Nucleic acids

Question 1

What is the basic composition of a nucleic acid?

Answer 1

• 4 different nucleotides

- Sugar-phosphate (ribose or deoxyribose)

Question 2

How are the nucleotides linked together?

Answer 2

Phosphodiester bond forming between the 5’ and 3’ hydroxyl group on adjacent nucleotides

Question 3

Which nucleic acid are purines and which are pyrimidines?

Answer 3

purines - Adenine, Guanine

pyrimidines- Cytosine, Uracil, Thymine

Question 4

How does the bond between the sugar and base differ for purines and pyrimidines?

Answer 4

glycosidic linkage between C1’ of sugar and:
N9 of purine
N1 of pyrimidine

Question 5

What is a nucleoside?

Answer 5

Base + Sugar

Question 6

What are the nucleoside names for A, C, G and T?

Answer 6

A - deoxyadenosine
C - deoxycytidine
G - deoxyguanosine
T - deoxythymidine

Question 7

What are the main structural elements of DNA?

Answer 7

• Right-handed double helix
• 2 anti-parallel strands
• sugar-phosphate backbone
• Alternating major and minor grooves

Question 8

What are the main interactions between components of DNA?

Answer 8

• H-bonds occurring between base pairs
• Base stacking accumulates van der Waals forces
• Core is hydrophobic
• Exterior phosphate groups interact with water

Question 9

How many H-bonds are formed between:

a) A + T
b) G + C

Answer 9

a) 2

b) 3

Question 10

What is the most common conformation of the sugar?

Answer 10

• One atom ‘puckered’ (out of plane)
• Called ‘endo’ as on the same side as C5’
• Most commonly C2’ and C3’

Question 11

Describe the B form of DNA

Answer 11

• most common
• bases are perpendicular to the helical axis
• ~10 bases per turn
• C2’ endo pucker
• Uneven grooves

Question 12

Describe the A form of DNA

Answer 12

• Less common and usually occurs when DNA is dehydrated, on double stranded RNA or DNA/RNA hybrids
• Bases tilted with respect to the helix axis
• C3’ endo pucker

Question 13

Describe the Z form of DNA

Answer 13

• extremely uncommon, adopted by DNA with alternating G & C residues
• Left handed helix
• Phosphoryl groups of the backbone are ‘zigzagged’
• C2’ and C3’ endo puckers
• 12 bases per turn

Question 14

How does DNA replication differ on the leading and lagging strand?

Answer 14

Leading strand - DNA polymerase, continuous replication
Lagging strand - Primase synthesises RNA to act as a ‘primer’ for DNA elongation to form Okazaki’s fragments which are later joined by the enzyme ligase

Question 15

What catalyses the pairing of t-RNA with an amino acid?

Answer 15

aminoacyl-tRNA synthase

Question 16

What are the start codons and stop codons?

Answer 16

start - UAA, UAG, UGA

stop - AUG

Question 17

What is exogenous and endogenous DNA damage?

Answer 17

exogenous - external factors

endogenous - celullar processes

Question 18

What can a chemical change to the DNA structure cause?

Answer 18

Abnormal base-pairing can propagate during cell division and cause altered function/carcinogenesis

Question 19

What can physical changes to the DNA cause?

Answer 19

Can prevent replication/transcription leading to cell death

Question 20

Define spontaneous deamination

Answer 20

Where cytosine undergoes spontaneous deamination to uracil which can go on to pair with adenine instead of guanine

Question 21

How is spontaneous deamination repaired?

Answer 21

Enzyme DNA-glycosylase removes any uracil found in DNA

Question 22

How does DNA alkylation occur?

Answer 22

• Electrophilic chemicals can alkylate DNA at various positions blocking translation/transcription
• Commonly O6 methylguanine can pair with T instead of C, inducing a mutation

Question 23

What are thymine dimers and how are they caused?

Answer 23

• UV radiation can cause photochemical cross-linking of pyrimidine bases forming cyclobutane ring which distorts the DNA strand

Question 24

How are thymine dimers repaired?

Answer 24

bacteria - DNA photolygase

higher organisms - excision repair