Nucleic Acid Discovery And Structure

Question 1

Name some functions of dna allowed because of the double helical structure of it

Answer 1

Storage within cells

Accessible for transcription(by proteins looking for sequences)

Replication possible

Meiosis - crossing over possible

Genome stability / repair

Question 2

Explain the griffiths experiment to how they found dna could be the thing ‘transforming’ in strains of strep

Answer 2

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

Question 3

What properties did the transforming agent have that showed it was dna in griffiths experiment

Answer 3

Contained phosphorus

Was destroyed by deoxyribonuclease enzymes

Wasn’t killed by proteases

= suggests it was dna not protein

Question 4

Explain the Harvey and chase experiment that lead to discovery of dna being genetic material- not proteins

Answer 4

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

Question 5

What is the proper name for bases nucleic acids?

Answer 5

Heterocyclic bases

Question 6

What makes up heterocyclic bases that are purines (A,G)

Answer 6

1 pyrimidine N ring (1-6 N)

1 imidazole N ring (7,8,9 N)

Question 7

What makes up pyrimidines (C,T,U)

Answer 7

1 pyrimidine ring (6N)

Question 8

What is important about the N at 9’ on purines ?

Answer 8

That it what attaches to C1 of sugar ribose and deoxyribose

Question 9

What makes adenine recognisable apart from its ring structure

Answer 9

It has an NH2 region attached to its pyrimidine ring

Question 10

What makes guanine and cytosine recognisable apart from its ring structure

Answer 10

Guanine and cytosine both have double O bond

Also an NH2 attached

Question 11

What makes thymine recognisable from the rest

Answer 11

On its pyrimidine ring it has a CH3 group

Question 12

In nucleic acids there are 2 sugar types - deoxyribose and ribose. What carbohydrate structure do they have?

Answer 12

A furanose structure (5 carbon ring and HOC2 at 5’

Question 13

What makes ribose and deoxyribose different

Answer 13

Ribose has an OH on the C2

Deoxyribose only has a H on the C2

Question 14

At what carbon does phosphate and a base attach on the sugars (via the OH group)

Answer 14

Phosphate - at 5’ (and 3’ if in polynucleotide strand)

Base at C1

Question 15

What are nucleosides

Answer 15

A base and sugar joined at N9/N1 and C1

Present in both dna and rna

Question 16

What are the nucleosides called in dna and rna and what’s the difference

Answer 16

RNA- adenosine,guanosine,cytidine, uridine

Dna - deoxyadenosine, deoxyguanosine,deoxycytidine, thymidine

Only difference is the OH on the C2 carbon not present in deoxynucleoside

Question 17

What are the nucleotides called in RNa and dna (base,phosphate,sugar)

Answer 17

Rna - adenylate, guanylate, cytidylate, uridylate

Dna - deoxyadenylate, deoxyguanylate,deoxycytidylate, thymidylate

Question 18

Why is deoxyadenylate special ?

Answer 18

The phosphate can be at both 5’c or at 3’C

Question 19

Why is a phosphate attached by a ‘phosphodiester’ bond when in a polynucleotide strand

Answer 19

Because it is attached to 1 sugar at C3’ and another sugar at C5’

= 2 ester bonds

Question 20

Why is dna more stable than RNA so used as a long term store?

Answer 20

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

Question 21

What is it called when bases are able to hydrolyse the C2 OH on ribose sugars

Answer 21

Base catalyses hydrolysis

This causes the breakage of phosphate back bond when base attacks the Oh

Question 22

What are ‘chargaffs rules’ about the base ratio

Answer 22

1- A and T are equal and C and G are equal

2- AT pairing can vary aswell as CG pairing in different individuals

Question 23

X-ray fibre diffraction was used to suggest the helical structure of dna. Explain the process of how this works

Answer 23

Dna is strawed out into thin fibres and then an X-ray beam is shone

The angle/diffraction site is then detected

Question 24

How did the St. Andrew’s Cross diffraction pattern determine the helixes

Answer 24

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

Question 25

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?

Answer 25

34A between repeating units (turn of the helixes)

3.4 A between base pairs

Question 26

Explain the basic structure of the alpha helix found by Watson and crick

Answer 26

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

Question 27

Base pairs are held by H bonds. Who is the donor and acceptor of the H bond?

Answer 27

N-H is the donor

O is the acceptor

Question 28

Why does guanine and cytosine have 3 bonds instead of 2

Answer 28

Because they both have a double bonded O on their rings

And also the NH2 groups

Question 29

The backbone enforced the A-T and C-G base pairing. Why do these have to be

Answer 29

Because other pairs would be too small, or too large, or misalign the donor from the acceptors

This would change the backbone structure

Question 30

What 3 things give the double helix it’s structural stability

Answer 30

Hydrophobic effect- hydrophobic bases are inside and phosphate backbone outside

Base pairs H bonds

Stacked base pairs (van der waal stacking force)

Question 31

What is the importance of the phosphate backbone being negative /acidic (PO43-)

Answer 31

Allows binding of proteins such as transcription factors or histones

Which are usually positively charged = attract

Question 32

What is the major and minor grooves of the dna structure

Answer 32

The distance between phosphate backbones from one side of helix and the other (in 3D shape)

Question 33

The major groove is called ‘information rich’ why is this

Answer 33

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

Question 34

Why is minor groove information poor?

Answer 34

Backbones are close together on this side of the helix

The base sequence is not easily read by proteins etc

Question 35

What happens if the proteins such as transcription factors try to bind to minor groove

Answer 35

They will alter the dna structure

They have to pull backbone apart to read sequence

Question 36

What 3 dna structures are there (B dna being the Watson and crick model) and what are the slight differences

Answer 36

A dna units are shorter

But wider in diameter than B dna

Z dna is left handed helix and is longer repeating units

Question 37

What 4 ways do RNA single strands try to get a double helix (better for them)

Answer 37

1- can match base pairs
2- mismatched base pairs
3- unmatched regions
4- tertiary interactions

Question 38

What are tertiary interactions in single stranded rna

Answer 38

When base pairs form bonds with other base pairs

Question 39

What is the structure of single stranded things usually called

Answer 39

Stem loop structures

Question 40

Why does DNA double stranded absorb more?

Answer 40

More UV is absorbed by dna