DNA structure and replication

Question 1

Gene definition

Answer 1

Basic physical and functional unit of heredity. Each gene is made up of DNA, with some genes coding for a particular protein. Specify phenotype at a gross level.

Question 2

Structure of a nucleotide

Answer 2

A nitrogenous base, five carbon monosaccharide -aldopentose - and phosphoric acid.

Question 3

4 DNA bases

Answer 3

Adenine, Thymine, Cytosine and Guanine

Question 4

Two different types of base explained

Answer 4

Purine- two rings and pyrimidine- one ring

Question 5

Which two bases are purines?

Answer 5

Adenine and Guanine

Question 6

Which three bases are pyrimidines?

Answer 6

Thymine, Cytosine, Uracil

Question 7

How are purines formed?

Answer 7

Derived from pyrimidines by addition of an imidazole group. Both bases have all their atoms in the same plane

Question 8

What is a nucleoside?

Answer 8

Compound formed by a nitrogenous base, purine or pyrimidine and aldopentose.

Question 9

Difference between nucleotide and nucleoside

Answer 9

Nucleotide contains a bound phosphate

Question 10

Nucleic acid definition

Answer 10

Linear macromolecule formed by the polymerisation of units called nucleotides. Extreme 5’ end has a free phosphate. extreme 3’ end has an OH

Question 11

How are nucleic acids formed?

Answer 11

Nucleotides linked to each other by phosphodiester bonds between the carbon 5’ of one pentose with the 3’ carbon of another,

Question 12

DNA structure

Answer 12

Formed of two, complementary nucleic acid chains producing a double helix with a clockwise rotation

antiparallel- one chain moving from 5’-3’ direction whilst the other ie 3’-5’

strong, highly hydrophilic sugar-phosphate backbone, with nitrogenous bases inside.

Bases bound to each other by hydrogen bonds, Adenine and Thymine = two, cytosine and guanine= 3

Space between turns is adequate to fit a pyrimidine and purine, too small for two purines and too wide for two pyrimidines.

Question 13

How many base pairs between each turn?

Answer 13

5 base pairs

Question 14

What is another force between base pairs?

Answer 14

Van der Waals, further increases stability

Question 15

What does the coiling of the DNA form? + function

Answer 15

Major and minor grooves parallel to the direction of the turns on the double helix. Allow interactions with transcription factors and other molecules.

Question 16

At what stage of the cell cycle is DNA replicated?

Answer 16

S phase

Question 17

What is the process of DNA replication? + what does it mean?

Answer 17

Semi Conservative replication. New DNA molecules will have one parent strand and one newly synthesised daughter strand.

Question 18

Process of semi conservative replication

Answer 18

1. Initiator proteins bind at the replication origin
2. DNA helicase separates the DNA strands at the replication origin
3. SSB proteins bind, preventing the DNA chain from reannealing
4. RNA polymerase binds to the chain and begins synthesising a primer in the 5’-3’ direction on both leading and lagging strands
5. DNA polymerase then binds to the primers and synthesises the new chains.

Question 19

What is the origin of replication?

Answer 19

Particular sequence of the genome where DNA replication begins. Place where the initiator proteins bind.

Question 20

Are there multiple origins of replication + why?

Answer 20

There are multiple, in order to increase the rate of DNA replication . Between 30,000-50,000

Question 21

What bases are often found at origins of replication? + why?

Answer 21

AT, as they have two hydrogen bonds, instead of 3, so les energy required to separate them.

Question 22

Function of SSB proteins

Answer 22

• prevent complementary strands re-hybridising
• stabilise single strand structure
• straighten DNA, preventing hairpin helices forming

Question 23

Topoisomerase function

Answer 23

Provides further stability by allowing free rotation of sections of DNA by partially cutting the DNA strand which releases the tension. Does not use ATP as uses energy from tension build up

Question 24

Replication fork definition and function

Answer 24

A structure that forms within the long helical DNA during DNA replication, created by helices. Resulting structure has two prongs, each made up of a single strand of DNA, providing a template for the leading and lagging strands.

The replication forks move away from each other, enabling bi-directional polymerisation.

Question 25

What do the replication forks form?

Answer 25

Bubbles or replicons

Question 26

How does the DNA polymerase move down the template strand? + why

Answer 26

Clamp loader protein attach a sliding clamp, preventing the DNA polymerase from easily dissociating

Question 27

DNA polymerase characteristics (4)

Answer 27

1. Their substrates are the four deoxyribonucleoside tri-phosphates dATP, dGTP, dCTP, dTTP. Provide the raw materials for the synthesis and the energy
2. Work on a single DNA strand to insert complementary nucleotides.
3. Unable to bind free nucleotides and start a strand- require a primer
4. Only catalyse the 5’-3’ direction, thus form one leading and one lagging strand

Question 28

Replisome definition

Answer 28

All proteins involved in DNA replication that form a multi enzyme complex.

Question 29

DNA polymerase function

Answer 29

Covalently links the free OH group on the 3’ carbon on the growing chain of nucleotides to the alpha-phosphate on the 5’ carbon of the next deoxyribonucleoside triphosphate; this releases the beta and gamma groups as a pyrophosphate and forms a phosphodiester linkage.

The release of pyrophosphate provides energy for the DNA polymerase.

Question 30

Why do DNA polymerase molecules only synthesise in the 5’-3’ direction?

Answer 30

• requires a free OH bond

- proof reading function would remove a nucleotide

Question 31

Polymerisation on the lagging strand stages

Answer 31

• DNA polymerase cannot synthesise in the 5’-3’ direction therefore synthesised in short segments called Okazaki fragments
• multiple primers formed, multiple DNA polymerases bind at the start of each Okazaki fragment, allowing them to extend in the 5’-3’ direction until they reach the next fragment and detach
• new Okazaki fragments form closer to replication fork origin
• DNA polymerase back stitches
• RNA primers broken down by nuclease then replaced by nucleotides.
• DNA ligase joins Okazaki fragments together

Question 32

How does DNA polymerase prevent mutations?

Answer 32

Has a high affinity for correct base pairings, which are energetically more favourable, thus incorrect pairings are more likely to dissociate

• exonucleolytic proofreading

Question 33

Explain exonucleolytic proofreading

Answer 33

If an incorrect nucleotide binds, the DNA polymerase removes it.

Question 34

Telomere definition and structure

Answer 34

A region of repetitive nucleotide sequences at each end of a chromosome which protects it from deterioration or fusion with neighbouring chromosomes .

Contains consultive heterochromatic DNA

Question 35

Why does the lagging strand of each chromosome shorten during DNA replication?

Answer 35

RNA primer forms on the end of the lagging strand and then is removed by a nuclease. DNA polymerase is unable to bind without a primary, thus the daughter strand is shorter.

Question 36

How is DNA shortening prevented?

Answer 36

Telomerase, an enzyme with an RNA component binds. It is a reverse transcriptase, so enables a complementary strand of DNA to then be synthesised

Question 37

Function of telomerase in cancers

Answer 37

Continues the replication of damaged DNA, preventing cell senescence

Question 38

antisense vs sense

Answer 38

antisense strand is the template strand

sense strand is the complementary strand to the antisense strand (forming the mRNA)