Nucleic Acids

Nucleic acids are large molecules located in cell nuclei.

• Two main types: DNA (deoxyribose nucleic acid) and RNA (ribose nucleic acid); both play key roles in protein synthesis and the transfer of genetic information.

• Provide the basis for hereditary material.

• Elements contained: Carbon, Nitrogen, Oxygen, Phosphorus, Hydrogen.

• Structure: Large polymers formed from many nucleotides (monomers) linked together in a chain.

Individual Nucleotide Structure

• Pentose monosaccharide (sugar): Contains $5$ carbon atoms.

• Phosphate group: A negatively charged inorganic molecule ($\text{PO}_4^{2-}$).

• Nitrogenous base: Complex organic molecule containing $1$ or $2$ carbon rings plus nitrogen.

Nucleotides

• Linked together by condensation reactions to form polymers (polynucleotides).

• Phosphodiester bonds: The phosphate group at the $5'$ carbon of the pentose sugar of one nucleotide forms a covalent bond with the hydroxyl ($\text{-OH}$) group at the $3'$ carbon of the pentose sugar of an adjacent nucleotide.

• Phosphodiester bonds form a long, strong sugar-phosphate backbone with a nitrogenous base attached to each sugar.

• Phosphodiester bonds can be broken via hydrolysis (the reverse of condensation reactions), releasing individual nucleotides.

Deoxyribonucleic Acid (DNA)

• Sugar in DNA: Deoxyribose (a sugar containing one less oxygen atom than ribose).

• DNA consists of nucleotides with $4$ different bases, divided into $2$ main groups: Pyrimidines and Purines.

Pyrimidines

• Smaller bases with single carbon-ring structures.

• Thymine (T), Cytosine (C).

Purines

• Larger bases with double carbon-ring structures.

• Adenine (A), Guanine (G).

The Double Helix

• DNA molecules vary in length from a few to millions of nucleotides.

• Made up of $2$ polynucleotide strands coiled into a double helix.

• Held together by hydrogen bonds between complementary bases.

• Each strand has a phosphate group ($5'$) at one end and a hydroxyl group ($3'$) at the other end.

• Both strands run in opposite directions (antiparallel).

Base Pairing Rules

• Adenine + Thymine: Form $2$ hydrogen bonds and always pair with each other.

• Cytosine + Guanine: Form $3$ hydrogen bonds and always pair with each other (complementary base pairing).

• A pyrimidine base always binds to a purine base, resulting in a constant distance between the DNA backbones (parallel polynucleotide chains).

• Complementary base pairing means DNA always contains equal amounts of adenine and thymine, as well as equal amounts of cytosine and guanine.

• The sequence of bases along a DNA strand carries the genetic information of an organism in the form of a code.

Ribonucleic Acid (RNA)

• Plays an essential role in transferring genetic information from DNA to proteins that make up enzymes and body tissues.

• DNA stores all genetic information of an organism but cannot supply this information directly to protein synthesis sites because eukaryotic chromosomes are very long molecules comprising hundreds of genes.

• RNA transcribes (copies) a gene-sized section of DNA into a short messenger RNA (mRNA) molecule.

  • Individual mRNA molecules are much shorter than a DNA chromosome.

• RNA nucleotides differ from DNA nucleotides:

  • Pentose sugar is ribose rather than deoxyribose.

  • Thymine (T) is replaced by Uracil (U).

• RNA nucleotides form polymers via phosphodiester bonds formed in condensation reactions.

• RNA polymers are small enough to leave the nucleus and travel to ribosomes, where they are central to protein synthesis.

• After protein synthesis, RNA molecules are degraded in the cytoplasm; phosphodiester bonds are hydrolysed, releasing RNA nucleotides to be reused.

Thymine vs. Uracil

• Both thymine and uracil are pyrimidines that form $2$ hydrogen bonds with adenine, so base pairing rules still apply.

• RNA nucleotides bind to DNA to make copies of particular sections of DNA.

DNA Extraction

DNA can be extracted from plant material using the following procedure:

1. Grind sample in a mortar and pestle: Breaks down the cell wall.

2. Mix sample with detergent: Breaks down the cell membrane, releasing cell contents into solution.

3. Add salt: Breaks hydrogen bonds between DNA and water molecules.

4. Add protease enzyme: Breaks down proteins associated with DNA in nuclei.

5. Add a layer of alcohol (ethanol) on top of sample: Causes DNA to precipitate out of solution.

6. Observe DNA: DNA appears as white strands forming between the sample layer and alcohol layer; can be collected by spooling it on a glass rod.