Lesson 15: Nucleic Acids Part 1 Flashcards
(29 cards)
2 types of nucleic acids
deoxyribonucleic acid (DNA) and ribonucleic acid (RNA)
in all nucleic acid polymers, the repeating monomeric unit is the ()
nucleotide
nucleotide:
nitrogenous base, 5 carbon ribose or deoxyribose sugar, phosphate
what is the major difference at the backbone level of RNA and DNA
the 2’ -OH (RNA) or -H (DNA) is the only difference
both DNA and RNA are highly flexible molecules
1 - nucleic acids must be highly flexible
2 - genetic material needs to store information
3 - needs to be mutable
4 - access and replicate
heterocyclic purines and pyrimidines are found in DNA and RNA
purines:
- adenine: 6 amino purine
- guanine: 2 amino 6 Oxy purine
pyrimidines
- cytosine: 2 oxy 4 amino pyramidine (DNA)
- uracil: (2,4 dioxy pyrimidine (RNA)
- thymine: 2,dioxy 5 metyl pyrimidine (DNA)
be sure to know the H-bond receptors and donors
what form do riboses exist in in DNA and RNA
furanose form
ribofuranose rings are ()
puckered
nucleoside and nucleotide sugars
beta-D ribose: RNA
beta - D - deoxyribose: DNA
bases for RNA/adjacent nucleoside
Adenine (A) - Adenosine
Guanine (G) - Guanosine
Cytosine (C) - Cytidine
Uracil (U) - Uridine
bases for DNA/adjacent nucleoside
Adenine (A) - Deoxyadenosine
Guanine (G) - Deoxyguanosine
Cytosine (C) - Deoxycytidine
Thymine (T) - Deoxythymidine
How is the nitrogenous base attached to a sugar
- N-glycosyl or glycosidic linkage: base to sugar
- glycosidic linkage is between 1’ position of pentose and 1 position of a pyrimidine
- glycosidic linkage is between 1’ position of pentose and 9 position of a purine
the phosphate backbone is a strong acid/base
acid
the net charge of the phosphate at pH7 will be positive/negative
negative
the phosphate group of the nucleotide is ()
polyprotic
- both pKa values are less than 7; negative. charge at physiological PH
the bases exist in different tautomeric forms
- for both purines and pyrimidine, the amino and keto tautomer are lower energy and more stable at pH 7 compared to their respective Imino and Enol tautomeric forms
Guanine/thymine: keto/enol
Adenine/cytosine: amino/imino
syn and anti conformation of nucleotides: rotation around the lycosidix (N-glycosyl) bond - which is more stable
- the anti conformation reduces steric and electrostatic clashes
- this is particularly evident for purine bases
nucleuc acids have conjugated ring systems and absorb UV light
- where is the max absorbance
- how dos this compare to proteins (W,Y,F)
- 260 nM
- nucleic acids do absorb to a lesser extend at 280 nm (compared to other proteins)
^^ we can utalize this property to calculate concentration of Nucleic Acid in solution - free purines and pyrimidiens are weakly basic, hence the name nigrogenous bases
- the aromaticity of the bases leads to electron delocalization in the rings, leading to the partial double bond character and planarity
- purines and pyrimidine rings are hydrophobic and insoluble at pH 7 –> this leads to hydrophobiic stacking of bases within DNA and RNA
the 3- –> 50 phosphodiester linkage : what is an ester
acid + alcohol –> ester
phosphodiester linkage is an example of metastability:
the free energy of phosphodiester bond formation is +25kJ/mol
free energy of hydrolysis:
-25kJ/mol
- thermodynamically, this process is favored
example of metastability:
the free energy favors hydrolysis; however the time scale in biological systems kinetically favors formation of phosphodiester linkage
how are successive nucleotides linked
- covalently through 5’ phosphate of one nucleotide and 3’ -OH of the next
- all phosphodiester bonds in DNA and RNA have the same orientation along the chain
- this gives each linear strand a specific polarity with a distinct 5’ and 3’ end
