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set 4 Flashcards

1
Q

what defines where rna polymerase binds in bacteria

A

the promoter

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2
Q

how can the promote be identified

A

by its similarity with its consensus sequence

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3
Q

whree do other transcription regulatory proteins often bind

A

near the promoter

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4
Q

where are the major bacterial promoters consensus sequences located

A

10 and 35 base pairs upstream of the transcription startpoint

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5
Q

what is the spacing between the promoter transcription sequences

A

17 +/- 1

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6
Q

UTR

A

Untrasnlated region

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7
Q

what is the -10 region of the promoter sonsensus sequence

A

5’TATAAT3’

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8
Q

what is the -35 region of the promoter consensus sequence

A

5’TTGACA3’

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9
Q

where were the bacterial sequences lined up to discover the consensus sequences of the bacterial promoters

A

at the transcription startpoint

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10
Q

what are the four steps in bacterial transcription

A
  1. promoter recognition
  2. transcription initiation
  3. chain elongation
  4. chain termination
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11
Q

how does RNA polymerase initiate transcription

A
  1. holoenzyme loosely attatched to dna find the promoter sequence and binds tightly to form a closed promoter sequence with the main interaction being between the polymerase and the -35 region
  2. the holoenzyme unwinds 14 bp of dna around the -10 position to form the open promoter complex with the primary interaction being between the polymerase and the -10 region
  3. the holoenzyme initiates rna synthesis at the +1 site
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12
Q

where does the holoenzyme initiate rna synthesis

A

at the +1 site

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13
Q

does the position of the RNA polymerase holoenzyme at the promoter change very much in foinf from the closed complex to the open complex

A

no

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14
Q

when does the sigma subunit dissociate from the holoenzyme

A

shortly after transcription (until the first 8-10 RNA nucleotides have been joined)

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15
Q

how is the transcription bubble affected during transcription

A

it is unwound ahead of the enzyme to maintain 14 bp and the double helix reforms behind the rna polymerase

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16
Q

when can a second round of transcription begin after the first round iniates

A

shortly after

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17
Q

intrinsic termination

A

mechanism that depends only on the presence of repeat sequences in the rna transcript to form a secondary structure that is needed for termination

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18
Q

rho dependent termination

A

requires a different termination sequence and a rho protein

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19
Q

what type of termination does most bacterial terminal undergo

A

intrinstic termination

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20
Q

transcription

A

a seqence of bases in one nucleic acid is used to generate a sequence of bases in another nucelic acid based on specific base base pairing not much different from dna repliaction

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21
Q

translation

A

a sequence of bases in a nucelic acid is used ot generate a sequence of amino acids in a protein
requires the conversion of a base sequence to an amino acid sequence

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22
Q

what is a fundamental stumbling block in the discovery of protein synthesis

A

there were 20 amino acids in proteins and only 4 baes found in dna

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23
Q

how many bases does it take to provide sufficient combinations that there is at least one for each amino acid

A

3

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24
Q

what are the possibilities for arranging. grouping three bases in an rna chain

A

overlapping
punctuated
unpunctuated

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25
overlapping code
can have 1, or 2 base overlap
26
punctuated code
has spaces in between three bases
27
unpunctuated code
has no spaces in between each group of three bases
28
what is the makeup of genetic code
three nucleotides to make up a codon no overlapping of codons unpunctuated
29
sidney brenner
identidied the amino acid following lysine in a large number of protiens... found 17 different amino acids reasoning that overlapping code would have permitted no more than four so therefore an overlapping code isnt possible bc it would have restricted evolutionary flexibility and was unsuported by obersvation
30
what did heinz frankel conrat study
single nucleotide substitutions
31
what did heinz frankel conrats study show
that single nucleotide changes caused by nitrous oxide led to single amino acid changes in the tabacco mosaic virus TMV coat protein
32
what does T4 rII encode
a gene for cell lysis
33
what does r in T2 rII stand for
rapid
34
what do the r* phage cells do
lyse cells slowly and form small plaques
35
what do r- phage cells do
lyse cells more rapidly so the phage can reinfect other cells more quickly therefore they form larger plaques
36
what was the proof for triplet genetic code come from
researchers CRICK BRENNER AND WATTS TOBIN created mutations by inserting of deleting single base pairs in the rII gene of bacteriophage T4
37
how many different ways are there to decode dna sequence
six you can start at the first, second, or third base pair and you can start from the top or bottom
38
frameshift mutations
mutations that alter the reading frame. they alter the sense of the translated message
39
what did crick, brenner, and watts tobin create
frameshifts
40
what was crick, brenner and tobins experimental results
they saw the single nucleotide additions into or deletions out of the rII gene of T4 bacteriophage cause frameshift mutations reversion mutation restored the reading frame crick and colleagues also concluded that the genetic code is read continuously with no gaps or pauses between the codons
41
codon
group of three consecutive nucleotides
42
how many different codons are there
64
43
what does the 64 codons and 20 amino acids lead to
redundancy
44
start codon
AUG
45
stop codons
UAG UAA UGA
46
Who performed the experiment that laid the groundwork for deciphering the genetic code-POLY U EXPERIMENTS
marshall nirenberg and hans matthaei
47
who pioneered the use of in vitro translation systems
marshall nirenberg and hans matthaei
48
what is in vitro translation system
rna template ribosomes and other necessary stuff individual radio labelled amino acids suitable reaction buffer (ph, salt conc)
49
what is used to precipitate proteins in in vitro translation system
trichloroacetic acid TCA
50
what did marshall nirenberg and hans matthaei first test in their in vitro systems
artifical mrna
51
what did the poly u chain produce
phenylalanine Phe
52
what was marshall nirenberg and hans matthaei experiment
combine synthetic rna made of only uracil with cell sap derived from e coli and added it to each of 20 test tubes the chain of repeating bases forced a protein chain to be made of one repeating amino acid Phe
53
what does poly c create
polyproline/ proline
54
poly a
polylysine
55
what is soluble in trichloracetic acid
polylysine
56
who tried a similar experiment to marshall and hans
watson and ochoa
57
what did gobind khorana do
expanded the range of template rnas by synthesizing mrna molecules with repeating di, tri and tetranucleotides and used them for in vitro transltaion reactions
58
what did alternating UC polypeptide product
serine and leucine
59
who used trinucleotides as templates to resolve ambiguities in previous experiemtns
marshall niremberg and philip leder
60
marshall niremberg and philip leder experiment
added each mini rna trinucleotide into in vitro translation systems and each system contained all 20 amino acids but only one of them was labelled with C14 at a time isolated the ribosome trna-mrna complexes and determined which mini rna trinucleotide was associated with which labelled amino acid
61
valine
GUC
62
who tested all 64 cosons and identified 61 plus the three stop codons
marshall niremberg and philip leder
63
what are more than one codon that specifies an amino acid called
synonymous codons
64
what has the message to be decoded
mrna
65
what are the adaptor molecules
tRNA
66
what forms catalysis of peptide bond formation
ribosomes
67
what helps everything work
extra factors
68
what did crick speculate
that a seperate enzyme is rewuired to join each adaper to its own amino acid
69
who discovered enzyme adapers in protein fomratio
mahlon hoagland and paul zamecnik
70
what was referred to as soluble rnas
tarnsfer rnas
71
similarities and differences between transfer rnas
has similar structure and function and different nucleotide sequences
72
is synthesis and processing of trna similar or differnt in bacteria and eukaryotes
different
73
differences of processing tRNA in eukaryotes and bacteria
eukatyoes individually transcribe each tRNA gene bacteria tRNAs are cotranscribed with rRNAs whle others are co transcribed as part of other large pre existing tRNA transcripts in all cases the pre tRNA must be processed into individual tRNA molecules
74
what five RNA sections are in the E coli transcription
``` 16s rRNA tRNA tRNA 23S rRNA 5S rRNA ```
75
what is the secondary structure of tRNAs
cloverleaf
76
what is covalently bonded at the 3' OH end of the tRNA
amino acid
77
modified bases of tRNA
dihydrouracil D | pseudouracil Y
78
what does the anticodon loop contain
anticodon triplet
79
tertiary structure of tRNA
L shape
80
what is the acceptor end of the tRNA
the 3' OH which can covalently attach to amino acid
81
what bond forms with ribosones and amino acid
peptide bond
82
what does the anticodon loop do in tRNA
exposed to be available for base pairing with the matching mRNA codon
83
what enzymes covalently attach amino acids to tRNA
aminoacyl tRNA synthetases aaRS
84
charged tRNAs
tRNAs used during translation that carry amino acids
85
uncharged tRNAs
tRNAs without amino acid
86
what do aaRS enxymes recognize
the specific tRNA | the matching amino acid
87
what is crucial for the integrity of the genetic code
correct charging of each tRNA
88
what do aaRS enzymes do
contact several points on the tRNA in the recognition process. the acceptor stem of the correct tRNA fits into the active site of the enzyme
89
what does the active site of the aaRS enzyme accomidate
the amino acid to be added to the tRNA | ATP which provides the energy and leaving group for amino acid attatchment
90
what does the specific amion acid with wich a tRNA supposed to be charged indicate
the three leter superscript
91
what does the actual amino acid attatched to a tRNA indicate
the three leter pre-
92
who determined that the gentic code derives its specificty from interaction between tRNA and mRNA NOT THE AMINO ACID
chaperville
93
what was chapervilles experiment
prepared normal cys-tRNAcys and then treated it with raney nickel which converted the covalently attached cystine to alanine to produce ala-tRNAala this was used in an in vitro tralslation reaction resulting in polypeptide containing ala instead of cys
94
chapervilles result
the fidelity of aminoacyl-tRNA synthetases in recognizing each of the tRNAs and correctly charging them is extremely important
95
how many tRNA molecules do many organisms product
30 to 40 which is less than 61 codons
96
third base wobbles
the wobble hypothesis - relaxation of the strict complementary watson-crick base pairing rules at the third base of the codon
97
isoaccepting tRNAs
a tRNA molecule with different anticodons to recognise the same amino acids
98
wobble position
the third base whichi s not perfectly matched
99
where is inosine found
in some cases its found at the wobble position of tRNA
100
what can inosine pair with
U C A
101
ribosomes
the machines that carry out protein synthesis
102
what do ribosomes contain
ribonucleoprotein complexes which contain both ribosomal RNAs and proteins
103
what direction do ribosomes translate mRNA
from the 5' to the 3'
104
ARE S=RIBOSOMES RIBOZYMES
yes
105
what is the catalytic molecule in eukaryotes and prokaryotes that carries out protein synthesis
23S rRNA in bacteria | 28S rRNA in eukaryotes
106
how many subunits compose ribosomes
2- large and small

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