07c: Control Of Gene Expression

Question 1

Lac operon is present in (bacteria/mammals)

Answer 1

Bacteria

Question 2

Lac operon is suppressed when:

Answer 2

Enough glucose in cell so it doesn’t need to use other sugars

Question 3

The lac operon genes are (mono/poly)cistronic, which means:

Answer 3

Polycistronic; the genes for all proteins are right next to each other

Question 4

List the order in which the genes in lack operon are present.

Answer 4

1. Regulatory gene (i)
2. Promoter (CRP then O)
3. Z then Y then A genes

Question 5

Which genes in lac operon fall under the general “operon”?

Answer 5

All except regulatory gene (i)

Question 6

What’s the regulatory gene in lac operon? What’s its function?

Answer 6

The i gene (repressor)

Question 7

The Z gene in lac operon codes for (X) which has what function?

Answer 7

X = beta galactosidase

Breaks down lactose to glucose and galactose

And converts lactose to allolactose

Question 8

The Y gene in lac operon codes for (X) which has what function?

Answer 8

X = galactoside permease

Allows lactose to enter cell

Question 9

The A gene in lac operon codes for (X) which has what function?

Answer 9

X = thiogalactoside transacetylase

Unknown function..

Question 10

If a significant amount of glucose present in cell, what happens in terms of lac operon?

Answer 10

Repressor expressed and binds operator (RNA pol binding and transcription of lac operon blocked)

Question 11

(X) is an isomer of lactose. What’s its role in the lac operon?

Answer 11

X = allolactose

Binds repressor, changing conformation and preventing it from binding operator

Question 12

High glucose levels means (low/high) cAMP levels.

Answer 12

Low

Question 13

How do cAMP levels come into play for the lac operon?

Answer 13

At very low glucose level, cAMP high and binds CRP. This complex binds promoter region of operon to stimulate high level transcription

Question 14

Almost all transcription factors bind (X) to the (Y) groove of DNA.

Answer 14

X = alpha helix
Y = major

Question 15

T/F: all transcription factors act as dimers.

Answer 15

False - many do, but not all

Question 16

T/F: the helix-turn-helix motif is found in both bacteria and euk.

Answer 16

True

Question 17

CRP, aka (X), has which transcription factor(s)?

Answer 17

X = cAMP binding protein

Helix-turn-helix

Question 18

Describe interaction of CRP with DNA, in terms of its motif.

Answer 18

Helix-turn-helix motif;

Recognition helix (3) interacts with major groove of DNA and is connected via turn to stabilization helix (2)

Question 19

When CRP interacts with DNA, it acts as (monomer/dimer/multimer).

Answer 19

Dimer

Question 20

T/F: very few transcription factors have beta sheet motifs.

Answer 20

True

Question 21

Motifs like helix-turn-helix have (strong/moderate/weak) interaction with DNA due to which bond(s)?

Answer 21

Strong interaction due to many weak hydrogen bonds

Question 22

How many molecules of Zn are used in the Zn finger motif?

Answer 22

1 or more

Question 23

What are the key residues found in Zn finger motif?

Answer 23

Repetitive motif of:

2 cys and 2 hys
OR 4 cys

With 12 AA bunch right in middle (forms finger)

Question 24

When Zn finger interacts with DNA, it acts as (monomer/dimer/multimer).

Answer 24

Multimer (can’t be dimer)

Question 25

Describe primary structure of leucine zipper.

Answer 25

35 AA stretch with leucine sticking out every 7 AA (interact to form coiled coil/zipper alpha helix Bottom has basic region alpha helices that bind DNA

Question 26

What's bZIP?

Answer 26

Same motif as leucine zipper, but Arg or His replace leucine

Question 27

The basic Helix-loop-helix is most similar to which other motif?

Answer 27

Leucine zipper, but there's a non-helical loop in the zipper helix

Question 28

List steps that take place to allow estrogen to affect transcription.

Answer 28

1. Estrogen enter cell 2. Estrogen receptor (ER) released from HSP and bind estrogen 3. ER-Estrogen complex enters nucleus and dimerizes with a second complex 4. Binding of dimer to ERE (estrogen response element) on DNA

Question 29

Promoters of housekeeping genes are likely (hypo/hyper)-methylated.

Answer 29

Hypo methylated

Question 30

How do (methylated/unmethylated) CpG islands in the (X) region of the gene block expression?

Answer 30

Methylated; X = promoter 1. Physically preclude transcription factor recruitment 2. MeCP2 protein binds methyl groups and prevents transcription by recruiting chromatin remodeling factors

Question 31

What's MeCP2 and what's its function?

Answer 31

Methyl CpG binding protein 2; binds methylated CpG islands in promoter and recruits chromatin remodeling factors (blocking gene transcription)

Question 32

T/F: methylated CpG islands in promoter always inhibit gene expression.

Answer 32

False - not always

Question 33

Igf2, aka (X), is a unique gene in that:

Answer 33

X = insulin-like growth factor 2 Imprinted gene that paternal gene (methylated) is expressed and maternal gene (unmethylated) is not

Question 34

Why is the (paternal/maternal), (methylated/unmethylated) Igf2 gene expressed?

Answer 34

Paternal; methylated Prevents binding of a repressor

Question 35

What are methods that can impact nucleosome structure and thus gene expression?

Answer 35

1. Positive super helical tension 2. ATP-driven chromatin remodeling 3. Covalent modification of Histone tails

Question 36

T/F: Chromatin remodeling requires ATP.

Answer 36

True

Question 37

Chromatin remodeling factors interact with (X) terminal of (Y) and use (Z) to (open up/close) nucleosome.

Answer 37

``` X = C Y = RNA Pol II Z = ATP ``` Open up

Question 38

Covalent modification of Histone tails includes which three processes?

Answer 38

1. Methylation 2. Phosphorylation 3. Acetylation

Question 39

Which residues can be methylated on Histone tails?

Answer 39

Lys or Arg

Question 40

Which residues can be phosphorylated on Histone tails?

Answer 40

Ser

Question 41

Which residues can be acetylated on Histone tails?

Answer 41

Lys

Question 42

Which enzyme is responsible for methylation of Histone tails?

Answer 42

Histone lysine methyltransferase Or protein Arg methyltransferase

Question 43

Covalent modification of Histone tails involves which terminus?

Answer 43

N-terminus

Question 44

Which enzyme is responsible for acetylation of Histone tails?

Answer 44

HAT (Histone acetyl transferase)

Question 45

Which enzyme is responsible for deacetylation of Histone tails?

Answer 45

HDAC (Histone deacetylase)

Question 46

Acetylation in general affects the charge on the Histone tail in which way?

Answer 46

Makes it less positively charged

Question 47

Binding of thyroid hormone to its receptor has what effect on transcription?

Answer 47

Changes HDAC domain to HAT domain, leading to acetylation and activation of transcription

Question 48

List the one Histone tail modification that represses transcription.

Answer 48

Methylation of lysine