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Molecular Biology > Lecture 5 Regulation of Transcription > Flashcards

Lecture 5 Regulation of Transcription Flashcards

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AP® Biology flashcards Biology 101 flashcards
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
Q

transactivation domain

A
  • activates transcription via protein-protein interactions
  • structurally more elusive
26
Q

dimerization domain

A
  • most transcription factors bind DNA as homodimers or heterodimers
27
Q

DNA binding domain

A

most common recognition alpha helical domain of protein and 5 base pairs within major groove of DNA double helix interact

28
Q

helix-turn-helix

A
  • 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
Q

zinc finger

A
  • 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
Q

basic leucine zipper

A
  • 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
Q

basic helix-loop-helix

A
  • coiled-coil and a helix that fits in the major groove\
  • four helices joined by a loop
32
Q

beta sheets

A
  • mediate DNA recognition
  • immunoglobins are entirely made of beta sheets
33
Q

role of transcription factors in gene regulation

A

influence the rate of transcription of specific genes either positively or negatively

34
Q

transcription factor repressors

A

block general transcription machinery

35
Q

transcription factor activators

A

increase the rate of transcription

36
Q

regulating transcription regulation in bacteria

A
  • 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
Q

CAP Catabolite Activator Protein

A
  • regulate the lac operon
  • enhances RNA polymerase by binding to the CTD
38
Q

lac operon

A

responds to low glucose levels in the cell by allowing it to metabolize lactose instead if lactose is present

39
Q

lacZ

A

breaks down lactose

40
Q

lacY

A

brings lactose into the cell

41
Q

lacA

A

moves harmful things out

42
Q

lactose levels

A

when lactose is absent the repressor binds to the lac operator and transcription if OFF

43
Q

glucose levels

A
  • 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
Q

classes or proteins that regulate transcription

A
  1. general (basal) transcription machinery
  2. transcription factors
  3. transcriptional coactivators and repressors
45
Q

main classes of coactivators

A
  • chromatin modification complexes
  • chromatin remodeling complexes
46
Q

Histone modification

A
  • acetylation of lysines
  • methylation of lysines and arginines
  • ubiquitinylation of lysines
  • phosphorylation of serines and threonines
47
Q

histone methyltransferase (HMT)

A
  • directs methylation
  • the methyl groups increase the bulk of histone tails but do not alter the electric charge
48
Q

histone demethylase

A

removes methyl groups

49
Q

intrinsic regulator

A
  • allows trp to be expressed or not
50
Q

low trp

A
  • ribosome stalls
  • 2 and 3 form a stem loop
  • transcription continues
51
Q

high trp

A
  • ribosome proceeds
  • terminator forms at blocks 3 and 4
52
Q

riboswitches

A
  • can directly bind a structure that controls RNA secondary structure
  • helps regulate transcription or translation
  • usually in prokaryotes
53
Q

regions of a riboswitch

A
  • aptamer
  • expression platform
54
Q

aptamer

A
  • binds to the metabolite
55
Q

expression platform

A

controls transcription or translation

56
Q

adenine riboswitch

A
  • regulates adenine synthesis
  • gene expression depends on if a terminator or anti-terminator forms
57
Q

low adenine

A

RNA structure in regions 2+3 form an anti-terminator and transcription proceeds (also similar to low levels of trp)

58
Q

high adenine

A

regions 3+4 form a terminator and transcription stops

59
Q

lysine riboswitch

A

no lysine - mRNA forms anti-terminator hairpin and transcription proceeds
yes lysine- aptamer-sensing domains bind lysine triggering formation of a transcription terminator

60
Q

TYPE III S-adenosyl methionine (SAM) riboswitch

A
  • 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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