2200 set 3 Flashcards
(116 cards)
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
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
3
Q
how many protein subunits does the pol III holoenzyme contain
A
11 including the two pol III core polymerases
4
Q
what are the tau proteins joined to
A
a protein complex called the clamp loader
5
Q
how many protein subunits form the sliding clamp
A
two or three
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
7
Q
what ensures greater processivity of pol III
A
the sliding clamp
8
Q
how many subunits form the sliding clamp in bacteria
A
two identical subunits (ring has a top half and a bottom half)
9
Q
how wide is the central hole in the sliding clamp
A
35 A
10
Q
how many subunits form the sliding clamp in eukaryotes called PCNA
A
Three identical subunits
11
Q
what does PCNA stand for
A
proliferating cell nucelar antigen
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
13
Q
what is the clamp loader complex similar to
A
dna c
14
Q
what model represents dna replication
A
the trombone model of dna replication
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
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
17
Q
how many real errors are present in replication
A
one in every billion nuceloties in e coli
18
Q
how many mistakes does dna polymerases make
A
one per every hundred thousand nucleotides
19
Q
what is the proofreading repair ability of dna polymerase enzymes due to
A
the 3’-5’ exonuclease activity
20
Q
what has the 3’-5’ exonuclease activity
A
pol I (the third out of three activities) pol III (E subunit)
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
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
23
Q
what are mispairings called
A
wobble
24
Q
why does wobble occur
A
because dna dobule helix is flexible and able to accomidate slightly misshaped pairings
25
how many rounds of synthesis does it take ot generate a heritable mutation due to wobble
it takes a second round of synthesis
26
where do the mi-shaped/ wobble pairs arise on which strand
could occur on either the parental or offspring strand
27
transition mutationos
keep chemical nature the same (AT-GC)
28
transversion mutations
change the chemical nature of the baes (AT-CG)
29
what are the steps to proofreading in dna polymerase
- 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
30
what untangles and seperates the two daughter dna strands from each other
special topoisomerases
31
the end problem
the challenges that linear/human chromosomes present when they are being copied because without a solution, the chromosomes will continue to get shorter
32
what are the necesarry steps to solve the end problem in dna
use permuted or concatenated end sequences or temporary circulazation like found in some bacteriophages.
use special end sequences and a special enzyme (tomerase)
33
what are telomeres
repetitive sequences at the end of chromosomes that consist of hundreds of 6bp repeats, 2 to 20 kb in length overall
34
what is the telomere repeat in humans
TTAGGG
35
what is the telomere repeat in tetrahymena
TTGGGG
36
what synthesizes telomeres
telomerase
37
what is telomerase made of
a protein part and a RNA part
38
what does the rna part of telomerase do
acts as a template for copying to synthesize the DNA telomere sequences
39
what is an example of reverse transcriptase
telomerase- RNA directed DNA polymerase
40
who discoverdd that chromosomes are protected by telomeres and the enzyme telomerase
elizabeth blackburn
carol greider
jack szotak
41
what happens after the dna strand is sufficiently elongated by telomerase
dna polymerase can complete the lagging strand against the dna made by telomerase
42
what does TERT stand for
telomerase reverse transcriptase
43
what cuases mice to have developmental defects
mice that are homozygous for loss of function mutations of the TERT gene have developmental defects
44
when are the TERT defects observed in mice
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
45
what is apoptosis
programmed cell death
46
why is telomere length important
its important for chromosome stability, cell longevity and reproductive sucess
47
where is telomerase active
in germ line cells and some stem cells in eukaryotes
48
do differentiated somatic cells and cells in cutlure have telomerase
no and they have limited life spans
49
what does reactivation of telomerase in somatic cells lead to
aging cells that continue to proliferate which is a feature of many types of cancer
50
what is one of the most common mutations in cancers of all types
TERT reactivation
51
dyskeratosis congentia
disorder associated with a loss of function of the DKC1 gene that encodes a protein needed for normal telomerase function
52
symptoms of dyskeratosis congentia
skin and nail abnormalities, loss of vision and hearing, and abnormalities of blood cell formation
53
what are the two critical differences between dna and rna nuceloties
thymine is replaced by uracil
| the sugar ribose is used rather than deoxyribose wich has a 2'OH
54
how similar are the sugar phosphate backbones in dna and rna
the similar sugars lead to formation of nearly identical backbones in the molecules
55
how different are the sugar phosphate backbones in dna and rna
when rna forms a double stranded helix, it will be in the A form whereas dna is in the B form
56
what causes inherent stability in rna at ph>7
the aditional OH group
57
transcription
the process of copying a region of DNA into a molecule of RNA
58
functional rnas
do not encode proteins but instead the rnas themseves preform functional roles in the cells
59
transfer rna (tRNA)
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
ribosomal rna (rRNA)
folds and assembles along with numerous proteins to form ribosomes
61
list the functional rnas
```
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
small nucelar rna
of various types is found in the nucleus of eukarytoes and plays a role in mRNA processing and splicing
63
micro rna and small interfering rna
are active in plant and animal cells and are involved in posttranscriptional regularion of mrna
64
ribozymes
rnas in eukaryotic cells which have catalytic activity
65
CRISPR RNA
found in bacterial cells and plays a role in defending the host from attack by bacteriophage
66
mRNA
is produced by protein producing genes and is the short lived intermediaty between dna and protein
67
which is the only type of rna that undergoes translation
mRNA
68
what is transcription of mRNA usually followed by
post transcriptional processing
69
who speculated that rna might play a role in using dna to direct protein synthesis
francis crick
70
who used the pulse chase technique
Elliot Volkin and Lazarus Astrachan
71
what is the pulse chase technique
-expose newly infected cells to a brief pulse of radioactively labelled phosphate and then followed with a chase of nonradiactive phosphate
72
what was the point of the pulse chase experiment
to identify what molecules are synthesized immediately after bacteriophage infection
73
what did infection stimulating a bust of transcriptional activity which quickly dissipate during the chase indicated in the pulse chase experiment
a rapid breakdown of the rna molecules
74
what was the conclusion of the pulse chase experiment
that RNA synthesis was necessary for formation of new phage proteins
75
what did Sydney Brenner and Francois Jacob and Matt Meselson find
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
who came up with the central dogma of molecular biology
francis crick
77
how does transcription differ from replication
- 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
what is the main level of control in rna synthesis
transcriptional level
79
transcriptional level
on or off
| lots or little
80
processing level
rna can be processed in several ways to produce several products (alternative splicing)
81
rma stability level
rnas can be specifically targeted and eliminated (degration, getting rid of rna)
82
what affects how much RNA is produced
transcription level
processing level
rna stability level
83
what affects how much mRNA is produced and therefore how much PROTEIN is produced
transcription level
processing level
rna stability level
translational level control
84
translational level control
the rate of translation into protein can be altered. rnas can be stored for later use
85
what is the overall amount of any gene produced an effect of
the net effect of all of the steps that affect how much a protein is product
86
what is the difference between rna and dna
rna dosent need a primer and when the first two nucleotides are joined, the 5' nucleotide keeps it triphosphate in place
87
does rna polymerase recruit nucleotides
no the process is one of random trial
88
process of rna polymerase adding nucelotides
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
what is the first base of a new RNA molecule typicalle
a purine
90
coding region of the gene
the portion that contains information needed to synthesize the function (RNA or protein) product
91
where are signals that regular the expression of rna or product found
ourside the coding region
92
what does a strong connection of rna polymerase on dna mean for the amount of product formed
lots of product
93
where does rna transcriptase start streamwise of the coding region
starts upstream 5' and ends downstream 3' of the coding region
94
what is the first nucleotide in the RNA transcript
+1 nucelotide
95
the promoter
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
the terminal region
regulates cessation of transcription and is downstream 3' to the coding region
97
sense strand
the dna strand not being read= coding streand
98
antisense strand
the dna strand being read= template strand
99
what sequences does the rna strand have
the same as the coding strand
100
how many bp are unwound in DNA in the transcription bubble
14
101
how many rna nucleotides remain paired with dna inside the transcription bubble
8
102
operons
groups or clusters of genes in bacteria. often consist of genes relating to a simiilar metabolic function
103
how is the expression of genes in operons regulated
its regulated collectively
104
how many TYPES of RNA polymerases are there in bacteria
one
105
how many variations of rna polymerase are there in bacteria
three types
106
what is bacterial rna polymerase composed of
a core enxyme that normally consists of five subunits
107
what can the core enzyme in rna polymerase do
it can make rna byt it cant do that at specific places meaning it cant recognize promoters
108
what is the sixth subunit of rna polymerase
it confers specifically on rna polymerase. SIGMA subunit.
109
what is the core enzyme of rna polymerase composed of
two identical a subunits
two non identical beta subunits
a w subunit
110
what is the stoichiometry of the core enzyme of rna polymerase
a2BB'w
111
what is the stoichiometry of the holoenzyme rna polymerase
a2BB'wsigma
112
what can bind to the promoter and initiate specific transcription
the holoenzyme rna polymerase
113
what is the sigma-70-subunit
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
how many different sigma subunits can E coli produce
7 different subunits
115
what is the principle subunit in e coli
sigma 70
116
what three sigma subunits are present in E coli under normal growth conditions
70, 54,28
