nucleic acids Flashcards
nucleotide
nucleic acid monomer
1. phosphate group
2. nitrogenous base (A, U, G, C, or T)
3. pentose sugar
nucleoside
only pentose sugar and nitrogenous base
difference between RNA and DNA pentose
rna has 2’ OH whereas DNA is missing 2’OH
purine
A and G
- 2 rings
pyrimadines
T, U, C
1 ring
uracil structure compared to thymine
demethylated version of thymine
how do adenine and guanine differ
adenine (amine) guanine (carbonyl group)
what differentiates cytosine from other pyrimidines
only pyrimadine with a primary amine
phosphate group
PO4 3-
- interact with 3’ and 5’ OH to form phosphodiester bonds
3’ OH
points down
5’ OH
points up
nucleoside diphsophates
have two phosphate groups attatched
nucleoside triphosphate
has 3 p groups
adenosine triphosphate
ATP
- adenine, bound by 3 phosphate groups
similar to gtp
3’5’ - cyclic adenosine monophosphate
CAMP
phosphideister bonds
bond between p group and 3’ or 5’ end of sugar
C-O-P-O configuration
nucleotide cofactors
FAD, NAD, FMN, NADP, coA
viral genome
can be double or single stranded dna or rna
base pairing
c—g
a–t
a–u
how many hydrogen bonds are in the G-C bond
3
how many hydrogen bonds are in the AT bond
2
chargoff’s rule
purines and pyrimidines exsist in a 1:1 ratio (DNA only)
amount of g = amount of c
amount of a = amount of T
purpose of hydrogen bonding between nitrogenous bases
stabilizes the double stranded structure
base stacking
hydrophobic interaction between nitrogenous bases on the same strand
double helix
structure of DNA with antiparallel DNA strands
BDNA
double helix
structure of DNA with antiparallel DNA strands
BDNA
Bdna
typical dna of human genome
right handed
10.5 bases/turn
ADNA
dehydrated form of BDNA that is formed by DNA RNA hybrid helicies
right handed
tighter than bdna with 11 bases per turn
ZDNA
DNA that has been methylated
LEFT HANDED
Looser
12 bases per turn
supercoiling
torsinal strain
dna is usually negatively supercoiled
hybridization
process where complimentary base pairs hydrogen bond
can be with entire DNA strand or an oligonucleotide
inconsistencies result in decreased favorability of hybridization
thermal denaturation
temperature raised high enough to break hydrogen bonds between the strands of dna
Tm
melting temperature of DNA denaturation
when half of DNA exists in unbound form
- depends on content of c-g and a-t bonds
PCR
annealing of complimentary dna
dna is repeatedly heated to a temp above melting point and allowed to cool in a process known as thermal cycling
during cooling: DNA becomes template for DNA polymerase enzyme to amplify DNA within target region defined by primers
- amplify a sequence
what techniques are utilized in PCR
denaturation (at high temps) and reannealing (lowering temp)
