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Biology Exam 3 > Control of Gene Expression > Flashcards

Control of Gene Expression 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
what other factors can a repressor attract?
- -chromatin remodeling complexes - -histone deacetylase - -histone methyl transferase
26
chromatin remodeling complex recruitment
repressor can recruit these to fold up DNA and make promoter site unavailable
27
histone deacetylase attraction to promoter
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
histone methyl transferase to ______ histones
this will methylate histones recruited by repressor proteins resulting in other proteins binding to methylated histones keeping DNA transcriptionally silent
29
list the ways repressor proteins can stop transcription
1. bind activator/DNA 2. block assembly of machinery 3. attraction of other factors
30
gene regulatory proteins acting as a committee
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
how is the function of gene regulatory proteins regulated?
1. synthesis 2. ligand binding 3. covalent modification 4. addition of subunit 5. unmasking 6. nuclear entry 7. proteolysis
32
synthesis
regulatory proteins are only made when wanted
33
ligand binding
regulatory proteins can't work until a ligand binds
34
covalent modification
--phosphorylation | proteins are not active until modified
35
unmasking
an inhibitor is bound normally but once removed = activation
36
nuclear entry
regulatory proteins are only active if located w/in nucleus
37
proteolysis
the regulatory protein is normally membrane bound becomes active when released from membrane
38
RNA alternative splicing - activators vs. repressors
activators can recruit splicing machinery repressors can stop them from being able to bind
39
RNA modifications
these provide stability poly A tail 5' cap
40
iron excess responses
ferritin made no transferrin receptor made thus unable to uptake Fe into cells
41
iron starvation response
no ferritin made transferrin receptors made thus Fe is taken into cells
42
IRE's
iron responsive elements recognition sites for binding when in iron excess
43
IRP
iron responsive regulatory protein | when in iron starvation
44
binding of IRPs to block translation
to IRE at 5' ferritin mRNA = no ferritin made = translation blocked if this does not happen mRNA is made so ferritin is made
45
binding of IRPs to allow translation
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
ferritin
is made when in excess of Fe | binds to receptors to make cells uptake iron for storage when excess iron
47
transferrin receptors
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
iron starvation: IRP/IRE
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
iron excess: IRP/IRE
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
microRNA function
small, non-coding regulatory RNAs to regulate mRNA 22 nucs long function to silence expression of specific mRNA targets
51
microRNA binding
bind to complementary sequences in the 3' UT end of mRNA will induce degradation or just block translation
52
microRNA targets for binding
have widespread binding sites and repress hundreds of mRNAs or effect an entire program
53
post-translational modification of proteins: why?
required for protein to be functional/active
54
protein post-translational modifications
1. by protein kinases 2. glycosylated 3. bind to other subunits/partners 4. modifying enzymes act on protein
55
proteins modified by protein kinases
phosphorylation
56
modifying enzymes that act on protein: example
Hsp help refold proteins so that can function properly activated at high temperatures
57
regulation of proteins by degradation
proteasome removes and recycles misfolded/old proteins proteins are flagged w/ ubiquitin on lysine side chains
58
interior of proteosomes
a hollow chamber w/ proteasomes inside ATP dependent recognizes proteins w/ ubiquitin flags recycles ubiquitin after binding bad proteins
59
addition of ubiquitin
using E1 enzymes | to add ubiquitin to lysine side chains on protein
60
coordinated gene expression
genes coordinate their expression in response to needs of the cell
61
DNA methylation
dna can be regulated by proteins dna can be covalently modified to induce activation/suppression methylation can be inherited from parents
62
genomic imprinting
- -differential expression of genetic material depending on parent of origin - -associated disorder prader willi syndrome
63
PWS
prader willi syndrome caused by paternal deletion on chromosome 15
64
PWS clinical presentation
infantile hypotonia poor suck-feeding issues stage two - childhood obesity - uncontrollable eating - hyperphagia mental and behavior problems
65
PWS inheritance
deletion expressed if missing from dad even if proper genes exist in DNA inherited from mom due to genomic imprinting
66
random X chromosome inactivation
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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