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BIOL 239 > Week 7 > Flashcards

Week 7 Flashcards

Transcription and Translation

1
Q

define: transcription

A

process by which the polymerization of ribonucleotides guided by complementary base pairing produces an RNA transcript of a gene (DNA -> RNA)

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2
Q

in which direction are nucleotides added

A

5’-to-3’

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3
Q

what is in place of thymine in RNA

A

uracil

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4
Q

which enzyme catalyzes transcription

A

RNA polymerase

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5
Q

define: promoters

A

DNA sequences near the beginning of genes that signal RNA polymerase where to begin transcription

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6
Q

define: terminators

A

sequences in the RNA produces that tell RNA polymerase where to stop (encoded by DNA)

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7
Q

define: open reading frame (ORF)

A

region between the start and stop codons

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8
Q

are the start and stop codons located at the ends of mRNA

A

no, since they are nested within the promoter and terminator regions

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9
Q

what are the three steps of transcription

A

initiation, elongation, and termination

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10
Q

define: RNA polymerase holoenzyme

A

RNA polymerase + sigma factor

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11
Q

what two things does the sigma factor do

A
  1. reduces RNA polymerase’s general affinity for DNA
  2. increases RNA polymerase’s affinity for the promoter
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12
Q

what happens when RNA polymerase binds to the promoter

A

the RNA polymerase unwinds part of the double helix

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13
Q

define: open promoter complex

A

complex formed between the RNA polymerase holoenzyme and an unwound promoter

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14
Q

when does the sigma factor get released

A

after the first few nucleotides of the RNA are synthesized

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15
Q

what is the average speed of RNA synthesis

A

50 nucleotides per second

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16
Q

define: transcription bubble

A

region of DNA unwound by RNA polymerase

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17
Q

what causes the RNA to get displaced during transcription

A

reformation of DNA helix

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18
Q

when can the next instance of transcription happen on a strand of DNA

A

once RNA polymerase has moved off the promoter

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19
Q

on which strand of DNA does transcription occur

A

the template strand

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20
Q

define: coding strand

A

the strand of DNA that has the same sequence as mRNA (with T replaced by U)

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21
Q

are the promoter and terminator sequences present in mRNA

A

no

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22
Q

what are the two methods of transcription termination

A
  1. rho-dependent
  2. rho-independent
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23
Q

what causes a hairpin loop to be formed in rho-independent termination

A

transcription of six adenines

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24
Q

what bonds are primarily present in a hairpin loop

A

C-G bonds

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25
why does the hairpin loop form
hydrogen bonds between A-U are weaker than C-G
26
what happens after a hairpin loop is formed
the RNA polymerase becomes weakly associated with the DNA and falls off
27
does a frame shift mutation in one gene affect the sequence of another gene
no, since each genes has its own transcription start/stop
28
in which type of cell does RNA processing occur
only in eukaryotes
29
what is added to the 5' end of eukaryotic mRNA
a methylated cap
30
what is the structure of a methylated cap
a guanidine triphosphate in reverse orientation to the 5' end with a methyl group, and methyl groups to one or more of the succeeding nucleotides in the RNA
31
what is at the 5' end of prokaryotic mRNA
a triphosphate
32
what is added to the 3' end of eukaryotic mRNA
poly-A tail
33
what is the structure of a poly-A tail
100-200 adenosines
34
how does the poly-A tail get added
ribonuclease cleaves the primary transcript (11-30 nucleotides downstream of the polyadenylation signal) to form a new 3' end and the poly-A polymerase adds As onto this new 3' end
35
define: polyadenylation
the addition of the poly-A tail to the 3' end
36
what is the purpose of the cap and tail in eukaryotic RNA
- prevent degradation since it has to be transported to the cytoplasm - to enable ribosomes to initiate translation
37
what are the forms of mRNA processing
1. addition of methylated cap 2. addition of poly-A tail 3. RNA splicing
38
define: RNA splicing
the removal of introns
39
define: exons
coding sequences for the protein product
40
what carries out splicing
spliceosome
41
why don't some RNA transcripts require a spliceosome
they are self-splicing
42
where are introns found
in the DNA and primary transcript, not in the mature RNA
43
what are the three short regions used for splicing
splice donors, splice acceptors, and branch sites
44
define: alternative splicing
a single mRNA transcript can be spliced in different ways to produce different mature mRNA molecules
45
in what phyla is alternative splicing the highest
in mammals
46
does the number of genes indicate complexity
no, but alternative splicing may
47
define: trans-splicing
form of alternative splicing in which an exon from one transcript can be joined to an exon from a different transcript
48
define: translation
process in which the genetic code carried by mRNA directs the synthesis of proteins from amino acids
49
how long are tRNA
74 to 95 nucleotides long
50
what do tRNA carry
- some modified bases produced by chemical alterations of the A, G, C, and U nucleotides - one particular amino acid
51
what is an example of a modified base that tRNA contains
inosine, a modification of adenosine
52
what does aminoacyl-tRNA synthetase catalyze
the attachment of a tRNA to its cognate amino acid
53
how is the correct order of amino acids determined
base pairing between an mRNA codon and a tRNA anticodon
54
what do the wobble rules refer to
the ability for some tRNAs to recognize more than one codon for the amino acid they carry
55
where can inosine be found in tRNA
in the anticodon when more than one codon can be recognized
56
what are ribosomes composed of
protein and rRNA
57
what is the function of ribosomes
the sites of protein synthesis
58
what are the three function sites of ribosomes
- A: aminoacyl binding site - P: peptidyl binding site - E: exit tRNA binding site
59
what is the *E. coli* Shine-Dalgarno sequence
AGGAGG
60
what recognizes the *E. coli* Shine-Dalgarno sequence
complimentary sequences in the 16S rRNA of the 30S subunit
61
what are Shine-Dalgarno sequences usually rich in
purines
62
what are the three steps of translation
initiation, elongation, termination
63
how does initiation happen in prokaryotes
30S ribosomal subunit binds to Shine-Dalgarno sequence in presence of tRNA carrying formylmethionine and then the 50S ribosomal subunit binds
64
what are 30S ribosomal subunits escorted by
initiation factor (IF) proteins
65
compare tRNA-FMet and tRNA that carries unmodified methionine
- they have the same anti-codon - rest of the tRNA is unique
66
what is an example of another start codon used in prokaryotes
*Mycobacterium tuberculosis* occasionally uses GUG
67
where does the 50S ribosomal subunit get placed in prokaryotic initiation
binds in a way such that tRNA-FMet is placed in the P site of the ribosome
68
what escorts the next tRNA into the A site of the ribosome
elongation factors (EFs)
69
what catalyses the formation of peptide bonds between amino acids
peptidyl transferase
70
when does the amino acid get released from its tRNA in P site
after the peptide bond between the amino acids in the P and A sites are formed
71
what happens to a free tRNA when it enters the E site
it gets released
72
what recognizes stop codons
a release factor
73
what is a nonsense codon
a stop codon (there is no corresponding tRNA)
74
how does initiation happen in eukaryotes
the 40S ribosome subunit recognizes and binds to the 5' methylated cap, it then scans along the mRNA unit it find the initiation of translation sequence
75
what amino acid does the initiator tRNA carry in eukaryotes
Met
76
define: polyribosome
complex of several ribosomes translating from the same mRNA
77
where does replication, transcription, and translation occur in prokaryotes
in the cytoplasm
78
where does replication, transcription, and translation occur in eukaryotes
- replication and transcription: in the nucleus - translation: in the cytoplasm
79
how long does mRNA live in prokaryotes vs eukaryotes
- prokaryotes: seconds - eukaryotes: minutes to hours
80
what is included in posttranslational processing
- enzyme removes methionine - cleavage of long polypeptides into smaller polypeptides - addition of chemical constituents to an amino acids (e.g. phosphorylation)
81
what are the four types of mutations on gene expression
- silent mutation - missense mutation - nonsense mutation - frameshift mutation
82
where are the two locations mutations can occur
1. within the coding sequence 2. outside the coding sequence

BIOL 239 (12 decks)

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