Control of Gene Expression

Question 1

Parts of the lac operon

Answer 1

Regulatory Gene: binds repressor
Promoter- has the operator and CRP gene
z gene: beta galactosidase –> lactose –> glucose + galactose
y gene: galactoside permease –> lactose –> into cell
a gene: thiogalactoside transacetylase –> ?

^genes right next to eachother: polycistronic message

Question 2

lac operon- glucose only

Answer 2

1) regulatory gene creates mRNA for repressor protein
2) repressor binds to operator
3) RNA polymerase cannot bind promoter
4) transcription blocked

Question 3

lac operon- little lactose present

what does beta galactosidase make?

Answer 3

beta galactosidase
lactose –> glucose + galactose

OR

lactose –> allolactose (isomer)

Question 4

What happens when little lactose present in the lac operon?

Answer 4

1) regulatory gene creates mRNA for repressor protein
2) allolactose binds to repressor
3) repressor cannot bind operator
4) RNA polymerase binds to promoter
5) transcription…but at a LOW level

Question 5

How are cAMP and glucose levels related?

Answer 5

increase glucose, decrease cAMP

decrease glucose, increase cAMP

Question 6

lac operon: lots of lactose and glucose

Answer 6

1) high CRP levels –> but doesn’t do anything
2) RNA pol binds to promoter
3) low transcription

Question 7

lac operon: lots of lactose and little glucose

Answer 7

1) CRP and cAMP bind leading to a conformational change in CRP
2) bind onto the promoter
3) Stimulates binding of RNA polymerase to the promoter
4) Transcription level is high

Question 8

Helix-turn-Helix motif (transcription motif)

Answer 8

Recognition binds major groove
dimer alpha helices are bound to the major groove of DNA

H bonding between bases on DNA and the protein end up becoming really strong since there are so many bonds made –> this makes this process very specific
ie: CRP (cAMP receptor protein)

Question 9

Function of CRP

Answer 9

acts as a dimer on the major groove to give a wide array of protein possibilities for interactions

Question 10

Pitt Hopkins Syndrome

Answer 10

Creates mutation in the basic region of a transcription factor…affects DNA binding of the transcription factor

Arg 576 highly conserved and essential for DNA recognition

Question 11

Zn (transcription motif)

Answer 11

alpha helices bind major groove
not a dimer

Use of 1 or more molecules of Zn
Repetitive motif of 2 cystine and 2 histidine (or cystine) residues in the sequence

Repetitive so can maker different fingers
Also has specific and strong interactions with DNA

Question 12

Leucine Zipper/bZip (transcription motif)

Answer 12

dimer alpha helices are bound to the major groove of DNA

Has 2 parts:
1) Zipper alpha helix: coil formed so that leucines stick out on one side –> hydrophobic interactions

2)Basic region DNA binding alpha helix: this is the part that interacts with DNA

Question 13

Basic helix-loop-helix (transcription motif)

Answer 13

dimer alpha helices are bound to the major groove of DNA
has alpha helix non helical loop alpha helix on the top

Bottom is a basic region- DNA binding and an alpha-helix

Question 14

How do you make different zipper motifs?

Answer 14

Different amino acids can replace the leucines on the zipper alpha helix

ie: arginine, histidine

Question 15

Ways to regulate transcription factors

Answer 15

1- protein synthesis
2- ligand binding
3- protein phosphorylation 
4- Addition of subunit
5- unmasking
6- Stimulation of nuclear entry
7- release from membrane

Question 16

How do estrogen receptors work?

Answer 16

Estrogen receptor and ligand estrogen bind to estrogen response element (ERE)

this binding unmasks the receptor and allows for transfer into the nucleus –> bind to coactivaters in nucleus –> transcription

Question 17

DNA methylation and cancer

Answer 17

DNA methylation suppresses the expression of tumor suppressor genes in cancer

Question 18

How does methylation block gene expression?

Answer 18

1) Methylated CpG islands inhibits transcription by physically precluding transcription factor recruitment
2) Methylated CpG binding protein 2 (MeCP2) binds to methyl groups and prevents transcription by recruiting chromatin recruiting factors

Question 19

Rett Syndrome

Answer 19

mutation in MeCP2 gene –> over transcription

Question 20

Methylation can also lead to gene activation

Answer 20

ie: Igf2

Insulin-like growth factor- imprinted gene

Question 21

Why in Igf2 are the paternal genes expressed even if they are methylated?

Answer 21

Methylation is at a DMR (differentiated methylated region) and promoter is open. Methylation at this regulatory region of the paternal chromosome prevents binding of a repressor to the region and transcription can occur

Question 22

Cutaneous T-cell lymphoma

Answer 22

Treated with HDAC inhibitor so that tumor surpressor gene expression increases

HDAC inhibitor –> more acetylation of histones

Question 23

Nucleosomes and gene expression

Answer 23

Positive superhelical tension

ATP-driven chromatin remodeling
-remodeling factors interact with C terminal of large subunit of RNA polymerase II and use ATP to open up nucleosome

Covalent Modification of histone tails
-Methylation of lysine or arginine (HMT

Question 24

3 ways of modifying histone tails

Answer 24

1) Acetylation of lysines
2) Phosphorylation of serines
3) Methylation of lysines and arginines

Question 25

Acetylation of histone tails

Answer 25

acetylation thru HAT reduces amount of + charge –> becomes loosely associated with DNA backbone –> can do transcription!

HDAC deacetylates and pushes reaction opposite way

Question 26

Thyroid Hormone Receptor- HAT and HDAC

Answer 26

Thyroid receptor and Reitinoid X receptor when attached to DNA both are attached to one another –> attratcs a co-repressor –> deacetylates histones –> tightly wrapped DNA –> transcription not initiated

Thyroid Hormone (T3) changes conformation of TR/RXR –> corepressor doesn’t bind –> coactivator with HAT can attach –> transcription!

Question 27

Methylation on lysine

Answer 27

can activate and repress!