Lecture 1-4 DNA Structure

Question 1

What is a gene

Answer 1

A fundamental, physical and functional unit of heredity

Question 2

What is the shape of a purine

Answer 2

Heterobicylic purine ring (A and G)

Question 3

What is the shape of a pyrimidine

Answer 3

Heterocyclic purine ring (T and C)

Question 4

What is a nucleoside and nucleotide

Answer 4

Nucleoside (base plus sugar)

Nucleotide (base plus sugar plus phosphate)

Question 5

What are the components of the primary structure of DNA

Answer 5

made up of deoxyribose, phosphate and purine and pyrimidine bases.
DNA has polarity

Question 6

Name the covalent links between components of primary structure of DNA

Answer 6

Backbone - alternating deoxyribose and phosphate groups

Purine and pyrimidine bases - side chains to backbone

Question 7

Explain Acid Chemical DNA hydrolysis

Answer 7

Acid hydrolysis - requires strong acid and heat, breaks N-glycosidic bonds between bases and deoxyribose. Also breaks phosphate ester bonds in DNA backbone, products are free bases, phosphate and polymer of deoxyribose

Question 8

Explain Alkaline Chemical DNA hydrolysis

Answer 8

DNA is stable to base hydrolysis, RNA is rapidly degraded in alkaline solution in presence of ‘2OH which can attack phosphate ester bond in presence of base

Question 9

Difference between Exonuclease Enzymatic DNA hydrolysis and endonuclease Enzymatic DNA hydrolysis

Answer 9

Exonucleases cut DNA or RNA from ends of strands, most exonucleases cut single strand DNA and cleave RNA.
Endonuclease cut within DNA or RNA strand. Mostly cut double strand DNA

Question 10

Summarize the secondary structure of DNA

Answer 10

Two chains coiled about an axis 
Opposite polarity of chains 
      - Deoxyribose phosphate backbone
      - bases to centre
Chains linked by H bonds between bases
Base pairs separated by 0.34nm
Base pairs rotate 36' (10 pairs per turn of helix)

Question 11

What are the interactions maintaining DNAs double Helix structure

Answer 11

1. Hydrogen bonding between pairs (G - C 3 bonds, A - T 2 bonds) only those pairs fit, gives rise to specificity.
2. Stacking interactions (hydrophobic and van der waals) large contribution to stability

Question 12

Describe the evidence that led Watson and Crick to determine double helical structure

Answer 12

X-Ray diffraction study
- Regular repeating structure means a diffraction
pattern is fromed. X shape indicated helix, intesity
of spots indicated double helix
0.34nm = 1 turn of helix also found
DNA base composition data: Chargaffs ratio
- Ratio of A - T = 1 and ratio of G - C = 1
Purine must always be attached to pyrimidine

Question 13

Why is the 36 degree twist important inbetween bases

Answer 13

The 36 degree twist positions the adjacent bases in Van Der Waal contact distance and faces of base pairs are hydrophobic and being in Van der Waal contact distance makes it a stabilizing hydrophobic interaction

Question 14

How do proteins recognize specific sequences in DNA?

Answer 14

Make specific interactions with groups on the edges of the base pairs
Specificity by proteins binding to either major or minor groove

Question 15

Name the four conditions that result in DNA denaturation

Answer 15

1. Low salt concentration - high salt conc ‘shield’ the negative charges on each phosphate
2. Extremes of pH - high or low pH changes ionisation states of hydrogen bonding groups
3. Elevated temperature - High temperature increases thermal motion
4. Association of DNA with proteins - sequence specific interactions in grooves of DNA

Question 16

Why does melting behaviour of DNA depend on base composition?

Answer 16

G - C have three hydrogen bonds and A - T have two, meaning the more G - C in the sequence the harder it is to melt.

Question 17

Why is DNA structure a compromise between stability and accessibility?

Answer 17

Cells need stability of genetic information

Cells need to be able to access genetic information

Question 18

Why can RNA be hydrolysed by alkaline but DNA can’t?

Answer 18

The -OH group on the 2’-position of ribose in RNA facilitates base hydrolysis.
DNA does not have an -OH group at 2’-position on its deoxyribose. Stable to base hydrolysis.
RNA is less suited for long term information storage than DNA because of this reactivity/instability.