Lesson 15: Nucleic Acids Part 1

Question 1

2 types of nucleic acids

Answer 1

deoxyribonucleic acid (DNA) and ribonucleic acid (RNA)

Question 2

in all nucleic acid polymers, the repeating monomeric unit is the ()

Answer 2

nucleotide

Question 3

nucleotide:

Answer 3

nitrogenous base, 5 carbon ribose or deoxyribose sugar, phosphate

Question 4

what is the major difference at the backbone level of RNA and DNA

Answer 4

the 2’ -OH (RNA) or -H (DNA) is the only difference

Question 5

both DNA and RNA are highly flexible molecules

Answer 5

1 - nucleic acids must be highly flexible
2 - genetic material needs to store information
3 - needs to be mutable
4 - access and replicate

Question 6

heterocyclic purines and pyrimidines are found in DNA and RNA

Answer 6

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)

Question 7

be sure to know the H-bond receptors and donors

Question 8

what form do riboses exist in in DNA and RNA

Answer 8

furanose form

Question 9

ribofuranose rings are ()

Answer 9

puckered

Question 10

nucleoside and nucleotide sugars

Answer 10

beta-D ribose: RNA
beta - D - deoxyribose: DNA

Question 11

bases for RNA/adjacent nucleoside

Answer 11

Adenine (A) - Adenosine
Guanine (G) - Guanosine
Cytosine (C) - Cytidine
Uracil (U) - Uridine

Question 12

bases for DNA/adjacent nucleoside

Answer 12

Adenine (A) - Deoxyadenosine
Guanine (G) - Deoxyguanosine
Cytosine (C) - Deoxycytidine
Thymine (T) - Deoxythymidine

Question 13

How is the nitrogenous base attached to a sugar

Answer 13

• 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

Question 14

the phosphate backbone is a strong acid/base

Answer 14

acid

Question 15

the net charge of the phosphate at pH7 will be positive/negative

Answer 15

negative

Question 16

the phosphate group of the nucleotide is ()

Answer 16

polyprotic
- both pKa values are less than 7; negative. charge at physiological PH

Question 17

the bases exist in different tautomeric forms

Answer 17

• 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

Question 18

syn and anti conformation of nucleotides: rotation around the lycosidix (N-glycosyl) bond - which is more stable

Answer 18

• the anti conformation reduces steric and electrostatic clashes
• this is particularly evident for purine bases

Question 19

nucleuc acids have conjugated ring systems and absorb UV light
- where is the max absorbance
- how dos this compare to proteins (W,Y,F)

Answer 19

• 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

Question 20

the 3- –> 50 phosphodiester linkage : what is an ester

Answer 20

acid + alcohol –> ester

Question 21

phosphodiester linkage is an example of metastability:

Answer 21

the free energy of phosphodiester bond formation is +25kJ/mol

Question 22

free energy of hydrolysis:

Answer 22

-25kJ/mol
- thermodynamically, this process is favored

Question 23

example of metastability:

Answer 23

the free energy favors hydrolysis; however the time scale in biological systems kinetically favors formation of phosphodiester linkage

Question 24

how are successive nucleotides linked

Answer 24

• 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

Question 25

RNA is hydrolyzed rapidly under what conditions

Answer 25

alkaline conditions
- DNA is not (No 2’OH in DNA)

Question 26

what is the backbone of DNA and RNA subjected to

Answer 26

non-enzymatic hydrolysis of phosphodiester bonds

Question 27

nucleic acids are highly flexible due to

Answer 27

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

Question 28

how does the nucleic acid flexion compare to the tortion angles in polypeptides

Answer 28

much more flexible (increased number of conformational states) compated to the torsion angles discussed with polypeptides

Question 29

is simple condensation with the removal of H2O sufficient to form a phosphodiester linkage in vivo?

Answer 29

NO – bond synthesis requires “activated nucleotides”