Nucleic Acid Discovery And Structure Flashcards
Name some functions of dna allowed because of the double helical structure of it
Storage within cells
Accessible for transcription(by proteins looking for sequences)
Replication possible
Meiosis - crossing over possible
Genome stability / repair
Explain the griffiths experiment to how they found dna could be the thing ‘transforming’ in strains of strep
They took dead pathogenic strain and a non pathogenic strain and this formed progenies that were pathogenic- suggesting something was transformed within the cell to make it pathogenic
What properties did the transforming agent have that showed it was dna in griffiths experiment
Contained phosphorus
Was destroyed by deoxyribonuclease enzymes
Wasn’t killed by proteases
= suggests it was dna not protein
Explain the Harvey and chase experiment that lead to discovery of dna being genetic material- not proteins
They took a bacteriophage and it had proteins labelled in S and dna was labelled with P
The ecoli was injected by bacteriophage
The bacteriophage was only able to replicate when the P radioactive was present, didn’t replicate when only S
This suggests dna was the thing that encoded for proteins to be assembled into bacteriophages
What is the proper name for bases nucleic acids?
Heterocyclic bases
What makes up heterocyclic bases that are purines (A,G)
1 pyrimidine N ring (1-6 N)
1 imidazole N ring (7,8,9 N)
What makes up pyrimidines (C,T,U)
1 pyrimidine ring (6N)
What is important about the N at 9’ on purines ?
That it what attaches to C1 of sugar ribose and deoxyribose
What makes adenine recognisable apart from its ring structure
It has an NH2 region attached to its pyrimidine ring
What makes guanine and cytosine recognisable apart from its ring structure
Guanine and cytosine both have double O bond
Also an NH2 attached
What makes thymine recognisable from the rest
On its pyrimidine ring it has a CH3 group
In nucleic acids there are 2 sugar types - deoxyribose and ribose. What carbohydrate structure do they have?
A furanose structure (5 carbon ring and HOC2 at 5’
What makes ribose and deoxyribose different
Ribose has an OH on the C2
Deoxyribose only has a H on the C2
At what carbon does phosphate and a base attach on the sugars (via the OH group)
Phosphate - at 5’ (and 3’ if in polynucleotide strand)
Base at C1
What are nucleosides
A base and sugar joined at N9/N1 and C1
Present in both dna and rna
What are the nucleosides called in dna and rna and what’s the difference
RNA- adenosine,guanosine,cytidine, uridine
Dna - deoxyadenosine, deoxyguanosine,deoxycytidine, thymidine
Only difference is the OH on the C2 carbon not present in deoxynucleoside
What are the nucleotides called in RNa and dna (base,phosphate,sugar)
Rna - adenylate, guanylate, cytidylate, uridylate
Dna - deoxyadenylate, deoxyguanylate,deoxycytidylate, thymidylate
Why is deoxyadenylate special ?
The phosphate can be at both 5’c or at 3’C
Why is a phosphate attached by a ‘phosphodiester’ bond when in a polynucleotide strand
Because it is attached to 1 sugar at C3’ and another sugar at C5’
= 2 ester bonds
Why is dna more stable than RNA so used as a long term store?
The OH at C2 of the ribose sugar is able to be hydrolysed causing a free phosphate by bases in rna
The OH isn’t present at C2 of dna
What is it called when bases are able to hydrolyse the C2 OH on ribose sugars
Base catalyses hydrolysis
This causes the breakage of phosphate back bond when base attacks the Oh
What are ‘chargaffs rules’ about the base ratio
1- A and T are equal and C and G are equal
2- AT pairing can vary aswell as CG pairing in different individuals
X-ray fibre diffraction was used to suggest the helical structure of dna. Explain the process of how this works
Dna is strawed out into thin fibres and then an X-ray beam is shone
The angle/diffraction site is then detected
How did the St. Andrew’s Cross diffraction pattern determine the helixes
The diffraction pattern had a 60• angle to it (cross)
These angles are made by the turn of a helix - didn’t know it was double at this point
There were dominant diffraction spots on the X-ray fibre diffraction experiment. The spaces between these were found at 34 A and 3.4 A (anxrams)
What did these represent (found by Watson and crick) in the double alpha helix?
34A between repeating units (turn of the helixes)
3.4 A between base pairs
Explain the basic structure of the alpha helix found by Watson and crick
2 anti parallel polynucleotide strands
Base pairs found
5’ to 3’ strand had a free phosphate
3’ to 5’ strand had a free OH on C3
RIGHT HANDED HELIX
Base pairs are held by H bonds. Who is the donor and acceptor of the H bond?
N-H is the donor
O is the acceptor
Why does guanine and cytosine have 3 bonds instead of 2
Because they both have a double bonded O on their rings
And also the NH2 groups
The backbone enforced the A-T and C-G base pairing. Why do these have to be
Because other pairs would be too small, or too large, or misalign the donor from the acceptors
This would change the backbone structure
What 3 things give the double helix it’s structural stability
Hydrophobic effect- hydrophobic bases are inside and phosphate backbone outside
Base pairs H bonds
Stacked base pairs (van der waal stacking force)
What is the importance of the phosphate backbone being negative /acidic (PO43-)
Allows binding of proteins such as transcription factors or histones
Which are usually positively charged = attract
What is the major and minor grooves of the dna structure
The distance between phosphate backbones from one side of helix and the other (in 3D shape)
The major groove is called ‘information rich’ why is this
The long distance between backbones allows accessibility or molecules such as proteins to bind
Able to read the base sequence easily because backbone isn’t in the way
Why is minor groove information poor?
Backbones are close together on this side of the helix
The base sequence is not easily read by proteins etc
What happens if the proteins such as transcription factors try to bind to minor groove
They will alter the dna structure
They have to pull backbone apart to read sequence
What 3 dna structures are there (B dna being the Watson and crick model) and what are the slight differences
A dna units are shorter
But wider in diameter than B dna
Z dna is left handed helix and is longer repeating units
What 4 ways do RNA single strands try to get a double helix (better for them)
1- can match base pairs
2- mismatched base pairs
3- unmatched regions
4- tertiary interactions
What are tertiary interactions in single stranded rna
When base pairs form bonds with other base pairs
What is the structure of single stranded things usually called
Stem loop structures
Why does DNA double stranded absorb more?
More UV is absorbed by dna
