molbio FINALLLL Flashcards
1
Q
Eukaryotic and bacterial genes are interrupted by non coding DNA (t/f)
A
false, only eukaryotic
2
Q
RNA poly CANNOT distinguish between coding and non coding regions, it will transcribe everything (t/f)
A
true
3
Q
Purpose of splicing
A
cell must remove non coding RNA from the primary transcript
4
Q
Eukaryotes add ______ and ______ to the ends of a transcript
A
cap to 5’
poly A tail to 3’
5
Q
splicing and capping occur in….
A
the nucleus, before mRNA moves to cystoplasm
6
Q
post transcript process
A
- capping
- splicing
- poly adenylation
7
Q
introns occur in…
A
mRNA, tRNA, rRNA
introns are surrounded by EXONs
8
Q
how many introns do mRNA contain, vs tRNA
A
0-362
0-1
9
Q
exons contain the sequence that will appear in a mature RNA product (t/f)
A
true
10
Q
introns are present in ____ but not _____
A
genes, mature RNA
11
Q
RNA splicing definition
A
cutting introns out of immature RNA, and stitching exons together
^^^simulstaneous
12
Q
primary transcript has both ____ and ____
A
introns, exons
13
Q
stages of mRNA synthesis/splicing
A
stage 1: synthesis of primary transcript
-an mRNA precursor, with introns copied from the gene
-the precursor is part of (hnRNAs)
stage 2: mRNA maturation
-splicing
14
Q
splicing must be _____ , it cannot disrupt the _____
A
precise, codons
15
Q
splicing signals in nuclear mRNA precursors are _____
A
uniform.
first 2 bases of introns will be GU
last 2 bases will be AG
16
Q
5’ and 3’ splice sites have _________ , that extend beyond ______
A
consensus sequences
GU and AG motifs
17
Q
whole ___________ - sequences are important to correct splicing
A
consensus
18
Q
mutated consensus seq can lead to
A
abnormal splicing
19
Q
splicing of nuclear mRNA precursors
A
the TWO STEP MODEL
- 2’ OH’ group of adenosine nucleotide in the middle of the intron will attack the phosphodiester bond in between the 1st exon, and G beginning of intron.
-forms loop lariat, and separates the first exon from intron.
-3’ OH group left at the end of the 1st exon will attack the phosphodiester bond linking the intron to the 2nd exon, forming the exon-exon phosphodiester bond, and releasing intron in lariat form at the same time
20
Q
spliceosomes are created inside the
A
nucleus
21
Q
splicing takes place on the
A
spliceosome
22
Q
spliceosomes contain
A
pre mRNA
snRNPs
protein splicing factors
^^^these recognize key splicing signals and direct splicing.
23
Q
snRNPs stands for ____ and contain ____
A
small nuclear ribonuclear proteins
rRNA+proteins
24
Q
The five snRNAs
A
U1, 2, 4, 5, 6
25
All 5 snRNAs join the ______ to play crucial role in splicing
spliceosome
26
spliceosome components and cycle
-proteins and RNA
-assembly, splicing activity, disassembly
27
by controlling assembly of ____, a cell can regulate quality/quantity of splicing, to regulate ____
spliceosome
gene expression
28
spliceosome cycle: assembly
-starts by binding U1 to splicing substrate, forming commitment complex- used to splice out the intron
-U2 joins complex because of ATP, and is followed by the others
-U6 leaves U4, and dislocates U1 at the 5', this step depends on ATP, and will activate the spliceosome, allowing U1 and U4 to be released.
29
alternative splicing
- will have profound effects on genes protein products
- can make a difference between secreted/membrane bound protein, and activity/inactivity
30
alternative splicing of ______ will mean many different products.
the same pre mRNA
31
many genes have ______ splicing patterns, some having thousands
more than 2
32
alternative splicing occurs in ...
less than 50 % of human genes
33
self splicing RNAs occur ....
without a spliceosome- it splices naturally
34
example of self splicing RNA
tetrahymena 26s rRNA gene has an intron, and self splices
35
Group of self splicing RNAs
group 1 introns, some group 2 introns
36
group 1 inrons
self splicing:
reaction starts by attack by guanine nucleotide on 5'
-this will add G to the 5' end of intron, and release first exon
now the first exon will attack the 3'
-this will ligate 2 exons together, and release the linear intron
-the intron will cycle twice, losing nucleotides each time, then linearize a last time.
37
group 2 introns
self splicing:
these self splice by using A-branched lariat intermediate, like a spliceosome lariat.
-this occurs w/ free guanosine attacking OH group
-secondary structures of the splicing complexes with sliceosome systems and group 2 introns are very similar
38
mRNAs will ____ at 5' end and _______ at 3' end
cap
polyadenylate
39
capping
a significant amount of methylation clustered at 5' end of mRNA
40
cap studies used mRNA because
easier to purify
41
the B-phosphate of a nucleoside triphosphate....
remains only in the 1st nucleotide in an RNA
-linkage is a triphosphate
42
what is the 5' cap made of
modified guanine: 7 methylguanosine
43
reovirus cap structure
the modified guanine (7methylguanosine) gives 1 positive charge
triphosphate link gives 3 negative charges
phosphodiester bond gives 1 negative charge
terminal phosphate gives 2 negative charges
44
reovirus cap is the...
base hydrolysis of viral mRNA followed by ion exchange chromatography
45
cap synthesis
1. RNA triphosphate removes terminal phosphate from pre mRNA
2. Guanylyltransferase adds capping GMP from GTP
3. a methyltransferase will methylate N7 of capping guanosine
4. methyltransferase catalyzes 2' O methylation of penultimate nucleotide
46
cap synthesis occurs
early in transcription before chain gets to be 30 nt long.
47
guanylyl transferase function
--add
48
methyltransferase function
--add
49
What is the purpose of capping>
1. protects mRNA from degradation
2. enhance translation of mRNA
3. transport mRNA out of nucleus
4. helps splice mRNAs
50
polyadenylation is found...
in 3' end of mature mRNA.
its not a part of DNA it is added.
51
polyadenylation
adding a poly A to RNA
-long chain of AMP residues is called poly A tail
52
heterogenous nuclear mRNA is...
a precursor to mRNA
53
the cut and falling of RNA poly is...
simultaneous.
54
eukaryotic mRNAs/their precursors have a chain of AMP residue about ...
250nt long, at their 3' ends
55
Poly A is added _______ by an enzyme called _____
post transcriptionally
poly A polymerase
56
poly A is not a product of transcription , it is not encoded in DNA (t/f)
true
57
functions of Poly A
-enhances lifetime and translation of mRNA
-required for transport of mRNAs from nucleus to cytoplasm
58
mechanism of poly A
-transcription of eukaryotic genes extends beyond polyadenylation site
-the transcript is cleaved, and polyadenylated at 3' end
59
polyadenylation signals
-minimum polyad signal:
-AAUAA motif, about 20nt upstream of a polyad site in preMRNA
-followed 23 bp later by GU rich motif
-followed immediately by U rich motif
60
polyadenylation involves both:
-pre mRNA cleavage
-polyad at the cleavage site
61
cleavage in mammals requires these proteins:
CPSF, CstF, CF1, CF2, Poly A polym, RNA poly 2
^^^CF1 and CF2 are used to cut
62
Initiation of Polyad
-2 proteins participate in this initiation:
CPSF binds to the AAUAAA motif
Poly A polymerase
63
signal for initiation of Polyad
AAUAAA followed by 8nt
-when polyA reaches 10nt length, further polyad becomes independent of the AAUAAA signal, and will depend on the polyA itself.
64
elongation of PolyA
-requires a specificity factor: Poly A binding protein 2 (PAB2)
-PAB2 binds to a pre initiatied oligoA
-this will aid poly A polymerase in elongating the poly A to 250 nt or more.
65
PAB2
PAB2 acts independently of AAUAAA motif
PAB2 depends only on poly A
its activity is enhanced by CPSF
66
model for polyadenylation
-factors assemble on the pre mRNA, guided by motifs
-cleavage occurs
-polymerase initiates polyA synthesis
-PAB2 allows rapid extension of the oligo A to full length
67
RNA processing during transcription
all 3 RNA processes occur during transcription.
-splicing- occurs when transcript is still underway
-capping- occurs when nascent mRNA is 30nt long, and when the 5' end of RNA emerges from polymerase
-polyadenylation occurs when mRNA is cut at the polyad site
68
binding CTD of RPB1 to mRNA process proteins
CTD of RPB1 of RNA poly 2 is involved in all 3 types of RNA processing,
capping, splicing, and polyad bind directly to the CTD which serves as a platform.
69
termination of transcription by RNA poly 2 occurs in 2 steps
1. transcript will have a co -transcript cleavage (CoTC), within the termination region downstream of the polyad site
2. cleavage and polyad occur at the polyA site, signals the polymerase to leave the template
70
translation is...
-ribosomes reading the genetic message in mRNA, and making the corresponding protein.
71
ribosomes are _______ factories
protein making
72
transfer RNAs (tRNAs) are ________ that bind an AA at one end, and _______ at the other end
adaptors
interact with mRNA
73
2 main components of translation
ribosome and tRNA
74
last three nucleotides of tRNA
CCA
75
what has to occur before initiating translation?
-make aminoacyl tRNAs: AAs must be covalently bound to tRNAs
-dissociation of ribosomes into their 2 subunits:
the cell will make the initiation complex on the small ribosomal subunit. the two subunits must separate.
76
translation initiation complex is assembled on ...
small ribosomal subunits.
77
what is tRNA charging
the process of bonding tRNA to amino acids
78
all tRNAs have the same 3....
same 3 bases on the 3' end (CCA)
79
terminal adenosine is the
target for charging with amino acid
80
during tRNA charging, an amino acid is attached by...
ester bonds between its carboxyl group and 2' or 3' hydroxyl group of terminal adenosine of tRNA
81
Two step charging
this is done for the aminoacyl tRNA synthetases to join amino acids to their tRNAs:
1. activation of AA with AMP from ATP
2. energy from aminoacyl-AMP is used to transfer the AA to the tRNA
82
E coli ribosomes dissociate into subunits at....
the end of each round of translation.
this is promoted by RRF and EF-G
83
RRF
ribosomal removal factor
84
IF3 binds to free 30S subunit to...
prevent reassociation with 50s subunit, to form a whole ribosome.
85
50s and 30s subunits combine to make...
70s subunit
86
IF3
binds by itself to the 30s subunit, stabilized by IF1 and IF2.
87
IF2
IF2 can bind alone, but it is stabilized with the help of IF1 and IF3.
88
IF1 cannot...
bind alone.
89
IF2 brings...
charged tRNA
90
Once the ribosomal subunits are dissociated, the cell builds a 30S initiation complex
includes:
-mRNA
-Aminoacyl tRNA (fMet-tRNA)
-Initiation factors (IFs)
91
when mRNA binds to 30s...
-16s rRNA can interact, and AUG will fit on top of the P site of 30s.
-tRNA will bind to the AUG, with an f-met unit.
-now, 50s subunit can bind, and it will bind with f-met unit.
92
Prokaryotic initiation codons:
AUG (most common)
GUG
UUG
93
the initiating aminoacyl tRNA
N-formyl-methionyl-tRNA
94
N formyl methione (fMet)
is the first amino acid incorporated to the polypeptide
-its usually removed from the mature protein
95
the 30s initiation complex is formed from...
a free 30s ribosomal subunit + mRNA + fMet-tRNA
96
the binding between the 30s prokaryotic ribosomal subunit and the initiation of mRNA depends on..
the base pairing with:
-Shine Dalgarno seq (upstream of the initiation)
-complementary seq of the 3' end of 16s RNA
97
the Shine dalgarno seq is complementary to
the 3' end of 16s e coli rRNA.
-mediated by IF3, all 3 IF factors will bind.
IF1 and 2 will assist.
98
ribosome binding occurs when theres...
3 or more base pairs
99
____ is the first tRNA and the major factor promoting the binding of fMet-tRNA to the _______
IF2.
-30s initiation complex.
** IF1 and IF3 are necessary for support.
100
______ is required for IF2 binding, but _____ is not hydrolyzed in the process.
GTP
GTP
101
the complete 30s initiation complex:
-30s ribosomal subunit
-mRNA
-fMET-tRNA
-GTP
-IF1, IF2, IF3
102
GTP is hydrolyzed after...
the 50s subunit joins the 30s complex to make the 70s initiation complex.
103
GTP hydrolysis is carried out by ...
IF2 with the 50s ribosomal subunit.
104
Purpose of hydrolysis
-release IF2 and GTP from the complex so that the polypeptide elongation can start.
105
Bacterial translation initiation
1. RRF + EF-G dissociate the 70s ribosome into 50s and 30s.
2. IF3 binds to 30S, prevents subunit re associating
3. IF1 and IF2/ GTP alongside IF3 binds.
4. binding of mRNA and fMEt-tRNA to form the 30S initiation complex
5. binding of 50s with loss of IF1 and IF3
6. IF2 dissociation with simultaneous GTP hydrolysis.
106
binding of mRNA and fMEt-tRNA to form the 30S initiation complex
-can bind in any order
-IF2 sponsors fMET-tRNA
-IF3 sponsors mRNA
107
Eukaryotic initiation of translation
-starts with methionine
-initiating tRNA differs from interior tRNA
-no shine dalgarno
-mRNA have caps on 5' end
-no ribosome binding site
108
bacterial initiation of translation
-n formyl methionine
-shine dalgarno sequence, shows ribosomes where to start
109
eukaryotic 40s ribosomal subunits locate the start codon by...
binding to 5' cap first, then scanning downstream to find the 1st AUG that is favorable (Kozaks rules)
-5-10% of the time, the 1st AUG will be passed in search of a better one
110
Translation with a short ORF
-ribosomes will initiate at an upstream AUG
-translate short ORF
-continue scanning
-reinitiate at a downstream AUG
111
Secondary structure near the 5' end of an mRNA can have pos or neg effects:
-a hairpin past an AUG can force a pause by ribosome subunit and stimulate translation
-stem loop between cap and initiation site can block scanning, and inhibit translation
112
bacterial and eukaryotic translation initiation both require IF's (t/f)
true
113
eukaryotic system is more complex than bacterial (t/f)
true.
-it has scanning process and factors to recognize the 5' cap.
114
the eIF4F
-cap binding protein
-composed of three parts: eIF4E, eIF4A, eIF4G
-the three parts together form eIF4F
115
eIF4E
24kD, cap binding activity
116
eIF4A
50kD
117
eIF4G
220kD
118
function of eIF4A
-RNA helicase:
-unwinds hairpins found in 5' leaders of eukaryotic mRNA
-unwinding is ATP dependent
-eIF4A needs help from eIF4B (stims helicase and binding to mRNA)
119
function of eIF4G
-scaffold protein, it will bind to other proteins:
eIF4E, eIF3, Pab1p
-interacting with these proteins lets eIF4G recruit 40s ribosomal subunits to mRNA, and stim translation
120
eIF3
40s ribosomal subunit binding protein
121
Pab1p
poly A binding protein
122
polio virus shuts down host cell's ability to...
translate any capped mRNA
-polio has RNA that serves as mRNA
-a viral protease cleaves off aminoterminal domain of eIF4G
-only viral RNA gets translated through IRES in viral mRNA
123
during polio, the DNA is not capped/methylated, but ....
it is still translated in the cell
124
IRES
internal ribosome entry site
125
eIF4G as an Adaptor step 1
1. cap recognition:
eIF4G is an adapter between eIF4E (which is bound to the cap) and eIF3 (bound to 40s subunit) that helps recruit 40s subunit to a site near the cap
126
eIF4G as an Adaptor step 2
2. IRES recognition:
IRES interacts with the remnant of eIF4G recruiting 40S subunit.
127
eIF4G as an Adaptor step 3
3. Cap and poly A recognition: synergism between cap and poly A.
the eIF4E bound to the cap and Pab1p bound to poly A both bind to eIF4G
-now the initiation process is done, and the ribosome will translate.
128
The Shine-Dalgarno sequence is found in
mRNA
129
This initiation factor is involved in binding tRNA to the ribosome.
eIF2
130
This initiation factor is a Cap binding protein
eIF4F
131
This initiation factor binds to the 40S subunit and inhibits reassociation of the 40S and 60S subunits
eIF3
132
This initiation factor binds to the 60S subunit and inhibits reassociation of the 40S and 60S subunits
eIF6
133
The first amino acid in all mature proteins in prokaryotes is an N-formyl-methionine (t/f)
false
134
The 30S initiation complex does not include
5S rRNA
135
this SnRNP base pairs with 5' splice site of mRNA
U1
136
this SnRNP base pairs with the conserved sequence at splicing branch point
U2
137
this SnRNP associates with last nucleotide in one exon and the first nucleotide in the next exon
U5
138
this SnRNP base pairs with 5' end of the intron
U6
139
The snRNPs are usually involved in which of the following?
splicing
140
Splicing signal sequence has _________ bases at 5' end, and _________ bases at the 3' end of the introns.
GU, AG
141
The process by which introns are removed from immature mRNA is called ______________.
RNA splicing
142
The semidiscontinuous nature of DNA replication was proven by the discovery of _____________
Okazaki fragments.
143
OriC is called an origin of DNA replication in ________.
E coli
144
In _______________ replication of DNA the two parental strands stay together and the two new daughter strands are produced.
semiconservative
145
_______________ introduces transient single stranded or double stranded breaks in DNA.
topoisomerase
146
The correct order of the steps of 5'-Cap synthesis based on the following:
1 The terminal phosphate is removed from the pre-mRNA.
2 A capping GMP is added to the pre-mRNA.
3 N7 of the capping guanine is methylated.
4 The 2'-O-methyl group of the penultimate nucleotide is methylated
147
Functions of the mRNA cap include all EXCEPT
helps regulate expression of the mRNA
148
The poly(A) tail of eukaryotic mRNA is exactly 150 nucleotides in length. (t/f)
false. 250
149
The polyadenylation of pre-mRNA does not require
RNA polymerase I
150
The _______ has ribosome-dependent GTPase activity.
IF-2
151
During protein translation, elongation takes place in this order:
1. EF-Tu, with GTP, binds an aminoacyl-tRNA to the ribosomal A site.
2. Peptidyl transferase forms a peptide bond between the peptide in the P site and the newly arrived aminoacyl-tRNA in the A site.
3. EF-G, with GTP, translocates peptidyl-tRNA to the P site
152
Ribosome recycling factor (RRF) resembles a tRNA molecule. (t/f)
true
153
elongation is similar in bacteria and eukaryotes (t/f)
true
154
mRNA read AND synthesized in the _ to _ direction
5' to 3'
155
proteins are made in the __ to ___ direction
amino to carboxyl
156
the ______ terminal amino acid is added first
amino
157
genetic code
set of 3 codons in mRNA that represent the 20 AA's in proteins
158
mutations show their effect....
down stream
159
types of frameshift mutations
add a base
delete a base
cross _ and _
add 3 bases
160
adding 3 bases to a sequence will change .... as opposed to adding 1 base
very little
1 base changes a lot
161
in mRNA codons instruct the ribosome to...
incorporate specific AA's into a polypeptide
162
genetic code can overlap (t/f)
false. each base is apart of 1 codon only.
163
the genetic code doesnt have gaps or commas (t/f)
true
164
3 codon sequence for methionine
AUG
165
the stop. codons
UAA
UAG
UGA
166
Not all amino acids will make a tRNA...
this will conserve energy.
167
types of degeneracy in genetic code:
-isoaccepting species of tRNA: bind to the same AA, but recognize different codons
-wobble
168
wobble
the 3rd base of a codon is allowed to move slightly from its position to form a non-Watson Crick pair with the anticodon.
169
wobble allows the same,,,
aminoacyl-tRNA to pair with more than one codon
170
wobble pairs are....
GU
IA
171
in wobble, _____ has to be W-C pairing,
2/3.
the third can wobble.
172
genetic code is universal. (t/f)
false.
173
eukaryotic nuclei and _____ along with at least one bacterium can have altered code
mitochondria
174
mitochondrial genomes and nuclei of at least one....
yeast have sense of codon changed from one AA to another. theyll have their own cellular machinery.
175
there can be ______ from the universal genetic code
deviations
176
EF-T
T for transfer.
transfers aminoacyl tRNAs to the ribosome.
-involved in 1st step of elongation
-its made of 2 different proteins: Tu's and T's.
Ef-Tu: unstable
Ef-Ts: stable
177
EF-G
-G for GTPase
-EF-G is in the 3rd step of elongation.
178
GTP and _____are needed for translocation
EF-G
179
a new round of elongation will occur if ...
EF-G is released from the ribosome, which depends on GTP hydrolysis.
180
as the elongation cycle repeats...
it will add AA's one at a time
-it will grow the polypeptide, until ribosome reaches a stop codon-now time for termination.
181
mutations can create termination codons in mRNA...
causing premature termination of translation.
182
amber mutation
creates UAG
183
ochre mutation
creates UAA
184
opal mutation
creates UGA
185
stop codon suppression
suppresses the stop codon, AUG to AUC
186
release factors recognize...
stop codons
187
prokaryotic tranlation termination is mediated by 3 factors:
-RF1 recognizes UAA and UAG
-RF2 recognizes UAA and UGA
-RF3 is GTP binding, helping bind RF1 and RF2 to ribosome.
188
eukaryotes have 2 release factors:
eRF1 recognizes all 3 termination codons
eRF3 is ribosome dependent GTPase, helping eRF1 release the finished polypeptide
189
eukaryotic ribosomes are released by
eIF3
-aided by eIF1, eIFA, and eIF3j
190
prokaryotic ribosomes need help from ____ and ____
RRF
EF-G
-RRF resembles a tRNA, binding to ribosome A site, but using a position not normally taken by tRNA.
-collaborates w EF-G in releasing 50s subunit or the whole ribosome.
191
double helix model states the two strands are
complementary
192
DNA replication is....
bidirectional
semi conservative
requires primers
half discontinuous
193
In DNAs semidiscontinuous replication ...
template is read 3' to 5'
synthesized 5' to 3'
194
The transcript bubbles limitation
it can only read 2kilo bp
195
in semi discontinuous the _____ strand is replicated continuously, and the _______ strand is replicated discontinously in _______
leading
lagging
okazaki fragments
196
okazaki fragments in e coli are initiated with rna primers ______ long
10-12 nt
197
primers can be hard to detect in cells because of
enzymes that attack RNAs
198
dna replication starts with bubble:
area where parental strands are seperated and new dna is synthesized
199
bidirectional replication fork
two replicating forks moving oppositely away from the origin
200
replicon
dna with one origin of replication
201
there are _______ dna polymerases in E coli
pol 1
pol 2
pol 3
202
dna pol 1
versatile enzyme with 3 activities:
-dna pol
- 3' to 5' exonuclease
-5' to 3' exonuclease
203
proteolytic treatment of dna pol 1
creates 2 polypeptides:
klenow fragment
smaller fragment
204
klenow fragment
has both polymerase, and the 3' to 5' exo nuclease activity, serving as proofreading.
if mistake, pol 1 pauses, exonuclease removes mistake.
205
5' to 3' exonuclease
allows pol 1 to degrade the strand ahead of the polymerase
-in one pass it will remove and replace the strand.
206
dna poly 2 and 3
pol 2 is NOT required for DNA replication
pol 3 is the only dna poly REQUIRED for dna replication, and is the enzyme to replicate bacterial DNA
207
DNA pol 1 appears mostly active as....
DNA repair
208
DNA pol 3 holoenzyme
-dna pol is in the alpha (aka synthesis)
-3' to 5' exonuclease is in the 3 subunit
-O subunit is unknown
-y is for atp-ase
-B subunit + the other 8 subunits make up the holoenzyme
209
dna dependent ATPase is in the ....
y - complex , with 5 subunits .
210
these subunits make up the core polymerase
alpha
3
O
211
T subunit
helps in dimerization of core
212
primers are made of ____ which helps mark them for degredation
RNA
213
only a ________ can serve as a primer for pol 3 holoenzyme
base paired nucleotide
214
strand unwinding
requires energy and enzymes
the helicase enzyme unwinds dsDNA, then its readu for SS DNA bind protein.
215
prokaryotic single strand DNA binding proteins
bind ssDNA much more strongly than dsDNA
-help helicase
help it from re annealing
-protect from degradation
-ESSENTIAL for prokaryotes
216
topoisomerases
helicase use ATP to unwind, causing supercoil.
topoisomerase will release stress and prevent supercoil
217
two types of topoisomerase:
type 1: temporary nicks in the SS
type 2: (the GYRASE) introduce single or ds breaks in DNA and allow it to change form.
218
topoisomerase process
binds with G-seg, uses T-seg, then repairs G-seg.
-holds onto one strand, allows T seg, repairs.
219
mismatch repair recognizes parental strand by...
methylated A in GATC seq
220
mismatch repair
-recognizes parental strand
-corrects mismatch in new strand
-eukaryotes use part of repair system
-distinguish strands at mismatch
221
methylated =_____ DNA
unmethylated = _____ DNA
original
new
222
the nick in a strand corresponds to a
methyl group
223
exonuclease ___
DNA poly 3 holoenzyme ____
DNA ligase _____
cuts
extends
fills gap
224
DNA ligase
makes phosphodiester bonds with opposing DNA ends
225
DNA helicase will _____ DNA
primase will ensure the ____
open up
continuation of making protein
226
initiation of DNA replication means....
primer synthesis
227
DNA poly cant synthesize without ____ which is made by _____
primers
DNA primase (DNA G)
228
primosome
collection of proteins needed to make primers
229
in e coli the primosome contains
DNA helicase (DNA B)
DNA primase (DNA G)
230
primosome is assembled at the....
oriC
231
the e coli oriC is a ____ bp DNA with 2 regions:
245 bp
the DUE and the DOR (protein binding, and DNA unwinding)
232
what does DOR stand for
DNA A oligomerization region
233
DNA A, ATP, HU... will only bind at
oriC
234
DNA A binds to oriC at the
DNA A boxes 9 mers
helps rna poly and HU protein melt DNA
235
DNA B (helicase) binds to the
open complex and helps binding of primase to complete the primosome
-unwinds DNA as replisome progresses
236
primosome will stay with the _____ and repeatedly prime the ______ synthesis on lagging strand
replisome
okazaki fragment
237
pol 3 holoenzyme synthesizes DNA at a rate of
730nt/sec to 1000nt/sec
238
pol 3 core alone
very poor polymerase
will fall off of template after 10 nt and take 1 min to reassociate
239
the B subunit of holoenzyme
-keeps pol engaged with template
-called sliding clamp
240
core poly + B subunit
replicates DNA processively at 1000nt/sec
-B subunit forms a ring shaped dimer to fit around DNA template, and interacts w alpha unit to tether the whole polymerase and template together
241
in eukaryotes what is the processivity factor, similar to the B clamp
PCNA. PCNA will form trimer, which forms ring to encircle DNA and hold it to template
242
the B clamp will be replaced with...
core subunit
243
the B subunit needs help from...
y - complex to load onto DNA template, and y complex will not remain afterwards.
244
clamp loading is _____ dependent
ATP
ATP changes shape of loader, so that the S subunit can bind to a B subunit, and allow for the encircling and opening of clamp
245
the pol 3 holoenzyme is.....
double headed
246
there are 2 core polymerases attached through two _ subunits to a ______
T
y complex.
one core ensures continuous synth of leading strand
one core performs discontinous synth of lagging strand
247
the y comlpex serves as a ...
clamp loader, to load the B clamp to a primed DNA template
248
After the B clamp is loaded...
the B clamp loses affinity for y complex, and associates with core polymerase
249
the y complex and B clamp help....
core poly with processive synthesis of Okazaki fragment
250
when the okazaki fragment is complete, the B clamp...
loses affinity for the core poly, and associates again with y complex, clamp recycles.
251
bacterial replication
2 replication forks approach each other at the terminus region
252
termination of replication for phage
phage produces long/linear concatemers, that grow until the genome sized piece is cut off, and put onto the phage head.
253
terminus region has ____ bp terminator sites, that bind to specific proteins: the ___
22
TUS
254
TUS stands for
terminus utilization substance
255
termination of DNA rep process
replicating forks enter terminus, pause, leave 2 daughter duplexes tangled, and must seperate.
256
what enables decatenation
topoIV decatenates the daughter duplexes
257
DNA _____ acts as a swivel during DNA replication
gyrase
258
two stage model for decatenation
-denaturation of remaining parental double helix (it still remains tangled together)
-repair synthesis fills in the single stranded gaps
-decatenation (topoIV) seperates daughter duplexes
259
where are telomeres located
the ends of eukaryotic chromosomes
260
one strand of telemores contains:
-tandem repeats of short G rich regions
261
Telomerase enzyme makes...
G rich telomere strand
Telomerase has a short RNA, that serves as a template for telomere synthesis.
262
telomeres help ...
- prevent degradation
-and extends chromosome ends by using their own template
-then fold in on themselves to secure
263
lagging strand is efficient because of
-differential affinity clamp B clamp
-looping
-Okazaki fragments
264
the 5' end can never be...
extended.
this means a gap is made, which can be aided by telomerase, which CAN extend the 3' end.
265
steps of telomere formation
-elongation
-translocation
-elongation
-primer synthesis
-DNA replication
-primer removal
266
all eukaryotes protect their _______ from nucleases, and ds break repair enzymes
telomeres
267
eukaryotes have telomere ________
binding proteins
268
telomere binding proteins
protect from degradation
hide telomere ends from DNA repair factors
269
telomeres are linear (t/f)
false.
they form a DNA t-loop.
270
Why is t loop formed
single stranded 3' end of telomere invading the ds telomere DNA upstream
271
function of telomere
prevent chromosome degradation and prevent DNA repair from finding ends of chromosomes
272
telomere binding proteins
called "shelterin"
theres 6:
TRF1
TRF2
TIN2
POT1
TPP1
RAP1
273
TRF1 and TRF2...
homologous. they bind to the ds part of telomeres.
274
telomere binding protein TRF1
-binds to ds part of telomeres, TTAGG repeat binding factor
275
telomere binding protein TRF2
homologous to TRF1, binds to ds part of telomeres
276
telomere binding protein POT1
protects telomeres, binds ss 3' tail of telomeres
277
telomere binding protein TPP1
POT1 binding protein
278
telomere binding protein TIN2
TRF1 interacting factor, and organizes.
279
telomere binding protein RAP1
repressor activator protein
