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Genetics - BIO 2306 > Ch 13 Transcription > Flashcards

Ch 13 Transcription Flashcards

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1
Q

compare and contrast RNA and DNA

A

DNA:
- deoxyribose sugar
- no 2’-OH group
- A,G,C,T nucleotides
- usually double stranded
- stable
RNA:
- ribose sugar
- has 2’-OH group
- A,G,C,U nucleotides
- usually single stranded
- degraded easily

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2
Q

class of RNA: structural and functional components of ribosome, participating in protein assembly

A

ribosomal RNAs (rRNAs)

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3
Q

class of RNA: carries genetic code for proteins

A

messenger RNA (mRNAs)

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4
Q

class of RNA: precursor molecule that is modified to become mRNA

A

pre-messenger RNA (pre-mRNAs)

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5
Q

class of RNA: helps incorporate amino acids into polypeptide chain

A

transfer RNA (tRNAs)

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6
Q

class of RNA: processing of pre-mRNA into mRNA

A

small nuclear RNAs (snRNAs)

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7
Q

class of RNA: processing and assembly of rRNA

A

small nucleolar RNAs (snoRNAs)

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8
Q

class of RNA: inhibit RNA translation (RNAi)

A

micro RNAs (miRNAs)

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9
Q

class of RNA: degradation of RNA molecules (RNAi)

A

small interfering RNAs (siRNA)

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10
Q

class of RNA: suppress transcription of transposable elements in reproductive cells

A

Piwi-interacting RNAs (piRNA)

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11
Q

class of RNA: assist destruction of foreign DNA

A

CRISPR RNA (crRNA)

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12
Q

snRNAs that combine with small protein subunits

A

small nuclear ribonucleoproteins (snRNPs)

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13
Q

process of RNAs synthesized from a DNA template

A

transcription

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14
Q

three major components of transcription

A

DNA template –> single strand used
RNA strand transcribed complementary to template strand
transcription unit

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15
Q

DNA strand used for transcription

A

template strand (negative/noncoding strand)

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16
Q

two other names for template strand

A

noncoding strand
negative strand

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17
Q

other DNA not used for transcription

A

nontemplate strand (positive/coding strand)

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18
Q

two other names for nontemplate strand

A

coding strand
positive strand

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19
Q

why is the nontemplate strand called the coding strand?

A

it is identical to the RNA strand transcribed, except T=U

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20
Q

stretch of DNA that encodes RNA molecule and sequences needed for transcription

A

transcription unit

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21
Q

three components of transcription unit

A

promoter
RNA-coding region
terminator

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22
Q

DNA sequence (upstream) that transcription apparatus recognizes and binds to

A

promoter

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23
Q

first nucleotide to be transcribed

A

transcription start site

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24
Q

DNA sequence copied into RNA

A

RNA-coding region

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25
Q

sequence (downstream) that is copied into RNA and transcription stops

A

terminator

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26
Q

substrates required to build RNA

A

ribonucleoside triphosphates (rNTPs)
transcription apparatus

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27
Q

bacterial RNA polymerase

A

(only one RNA polymerase) - transcribes mRNA, tRNA, and rRNA

28
Q

what subunits is core RNA polymerase composed of

A

five subunits: 2 alpha, 1 beta, 1 beta prime, and 1 omega

29
Q

catalyzes elongation of RNA by addition of RNA nucleotides

A

core RNA polymerase enzyme

30
Q

joins with core enzyme to form holoenzyme

A

sigma factor

31
Q

controls binding of RNA polymerase to promoter

A

RNA polymerase holoenzyme

32
Q

what happens if no sigma factor is present?

A

transcription starts at a random start point

33
Q

difference between bacterial and eukaryotic RNA polymerases

A

bacteria only have one RNA polymerase that synthesizes all RNA classes
eukaryotes have multiple (three main types of RNA polymerases that synthesize different RNA classes)

34
Q

polymerase that transcribes large rRNAs

A

RNA polymerase I

35
Q

polymerase that transcribes pre-mRNAs

A

RNA polymerase II

36
Q

polymerase that transcribes tRNAs

A

RNA polymerase III

37
Q

set of most commonly encountered nucleotides among sequences

A

consensus sequence

38
Q

describe bacterial promoter

A

consists of -35 consensus sequence and -10 consensus sequence

39
Q

Pribnow box; most common consensus sequence that lies 10 nucleotides upstream of start site in promoter (TATAAT)

A

-10 consensus sequence

40
Q

common consensus sequence that lies 35 nucleotides upstream of start site in promoter (TTGACA)

A

-35 consensus sequence

41
Q

substitutions within -10 and -35 consensus sequences that slow down rate of transcription

A

down mutations

42
Q

substitutions within -10 and -35 consensus sequences that increase rate of transcription

A

up mutations

43
Q

describe bacterial initiation of transcription

A
  • sigma factor joins with core RNA polymerase to form holoenzyme
  • holoenzyme binds to -35 and -10 consensus sequences in promoter tightly and unwinds DNA
  • complementary rNTP incorporated to transcription start site
  • 2 phosphate groups cleaved for each rNTP added to 3’ end of growing RNA molecule
  • sigma factor released and RNA polymerase moves beyond promoter
44
Q

explain abortive initiation

A

while RNA polymerase complex is attached to the promoter, short transcripts are generated and released before it transitions to elongation

45
Q

describe bacterial elongation of transcription

A
  • RNA polymerase changes shape & leaves promoter
  • RNA poly continues to add nucleotides and transcribe downstream
  • RNA poly unwinds DNA at leading (downstream) edge and rewinds DNA at trailing (upstream) edge
  • RNA poly proofreads by backtracking
46
Q

area on DNA where transcription takes place

A

transcription bubble

47
Q

RNA poly slides backward along template strand

A

backtracking

48
Q

what kind of supercoiling is generated when RNA poly unwinds DNA at leading/downstream edge

A

positive supercoiling

49
Q

what kind of supercoiling is generated when RNA poly unwinds DNA at trailing/upstream edge

A

negative supercoiling

50
Q

describe bacterial termination of transcription

A
  • RNA transcribes the terminator
  • RNA stops synthesizing RNA
  • new RNA released from RNA poly and dissociates from DNA template
  • RNA poly detaches
51
Q

describe rho-independent terminators

A

termination w/o rho factor
- inverted repeats in DNA cause transcribed RNA to form hairpin structure
- string of adenine nucleotides follow inverted repeats to produce string of uracil nucleotides in after hairpin
- causes RNA poly to pause
- hairpin structure destabilizes DNA-RNA pairing and RNA molecule separates

52
Q

describe rho-dependent terminators

A

termination in presence of rho factor
- rho binds to unstructured region of RNA and moves towards 3’ end
- RNA poly encounters terminator sequence and pauses
- rho uses helicase activity to unwind DNA-RNA hybrid and ends transcription

53
Q

accessory proteins that bind to DNA sequences and affect levels of transcription

A

transcription factors

54
Q

transcription factors that combine with RNA poly and mediator to form basal transcription apparatus

A

general transcription factors (TFs)

55
Q

complex of TFs + RNA poly + mediator that assembles on promoter and initiates transcription

A

basal transcription apparatus

56
Q

transcription factors that stimulate assembly of basal transcription apparatus to increase levels of transcription

A

transcriptional activator proteins (TAPs)

57
Q

which RNA polymerase transcribes genes in eukaryotes

A

RNA Poly II

58
Q

parts of eukaryotic promoter

A

core promoter
regulatory promoter

59
Q

describe the core promoter

A

immediately upstream from start site where basal apparatus binds
TATA box consensus sequence located -25 upstream

60
Q

describe the regulatory promotor

A

immediately upstream of core promoter
TAPs bind and effect rate of transcription initiation

61
Q

more distant sequences that regulate transcription if TAPS bind to them

A

enhancers

62
Q

describe eukaryotic initiation of transcription

A

assembly of basal transcription apparatus
- TFIID contains TATA-binding protein that binds to TATA box within core promoter
- TAPs at regulatory promoter interact with basal transcription apparatus thru mediator
- TAPS at enhancers interact with basal transcription apparatus by forming loop in DNA
DNA unwinds to produce template strand

63
Q

describe eukaryotic elongation of transcription

A
  • DNA enters RNA Poly II through cleft and unwinds
  • nucleotides added to growing 3’ end of RNA molecule
  • hybrid DNA-RNA hits wall of amino acids and bends at right angle, positioning it at polymerase active site
  • new RNA separates from DNA and exits
64
Q

describe eukaryotic termination of transcription

A
  • RNA poly II transcribes well past coding sequences
  • pre-mRNA cleaves at specific sites
  • Rat1 exonuclease attaches to 5’ end of RNA and moves toward RNA polymerase, degrading RNA
  • Rat1 reaches polymerase and transcription terminates
65
Q

is transcription in archaea more similar to transcription in eukaryotes or prokaryotes?

A

eukaryotes

Genetics - BIO 2306 (20 decks)

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