Nucleotides and DNA

Question 1

Nucleotides in the monomer form are used for?

Answer 1

Metabolism (ATP), enzyme cofactors (NAD+) and signal transduction (cAMP).

Question 2

Nucleoside

Answer 2

Nitrogenous base and pentose.

Question 3

PO4 is what a neutral pH?

Answer 3

Negative.

Question 4

PO4 is typically attached to which position?

Answer 4

5’

Question 5

Nitrogenous bases are…

Answer 5

Derivative of pyrimidine or purine, planar or almost planar, absorb UV light around 250-270nm.

Question 6

Difference between ribo and deoxyribo

Answer 6

Deoxyribo has no O at 2’ carbon.

Question 7

N-glycosidic bond

Answer 7

Pentose is attached to the nitrogenous base. Quite stable towards hydrolysis.

Question 8

Where does the N-glycosidic bond form in pyrimidines?

Answer 8

N1 position of N base.

Question 9

Where does the N-glycosidic bond form in purines?

Answer 9

N9 position of N base.

Question 10

Syn conformation

Answer 10

Angle near 0 in N-glycosidic bond.

Question 11

Anti conformation

Answer 11

Angle near 180 in N-glycosidic bond. Normal B-DNA.

Question 12

Ring pucker limits what?

Answer 12

The angle of torsion possible for the N-glycosidic bond.

Question 13

How do nucleotides connect to one another?

Answer 13

Phosphodiester bonds, connected from 3’ carbons to 5’ carbons.

Question 14

How are DNA/RNA strands held together?

Answer 14

Hydrogen bonding.

Question 15

What was the waston and crick model of B-form DNA?

Answer 15

10.5 base pairs, or 3.6nm, per turn of helix.

Question 16

RNA is unstable under…

Answer 16

Alkaline conditions. The OH at the 2’ position acts as a nucleophile.

Question 17

What remains intact during DNA denaturation?

Answer 17

Covalent bonds and genetic code.

Question 18

What is lost during DNA denaturation?

Answer 18

Hydrogen bonds and base stacking.

Question 19

What induces denaturation?

Answer 19

High temperature or change in pH.

Question 20

Tm

Answer 20

Mid point of melting

Question 21

What increases Tm (DNA denaturation)?

Answer 21

High CG composition, longer DNA and high salt.

Question 22

Deamination

Answer 22

Cytosine to uracil, very slow reactions.

Question 23

Depurination

Answer 23

N-glycosidic bond is hydrolyzed, significant for purines.

Question 24

UV light induces…

Answer 24

Dimerization of pyrimidines.

Question 25

cAMP

Answer 25

Second messenger, activates protein kinase A activity.

Question 26

What ends are new nucleotides added to?

Answer 26

3’ end (to the 3’-OH).

Question 27

How are trinucleotides added in DNA elongations?

Answer 27

The nucleophilic OH group at the 3’ end of the growing chains attacks the alpha phosphate of the incoming trinucleotide.

Question 28

How is the 3’ OH made a more powerful nucleophile?

Answer 28

By near by Mg+ ions.

Question 29

Primer

Answer 29

Contains 3’ - OH to begin the first DNA polymerase catalyzed reaction, commonly made of RNA.