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BIOC 302 Part 2 > RNA: Transcription and Processing > Flashcards

RNA: Transcription and Processing Flashcards

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1
Q

transcription

A
  • DNA directed synthesis of RNA by RNA polymerase
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2
Q

RNA polymerase similarities to DNA polymerase (2)

A
  • requires Mg+

- catalytic mechanism

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3
Q

RNA polymerase differences to DNA polymerase (4)

A
  • doesn’t require primer
  • does not have proof-reading activity
  • does not use topoisomerase to relieve supercoils
  • does not require helicase (built into RNA pol.)
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4
Q

types of RNA (3)

A
  • mRNA
  • tTNA
  • rRNA
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5
Q

mRNA (4)

  • full name
  • percentage of all RNA
  • function
  • number of possible sequences
A
  • messenger RNA
  • about 5% of RNA
  • encodes proteins
  • thousands - millions of different sequences
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6
Q

tRNA (5)

  • full name
  • percentage of all RNA
  • function
  • number of possible sequences
  • size
A
  • transfer RNA
  • about 15% of all DNA
  • transfers amino acids to ribosomes
  • at least 1 sequence per amino acid (usually about 40 tRNAs)
  • smaller than mRNA usually
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7
Q

rRNA (3)

  • full name
  • percentage of all RNA
  • function
A
  • ribosomal RNA
  • about 80% of all RNA
  • major part of ribosomes: play structural and catalytic role in ribosomes
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8
Q

other RNA (3)

  • examples
  • percentage of all RNA
  • function
A
  • miRNA, snRNA
  • less than 1%
  • involved in regulation of gene expression, studied in epigenetics
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9
Q

what are the main components of a gene (4)

A
  1. protein coding region
  2. transcription start site/+1 site
  3. promoter region
  4. terminator sequence
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10
Q

promoter region

  • location
  • function
A
  • sequence of DNA upstream of TSS

- binding of RNA polymerase occurs heres

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11
Q

terminator sequence

A
  • involved in termination of transcription
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12
Q

RNA transcript

A
  • protein coding region, 5’ untranslated region, and 3’ untranslated region
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13
Q

template strand/non-coding strand (2)

A
  • strand of DNA that serves as a template during transcription
  • complementary to coding strand
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14
Q

coding strand/non-template strand (2)

A
  • has exact same sequence as unprocessed DNA (preRNA) except U is used instead of T
  • gene sequences are always written as the coding sequence
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15
Q

what are the common features of bacterial promoters (3)

A
  1. -10 sequence
  2. -35 sequence
  3. UP element
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16
Q
  • 10 sequence (2)
A
  • consensus sequence TATAAT

- recognized by sigma-factor

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17
Q
  • 35 sequence
A
  • consensus sequence: TTGACA
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18
Q

UP element (2)

A
  • less common

- associated with strong transcription, so it is usually found in housekeeping genes

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19
Q

RNA polymerase holoenzyme

A

RNA polymerase core + sigma-factor

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20
Q

sigma-factor (2)

A
  • can attach to DNA

- different sigma-factors recognize different -10 sequences

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21
Q

sigma-switch

A
  • change in sigma-factor on an RNA polymerase
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22
Q

closed complex

A
  • RNA polymerase holoenzyme bound to promoter on coding strand
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23
Q

open complex

A
  • RNA polymerase bound to coding strand when DNA double helix is opened
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24
Q

what direction does the RNA chain grow in elongation of transcription

A
  • 5’ -> 3’ direction
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25
NasU protein
- binds to core RNA polymerase during elongation instead of sigma/replaces sigma
26
transcription bubble
- where transcription occurs | - region of denatured DNA enclosed by RNA polymerase that contains nascent RNA and RNA-DNA hybrid double helix
27
how long is the RNA-DNA hybrid double helix
- 8bp
28
what are the 2 common mechanisms used during transcription termination? (2)
- rho-independent termination | - rho-dependent termination
29
what is unique to pho-independent termination?
- palindromic sequence that causes the formation of a stem-loop structure
30
what is unique to pho-dependent termination?
- rut element that binds rho-helicase
31
what are the key differences between transcription in eukaryotes vs prokaryotes (4)
1. chromatin must be reorganized prior to transcription 2. activation of transcription can occur over long distances 3. there are 3 different RNA polymerases 4. RNA must be processes before it is ready for translation
32
what does RNA polymerase I produce (3)
- 18S rRNA - 58S rRNA - 28S rRNA
33
what does RNA polymerase II produce (3)
- mRNA - miRNA - snRNA
34
what does RNA polymerase III produce (2)
- tRNA | - 5S rRNA
35
what is the unit "s" that is used to classify rRNA? (2)
- 1 svedberg | - centrifugation unit
36
how is DNA accessibility regulated in eukaryotes?
- changing state of histone proteins
37
euchromatin (2) - definition - enzyme
- describes DNA when it is "wrapped" loosely around histones and is actively transcribed - this DNA type of produced by histone acetyl transferases
38
heterochromatin (2) - definition - enzyme
- describes DNA when it is "wrapped" tightly around histones and is not transcribed - this DNA type of produced by histone deacetylases
39
histone acetyl transferases (HATs) (3)
- enzymes that add acetyl groups to lysine residues of histones - makes histones less positive and electrostatic forces between histones and DNA weaker - this enzyme turns the gene "on"
40
histone acetylases (HDACs)
- enzymes that remove acetyl groups from lysine residues of histones - makes histones more positive and electrostatic forces between histones and DNA stronger - this enzyme turns the gene "off"
41
how do cells characterize their genome into heterochromatin and euchromatin (2)
- euchromatin and heterochromatin are specific to each cell type - can change over time and in different environments
42
how can chromatin be modified? (3) - methods (2) - affect
- acetylation of histones - methylation of chromatin and DNA - this will affect transcription rate
43
cis elements (3) - definition - examples (3) - effect
- parts of DNA that can affect transcription over long distances in eukaryotes - enhancers, silencers, and insulators - binding sites for different trans-factors (proteins) that will interact with the promoter and affect transcription initiation
44
enhancers
- enhance transcription
45
silencers
- inhibit transcription
46
isulators
- prevent action of other cis-elements
47
eukaryotic promoters and RNA polymerase
- each RNA polymerase has its own type of promoter
48
common elements of RNA polymerase promoters (2)
- TATA box (-30 region) | - CAAT box (-40 to -150 region; varies)
49
promoter
- binding site for RNA polymerase and transcription factors
50
what is required for transcription (2)
- RNA polymerase and help from transcription factors | - usually gene-specific TFs are needed to initiate transcription
51
transcription factors for RNA polymerase II
- TFII
52
transcription factors for RNA polymerase I
- TFI
53
TATA binding proteins (2)
- TFIID | - TFIIA
54
eukaryote closed complex
- TFII and RNA polymerase II bound to the promoter with no DNA unwinding
55
eukaryote open complex
- TFII and RNA polymerase II bound to the promoter with DNA unwinding
56
RNA polymerase II "tail" (2) - what it is - what happens to it during transcription initiation
- C-terminus of RNA polymerase | - phosphorylated at multiple sites by TFIIs
57
what happens to RNA polymerase and the TFs after transcription starts? (2)
- RNA polymerase II leaves the promoter and begins synthesis of RNA - general TFs are left behind and dissociate with DNA
58
example of a gene-specific transcription factor
- SREBP binds to SRE to initiate transcription of HMG-CoA reductase
59
how does elongation differ in eukaryotes from prokaryotes? (2)
- more complex | - require elongation factors
60
how does termination differ in eukaryotes from prokaryotes?
- can require termination factors or be done in factor-independent way
61
pre-mRNA (2)
- nascent mRNA that must undergo modifications before it is ready for translation - present in eukaryotic cells
62
capping - definition - purpose
- addition of 5' cap | - helps ribosomes recognize RNA
63
what enzymes are used for capping pre-mRNA (2)
- step 1: phosphohydrolase | - step 2: guanylyltransferase
64
polyadenylation
- addition of polyadenine (polyA) tail at 3' end of mRNA
65
purpose of polyadenylation (2)
- helps ribosome to recognize mRNA | - plays role in RNA stability
66
how does polyA tail length affect mRNA
- longer tails lead to longer lifespan for mRNA as tail is degraded over time and tail confers stability of the RNA
67
splicing
- removal of introns from pre-mRNA prior to translation in eukaryotic cells
68
exons
- amino acid coding sequences in eukaryotic pre-mRNA
69
introns
- amino acid non-coding sequences in eukaryotic pre-mRNA
70
alternative splicing
- splicing of different exons out of pre-mRNA to produce different proteins
71
group I introns (2)
- free guanosine serves as 1st nucleophile | - 3' OH of upstream exon serves as 2nd nucleophile
72
group II introns (3)
- 2' OH of adenosine in middle of intron serves as first nucleophile - 3' OH of upstream exon serves as 2nd nucleophile - lariat is formed as product
73
ribozymes (2)
- catalytic RNAs | - ex. group I and group II introns
74
spliceosome mediated introns (2)
- requires several proteins and Mg2+ | - evolved from group II, so lariat is formed
75
how are tRNAs and rRNAs processed?
- bases can be modified
76
RNA editing
- change in nucleotide sequence after transcription that leads to change in protein sequence
77
example of RNA editing
- ApoB 100 in LDL (100% of protein) - no editing - ApoB 48 in chylomicrons (48% of protein) - post transcriptional editing of C -> U (deamination) in the intestines, leading to a premature stop codon

BIOC 302 Part 2 (7 decks)

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