Lesson 15: Nucleic Acids Part 1 Flashcards
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
RNA is hydrolyzed rapidly under what conditions
alkaline conditions
- DNA is not (No 2’OH in DNA)
what is the backbone of DNA and RNA subjected to
non-enzymatic hydrolysis of phosphodiester bonds
nucleic acids are highly flexible due to
1: conformations of ribose
2: rotation around contiguous phosphodiester linkages
3: rotation around glycosidic linkage - free rotation around 6 bonds and limited dynamics in the 7th
how does the nucleic acid flexion compare to the tortion angles in polypeptides
much more flexible (increased number of conformational states) compated to the torsion angles discussed with polypeptides
is simple condensation with the removal of H2O sufficient to form a phosphodiester linkage in vivo?
NO – bond synthesis requires “activated nucleotides”
