Chapter 2 & 4 - Nucleic Acids

Question 1

How many nucleotides is one DNA turn made up of?

Answer 1

10.5

Question 2

How wide is the minor groove?

Answer 2

12 Å or 1.2 nm

Question 3

How wide is the major groove?

Answer 3

22 Å or 2.2 nm

Question 4

How wide is a double helix?

Answer 4

20 Å

Question 5

What is the centre-to-center distance between adjacent nucleotide pairs?

Answer 5

3.4 Å

Question 6

At which carbon on the sugar is the H attached to in deoxyribose?

Answer 6

At carbon 2.

Question 7

Which carbon carries the nitrogen base with a glycosidic bond?

Answer 7

Carbon number 1.

Question 8

Which are carbons are the reactive moieties on deoxyribose?

Answer 8

The 3’ OH is the reactive moiety for formation of phopshopdiesterbonds. The 5’ OH is another reactive moiety.

Question 9

How does phophodiester bond formation occur?

Answer 9

When adding nucleotides to the 3′ end of a polynucleotide chain the polymerase catalyzes the nucleophilic attack of the 3′-hydroxyl group terminus of the polynucleotide chain on the α-phosphate group of the nucleoside triphosphate that is added. For the initiation of this reaction, DNA polymerases require a primer with a free 3′-hydroxyl group already base-paired to the template and cannot start from scratch by adding nucleotides to a free single-stranded DNA template.

(Adenine-deoxyribose-triphosphate –> triphosphate attached to the 5’ carbon. Phosphates are connected by high energy bonds. The 3’ OH groups acts as the nucleophile ad donates a pair of electrons to the phosphate.)

Question 10

How does Glycosidic bond/linkage occur?

Answer 10

OH group the 1’carbon reacts with the H (N9) of the nitrogenous base and releasing a water molecule.

Question 11

At which positions on the bases do hydrogen bond formation occur?

Answer 11

A:T
Adenine and thymine match up so that a hydrogen bond can form between the exocyclic amino group at C6 and adenine at the carbonyl at C4 in thymine.Hydrogen bond can form between N1 of adenine and N3 of thymine.

G:C
NH2 at C2 on guanine hydrogen-bonds with a carbonyl at C2 on cytosine. N1 of guanine and N3 of cytosine form a bond. And the carbonyl at C6 of guanine can form a hydrogen bond with the NH2 at C4 of cytosine.

Question 12

What is an amino acid?

Answer 12

Imino acid = contains both an imine (C=NH) and a carboxyl group.

Question 13

Explain base stacking.

Answer 13

Induces by dipole-dipole and partial charge interaction between rings of the bases. (G:C have stronger stacking interactions)

Question 14

How are the 3’ and 5’ ends chemically different?

Answer 14

The 3’ end carries an unlike -OH group attached to the 3’ position on the sugar ring; the 5’ carries a free phosphate group attached to the 5’ position on the sugar ring.

Question 15

How does the chemical information differ between the major and minor groove?

Answer 15

Major groove ADHM

Minor groove ADA/AHA (symmetrical)

Question 16

What does hyperchomicity mean?

Answer 16

When the temperature of a solution of DNA is raised to near boiling point of water, the optical density at 260 nm markedly increases. The DNA duplex absorbs less ultraviolet light (40%) than do individual DNA chains.

Question 17

What is the linking number?

Answer 17

The number of times one strand would have to be passed through the other in order to have both strands completely separated. The linking number is a constant of cccDNA.

Question 18

What is twist?

Answer 18

Number of times one strand crosses in-front of the other strand.

Question 19

During which conditions do B and A form of DNA exist?

Answer 19

B DNA –> high humidity (physiological conditions)

A DNA –> low humidity

Question 20

Explain syn and anti in DNA?

Answer 20

In right handed DNA the glycosidic bond is always in the anti conformation. In the left handed helix, the glycosidic bond is int he anti conformation at pyrimidine residues and in the sun conformation at purine residues.

Question 21

What are the differences between the A, and Z form of DNA?

Answer 21

A form –> short and broad, right handed, 11 bp per turn , helix axis location through the major groove, major groove is narrow but deep, minor groove is broad but shallow.

Z form –> elongated and slim, 12 bp per turn, left handed, helix axis location though the minor groove, major groove is flattened out, minor groove is extremely narrow but very deep.

Question 22

What is writhe?

Which two form of writhe are there?

Answer 22

The total number of interwound and /or spiral writhes in cccDNA.
Interwound or

Question 23

What does superhelical density mean biologically?

Answer 23

Negative supercoils can be though of as a store of three energy that aids in process that require strand separation, such as DNA replication and transcription. Because LK=Tw+Wr, negative supercoils can be covered into untwisting of the double helix. regions of negatively supercoiled DNA, therefore have a tendency to unwind partially.

Question 24

What is superhelical density?

Answer 24

Sigma= Delta LK / LK*

Question 25

What is the function fo DNA gyrase?

Answer 25

A type II topoisomerase that introduces negative supercoils.

Question 26

How do Ethidium Ion cause DNA to unwind?

Answer 26

Ethidium is a large, flat, multi ringed cation. Its planar shape enables ethidium to slip, or intercalate, between the stacked base pairs of DNA.