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Biol 207 > Topic 7-1 > Flashcards

Topic 7-1 Flashcards

1
Q

under the microscope, DNA molecules undergoing transcription exhibit:

A

Christmas-tree-like structures

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2
Q

what are the RNA subunits?

A

rNTPs (ribonucleoside triphosphates)

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3
Q

what are the DNA subunits?

A

dNTPs (deoxyribonucleoside triphosphates)

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4
Q

what is the difference between RNA sugars and DNA sugars?

A

RNA has a hydroxyl group on the 2’ carbon

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5
Q

why is RNA more unstable than DNA?

A

bc of the 2’OH

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6
Q

what is the difference between RNA bases and DNA bases?

A

RNA contains uracil, adn DNA contains thymine

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7
Q

true or false: RNA has no secondary structure

A

false. RNA is single stranded but can contain many types of secondary structure

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8
Q

a flexible secondary shape can allow some RNA to act as:

A

ribozymes/ catalytic RNA

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9
Q

what are the four main functions of ribozymes?

A

1) cut/edit out own sequence
2) connect RNA olecules together
3) replicate other RNA
4) catalyze peptide bond formation b/w a.a.

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10
Q

there are many classes of RNA, what are the four that we focus on in this class?

A
  • ribosomal RNA (rRNA)
  • messenger RNA (mRNA)
  • transfer RNA (tRNA)
  • CRISPR RNA (crRNA)
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11
Q

what is transcription?

A

the synthesis of an RNA molecule from a DNA template

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12
Q

what are the three major components required for RNA transcription?

A
  • a DNA template
  • ribonucleotide triphosphates
  • the transcription apparatus (proteins necessary for catalysing the synthesis of RNA)
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13
Q

unlike replication, transcription is _________ in what DNA sequences are transcribed

A

highly selective

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14
Q

during transcription, RNA molecules are synthesized in the _______ direction, and is both _______ and _______ to the DNA template strand

A

5’ –> 3’, complementary, antiparallel

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15
Q

a stretch of DNA encoding RNA molecule and sequences necessary for transcription (promoter, RNA coding region, terminator)

A

transcriptional unit

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16
Q
  • contains sequences that the transcriptional apparatus recognize and bind
  • dictates which DNA strand is the template strand and transcription start site
    these are characteristics of the:
A

promoter

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17
Q
  • contains sequences that signal to end transcription
  • usually part of the RNA coding sequence and resulting transcript
    these are characteristics of the:
A

terminator

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18
Q

the first nucleotide transcribed is numbered ____ and numbering ___ downstream. nucleotides upstream of the start site are numbered ___

A

+1, increases, negative

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19
Q

RNA polymerase and array of accessory proteins

A

transcriptional apparatus

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20
Q

a large multimeric enzyme (contains several polypeptide chains)

A

RNA polymerase

21
Q

the core enzyme of RNA polymerase contains these five subunits:

A
  • alpha (2)
  • beta
  • beta prime
  • omega
22
Q

what is the function of the core enzyme of RNA polymerase?

A

catalyzes addition of rNTPs, thus elongation of RNA molecule

23
Q

different accessory proteins regulate:

A

special transcriptional functions

24
Q

what are the three main transcriptional stages?

A

1) initiation
2) elongation
3) termination

25
Q

transcriptional appratus that assembles on promoter and begins RNA synthesis

A

initiation

26
Q

what are the four main steps of initiation?

A

1) promoter recognition/ binding
2) formation of transcription bubble
3) creation of first bonds between rNTPs
4) escape of transcriptional apparatus from promoter

27
Q

critical step for regulating selective gene expression (when and how frequent)

A

promoter recognition and binding

28
Q

the promoter sequence encodes three key pieces of information:

A
  • where to start
  • which is the template strand
  • which direction to move
29
Q

set of most commonly encountered nucleotides among sequences with considerable similarity or consensus. similar location w/ respect to start site

A

consensus sequence

30
Q

most bacterial promoters have two:

A

consenseus sequences

31
Q

the pribnow (TATAAT) box

A

located -10 bp upstream of the start site

32
Q

TTGACA promoter

A

located -35 bp upstream of the start site

33
Q

a bacterial accessory protein that binds to the core RNA polymerase (forming the holoenzyme)

A

sigma factor

34
Q

stabilizes polymerase binding to proper promoter start sites ensuring initiation of gene transcription

A

sigma factor

35
Q

true or false: the signma factor is required only for promoter binding and initiation and detaches after a few RNA nucleotides have been added

A

true

36
Q

the holoenzyme changes structure leading to tighter binding and unwinding of DNA to form the:

A

transcription bubble (nucleotides -12 to +2)

37
Q

as subsequent rNTPs are added to the RNA molecule, ______ are cleaved in the rxn

A

two phosphates

38
Q

polymerase changes shape again such that it “lets loose” of consenses sequences in promoter and is free to:

A

move and transcribe downstream

39
Q

what are the three main processes involved in elongation?

A
  • unwinding DNA at downstream edge of bubble
  • adding nucleotides to RNA molecule
  • rewinding DNA at upstream edge
40
Q

DNA _______ ahead of bubble, negative _______ behind bubble

A

supercoiling, supercoiling

41
Q

likely relieve supercoiling

A

topoisomerases

42
Q

a “pause” in transcription caused by backbacking, where:

A

polymerase slides backward along the DNA template

43
Q

transcriptional pausing is important for:

A

proofreading

44
Q

what are the three main steps of termination?

A

1) RNA polmerase stops RNA synthesis
2) RNA molecule is released from polymerase and dissociates from DNA
3) polymerase detaches from DNA

45
Q

what are the two major types of termination mechanisms?

A

rho-dependent and rho-independent

46
Q

genes with the rho-dependent terminator have two features:

A
  • RNA sequence where rho binds, called the Rut (rho utilization) site
  • terminator sequence causes polymerase to pause (allows rho to advance towards transcription site)
47
Q

the rho protein has ________ activitiy that unwinds the RNA:DNA hybrid thus terminating transcription

A

helicase

48
Q

genes with the rho-independent terminator have two features:

A
  • inverted repeats - two sections of terminator have complementary (inverted strands)
  • string of ‘A’s in the DNA template follows last inverted repreat (string of ‘U’s in RNA)
49
Q

in rho-independent termination, the string of uracil causes polymerase to pause, allowing ________ to form

A

the inverted repeat hairpin

Biol 207 (34 decks)

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