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BIOL2500 > Unit 02.2: DNA Transcription > Flashcards

Unit 02.2: DNA Transcription Flashcards

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1
Q

who introduced the concept of the central dogma?

A

crick

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2
Q

what are the functions of RNA?

A
  • provides info for making proteins
  • regulation of translation
  • processing RNA
  • maintaining chromosome ends
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3
Q

what makes RNA versatile?

A
  • single stranded
  • can base pair with other RNAs
  • can have enzymatic activity
  • can be regulated by other molecules
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4
Q

who used the pulse chase experiments to show RNA export and that RNA can be used to make proteins?

A

volkin and astrachan

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5
Q

can RNA form hairpins?

A

yes!

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6
Q

what are the 2 classes of RNA?

A

messenger RNA and non coding RNA

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7
Q

what are some examples of non coding RNA?

A
  • ribosomal RNA (rRNA)
  • transfer RNA (tRNA)
  • small nuclear RNA (snRNA)
  • micro RNA (miRNA)
  • small interfering RNA (siRNA)
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8
Q

what is the function of snRNAs?

A

mRNA processing and intron removal

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9
Q

what is the function of miRNAs and siRNAs?

A

regulation

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10
Q

what is the direction of transcription?

A

5’ to 3’

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11
Q

describe transcription initiation in bacteria.

A

RNA Polymerase binds to the template strand of DNA at the Pribnow Box and the -35 consensus sequence located within the promoter

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12
Q

why is the consensus sequence called a consensus sequence?

A

bc the sequence is almost identical in all promoters

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13
Q

prokaryotic RNA Polymerase is a _____, composed of several subunits

A

holoenzyme

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14
Q

what subunits makeup prokaryotic RNA polymerase?

A

2 a units, one β subunit, one β’ subunit, one ω subunit and a σ factor

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15
Q

what is the function of the two a subunits in prokaryotic RNA Polymerase

A

help assemble the enzyme

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16
Q

what is the function of the β subunit in prokaryotic RNA Polymerase?

A

active in catalysis

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17
Q

what is the function of the β’ subunit in prokaryotic RNA Polymerase?

A

binds DNA

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18
Q

what is the function of the ω subunit in prokaryotic RNA Polymerase?

A

helps assemble enzyme

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19
Q

what is the function of the σ factor in prokaryotic RNA Polymerase?

A

binds to promoter until transcription begins, initiating first unwinding, after which it dissociates from the core enzyme

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20
Q

describe transcription elongation in prokaryotes.

A
  • RNA polymerase moves along DNA, unwinding and rewinding DNA as it moves along, maintaining the transcription bubble.
  • adds nucleotides (ATP, GTP, UTP, CTP) complementary to template strand.
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21
Q

is transcription slower than DNA replication?

A

yes!

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22
Q

are only the protein coding segments of DNA transcribed?

Study These Flashcards
A

no! transcription continues beyond the coding region, forming the 3’ UTR

23
Q

describe factor independent termination in prokaryotes. which eukaryotic form of termination is it analogous to?

Study These Flashcards
A
  • a GC rich stretch is transcribed (forming a hairpin) followed by a series of As
  • the presence of this hairpin loop causes RNA Polymerase to dissociate from DNA

analogous to the allosteric model

24
Q

describe rho-dependent termination in prokaryotes. which eukaryotic form of termination is it analogous to?

Study These Flashcards
A
  • rho factor protein recognizes and binds to a rut site upstream of where RNA Polymerase naturally pauses transcription (rut site consists of a sequence rich in Cs and poor in Gs)
  • once bound, Rho travels to 3’ end of the transcript, bumping into RNA polymerase, unwinding the last bit of the DNA-RNA base pairing
  • RNA Polymerase dissociates

analogous to torpedo model

25
why is eukaryotic transcription more complicated than prokaryotic?
1. eukaryotes have larger genomes, and genes that are much further apart 2. eukaryotes have 3 different RNA polymerases all of which also need GTFs to bind to promoters and carboxy-terminal domains to coordinate RNA processing 3. transcription takes place in nucleus but needs to then leave (post transcriptional modifications) 4. eukaryotic DNA is packed into tight chromatin (much tighter than prokaryotic DNA!!)
26
which RNAs does RNA Polymerase 1 synthesize?
rRNA (except 5s rRNA)
27
which RNAs does RNA Polymerase 2 synthesize?
mRNA, some miRNAs and snRNAs
28
which RNAs does RNA Polymerase 3 synthesize?
tRNA, 5s rRNA, some snRNAs
29
describe transcription initiation for mRNA in eukaryotes.
1. general transcription factors help bind RNA polymerase 2 to DNA promoters 2. once all TFs join, the preinitiation complex is formed 3. once preinitiation complex is formed, transcription starts at the +1 nucleotide
30
in what order do the TFs come in to help initiate transcription in eukaryotes? what do they each do?
1. TFIID (made up of TATA binding protein and TBP associated factor) binds to TATAA box, forming initial committed complex. 2. TFIIA, TFIIB, TFIIF join the initial committed complex along with RNA Polymerase 3. TFIIE and TFIIH join, forming the preinitiation complex
31
what is the function of the carboxy terminal domain (CTD)?
prepares pre-mRNA transcript for modification as it is being transcribed
32
the CTD has what repeating a^2 sequence?
tyrosine-serine-proline-threonine-serine-proline-serine
33
what does the phosphorylation of the 5th position serine signal?
the binding of the 5' cap
34
describe transcription termination when RNA Pol 1 is used.
proteins bind to terminator elements on DNA
35
describe transcription termination when RNA Pol 3 is used.
there is a poly u stretch, similar to prokaryotic factor independent termination.
36
describe the torpedo model of termination when RNA Pol 2 is used
1. transcription continues past a cleavage site where the pre-mRNA is then cleaved 2. 5' end of cleaved mRNA digested by Xrn2 until it reaches RNA Pol 2, causing it to dissociate 3. interacts w/ serine 2 in CTD
37
describe the allosteric model of termination when RNA Pol 2 is used
- transcription past cleavage site causes elongation factors to dissociate, causing a confirmational change in the RNA polymerase, which causes RNA Polymerase 2 to dissociate from DNA
38
what is the purpose of the 5' cap on mRNA?
protects mRNA from degradation as its being transported across nuclear envelope and as introns are spliced.
39
describe the process by which the 5' cap is added.
1. RNA triphosphatase removes one of three phosphate from first nucleotide. 2. guanylyl transferase adds a guanine to the 5' end of mRNA 3. this produces a weird but very stable 5' to 5' bond, forming a triphosphate linkage. 4. added guanine gets methylated by 7-methyltransferase, finishing up the cap.
40
how long is the pre mRNA when the 5' cap is added?
about 25 bp
41
describe the steps by which the 3' end of the mRNA is polyadenylated.
1. cleavage and polyadenylation specificity factor (CPSF) binds to AAUAAA region upstream of poly-A (cleavage) site 2. cleavage stimulating factor (CStF) binds to uracil rich sequence downstream of poly-A site. 3. other cleavage factors (CFI, CFII) join complex along with polyadenylate polymerase (PAP) 4. complex cleaves 15-30 nucleotides downstream of the AAUAAA 5. once cut, the pre-mRNA has 50-250 adenosines added to its 3' end, creating the poly-A tail
42
what are some functions of the poly-A tail?
- transport of mRNA - protection of mRNA from degredation - enhances translation by enabling ribosomal recognition of mRNA - acts as a timer
43
what defines the 5' and 3' spice sites
most 5' spice sites start with GU, while most 3' splice sites start with AG.
44
splicing removes _____ and joins together the _____
introns, exons
45
what is the protein complex that removes introns?
spliceosomes
46
T/F; pre-mRNAs can be spliced in different ways depending on the gene we want transcribed.
true!
47
what is alternative splicing?
when an intron in one gene may be an exon in another gene depending on the protein
48
which a^2 are negatively charged?
aspartate and glutamate
49
which structure on aspartate and glutamate causes them to be negatively charged?
carbolixic acid on R-grp
50
which a^2 are positively charged?
lysine, arginine, histidine
51
which structure on lysine, arginine, and histidine causes them to be positively charged?
amino group on R-grp
52
which a^2 are polar uncharged?
serine, threonine, tyrosine, cysteine, asparagine, and glutamine
53
what is the only a^2 that can make covalent bonds?
cysteine
54
who proposed the one gene one polypeptide hypothesis?
beadle and tatum

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