Topic 2 ( 2.11 to 2.15) + 2.5 9 (DNA and nucleotides) Flashcards
What is DNA
Deoxyribonucleic acid
It is a polymer made of nucleotides
It is made of 2 anti-parallel strands that are joined by complimentary base pairing (forming hydrogen bonds between opposite strands)
It has a sugar phosphate backbone (created by phosphodiester bonds between adjacent nucleotides)
and is wound into a double helix
What is DNA replication
The process of creating a new double helix
What did Meselson and Stahl do
They performed an experiment which proved Watson and Cricks hypothesis was correct
That DNA was made of two strands which replicate semi conservatively
What is semi conservative DNA replication
Two DNA copies are produced in replication one contains the parent DNA (a template strand) and one containing new DNA
What is density gradient centrifugation
A method of separating cells / materials based of their identity
What was done in the Meselson and Stahl experiment
-E-coli was grown in a medium using the heavy isotope of hydrogen 15N, to give the parental DNA a higher than normal density
-14N was then added in excess to the solution and the E-coli were grown, so that future DNA would have a lower gradient
- They took a DNA sample at each generation and used density gradient centrifugation to see how parental and daughter DNA was distributed
- They took UV photos of the DNA ‘bands’ which allowed them to see the different densities
What did Meselson and Stahl observe from the parent DNA and its replicated daughter DNA
The parent DNA was made entirely of 15N
After the first replication cycle the density centrifugation only showed a band of half 15N and half 14N (intermediate density)
After the 2nd replication cycle, the density gradient centrifugation showed a band of 15N and 14N as well as a band of only 14N
What did Meselson and Stahl’s experiment tell them
- the nitrogen in each DNA divided evenly between the two subunits of DNA
- Each new double helix contained one parental subunit which supported semi-conservative replication
- For every parental DNA (every template strand) two new DNA molecules were made
Why did Meselson and Stahl use Nitrogen
All DNA has nitrogen due to the nitrogenous bases
Why does the ratio of 15N to 14N slowly decrease (Meselson and Stahl)
No new 15N was added to the solution, so it is only present in the 1st template strands
as more DNA replication occurs, all new strands will be made of 14N, as it was added in excess to the E-coli
What is the 3’ (3 prime) and 5’ (5 prime) ends of DNA (same with RNA as both are pentose sugars)
The 3’ end is where the chain of DNA / RNA ends at the third carbon
The 5’ end is where the chain of DNA / RNA ends at the 5th carbon
How does DNA polymerase write the new nucleotides
DNA polymerase places nucleotides in the opposite direction of DNA
At the 3’ end of the template strand, the DNA polymerase would put at 5’ end nucleotide
This ensures DNA is anti-parallel
How is DNA replicated
(excluding lagging and leading strands)
-Hydrogen bonds are broken by helicase
- Single strand binding proteins prevent the two strands from reforming hydrogen bonds with each other
-DNA primase then places RNA primers to signal DNA polymerase
-DNA polymerase writes from 5’ to 3’
- Two identical double helix’s of DNA are formed
What is the leading strand (DNA replication)
The Template strand which is read 3’ to 5’ is the strand that produces the leading strand. DNA polymerase moves in the 5’ direction so it continously summons nucleotides
The leading strand itself would be antiparallel so 5’ 3’
What is the lagging strand (DNA replication)
The Parent DNA strand that produces the lagging strand is read in the 5’ to 3’ end
As the DNA unravels a new 3’ end is revealed. This results in new primers having to be placed making okazaki fragments.
The antiparallel strand (which is the lagging strand) is 3’ to 5’
What are okazaki fragments
Fragments of DNA made at the lagging strand
How is the lagging strand made (DNA replication)
DNA Polymerase placed nucleotides from 3’ to 5’
As the DNA unravels new primers have to be placed so that nucleotides can be arranged
This form okazaki fragments as the primers prevent the nucleotides from joining together
The Okazaki fragments are the joined together in a reaction catalyzed by DNA ligase
Why is there a lagging and leading strand
DNA strands are antiparallel
one is 5’ to 3’
one is 3’ to 5’
DNA polymerase reads from 3’ to 5’ so when the new 5’ end opens new primers have to be placed. (As DNA wants
This creates a lagging strand
on the 5’ 3’ strand DNA nucleotides can be placed continuously
Why does DNA polymerase ‘Read up write down’
To ensure the strands are antiparallel
it reads from 3’ to 5’ - This means that it scans and places nucleotides towards the 5’ end
it writes 5’ to 3’ - this means the nucleotides it places form a strand that is antiparallel
What is topoisomerase
An enzyme that prevents DNA from super coiling during DNA replication
What is gyrase
The enzyme that causes DNA to unwind during DNA replication
What is conservative replication
A theory that in DNA replication two double helixes were produced, one entirely made of parent DNA and one made of daughter DNA
What is Dispersive replication
A DNA replication theory that in the two replicated DNA double helixes contained random combinations of parental and daughter DNA in both strands of each double helix
What is Primase
An enzyme that places RNA primers during DNA replication to signal DNA polymerase
What is DNA Helicase
AN enzyme that breaks the hydrogen bond between opposite nucleotides during DNA repliction.
What is DNA polymerase
An enzyme that catalyses the addition of nucleotides to the end of DNA and causes phosphodiester bonds to form between adjacent nucleotides
What is DNA ligase
A enzyme that joins okazaki fragments together (causes phosphodiester bonds to form)
Why is DNA a polymer
It is made up of a chain of repeating nucleotides (monomers)
What does it mean that DNA is antiparallel
It is parallel but the strands are running in opposite directions
What are DNA nucleotides made of
Deoxyribose sugar
A phosphate group
A purine or pyrimidine nitrogenous base
What are the 4 nitrogenous bases and how they bind
adenine to thymine
cytosine to guanine
What are the 4 different DNA nucleotides called
adenosine
thymidine
guanosine
cytidine
How is the sugar phosphate backbone formed
The deoxyribose sugar of one nucleotide form a phosphodiester bond with the phosphate of another nucleotide
Which nitrogenous bases are purine
Adenine
Guanine
Which nitrogenous bases are pyrimidine
Thymine
Cytosine
What is a purine base
A nitrogenous base made of a pyrimidine ring and a imidazole ring
(2 rings)
What is a pyrimidine base
A nitrogenous base made of a pyrimidine ring
(1 ring - 6 sided)
How many hydrogen bonds form between adenine and thymine
2 hydrogen bonds
How many hydrogen bonds form between guanine and cytosine
3 hydrogen bonds
Why can purine bases only bond to pyrimidine bases
(and visa versa)
Purine base are 2 ringed and pyrimidine have 1 ring.
in order to keep DNAs structure uniform, 2 rings must always form hydrogen bonds with 1
(purine - purine = too large)
(pyrimidine - pyrimidine = too small)
Why is DNA made from two strands
Facilities DNA replication
Protects DNA bases
Provides structural support
What is the 3’ (3 prime) and 5’ (5 prime) ends of DNA (same with RNA as both are pentose sugars)
The 3’ end is where the chain of DNA / RNA ends at the third carbon
The 5’ end is where the chain of DNA / RNA ends at the 5th carbon
