3.1.5 Nucleic acids are important information-carrying molecules

Structure of DNA and RNA

dna structure: nucleotide

• monomers of nucleic acid

• the basic building block of DNA

each DNA nucleotide consists of:

• pentose sugar (deoxyribose)

• phosphate group

• nitrogenous base: A, T, C, G

the bonding inside a nucleotide

• ester bond → phosphate to sugar

• glycosidic bond → base to sugar

dna structure: polynucleotide

• DNA as a polymer

→ DNA + RNA are polymers of nucleotides joined together by condensation reactions forming phosphodiester bonds

phosphodiester bonds

• forms between a phosphate of one nucleotide + 3’ carbon of next sugar

• produces a sugar phosphate back bone

• directionality of a phosphodiester bond = one strand runs from 5’ to 3’ + complementary strand runs antiparallel (3’ to 5’)

• DNA polymerase can only add nucleotides to the 3’ OH → making strand directionality biologically essential

what does DNA do? What does RNA do?

• DNA hold genetic infomation

• RNA transfers genetic information from DNA to the ribosomes

double helix structure

→ DNA has a double helix structure with 2 phosphate backbones twisted around each other

→ held together by hydrogen bonds bet. base pairs

→ twisted into a right-handed double helix

complementary base pairing

A - T ( Adenine + Thymine) = 2 hydrogen bonds

C - G (Cytosine + Guanine) = 3 hydrogen bonds

→ there are more C -G pairs = more stability due to more H bonds

→ base pairing ensures DNA replication accuracy

Purines vs pyrimidines

purines = A,G → double ring, bigger

pyrimidines = C,T,U → single ring, smaller

• a purine must pair with a pyrimidine: maintains constant helix width → key structural property

DNA

sugar :

bases

structure

stability:

sugar : deoxyribose

bases : A,T.C,G

structure: double stranded

stability: very stable ( no 2’OH)

RNA

sugar: ribose

bases: A, U, G ,C ( U replaces T)

structure: single stranded

stability: less stable ( reactive 2’OH)

RNA : mRNA + tRNA

mRNA = carries genetic code to ribosomes

tRNA = carries amino acids during translation (RNA transfers DNA code to ribosomes + is translated into polypeptides)

hydrogen bonds

• hold the 2 antiparallel strands together

• allows:

• stability (many form collectively strong strcutures)

• replication (easy to break)

Purpose of DNA Replication

• Occurs before cell division to ensure each daughter cell receives a full set of DNA.

• Ensures genetic continuity between generations of cells.

• Happens in S phase of interphase.

Semi-Conservative Replication step 1

• DNA helicase breaks the hydrogen bonds between complementary bases.

• The double helix unwinds to form two separate strands

Semi-Conservative Replication step 2

• Each exposed polynucleotide strand then acts as a template

• Free-floating DNA nucleotides are activated by phosphorylation

Semi-Conservative Replication step 3

• Free-floating DNA nucleotides line up with complimentary bases

• Hydrogen bonds form between the bases on the original and new strand

Semi-Conservative Replication step 4

• The enzyme DNA polymerase catalyses condensation reactions between nucleotides.

• This forms phosphodiester bonds between the phosphate of one nucleotide and the sugar of the next.

• The strand twists to form a double helix

• Each of the new DNA molecules contain one template strand and one new strand.

Semi-Conservative Replication step 5

Energy for bond formation

• Free nucleotides exist as activated nucleotides (nucleoside triphosphates).

• When two phosphate groups are removed, energy is released, which is used to form phosphodiester bonds.

• This drives the polymerisation of the new strand.

Semi-Conservative Replication step 6

Two new double helices form

• Once the strands are fully synthesised, each new molecule rewinds into a double helix.

• Each daughter DNA molecule contains:

  • One original strand (from the parent DNA),

  • One newly synthesised strand.

Semi-Conservative Replication why is it called that?

This process is called semi-conservative replication because half of each DNA molecule is conserved (kept) from the original parent DNA molecule.

This ensures genetic continuity, meaning:

• All daughter cells receive identical DNA,

• Correct genetic information is passed from one generation of cells to the next.

Evidence for Semi-Conservative Replication — Meselson & Stahl (1958)

Experimental design

• Grew E. coli in 15N (heavy nitrogen) → DNA becomes heavy.

• Moved bacteria to 14N medium.

• Extracted DNA after generations and centrifuged it to separate by density.

• Why nitrogen?

  • All DNA bases contain nitrogen.

  • DNA made in 15N medium is denser than DNA made in 14N medium.

  Results Generation 0 (in 15N)

  • One heavy band low in centrifuge tube.

  After 1 generation in 14N

  • One intermediate (hybrid) band → supports semi-conservative model.

  After 2 generations

  • Two bands:

    • Light band (new DNA from 14N)

    • Intermediate hybrid band
      → Confirms semi-conservative replication.

Why it disproves the conservative model

• Conservative replication would produce:

  • One heavy band

  • One light band

• But the first generation showed only hybrid, not two distinct bands

Test for Non-Reducing Sugars

• Add Benedict’s reagent to the sample and heat in a boiling water bath.

• If the solution stays blue, no reducing sugar is present.

• Add dilute hydrochloric acid to a fresh sample and heat to hydrolyse non-reducing sugars.

• Neutralise the mixture using sodium hydrogencarbonate.

• Add Benedict’s reagent again and heat.

• A brick-red precipitate shows that a non-reducing sugar was originally present.

pH

a measure of the concentration of hydrogen ions in an aqueous solution

. Free hydrogen ions (H⁺) do not exist independently in water.

• They immediately associate with water molecules to form hydronium ions (H₃O⁺).

• In biology, we simplify this and refer to hydrogen ion concentration, [H⁺].

This matters because biological reactions occur in aqueous solutions.

The pH scale

• measures acidity and alkalinity

• logarithmic scale, not linear.

• means:

• A change of 1 pH unit represents a tenfold change in hydrogen ion concentration.

• A change of 2 pH units represents a hundredfold change.

• This explains why small changes in pH can have large biological effect

pH CALCULATIONS

pH = −log₁₀[H⁺] • [H⁺] = 10⁻ᵖᴴ

in detail:

• pH values are always given to 2 decimal places.

• You are not expected to calculate logs without a calculator, but you must interpret changes.

WHY pH MATTERS IN BIOLOGY

All enzymes are proteins.

• Proteins have a tertiary structure held together by: – Hydrogen bonds – Ionic bonds

• Hydrogen ions affect the charge of amino acid side chains.

• Changing pH alters: – Ionic interactions – Hydrogen bonding

This changes the shape of the enzyme, especially the active site.

pH AND ENZYME ACTIVITY (optimum pH)

• Each enzyme has an optimum pH

At the optimum pH:

• The active site has the correct shape

• Enzyme–substrate complexes form efficiently

pH AND ENZYME ACTIVITY (Deviations from optimum pH)

Increased or decreased [H⁺] disrupts bonds

• Active site shape changes

• Fewer enzyme–substrate complexes form

• Reaction rate decreases

pH AND ENZYME ACTIVITY (Extreme pH)

Hydrogen and ionic bonds break permanently

• Tertiary structure is lost

• Enzyme is denatured (irreversible)

pH AND ENZYME ACTIVITY (Examples)

• Pepsin – optimum pH ≈ 2 (stomach)

• Trypsin – optimum pH ≈ 8 (small intestine)