Lecture 1: Introduction; DNA structure, genes, genomes

Question 1

Name all pyrimidine nucleotides

Answer 1

Cytosine, uracil, thyamine

Question 2

what does the pyrimidine structure look like

Answer 2

Single ring

Question 3

Name all purine nucleotides

Answer 3

Guanine, adenine

Question 4

What does the purine structure look like

Answer 4

Double ring

Question 5

What’s the structural difference between oxy- and deoxyribose ribose sugars

Answer 5

Deoxyribose sugars have a H bonded at C2 as opposed to an OH

Question 6

What is a nucleoside

Answer 6

Base + sugar

Question 7

What is a nucleotide

Answer 7

nucleoside + phosphate

Question 8

What direction is DNA synthesised

Answer 8

5’ to 3’

Question 9

Where does the phosphodiester bond form between two ribose sugars

Answer 9

Between the C3 of the 5’ ribose and the C5 of the 3’ ribose

Question 10

What are the three main forms of DNA double helix?

Answer 10

A, B and Z

Question 11

What forms of DNA are right handed

Answer 11

A and B

Question 12

What forms of DNA are left handed

Answer 12

Z form

Question 13

What is the diameter of A, B, and Z forms of DNA from largest to smallest

Answer 13

A (~26Å) then B (~20Å) then Z (18Å)

Question 14

How many bases are there per helical turn for A, B, and Z forms of DNA

Answer 14

A = 11
B = 10.5
Z = 12

Question 15

How much does the helix rise per base pair for DNA forms A, B, and Z.. From largest to smallest

Answer 15

Z (3.7Å) then B (3.4Å) then A (2.6Å)

Question 16

What is the difference between plextonemic and paranemic forms of DNA

Answer 16

Plectonemic = intertwined (helix)
Paranemic = linear (no helix)

Question 17

What is meant by positive and negative super coiling

Answer 17

Positive super coiling = number of bases per helical turn increases (less tight)
Negative super coiling = number of bases per helical turn decreases (tighter)

Question 18

Where does the Z form of DNA occur

Answer 18

Regions of alternating purine-pyrimidine sequences (e.g., CGCGCGC)

Question 19

What happens to the bases in the A-form of DNA

Answer 19

They tilt

Question 20

What forms of double helix can RNA only form

Answer 20

A and Z

Not B due to ribose preferences

Question 21

What is GC content and what can be inferred from its abundance

Answer 21

GC content is the amount of GC bases within a strand
High GC% = higher melting point
Low GC% = lower melting point

Question 22

What is GC content and what can be inferred from its abundance

Answer 22

GC content is the amount of GC bases within a strand
High GC% = higher melting point
Low GC% = lower melting point

Question 23

When does a DNA hairpin form

Answer 23

When the bases along the DNA strand inversely match each other
(e.g., TGCGATactcATCGCA)

Question 24

When does a DNA cruciform form

Answer 24

When the bases along both DNA strands inversely match each other
Double hairpin