Exam 2 Flashcards
(209 cards)
1
Q
What are the pyrimidines?
A
Cytosine
Uracil
Thymine
2
Q
What are the purines?
A
Adenine
Guanine
3
Q
What is the only nucleotide explicit to DNA?
A
thymine
4
Q
What is the only nucleotide explicit to RNA?
A
uracil
5
Q
Are purines or pyrimidines a 6 atom ring?
A
pyrimidines
6
Q
Are purines or pyrimidines a 9 atom ring with 2 rings?
A
purines
7
Q
Why are bases insoluble in water?
A
aromaticity
8
Q
What are nucleosides?
A
nitrogen base + sugar
9
Q
What bond links bases to sugars in nucleosides?
A
beta–glycosidic bond
10
Q
What number type are sugars in DNA?
A
pentose
11
Q
_________ makes nucleosides more water soluble than free bases
A
sugars
12
Q
What does the hydroxyl group of at the 2-position affect?
A
susceptibility to hydrolysis
secondary structure
13
Q
Why is DNA more stable?
A
it has an H and not an OH
14
Q
What do syn and anti nucleosides look like?
A
syn: base on same side as sugar
anti: base on opposite side as sugar
15
Q
What are the 4 common ribonucleosides?
A
- cytidine
- uridine
- adenosine
- guanosine
(–ine)
16
Q
What is the two and four letter symbol for deoxyadenosine?
A
dA
dAMP
17
Q
What is the two and four letter symbol for deoxyguanosine?
A
dG
dGMP
18
Q
What is the two and four letter symbol for deoxythymidine?
A
dT
dTMP
19
Q
What is the two and four letter symbol for deoxycytidine?
A
dC
dCMP
20
Q
What is the one and three letter symbol for adenosine?
A
A
AMP
21
Q
What is the one and three letter symbol for guanosine?
A
G
GMP
22
Q
What is the one and three letter symbol for uridine?
A
U
UMP
23
Q
What is the one and three letter symbol for cytidine?
A
C
CMP
24
Q
Some minor nucleosides have “methyl” in the beginning of their name; these nucleosides are an example of a _____________ marker
A
epigenetic marker
25
N6-Methyladenosine is a minor DNA nucleoside common in _________ but not found in __________?
bacteria
eukaryotes
26
What 2 ways are minor DNA nucleosides helpful?
1. markers own DNA to protect from degradation and degrade of bacterial DNA
2. mark genes that need to be activated
27
The minor RNA nucleoside, ____________, is found in the wobble position
inosine
28
What are 2 minor RNA nucleosides?
1. inosine
2. pseudouridine
29
nucleosides are ___________ for nucleic acids
substrates
30
What is known as the energy carrier for nucleosides?
5'-triphosphate
31
Where is energy stored in nucleotides?
phosphoric bond
32
What does GTP drive?
protein synthesis
33
What does CTP drive?
lipid synthesis
34
What does UTP drive?
carb metabolism
35
What do cyclic nucleotides regulate?
regulators of cellular metabolism
(found in all cells)
36
What are polynucleotides?
chains of nucleic acids
37
What bond links nucleic acids?
3'-5' phosphodiester bonds
38
What is the charge of DNA's back bone?
negative
39
Is DNA or RNA more stable?
DNA
40
What are the 5 types of RNA?
1.ribosomal RNA
2. messenger RNA
3. transfer RNA
4. small nuclear RNA
5. small non-coding RNA
41
What are the 2 fundamental chemical differences between DNA and RNA?
1. DNA contains 2-deoxyribose instead of ribose
2. DNA contains thymine instead of uracil
42
How does nature solve this issue of cytosine spontaneously deaminating into uracil?
uses thymine with a 5-methyl group to replace uracil
43
What is Chargaff's rule?
A=T
G=C
44
What did Rosalind Franklin do?
x-ray fiber diffraction to find the helix
45
What did Watson and Crick do?
base pairing and double helix
46
How many hydrogen bonds does A:T have?
two
47
How many hydrogen bonds does G:C have?
three
48
What regions of DNA are most stable?
G:C rich regions
49
Describe the major groove of DNA
large enough to accommodate an alpha helix from a protein
50
How is DNA antiparallel?
the two stands run in the opposite direction of each other
51
What is the consequence of DNA being antiparallel?
complementary strands
52
Base pairing is done by ____________ bonds
hydrogen
53
What is the only known left-handed DNA?
Z-DNA
54
What is the most common DNA?
B-DNA
55
What DNA is dehydrated?
A-DNA
56
What DNA is right handed?
A-DNA
B-DNA
57
What are 2 ways to sequence nucleic acids?
1. Chain termination (sanger)
2. base specific chemical cleavage
58
How are dideoxynucleotides used in chain termination sequencing?
they are randomly added to DNA being synthesized by DNA pol causing chain termination
59
How does base specific chemical cleavage sequencing work?
like sanger but chain is terminated by chemical agents
60
Can the secondary structure of DNA be denatured then renatured?
yes
61
what is reeannealing?
reassociation of the DNA strands into double helix
62
The rate of re-association is___________ proportional to genome complexity
inversely
63
What is the tertiary structure of DNA?
supercoils
64
What is the job of topoisomerase?
relaxing supercoils
65
o
o
66
What is the difference between toroidal and interwound supercoils?
toroidal: spirals out
interwound: spirals in
67
how do you find linking number?
L = twists + writhe
68
What are twists and writhes?
twists: number of helical turns
writhe: number of times helix crosses over on itself
69
_________ super coils makes it easier for DNA to unwind
negative
70
How is torsional stress on molecules resovled?
DNA is unwound
71
What is a type of topoisomerase?
gyrase
72
what does DNA gyrase do?
introduce negative supercoils
73
What are bacterial DNA gyrase inhibitors known for?
antibiotics
74
Supercoiled DNA in a torodial form wraps around ____________-
protein spools
75
What is an an example of a protein spool?
histones
76
What are the 3 parts of a chromosome?
1. origin of replication
2. two telomeres
3. centromere
77
_________ is the genetic material for cellular organisms
DNA
78
Why is DNA replication semiconcervative?
the replication DNA is made of one new strand and one old strand
79
What did Meselson and Stahl's experiment prove?
DNA replication is semiconservative
N14 and N15 created mixed strands
80
How is DNA replication bidirectional?
two replication forks which move in opposite directions
81
How id DNA replication semi-discontinous?
one strand synthesizes smoothly and one in fragments (lagging)
82
What does DnaA do in bacterial DNA replication?
initiator
83
What does DnaB do in bacterial DNA replication?
unwinds DNA
84
What does DnaG do in bacterial DNA replication?
primase
85
What does DnaC do in bacterial DNA replication?
helicase inhibitor
86
Where does DNA polymerase add nucleotides?
3' end
87
What is the purpose of 3'-5' exonuclease activity in DNA polymerase I?
proof reading
removes incorrect nucleotides
88
What is the purpose of 5'-3' exonuclease activity in DNA polymerase I?
removes primer
89
What fixes the nick between Okazaki fragments during DNA replication?
DNA ligase
90
DNA polymerase III uses an _________ primer for DNA synthesis
RNA primer
91
What is the "real" DNA polymerase for bacteria?
DNA polymerase III
92
What is special about the beta subunit of bacterial DNA polymerase III?
it forms a ring around DNA
93
supercoiling must be compensated by ___________
DNA gyrase
94
why do eukaryotes have multiple origins of replication?
there are so many genes
95
The earlier in S phase the DNA is replicated the ________ condensed it is
less condensed
96
What was identified as the origin of replication identified in yeast?
ARS (autonomously replicated sequence)
97
What is ORC?
origin of replication
98
o
o
99
What does MCM, Cdt1 and Cdc6 do in DNA replication?
loads helicase
100
At ORC what is formed to start DNA replication?
Pre-RCs (prereplication complex)
101
______ proteins are replication licensing factors
MCM
102
__________ complexes control cell cycle
cyclin-Cdk
103
What are the 3 major cyclin types?
1. G1/S-cyclin-Cdks
2. S-cyclin-CDKs
3. M-cyclin-CDKs
104
What does G1/S-cyclin-Cdks trigger?
trigger progression through the start checkpoint
105
What does S-cyclin-CDKs trigger?
trigger DNA replication
106
What does M-cyclin-CDKs trigger?
triggers mitosis
107
What does the inactive state of Cdk look like?
T loop
108
What does the partially active state of Cdk look like?
cyclin is bound
109
What does the active state of Cdk look like?
Cdk is phosphorylated
110
Checkpoints of the cell cycle depend on ________ and ________
cyclin and Cdk
111
DNA replication occurs _______ per cell cycle
once
112
What are the two steps to ensure only one DNA replication per cell cycle?
1. licensing of replication (late M or early G1)
2. activation of replication (S phase)
113
What did cell-fusion experiments give evidence of?
re-replication block
114
_____ phase cytoplasm contains all the factors needed to drive G1 nucleus to DNA synthesis
S phase
115
What are the 3 mechanisms that prevent re-replication?
1. inhibition of MCM2-7 loading by geminin
2. replication-dependent Cdt-1 degradation
3. Cdk-dependent inhibition pf pre-RC formation
116
What are the two challenges of tightly packed DNA for replication?
1. DNA template needs to be accessed
2. nucleosomal organization has to be reproduced on daughter strands
117
What does PCNA do in chromatin restoration?
sliding clamp that scans for damage
directs DNA methylation
118
What is endoreduplication?
DNA replication without cytokinesis
119
___________ is replication of DNA with completion of mitosis but not cytokinesis
polyploidy
120
___________ is repeated replication of DNA without forming new nuclei
polyteny
121
What enzyme maintains telomere length?
telomerase
122
Telomerase uses an internal ______ template
RNA
123
telomerase uses _______ transcriptase activity
reverse transcriptase
124
What cell type lacks telomerase causing shortening telomeres?
somatic
125
What did Howard Temin discover?
RNA-directed DNA polymerase (reverse transcriptase)
DNA is an intermediate in RNA tumor virus replication
126
What is RNA-directed DNA polymerase also known as?
reverse transciptase
127
What are the three enzymes involved in reverse transcriptase?
1. RNA-directed DNA polymerase
2. RNase H
3. DNA-directed DNA polymerase
128
What does DNA-directed DNA polymerase do in reverse transcriptase?
makes DNA duplex (seconda DNA strand) after RNase H destroys the viral genome (RNA removed)
129
What does RNase H do in reverse transcriptase?
degrades RNA in the DNA:RNA hybrids
130
All RNA tumor viruses contain ____________
reverese transcriptase
131
What has reverse trancriptase aided in the treatment of?
AIDs
132
What is the process of reverse transcriptase?
complementary DNA is synthesized using a strand of RNA
133
An _________ primer is required for reverse transcriptase
unusual primer
134
What was the first approved drug/nucleoside to treat aids?
AZT
135
What substrate of AZT binds to HIV reverse transcriptase?
AZTTP
136
___________ recombination involves similar DNA sequence
homologous
137
____________ recombination involves very different nucleotides sequences
non-homologous
138
_________________ is the enzymatic insertion of transposon
transposition
139
________________ and ______________ play a significant role in evolution
non-homolgous recombination
transpositions
140
What did Meselson and Weigle's experiment show?
recombination of chromosomes (using heavy and light phages)
141
What are the 6 steps of Holliday Model Homologous Recombination?
1. SYNAPSIS -- two homologous DNA duplexes align
2. SINGLE STRAND NICK
3. STRAND INVASION -- partial strand unwinding
4. LIGATION -- Holliday junction created
5. BRANCH MIGRATION -- unwinding then rewinding of two duplexes
6. STRAND EXCHANGE -- nick introduced to fix Holliday junction
142
What enzyme initiates the Holliday model and makes a nick and unwinds the DNA?
RecBDC
143
What enzyme is responsible for strand invasion in the Holliday model?
RecA
144
What enzyme is responsible for branch migration in the Holliday model?
RuvA RuvB
145
What enzyme is responsible for strand exchange?
RuvC
146
What enzyme has helicase, nuclease, and ATPase activity?
RecBCD
147
What is a x (chi) site?
recombinational hotspot
148
Why do bunny ears form when RecBCD unwinds DNA?
the rate of unwinding is faster than the rate of ssDNA release
149
What enzyme in the Holliday Model aids in homologous pairing?
RecA
150
RecA forms a __________ with a groove to accommodate the ssDNA
helical filament
151
Once RecA:ssDNA complex is bound what happens?
it binds to dsDNA to search for a homologous region
152
What is the loop called made by RecA in strand invasion of Holliday model?
D loop
153
What class of enzymes solve the Holliday junction?
Ruv
154
What Ruv cleaves the Holliday junction to fix it?
RuvC
155
Gene transfer techniques make it possible to introduce genes into animals by _________
transfection (transgenic animals)
156
What did Barbara McClintock discover?
transposons
157
What are class I transposons called?
retrotransposons
158
What is the phrase used to describe class I (retrotransposons) transposons?
copy and paste
159
What are class II transposons called?
DNA transposons
160
What is the phrase used to describe class II (DNA transposons) transposons?
cut and paste
161
How do class I (retrotransposons) work?
RNA is reverse transcribed into DNA and DNA is inserted back into genome in a new spot
162
What class of transposons require RNA intermediate?
Class I (retrotransposons)
163
What are transposase?
target sequence for transposons
164
Can RNA and DNA have mutations?
yes
165
Mutations are usually ________ to gene function
deleterious
166
Are mutations usually recessive or dominant?
recessive
167
Can DNA be replaced?
No, so it must be fixed
168
What does the Ames test indicate?
the mutagenic potential of a chemical
169
How does the Ames test work?
Bacteria with a mutation causing no HIS production so the bacterial will not be able to grow without HIS in environment
The bacteria is introduced to a chemical that mutates the HIS gene and now it can grow even without the presence of HIS
170
What are 3 major DNA repair systems?
1. double stranded breaks
2. direct reversal
3. single-stranded damage repair
171
Why is double stranded breaks a dangerous DNA repair system?
the broken of strands cannot be recovered
172
How does the DNA repair system, direct reversal work?
chemical reactions reverse the damage of DNA
173
What does the DNA repair system, single-stranded damage repair, rely on to guide repair?
complementary strand
174
What are 3 examples of single strand damage repair?
1. mismatch repair
2. base excision reapir
3. nucleotide excision repair
175
What mechanism does double stranded DNA breaks use to repair?
NHEJ
176
In NHEJ for double stranded breaks, what enzyme recruits the two exposed ends?
Ku70/80
177
double stranded break repairs cause _________ to form when its HOMOLOGOUS DNA recombination
D loops
178
pyrimidine dimers can be repaired by __________
photolyase
179
In base excision repair, __________ removes damaged bases creating _________
DNA glycosylase
AP sites
180
How do AP endonucleases reverse chemical damage?
cleave DNA backbone so that exonuclease can remove several residues and new ones added
181
What repair system repairs large regions not just bases?
nucleotide excision repair
182
What does photolyase break to fix chemical mutations?
rings
183
Base excision repair uses specific ______________
DNA glycosylases
184
What is an AP site?
where DNA glycosylase has removed damaged nucleotides
185
Why is uracil glycosylase important?
removes U from DNA because C spontaneously deaminates into U
186
What polymerase synthesizes new DNA at AP sites?
DNA pol I
187
What enzyme seals AP sites?
DNA ligase
188
__________ remove DNA segments for nucleotide excision repair?
excinuclease
189
Nucleotide excision repair in bacteria uses _________ exinucleases
ABC
190
Do human or bacteria have larger sections removed in nucleotide excision repair?
humans
191
Mismatch repair systems _______ DNA duplexes for mismatched bases
scans
192
How do repair enzymes know which strand is correct in bacterial methyl-directed mismatch repair?
The errors will be in unmethylated sections
193
What proteins are involved in bacteria methyl-directed mismatch repair?
Mut
194
Why is Nitrosoguanidine used in labs?
mutagen in labs
195
Mutations in the ____________ cause Meier-Gorlin syndrome
pre-replication complex
196
Do DNA polymerases require primers?
yes
197
What DNA polymerase lengthens Okazaki framgents?
DNA polymerase I
198
What DNA polymerase removes primers?
DNA polymerase I
199
Which DNA polymerase is very processive?
DNA polymerase III
200
Which DNA polymerase is specific for the lagging strand in bacteria?
DNA polymerase I
201
DNA polymerase III can work on _______ strands in bacteria
both
202
What DNA polymerase fills in Okazaki fragments in eukaryotes?
DNA polymerase I
203
In eukaryotes, the epsilon subunit of DNA polymerase I works of the ________ strand
leading
204
In eukaryotes, the delta subunit of DNA polymerase I works of the ________ strand
lagging
205
What DNA polymerase was the first discovered?
I
206
Which DNA polymerase has 5'-3' and 3'-5' exonuclease activity?
DNA polymerase I
207
Is DNA polymerase III found in eukaryotes?
No only in prokaryotes
208
Which DNA polymerase is enormously processive?
DNA polymerase III
209
Which DNA polymerase has the beta subunit ring?
DNA polymerase III
