Gene Regulation

Question 1

what are cis regulatory elements

Answer 1

proteins that bind to DNA itself - enhancer sequence, basal promoter sequence, proximal control region

Question 2

what are trans regulatory elements

Answer 2

proteins that bind to the cis regulatory elements - enhancers, transcription factors

Question 3

what does the basal promoter sequence consist of

Answer 3

TATA box and CAAT box

Question 4

what is promoter region responsible for

Answer 4

interaction of RNA pol II with its associated factors

Question 5

whats the point of having both a basal and upstream promoters

Answer 5

allow for tight regulation

Question 6

what do transcription factors do

Answer 6

help to grant specificity to RNA pol II regulated transcription

Question 7

what promotes high levels of transcription?

Answer 7

enhancer, proximal promoters

Question 8

level of expression with just the basal transcription machinery

Answer 8

low

Question 9

where can enhancer be found

Answer 9

before gene, introns, or after gene

Question 10

examples of eukaryotic transcription factors that must dimerize to function

Answer 10

leucine zipper, helix-turn-helix, zinc finger

Question 11

what are DNA binding domain

Answer 11

part of transcription factors that only bind to certain DNA sequences

Question 12

advantages of forming a dimer

Answer 12

adds an element of complexity and versatility

Question 13

what does enhancer do to basal transcription apparatus

Answer 13

it stabilizes it thus increasing transcription levels

Question 14

three modes of repressor action for transcription factors

Answer 14

quenching, blocking, competition

Question 15

when does quenching occur with repressor proteins

Answer 15

repressor protein binds directly to the activator and hence can’t bind enhancer

Question 16

when does competition occur with repressor protein

Answer 16

activator and repressor compete for binding to the enhancer

Question 17

when does blocking occur with repressor protein

Answer 17

repressor binds to activation domain of the activator and now cant interact with basal transcriptional machinery

Question 18

if repressor protein binds to the activation domain of the activator, can it still bind to the DNA

Answer 18

yeah but it is non functional

Question 19

advantage of different genes having the same cis regulatory sequence

Answer 19

multiple genes can be regulated together - turned on and off at same time etc

Question 20

short sequences of DNA within a gene promoter region that are able to bind a specific transcription factor and regulate transcription of genes

Answer 20

response elements

Question 21

what allows the hypoxia inducible factors to bind and regulate transcription of genes

Answer 21

short DNA sequences (HREs) in the promoter of the genes

Question 22

how do hypoxia element factors work

Answer 22

they (HIF alpha and HIF beta) must dimerize before they can bind to DNA sequences and regulate expression

Question 23

what type of elements are the hypoxia inducible factors

Answer 23

cis regulatory elements

Question 24

most oxygen breathing species express what highly conserved transcriptional complex

Answer 24

HIF-1

Question 25

what does HIF do

Answer 25

allows for coordinated cellular response to low oxygen tension

Question 26

name giving to normal cells with oxygen stress

Answer 26

normoxia

Question 27

fate of HIF-1 alpha under normal oxygen conditions

Answer 27

they are degraded by proteasomes in the cytoplasm and genes for hypoxia response are not expressed

Question 28

fate of HIF-1 alpha under low oxygen state

Answer 28

HIF-1 alpha is not degraded and it enters cell nucleus where it forms dimer with HIF-1 beta allowing it to bind to DNA of target genes carrying hypoxia response element (HRE)

Question 29

Induction of expression of a family of genes by transcription factor binding to a common enhancer sequence of many different genes is an example of?

Answer 29

cells in hypoxia state

Question 30

what happens inside a tumor that causes it to grow

Answer 30

so there is no oxygen inside a tumor hence HIF-1 alpha is not degraded. HIF-1 alpha stimulates angiogenesis (development of new blood vessels) hence giving supply for tumor to grow

Question 31

reason why we learn about hypoxia in relation to how we should treat tumor

Answer 31

if we could find a way to inhibit HIF-1 alpha and beta inside tumors we can stop its growth

Question 32

glucocorticoid receptors is what type of transcription factor

Answer 32

zinc finger TF

Question 33

What does activated glucocorticoids receptor do in nucleus and cytosol

Answer 33

upregulates expression of anti inflammatory genes in nucleus represses expression of pro inflammatory proteins in cytosol

Question 34

glucocorticoids is used as treatment for

Answer 34

glucocorticoid deficiency and to suppress the immune system

Question 35

key thing to note about glucocorticoid response elements DNA sequence

Answer 35

they are inverted repeats

Question 36

what happens to glucocorticoid receptors in cytoplasm in absence of glucocorticoids

Answer 36

become part of an inactive multi-protein complex

Question 37

when happens when cortisol (glucocorticoids) is present in cytoplasm

Answer 37

its receptors dissociate from the multi protein complex, dimerizes, and moves to the nucleus

Question 38

what do glucocorticoids receptors do in nucleus

Answer 38

induce or repress target genes also bind response element DNA in the promoter regions of glucocorticoid-responsive genes

Question 39

what is the myc/max system

Answer 39

regulatory mechanism that switches between gene activation and repression

Question 40

in absence of myc, what does max do

Answer 40

max dimers with itself (homodimer) and represses gene transcription

Question 41

what does myc do with its transcriptional regulation domain

Answer 41

it has to dimer with max first before it can bind to DNA then regulates expression of genes involved in cell cycle progression

Question 42

when is max expressed and myc not

Answer 42

in non proliferating cells

Question 43

in presence of myc what happens

Answer 43

myc and max dimerize (heterodimer) and activate gene expression

Question 44

difference between myc/max heterodimer and max homodimer

Answer 44

myc/max - gene expression (more favorable) | max/max - gene suppression

Question 45

problem with myc over expression in tumors/cancers

Answer 45

it will favor forming the heterodimer with max and will promote cell proliferation

Question 46

Processes long primary- miRNAs to pre-miRNA hairpin structures

Answer 46

Drosha

Question 47

Base pairing between miRNA and target mRNA give what

Answer 47

target specificity

Question 48

what happens if specificity is not complete with miRNA

Answer 48

one miRNA can silence many mRNA

Question 49

what further processes pre-miRNA to single stranded RNA and initiates the formation of the RNA-induced silencing complex (RISC)

Answer 49

dicer

Question 50

is it common in human for mRNA to be regulated by miRNA

Answer 50

yeah

Question 51

how does miRNA regulate gene expression in mRNA

Answer 51

it binds to the 3' UTR and base pairs to it preventing interaction of translational machinery with the 5' cap structure basically prevents mRNA from getting translated

Question 52

miRNA are normally involved in what type of regulation

Answer 52

cell proliferation

Question 53

what happens to the genes that code for miRNA in tumor cells

Answer 53

amplified so they proliferate uncontrollably

Question 54

short interfering RNA (siRNA) is processed by what type of enzyme

Answer 54

dicer

Question 55

Double stranded RNA Often transcribed of two opposable promoters in a gene delivery vector

Answer 55

siRNA