Molecular Biology & Genetics 1 - DNA Structure & Replication Flashcards
What did Chargaff investigate?
The different amounts of A, T, C, and G in different species
What did Chargaff find?
That there is different amounts of each base in different species and the amounts of A and T were similar within a species and so were C an G
What was Chargaff’s conclusion?
There is significant DNA variation between species, thus DNA could be the genetic material
What was Chargaff’s first rule?
A=T and C=G
What was Chargaff’s second rule?
The composition of DNA varies between species
What happened after it was proven that DNA was the genetic material?
It was discovered that the DNA structure is a double stranded helical molecule with particular features
What did the X-ray diffraction pattern of DNA show?
DNA has a helical structure, the bases are arranged perpendicular to the length of the DNA molecule and it is double stranded
What wasn’t shown by the X-ray diffraction pattern of DNA?
The arrangement of the bases
What was indicated in the X-ray diffraction pattern that allowed inferences to be made about base arrangement in DNA?
There is a constant diameter which meant that the base pairs must each include a purine and a pyrimidine (A=T and C=G)
How are nucleotides connected?
Nucleotide monomers are joined together with phosphodiester bonds which are covalent to form a polynucleotide = nucleic acid (deoxyribonucleic acid for DNA)
How does the phosphodiester bond form?
The hydroxyl group (OH) on the 3rd carbon of one nucleotide reacts with the phosphate group attached to the 5th carbon on another molecule
What is the product of phosphodiester bonds forming?
Water
How are DNA and RNA synthesised?
They are synthesised in the 3’ to 5’ direction meaning that new bases attach to the 3’ end
What is the direction of the two DNA strands?
The two strands are antiparallel and form a double stranded helix which isn’t uniform
What stabilises the DNA structure?
Hydrogen bonds between the complementary base pairs
How many hydrogen bonds between A and T?
2
How many hydrogen bonds between C and G?
3
What did the Watson Crick Model of DNA provide?
A stimulus for deciphering the genetic code and a possible mechanism for DNA replication
What happens during semi-conservative replication of DNA?
Each DNA strand of the double helix is used as a template strand for the synthesis of two new strands. Complimentary bases join with each other
What is the result of semi-conservative replication?
2 strands of DNA which each contain one parent (old) strand and one new strand which is why it is called semi-conservative
Why does DNA replication need to occur?
So that when the body needs to make new cells, each cell has a copy of the genetic information
When are new cells made?
At different growth stages, pregnancy and repair of injury
What direction do the parental template strands run in?
3’ to 5’
How many pairs of chromosomes are in humans?
23
How are chromosomes described?
large linear
Where does replication occur and why?
In regions which are rich in AT as this means there is less force holding the strands together and they’re easier to pull apart
How is Eukaryotic DNA Replication described?
Bidirectional
What is needed for a DNA copy to be made?
Progressive addition of new nucleotides, a starting point for new nucleotide addition, unwinding of the helical double-stranded DNA, release of tension, prevention of double-stranded DNA reforming and protection of it, joining of end of newly synthesised strands together
What enzyme allows for the progressive addition of new nucleotides?
DNA polymerase III
What enzyme gives a starting point for nucleotide addition?
Primase
What unwinds the helical double-stranded DNA?
Helicase
What releases the tension in DNA?
Topoisomerase
What prevents the double helix reforming and protects it?
Single strand DNA binding proteins
What joins newly synthesised fragments together?
DNA Ligase
What is the leading strand?
It is the strand which forms first and is continuously synthesised in the 5’ to 3’ direction
What is the lagging strand?
It is formed second and discontinuously synthesised in the 5’ to 3’ direction as Okazaki fragments
Replication is semi-
Discontinuous
What happens as the replication bubble gets larger?
Theleading strand gets longer and more fragments are added to the lagging strand
What is primase?
A type of RNA polymerase that makes and RNA primer which has an internal 3’ OH group to be used as a starting point for DNA polymerisation
How does primate move?
When making fragments it jumps further back each time a new fragment is added to begin each one
What do single strand binding proteins do?
Bind to the single strand and prevent the parental strands from coming back together and being degraded
What does DNA polymerase III need?
An OH group which the phosphate group of the incoming nucleotide can be attached to
What is DNA polymerase III?
An enzyme that synthesises a new NDA strand by adding nucleotides complementary to the parental strands. Single stranded binding proteins are kicked off as it does this.
What does helices do?
Unwinds the DNA strand and creates tension at the replication fork
What is the function of topoisomerase?
Cuts the DNA strand at the replication fork, allows them to unwind and releases the tension. Then joins them back together
What are the two types of activity of DNA polymerase I?
RNase Activity and DNA polymerase activity
What is the RNase activity of DNA polymerase I?
RNase H is an endonuclease enzyme that recognises DNA:RNA hybrids and degenerates the RNA part (the RNA primer)
What is the DNA polymerase activity of DNA polymerase I?
Synthesises DNA by adding nucleotides complementary to the parent DNA template of the lagging strand in areas where the RNA primer was. Uses the OH group of the next group to extend it unto the following fragment but doesn’t connect them
What is the main function of DNA Ligase?
To join newly synthesised Okazaki fragments together (creates phosphodiester bonds), once the RNA primers have been removed and replaced by DNA nucleotides
What is the second function of DNA Ligase?
Connects the newly synthesised fragments from multiple replication bubbles (leading strand of one bubble joins to the Okazaki fragments of another)
When can DNA errors be repaired?
During replication using an exonuclease and after replication using an endonuclease
The error rate of DNA polymerase III is…
low (has high accuracy)
How does DNA polymerase III remove errors?
It has a proofreading mechanism which checks newly inserted nucleotide bases against the template. These types of incorrect bases are removed by a 3’ to 5’ exonuclease activity of DNA Pol III and then synthesis continues
What can cause DNA damage or errors?
Incorrectly inserted bases aren’t corrected by DNA Pol III, radiation damage and chemical modification of bases
What does ENDOnuclease do?
Takes out a section of DNA which includes the incorrect base as well as nucleotides either side. A DNA polymerase uses the 3’ OH group to fill the gap with new DNA and the new DNA is joined to the existing DNA by Ligase
Why is it important errors in DNA are corrected?
If not corrected, the DNA error becomes part of the DNA template and every strand made from it will have the error. Therefore it will be a permanent change in the DNA (mutation)
What is the Polymerase Chain Reaction?
The in vitro (test tube) method of making multiple DNA copies so that there is enough DNA material to work with
What happens during the Polymerase Chain Reaction?
There is a rapid exponential increase of DNA molecules with only the ‘targeted’ DNA region being copied. Heating and cooling are utilised in this method
What are the 3 stages of the Polymerase Chain Reaction?
Denaturation, Annealing and Extension
What happens during denaturation?
The temperature is increased to separate the DNA strands
What happens during annealing?
The temperature is decreased to allow the primers to base pair to the complimentary DNA template
What happens during extension?
Polymerase extends primer to form new DNA strand
What is the DNA template in the Polymerase Chain Reaction?
DNA molecule to which complimentary nucleotides can be matched to make identical copies via DNA synthesis
What is the function of the primers in the Polymerase Chain Reaction?
Provide a 3’ OH group which is essential to initiate DNA synthesis as well as defining the region of the DNA molecule to be replicated
What is the function of DNA polymerase in the Polymerase Chain Reaction?
An enzyme which adds nucleotides
What are dNTPs in the Polymerase Chain Reaction?
Free nucleotides (equal amounts of A, T, C and G)
