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stupid orgo > 2200 set 3 > Flashcards

2200 set 3 Flashcards

1
Q

how can we ensure that the leading and lagging strands are getting made at the same ratee

A

each replisome complex carries out replication of the leading and lagging strand simultaneously. the two dna pol III core enzymes are each tethered to a larger complex by the tau protien

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2
Q

what are the three subunits of pol III complex

A

a (dnaE gene) has the polymerase activity
E (dnaQ) has 3’-5’ exonucease activity
theta (holE) stimulates the E subunits proofreading

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3
Q

how many protein subunits does the pol III holoenzyme contain

A

11 including the two pol III core polymerases

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4
Q

what are the tau proteins joined to

A

a protein complex called the clamp loader

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5
Q

how many protein subunits form the sliding clamp

A

two or three

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6
Q

what keeps pol III core attatched to the dna strands, preventing dissociation and enhancing the rate of productive synthesis

A

the sliding clamp

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7
Q

what ensures greater processivity of pol III

A

the sliding clamp

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8
Q

how many subunits form the sliding clamp in bacteria

A

two identical subunits (ring has a top half and a bottom half)

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9
Q

how wide is the central hole in the sliding clamp

A

35 A

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10
Q

how many subunits form the sliding clamp in eukaryotes called PCNA

A

Three identical subunits

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11
Q

what does PCNA stand for

A

proliferating cell nucelar antigen

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12
Q

what helps the sliding clamp get onto the dna

A

the clamp loader complex does this by attaching to the sliding clamp and temporarily opening the subunits so that dna can be put in the subunit

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13
Q

what is the clamp loader complex similar to

A

dna c

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14
Q

what model represents dna replication

A

the trombone model of dna replication

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15
Q

what is the problem of chromatin

A

in eukaryotic cells, the presence of nucleosomes presents a barrier to replisomes and dna replication and you would also need to double the amount of nucelosomes and need to make new histones

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16
Q

how is the problem of chromatin solved

A

as the replication fork passes, old nucleosomes dissasmble into H2A-H2B dimers and H3-H4tetramers and then the old and new tetramers associate with the dimers that may be a mix of old and new

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17
Q

how many real errors are present in replication

A

one in every billion nuceloties in e coli

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18
Q

how many mistakes does dna polymerases make

A

one per every hundred thousand nucleotides

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19
Q

what is the proofreading repair ability of dna polymerase enzymes due to

A

the 3’-5’ exonuclease activity

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20
Q

what has the 3’-5’ exonuclease activity

A 
pol I (the third out of three activities)
pol III (E subunit)
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21
Q

what was the original idea that caused errors in dna

A

because a base transiently adopted it tauomer conformation and this led to pairing with the “wrong” partner base

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22
Q

what actually causes erros in dna replication

A
  • mispairing between different (non tautomeric) chemical forms of bases (with extra proton, A with G)1
  • normal bases that bond inappropriately because of a slight shift in position of the nucleotide in space
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23
Q

what are mispairings called

A

wobble

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24
Q

why does wobble occur

A

because dna dobule helix is flexible and able to accomidate slightly misshaped pairings

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25
Q

how many rounds of synthesis does it take ot generate a heritable mutation due to wobble

A

it takes a second round of synthesis

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26
Q

where do the mi-shaped/ wobble pairs arise on which strand

A

could occur on either the parental or offspring strand

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27
Q

transition mutationos

A

keep chemical nature the same (AT-GC)

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28
Q

transversion mutations

A

change the chemical nature of the baes (AT-CG)

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29
Q

what are the steps to proofreading in dna polymerase

A
  • newly incorporated mismatched nucelotide destabilizes the base pair at the growing end of the strand
  • the mimatched end of the just synthesized dna strand is displaced into the proofreading site of the enzyme(3’-5’ exonuclease)
  • several nucleotides att eh growing end are removed by the exonuclease
  • the 3’ end returns to the polymerae active site and incorporation of new nucleotides resumes
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30
Q

what untangles and seperates the two daughter dna strands from each other

A

special topoisomerases

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31
Q

the end problem

A

the challenges that linear/human chromosomes present when they are being copied because without a solution, the chromosomes will continue to get shorter

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32
Q

what are the necesarry steps to solve the end problem in dna

A

use permuted or concatenated end sequences or temporary circulazation like found in some bacteriophages.
use special end sequences and a special enzyme (tomerase)

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33
Q

what are telomeres

A

repetitive sequences at the end of chromosomes that consist of hundreds of 6bp repeats, 2 to 20 kb in length overall

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34
Q

what is the telomere repeat in humans

A

TTAGGG

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35
Q

what is the telomere repeat in tetrahymena

A

TTGGGG

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36
Q

what synthesizes telomeres

A

telomerase

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37
Q

what is telomerase made of

A

a protein part and a RNA part

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38
Q

what does the rna part of telomerase do

A

acts as a template for copying to synthesize the DNA telomere sequences

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39
Q

what is an example of reverse transcriptase

A

telomerase- RNA directed DNA polymerase

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40
Q

who discoverdd that chromosomes are protected by telomeres and the enzyme telomerase

A

elizabeth blackburn
carol greider
jack szotak

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41
Q

what happens after the dna strand is sufficiently elongated by telomerase

A

dna polymerase can complete the lagging strand against the dna made by telomerase

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42
Q

what does TERT stand for

A

telomerase reverse transcriptase

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43
Q

what cuases mice to have developmental defects

A

mice that are homozygous for loss of function mutations of the TERT gene have developmental defects

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44
Q

when are the TERT defects observed in mice

A

fourth and fifth generations due to loss of telomere length with each generation. by the 4th or 5th generations, shortening is critial and apoptosis is induced

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45
Q

what is apoptosis

A

programmed cell death

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46
Q

why is telomere length important

A

its important for chromosome stability, cell longevity and reproductive sucess

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47
Q

where is telomerase active

A

in germ line cells and some stem cells in eukaryotes

48
Q

do differentiated somatic cells and cells in cutlure have telomerase

A

no and they have limited life spans

49
Q

what does reactivation of telomerase in somatic cells lead to

A

aging cells that continue to proliferate which is a feature of many types of cancer

50
Q

what is one of the most common mutations in cancers of all types

A

TERT reactivation

51
Q

dyskeratosis congentia

A

disorder associated with a loss of function of the DKC1 gene that encodes a protein needed for normal telomerase function

52
Q

symptoms of dyskeratosis congentia

A

skin and nail abnormalities, loss of vision and hearing, and abnormalities of blood cell formation

53
Q

what are the two critical differences between dna and rna nuceloties

A

thymine is replaced by uracil

the sugar ribose is used rather than deoxyribose wich has a 2’OH

54
Q

how similar are the sugar phosphate backbones in dna and rna

A

the similar sugars lead to formation of nearly identical backbones in the molecules

55
Q

how different are the sugar phosphate backbones in dna and rna

A

when rna forms a double stranded helix, it will be in the A form whereas dna is in the B form

56
Q

what causes inherent stability in rna at ph>7

A

the aditional OH group

57
Q

transcription

A

the process of copying a region of DNA into a molecule of RNA

58
Q

functional rnas

A

do not encode proteins but instead the rnas themseves preform functional roles in the cells

59
Q

transfer rna (tRNA)

A

are encoded in dozens of forms and are covalently joined with an amino acid which they transport into the ribosome for inclusion into a growing protein chain

60
Q

ribosomal rna (rRNA)

A

folds and assembles along with numerous proteins to form ribosomes

61
Q

list the functional rnas

A 
t-RNA-transfer RNA
r-RNA-ribosomal RNA
snRNA-small nuclear RNA
miRNA-micro RNAs
siRNA-small interfering RNAs
ncRNA-non-coding RNA
crRNA-CRISPR RNA
62
Q

small nucelar rna

A

of various types is found in the nucleus of eukarytoes and plays a role in mRNA processing and splicing

63
Q

micro rna and small interfering rna

A

are active in plant and animal cells and are involved in posttranscriptional regularion of mrna

64
Q

ribozymes

A

rnas in eukaryotic cells which have catalytic activity

65
Q

CRISPR RNA

A

found in bacterial cells and plays a role in defending the host from attack by bacteriophage

66
Q

mRNA

A

is produced by protein producing genes and is the short lived intermediaty between dna and protein

67
Q

which is the only type of rna that undergoes translation

A

mRNA

68
Q

what is transcription of mRNA usually followed by

A

post transcriptional processing

69
Q

who speculated that rna might play a role in using dna to direct protein synthesis

A

francis crick

70
Q

who used the pulse chase technique

A

Elliot Volkin and Lazarus Astrachan

71
Q

what is the pulse chase technique

A

-expose newly infected cells to a brief pulse of radioactively labelled phosphate and then followed with a chase of nonradiactive phosphate

72
Q

what was the point of the pulse chase experiment

A

to identify what molecules are synthesized immediately after bacteriophage infection

73
Q

what did infection stimulating a bust of transcriptional activity which quickly dissipate during the chase indicated in the pulse chase experiment

A

a rapid breakdown of the rna molecules

74
Q

what was the conclusion of the pulse chase experiment

A

that RNA synthesis was necessary for formation of new phage proteins

75
Q

what did Sydney Brenner and Francois Jacob and Matt Meselson find

A

that E coli infected with bacteriophage T2 used existing bacterial ribosomes and a “messenger” molecule to encode phage proteins. the rna that directed the synthesis of phage proteins was unstable and degraded quickly and was called messenger rna

76
Q

who came up with the central dogma of molecular biology

A

francis crick

77
Q

how does transcription differ from replication

A
  • enzymes are different (DNA dependant RNA polymerases)
  • small region of dna copied at a time (dna unwinding is relatively minimal)
  • some regions are copied at high levels and some are low and this can be changed in reponse to enviromental changes or by regulators
78
Q

what is the main level of control in rna synthesis

A

transcriptional level

79
Q

transcriptional level

A

on or off

lots or little

80
Q

processing level

A

rna can be processed in several ways to produce several products (alternative splicing)

81
Q

rma stability level

A

rnas can be specifically targeted and eliminated (degration, getting rid of rna)

82
Q

what affects how much RNA is produced

A

transcription level
processing level
rna stability level

83
Q

what affects how much mRNA is produced and therefore how much PROTEIN is produced

A

transcription level
processing level
rna stability level
translational level control

84
Q

translational level control

A

the rate of translation into protein can be altered. rnas can be stored for later use

85
Q

what is the overall amount of any gene produced an effect of

A

the net effect of all of the steps that affect how much a protein is product

86
Q

what is the difference between rna and dna

A

rna dosent need a primer and when the first two nucleotides are joined, the 5’ nucleotide keeps it triphosphate in place

87
Q

does rna polymerase recruit nucleotides

A

no the process is one of random trial

88
Q

process of rna polymerase adding nucelotides

A

first the correct ntp is positioned in the active site of the enzyme and then a nucleophilic displacement reaction leadas to formation of the phosphodiester bond

89
Q

what is the first base of a new RNA molecule typicalle

A

a purine

90
Q

coding region of the gene

A

the portion that contains information needed to synthesize the function (RNA or protein) product

91
Q

where are signals that regular the expression of rna or product found

A

ourside the coding region

92
Q

what does a strong connection of rna polymerase on dna mean for the amount of product formed

A

lots of product

93
Q

where does rna transcriptase start streamwise of the coding region

A

starts upstream 5’ and ends downstream 3’ of the coding region

94
Q

what is the first nucleotide in the RNA transcript

A

+1 nucelotide

95
Q

the promoter

A

the set of dna sequences that controls the acess of RNA polymerases to the gene and is immediately upstream 5’ of the transcription startpoint

96
Q

the terminal region

A

regulates cessation of transcription and is downstream 3’ to the coding region

97
Q

sense strand

A

the dna strand not being read= coding streand

98
Q

antisense strand

A

the dna strand being read= template strand

99
Q

what sequences does the rna strand have

A

the same as the coding strand

100
Q

how many bp are unwound in DNA in the transcription bubble

A

14

101
Q

how many rna nucleotides remain paired with dna inside the transcription bubble

A

8

102
Q

operons

A

groups or clusters of genes in bacteria. often consist of genes relating to a simiilar metabolic function

103
Q

how is the expression of genes in operons regulated

A

its regulated collectively

104
Q

how many TYPES of RNA polymerases are there in bacteria

A

one

105
Q

how many variations of rna polymerase are there in bacteria

A

three types

106
Q

what is bacterial rna polymerase composed of

A

a core enxyme that normally consists of five subunits

107
Q

what can the core enzyme in rna polymerase do

A

it can make rna byt it cant do that at specific places meaning it cant recognize promoters

108
Q

what is the sixth subunit of rna polymerase

A

it confers specifically on rna polymerase. SIGMA subunit.

109
Q

what is the core enzyme of rna polymerase composed of

A

two identical a subunits
two non identical beta subunits
a w subunit

110
Q

what is the stoichiometry of the core enzyme of rna polymerase

A

a2BB’w

111
Q

what is the stoichiometry of the holoenzyme rna polymerase

A

a2BB’wsigma

112
Q

what can bind to the promoter and initiate specific transcription

A

the holoenzyme rna polymerase

113
Q

what is the sigma-70-subunit

A

one polypeptide
four distinct folded domains
each domain is positioned in a diffrent place in the holoenzyme
the sixth subunti of the holoenzyme rna polymerase

114
Q

how many different sigma subunits can E coli produce

A

7 different subunits

115
Q

what is the principle subunit in e coli

A

sigma 70

116
Q

what three sigma subunits are present in E coli under normal growth conditions

A

70, 54,28

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