Dna Structure And Replication

Front 1

Why is DNA important?

Back 1

- Encodes our genes
- Molecular basis for inheritance
- Contains code for all other cellular molecules
- Of complementary structure, allows replication and reading of the code
-Varieations in DNA sequence leads to phenotypic differences and susceptibility to disease
-Defects in DNA replication and repair lead to many diseases

Front 2

Describe the structure of overall DNA

Back 2

- Sugar+phosphate (backbone) and nitrogenous base = nucleotide

- Double stranded molecule coiled = DNA double helix

- Each strand has a 5 prime end and a 3 prime end (written 5' and 3')

Front 3

What is a Nucleoside?

Back 3

Nucleotide without the phosphate group (i.e. sugar backbone and nitrogenous base)

Front 4

Spell out the names of the nitrogenous bases

Back 4

- Adenine

- Cytosine

- Thymine

- Guanine

Front 5

Classsify the DNA's nitrogenous bases

Back 5

- Purine: A, G (remember Pure And Good - two o, so double ringed structure)

- Pyrimidine: T, C (the other one with one ring)

Front 6

Describe the hydrogen bonding pattern in A-T and C-G base pairs

Back 6

A-T: 2 hydrogen bonds

C-G: 3 hydrogen bonds (think G has three straight lines in it)

Front 7

In the Anti-parallel DNA strand, how is the 3' different from the 5' end.

Back 7

- 3' end: unlinked OH group on the sugar backbone

- 5' end: Free phosphate group on the sugar backbone

Front 8

Describe the Compaction of the DNA at Interphase and metaphase of mitosis

Back 8

- Each cell has ~ 2 metres of DNA

~ 1,000x compaction at interphase

~ 10,000x compaction at metaphase

Front 9

Name the main stages of mitosis

Back 9

Interphase, Prophase (early and late), (prometaphase before) Metaphase, Anaphase, Telophase, Cytokinesis

(remember IPMATC or "I'll Probably Make Another Telephone Call)

Front 10

Describe vaguely what happens at each mitotic stage

Back 10

Interphase : the interval, chromosomes are invisible

Prophase: the first, chromosomes are visible

Metaphase: M for middle, chromosomes line up on the cell's equator

Anaphase: A for Apart, chromosomes split apart

Telophase: chromosomes once again invisible within their own nuclei

Cytokinesis: formation of two distinct daughter cells

Front 11

What protein is DNA wrapped around?

And How many types of this protein are there?

Name them.

Back 11

- Histone protein

- 5 types: 1 Linker Histone, 4 Core histones

- Linker histone: Histone H1

- Core histones: H2A, H2B, H3, H4

Front 12

Describe compaction of DNA from loose strands to mitotic chromosome

Back 12

- Short region DNA double helix: 2nm

- Nucleosomal fibre: 11nm

- Chromatin fiber of packed nucleosomes: 30nm

- Section of chomosome in extended form (chromatine loops): 300nm

- Condensed section of chromosome (condensed chromatine loops): 700nm

Bold section are coiled 1,000x

- Entire mitotic chromosome: 1400nm

This section is coiled 10,000x

Front 13

Indepth look at the Nucleosomal fibre

Back 13

~200 nucleotide pairs of DNA between linker DNA and furthest end of core histone

Front 14

Visual representation of compaction DNA sections

Back 14

Front 15

Visual representation of compaction DNA sections

Back 15

Front 16

DNA replication semi-conservative, why?

Back 16

Each daughter DNA contains half of a new strand and half a template (original) strand

Front 17

Where does replication start

Back 17

At origins fo replication

Front 18

State the direction in which replication occurs

Back 18

Always 5' to 3' direction (therefore leading strand always at 5')

Front 19

What is an Okazaki Fragment

Back 19

Discontinuously synthesised DNA fragments associated with the lagging strand template (5' to 3') - these require RNA priming, which serve as beginning of the Okazaki fragments

Front 20

What is a replication bubble

Back 20

Enclosed area within which replication occurs

Front 21

What is a replication fork

Back 21

Point at which the two DNA strands separate to allow replication of DNA

Front 22

Which enzyme prevents DNA supercoiling

Back 22

Tropoisomerase (acts by cutting strand of DNA to relax the supercoiling of the DNA as it unwinds for replication)

Front 23

Describe the action of antibiotics on DNA replication, when Topoisomerase is targeted.

Back 23

Supercoiling of the DNA and the double strand breaks, therefore replication prevented

Front 24

Given an example of an anti-biotic which targets Tropoisomerase in E.coli

Back 24

Quinolones

Front 25

Which antibiotics target nucleotide synthesis?

which types of bacteria species do they target?

Back 25

Co-trimoxazole = Trimethoprim - Sulfamethoxazole in a 1/5 ratio

aerobic Gram-positive and Gram-negative species

Front 26

Give examples of Fluoroquinolones

Back 26

Nalidixic acid

Ciproflaxin

Levofloaxacin

Gemifloxacin

Front 27

Which enzyme in DNA replication do Fluoroquinolones target?

Back 27

Topoisomerases

Front 28

What type of bacteria species are targeted by Fluoroquinolones?

Back 28

Aerobis Gram-positive and Gram-negative species,

some anaerobic Gram-negative species

and M.tuberculosis

Front 29

Give a special characteristic of DNA Polymerase

Back 29

It has both additive and editing section for replication and repair of errors during replication

Front 30

How are replication mistakes detected, and edited?

Back 30

DNA polymerase proofreads the nucleotides layed down, using 3' to 5' exonuclease proofreading (cleaving nucleotides one at a time from the end of a polynucleotide chain).

The scan is in the opposite direction to replication, and if nucleatide is mismatched the entire holoenzyme backs up and repairs the fault in a 3' to 5' direction.

Before continuing replication (5' to 3' end).

Front 31

Which enzyme fuses DNA nucleotides together?

Back 31

DNA ligase

Front 32

Which enzyme cuts DNA strands?

Back 32

DNA nuclease

Front 33

What are the 3 methods of general DNA repair?

Back 33

Base excision repair

Nucleotide excision repair

Mismatch repair

Front 34

Explain what is meant by "Base excision repair" (hint: recognition of specific non-bulky lesions)

Back 34

DNA repair method: DNA Glycosylase initiates the repaire - recognizes and removes specific damaged/innappropriate bases.

This forms AP sites

AP sites cleavaged by AP endonuclease.

Resolting single strand has correct nucleotide added by DNA Polymerase. DNA Ligase allow the sugar-phosphate backbone to be sealed.

Front 35

Explain what is meant by "Nucleotide excision repair"

Back 35

Repair to DNA damaged by UV light (UV damages results in large damage).

Damaged single strand recongnised, cut by DNA Nuclease.

DNA segment containing the abnormality is removed by DNA Helicase.

Undamaged single strand used by DNA polymerase as template for synthesis of a short complementary strand.

DNA ligase carries out final ligation.

Front 36

Explain what is meant by "Mismatch repair"

Back 36

Strand-specific repair.

MutS binds to mismatched base pair

MutL scans nearby DNA for nick and triggers strand removal to the mismatch

Front 37

What are the names of the Mismatch Proofreading Proteins?

Back 37

MutS

MutL

Front 38

What is DNA Nick?

Back 38

Discontinuation in a double stranded DNA molecule, where there is no phosphodiester bond between adjacent nucleotides of one strand.

Occurs due to damage or enzyme action.

Front 39

What 2 repairs can be done on Double strand breaks?

Back 39

- Non-homologous end joining

- Homologous recombination

N.B. At breakage site, loss of nucleotides due to degradation from ends

Front 40

What is Non-homologous end joining?

Back 40

broken strands joined and loss of nucleotides not rectified.

Segment now altered, possible loss genes

Front 41

What is Homologous end-joining?

Back 41

Copying process involving homologous recombination.

i.e. locate its identical 2nd chromosome and copies it to completely restore the broken DNA sequence

Front 42

Clinical consequences of defective repair mechanism.

A) Nucleotide excision repair

Give Name and Phenotype

Back 42

N: Xeroderma pigmentosum (XP)

P: Skin cancer, cellular UV sensitivity, neurological abnormalities

Front 43

Clinical consequences of defective repair mechanism.

B) Mismatch repair

Give Name and Phenotype

Back 43

N: MutS, MutL

P: Colon Cancer

Front 44

Clinical consequences of defective repair mechanism.

C) Repair of homologous recombination

Give Name and Phenotype

Back 44

N: BRCA2

P: Breast & ovarian cancer

Front 45

What is Topoisomerase?

Back 45

An enzyme that regulate the winding and unwinding of the DNA i.e. at Replication and Transcription