Primary Structure of Nucleic Acids

Question 1

What are the similarities between DNA and RNA?

Answer 1

They are both linear polymers composed of varying sequences of four different nucleotides.�

Question 2

What is a nucleotide composed of?

Answer 2

A pentose sugar, a phosphate group and an organic nitrogenous base�.

Question 3

What is the pentose sugar in RNA? Draw it.

Answer 3

Ribose. Has OH on 2’ carbon.

Question 4

What is the pentose sugar in DNA? Draw it.

Answer 4

Deoxyribose. Has H on 2’ carbon.

Question 5

How is the steric strain of the planar pentose sugar ring relieved? Draw it.

Answer 5

By puckering causing the 2’ and 3’ carbon to be out of the plane.

Question 6

How are phosphate groups attached to free nucleotides?

Answer 6

They are bonded to the oxygen group of the 5’ carbon in the pentose sugar via a PHOSPHOESTER BOND (P-O-C).

Question 7

What is nuceleotide with one, two or three phosphate called?

Answer 7

Respectively: 
Nucleotide monophosphate (eg. AMP)
Nucleotide diphosphate (eg. ADP)
Nucleotide triphosphate (eg. ATP)

Question 8

How is the base bonded in to the nucleotide structure?

Answer 8

It is joined by a Beta glycosidic bond to the 1’ carbon in the pentose sugar. It sits in the plane above the pentose sugar ring this means there are two planar rings - sugar and base.

Question 9

What are the two types of bases?

Answer 9

Purines and Pyrimidines.

Question 10

Describe the structure of a purine and state which bases are purines.

Answer 10

The purines are formed of two rings - a five membered ring fused with a six membered ring.
Adenine and Guanine are purines.

Question 11

Describe the structure of a pyrimidine and state which bases are pyrimidines.

Answer 11

Pyrimidines are a single six membered ring.

Thymine, Uracil and Cytosine are pyrimidines.

Question 12

What bases are keto bases and why?

Answer 12

Guanine, Thymine and Uracil.
Guanine (purine) is because at position 6 the group attached is C=O.
Thymine and Uracil (pyrimidine) are keto bases because at position 4 there is a C=O group.

Question 13

What bases are amino bases and why?

Answer 13

Adenine and Cytosine.
Adenine (purine) is an amino base because it has the group C-NH2 at position 6.
Cytosine (pyrimidine) is an amino base because it has the group C-NH2 at position 4.

Question 14

Draw the structure of Adenine, Thymine, Cytosine and Guanine.

Answer 14

See whiteboard photos on phone.

Question 15

What is a nucleoside?

Answer 15

Sugar + base

Question 16

What is a nucleotide?

Answer 16

Sugar + base + phosphate

Question 17

What are the names of the nucleosides of RNA?

Answer 17

Adenosine, Guanosine, Cytidine, Uridine.

no thymine as this is not present in RNA

Question 18

What are the names of the nucleosides of DNA?

Answer 18

Deoxyadenosine, Deoxyguanosine, Deoxycytidine and (Deoxy)thymidine.

Question 19

Describe how nucleotides polymerise?

Answer 19

The alpha phosphate group (one closest to carbon) of the free nucleotide triphosphate undergoes nucleophilic attack from the 3’ C-OH group of the nucleotide at the 3’ end of the growing chain.
A phospodiester bond forming between the two and the elimination of pyrophosphate (two phosphate groups).

Question 20

What catalyses the polymerisation of nucleotides and what fuels it?

Answer 20

The reaction is catalysed by polymerase enzymes and fueled by the energy-rich phosphoanhydride bonds (P-O-P).

Question 21

Which group is the phosphate attached to and how does this creat directionality?

Answer 21

The phosphate on the free nucleotide is attached to the 5’ carbon. This means that after it joins the nucleotide chain at the 3’ carbon there will be a free 5’ phosphate group at one end (5’ end) and there will be a free 3’ O-H group at the other end (3’ end). Giving the polymers (DNA and RNA) direction they go 5’ to 3’.

Question 22

What about RNA makes it less stable than DNA?

Answer 22

It has an OH group on the 2’ carbon (where DNA has H) this makes it susceptible to base catalysed hydroylsis whereby the phosphate bonds to both OH groups on the 3’ and 2’. This causes the loss of the nucleotide and shortening of the RNA chain. This is why DNA is more suited to being the hereditary material.

Question 23

What are some additional roles of nucleotides?

Answer 23

The high free energy of the phosphoanhydride bond in ATP is used to fuel many biochemical reactions.
Some nucleotides work as intracellular signalling molecules (eg. cAMP).
Also some nucleotides can work as intracellular neurotransmitters - therefore regulating cell and organism behaviour.