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genetics > chapter 8 part 2 > Flashcards

chapter 8 part 2 Flashcards

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Biology 101 flashcards
1
Q

most common eukaryotic promoter consensus sequence

A

TATA box located at position -25

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2
Q

what is another name for the TATA box?

A

Goldberg-Hogness box

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3
Q

what consensus sequence in eukaryotes is often found near the -80 position

A

CAAT box

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4
Q

what consensus sequence in eukaryotes is often found near the -90 position

A

GC-rich box
(5’-GGGCGG-3’)

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5
Q

what helps RNA pol II recognize and bind to promoter sequences?

A

proteins called transcription factors

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6
Q

what is the principle binding site for eukaryotes during promoter recognition

A

TATA box

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7
Q

where do transcription factors bind

A

nearby regulatory sequences and interact with RNA polymerase

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8
Q

TFII factors

A

TFs that interact with pol II

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9
Q

eukaryotic promoter recognition steps

A
  1. TFIID binds TATA box sequence and TBP-associated factor (initial committed complex)
  2. TFIIB, TFIIF, and RNA pol II join complex (minimal initiation complex)
  3. joined by TFIIE and TFIIH (complete initiation complex)
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10
Q

TFIID

A

multisubunit protein containing TATA-binding protein (TBP)

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11
Q

initial committed complex

A

assembled TFIID bound to TATA box

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12
Q

minimal initiation complex

A

when TFIIB, TFIIF, and RNA pol II join initial committed complex

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13
Q

completely initiation complex

A

minimal initiation complex joined by TFIIE and TFIIH

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14
Q

what does the complete initiation complex contain?

A

multiple proteins referred to as general transcription factors

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15
Q

Band Shift Assay

A
  • fragments of DNA containing suspected fragments isolated
  • mixed with RNA polymerase/transcription factors
  • fragments that bind to RNA pol/tf have slower electrophoretic migration than unbound
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16
Q

is the exact location of RNA pol binding in band shift assay known?

A

no

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17
Q

DNA footprint protection assay

A
  • first few steps indentical to band assay
  • all fragments end-labeled with p32
  • Dnase I added to each reaction
  • all fragments subjected to electrophoresis
  • gaps represent “footprint protection” by presence of bound transcriptional protein
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18
Q

Dnase I function

A

randomly cleaves DNA not protected by proteins

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19
Q

what do mutations inside the consensus region do

A

significantly reduce levels of transcription

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20
Q

what do mutations outside consensus region do

A

have non-significant effects on transcription

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21
Q

what do enhancer sequences do

A

increase level of transcription of specific genes

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22
Q

are enhancers DNA and RNA sequences?

A

DNA

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23
Q

where are enhancer sequence in comparison to the gene

A
  • can be upstream or downstream
  • often very different from gene sequence
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24
Q

what do enhancer sequences bind to

A

activator proteins and associated co-activators that interact with the TF attached to promoters

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25
Q

what do the activator/coactivator proteins form in enhancer sequences

A

protein bridge that links enhancer proteins to initiation complex at promoter

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26
Q

silencer sequences

A

DNA elements that act at a distance to repress transcription of target genes

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27
Q

what do silencers bind to

A

transcription factors called repressor proteins

28
Q

repressor proteins

A

induce bends in the dNA to reduce transcription

29
Q

where are silencers located

A
  • upstream or downstream
  • variable distances
30
Q

where are ribosomal genes found

A

nucleolus

31
Q

nucleolus

A

nuclear organelle containing rRNA and multiple copies of genes encoding rRNA

32
Q

what is transcription with RNA pol I similar to

A

that of RNA pol II

33
Q

how many functional sequences do RNA pol I promoters have near start of transcription

A

2

34
Q

2 functional sequences of RNA pol I promoters

A
  1. core element
  2. upstream control element
35
Q

core element

A
  • stretches from -45 to +20
  • initiation of transcription
  • bound by sigma-like factor 1 (SL1) protein
36
Q

upstream control element

A
  • spans from -100 to -150
  • increases transcription level
  • bound by upstream binding factor 1 (UBF1)
37
Q

what do most RNA pol III promoters have

A

internal control region

38
Q

are ICRs within or outside of the transcribed region?

A

within the transcribed region

39
Q

internal control region composition

A

2 short DNA sequences:
- box A and box B or C

40
Q

how many base pairs separate box A and box B/C in the internal control region

A

25

41
Q

what kind of proteins bind to the boxes in the internal control region

A

TFII proteins

42
Q

where does transcription begin in the internal control region

A

near box A

43
Q

what does archaeal promoter/transcription resemble?

A

simplified version of eukaryotic pol II

44
Q

transcription promotion in archaea

A
  • 2 proteins homologous to eukaryotic tf identify 2 promoter consensus regions
  • TATA-binding protein (TBP) binds to TATA box
  • TFB binds to TFB-recognition element (BRE) upstream of TATA box
  • RNA pol then binds
45
Q

are bacterial or eukaryotic transcripts more stable

A

eukaryotic

46
Q

where does transcription occur in eukaryotes

A

nucleus

47
Q

where does translation occur in eukaryotes

A

cytoplasm

48
Q

are introns found in bacterial transcripts?

A

no

49
Q

pre-mRNA

A

initial eukaryotic gene mRNA, fully processed to become mature mRNA

50
Q

modifications in post-transcriptional processing

A
  1. 5’ capping
  2. 3’ polyadenylation
  3. intron splicing
51
Q

when does 5’ capping start

A

after first 20-30 nucleotides of mRNA have been synthesized

52
Q

guanylyl transferase

A

adds guanine to 5’ end of pre-mRNA to form unique 5’ to 5’ nucleotide bond

53
Q

what do additional enzymes do during mRNA 5’ capping

A

methylates newly added guanine and nearby nucleotides

54
Q

functions of 5’ capping

A
  1. PROTECTION of mRNA from degradation
  2. TRANSPORT of mRNA out of nucleus
  3. subsequent intron SPLICING
  4. enhance TRANSLATION` efficiency by orienting ribosome on mRNA
55
Q

3 steps of 5’ capping

A
  1. guanylyl transferee removes y (3rd) phosphate of 5’ end of mRNA (leaves 2 phosphates)
  2. guanine to be added loses 2 phosphates to become monophosphate
  3. guanylyl transferase joins guanine monophosphate to 5’ mRNA by 5’ to 5’ triphosphate lihnkage
56
Q

name of bond between phosphates in 5’ capping

A

5’ to 5’ triphosphate linkage

57
Q

overview of 3’ polyadenylation

A

3’ end of pre-mRNA modified by action of several enzymes that remove a section of 3’ message and replace it with a string of adenines

58
Q

functions of polyadenylation

A
  1. facilitated TRANSPORT of mature mRNA across nuclear membrane through pore complex to cytoplasm
  2. PROTECTS mRNA from degradation
  3. enhances TRANSLATION by enabling ribosomal recognition of mRNA
59
Q

steps of polyadenylation

A
  1. cleavage/polyadenylation specificity factor binds near signal sequence
  2. cleavage-stimulating factor binds to uracil-rich region downstream
  3. CFI, CFII, and polyadenylate polymerase also bind
  4. pre-mRNA cleaved 15-30 nucleotide downstream poly. signal
  5. 3’ end of mRNA undergoes addition of 20-2000 A
  6. poly-A-binding protein joins A tail to increase rate of addition
60
Q

polyadenylation signal sequence

A

5’ - AAUAAA - 3’
- downstream of stop codon

61
Q

what happens to mRNA released by cleavage during polyadenylation

A

later degraded

62
Q

how are 20-200 A added to 3’ end of cut pre-mRNA

A

through action of CPSF and PAP

63
Q

when does poly-A-binding protein join adenine tail

A

after addition of first 10 proteins

64
Q

how are polyadenylation and transcription termination connected

A

by activity of specialized RNase (Torpedo)

65
Q

Torpedo model of transcription termination

A
  • after 3’ cleavage/polyadenylation, uncapped transcript still attached to RNA pol
  • digest residual transcript like torpedo
  • RNase catches up to polymerase and triggers termination

genetics (37 decks)

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