14: Nucleic acid structure Flashcards
What is the difference between thymine and uracil?
thymine - Ch3 grp
uracil - H
What are the characteristics of the ring structures of nitrogenous bases?
flat - relatively hydrophobic, edges have hydrogen bonding groups
How are nitrogenous bases categorized by structure?
purine: double ring of 5C and 6C - adenine and guanine
pyrimidine: 6C ring - thymine, uracil, cytosine
What is the purpose of the N in all nitrogenous bases?
makes N-glycosidic bonds to make nucleoside
What is the structure of a nucleoside?
sugar (ribose or deoxyribose) + base
N on base attached to 1’ C on sugar through N-glycosidic bond
difference between ribonucleoside and deoxyribonucleoside?
ribose - OH
deoxyribose - H (reduced ribose by O removal from 2’ carbon)
What is the structure of a nucleotide?
base + sugar + phosphate(s)
up to 3 phosphates
phosphate adds to 3’ C of sugar
What is the structure of a polynucleoside?
What is the bond used?
How is the sequence of polynucleotides written?
5’ end usually but not always has a phosphate group
phosphodiester bond of 3’ C of 1 sugar to phosphate group to the 5’ C of the next sugar (RNA and DNA)
written 5’ to 3’
What is B-DNA structure?
left hand or right hand, sugar phosphate backbone, antiparallel double helix
What is the evidence for B-DNA structure?
- char gaffs rule (amt of A=T, amt G=C to matter tissue or species)
- x-ray diffraction pattern
- structures of bases (enols vs ketone form)
What are the forces stabilizing the double helix?
- base stacking (important)
- flat nitrogenous bases stack protecting hydrophobic surface drives folding and stability - base pairing (HB) have constant width for each BP (10.85 A)
hydrophobic bases inside and sugar and phosphate (neg charge) are hydrophilic
What are the major and minor grooves? Why does this occur?
allows for proteins to interact with DNA by proteins sticking into correct grooves
major groove has more info and has more distance between backbone and base and this occurs bc the BP are not directly 180º from each over
What are the dimensions of B-DNA?
minor groove + major groove height = 10 BP = 34A
20A width
What is the effect of increasing temperature on nucleic acid?
How is this measured?
denaturation - separating strands
annealing (renature) reversible possible if temperature change is gradual so that BP will occur correctly
measured with absorbance of 260nm (absorbed better by single stranded DNA)
As length of BP increases, melting temperature…
increases
- more base stacking + pairing interactions = more difficult to pull strands apart