DNA structure and replciation Flashcards
(42 cards)
1
Q
Why is DNA important
A
- DNS encodes for genes
- Molecular basis for inheritance
- Contains the code for all other cellular molecules
- Complimentary structure allows it to be replicated and the code to be read
- Variations in DNA sequence lead to phenotypic differences and susceptibility to disease
- Defects in DNA replication and repair lead to many diseases
2
Q
what is a nucleotide made out of
A
- made out of a nitrogenous base, a pentose sugar called deoxyribose and a phosphate group
3
Q
what do nucleotides join together to make
A
they join together to make a DNA strand
4
Q
what happens when DNA wraps around histone proteins
A
they form nucleosomes
5
Q
what do nucleosomes form during compaction
A
chromatins
6
Q
describe the structure of the DNA
A
- They have an antiparallel strand which means they go in opposite directions, one goes 5 to 3 and the other goes 3 to 5 direction
- There are two groups purine and pyrimidine - The nucleotides are joint by phosphodiester bonds between the phosphate group of one nucleotide and the carbon on another nucleotide
- GC are held together more tightly due to 3 hydrogen bonds, this affects structure and function of the chromosome
- No bonds between adjacent nucleotides other than the sugar phosphate backbone
7
Q
what are the purine bases
A
adenine and guanine
8
Q
what are the pyrimidine bases
A
thymine and cytosine
9
Q
how many rings does purine have versus how many rings does pyrimidine have
A
purine has two nitrogenous bases whereas pyrimidine has 1 nitrogenous base
10
Q
how many hydrogen bonds join A and T
A
2
11
Q
how many hydrogen bonds join C and G
A
3
12
Q
whats the difference between 5 prime and 3 prime ends
A
- In the 5 direction there is a free phosphate group on the sugar backbone whereas in the 3 position there is an unlinked OH group on the sugar backbone
13
Q
what is the central dogma
A
- DNA sequence is the template for RNA
- DNA is transcribed and it becomes RNA and forms base triplets
- Base triplets join to amino acids during translation and forms a protein
14
Q
what does each cell have
A
2 metres of DNA
15
Q
what are the core proteins that make up the histone that the nucleosome wraps around
A
- made up of 8 histone molecules these are called core histone proteins
- 2x H2A
2x H2B
2x H3
2x H4
and there is only one linear histone called H1
16
Q
describe the compaction of nucleotides into the nucleosomes and nucleosomal fibre
A
- DNA wraps around a histone twice, to give the nucleosomal fibre
- DNA between the two nucleosomes is called linker DNA
17
Q
describe the compaction of nucleosomes into chromatin
A
- nucleosomal fibre is folded into chromatin
- Forms a 30-nanometre chromatin fibre is formed of the way the nucleosomes bend
- The 30 nm chromatin fibre has to fold, it loops and folds around
- At interphase it is 1,000x compaction and at metaphase it is 10,000 x compaction
- chromatin is further supercoiled into chormosomes
18
Q
describe the structure of semi-conservative replication
A
- Semiconservative replication happens in S phase (synthesis phase)
- Both the parent strands are used as a template once they separate this allows new DNA to pair to the strands if they have complimentary nitrogenous bases
- The process is called semi-conservative replication as there is always part of the original DNA that remains in the strand.
19
Q
describe semiconservative replication
A
- DNA helicase unwinds the double helix breaking the hydrogen bonds
- Results in 2 separate strands
- 2 unwound strands used as templates to create 2 complementary DNA strands
- 2 strands: the leading strand (3’ to 5’) and the lagging strand (5’to3’)
- Strand separation creates a replication form
- Origins of replication is where the replication fork forms and the origin spreads along the whole strand resulting in 2 daughter strands fir each parent strand
- New complementary daughter strand must be created in 5’ to 3’ direction - At the leading strand
- Strand is read 3 to 5
- RNA primase binds to the end of the strand and lays down a primer segment this is the start point for replication
- DNA polymerase binds next to the primer and reads along the strand adding new nucleotides creating complementary strands
- Complementary strand created in the 5 to 3 direction, DNA polymerase can only add nucleotides this way
- DNA ligase travels and seals new DNA sequence resulting in daughter strand - The lagging strand
- New complementary strand created in fragments (DNA polymerase can only create in 5 to 3 direction)
- Several primers made along the strand by RNA primase these are known as okazaki fragments
- DNA polymerase continues to add complementary nucleotides after primers in 5 to 3 direction
- DNA ligase travels and seals new DNA sequence resulting in daughter strand
20
Q
what does topoisomerase enzymes do
A
prevents supercoiling of DNA and allows it to relax again
21
Q
what do quinolone do
A
- Quinolones target topoisomerase enzyme and lead to supercoiling of DNA and causes the double strand to break
22
Q
describe the example of quinolone targeting topoisomerase
A
- An example on quinolones targeting topoisomerase is in E.coli bacteria, in E.coli there is a closed circular template when it goes through DNA replication there is an unwound duplex and an overwound region, topoisomerase prevents the supercoiling of DNA and therefore the quinolones targeting these means that the e.coli can no longer replicate
23
Q
give an example of quinolone antibiotics targeting topoisomerase
A
- fluroquinolones - they cause the DNA to supercoil and the double strand to break
24
Q
give some examples of fluroquinolones
A
- nalidixic acid
- ciproflaxacin
- levofloxacin
- gemifloxacin
25
what target topoisomerase do fluroquinolones target
- aerobic gram-positive and gram-negative species,
- some anaerobic gram-negative species
- M.tuberculosis
26
give an example of antibiotics that target nucleotide synthesis
- Trimethoprim – sulfamethoxaole
27
name an example of trimethoprim-sulfametoxoaole
- co-trimoxaxzole =trimethoprim:sulfamethoxazole = 1:5
28
what target nucleotide synthesis does trimethoprim sulfamethoxaolet target
aerobic gram-positive and gram-negative species
29
what does DNA polymerase have
- DNA polymerase has separate sites for DNA synthesis and editing
- One part is used for adding the nucleotides
- One part detects where the code is abnormal and induces the editing system
30
describe the editing process
- DNA polymerase synthesises DNA during semi-conservative replication
1. If the DNA polymerase adds an incorrect nucleotide and the polymerase detects this
2. Polymerase removes the incorrect nucleotides by 3 to 5 editing
3. Then the correctly paired 3 end allows addition of the next nucleotide
4. Synthesis continues in the 5 to 3 direction
31
define single strand defects
abnormal replication that only affects one strand
32
what are the single strand defects
- Base excision repair
- Nucleotide excision repair
- Mismatch repair
33
describe base excision repair
- For example a there is a chemically abnormal cytosine and it has become a uracil and therefore it is wrong joined to the G,
- Uracil DNA glycosylase removes the U from the base
- Another enzyme removes the sugar-phosphate backbone
- The DNA polymerase adds new nucleotides and the DNA ligase seals the nick
34
describe nucleotide excision
- There is a pyrimidine dimer, this is a joint between the nitrogenous groups
- A nuclease removes DNA strand (in bacteria removes 12 nucleotides) by DNA helicase
- DNA ligase and polymerase replace the whole strand
35
describe DNA mismatch repair
- MutS binds to the mismatched base pair and MutL Looks nearby DNA for nick and triggers strand removal to the mismatch
- Error in a newly made strand
- Therefore there is binding of mismatch proofreading proteins
- MutS binds to mismatched base pair and MutL DNA starts scanning and detects a nick in the new DNA strand
- The strand is then removed
- And DNA is repaired
36
what are double strand breaks
abnormality with both strands
37
what are the two types of double strand breaks
- Non-homologous end joining
| - Homologous recombination
38
describe what happens when there is a double strand break
- There is an accidental break
- This leads to loss of nucleotides due to degradation from ends due to enzymes cleaning them up therefore they are no longer complimentary to each other, smooth ends are created
- It can either go to non-homologous end joining or homologous end joining
- Non-homologous end joining Is when the region has altered segment due to missing nucleotides, the two ends join together and DNA nucleotides are lost
- In homologous end joining is when a copying process is used involving homologous recombination, this is the complete sequence restored by copying from the second chromosome
39
what are some examples of inherited DNA repair defects
- xeroderma pigmentosum
- mutS and mutL
- BRCA2
40
describe the affected process that xeroderma pigmentosum affects and the phenotype it causes
- affected process that no longer works is; Nucleotide excision repair
- phenotype is:Skin cancer, cellular UV sensitivity, neurological abnormalities
41
Describe the affected process that MutL and MutS affects and the phenotype that it causes
- affected process: mismatch repair
| - phenotype: colon cancer
42
Describe the affected process that BRCA2 affects and the phenotype that it causes
- affected process; repair by homologous recombination
| - phenotype caused; breast and ovarian cancer
