Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

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

RNA: Transcription and Processing Flashcards

1
Q

transcription

A
  • DNA directed synthesis of RNA by RNA polymerase
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

RNA polymerase similarities to DNA polymerase (2)

A
  • requires Mg+

- catalytic mechanism

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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.)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

types of RNA (3)

A
  • mRNA
  • tTNA
  • rRNA
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

promoter region

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

- binding of RNA polymerase occurs heres

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

terminator sequence

A
  • involved in termination of transcription
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

RNA transcript

A
  • protein coding region, 5’ untranslated region, and 3’ untranslated region
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

template strand/non-coding strand (2)

A
  • strand of DNA that serves as a template during transcription
  • complementary to coding strand
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

what are the common features of bacterial promoters (3)

A
  1. -10 sequence
  2. -35 sequence
  3. UP element
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q
  • 10 sequence (2)
A
  • consensus sequence TATAAT

- recognized by sigma-factor

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q
  • 35 sequence
A
  • consensus sequence: TTGACA
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

UP element (2)

A
  • less common

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

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

RNA polymerase holoenzyme

A

RNA polymerase core + sigma-factor

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

sigma-factor (2)

A
  • can attach to DNA

- different sigma-factors recognize different -10 sequences

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

sigma-switch

A
  • change in sigma-factor on an RNA polymerase
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

closed complex

A
  • RNA polymerase holoenzyme bound to promoter on coding strand
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

open complex

A
  • RNA polymerase bound to coding strand when DNA double helix is opened
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

what direction does the RNA chain grow in elongation of transcription

A
  • 5’ -> 3’ direction
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

NasU protein

A
  • binds to core RNA polymerase during elongation instead of sigma/replaces sigma
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

transcription bubble

A
  • where transcription occurs

- region of denatured DNA enclosed by RNA polymerase that contains nascent RNA and RNA-DNA hybrid double helix

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

how long is the RNA-DNA hybrid double helix

A
  • 8bp
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

what are the 2 common mechanisms used during transcription termination? (2)

A
  • rho-independent termination

- rho-dependent termination

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

what is unique to pho-independent termination?

A
  • palindromic sequence that causes the formation of a stem-loop structure
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

what is unique to pho-dependent termination?

A
  • rut element that binds rho-helicase
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

what are the key differences between transcription in eukaryotes vs prokaryotes (4)

A
  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
Q

what does RNA polymerase I produce (3)

A
  • 18S rRNA
  • 58S rRNA
  • 28S rRNA
33
Q

what does RNA polymerase II produce (3)

A
  • mRNA
  • miRNA
  • snRNA
34
Q

what does RNA polymerase III produce (2)

A
  • tRNA

- 5S rRNA

35
Q

what is the unit “s” that is used to classify rRNA? (2)

A
  • 1 svedberg

- centrifugation unit

36
Q

how is DNA accessibility regulated in eukaryotes?

A
  • changing state of histone proteins
37
Q

euchromatin (2)

  • definition
  • enzyme
A
  • describes DNA when it is “wrapped” loosely around histones and is actively transcribed
  • this DNA type of produced by histone acetyl transferases
38
Q

heterochromatin (2)

  • definition
  • enzyme
A
  • describes DNA when it is “wrapped” tightly around histones and is not transcribed
  • this DNA type of produced by histone deacetylases
39
Q

histone acetyl transferases (HATs) (3)

A
  • 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
Q

histone acetylases (HDACs)

A
  • 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
Q

how do cells characterize their genome into heterochromatin and euchromatin (2)

A
  • euchromatin and heterochromatin are specific to each cell type
  • can change over time and in different environments
42
Q

how can chromatin be modified? (3)

  • methods (2)
  • affect
A
  • acetylation of histones
  • methylation of chromatin and DNA
  • this will affect transcription rate
43
Q

cis elements (3)

  • definition
  • examples (3)
  • effect
A
  • 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
Q

enhancers

A
  • enhance transcription
45
Q

silencers

A
  • inhibit transcription
46
Q

isulators

A
  • prevent action of other cis-elements
47
Q

eukaryotic promoters and RNA polymerase

A
  • each RNA polymerase has its own type of promoter
48
Q

common elements of RNA polymerase promoters (2)

A
  • TATA box (-30 region)

- CAAT box (-40 to -150 region; varies)

49
Q

promoter

A
  • binding site for RNA polymerase and transcription factors
50
Q

what is required for transcription (2)

A
  • RNA polymerase and help from transcription factors

- usually gene-specific TFs are needed to initiate transcription

51
Q

transcription factors for RNA polymerase II

A
  • TFII
52
Q

transcription factors for RNA polymerase I

A
  • TFI
53
Q

TATA binding proteins (2)

A
  • TFIID

- TFIIA

54
Q

eukaryote closed complex

A
  • TFII and RNA polymerase II bound to the promoter with no DNA unwinding
55
Q

eukaryote open complex

A
  • TFII and RNA polymerase II bound to the promoter with DNA unwinding
56
Q

RNA polymerase II “tail” (2)

  • what it is
  • what happens to it during transcription initiation
A
  • C-terminus of RNA polymerase

- phosphorylated at multiple sites by TFIIs

57
Q

what happens to RNA polymerase and the TFs after transcription starts? (2)

A
  • RNA polymerase II leaves the promoter and begins synthesis of RNA
  • general TFs are left behind and dissociate with DNA
58
Q

example of a gene-specific transcription factor

A
  • SREBP binds to SRE to initiate transcription of HMG-CoA reductase
59
Q

how does elongation differ in eukaryotes from prokaryotes? (2)

A
  • more complex

- require elongation factors

60
Q

how does termination differ in eukaryotes from prokaryotes?

A
  • can require termination factors or be done in factor-independent way
61
Q

pre-mRNA (2)

A
  • nascent mRNA that must undergo modifications before it is ready for translation
  • present in eukaryotic cells
62
Q

capping

  • definition
  • purpose
A
  • addition of 5’ cap

- helps ribosomes recognize RNA

63
Q

what enzymes are used for capping pre-mRNA (2)

A
  • step 1: phosphohydrolase

- step 2: guanylyltransferase

64
Q

polyadenylation

A
  • addition of polyadenine (polyA) tail at 3’ end of mRNA
65
Q

purpose of polyadenylation (2)

A
  • helps ribosome to recognize mRNA

- plays role in RNA stability

66
Q

how does polyA tail length affect mRNA

A
  • longer tails lead to longer lifespan for mRNA as tail is degraded over time and tail confers stability of the RNA
67
Q

splicing

A
  • removal of introns from pre-mRNA prior to translation in eukaryotic cells
68
Q

exons

A
  • amino acid coding sequences in eukaryotic pre-mRNA
69
Q

introns

A
  • amino acid non-coding sequences in eukaryotic pre-mRNA
70
Q

alternative splicing

A
  • splicing of different exons out of pre-mRNA to produce different proteins
71
Q

group I introns (2)

A
  • free guanosine serves as 1st nucleophile

- 3’ OH of upstream exon serves as 2nd nucleophile

72
Q

group II introns (3)

A
  • 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
Q

ribozymes (2)

A
  • catalytic RNAs

- ex. group I and group II introns

74
Q

spliceosome mediated introns (2)

A
  • requires several proteins and Mg2+

- evolved from group II, so lariat is formed

75
Q

how are tRNAs and rRNAs processed?

A
  • bases can be modified
76
Q

RNA editing

A
  • change in nucleotide sequence after transcription that leads to change in protein sequence
77
Q

example of RNA editing

A
  • 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)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions