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Biology Exam 3 > Control of Gene Expression > Flashcards

Control of Gene Expression Flashcards

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AP® Biology flashcards Biology 101 flashcards
1
Q

what are recognition sequences?

A

recognition sites for DNA binding proteins

can be close or far away from gene

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2
Q

what are gene regulatory proteins?

A

transcription factors that will bind and activate genes

associate w/ the major groove of DNA structure

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3
Q

gene regulatory proteins and their binding locations

A

protein surface is completely complimentary to surface of DNA binding region

contact has 4 possible configurations of base pairs
w/ 10-20 interactions

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4
Q

parts of gene regulatory proteins

A

DNA binding module
activation module
dimerization module
regulatory module

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5
Q

what modules are always present vs. could be present on gene regulatory proteins?

A

always – DNA binding, activation modules

might – dimerization, regulatory modules

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6
Q

dimerization module

A

could be present

forms dimers w/ other protein subunits

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7
Q

regulatory module

A

could be present

regulate the transcription factor

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8
Q

evidence for transcription factors being modular

A

using experiments where we cut out portions of the gene regulatory proteins we discovered that they are modular

aka certain regions do a specific thing

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9
Q

what are the 4 different structural motifs?

A

helix turn helix
zinc finger motif
leucine zipper
helix loop helix

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10
Q

what is the most common structural motif?

A

helix turn helix

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11
Q

2 alpha helices connected by a short chain of amino acids

A

helix turn helix

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12
Q

helix turn helix

A

turned at fixed angle
-the longer helix has the recognition and dna binding modules

-dna side chains recognize dna binding site

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13
Q

zinc finger motif

A
  • -a zn atom located at the base of a finger-like structure
  • -zinc finger domains found in clusters
  • -have multiple contact points w/ dna = stabilization
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14
Q

2 alpha helical strands that contact DNA like a clothespin

A

leucine zipper motif

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15
Q

leucine zipper

A
  • -activation and dimerization modules overlap
  • -forms hydrophobics interactions between 2 helices = zipper
  • -leucine every 7 amino acids
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16
Q

helix loop helix

A

a short alpha helix chain connected by a loop to a second chain

  • -existing as a homo or heterodimer
  • -3 modules: dna binding, dimer, activation
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17
Q

3 ways to identify transcription factors

A

EMSA
affinity chromatography
CHIP

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18
Q

electrophoretic mobility shift assay

A

EMSA
a gel mobility shift assay that detects sequence specific DNA binding proteins using a radioactive DNA fragment

after running a electrophoretic gel – the protein w/ smallest protein moves farthest – backpack example

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19
Q

affinity chromatography

A

to ID DNA binding proteins = purification

  1. ID a dna binding protein
  2. isolate
  3. use only 1 promoter recognition sequence
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20
Q

chromatin immuno-precipitation

A

CHIP
used when you don’t know what the regulatory protein binds to

–allowing you to ID sites in genome that a known protein binds to

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21
Q

CHIP use

A

used in living cells

PCR product at end so you can ID DNA sequence

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22
Q

how does histone acetylation effect binding to DNA

A

makes it easier to remove histones

thus easier access to DNA

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23
Q

activator and repressor protein competition

A

their binding sites might overlap and they can compete for binding

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24
Q

activator and repressor proteins both bind DNA

A

repressor can then bind to the activator to inhibit transcription = masking
or
repressor can bind to other DNA to block assembly of transcription machinery

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25
Q

what other factors can a repressor attract?

A
  • -chromatin remodeling complexes
  • -histone deacetylase
  • -histone methyl transferase
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26
Q

chromatin remodeling complex recruitment

A

repressor can recruit these to fold up DNA and make promoter site unavailable

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27
Q

histone deacetylase attraction to promoter

A

repressor proteins can attract this which results in

it is harder to remove/remodel deacetylated histones – thus harder to free DNA from it’s coiled structure

28
Q

histone methyl transferase to ______ histones

A

this will methylate histones

recruited by repressor proteins

resulting in other proteins binding to methylated histones keeping DNA transcriptionally silent

29
Q

list the ways repressor proteins can stop transcription

A
  1. bind activator/DNA
  2. block assembly of machinery
  3. attraction of other factors
30
Q

gene regulatory proteins acting as a committee

A

the same protein can act as a activator or repressor depending on what proteins have assembled together

aka = committee of proteins together will = an activator or repressor

31
Q

how is the function of gene regulatory proteins regulated?

A
  1. synthesis
  2. ligand binding
  3. covalent modification
  4. addition of subunit
  5. unmasking
  6. nuclear entry
  7. proteolysis
32
Q

synthesis

A

regulatory proteins are only made when wanted

33
Q

ligand binding

A

regulatory proteins can’t work until a ligand binds

34
Q

covalent modification

A

–phosphorylation

proteins are not active until modified

35
Q

unmasking

A

an inhibitor is bound normally but once removed = activation

36
Q

nuclear entry

A

regulatory proteins are only active if located w/in nucleus

37
Q

proteolysis

A

the regulatory protein is normally membrane bound

becomes active when released from membrane

38
Q

RNA alternative splicing - activators vs. repressors

A

activators can recruit splicing machinery

repressors can stop them from being able to bind

39
Q

RNA modifications

A

these provide stability

poly A tail
5’ cap

40
Q

iron excess responses

A

ferritin made
no transferrin receptor made
thus unable to uptake Fe into cells

41
Q

iron starvation response

A

no ferritin made
transferrin receptors made

thus Fe is taken into cells

42
Q

IRE’s

A

iron responsive elements
recognition sites for binding
when in iron excess

43
Q

IRP

A

iron responsive regulatory protein

when in iron starvation

44
Q

binding of IRPs to block translation

A

to IRE at 5’ ferritin mRNA
= no ferritin made
= translation blocked

if this does not happen mRNA is made so ferritin is made

45
Q

binding of IRPs to allow translation

A

to IRE at 3’ transferrin receptor mRNA
= transferrin made
= mRNA stable

if this does not happen RNA degrades and no transferrin receptor is made

thus no iron taken into cell

46
Q

ferritin

A

is made when in excess of Fe

binds to receptors to make cells uptake iron for storage when excess iron

47
Q

transferrin receptors

A

found on basal cell membranes
uptake iron into cells
normally cells store iron but if in starvation these need to be blocked so that iron is not stored inside cells

48
Q

iron starvation: IRP/IRE

A

IRP binding to IRE of ferritin
no mRNA made
because we don’t need to store Fe

IRP binds to IRE at 3’
=transferrin made to collect more iron

49
Q

iron excess: IRP/IRE

A

too much iron in blood - must store excess in cells
ferritin needed but not TfR

IRP binds to iron and is inactivated

  • -ferritin made w/o suppression
  • -w/o binding of IRP TO TfR IRE – no transferrin made
50
Q

microRNA function

A

small, non-coding regulatory RNAs to regulate mRNA

22 nucs long

function to silence expression of specific mRNA targets

51
Q

microRNA binding

A

bind to complementary sequences in the 3’ UT end of mRNA

will induce degradation or just block translation

52
Q

microRNA targets for binding

A

have widespread binding sites and repress hundreds of mRNAs or effect an entire program

53
Q

post-translational modification of proteins: why?

A

required for protein to be functional/active

54
Q

protein post-translational modifications

A
  1. by protein kinases
  2. glycosylated
  3. bind to other subunits/partners
  4. modifying enzymes act on protein
55
Q

proteins modified by protein kinases

A

phosphorylation

56
Q

modifying enzymes that act on protein: example

A

Hsp
help refold proteins so that can function properly

activated at high temperatures

57
Q

regulation of proteins by degradation

A

proteasome
removes and recycles misfolded/old proteins

proteins are flagged w/ ubiquitin on lysine side chains

58
Q

interior of proteosomes

A

a hollow chamber w/ proteasomes inside
ATP dependent

recognizes proteins w/ ubiquitin flags

recycles ubiquitin after binding bad proteins

59
Q

addition of ubiquitin

A

using E1 enzymes

to add ubiquitin to lysine side chains on protein

60
Q

coordinated gene expression

A

genes coordinate their expression in response to needs of the cell

61
Q

DNA methylation

A

dna can be regulated by proteins

dna can be covalently modified to induce activation/suppression

methylation can be inherited from parents

62
Q

genomic imprinting

A
  • -differential expression of genetic material depending on parent of origin
  • -associated disorder prader willi syndrome
63
Q

PWS

A

prader willi syndrome

caused by paternal deletion on chromosome 15

64
Q

PWS clinical presentation

A

infantile hypotonia
poor suck-feeding issues

stage two - childhood obesity - uncontrollable eating - hyperphagia

mental and behavior problems

65
Q

PWS inheritance

A

deletion expressed if missing from dad even if proper genes exist in DNA inherited from mom

due to genomic imprinting

66
Q

random X chromosome inactivation

A

females are XX
but the body cannot have segments of the same chromosome active

so in some areas of body one X is turned off while somewhere else the opposite is true

it is completely random and complex

Biology Exam 3 (9 decks)

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