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biochemistry 2 > regulation of gene expression > Flashcards

regulation of gene expression Flashcards

1
Q

how does tretinoin reduce ance and skin wrinkle?

A

normalizes skin cycle and reduces expression of NO (which is pro-inflammatory)

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2
Q

what is tretinoin?

A

all-trans retinoic acid

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3
Q

what does tretinoin bind to?

A

RAR and RXR

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4
Q

what does tretinoin increase expression of?

A

type 1 collagen

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5
Q

access to promotor is restricted by?

A

chromatin structure

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6
Q

RNA polymerase binds to DNA at the _____,

A

promotor

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7
Q

where do regulatory proteins bind to

A

promotor

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8
Q

housekeeping genes vs regulated genes

A

housekeeping are expressed all the time bc needed for survival, regulated are expressed only when necessary

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9
Q

positive regulation

A

cells off to cells turned on

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10
Q

which proteins are normally multimeric

A

regulatory proteins

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11
Q

downstream promotors

A

right side

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12
Q

upstream promotors

A

left side

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13
Q

most common aa involved?

A

asn, glu, gln, lys, arg

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14
Q

regulatory protiens have DNA binding ____

A

domains/motifs

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15
Q

what does the interaction between dna and aa involve

A

H-bonds

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16
Q

helix-turn-helix domain

A

20 AA with 2 alpha segments, one acts as a recognition helix

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17
Q

zinc finger domain

A

30 AA long

loops crossed linked w Zn2+

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18
Q

why would there be many zinc fingers??

A

bc DNA binding is weaker

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19
Q

along with DNA binding domains what can zinc fingers also act as ?

A

RNA binding motif

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20
Q

Leucine zipper ( part of regulatory protiens that helps with the binding to DNA)

A

leu occurs at every 7th position

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21
Q

regulatory proteins have 2 things

A

protein interaction domains and DNA binding motifs to interact with other TF at the promoter region

22
Q

euchromatin is accessable or non accessable?

A

loosely packed/ accessible

23
Q

which chromatin structure is tightly packed??

A

heterochromatin

24
Q

nucleosome has how many histone proteins

A

2 of each of the 4 histone protiens ( H2A,H2B,H3,H4)

25
Q

what is H1 proteins role??

A

linker protein/ glues together multiple nucleosomes

26
Q

which chromatin is depleted of H1 and replaced with histone variants

A

eurchromatin ( transcriptionally active)

27
Q

which enzymes replace H1 with histone variants?

A

SNF/SWI enzymes

28
Q

which nucleotide gets methylated in modification?? and in what bond?

A

cytosine in the CpG bond

29
Q

which is more common histone modification or DNA modification?

A

histone- can be methylated, phosphorylated, acetylated ect…
DNA only methylated on cytosine

30
Q

phosphorylation on histones occur on which AA?

A

Serine and threonine

31
Q

histone methylation can occur only on which AA’s?

A

LYS and ARG

32
Q

acetylation, ubiquitination and sumolyation occur on which AA in histones??

A

LYSINE

33
Q

what is histone acetylation regulated by??

A

HAT ( histone acetylation transferase) and HDAC’s (histone de-acetylation)

34
Q

why would you acetylate a histone??

A

allows for chromatin to be exposed to TF and binding proteins for transcription to occur. acetylation is regulated by HAT and HDAC enzymes

35
Q

describe the assembly of the pre-initiation complex

A

goal is to stimulate poly2 to transcribe
first, activators bind to enhancers
then histone/nucleosome modification begins w mediator??
then, TATA binding protiens (TBP) and Transcription factor 2B come in and bind to the promotor
Basal TF and RNA polymerase 2 bind to start site and TF2H stimulate poly 2 to transcribe

36
Q

what stimulates RNA polymerase to transcribe after pre-initiation complex has formed

A

TF2H

37
Q

what is the mediators role in the pre-initiationcomplex?

A

enhance and promote connection (structurally through stacking and functionally through activating protiens or TF that then go to promotor region)

38
Q

HMG

A

high mobility group

39
Q

what does HMG do?

A

bends DNA

40
Q

UAS

A

upstream activator sequence

41
Q

lncRNA

A

long non-coding RNA, acts as an enzyme

42
Q

can lncRNA be an inhibitor?

A

yes

43
Q

what are HRE’s?

A

hormone response elements- a short sequence of DNA in the promotor region- steroid hormones ( such as retinoic acid, vitD, thyroid hormone) binds to it acting as a TF

44
Q

how do steroids/ hormones elicit an intracellular response

A

they bind to NR inside the cytoplasm, NR dimer attaches to HRE (hormone response element ) thereby altering gene expression

45
Q

describe NR structure

A

lots of domains- need DNA binding domains such as ZInc fingers and binding sites for the hormones and a region that activates transcrition of the reguated gene

46
Q

Type 1 vs Type 2 NR

A

Type 1 is found in cytoplasm bound to HSB and only dimerized MR can go through nucleus

47
Q

introns

A

do not code and get spliced out

48
Q

exons

A

code for genes

49
Q

what are translational regulators

A

bind to mRNA using same principle that TF bind to DNA

50
Q

micro RNA (endogenous )

A

silence genes by binding to the mRNA and prevent translation

51
Q

difference between Micro RNA and siRNA

A

microRNA is endogenous whereas siRNA is synthesized using science

52
Q

SiRNA

A

once bind to mRNA- inhibits its translation

biochemistry 2 (7 decks)

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