Lecture 3: Nucleic Acid Biology Flashcards
What is a Nucleotide?
The basic unit of a nucleic acid
What is the difference between nucleotide and nucleoside?
Nucleoside is not an acid
How are nucleotides joined together to form nucleic acids?
Through phosphoediester bonds. Phosphodiester bond links C3’-OH of one nucleotide with C5’-phosphate of the next
Free purines and pyrimidines are….
Weak bases
Purines and pyrimidines in DNA/RNA are….
Aromatic
Purines/pyrimidines are hydrophobic…meaning….
At neutral pH uncharged, thus they strongly repel water
What do planar rings do to minimize contact with water?
The planar rings “stack” on top of each other in nucleic acids
B form DNA
•Watson and Crick DNA structure
•Right-Handed Helix
•Most stable under physiological conditions
Helical sense Diameter for B form DNA
20 A
(A form is wider, Z form is smaller)
Base pairs per helical turn for B form DNA
10.5
(A form is more, Z form is even more)
Helix rise per base pair for B form DNA
3.4 A
(A form is smaller, Z form is bigger)
Hairpin
•When one strand is involved
•Within-strand palindrome pairing
•Very common in RNA
Cruciform
•When two strands are involved
•Extent in vivo not known
Tm…..
Temperature at which DNA is 50% melted (unpaired)
Tm is proportional to
GC content
DNA can be dissociated (melted) by
Increasing T
Melting can be followed by measuring UV absorbance at
260 nm
Deamination of bases
•Cytosine to uracil is most common
•1 per 10^7 per 24 hours (around 100/cell/day)
Hydrolysis of N-glycosidic bond
•removes base
•result is apurnic/apyrimidinic site (depurination more common)
•1 per 10^5 per 24 hours (10,000/cell/day)
UV-induced crosslinking
•adjacent thymines crosslinked into one of two products
•result is a DNA kink that can lead to a double-strand break
Deaminating agents
•Sodium nitrite
•Sodium nitrate
•Nitrosamine
Alkylating agents
•Dimethynitrosamine, Dimethylsulfate, Nitrogen mustard
•Can cause mispairing, crosslinking of bases
Greatest contributor to DNA damage
Oxidative damage
