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MBG 2040 > transcription > Flashcards

transcription Flashcards

1
Q

RNA structures

A

primary: nucleotide sequence
secondary: folding due to H-bonding between complementary bases on the same strand
tertiary: have intrastrand binding
quaternary: RNAs interact as functional units
- due to all these structures RNA has more functions than RNA

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2
Q

Why is RNA less stable than DNA

A
  • presence of a 2’-OH group in ribose, causes it to react intramolecularly resulting at the 3’OH site resulting in phosphate bond breakage
  • single-stranded
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3
Q

Why do we use an unstable RNA rather than DNA?

A
  • a carry on from evolution (RNA evolved first)
  • can form many tertiary structures allowing it to have many different functions
  • easily temporary and degraded molecule offers a way of controlling its level (ex: shutting off expression)
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4
Q

coding region

A

tells you which amino acid to put in your proteins

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5
Q

coding region and gene expression in prokaryotes

A
  • often a single continuous unit
  • transcription, translation and mRNA degradation occur simultaneously
  • DNA is free in the cytoplasm
  • ribosomes bind to mRNA while being synthesized and start making protein
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6
Q

what do ribosomes translate

A
  • they translate the RNA as its being synthesized from DNA to save time
  • never translate the DNA because you don’t want to damage it
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7
Q

introns and exons

A

exons: protein-coding segments
introns: non-coding segments

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8
Q

environments of DNA and RNA in eukaryotes

A
  • transcription is in the nucleus
  • translation is in the cytoplasm
  • mRNA has to be modified before it gets translated
  • ## environment is more hostile to mRNA
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9
Q

At what rate does translation happen after transcription in eukaryotes

A
  • not coupled like in prokaryotes!
  • RNA transcripts are made in the nucleus then are transported to the cytoplasm
  • the first RNA made is a primary transcripts, when introns are removed the mRNA is able to come out of the nucleus
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10
Q

transfer RNAs (tRNA)

A
  • adaptors between amino acids and the codons in mRNA
  • involved in translation - translate the genetic code to protein
  • clover shaped
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11
Q

messenger RNAs (mRNA)

A
  • intermediates that carry genetic information from DNA to the ribosomes
  • usually linear
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12
Q

ribosomal RNA (rRNA)

A
  • structural and catalytic components of ribosomes
  • circular, binds to mRNA
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13
Q

types of RNAs only found in eukaryotes

A
  • small nuclear RNAs (snRNA, snoRNA)
  • micro RNAs (miRNA, siRNA, Crispr RNA)
  • long noncoding RNA
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14
Q

RNA synthesis

A
  • happens in 5’ to 3’ direction using 3’ to 5’ DNA template strand, complementary and anti-parallel to DNA template strand
  • if you want RNA to have the same sequence as strand A make it from strand B
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15
Q

coding vs non-coding DNA strand

A

coding:
- strand you want to copy sequence of
- aka “non-template” or “sense” strand
non-coding:
- strand you use as a template for mRNA (opposite sequence)
- aka “template” or “antisense” strand

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16
Q

why can transcription utilize either DNA strand

A
  • there are multiple genes on a chromosome that are located on either strand
  • no matter which strand contains the gene, transcription will always occur in the 5’ to 3’ direction
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17
Q

transcription as a chemical reaction

A

RNAn + rNTP -> RNAn+1 + PPi

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18
Q

general features of RNA synthesis

A
  • precursors are rNTPs
  • only one strand of the DNA is used as the template
  • catalyzed by RNA polymerase
  • RNA molecule is identical to non-template 5’ to 3’ strand and complimentary to 3’ to 5’ template
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19
Q

structure of gene for transcription in prokaryotes

A

contains…
- promotor
- transcription start site
- RNA-coding region
- terminator
- transcription termination site

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20
Q

promotor region

A
  • regulates the rate of transcription
  • where RNA polymerase binds and initiates transcription from
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21
Q

terminator

A
  • signals transcription to stop
  • is encoded in the RNA (unlike promotor)
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22
Q

steps in prokaryotic transcription

A
  1. initiation
  2. elongation
  3. termination
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23
Q

initiation

A
  • RNA polymerase binds, unwinds and joins the first 2 nucleotides
  • initiation of RNA synthesis DOES NOT require a primer
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24
Q

elongation

A
  • complementary nucleotides continue to be added
  • localized DNA unwinding ahead of RNA polymerase generates a transcription bubble
  • transcription bubble moves with RNA polymerase and unwound DNA behind it rewinds, RNA starts to stick out
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25
Q

termination

A
  • transcription stops when RNA polymerase reaches the “terminator” region of the gene
  • newly synthesized RNA together with RNA polymerase is released
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26
Q

components of E. coli RNA polymerase

A

core (a2,B,B’,w): transcribes any DNA sequence - not gene specific

holoenzyme(a2,B,B’,w,o): specific for transcribing genes

27
Q

alpha subunit of RNA poly

A

involved in assembly of the tetrameric core

28
Q

beta subunit of RNA poly

A

contains the ribonucleoside triphosphate (rNTP) binding site

29
Q

beta-prime subunit of RNA poly

A

contains the DNA template binding region

30
Q

omega subunit of RNA poly

A

helps to stabilize the tetrameric core

31
Q

sigma subunit* of RNA poly

A

binds to the RNA poly tetrameric core, assists in correct initiation of transcription - specifically at promoter region
- give the RNA poly specify for a gene

32
Q

initiation of transcription in prokaryotes

A
  • recognition of 2 important promoter sequences
    a -35 element: 5’TTGACA3’
    a -10 element: TATAAT box
  • transcription initiates about 5-9 base pairs down from -10 sequence, the +1 position is a purine
33
Q

transcription elongation in prokaryotes

A
  • occurs when sigma factor is released in order for RNA poly to move along template strand
34
Q

transcription termination in prokaryotes

A
  • rho-independent (doesn’t use terminator proteins)
  • commons mechanism is weak H-bonding at U:A residues that allows mRNA to release from DNA when RNA poly pauses at terminator
  • RNA hybridizes with itself
35
Q

polymerases involved in eukaryotic transcription

A

RNA poly I: transcribes larger rRNAs
RNA poly II: transcribes pre-mRNA, some snRNAs, snoRNAs, some miRNAs
RNA poly III: transcribes tRNAs, small rRNAs, some snRNAs, some miRNAs

36
Q

specific promoter sequences for genes transcribed by RNA poly I, II and III

A
  • ## promoter-specific accessory proteins recognize each specific type of promotor and recruit appropriate poly for transcription
37
Q

activators

A
  • specific for a gene and bind general transcription factors so they can bind DNA. to a particular gene
38
Q

promotors in eukaryotes

A
  • consists of a regulatory promoter and a core promoter
  • core promotor contains -35, -25, +1 and +30 sequences
    -35: TFIIB recognition element
    -25: TATA box
    +1: initiator element
    +30: downstream core promoter
39
Q

initiation of transcription in eukaryotes

A
  • involves assembly of general transcription factors
  • TFIID assembles first at the TATA box followed by the remaining TFs
  • this forms the preinitiation complex
  • the “mediator” permits interactions with other activator proteins bound to regulatory regions or enhancers
  • DNA loops out allowing bound proteins to interact with BTA
40
Q

core promoters in eukaryotes

A
  • assemble the transcriptional machinery, but enhancers determine how efficiently they transcribe
41
Q

distinct enhancers

A
  • contain different cofactors which can increase or not increase transcription by RNA poly II
  • most are far removed from the promoters they influence and must bend the DNA to interact with promoter
42
Q

elongation in transcription for eukaryotes

A
  • many of the general transcription factors remain at the promoter for quick re-initiation with a new pol.II
  • a transcription bubble is generated by RNA:DNA binding
  • ensures free RNA3’-OH terminus is available for new rNTP addition
43
Q

termination of transcription in eukaryotes

A
  • involves cleavage of pre-mRNA and 5’ to 3’ degradation of remaining RNA
  • terminates when Rat1 exonuclease reaches RNA Poly
44
Q

Colinerity

A
  • in prokaryotes, the coding region of a gene is not interrupted: the sequence of the gene is co-linear with the amino acid sequence
  • the number of nucleotides in the gene is proportional to the number of amino acids in the protein
45
Q

RNA molecules and processing in prokaryotes

A

the sequence of mRNA corresponds to the sequence of the gene from which it was transcribed

46
Q

RNA molecules and processing in eukaryotes

A
  • genes are often interrupted
  • the removal of introns is required to form the mRNA that will be translated into a polypeptide
    3 main steps of processing: addition of 7-methyl guanosine cap, polyA tail and removal of introns
47
Q

the 7’methyl guanosine cap (5’ cap)

A
  • occurs early in the elongation process
  • added to pre-mRNA via the unique 5’-5’ phosphate linkage
48
Q

3’ PolyA tail

A
  • pre-mRNA is cleaved 11-30 nt following 5’AAUAAA3’ sequence and then a long string of about 200 “A” residues is added by PolyA polymerase
49
Q

the removal of introns

A
  • must happen precisely in order to fuse 3’ of one exon to 5’ of the next
  • every intron has 2 conceived sequences required for removal
    1) 5’ and 3’ splice sequences containing “GU and AG” respectively
    2) intron branch point: a concerted “A” residue
  • happens by RNA splicing via spliceosomes
50
Q

spliceosomes mechanism

A

1) snRNP assembly: U1 binds to 5’ splice site and U2 binds to branch site
2) 5’ splice site is cleaved
3) 3’ splice site is cleaved
4) the exons join together
- U1 and U2 draw ends of intron together to cleave

51
Q

lariat formation

A

involves a unique linkage between the 5’ phosphate of the G and the 2’OH of the A
- formation is made after 3’ splice site is cleaved

52
Q

how can one gene make many different proteins?

A
  • splicing of introns can occur in many different ways to give different proteins
53
Q

alternative splicing

A
  • either 2 introns are removed to yield one mRNA OR 2 introns and an exon are removed to yield a different mRNA
  • more common
54
Q

Multiple 3’ cleavage sites (splicing)

A
  • cleavage may be at 3’ site1 or at 3’ site2
    -mRNA products of different lengths are produced after splicing
55
Q

RNA editing

A

changes the information content of genes by…
- changing the structures of individual bases
- modification of mRNA by endogenous guide RNAs
- inserting or deleting nucleotides

56
Q

guide RNAs (gRNA)

A
  • direct the insertion of uridine bases into the mRNA by repair polymerase
  • gRNA serves as a template for addition, deletion or alteration of bases
  • ## makes new codons that specify new amino acids in the protein
57
Q

editing of apoplipoprotein-B mRNA

A
  • RNA editing of ApoB changes C to U converting glutamine codons (CAA) to stop codons (UAA) which truncates the protein and gives it a different function with respect to lipid binding
58
Q

transfer RNA (tRNA)

A
  • clover-shaped adaptors between the AAs and codons in mRNA
  • the anticodon of tRNA pair with the codon of mRNA
  • contain modified ribonucleotides
59
Q

ribosomal RNA (rRNA)

A
  • key components of the ribosome
  • synthesis of rRNA and ribosomes happens in the nucleolus
  • in prokaryotes there is no nucleolus so this process happens in the cytoplasm
60
Q

synthesis and processing ribosomal RNAs

A
  • methyl groups are added to specific bases and to the 2’-carbon atom of some ribose sugars
  • the RNA is cleaved into several intermediates and then trimmed
  • in prokaryotes made in 1 transcript and spliced out, also forms a tRNA
61
Q

snRNAs

A
  • act in complexes with proteins
  • plays in post-transcriptional processing of RNA such as splicing
62
Q

snoRNAs

A

in eukaryotes, guide the enzymatic chemical modifications of rRNAs, tRNAs and snRNAs

63
Q

small micro RNAs

A
  • regulate the control of gene expression in different ways

MBG 2040 (23 decks)

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