Lecture 1: Introduction; DNA structure, genes, genomes Flashcards
Name all pyrimidine nucleotides
Cytosine, uracil, thyamine
what does the pyrimidine structure look like
Single ring
Name all purine nucleotides
Guanine, adenine
What does the purine structure look like
Double ring
What’s the structural difference between oxy- and deoxyribose ribose sugars
Deoxyribose sugars have a H bonded at C2 as opposed to an OH
What is a nucleoside
Base + sugar
What is a nucleotide
nucleoside + phosphate
What direction is DNA synthesised
5’ to 3’
Where does the phosphodiester bond form between two ribose sugars
Between the C3 of the 5’ ribose and the C5 of the 3’ ribose
What are the three main forms of DNA double helix?
A, B and Z
What forms of DNA are right handed
A and B
What forms of DNA are left handed
Z form
What is the diameter of A, B, and Z forms of DNA from largest to smallest
A (~26Å) then B (~20Å) then Z (18Å)
How many bases are there per helical turn for A, B, and Z forms of DNA
A = 11 B = 10.5 Z = 12
How much does the helix rise per base pair for DNA forms A, B, and Z.. From largest to smallest
Z (3.7Å) then B (3.4Å) then A (2.6Å)
What is the difference between plextonemic and paranemic forms of DNA
Plectonemic = intertwined (helix) Paranemic = linear (no helix)
What is meant by positive and negative super coiling
Positive super coiling = number of bases per helical turn increases (less tight)
Negative super coiling = number of bases per helical turn decreases (tighter)
Where does the Z form of DNA occur
Regions of alternating purine-pyrimidine sequences (e.g., CGCGCGC)
What happens to the bases in the A-form of DNA
They tilt
What forms of double helix can RNA only form
A and Z
Not B due to ribose preferences
What is GC content and what can be inferred from its abundance
GC content is the amount of GC bases within a strand
High GC% = higher melting point
Low GC% = lower melting point
What is GC content and what can be inferred from its abundance
GC content is the amount of GC bases within a strand
High GC% = higher melting point
Low GC% = lower melting point
When does a DNA hairpin form
When the bases along the DNA strand inversely match each other
(e.g., TGCGATactcATCGCA)
When does a DNA cruciform form
When the bases along both DNA strands inversely match each other
Double hairpin
