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genetics > chapter 8 part 2 > Flashcards

chapter 8 part 2 Flashcards

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Biology 101 flashcards
1
Q

Where is the principal binding site for transcription factors in most eukaryotic promoters?

A

the TATA box

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2
Q

where does transcription in eukaryotes take place?

A

the nucleus

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3
Q

Which structure, located in the promoter, facilitates the binding of RNA polymerase III to tRNA promoters?

A

internal control region (ICR)

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4
Q

what enzyme permits a 5’ capping of mRNA?

A

guanylyl transferase

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5
Q

Which DNA regulatory sequence interacts with activator proteins to increase the level of transcription?

A

enhancer

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6
Q

Which of the following research techniques would be used to verify that a DNA sequence of interest binds to a transcription factor?

A

band shift assay

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7
Q

what is the most common eukaryotic consensus sequence?

A

the TATA Box

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8
Q

what is the TATA box also called?

A

the Goldberg-Hogness box

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9
Q

where is the TATA Box located?

A

about the -25 position

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10
Q

whare is the CAAT box found?

A

-80 position

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11
Q

where is the GC-rich box found?

A

the -90 position

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12
Q

do prokaryotic promoters display more or less variation than eukaryotic promoters?

A

less

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13
Q

what helps RNA pol II bind to the promoter sequence?

A

transcription factos (TFs)

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14
Q

what is the principle binding site during promoter recognition?

A

the TATA Box

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15
Q

what do TFs bind to and what do they do?

A

nearby regulatory sequences and they interact with RNA polymerase

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16
Q

what are the TFs called that interact with Pol II?

A

TFII Factors

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17
Q

what does TFIID contain?

A

the TATA-Binding protein

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18
Q

what does the TFIID bind?

A

it binds the TATA Box sequence and the TBP-associated factor (TAF)

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19
Q

what froms the initial committed complex?

A

the TFIID bound to the TATA Box

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20
Q

what makes up the minimal initation complex?

A

the TFIIB, TFTTF, and RNA Pol ii

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21
Q

what form the complete initation complex?

A

TAFIIE and TFIIH

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22
Q

what are the proteins in the complete initiation complex referred to as?

A

the General Transcription Factors (GTFs)

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23
Q

what happens in Band Shift Assay?

A

-isolate fragements of DNA containing suspected DNA fragments
-DNA fragments r mixed with RNA pol and/or transcription factors
-the fragments that bind to the RNA/ TFS have slower electrophoretic migration that the unbound sequences
-inidcated that the DNA fragments r bound by transcriptional proteins

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24
Q

is exact location known in Band Shift Assay?

A

No- we just know that the DNA is bound by transcriptional proteins

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25
Q

what happens in DNA Footprint Protection Assay?

A

-first couple of steps are identical to band assay
-the fragments are labeled with 32P
-Dnase I is added to each reaction (DNA not protected by proteins is cleaved)
-All fragments from both reactions are subjected to electrophoresis

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26
Q

is exact location known in DNA Footprint Protection Assay?

A

Yes- we get to know where within a fragment a transcriptional protein binds

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27
Q

what does Dnase I do?

A

it randomly gets rid of DNA not protected by proteins

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28
Q

Mutations inside the consensus region significantly _________ levels of transcription

A

reduce

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29
Q

Mutations outside the consensus region have ________________ effects on transcription

A

non-significant

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30
Q

what do enhancer sequences do?

A

Increase the level of transcription of specific genes

31
Q

what do enhancer sequences bind?

A

activator proteins and co-activators that form a protein bridge

32
Q

what does the protein bridge in enhancers link?

A

links to proteins at the enhancer sequence to the initiation complex at the promoter

33
Q

why does the bridge bend the DNA?

A

so the enhancer sequence part and the initiation complex’s proteins are close enough to interact

34
Q

what are silencer sequences

A

-reverse of enhancer sequences
-DNA elements that act at a distance to REPRESS transcription of their target genes

35
Q

what do silencers bind?

A

transcription factors called repressor proteins that induce bend in DNA

36
Q

what do the bends do in the silencers?

A

it reduced transcription of the target gene

37
Q

where would silencer be loated?

A

upstream or downstream from their target gene- the distance varies

38
Q

what does RNA pol I do?

A

transcribes genes for rRNA

39
Q

where are ribosomal genes found?

A

in the nucleolus

40
Q

what is the nucleolus?

A

a nuclear organelle containing r RNA and multiple copies of genes encoding rRNA

41
Q

how many function sequences do RNA pol I promoters have?

A

2 (near the start of transcription)

42
Q

what are the two functional sequences that RNA Pol I Promoters have?

A
  • the core element
  • upstream control element
43
Q

core element

A

t (-24 to +20, needed for initiation of transcription, bound by sigma-like factor 1 (SL1) protein

44
Q

upstream control element

A

-100 to -150, increases level of transcription, bound by upstream binding factor 1 (UBF1)

45
Q

what is RNA Pol iii primarily responsible for transcription of?

A

tRNA genes, also does one rRNA, and other RNA-encoding genes

46
Q

what do most RNA pol ii promoters have?

A

an internal control region (ICR)

47
Q

what are ICRs

A

they are within the transcribes region
-typically contain dna sequences called box A and box B, or box A and box C
-25 bp seperate the two box regions
-TFII proteins bind to the two box region
-RNA pol iii n=binds to the complex and transcription begins near box A after proper RNA pol iii positioning

48
Q

how many proteins identify the two promoter consensus regions in archaea

A

two

49
Q

what is archaea transcription kind of similar too, just simplifed?

A

eukaryotic transcription

50
Q

how does transcription work in archaea

A

TATA-binding protein (TBP) binds to the TATA box and transcription factor B (TFB) binds to a TFB-recognition element (BRE) upstream do the TATA box. rna pol then binds

51
Q

____________ transcripts are more ________ than bacterial
transcripts

A

Eukaryotic
stable

52
Q

what are transcription and translation seperated in time and location in?

A

eukaryotes

52
Q

where does transcription occur in eukaryotes?

A

nucleus

53
Q

where does translation occur in eukaryotes?

A

cytoplasm

54
Q

what do eukaryotic transcripts have than bacterial don’t?

A

introns

55
Q

what is the initial eukaryotic gene mRNA called?

A

pre-mRNA

56
Q

what is the fully processed eukaryotic gene mRNA called?

A

mature mRNA

57
Q

what do mature mRNA modifications include?

A
  1. 5’ capping
  2. 3’ polyadenylation
  3. intron splicing
58
Q

when does guanylyl transferase come in to play?

A

after the first 20 to 30 nucleotides of mRNA have been synethesized

59
Q

what does guanylyl transferase do?

A

it adds a guanine to the 5’ end of the pre-MRNA - unique to a 5’ to 5’ nucleotide bond

60
Q

what are the several functions that the 5’ capping serves?

A

-protection of mRNA from degredation
-transport of mRNA out the nucleus
-intron splicing
-enhancing translation by efficiently orienting the ribosome on the mRNA

61
Q

what phosphate does guanylyl transferase remove?

A

the y (or 3’ phosphate) of the 5’ end of the mRNA, this leaves us two phosphates

62
Q

how many phosphates does the guanine to be added to the mRNA lose to become guanine monophosphate?

A

two

63
Q

what does guanylyl transferase join the guanine monophosphate by to the 5’ mRNA by?

A

a 5’ to 5’ triphosphate linkage

64
Q

what is pre-mRNA 3’ polyadenylation?

A

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

65
Q

what are the functions of polyadenylation?

A

-facilitate transport of mature mRNA across the nuclear membrane to cytoplasm
-protecting mRNA from degradation
-enhancing translation by enabling the ribosomal recognition of mRNA

66
Q

what type of eukaryotic transcripts dont undergo polyadenylation?

A

histone genes

67
Q

what are the steps of polyadenylation?

A
  1. cleavage and polyadenylation specificity factor (CPSF) binds near the polyadenylation signal sequence, downstream of the stop codon
    -followed by binding of cleavage stimulating factor (CstF) to a uracil rich region downstream of the polyadenylation signal sequence
    -. two other cleavage factors (CFI and CFII) and polyadenylate polymerase (PAP) also bind
  2. the pre-mrna is cleaved 15-30 nucleotides downstream of the polyadenylation signal sequence
  3. the 3’ end pf the cut-premRNA undergoes enzymatic addition of 20 to 200 adenines through the action of CPSF and PAP
  4. after addition of the first 10 adenines, molecules of poly-A-binding protein (PABII) join the adenine tail and increase the rate of addition of adenines
68
Q

what is the polyadenylation signal sequence?

A

5’ - AAUAAA - 3’

69
Q

what is the torpedo model of transcription?

A

it happens after the 3’ cleavage and polyadenylation when the resulting residual transcript is still attached to RNA pol ii

70
Q

_____________ and transcription termination are connected by the activity of a specialized ______.

A

polyadenylation, RNase

71
Q

what does the specialized RNase do?

A

it rapidly digests the residual transcript like a “torpedo” aimed at the residual mRNA attached to RNA pol II

72
Q

what does RNase do when it catches up to RNA pol II

A

it triggers termination with RNA pol II releasing from the DNA

genetics (23 decks)

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