Module 3

Question 1

name the components of nucleotides found in DNA

Answer 1

sugar, phosphate, nitrogenous base (adenine, guanine, thymine, cytosine)

Question 2

the nitrogenous base in DNA is attached to the sugars ___ carbon

Answer 2

first

Question 3

the phosphate in DNA is attached to the sugars ___ carbon

Answer 3

fifth

Question 4

a nucleotide is attached to another nucleotide through what component and which carbon in DNA

Answer 4

bond between phosphate group and sugar. phosphate attached between the third carbon of the previous sugar and fifth carbon of the current sugar

Question 5

why is the sugar called deoxyribose in DNA

Answer 5

its missing a hydroxyl group from the second carbon

Question 6

the backbone of DNA is bonded by what kind of bonds

Answer 6

phosphodiester

Question 7

what is the direction of the top strand typically in DNA? what about bottom

Answer 7

top 5’ to 3’ (Watson) and bottom 3’ to 5’ (crick)

Question 8

what kind of bonds do the bases make together

Answer 8

non covalent hydrogen bonds

Question 9

give the complementary bases and the amount of bonds

Answer 9

adenine and thymine, 2H bonds
cytosine and guanine 3H bonds

Question 10

what are the pyrimidines

Answer 10

thymine and cytosine (single ring)

Question 11

what are the purines

Answer 11

adenine and guanine (double ring)

Question 12

how many bases is one turn of the dna helix

Answer 12

10 bases

Question 13

what provides stability in the dna helix

Answer 13

1. hydrogen bonds between bases
2. stacking of bases, pi-pi interactions (sharing of electron probabilities)

Question 14

explain what the major and minor grooves are

Answer 14

base pair recognition and binding for proteins.
major: base pair specific info
minor: non specific
sequent and non sequent actions are possible on the DNA

Question 15

what differentiates DNA and RNA

Answer 15

DNA: double helix, two polynucleotide strands, H at carbon 2 in sugar, thymine
RNA: single polynucleotide strand, OH at carbon 2 in sugar, uracil

Question 16

whats in the position at these carbons in deoxyribose: 1,2,3,5

Answer 16

1: linked to nucleobase
2: H (which makes in dna instead of rna)
3: hydroxyl group
5: ribose sugar linked to phosphate

Question 17

what is this base

Answer 17

cytosine

Question 18

what is this base

Answer 18

adenine

Question 19

what is this base

Answer 19

uracil

Question 20

what is this base

Answer 20

thymine

Question 21

what is this base

Answer 21

guanine

Question 22

what are the 3 bases that have amine, NH2, group

Answer 22

cytosine, guanine and adenine

Question 23

what are the 4 bases that have a carbonyl group

Answer 23

1: cytosine, guanine
2: uracil, thymine

Question 24

which bases have 1 ring and which have 2

Answer 24

1: cytosine, uracil, thymine
2: adenine, guanine

Question 25

the pKa of the phosphate group in dna/rna is what? what does this mean for the charge of the molecule

Answer 25

1, it has a net negative charge, strong acid = eager proton donor = deprotonated = negative charge

Question 26

how do DNA and RNA degenerate? which degenerates faster and why?

Answer 26

their backbones undergo slow non-enzymatic hydrolysis to their phosphodiester bonds. RNA degenerates faster than DNA because of its OH at carbon 2 (more reactive hydroxyl group)

Question 27

from which carbon do you start counting in DNA?

Answer 27

the one bonded to the phosphate group

Question 28

what is a coupled reaction?

Answer 28

mixing a thermodynamically unfavorable reaction with a thermodynamically favorable one

Question 29

DNA polynucleotides are formed in which direction?

Answer 29

5' to 3'

Question 30

explain how new nucleotides are added in DNA

Answer 30

A new nucleotide (in the form of a deoxynucleotide triphosphate (dNTP)) is added to the 3' hydroxyl (-OH) group of the last sugar in the chain. - The incoming nucleotide is a dNTP with three phosphate groups - The 3' hydroxyl (-OH) of the growing chain reacts with the 5' phosphate group of the incoming nucleotide. - This reaction removes two phosphate groups (pyrophosphate) from the dNTP, leaving a dNMP. - A water molecule (H₂O) is released during the reaction, making it a condensation reaction - A phosphodiester bond forms between the sugar of the last nucleotide in the chain and the phosphate of the incoming dNMP. - This bond creates the sugar-phosphate backbone of DNA.

Question 31

why is dntp required for the growth of DNA polynucleotide chain

Answer 31

it makes the reaction favorable, G is negative (spontaneous)

Question 32

which compound is this

Answer 32

cytosine

Question 33

which compound is this

Answer 33

guanine

Question 34

which compound is this

Answer 34

adenine

Question 35

which compound is this

Answer 35

thymine

Question 36

Answer 36

uracil