MCB Lec 29

- Double stranded helix
- Contains a phosphate group, sugar, and base
- water soluble

2 hydrogen bonds between AT
3 hydrogen bonds between GC

Ribose (RNA) and deoxyribose (DNA) are both pentose sugars
■ Pentose comes from the pentose-phosphate pathway
■ OH group is present in RNA, making RNA more reactive and less stable

- N-glycosidic bond: bond between the base and the sugar
- Ester linkage: monophosphate bond
- Anhydride linkage: diphosphate bond
- Phosphoanhydride bond: triphosphate bond

Pyramids: Pyramids CUT
○ Cytosine
○ Uracil
○ Thymine
Purines: purines Are Good
○ Adenine
○ Guanine

Base + sugar
adenosine, guanosine, cytidine, uridine, thymidine
- Can be monophosphate, diphosphates, or triphosphate

Base + Sugar + PhosphaTe:
adenylate, guanylate, cytidylate, uridylate, thymidylate

adenosine monophosphate
- act as a handle in cofactors coenzymes
- conservative evolutionary feature

deoxyadenosine monophosphate

adenosine diphosphate

deoxyadenosine diphosphate

adenosine triphosphate

deoxyadenosine triphosphate

- greatly hindered;
- anti conformation in double helical strcutures (mostly)

- base and sugar are on opposite sides of the N-glycosidic bond
- base and sugar are on the same side of the N-glycosidic bond
- Z DNA has both (alternating syn and anti)

phosphodiester linkage

DNA
- 2' carbon stability
- RNA has OH group on 2' instead of H like DNA

OH group can activate as a nucleophile to attack the phosphate group, causing degradation of the RNA

enzyme that cleaves nucleic acids

- 5’-exonuclease cleaves the 5’ end
- 3’ exonuclease cleaves the 3’ end
- Endonuclease recognizes internal sits and cleaves to break it

- 3 H-bonds between base pairs GC; more stable
- 2 H-bonds between base pairs AT; less stable

Right handed helix: right handed thumbs up and twist

stacked bases in nucleic acids absorb less UV light than do unstacked bases

- single-stranded vs. double stranded because single-stranded absorbs more light
- Nucleic acids vs proteins
absorb light at 260 nm, proteins absorb light at 280 nm

the temperature at which half of the helical structure is lost
more stable = higher tm

Concentration of ions in the solution
- lead to more stacked bases = less UV absorbed
- more Na+ in solution = more stimulation of phosphate backbone = higher ™
DNA sequence
- high GC content, high Tm
- less UV light absorbed
Length of DNA
- longer = less UV absorbed

B DNA
A DNA
Z DNA

- most cellular DNA
- right handed helix
- most stable
- anti
- fully hydrated

- double-stranded RNA
- DNA/RNA hybrid
- dehydrated hydrated
- righthanded helix
- anti
- broadest

- not observed in living cells,
- left handed helix
- based on crystal structure
- CGCGCG
- alternating anti and syn
- narrowest

total base pairs/ base pairs per turn

linking number

Tw = Lk - Wr

ability to compare supercoiling of different length DNA molecules

they all pair up so remember to check

imino AC and vice versa

enol GT and vice versa