Nucleic Acids

Question 1

What are the parts of the primary structure of DNA?

Answer 1

bases, nucleosides, nucleotides then single strands

Question 2

What are bases?

Answer 2

nitrogenous bases = have high nitrogen content

• purine
• pyrimidine

Question 3

What is tautomerism?

Answer 3

DNA nucleotides recognise each other by their hydrogen bonds
- in the correct tautomeric form these bases have hydrogen bond acceptors and donors = which allow formation of hydrogen bonds and recognition of each other

Question 4

What are tautomers?

Answer 4

isomers of a compound the only differ in the position f their electrons and protons

Question 5

What are the purine bases?

Answer 5

single benzene ring - 6C
cytosine - found in DNA and RNA
thymine - found in DNA
uracil - found in RNA

Question 6

What are the pyrimidine bases?

Answer 6

two benzene rings - 6C and 5C
adenine - found in DNA and RNA
guanine - found in DNA and RNA

Question 7

Where are the hydrogen bond donors and acceptors for thymine and cytosine?

Answer 7

pyrimidine 
acceptors 
- nitrogen and oxygen atoms 
donors 
- hydrogen atoms on the nitrogen atoms

Question 8

Where are the hydrogen bond donors and acceptors for adenine and guanine?

Answer 8

purine 
acceptors
- nitrogen and oxygen atoms 
donors 
- hydrogen atoms on the nitrogen atoms

Question 9

What is a nucleoside?

Answer 9

nitrogenous base attached to a sugar

sugar - ribose or deoxyribose

Question 10

What is the difference between ribose and deoxyribose sugar?

Answer 10

RNA = ribose - has 2 OH groups on the ribose sugar ring
DNA = deoxyribose - has only 1 OH group on the ribose sugar ring (1 is missing from C2)

Question 11

What is a nucleotide?

Answer 11

phosphate esters of nucleosides

• base, sugar and phosphate
• phosphates are attached to the sugar by the free hydroxyl group on C5

phosphate groups give the nucleotides an overall negative charge

Question 12

What are the roles of nucleotides?

Answer 12

movement of energy within an organism - ATP
ATP = 3 phosphates, ribose sugar, adenine
metabolic regulator - cAMP
components of major coenzymes - NAD, FAD, coenzyme A
activated intermediates in biosynthesis

Question 13

How are the nucleotides in a single strand of DNA linked?

Answer 13

nucleotides are linked phosphate groups bridging two sugar units

sugar-phosphate groups form the backbone of the strand with the bases hanging off it

Question 14

What is the different between RNA and DNA?

Answer 14

RNA - usually single stranded
DNA
- usually double stranded
- the two strands are held together by hydrogen bonds
- the bonds runs in opposite directions forming a duplex

Question 15

How does Watson - Crick base pairing work?

Answer 15

dominant pattern of base pairing is formed
A-T has 2 hydrogen bonds
C-G has 3 hydrogen bonds
= A-T < C-G

Question 16

What features of the base pairing in Watson-Crick base pairing allows for isomorphous geometry?

Answer 16

For each pair the distance between the C-1’ atoms and the angle between the glycosidic bonds is the same.

Question 17

What is the primary structure of DNA?

Answer 17

order of attachment of nucleotides

Question 18

What determines the secondary structure of DNA?

Answer 18

shape of the base pairs
interaction between base pairs 
duplex of DNA
packing of DNA
structure of RNA

Question 19

What is the shape of the nucleotide pairs?

Answer 19

bases are in an aromatic ring - are planar

hydrogen bonds between the bases ensure that both bases are in the same plane

the sugars are more or less perpendicular to the plane of the bases - are puckered

sugar phosphate backbone is quite flexible - not responsible for the helical shape of DNA

Question 20

What is meant by pi stacking?

Answer 20

pi stacking occurs as heterocyclic bases in DNA tend to try to line up above one another = overlap

it occurs as aromatic rings have electrons above and below the plane of the ring and it is energetically favourable for them to overlap with other p-orbital in adjacent rings
- it is energetically favoured as it allows for the delocalisation of electrons

the bases tend to line up on top of each other at angle of approximately 30-40 degrees

Question 21

How does pi stacking affect the secondary structure of the DNA?

Answer 21

the overlap of the heterocyclic bases (aromatic) is a constraint on the sugar-phosphate backbone
- results in the formation of the helical shape = forced to twisting

Question 22

What is the difference between right handed and left handed DNA?

Answer 22

DNA is normally right handed but can be found as left handed under certain conditions
right handed - viewed as clockwise
left handed - viewed as anticlockwise

Question 23

What determines the shape of DNA?

Answer 23

the sequence of bases and the chemical environment

• the negative charges on the backbone phosphate will repel and stretch the strand
• if the bases are not all in the same plane but tilted to one another then the strand will bend

Question 24

What are the grooves in DNA and their causes?

Answer 24

minor and major grooves
- each is a different shape, size and contains a different chemical environment

minor
- occurs when strands are closer together
major
- occurs when strands are further apart

Question 25

Why are grooves important for drug discovery?

Answer 25

drugs binds to different grooves

proteins binds to different grooves

Question 26

What are histones and what is their function?

Answer 26

proteins that associate with DNA

enable it to fit inside the nucleus

• neutralises the negative charges on the phosphates groups = stops repulsion and separation
• histones can wrap around them and can enter the nucleus

Question 27

What are the areas in DNA that anti-cancer drugs can bind to?

Answer 27

two areas

• intercalation = between the base pairs
• groove binding = in the groove

Question 28

What is gene therapy?

Answer 28

involves the introduction of small pieces of DNA into a cell, which then allows for the synthesis of a required protein
- could be a required protein (cystic fibrosis) or a foreign toxic protein (targeting cancer cells)