 23

false; can occur as homodimer or heterodimer

Question 24

How many modules are there in the helix-loop-helix domain? What are they?

Answer 24

3; DNA binding domain, dimerization domain, activation domain

Question 25

What is hereditary spherocytosis (HS)?

Answer 25

a hemolytic anemia characterized by spherical and fragile RBCs that lyse and release hemoglobin

Question 26

What is the clinical presentation of hereditary spherocytosis?

Answer 26

hemolysis, anemia, splenomegaly note: presentation ranges from mild to severe anemia and can be fatal

Question 27

What is HS caused by?

Answer 27

mutations in genes for the erythrocyte membrane skeleton of RBCs

Question 28

Is HS dominantly or recessively inherited?

Answer 28

dominantly

Question 29

The erythrocyte membrane skeleton (EMS) confers what to RBCs?

Answer 29

durability and stability

Question 30

How many EMS passages are in the circulation?

Answer 30

1/2 million

Question 31

What is the incidence rate of HS?

Answer 31

1/2000 | note: HS is the most common hereditary anemia in people of Northern European Descent

Question 32

True or false? | HS can be caused by a mutation in zinc finger protein gene Klf1

Answer 32

true note: the Klf1 zinc finger protein binds to promoters of all genes in EMS - turns them on

Question 33

Where is the HS mutation found in the Klf1 gene?

Answer 33

GAA to GAT or Glutamic acid (Glu) to Aspartic acid (Asp) in exon 3 (zinc finger domain 2) note: the mutation causes there to be less RNA made from target promoter

Question 34

What is the chain of amino acids in the mutated form of Klf1 DNA binding motif?

Answer 34

Arg-Asp-Arg

Question 35

In normal Klf1, the R (Arg) interacts with E (Glu Acid) in RER to stabilize interaction with C in the major groove of what?

Answer 35

CACCC recognition sequence

Question 36

What is the result of the HS Klf1 mutation?

Answer 36

DNA cannot be unwound - no transcription

Question 37

In regards to detection of sequence-specific DNA proteins, how does affinity chromatography work?

Answer 37

DNA binding protein is isolated, then the purification of sequence specific binding proteins

Question 38

What does CHIP: chromatin immune precipitation allow one to identify?

Answer 38

allows identification of the sites in the genome that a regulatory protein binds; the pcr product at the end can be used to screen a microarray gene chip

Question 39

What is the gene control region of a typical eukaryotic gene?

Answer 39

DNA region involved in regulating and initiating transcription of a gene

Question 40

Does the gene control region of a typical eukaryotic gene include the promoter?

Answer 40

yes; where transcription factors and RNA polymerase II assembles

Question 41

Of the 25,000 human genes, __% encode gene regulatory proteins

Answer 41

8

Question 42

In regards to the gene control region of a typical eukaryotic gene, RNA polymerase and general transcription factors assemble at the promoter. Other gene regulatory proteins bind to regulatory sequences located where?

Answer 42

can be adjacent, far upstream, or in introns downstream of the promoter

Question 43

What is the model for Transcriptional activation?

Answer 43

DNA looping and a mediator complex allowing regulatory proteins to interact with the proteins that assemble at the promoter

Question 44

In regards to transcriptional activation, the mediator serves as an intermediary between what?

Answer 44

gene regulatory proteins and RNA polymerase II

Question 45

Gene activator proteins modify local chromatin structure. Histone acetylation does what?

Answer 45

makes it easier to remove histones - favors transcription

Question 46

What is the sequence of events starting from gene activation to transcription initiation?

Answer 46

gene activator protein binds to chromatin; chromatin remodeling; covalent histone modification; additional activator proteins bound to gene regulatory region; assembly of pre-initiation complex at the promoter; transcription initiation

Question 47

Gene repressors inhibit transcription in different ways. The first being that gene activators and repressers compete for the same what?

Answer 47

binding site

Question 48

Another way gene repressors inhibit transcription when both activator and repressor bind to DNA but the repressor also binds to what?

Answer 48

the activation domain of the activator protein - masks the activation surface

Question 49

Another way gene repressors inhibit transcription is by binding DNA and directly interacting (blocking) with what?

Answer 49

general transcription factors

Question 50

Another way gene repressors inhibit transcription is by recruiting a ___ ___ __ which returns the promoter to the pre-transcriptional nucleosome state

Answer 50

chromatin remodeling complex

Question 51

Another way gene repressors inhibit transcription is by recruiting a ___ ___ to the promoter which makes it harder to remove deacetylated histones

Answer 51

histone deacetylase

Question 52

Another way gene repressors inhibit transcription is by recruiting a ___ ___ ___ which methylates histones. These methylated histones are bound to proteins which act to maintain chromatin in a transcriptionally silent form..

Answer 52

histone methyl transferase

Question 53

True or false? depending on their composition, the complexes can be either activating or repressing. The same protein can be part of an activating or repressing complex

Answer 53

true

Question 54

What are the seven ways gene regulatory proteins are controlled?

Answer 54

1. synthesis 2. ligand binding 3. covalent modificaiton-phosphorylation 4. addition of subunit 5. unmasking 6. nuclear entry 7. proteolysis

Question 55

In regards to the globin genes, what are alpha like chains? and beta like chains?

Answer 55

alpha like: zeta and alpha beta like: epsilon, gamma, delta, and beta

Question 56

In regards to beta globin gene regulation, what do regulatory proteins bind to?

Answer 56

LCR