Nucleic acids part 1

Question 1

How is genetic information stored?

Answer 1

Genetic information is stored in DNA, specifically in the base-pair sequences of the DNA strands.

Question 2

What process is referred to as the central dogma (principle) of molecular biology?

Answer 2

DNA stores genetic info, RNA transcribes and translates this info through protein synthesis.

The overall process is the central dogma of molecular biology

Question 3

How do retroviruses’ genetic information transfer system differ from that of humans?

Answer 3

Retroviruses store genetic info as RNA not DNA - Uses host cell to reproduce.

Question 4

What are 2 examples of antiretroviral drugs and what retroviruses are they used to treat?

Answer 4

Retrovir (AZT) for HIV.

Acyclovir for herpes and shingles.

Question 5

What is the basic structure of a nucleic acid?

Answer 5

Nucleic acids are polymers of nucleotide monomers.

Question 6

What is the structure of the nucleic acid sugars in DNA and RNA?

Answer 6

In RNA, the sugar is a D-ribose ring with a ß-configuration.

In DNA the sugar is a 2’-deoxy-D-ribose ring with no hydroxyl group at C-2’.

Question 7

What are the basic structure of the DNA and RNA sugar phosphate backbones?

Answer 7

DNA is a chain of 2’-deoxy-D-ribose rings liked by 3’ to 5’ phosphodiester linkages.

RNA is a chain of D-ribose linked by 3’ to 5’ phosphodiester linkages.

Question 8

What are the 2 subclasses of nucleotides, which bases fall into which class, and what are the structures of the 2 subclasses?

Answer 8

Two classes - purines (adenine, guanine) and pyrimidines (cytosine, thymine).

Purines - bicyclic system, 5-membered ring fused to a 6-membered ring.

pyrimidines - 6-membered rings containing 2 nitrogens.

Question 9

How do the RNA bases differ from the DNA ?

Answer 9

In RNA, thymine is replaced by uracil

Question 10

What glycosidic linkage forms between the nucleotide bases and the ribose sugars?

Answer 10

The nucleotide bases are connected to the ribose sugars by a C-N bond at the C-1’ position.

The C-N bond replaces the N-H bond in the free nucleotide bases.

Question 11

What is the structure of a nucleoside unit?

Answer 11

A nucleoside is an aldopentose sugar linked to a purine or pyrimidine base.

Question 12

What is the structure of a nucleotide unit?

Answer 12

A nucleotide is the same as a nucleoside but is also bonded to a phosphate.

Question 13

What is an oligonucleotide?

Answer 13

A short length of single stranded DNA consisting of a number of linked nucleotides.

The nucleotides are connected by
3’,5’-phosphodiester bonds.

Question 14

Nucleotide bases are described as heterocyclic, what does this mean?

Answer 14

Nucleotides are heterocyclic as they contain a nitrogen atom in their ring.

Question 15

What can be said about the basicity of the nucleotide bases?

Answer 15

The nitrogen atoms within the nucleotide ring structure can act as a Brønsted-Lowry bases.

This means the nitrogen can accept a proton and become charged.

Question 16

What acid-base equilibria exists in the nucleotide bases?

Answer 16

The bases exist in equilibria with their deprotonated and protonated forms:

BH+ + H2O ⇌ B + H3O+

Question 17

18. How can the equilibrium constant, Ka be calculated?

Answer 17

Ka = [B] [H3O+] / [BH+]

Question 18

How can pKa be calculated, what is it a measure of and what does a large pKa value indicate?

Answer 18

pKa = -log Ka

The pKa value is a measure of the position of the equilibrium:

A large pKa indicates the equilibrium lies to the left hand side - indicates a strong base (B converys readily to BH+).

Question 19

Why is the heterocycle pyrrole a weak base?

Answer 19

In pyrrole, the nitrogen lone pair is involved in pi-bonding

The nitrogen lone pair is not available for accepting a proton making it a weak base.

Question 20

Which 2 heterocycles act as nucleophiles and what does this mean?

Answer 20

pyridine and imidazole have nitrogen lone pairs making them nucleophilic and meaning they can react with electrophiles.

Question 21

What is tautomerization and which bases can undergo tautomerization?

Answer 21

Tautomerization is the transfer of a hydrogen atom from one place to another within the same molecule.

The two related structures are called tautomers.

Pyridines with an -OH or NH2 group on the carbon adjacent to the heterocyclic nitrogen can undergo tautomerization.

Question 22

What are the two main types of nucleotide base tautomers that occur, and which form of these tautomers exist in an excess in the equilibrium?

Answer 22

Lactam / lactim tautomers - The C=O (am) adjacent to the heterocyclic carbon becomes a C-OH (im).

Amino / imino tautomers - The C-NH2 (a) adjacent to the heterocyclic carbon becomes a C=NH (i).

Question 23

What is a hydrogen bond?

Answer 23

A hydrogen bond is an electrostatic attraction between a hydrogen atom attached to a very electronegative element (such as O or N) and a lone pair of electrons

Question 24

What are hydrogen bond donors and hydrogen bond acceptors?

Answer 24

Donors - Functional groups with an O-H or N-H bond.

Acceptors - Functional groups with lone pairs of electrons.

Question 25

What is complementary hydrogen bonding?

Answer 25

If hydrogen bond donor and acceptor groups line up correctly on a pair of molecules they hydrogen bonding is complementary.

Question 26

How does complementary hydrogen bonding impact the hydrogen bonds that form between the two strands of DNA?

Answer 26

Hydrogen bonding occur between base pairs involving one purine and one pyrimidine.

Question 27

In DNA and RNA which bases are complementary with one another?

Answer 27

In DNA: A pairs with T and G pairs with C.

In RNA: A pairs with U and G pairs with C.

Question 28

How can tautomerization of the nucleotide bases in DNA lead to damage?

Answer 28

Tautomerization of carbonyl or amino groups in the nucleotide bases can cause a change in the hydrogen bonding pattern.

This can lead to incorrect base pairing. If this happens during transcription an incorrect base may be incorporated into the DNA copy.

Question 29

What is the error rate in DNA due to tautomerization and why does the expected error differ from the in vivo error?

Answer 29

It would be ~300,000 errors per cell division.

However it is 1 in 10^8 base pairs copied, due to the presence of proofreading enzymes that remove tautomerization-based mismatches.

Question 30

What is the phosphodiester linkage?

Answer 30

The sugar phosphate backbone is linked through the 3’-hydroxy of one of the sugars to the 5’ hydroxy of a second sugar.

Question 31

How are organic esters and phosphodiesters formed?

Answer 31

Acid + alcohol (- H2O) –> ester

The difference is that in phosphate esters more than one hydroxyl group can be replaced, whilst for an organic ester only one hydroxyl group is replaced.

Question 32

How does phosphodiester hydrolysis in RNA differ from phosphodiester hydrolysis in DNA?

Answer 32

RNA is much less stable to hydrolysis than DNA due to the presence of an -OH group at the 2’ position of the ribose ring.

Question 33

What is sugar-base link cleavage in DNA and what does it result in the generation of?

Answer 33

The sugar-base link (a C-N) bond is unstable to acid hydrolysis, especially in the purines.

Protonation at N-7 aids the hydrolysis of the nucleotide base to give abasic DNA.