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Bio 184 > 02/13 transcription > Flashcards

02/13 transcription Flashcards

1
Q

which strand is complementary to the mRNA transcript

A

the template strand

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2
Q

which strand matches the nucleotide sequence to the mRNA transcript

A

the coding strand

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3
Q

what are the general steps of initiation

A

The promoter is the recognition site for transcription factors that will bind with RNA po and form a closed promoter complex. This will later get opened to form an open promoter complex

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4
Q

what are the two main types of genes

A

structural- code for protein

non-structural- code for RNA type

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5
Q

how do transcription factors know when and where to bind

A

there are specific regulatory sequences that they “feel by braille” to and bind

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6
Q

which direction is downstream of a gene?

A

it is in the direction of the MRNA

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7
Q

what direction is upstream of a gene

A

it is away from the mRNA, these are generally regions where the promoter exists

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8
Q

for regions upstream of the +1 base, are they transcribed

A

no, these are not

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9
Q

is the first base in the mRNA transcript the start codon?

A

no, it is the 5’ UTR

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10
Q

is the promoter within the 5’ UTR region?

A

no it is not transcribed at all

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11
Q

what is the purpose of the -10 and -35 regions of the promoter

A

these are regions that reside within the major groove of the DNA, this is where transcription factor proteins will bind

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12
Q

what is a consensus sequence

A

A sequence with the most commonly occurring bases, they are essentially flexible recognition sequences

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13
Q

how do variations in the consensus sequence play a role?

A

they can affect the rate of RNA transcription

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14
Q

what is the sigma factor’s role?

A

it associates with RNA polymerase and scans the DNA for the consensus sequence of the promoter

at this consensus, it will synthesize a short spurt of RNA and then get released

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15
Q

how does RNA polymerase open the strand

A

it has a “helicase-like” activity and can break bonds

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16
Q

what is the primary difference between a DNA polymerase and an RNA polymerase

A

RNA polymerases do not require a primer to begin

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17
Q

does RNA polymerase have proofreading

A

no

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18
Q

what is rho dependent termination

A

it is a method of termination in bacteria

it requires the rho protein and a stem loop structure

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19
Q

what is rho independent termination

A

it is a method of termination in bacteria

it does not require rho protein but requires a stem loop and a U rich region

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20
Q

what do rho dependent and independent termination both depend on?

A

they depend on stem loop structures

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21
Q

what is a stem loop

A

it is a intramolecular secondary structure with complementary regions that form a loop

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22
Q

Describe the mechanism of rho dependent termination

A

rho protein recognizes its recognition sequence and binds to the RNA strand

the RNA polymerase is paused by the formation of a stem loop and the rho protein can catch up and dislodge it from the RNA transcript

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23
Q

without the formation of the stem loop, what would happen to the RNA polymerase

A

it wouldn’t know to stop and would continue transcribing

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24
Q

describe the mechanism of rho independent termination

A

it is facilitated by an allosteric binding site

another protein will bind to this site and cause the RNA polymerase to change shape and fall off of the template

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25
why does the mechanism of rho independent termination have to be U rich?
if it is U rich, there will be a loose interaction between the template and polymerase
26
how do eukaryotes differ in terms of polymerases to prokaryotes
eukaryotes have more specialized types of polymerases
27
what is the core promoter
it is found in eukaryotes and includes the TATA box which determines the start point of transcription
28
what are regulatory elements
they are sequences that influence gene transcription
29
what is a constitutive gene
it is a gene that is always on
30
what is a facultative gene
it is a gene that oscillate between being on and off
31
what are enhancers
they are regulatory elements that stimulate transcription
32
what are silencers
they are regulatory elements that inhibit transcription
32
how can regulatory elements act on promoters that are far away?
through the use of radial loops which brings the regions closer
33
What are cis acting elements
they are DNA sequences that only affect nearby genes
34
What is a trans-acting element
they are regulatory proteins that bind to DNA sequences from any region
35
what is the role of TFIID
it binds to the TATA promoter by seeking out an AT rich area
36
how is TFIID different from the sigma binding protein in prokaryotes
the sigma binding protein travels down WITH the RNA polymerase to locate the promoter while TFIID acts alone and signals the other proteins when it finds the promoter
37
what is the role of TFIIH (2)
It has helicase activity that opens the complex it phosphorylates the RNA polymerase, which gives it a negative charge and changes its structure via a covalent attachment of a phosphate group. This activates the RNA polymerase
38
what is the basal transcription apparatus comprised of
RNA pol II and 5 GTFS (general transcription factors)
39
what are GTFs
they are transcription factors necessary for all RNA transcription
40
What are STFs
they are specific transcription factors that bind to enhancers/ silencers that are specific to the gene
41
what is the primary 2 roles of a mediator protein
it acts to bridge signals and mediate interactions between STFs and RNA pol II it also aids in TFIIH's ability to phosphorylate RNA pol II
42
describe the role of the poly A sequence in eukaryotic termination
when the RNA polymerase moves downstream of the poly A sequence, it gets cleaved off by endonuclease activity, which separates the two RNA strands
43
What is the torpedo model of termination
an exonuclease enzyme degrades the remaining RNA in the 5'-3' direction until it catches up to RNA polymerase and dislodges it
44
how is the torpedo model similar to rho dependent termination? how is it different?
it is similar since an enzyme follows the RNA polymerase and dislodges it it is different since rho does NOT degrade the remaining RNA and it requires a stem loop
45
what is the allosteric model of termination
termination factors bind the the RNA polymerase and dislodges it
46
what termination process is the allosteric model of termination similar to?
it is similar to the rho independent model as they both involve the use of the allosteric binding site and termination by RNA polymerase dislodging
47
what is a key difference between eukaryotic and prokaryotic termination of transcription
the prokaryotic termination requires the use of a stem loop while the eukaryotic does not
48
when does the poly A tail get added
in post transcription
49
what does the pre-mRNA contain
start codon, introns, exons, stop codon
50
what does the pre-mRNA not contain
guanine cap, poly A tail, promoter
51
what are the three things that occur in post transcriptional processing
splicing of introns addition of poly A tail addition of guanine cap
52
true or false, nonstructural genes do not require post transcriptional processing
false, RNAs still need to undergo processing and splicing
53
describe RNA processing
nonstructural genes are often transcribed into larger RNA fragments and are then spliced by ribozymes to form smaller functional pieces
54
what is a ribozyme
it is an RNA that contains catalytic activity
55
what type of nuclease activity is used in RNA processing
endonuclease activity to internally cut the larger RNA
56
what are covalently modified bases
they are post-transcriptional modifications of RNA molecules
57
what does it mean when a bacteria has colinearity of gene expression
bacteria do not require additional processing steps as the coding strand directly codes for the mRNA sequence and the mRNA transcript directly codes for the polypeptide amino acid sequence
58
what are exons? introns?
exons are the codings sequences of the mRNA introns are the intervening sequences that disrupt the exons and need to be spliced out
59
why does the nucleus play an important role in the transcription to translation pipeline in eukaryotes
the nucleus has a nuclear envelope that gives time for the mRNA transcript to be modified bacteria cannot do this as they are immediate;y translated
60
what are the two types of introns?
self splicing and spliceosomes
61
what is the key difference between self-splicing and spliceosome introns
self-splicing introns will splice the same time everytime and do not require help from other proteins spliceosomes can cut differently and perform alternative splicing
62
what is a spliceosome comprised of
it is comprised of RNA and protein (snRNPs)
63
what type of activity do both self splicing introns and spliceosome introns have?
they both have ribozyme activity
64
why is it important that not every cell has the same type of spliceosome
different spliceosomes will cut the mRNA in different ways, this will result in a different RNA strand which will code for different types of polypeptides
65
What is the role of RNaseP
it is an ribozyme endonuclease that cuts the tRNA in post transcriptional modifications
66

Bio 184 (30 decks)

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