Lecture 2: Structure Of Nucleic Acids

Question 1

Structural feature of DNA facilitates what?

Answer 1

Replication and Transcription

Question 2

Key structural difference of RNA to DNA and its function

Answer 2

• Smaller and less stable than DNA

• Acts as a template for protein synthesis

Question 3

What are nucleic acids?

Answer 3

Unbranched polymers (polynucleotides) made up of nucleotide monomers

Question 4

Three characteristic (structural) components of nucleotides

Answer 4

• A nitrogenous base

• One or more phosphates

• A pentose sugar

Question 5

Phosphate Group is responsible for the acidic property of nucleic acids:

True or False

         O
         ||
O- — P — O
          |
          O-

Answer 5

True

[ Because of Phosphoric Acid ]

          O
          ||
HO — P — OH
           |
         OH

Question 6

What is the difference between DNA’s pentose (5 Carbons, read from the right) sugar and RNA’s?

What does that say about RNA?

Answer 6

2-Deoxyribose (No oxygen) (DNA) has an H, while Ribose (RNA) has an OH group.

RNA is more reactive and unstable because of the OH group.

Question 7

What are Purines and Pyrimidines? What are their differences?

Answer 7

Purines (Adenine & Guanine) have a double ring,

Pyrimidines (Thymine, Uracil, & Cytosine) have a single ring

Question 8

Difference between Nucleoside and Nucleotide

Answer 8

Nucleoside: Base + Sugar (joined by an N-glycosidic bond)

Nucleotide: Nucleoside + Phosphate (joined by a phosphoester bond)

Question 9

Structural features of the DNA structure

Answer 9

• Two strands running anti-parallel

• Sugar-phosphate backbone linked between the 3’ of one nucleotide to the 5’ carbon of the next via a phosphodiester bond

• Each strand has a 5’ end (phosphate) and a 3’ end (hydroxyl)

• 5’ end of one strand is paired with the 3’ end of the other strand

• Strands held together by H bonds between bases

• Bases are planar with respect to the sugar phosphate backbone (Bases are flat)

Question 10

Features of B-DNA’s structure (most common form in solution)

Answer 10

• Right-handed double helix (width 2nm)

• Hydrophobic core

• Hydrophilic backbone

• Major & Minor Grooves

• Helical structure brings bases-pairs closer together (spacing of 0.34 nm)

Question 11

Factors contributing to the stability and structure of the DNA double helix

Answer 11

• Backbones need to be separated as far as possible to avoid electrostatic repulsion and allow exposure to solvent

• Bases form mutually stabilising hydrogen bonds

• Bases stack to maximise interactions between aromatic rings

• Bases attracted to each other

Question 12

How many H-bond acceptors & donors are between Thymine (or Uracil) and Adenine?

Answer 12

1 donor (O)
1 acceptor (N-H) -> T or U

1 donor (H-N)
1 acceptor (N) -> A

Thymine (or U) and Adenine share 2 bonds

Question 13

How many H-bond acceptors and donors do Cytosine and Guanine have?

Answer 13

1 donor
2 acceptors -> Cytosine

2 donors
1 acceptors -> Guanine

Cytosine and Guanine share 3 bonds, so they are stronger than T (or U) and A paired together

Question 14

What do non-standard pairings do to DNA? (G&T, G&A, C&T)

Answer 14

They distort the geometry of the double helix. The distance between bases remains to be no longer 1.1 nm.

Question 15

Characteristics and functional features of the base stacking interactions

Answer 15

• Hydrophobic interactions drive the bases to the inside of the helix

• Aromatic rings of the bases are attracted to each other

Question 16

How do proteins bind to DNA?

Answer 16

Via the major and minor grooves

Question 17

What links bases and sugars together?

Answer 17

Glycosidic bonds

Question 18

Characteristics of glycosidic bonds between bases and sugars

Answer 18

• Approximately in the same place in all base-pairs

• Angled with respect to one another

Question 19

How do sequence-specific DNA binding proteins “read” the DNA code without unwinding the helix

Answer 19

They access chemical information in the grooves (chemical information rich – especially the M.G.)

Major Groove: Wider and more accessible

Minor Groove: Narrower but still accessible

Question 20

Define and describe the structure of the RNA

Answer 20

• Unbranched polymer of ribonucleotides (primary structure)

• Predominantly single-stranded but can form complex secondary and tertiary structure

• Moves in 5’ to 3’ direction

Question 21

Difference between DNA and RNA

Answer 21

DNA has Thymine while RNA has Uracil

Question 22

Why does DNA have thymine and not uracil?

Answer 22

More stable than Uracil, less chance of mutations forming

(-NH3 -> +H2O)

Uracil in DNA can be recognised & removed by DNA repair processes because it isn’t normally present in DNA

Question 23

Why does RNA have Uracil and not Thymine?

Answer 23

Thymine is methylated-Uracil (has CH3).

• It’s more energetically costly to produce.

• There is no biosynthetic pathway in cells to produce the thymidine ribonucleotide.

Question 24

Explain why RNA is intrinsically less stable than DNA

Answer 24

2’ Hydroxyl acts as an internal nucleophile in an internal displacement reaction.

That breaks the phosphodiester backbone.

2’-3’ -cyclic monophosphate is produced.

Question 25

Definition of glycosidic bond and where it occurs

Answer 25

The bond that is created after a condensation reaction between a deoxyribose sugar and a base (O is shared).