Genetics - DNA replication Flashcards
(80 cards)
1
Q
what important tasks do cells need to complete before they divide?
A
grow
copy its genetic material (DNA)
physically split into two daughter cells
2
Q
what two major phases is the cell cycle divided into?
A
interphase and mitosis (M) phase
3
Q
what happens during interphase?
A
G1, S, G2
the cell grows and makes a copy of its DNA
4
Q
During the mitotic phase, what happens?
A
the cell separates its DNA into two sets and divides its cytoplasm, forming two new cells
5
Q
at each cell division, what must a cell do?
A
it must copy its genome
it is essential that this process occurs accurately
6
Q
Semi-conservative replication?
A
DNA acts as a template for its own replication
7
Q
what type of replication does DNA replicate by?
A
semi-conservative replication
8
Q
what does DNA helicase do?
A
unwinds the DNA
9
Q
What does DNA polymerase do?
A
synthesises DNA 5’-3’ direction
10
Q
what does DNA topoisomerase do?
A
relieves the tension in DNA
11
Q
What does DNA primase do?
A
synthesises RNA primers
12
Q
what do ribonucleases do?
A
degrades RNA primers
13
Q
what does DNA ligase do?
A
joins DNA fragments
14
Q
what does telomerase do?
A
replicates the ends of the chromosome
15
Q
DNA unwinding?
A
DNA helicase
SSB
DNA topoisomerase
16
Q
DNA helicase function?
A
unwinds the DNA
uses ATP to propel itself along the DNA
17
Q
SSB? Function?
A
SSB - single-stranded DNA binding protein
Binds and keep the strands apart
18
Q
DNA topoisomerase function?
A
relieves the tension
19
Q
DNA synthesis process?
A
DNA polymerase requires a template
DNA polymerase requires a primer
A new strand of DNA is always synthesised in a 5’ to 3’ direction
it elongates from a free 3’OH
Synthesis begins at an origin replication
20
Q
DNA primase?
A
synthesises short RNA primer
21
Q
primer?
A
short segment of RNA complementary to the template with a 3’OH
22
Q
3’OH?
A
3 prime hydroxyl group
23
Q
DNA replication progresses in the –>
A
5’-3’ so replication on the leading strand is continuous
24
Q
As DNA replication cannot progress in the opposite direction…
A
replication on the lagging strand is discontinuous
25
Okazaki fragments?
the short DNA sequences (100-1000 nucleotides) synthesised on the lagging strand
26
DNA helicase results in the formation of a...
replication fork
27
exonuclease?
removes all of the RNA primers --> another DNA polymerase molecule fills these gaps with DNA nucleotides
28
How does the DNA polymerase remain attached to the DNA template?
by interaction with a protein called sliding clamp
29
when does a new sliding clamp come in?
a new clamp has to be loaded on the lagging strand as each Okazaki fragment is synthesised
30
What happens with the lagging strand?
DNA primase attaches RNA to template
DNA polymerase III adds nucleotides until it reaches the previous primer
RNase H digests the RNA primer, leaving a gap
DNA polymerase I fills in the gaps
DNA ligase then joins the fragments together
31
telomerase?
elongates parental strand
end problem
32
what are telomeres?
repetitive regions at the very ends of chromosomes are called telomeres
33
what do telomeres act as?
act as caps that protect the internal regions of the chromosomes, and they're worn down a small amount in each round of DNA replication
34
Depurination?
no DNA breaks
removal of purines
removal of guanine or adenine base to leave sugar-phosphate group
35
Deamination?
no DNA breaks
results in a C to U transition
e.g. conversion of cytosine to uracil
36
What is a gain of function mutation?
A DNA sequence change that leads to increased or alternative activity
37
What is a loss of function mutation?
A DNA sequence change that leads to decreased activity
38
silent mutation?
when a nucleotide substitution results in a different codon that still encodes the same amino acid - therefore the protein is unaffected in function and the phenotype of the organism is not significantly altered
39
Missense mutation?
when a nucleotide substitution results in a codon that encodes a different amino acid - therefore the primary protein sequence is altered which may be conservative or radical
40
what is a conservative substitution?
similar amino acid R group size and charge
similar protein shape and function
e.g. Gly --> Ala
41
radical substitution?
new amino acid R group different in charge or size
protein may have altered secondary or tertiary structure affecting function
42
consequences of missense mutation?
conservative substitution
radical substitution
disrupting functional or structurally important residues
43
Nonsense mutations?
when a nucleotide substitution results in a stop codon that stops translation, therefore the protein truncated and may not function properly or even at all
44
what is protein truncation?
shortening due to change of sequence resulting in stop codon
45
NMD?
nonsense mediated decay
a process during translation that detects transcripts with premature stop codons and degrades them
46
3 mechanisms for DNA repair
Excision
Repair
Joining
47
excision?
recognition and removal of damage
exonuclease
48
repair?
re-synthesis of missing DNA
DNA polymerase
49
Joining?
sealing the nick
DNA ligase
50
Mismatch repair?
DNA replication makes a mistake 1 in 10(7) nucleotides copied - mismatch repair reduces this to 1 in 10(9)
51
What do RNA primers provide when we are creating the lagging strand?
the 3' OH groups at regular intervals along the lagging strand template
52
when does the lagging strand stop?
it stops short of the end of the lagging strand template
53
why do chromosomes get progressively shorter during each replication cycle?
because there is an inability to replicate the ends as there is
no 3' OH group available to prime DNA synthesis
54
what solves the end replication problem?
solved by the enzyme telomerase
55
telomere?
G-rich series of repeats
56
where is a telomere found?
in the ends of chromosomes
57
what does telomerase do?
recognises the tip of an existing repeat sequence, using an RNA template within the enzyme
telomerase elongates the parental strand in the 5' to 3' direction and adds additional repeats as it moves down the parental strand
58
how is the lagging strand completed?
by DNA polymerase alpha, carries a DNA primase as one of its subunits - allows the ends to be completely copied in the new DNA
59
What is the problem in the lagging strand?
Okazaki fragments cannot cover the end of the chromosome
60
Why can the other primers throughout the lagging strand be replaced, apart from the end one?
there is no way to get the fragment started because the primer would fall beyond the chromosome end
61
What happens in each round of replication because of the problem in the telomeres?
part of the DNA at the end of a eukaryotic chromosome goes uncopied in each round of replication
62
part of the DNA at the end of a eukaryotic chromosome goes uncopied in each round of replication - what does this result in?
leaves a single-stranded overhang.
63
part of the DNA at the end of a eukaryotic chromosome goes uncopied in each round of replication - what happens over multiple rounds of cell division?
the chromosome will get shorter as this process repeats
64
what is telomerase?
an enzyme which is an RNA-dependent DNA polymerase, meaning an enzyme that can make DNA using RNA as a template
65
what is the solution for the problem caused in telomeres?
the enzyme binds to a special RNA molecule that contains the sequence complementary to the telomeric repeat
66
telomere solution, the enzyme binds to a special RNA molecule that contains the sequence complementary to the telomeric repeat - what happens after this?
telomerase recognises the tip of an existing repeat sequence and uses the RNA template within the enzyme to add additional repeats to the telomere DNA
67
Telomere - solution, telomerase recognises the tip of an existing repeat sequence and uses the RNA template within the enzyme to add additional repeats to the telomere DNA - what happens after this?
when the overhang is long enough, a matching strand can be made by DNA polymerase alpha, which has its own primase subunit - so DOESN'T NEED A PRIMER
68
how does the active site help with 'proof-reading' and 'fidelity'?
active site geometry only accommodates A-T & G-C base pairs
69
How is the 'proof-reading' carried out?
3' to 5' exonuclease activity
70
what can cause damage to DNA?
can be damaged as a result of UV light, ionising radiation exposure, toxic chemical agents, reactive oxygen species
71
What can DNA damage result in?
results in mutations in genes that can lead to altered coding for proteins resulting in loss or gain of functions
72
how many errors does a typical mammalian cell accumulate in its DNA every 24 hours?
many thousands of errors
73
What type of damage arises from UV light exposure?
Thymidine Dimers
74
What are the types of damages to the DNA?
Double stranded breaks, thymidine dimers, depurination, deamination
75
What kind of damage are we talking about when we say 'thymidine dimers'?
two adjacent thymine bases become covalently attached to each other --> leads to stalling of the replication machinery
76
Failure to repair thymidine dimer leads to?
this is the problem in xeroderma pigmentosum
77
what causes double stranded breaks?
some environmental factors such as high energy radiation
78
what happens during double stranded breaks?
chromosomes are literally split in two
79
In double stranded breaks, what depends on where the break is and how extensive the damage is?
depending on these two factors, large numbers and the information they encode can be lost
80
