DNA structure and replication Flashcards
Gene definition
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.
Structure of a nucleotide
A nitrogenous base, five carbon monosaccharide -aldopentose - and phosphoric acid.
4 DNA bases
Adenine, Thymine, Cytosine and Guanine
Two different types of base explained
Purine- two rings and pyrimidine- one ring
Which two bases are purines?
Adenine and Guanine
Which three bases are pyrimidines?
Thymine, Cytosine, Uracil
How are purines formed?
Derived from pyrimidines by addition of an imidazole group. Both bases have all their atoms in the same plane
What is a nucleoside?
Compound formed by a nitrogenous base, purine or pyrimidine and aldopentose.
Difference between nucleotide and nucleoside
Nucleotide contains a bound phosphate
Nucleic acid definition
Linear macromolecule formed by the polymerisation of units called nucleotides. Extreme 5’ end has a free phosphate. extreme 3’ end has an OH
How are nucleic acids formed?
Nucleotides linked to each other by phosphodiester bonds between the carbon 5’ of one pentose with the 3’ carbon of another,
DNA structure
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.
How many base pairs between each turn?
5 base pairs
What is another force between base pairs?
Van der Waals, further increases stability
What does the coiling of the DNA form? + function
Major and minor grooves parallel to the direction of the turns on the double helix. Allow interactions with transcription factors and other molecules.
At what stage of the cell cycle is DNA replicated?
S phase
What is the process of DNA replication? + what does it mean?
Semi Conservative replication. New DNA molecules will have one parent strand and one newly synthesised daughter strand.
Process of semi conservative replication
- Initiator proteins bind at the replication origin
- DNA helicase separates the DNA strands at the replication origin
- SSB proteins bind, preventing the DNA chain from reannealing
- RNA polymerase binds to the chain and begins synthesising a primer in the 5’-3’ direction on both leading and lagging strands
- DNA polymerase then binds to the primers and synthesises the new chains.
What is the origin of replication?
Particular sequence of the genome where DNA replication begins. Place where the initiator proteins bind.
Are there multiple origins of replication + why?
There are multiple, in order to increase the rate of DNA replication . Between 30,000-50,000
What bases are often found at origins of replication? + why?
AT, as they have two hydrogen bonds, instead of 3, so les energy required to separate them.
Function of SSB proteins
- prevent complementary strands re-hybridising
- stabilise single strand structure
- straighten DNA, preventing hairpin helices forming
Topoisomerase function
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
Replication fork definition and function
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.
What do the replication forks form?
Bubbles or replicons
How does the DNA polymerase move down the template strand? + why
Clamp loader protein attach a sliding clamp, preventing the DNA polymerase from easily dissociating
DNA polymerase characteristics (4)
- Their substrates are the four deoxyribonucleoside tri-phosphates dATP, dGTP, dCTP, dTTP. Provide the raw materials for the synthesis and the energy
- Work on a single DNA strand to insert complementary nucleotides.
- Unable to bind free nucleotides and start a strand- require a primer
- Only catalyse the 5’-3’ direction, thus form one leading and one lagging strand
Replisome definition
All proteins involved in DNA replication that form a multi enzyme complex.
DNA polymerase function
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.
Why do DNA polymerase molecules only synthesise in the 5’-3’ direction?
- requires a free OH bond
- proof reading function would remove a nucleotide
Polymerisation on the lagging strand stages
- 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
How does DNA polymerase prevent mutations?
Has a high affinity for correct base pairings, which are energetically more favourable, thus incorrect pairings are more likely to dissociate
- exonucleolytic proofreading
Explain exonucleolytic proofreading
If an incorrect nucleotide binds, the DNA polymerase removes it.
Telomere definition and structure
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
Why does the lagging strand of each chromosome shorten during DNA replication?
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.
How is DNA shortening prevented?
Telomerase, an enzyme with an RNA component binds. It is a reverse transcriptase, so enables a complementary strand of DNA to then be synthesised
Function of telomerase in cancers
Continues the replication of damaged DNA, preventing cell senescence
antisense vs sense
antisense strand is the template strand
sense strand is the complementary strand to the antisense strand (forming the mRNA)
