Structure, Function and Replication of DNA Flashcards
(252 cards)
1
Q
What does DNA contain?
A
genes
2
Q
What are genes? (2)
A
units of biological information and units of inheritence
3
Q
Is DNA a polymer or a monomer?
A
polymer
4
Q
What is a polymer?
A
a long strand (compound made up of a long chain of identical or similar units)
5
Q
what are the monomers of DNA called?
A
nucleotides
6
Q
What is a bacteriophage?
A
a virus that infects bacteria and reproduces inside of it using its viral DNA to hijack the host bacterial DNA
7
Q
What is phage T2?
A
A bacteriophage
8
Q
What is the genetic material of phage T2?
A
DNA
9
Q
Describe the method of Hershey and Chase’s 1952 experiment? (3)
A
1) they infected bacteria with phage T2 labelled with 32P in DNA and 35S in protein
2) they separated the phage (protein) coat and the infected bacteria
3) they isolated progeny phage
10
Q
What did Hershey and Chase find in 1952? (2)
A
The phage contained mostly 35S label and the infected bacteria mostly 32P. When progeny (offspring) of phage was isolated, they found 30% 32P and less than 1% of 35S (basically none)
11
Q
What do Hershey and Chase’s 1952 findings show?
A
- The DNA, not the viral protein enter the bacteria
- the DNA of the parent phages becomes part of the progeny phage
12
Q
How many parts does each DNA nucleotide have?
A
3
13
Q
What are the 3 parts of each DNA nucleotide?
A
- A sugar
- base
- phosphate group
14
Q
Why is the sugar 2’ deoxyribose (2 prime)?
A
the 2nd carbon of the sugar ring doesn’t have an oxygen attached (deoxy-)
15
Q
How does the deoxygenation of the 2nd carbon in the sugar affect stability?
A
It increases it
16
Q
How many phosphates in the phosphate group of DNA?
A
3
17
Q
what are the names of the 3 phosphate groups of DNA?
A
alpha (a), Beta (B) and Gamma (y)
18
Q
Where is the alpha phosphate positioned on the nucleotide?
A
closest to the sugar
19
Q
Where is the beta phosphate positioned on the nucleotide?
A
between the alpha and gamma phosphates
20
Q
where is the gamma phosphate positioned on the nucleotide?
A
furthest from the sugar
21
Q
How many bases are in DNA?
A
4
22
Q
What are the four bases?
A
Adenine, Guanine, Cytosine and Thymine
23
Q
What are the 2 types of DNA bases?
A
Purines and pyrimidines
24
Q
Which bases are purines?
A
Adenine and Guanine
25
Which bases are pyrimidines?
cytosine and thymine
26
What makes a base a purine?
They're made up of 2 carbon (2C) rings
27
What makes a base a pyrimidine?
They're made up of 1 carbon (1C) ring
28
Which part of the base attaches to the sugar in DNA?
the nitrogen
29
What type of bond joins the base and the sugar in a DNA nucleotide?
A B-N-glycosidic bond
30
What's the full name of the nucleotide with an A base?
2'-deoxyadenosine 5'-triphosphate (dATP)
31
What's the full name of the nucleotide with a G base?
2'-deoxyguanosine 5'-triphosphate (dGTP)
32
What's the full name of the nucleotide with a C base?
2'-deoxycytidine 5'-triphosphate (dCTP)
33
What's the full name of the nucleotide with a T base?
2'- deoxythymidine 5'-triphosphate (dTTP)
34
What happens to the phosphate group of a nucleotide when DNA is polymerising?
the alpha phosphate joins to the base of the other nucleotide and the B and Y phosphates are lost
35
What sort of bond joins 2 nucleotides together in DNA?
phosphodiester bond
36
Is DNA double or single stranded?
double
37
what shape does the double stranded DNA make?
A helix
38
Who discovered the double helix structure of DNA?
Watson, Crick and Franklin
39
Are the ends of DNA the same or different?
different
40
Does DNA have directionality?
yes
41
can DNA be read in 1 or 2 directions?
1
42
How is the directionality of the 2 strands in a DNA molecule described? what does this mean?
Antiparrallel organisation
| This means they go in opposite directions- 1 going 5' -> 3' on one and 3' --> 5' on the other
43
Is DNA a regular helix?
no
44
What are the 2 grooves in DNA?
Major and Minor
45
What's the advantage of having a major DNA groove?
enzymes can go in and read the DNA
46
What bonds hold the 2 strands of DNA together?
Hydrogen bonds
47
What's the hydrogen bonding between the 2 strands of DNA called?
complementary base pairing
48
What bases pair?
A to T
| C to G
49
How many hydrogen bonds between A and T?
2
50
How many hydrogen bonds between G and C?
3
51
Which is a stronger bond, that between A and T or that between G and C and why?
G and C has they have more hydrogen bonds
52
What do you call the amount of G + C nucleotides in an organism's DNA?
GC content
53
What's the GC content of human DNA?
40.3%- medium amount
54
can the DNA helix exist in different forms?
yes
55
What are the 3 forms of DNA helix?
A, B and Z
56
What's the main difference between A and B helix DNA?
A DNA has a narrow major groove but B DNA has a wide major groove
57
Which is the best known DNA helix?
B
58
In what conditions does A-DNA form?
When there;s not enough water (dehydrated conditions)
59
What's the structure of Z-DNA?
It's wound into a left handed helix
60
Where's Z-DNA found?
Found with B-DNA naturally in regions of human and other organism's DNA
61
Is Z-DNA biologically active?
yes
62
What's a Hydrogen bond?
A weak electrostatic attraction between an electronegative atom and a hydrogen atom attached to a second electronegative atom
63
What's the 3'-OH terminus?
The end of a polynucleotide that terminates with a hydroxyl group attached to the 3'-carbon of the sugar
64
What's the 5'- P terminus?
The end of a polynucleotide that terminates with a mono-, di- or tri- phosphate attached to the 5'- carbon of the sugar
65
What are the 2 roles of the genes in a cell?
- units of biological information
| - genes are units of inheritance
66
what's intergenic DNA?
part of DNA which aren't genes
67
what's the purpose of intergenic DNA?
mostly unknown, however believed to be involved in DNA replication
68
How long is a gene?
varies greatly
69
what's the unit of length of a DNA molecule?
Base Pair (number of base pairs) (BP)
70
How many BPs in 1 kilobase pair (kb)?
1000000 (million) BP
71
How many BPs in 1 megabase pair (mb)?
1000 BP (1 million)
72
How long are the shortest genes?
around 100 bps
73
How long are the longest genes?
around 2,400,00 bp
74
Do the longest genes contain 24000 times more information than the shortest?
no
75
What are genes split into (to make them discontinuous)?
introns and exons
76
what are exons?
parts of the gene which contain the information needed to make protein
77
what are introns?
information not needed to make a protein
78
How many introns does the average human gene have?
8
79
How many exons does the average human gene have?
9
80
What's the mean intron length?
3365 bp
81
what's the mean exon length?
145 bp
82
are genes directional?
yes
83
which direction are genes read in?
5'--> 3'
84
What's the process of reading gene information called?
gene expression
85
by which process do genes become RNA?
transcription
86
By which process does RNA become a protein?
translation
87
what are RNA and proteins?
functional end products of gene expression (sometimes RNA is the end product)
88
do proteins play many roles in the cell?
yes
89
name 3 types of protein..
any 3 from:
- structural proteins
- motor proteins
- catalytic proteins (enzymes)
- transport proteins
- storage proteins
- protective proteins
- regulatory proteins
90
Give an example of a structural protein
either collagen or keratin
91
give an example of a motor protein
myosin or dynein
92
give an example of an enzyme
hexokinase or DNA polymerase
93
give an example of a transport protein
hemoglobin or serum albumin
94
give an example of a storage protein
ovalbumin or ferritin
95
give an example of a protective protein
immunoglobulins or thrombin
96
give an example of a regulatory protein
insulin or somatostatin or somatotrophin
97
what's the structure of collagen?
long and thin
98
what does hemoglobin do?
transports O2 in RBCs
99
what does insulin do?
regulates sugar levels
100
do RNAs that do not translate play important roles in cells?
yes
101
what percent of RNA is coding RNA?
4%
102
what's the coding RNA?
mRNA (messenger)
103
what percent of RNA is noncoding?
96%
104
give 3 types of noncoding RNA
any 3 from
- rRNA
- tRNA
- snRNA
- snoRNA
- scRNA
- miRNA
- siRNA
105
What's rRNA?
ribosomal RNA
106
what's snRNA?
small nuclear RNA
107
What's tRNA?
transfer RNA
108
where are noncoding RNAs often found?
in intergenic regions
109
what does it mean if a gene is unique?
there's only one copy of this gene
110
what's a gene family?
a group of the same/similar genes
111
when do simple multi-gene families occur?
when genes are needed in large quantities
112
what's a complex multi-gene family?
where the genes aren't identical but have similar sequences- they code for similar but non- identical proteins
113
what's a tandem array?
a set of identical or very similar genes that are arranged one after the other in a group
114
do human globin genes form complex or simple multigene families?
complex
115
how many complex multigene families do globin genes form?
2
116
what are the 2 complex multigene families and where are they found?
the alpha-globin are on chromosome 16
| the beta-globin are on chromosome 11
117
when are hemoglobin genes expressed in humans?
at different stages in human development
118
By what process do genes in a multigene family arise?
gene duplication
119
what happens after gene duplication?
the sequences of the genes gradually change so the members of the gene family have slightly different sequences
120
the greater the time that has passed since the duplication....
... the more differences we see between the pair of genes
121
why do we see more differences between gene pairs after a longer time has passed?
more mutations to the base code have occured
122
what's a molecular clock?
a measure of the rate at which the sequence of a gene changes
123
what can molecular clocks show?
when a pair of genes were formed by duplication, allowing estimation of how long ago genes duplicated and diverted from each other (can study evolution)
124
what do you call genes that have lost their function?
pseudogenes
125
can pseudogenes become functional genes again?
yes, by mutation
126
How many pseudogenes are there in the alpha-globin family?
3
127
how many pseudogenes are there in the beta-globin familiy?
1
128
how does DNA replicate?
by semi-conservative replication
129
what is semi-conservative replication?
replication whereby half of the old information is included in the new molecule and the other half is new (gives 2 exact copies)
130
what were the other 2 possibilities of a mechanism for replication?
conservative and dispersive
131
How might conservative replication work?
- the parent molecule separates in to 2 strands
- semi-conservative replication occurs
- when strands rejoin the 2 old join together and the 2 new join together
132
what's dispersive replication?
where old and new DNA are mixed up in both strands
133
How might dispersive replication happen?
the parent molecule opens up into 2 strands
- a bit of new DNA is made
- the template switches repeatedly and old and new segments join
134
why was semi- conservative replication first thought impossible?
DNA is plectonemic- strands can't be separated without unwinding
many DNA molecules are circular making unwinding more difficult
135
what would happen if you made a double stranded cut to unwind circular DNA?
it would tighten up the helix
trying to unwind the DNA from one end would cause DNA at such a fast speed that the energy produced would destroy the DNA
136
which was the most popular theory of replication in the 1950s?
dispersive (due to the issue of unwinding)
137
What was the purpose of the meselson-stahl experiment?
to dsitinguish between the 3 modes of DNA replication and work out which occurs in E.coli bacteria
138
What was the method of the Meselson-Stahl experiment?
- A culture of bacteria were grown in a medium containing heavy Nitrogen (N15, instead of the normal N14)
- The bacteria colony was transferred to a growth medium containing normal Nitrogen (N14)
- Samples from this colony were removed after 20 minutes (1 cell division) and 40 minutes (2 cell division)
- The colonies were centrifuged
139
What were the findings of the Meselson-Stahl experiment?
- When grown in the heavy Nitrogen and centrifuged all bacteria appeared in the same band (15N), bacteria grown in normal Nitrogen (14) medium showed a higher up band (lighter)
- After one replication in lighter the medium, the bacteria band appeared in between where the 14 and 15 were
- after 2 replications, there was a band where N14 was and a band where the N14/15 was
140
Which method of replication did the meselson- stahl's findings support?
semi-conservative
141
what would meselson- stahl have seen if they had been conservative replication after 1 division?
2 bands- one for N14, one for N15
142
what would meselson and stahl have seen after one replication in dispersive replication?
what they did see- a band in between N14 and N15
143
what would meselson- stahl have seen after two divisions in dispersive replication?
one band- between N14 and N15 (same as first division)
144
which type of enzyme is reponsible for DNA strand separation/ unwinding?
DNA topoisomerases
145
What's the mode of action of a Type I DNA topoisomerase?
It makes a nick in 1 strand and passes the other through that nick to allow unwinding by releasing tension
146
What's the mode of action of a Type II DNA topoisomerase?
- it makes a double strand nick and one segment of DNA passes through the gap, unwinding this section, then the 2 cut strands are rejoined and the process repeats further down the strand
147
Which enzyme breaks the bonds between the base-pairs?
DNA helicase
148
what's the replication fork?
the open part of the DNA where the new strands of DNA are being synthesised
149
What's the process of DNA synthesis called? (2 names)
template-dependent DNA synthesis
and
DNA-dependent DNA synthesis
150
What enzyme carries out DNA-dependent DNA synthesis?
DN-dependent DNA polymerase
151
What direction is DNA synthesis always in?
5'-->3'
152
what's required to initiate the synthesis of a new DNA strand?
a primer
153
why is a primer needed to initiate the synthesis of a new DNA strand?
unknown
154
as well as synthesising DNA, what other function does DNA polymerase serve?
It can degrade DNA- exonuclease activity
155
How many types of exonuclease activity are there?
2
156
what are the names of the 2 types of exonuclease activity?
3'-->5'
and
5'-->3'
157
What happens during 3'-->5' exonuclease activity?
the polymerase can remove nucleotides it has just just inserted
this is called proofreading, allowing errors to be corrected
158
What happens during 5'-->3' exonuclease activity?
the polymerase can remove DNA already attached to the template
159
what are the 2 bacterial DNA polymerases?
I and III
160
what are the 2 eukaryotic DNA polymerases?
alpha (a) and delta
161
what's the function of DNA polymerase I?
DNA repair and replication
162
What's the function of DNA polymerase III?
main replicating enzyme- in bacteria
163
what's the function of DNA polymerase alpha?
priming during replication
164
what's the function of DNA polymerase delta?
main replicative enzyme- in eukaryotes
165
does DNA polymerase I have 3'-->5' activity?
yes
166
does DNA polymerase I have 5'-->3' activity?
yes
167
does DNA polymerase III have 3'-->5' activity?
yes
168
does DNA polymerase III have 5'-->3' activity?
no
169
does DNA polymerase alpha have 3'-->5' activity?
no
170
does DNA polymerase alpha have 5'-->3' activity?
no
171
does DNA polymerase delta have 3'-->5' activity?
yes
172
does DNA polymerase delta have 5'-->3- activity?
no
173
what must first happen at the replication fork?
the separated single strands must be protected
174
why must the the separated single strands be protected? (2)
they may just reattach to each other
or
be attacked by nucleases
175
what protects the separated single strands at the replication fork?
single-strand binding proteins (SSBs)
176
What's the leading strand?
The strand which can be synthesised by continuous DNA synthesis
177
Why can the leading strand be copied by continuous DNA synthesis?
It goes in the 5'-->3' direction (with the parent strand being read 3'-->5')
178
What's the primer for bacteria synthesis made of?
RNA
179
In bacteria, what makes the primer?
Primase enzyme
180
how long is the primer in prokaryotes?
4-15 nucleotides in length
181
What synthesises the new DNA strand after the primer has been made in prokaryotes?
DNA polymerase III
182
what happens after the primer attaches to the template stand in eukaryotic DNA?
the primer is extended by DNA polymerase alpha, which adds about 20 nucleotides
then DNA polymerase delta makes the rest of the new strand
183
How is DNA on the lagging strand synthesised?- generally
It's made in segments called Okazaki fragments
184
How are Okazaki fragments joined in bacteria?
DNA polymerase III stops when it reaches the RNA primer
DNA polymerase I continues synthesis
DNA ligase links the two DNA fragments
185
How are Okazaki fragments joined in eukaryotes?
DNA polymerase delta and helicase push aside the primer
FEN1 cuts the DNA at the branch point
there's still a missing phosphodiester bond between the okazaki fragments which is joined by DNA ligase
186
What does the enzyme telomerase do in eukaryotes?
prevents the ends of chromosomes from getting shorter
187
How does the enzyme telomerase prevent the ends of chromosomes from getting shorter?
it extends the parent DNA by adding the sequence TTAGGG several times so the final okazaki fragment can be primed
188
What's a genome?
the complete set of DNA molecules possessed by an organism
189
where does the replication of an E.coli genome begin?
the origin of replication (always the same position of the genome)
190
In E.coli, how is the direction of replication described?
bidirectional (goes in 2 directions)
191
describe the origin of replciation
- spans approx. 245 bp of DNA
| - contains 2 short repeat motifs (one is 9 nucleotides long, the other is 13)
192
what are origins of replication like in human DNA?
there are many on each chromosomal DNA molecule
| usually around 300kb apart from eachother
193
where do DNaA proteins bind?
close to the origin of replication
194
what happens to the DNA near the DNaA proteins?
it becomes wound around the barrel of these proteins
195
What does the winding of DNA around the DNaA proteins do?
causes torsional stress causing the base pairs at the origin of replication to break
196
what type of DNA is typically at the origin of replication? why?
A-T rich sequence
| because the bonds are weaker (2 H bonds rather than 3)
197
How is the prepriming complex formed and opened into replication forks?
by attachment of DNaB proteins to the origin on either end. This starts breaking base-pair bonds, opening up the DNA further, moving the replication forks further away from the origin of replication
198
What is synthesised as the double helix unzips?
new polynucleotides
199
what is DNaB?
a helicase enzyme
200
How is the primosome formed?
by the attachment of 2 primase enzymes
201
What do primase enzymes do at the primosome?
make the RNA primers that initiate replication
202
what's needed before DNA Polymerase III can begin to make DNA?
a special type of RNA polymerase that synthesizes the primers
203
describe events at the replication fork in E.coli?
- DNA topoisomerase separates the strands
- DNA helicase breaks base pairs
- single strand binding proteins (SSBs) protect the bare single strands
- primase makes primers on the lagging strand
- DNA polymerase III synthesizes DNA
- DNA polymerase I and DNA ligase joins up the okazaki fragment
- the gamma complex attaches and detaches polymerase III from the lagging strand
204
what's single binding proteins (SSBs) purpose?(2)
prevent attacks by nucleases- if the body treats the exposed single strand as viral genetic material
prevents base pairs from rejoining
205
describe events at the replication fork in humans?
- DNA topoisomerases separates strands
- helicase breaks base pairs
- SSBs protect the single bare strands
- primase/DNA polymerase alpha make primers on the lagging strand
- DNA polymerase delta synthesizes DNA
- FEN1 and DNA ligase join up the okazaki fragments
- the proliferating cell nuclear antigen (PCNA) holds DNA polymerase delta tightly onto the DNA
206
What is required due to the bidirectionality of replication in E.coli?
a point to stop (termination point) at (in case the replication in either direction is going at different speeds)
207
How many terminator sequences are there in the E.coli genome?
6
208
what binds to each of the terminator sequences in E.coli?
Tus protein
209
are the terminator sequences in E.coli directional? why?
- yes
- because they affect the direction at which the Tus protein binds, one side has protein oriented one way the other the opposite way
210
What do Tus proteins allow and disallow?
replication fork can pass in one direction but not the other
211
what's chromatin?
DNA extracted from the nucleus
| a DNA-protein complex
212
what structure is shown on the electron microscope image of chromatin?
beads-on-a-string structure (proteins are beads on DNA string)
213
How are the proteins distributed along DNA?
At regular intervals
214
what are the proteins in chromatin called?
histones
215
what do histones contain in high amounts?
basic amino acid content
216
what's a nucleosome?
the 'beads'
| an octamer of DNA wrapped around 8 histones
217
Which histones are found in a nucleosome?
2x H2A
2x H2B
2x H3
2x H4
218
How long is linker DNA between nucleosomes?
50-70 bp
219
What's Histone H1?
a linker histone
220
what does Histone H1 do?
attaches to the outside of the nucleosome
221
what is a chromatosome made up of?
nucleosome + DNA + linker histone
222
Is DNA static?
no (during replication it leaves the nucleosome package and remains in it when not in use)
223
How much does the beads on a string structure reduce the length of DNA?
by 1/6
224
What's the next level of packaging DNA?
30nm chromatin fibre
225
How much does the 30nm chromatin fibre reduce DNA length by?
another 1/7
226
are higher levels of packaging DNA after 30nm chromatin fibre understood?
no
227
what's the highest level of DNA packaging?
the metaphase chromosome
228
where is the metaphase chromosome found?
only in dividing cells (when chromosomes condense)
229
How is euchromatin seen under the microscope?
light areas
230
what does euchromatin contain?
active genes
231
what level of packaging is euchromatin at?
probably 30nm fibre
232
How is heterochromatin seen under the microscope?
dark areas
233
what does heterochromatin contain?
inactive genes
234
Is heterochromatin or euchromatin more densely packed?
heterochromatin
235
what's the difference between constitutive and facultative heterochromatin?
constitutive contains DNA that is tightly packed in all cells
facultative contains DNA that is tightly packed in some cells
236
what's the nuclear matrix?
a protein network which gives round structure to nucleus
237
what is euchromatin attached to and why?
the nuclear matrix to prevent the DNA from getting tangled up
238
what's the structure of a metaphase chromosome?
- centromere golds the daughter chromosomes together
| telomeres protect the ends
239
what do the centromeres contain?
special histones- CENP-A instead of H3
240
what do telomeres protect the ends of chromosomes from?
exonuclease attack
and
being mistaken for chromosome breaks and joining together
241
what are chromatids?
the arms of chromosomes
242
what forms telomeres?
telomerase
243
what's the karyogram?
a complete set of stained chromosomes
244
what does each chromosome show when stained?
a specific pattern of staining to that chromosome
245
what are the dark bands seen on chromosomes on the karyogram?
constitutive heterochromatin (where DNA/chromosomes are packaged more tightly)
246
define interphase
the period between cell divisions
247
what's a nuclease protection experiment?
a technique that uses nuclease digestion to determine the positions of proteins on DNA or RNA molecules
248
What's the UTR?
UnTranslated Region
249
what's a spacer?
an area of non-coding DNA between genes (different to introns which are non-coding within genes)
250
what's a cistron?
a section of DNA or RNA molecule that codes for a specific polypeptide in protein synthesis (a gene)
251
what 3 factors are required for the initiation of DNA replication in E.Coli?
Primase
DNA Helicase
DNaA
252
what's unusual about telomerase?
it contains an RNA component
