The structure of DNA and RNA as polymers of nucleotides joined by phosphodiester bonds. Semi-conservative replication of DNA. The structure of ATP and its hydrolysis to release energy.

What this dot point is asking

AQA wants you to describe DNA and RNA as polynucleotides built from nucleotides joined by phosphodiester bonds, state the complementary base-pairing rules, explain semi-conservative replication, and describe the structure of ATP and its hydrolysis to release energy.

The answer

The nucleotide

The bases are divided into:

• Purines (double ring): adenine (A) and guanine (G).
• Pyrimidines (single ring): cytosine (C), thymine (T) in DNA, and uracil (U) in RNA.

DNA structure

• The pentose sugar in DNA is deoxyribose.
• Nucleotides join by condensation reactions that form phosphodiester bonds between the phosphate of one nucleotide and the sugar of the next, creating a sugar-phosphate backbone.
• DNA is double-stranded: two polynucleotide strands wound into a double helix.
• The two strands are held together by hydrogen bonds between complementary bases: A pairs with T (2 hydrogen bonds) and C pairs with G (3 hydrogen bonds).
• The two strands run in opposite directions (antiparallel).

This structure suits DNA's role as a stable store of genetic information: the bases are protected on the inside, hydrogen bonds are strong in bulk but easy to separate for replication, and the molecule is long enough to store many genes.

RNA structure

• The pentose sugar is ribose.
• RNA is relatively short and usually single-stranded.
• It uses uracil (U) in place of thymine (so A pairs with U).
• mRNA carries a copy of a gene from DNA to ribosomes; this shorter, single strand is suited to leaving the nucleus and being broken down after use.

Semi-conservative replication

DNA copies itself semi-conservatively: each new (daughter) molecule contains one original strand and one newly synthesised strand.

1. DNA helicase breaks the hydrogen bonds between complementary bases, unwinding and unzipping the double helix into two single strands.
2. Each exposed strand acts as a template.
3. Free activated DNA nucleotides line up against the template by complementary base pairing (A-T, C-G).
4. DNA polymerase joins adjacent nucleotides by catalysing phosphodiester bonds, building each new strand.
5. The result is two identical DNA molecules, each with one conserved (old) and one new strand.

Meselson and Stahl (1958) confirmed this using nitrogen isotopes ($^{15}\text{N}$ "heavy" and $^{14}\text{N}$ "light"): after one round of replication in $^{14}\text{N}$, all DNA was of intermediate density - exactly what the semi-conservative model predicts, and what fully conservative or dispersive models did not.

ATP

Hydrolysis of ATP

ATP is the cell's immediate energy currency. Energy is released when the terminal phosphate bond is broken by hydrolysis, catalysed by the enzyme ATP hydrolase:

• ADP is adenosine diphosphate; $P_i$ is an inorganic phosphate group.
• A relatively small, manageable amount of energy is released, so little is wasted.
• The released $P_i$ can phosphorylate another molecule, making it more reactive (e.g. in active transport and muscle contraction).

Resynthesis of ATP

ATP is not stored; it is continuously regenerated by the reverse reaction - a condensation of ADP and $P_i$ catalysed by ATP synthase - using energy released during respiration (and, in plants, photosynthesis):

This rapid recycling is why a cell can run on a tiny pool of ATP yet meet large, fluctuating energy demands.

Worked example

Why this matters across 3.1

Nucleic acids are polymers built by condensation, like polysaccharides (see carbohydrates). Replication depends on enzymes such as helicase and polymerase (see enzymes), and genes ultimately code for proteins (see proteins). The phosphate groups in nucleotides and ATP are the inorganic phosphate ion $\text{PO}_4^{3-}$ (see water and inorganic ions). Lipids are not polymers, which makes a useful contrast (see lipids).

Try this

Q1. Describe the structure of a DNA nucleotide. [3 marks]

• Cue. A pentose sugar (deoxyribose); a phosphate group; a nitrogenous base (one of A, T, C or G); the three are joined by condensation.

Q2. Explain how the structure of DNA is suited to its function of storing genetic information. [4 marks]

• Cue. Long molecule stores much information; double helix/sugar-phosphate backbone protects bases and gives stability; many hydrogen bonds give overall stability but each is weak so strands separate for replication/transcription; base sequence codes for amino acid sequence; complementary base pairing allows accurate copying.

Q3. Explain why ATP is a better immediate energy source for the cell than glucose. [3 marks]

• Cue. ATP releases energy in a single step (glucose needs many); releases a small, usable amount so little wasted as heat; releasing a phosphate can phosphorylate and activate other molecules; rapidly resynthesised from ADP + Pi.