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MBG 2040 > Transcription and RNA Processing > Flashcards

Transcription and RNA Processing Flashcards

Lectures 4-7

1
Q

what are the differences between DNA and RNA?

A

URACIL
RNA has a ribose sugar (-OH group on 2’ C)
RNA has a tertiary structure, since it is single stranded (ex. tRNAs) and quaternary structure (functional units in the ribosome)

REMEMBER: if I had to pick between DNA and RNA, I would pick RNA since it has U in it

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2
Q

which nucleotide is PROMISCUOUS?

A

GUNANINE
pairs with C and U

REMEMBER: promiscuous Girl (begins with G)

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3
Q

which molecule is more stable, DNA or RNA?

A

DNA

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4
Q

what are some basic features of RNA?

A

unstable
easier to regulate
not segregated to nucleus
evolved first
can have many conformations

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5
Q

what are the types of RNA?

A

coding: mRNA
noncoding: tRNA, rRNA

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6
Q

how is RNA synthesized?

A

TRANSCRIPTION
5’ to 3’ direction, using 3’ to 5’ DNA template
complementary and antiparallel to DNA template
RNA strand wil MATCH noncoding strand

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7
Q

how is an rNTP added to the strand?

A

two phosphates cleaved off INCOMING rNTP, attaches to the 3’ OH group of the last rNTP in strand
nucleophilic attack
ALWAYS synthesized 5’ to 3’

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8
Q

what the subunits of the RNA holoenzyme?

A

alpha –> assembly of tetrameric core
beta –> rNTP bonding site
beta prime –> DNA template binding region
omega –> stabilize tertameric core
sigma –> binds to RNA polymerase tertrameric core and assists in correct initiation of transcription

PROKARYOTES
REMEBER: B - Beta - Binding site

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9
Q

what does the sigma factor bind to?

A

-35 and -10 consensus sequences
properly positions RNA polymerase to begin transcription

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10
Q

describe initiation in prokaryotes

A

once the holoenzyme is bound to the promoter, RNA polymerase is positioned over the transcription start site
unwinds DNA
NO PRIMER needed

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11
Q

describe elongation in prokaryotes

A

sigma factor released
rNTPs added 5’ to 3’ by RNA polymerase
transcription bubble moves with RNA polymerase and unwound DNA rewinds behind it

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12
Q

describe TERMINATION in prokaryotes

A

RNA polymerase reaches terminator region
upstream of where termination will take place
newly synthesized RNA and RNA polymerase released
can be rho dependent or independent

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13
Q

describe RHO DEPENDENT termination

A

rho binds to the RUT site (C-rich) and moves towards 3’ end of RNA
RNA polymerase encounters termination sequence and pauses, rho catches up
rho unwinds DNA-RNA hybrid and terminates transcription

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14
Q

describe RHO INDEPENDENT termination

A

2 common features: inverted repeates, 6-9 As
string of Us cause RNA polymerase to pause and the inverted repeats fold into a hairpin
DNA-RNA pairing is destabilized
separates from template, terminating sequence

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15
Q

how many RNA polymerases do eukaryotes have?

A

at least THREE
plants have FIVE

for reference: prokaryotes have 1

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16
Q

describe the elements of the mRNA stand during INITIATION in EUKARYOTES

A

-35 consensus sequence, -25 consensus sequence, +1 initiator element, +30 core-promotor element
regulatory promotor up to 100 NT upstream

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17
Q

describe the proteins involved in INITIATION in EUKARYOTES

A

TFII A, B, D, E, F, H

TFIID contains TATA BP and assembles to TATA box, followed by the rest of the TFs and RNA polymerase II

TFs bind to ENHANCER (upstream)
TFs bind to promotor forming PREINITIATION COMPLEX –> initiates basal transcription

MEDIATOR permits interactions with activator/repressor proteins

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18
Q

describe ELONGATION is EUKARYOTES

A

POLYMERASE II moves along template strand
TFs stay at promotor
DNA enters polymerase downstream through a CLEFT, BENDS at a 90 degree angle and separates
template strand enters pore
rNTPs added to 3’ end of chain
synthesized 5’ to 3’
RNA is separated from DNA through another cleft

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19
Q

what does it mean if two amino acids are COLINEAR?

A

in prokaryotes, the coding region of a gene is uninterrupted

number of NUCLEOTIDES is proportional to the number of AMINO ACIDS (3:1)

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20
Q

what are the primary regions in mature prokaryotic mRNA?

A

5’ untranslated region –> does not code for AAs, binds to ribsomal complex
shine-dalgarno sequence
protein coding region –> begins with start codon, ends with stop codon
3’ UTR –> does not code for AAs, affects stability of the mRNA and regulates translation

21
Q

when does translation happen in prokaryotes?

A

simultaneously to transcription (no processing in between)

22
Q

what modifications are made to eukaryotic pre-mRNA?

A

removal of introns
addition of 5’ cap
addition of poly A tail

23
Q

where are introns spliced? by what?

A

in the nucleus, by splicosomes
the order of exons is always kept in mature mRNA

24
Q

what are introns?

A

influence how genes are expressed
present in eukaryotic DNA
can have self splicing capabilities
removed from pre-mRNA

25
Q

how is the 5’ cap added?

A

1 of 3 phosphate groups are cleaved off pre-mRNA
guanine nucleotide added with phosphates (5’ to 5’ linkage)
methylation

NOTE: methyl guanosine is NOT transcribed

26
Q

where are the methyl groups added

A

7’ position of guanine
2’ OH of the first and/or second nucleotide
adenine can get 2 methyl groups

27
Q

what is the poly A tail?

A

50-250 As added to the 3’ end, WITHOUT a template
affects stability of mRNA, facilitates attachment of ribosomes, export out of the nucleus

28
Q

what are the splice sites?

A

5’ splice site (containing GU junction sequence) refers to the 5’ end of the intron
3’ splice site contains the AG junction sequence
intron branch point: conserved A 18-40 NTs upstream of 3’ splice site

29
Q

what are spliceosomes?

A

RNA/protein structure
contains 5 small nuclear RNAs (snRNAs): U1,2,4,5,6
300 small proteins

30
Q

describe the spliceosome assembly

A

U1 attaches to the 5’ splice site
U2 attaches to the branch point
complex of U4,5,6 joins spliceosome

31
Q

describe the process of RNA splicing

A

mRNA is cut at 5’ splice site
5’ end joins branch point (LAURIAT)
cut is made at the 3’ splice site
lauriat is released and DEGRADED
the exons fuse
2 TRANSESTERIFICATION reactions by U6 (one phosphodiester link replaces another)

32
Q

how is the lauriat formed?

A

5’ phosphate of G nucleotide binds with 2’ OH group of A nucleotide at the branch point

33
Q

why is RNA unstable?

A

the 2’ OH group can react intramolecularly with the 3’ OH group –> PHOSPHATE BOND BREAKAGE

34
Q

describe the pathway of alternative splicing?

A

EXONS spliced out with the introns, yielding a different mRNA

35
Q

describe the pathway of multiple 3’ cleavage sites

A

different cleavage sites are located in the 3’ direction of an exon
part of the exon is removed with the intron

36
Q

give an example of alternative splicing

A

thyroid cells and brain cells do this
thyroid cells produce calcitonin, brain cells produce calcitonin gene regulated peptide

37
Q

how can RNA be edited?

A

modification by guide RNAs
inserting or deleting uridine monophosphate residues
changing the structure of individual bases

38
Q

how does guide RNA edit mRNA?

A

guide RNA pairs with mRNA
loops form in guide RNA
guide RNA serves as a template for adding or deleting bases
mature mRNA is released
this PERMANENTLY modifies the mRNA

39
Q

describing RNA editing of ApoB

A

changes C to U (deamination)
creates a STOP codon (new protein)

40
Q

what modifications do tRNAs undergo?

A

removal of 5’ and 3’ sequences
removal of introns
nuclotides 5’-CCA-3’ added to 3’ end of tRNA*
modification of nucleotides –> RARE BASES

*REMEMBER: ACC –> the Air Canada Center

41
Q

describe the components of the prokaryotic ribosome

A

31 ribosomal proteins + 5S rRNA + 23s rRNA –> 50S subunit

21 ribosomal proteins + 16S rRNA –> 30S subunit

30S + 50S –> 70S

1 gene

42
Q

describe the components of the eukaryotic ribosome

A

49 ribosomal proteins + 5S rRNA + 5.8S rRNA + 23s rRNA –> 60S subunit

33 ribosomal proteins + 18S rRNA –> 40S subunit

60S + 40S –> 80S

2 gene

43
Q

where does rRNA synthesis occur?

A

eukaryotes: NUCLEOLUS
prokaryotes: CYTOPLASM

44
Q

what are snRNAs?

A

act in complexes with proteins
SPLICEOSOMES

45
Q

what are snoRNAs?

A

act in complexes with proteins
EUKARYOTES: guide modifications of rRNAs in nucleolus

46
Q

what are siRNA and miRNA

A

EUKARYOTES
regulate and control gene expression
double stranded RNA

47
Q

what are CRISPR RNAs?

A

PROKARYOTES
work with Cas9 to cleave foreign DNA

48
Q

what are LnCRNAs?

A

EUKARYOTIC
longer than miRNAs
control gene expression OR recruit proteins involved in DNA modification

MBG 2040 (6 decks)

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