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stupid orgo > set 4 > Flashcards

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
Q

overlapping code

A

can have 1, or 2 base overlap

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26
Q

punctuated code

A

has spaces in between three bases

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27
Q

unpunctuated code

A

has no spaces in between each group of three bases

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28
Q

what is the makeup of genetic code

A

three nucleotides to make up a codon
no overlapping of codons
unpunctuated

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29
Q

sidney brenner

A

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

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30
Q

what did heinz frankel conrat study

A

single nucleotide substitutions

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31
Q

what did heinz frankel conrats study show

A

that single nucleotide changes caused by nitrous oxide led to single amino acid changes in the tabacco mosaic virus TMV coat protein

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32
Q

what does T4 rII encode

A

a gene for cell lysis

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33
Q

what does r in T2 rII stand for

A

rapid

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34
Q

what do the r* phage cells do

A

lyse cells slowly and form small plaques

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35
Q

what do r- phage cells do

A

lyse cells more rapidly so the phage can reinfect other cells more quickly therefore they form larger plaques

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36
Q

what was the proof for triplet genetic code come from

A

researchers CRICK BRENNER AND WATTS TOBIN created mutations by inserting of deleting single base pairs in the rII gene of bacteriophage T4

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37
Q

how many different ways are there to decode dna sequence

A

six you can start at the first, second, or third base pair and you can start from the top or bottom

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38
Q

frameshift mutations

A

mutations that alter the reading frame. they alter the sense of the translated message

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39
Q

what did crick, brenner, and watts tobin create

A

frameshifts

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40
Q

what was crick, brenner and tobins experimental results

A

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

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41
Q

codon

A

group of three consecutive nucleotides

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42
Q

how many different codons are there

A

64

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43
Q

what does the 64 codons and 20 amino acids lead to

A

redundancy

44
Q

start codon

A

AUG

45
Q

stop codons

A

UAG UAA UGA

46
Q

Who performed the experiment that laid the groundwork for deciphering the genetic code-POLY U EXPERIMENTS

A

marshall nirenberg and hans matthaei

47
Q

who pioneered the use of in vitro translation systems

A

marshall nirenberg and hans matthaei

48
Q

what is in vitro translation system

A

rna template
ribosomes and other necessary stuff
individual radio labelled amino acids
suitable reaction buffer (ph, salt conc)

49
Q

what is used to precipitate proteins in in vitro translation system

A

trichloroacetic acid TCA

50
Q

what did marshall nirenberg and hans matthaei first test in their in vitro systems

A

artifical mrna

51
Q

what did the poly u chain produce

A

phenylalanine Phe

52
Q

what was marshall nirenberg and hans matthaei experiment

A

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
Q

what does poly c create

A

polyproline/ proline

54
Q

poly a

A

polylysine

55
Q

what is soluble in trichloracetic acid

A

polylysine

56
Q

who tried a similar experiment to marshall and hans

A

watson and ochoa

57
Q

what did gobind khorana do

A

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
Q

what did alternating UC polypeptide product

A

serine and leucine

59
Q

who used trinucleotides as templates to resolve ambiguities in previous experiemtns

A

marshall niremberg and philip leder

60
Q

marshall niremberg and philip leder experiment

A

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
Q

valine

A

GUC

62
Q

who tested all 64 cosons and identified 61 plus the three stop codons

A

marshall niremberg and philip leder

63
Q

what are more than one codon that specifies an amino acid called

A

synonymous codons

64
Q

what has the message to be decoded

A

mrna

65
Q

what are the adaptor molecules

A

tRNA

66
Q

what forms catalysis of peptide bond formation

A

ribosomes

67
Q

what helps everything work

A

extra factors

68
Q

what did crick speculate

A

that a seperate enzyme is rewuired to join each adaper to its own amino acid

69
Q

who discovered enzyme adapers in protein fomratio

A

mahlon hoagland and paul zamecnik

70
Q

what was referred to as soluble rnas

A

tarnsfer rnas

71
Q

similarities and differences between transfer rnas

A

has similar structure and function and different nucleotide sequences

72
Q

is synthesis and processing of trna similar or differnt in bacteria and eukaryotes

A

different

73
Q

differences of processing tRNA in eukaryotes and bacteria

A

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
Q

what five RNA sections are in the E coli transcription

A 
16s rRNA
tRNA
tRNA
23S rRNA
5S rRNA
75
Q

what is the secondary structure of tRNAs

A

cloverleaf

76
Q

what is covalently bonded at the 3’ OH end of the tRNA

A

amino acid

77
Q

modified bases of tRNA

A

dihydrouracil D

pseudouracil Y

78
Q

what does the anticodon loop contain

A

anticodon triplet

79
Q

tertiary structure of tRNA

A

L shape

80
Q

what is the acceptor end of the tRNA

A

the 3’ OH which can covalently attach to amino acid

81
Q

what bond forms with ribosones and amino acid

A

peptide bond

82
Q

what does the anticodon loop do in tRNA

A

exposed to be available for base pairing with the matching mRNA codon

83
Q

what enzymes covalently attach amino acids to tRNA

A

aminoacyl tRNA synthetases aaRS

84
Q

charged tRNAs

A

tRNAs used during translation that carry amino acids

85
Q

uncharged tRNAs

A

tRNAs without amino acid

86
Q

what do aaRS enxymes recognize

A

the specific tRNA

the matching amino acid

87
Q

what is crucial for the integrity of the genetic code

A

correct charging of each tRNA

88
Q

what do aaRS enzymes do

A

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
Q

what does the active site of the aaRS enzyme accomidate

A

the amino acid to be added to the tRNA

ATP which provides the energy and leaving group for amino acid attatchment

90
Q

what does the specific amion acid with wich a tRNA supposed to be charged indicate

A

the three leter superscript

91
Q

what does the actual amino acid attatched to a tRNA indicate

A

the three leter pre-

92
Q

who determined that the gentic code derives its specificty from interaction between tRNA and mRNA NOT THE AMINO ACID

A

chaperville

93
Q

what was chapervilles experiment

A

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
Q

chapervilles result

A

the fidelity of aminoacyl-tRNA synthetases in recognizing each of the tRNAs and correctly charging them is extremely important

95
Q

how many tRNA molecules do many organisms product

A

30 to 40 which is less than 61 codons

96
Q

third base wobbles

A

the wobble hypothesis - relaxation of the strict complementary watson-crick base pairing rules at the third base of the codon

97
Q

isoaccepting tRNAs

A

a tRNA molecule with different anticodons to recognise the same amino acids

98
Q

wobble position

A

the third base whichi s not perfectly matched

99
Q

where is inosine found

A

in some cases its found at the wobble position of tRNA

100
Q

what can inosine pair with

A

U C A

101
Q

ribosomes

A

the machines that carry out protein synthesis

102
Q

what do ribosomes contain

A

ribonucleoprotein complexes which contain both ribosomal RNAs and proteins

103
Q

what direction do ribosomes translate mRNA

A

from the 5’ to the 3’

104
Q

ARE S=RIBOSOMES RIBOZYMES

A

yes

105
Q

what is the catalytic molecule in eukaryotes and prokaryotes that carries out protein synthesis

A

23S rRNA in bacteria

28S rRNA in eukaryotes

106
Q

how many subunits compose ribosomes

A

2- large and small

stupid orgo (7 decks)

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