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Molecular Biology > Lecture 5 Regulation of Transcription > Flashcards

Lecture 5 Regulation of Transcription Flashcards

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1
Q

overview of transcriptional regulation

A

transcription and translation are uncoupled in euks

transcription - nucleus
translation - cytoplasm

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2
Q

repressors

A

regulatory proteins that decrease the level of transcripts form certain genes

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3
Q

activators

A

proteins that increase transcription

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4
Q

regulatory sequences

A

specific DNA regions to which regulatory proteins bind, upstream

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5
Q

transcription factors

A

interpret the info present in gene promoters and other regulatory elements and transmit the appropriate response to the RNA pol II transcriptional machinery

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6
Q

What turns on a particular gene?

A

unique combination of regulatory elements and the transcription factors that bind them

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7
Q

cis - acting regulatory elements

A
  • promoter elements, long-range regulatory elements
  • sequence of DNA
  • where trans factors bind
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8
Q

trans-acting transcription factors

A
  • regulatory proteins
  • bind to cis acting elements
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9
Q

gene promoter

A

collection of cis regulatory modules
- required for transcription initiation
- increase the frequency of initiation
- recognition site for RNA poll II general transcription factors

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10
Q

core promoter elements

A

overlap transcription start site
recognition site - by TFIID
may contain some, all, or none of the common motifs

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11
Q

upstream core promoter elements

A
  • BRE
  • TATA box
  • initiator
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12
Q

downstream core promoter elements

A
  • MTE
  • DPE
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13
Q

proximal promoter elements

A
  • CAAT box
  • GC box
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14
Q

long-range regulatory elements

A
  • can work far from the gene promoter
  • enhancer/silencer
  • insulators
  • locus control regions
  • matrix attachment regions
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15
Q

enhancers/silencer

A
  • increase and repress gene promoter activity respectfully
  • contain about 10 binding sites for several different transcription factors
  • can be upstream or downstream
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16
Q

insulators

A
  • chromatin boundary markers
  • enhancer/silencer blocking activity
  • recognized by specific DNA-binding proteins
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17
Q

locus control regions (LCRs)

A
  • organize and maintain a domain of active chromatin
  • upstream of beta globin gene cluster
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18
Q

co-regulators

A
  • recruited by specific regulatory proteins
  • co-activators/co-repressors help to control transcription
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19
Q

allosteric effectors

A
  • small molecules that can bind directly to the regulatory proteins and change their conformation
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20
Q

hyperacetylated chromatin

A

actively transcribed

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21
Q

hypoacetylated chromatin

A

levels of transcription are low

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22
Q

histone acetyltransferases

A

gene activation
- directs acetylation of histones at lysine residues
- reduces the overall positive charge of the histones

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23
Q

histone deacetylases

A

repress transcription
- catalyzes removal of acetyl group

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24
Q

three major domains of transcription factors

A
  • DNA binding domain
  • transactivation/repression domain
  • dimerization domain
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25
transactivation domain
- activates transcription via protein-protein interactions - structurally more elusive
26
dimerization domain
- most transcription factors bind DNA as homodimers or heterodimers
27
DNA binding domain
most common recognition alpha helical domain of protein and 5 base pairs within major groove of DNA double helix interact
28
helix-turn-helix
- read DNA through interactions with base pairs - euks = homeodomain - helix 3 fits in major groove and n terminal arm makes contact in minor groove
29
zinc finger
- many DNA binding folds - about 30 amino acids with an alpha helix and two beta strands around a central zinc ion - alpha helix to major groove - interacts with two cysteines and two histidine's
30
basic leucine zipper
- long alpha helices about 60 aa - hydrophobic leucine residues on the surface that zip together - n terminal splays and sits in the major groove
31
basic helix-loop-helix
- coiled-coil and a helix that fits in the major groove\ - four helices joined by a loop
32
beta sheets
- mediate DNA recognition - immunoglobins are entirely made of beta sheets
33
role of transcription factors in gene regulation
influence the rate of transcription of specific genes either positively or negatively
34
transcription factor repressors
block general transcription machinery
35
transcription factor activators
increase the rate of transcription
36
regulating transcription regulation in bacteria
- prevent RNA polymerase accessing promoter by using Trp repressor - when tryptophan levels are high the trp repressor binds and block RNA polymerase - can only bind if bound itself by tryptophan
37
CAP Catabolite Activator Protein
- regulate the lac operon - enhances RNA polymerase by binding to the CTD
38
lac operon
responds to low glucose levels in the cell by allowing it to metabolize lactose instead if lactose is present
39
lacZ
breaks down lactose
40
lacY
brings lactose into the cell
41
lacA
moves harmful things out
42
lactose levels
when lactose is absent the repressor binds to the lac operator and transcription if OFF
43
glucose levels
- low glucose (available lactose) = CAP binds strongly to the CAP operator enhancing transcription ON - high glucose (available lactose) = CAP does not bind the CAP operator, lac repressor is not bound so WEAK transcription
44
classes or proteins that regulate transcription
1. general (basal) transcription machinery 2. transcription factors 3. transcriptional coactivators and repressors
45
main classes of coactivators
- chromatin modification complexes - chromatin remodeling complexes
46
Histone modification
- acetylation of lysines - methylation of lysines and arginines - ubiquitinylation of lysines - phosphorylation of serines and threonines
47
histone methyltransferase (HMT)
- directs methylation - the methyl groups increase the bulk of histone tails but do not alter the electric charge
48
histone demethylase
removes methyl groups
49
intrinsic regulator
- allows trp to be expressed or not
50
low trp
- ribosome stalls - 2 and 3 form a stem loop - transcription continues
51
high trp
- ribosome proceeds - terminator forms at blocks 3 and 4
52
riboswitches
- can directly bind a structure that controls RNA secondary structure - helps regulate transcription or translation - usually in prokaryotes
53
regions of a riboswitch
- aptamer - expression platform
54
aptamer
- binds to the metabolite
55
expression platform
controls transcription or translation
56
adenine riboswitch
- regulates adenine synthesis - gene expression depends on if a terminator or anti-terminator forms
57
low adenine
RNA structure in regions 2+3 form an anti-terminator and transcription proceeds (also similar to low levels of trp)
58
high adenine
regions 3+4 form a terminator and transcription stops
59
lysine riboswitch
no lysine - mRNA forms anti-terminator hairpin and transcription proceeds yes lysine- aptamer-sensing domains bind lysine triggering formation of a transcription terminator
60
TYPE III S-adenosyl methionine (SAM) riboswitch
- no SAM = the Shine Dalgarno (SD) sequence is accessible for ribosome binding and transcription initiation ON - yes SAM = the shine Dalgarno sequence is base paired in a stem structure preventing ribosome binding OFF

Molecular Biology (2 decks)

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