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genetics midterm 2 > lecture 15, 16 > Flashcards

lecture 15, 16 Flashcards

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1
Q

what does RNA stand for

A

ribonucleic acid

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2
Q

what is RNA made from?

A

a DNA template

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3
Q

trasncription

A

the process of making RNA using DNA template

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4
Q

what are the four ribonucleotides found in RNA?

A

adenine, guanine, cytosine, and uracil

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5
Q

what are the ribonucleotides that pair with each other?

A

A to U, G to C

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6
Q

what is different about the structure of RNA vs DNA?

A

RNA has an OH group instead of H in DNA, making it less stable

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7
Q

what about RNA makes base-pairing slightly different?

A

when RNA folds, U can pair with A or G

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8
Q

what is the benefit behind U being able to bind with A or G?

A

more options in forming secondary structures

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9
Q

is RNA single or double stranded?

A

single stranded

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10
Q

what benefit comes out of RNA being single-stranded?

A

it is able to fold on itself to form secondary structures

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11
Q

ribozyme

A

RNA that can catalyze reactions

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12
Q

mRNA

A

encodes for proteins

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13
Q

functional RNA

A

involved in regulating gene function

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14
Q

can functional RNA encode for proteins?

A

no

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15
Q

which strand is RNA complementary to?

A

the template strand

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16
Q

which strand is RNA identical to with the exception of U swapped with T?

A

non-template strand

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17
Q

what is another name for the non-template strand?

A

coding strand

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18
Q

where does transcription start on the gene?

A

between the promoter and the first codon in a (+1) region

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19
Q

what RNA regions do not code/are considered untranslated regions?

A

5’ UTR and 3’ UTR

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20
Q

Where is the 5’ UTR located?

A

just before the first/start codon

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21
Q

where is the 3’UTR located?

A

after the stop codon

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22
Q

promoter

A

a region of DNA where RNA polymerase holoenzyme binds to initiate transcription for the gene

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23
Q

how far is the promoter from the (+1) site?

A

50-100 bps

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24
Q

when is a promoter considered active?

A

when the promote binds the RNA polymerase holoenzyme/when transcription occurs

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25
when is the promoter considered inactive?
when there is no transcription
26
what is the purpose of the -35 consensus sequence?
its a site that recognizes RNA pol
27
what is the purpose of the -10 consensus sequence?
to help RNA pol open DNA
28
What binds to the -35 and -10 consensus sites?
RNA pol sigma factor
29
What does the beta subunit do?
Harbors the catalytic site
30
what does beta prime subunit do?
assists in catalysis
31
what do alpha and omega factor subunits do?
regulation and assembly
32
transcription bubble
the single strand DNA region formed during transcription inside RNA pol
33
in prokaryotes, what are the two main termination mechanisms in prokaryotes
intrinsic and rho-dependent termination
34
intrinsic termination
occurs through RNA pol activity with the formation of a loop structure in the RNA that is rich in GC, followed by an upstream poly-U sequence
35
rho-dependent termination
RNA pol encounters a C-rich region and signals a pause in transcription, and the protein rho binds to the RNA to find the rut region and terminates transcription
36
in prokaryotes, where do transcription and translation occur?
In the cytoplasm
37
in eukaryotes, where do transcription and translation occur?
in the nucleus and cytoplasm respectively
38
how many RNA pol do prokaryotes have?
one
39
how many RNA pol do eukaryotes have?
three
40
what does eukaryotic DNA wrap around?
proteins (histones)
41
what needs to be removed/moved in eukaryotes for transcription to occur?
histones
42
what is the equivalent of mRNA in eukaryotes?
RNA pol II
43
what is the purpose of RNA pol I and RNA pol III?
to make functional RNA
44
RNA pol II
transcribes mRNA and some functional RNA
45
general transcription factors
protein complexes that help RNA pol II recognize and initiate transcription at the promoter
46
what do many RNA pol promoters use as a binding site for transcription?
a TATA box or an INR (in pol II)
47
what general transcription factor does RNA pol II mostly rely on?
TFIID
48
what does TFIID do?
binds the promoter at the TATA box via TBP
49
describe a summary of transcription initiation in eukaryotes
binding of TBP and TFIID -> formation of preinitiation complex- > RNA pol II begins elongation
50
what happens after RNA pol II synthesizes the RNA
It leaves the promoter and TFIID behind
51
what are the major transcriptional processes in eukaryotes?
(1) 5' Cap (2) splicing (3) polyadenylation
52
5' Capping process
7-methylguanosine attaches to the 5' UTR end with three phosphate groups
53
what is the purpose of the 5' capping process?
to protect the RNA from degradation and provides binding sites for proteins that assist in translation
54
splicing
an RNA transcription process that removes introns
55
what is the purpose of splicing?
to remove non-coding sequences from the pre-mRNA to make a "proper" mRNA for protein translation
56
polyadenylation
An RNA transcription process that adds a poly-A tail to the end of mRNA
57
what is the purpose of polyadenylation?
to protect the RNA from degradation and stimulates translation by interacting with translation machinery
58
open reading frame (ORF)
the nucleotide sequence from start to stop but does not include stop
59
coding sequence (CDS)
the nucleotide sequence from start to stop that will appear in the mRNA that will appear in the mRNA
60
in prokaryotes, what is ORF equal to?
CDS
61
in eukaryotes, what is ORF equal to?
CDS + introns
62
pre-mRNA
RNA that has not been processed yet
63
What do all introns require?
GU at the 5', AG at the 3', and an A in between, but closer to 3'
64
snRNPs
small protein complexes involved in splicing
65
describe how a spliceosome is constructed
U1 and U2 SNPs bind to the 5' splice site (U1) and internal A (U2) , then U4-5-6 complex joins to complete the full spliceosome
66
describe how the spliceosome functions following assembly
some U SNPs are displaced followed by the formation of a Lariat structure, where 1 end of the intron attaches to the internal A while the other is cleaved, concluded by the joining of the exons
67
list the different types of functional RNA
tRNA, rRNA, snRNA, miRNA, siRNA, piRNA
68
tRNA
transfer RNA; carries amino acids to the ribosome for protein synthesis
69
Which RNA polymerase transcribes tRNA?
RNA pol III
70
rRNA
ribosomal RNA; RNA components of the ribosome that have structural and enzymatic activities
71
Which RNA polymerase transcribes rRNA?
RNA pol I except 5S rRNA (transcribed by RNA pol III)
72
snRNA
small nuclear RNA; involved in the splicing of eukaryotic RNAs into mRNA
73
Which RNA polymerase transcribes snRNA?
RNA pol II and RNA pol III
74
miRNA
micro RNA; regulates translation and infection via regulating RNA stability
75
siRNA
small interfering RNA; help prevent mobilization of transposons and viruses
76
piRNA
piwi-interacting RNA; control transposition (jumping genes that could be harmful)
77
how is siRNA formed?
using the enzyme DICER
78
DICER
an enzyme that chops up double-strand RNA
79
describe the siRNA formation process and function
DICER chops double-stranded RNA into siRNA and mRNA where siRNA is bound to RISC and separated, then mRNA is bound to RISC and degrades it
80
Why is it important for RISC to degrade mRNA?
in the event that some mRNA could be harmful if translated or if its not meant to be expressed as a protein
81
how is miRNA formed?
using the enzyme DICER for processing
82
describe the miRNA formation process and function
DICER processes the RNA and removes the hairpin loop, then is transferred into RISC and separated, in which miRNA uses it in identifying mRNA targets to repress translation or degrade mRNA
83
what is the key difference between miRNA and siRNA?
siRNA is rapid degradation of mRNA before it approaches translation, miRNA is controlled and more flexible
84
what genes utilize miRNA over siRNA?
endogenous genes; genes that are naturally present in an organism
85
RNA decay
The process by which RNA is destroyed over time

genetics midterm 2 (6 decks)

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