Study Notes: DNA, Genes, and Chromosomes (3.1.7 & 3.1.8)

Welcome to one of the most fundamental and exciting chapters in Biology! Here, we dive into the molecule of life: DNA. Understanding DNA, genes, and chromosomes is like learning the secret blueprint that dictates everything about an organism, from its smallest cellular function to its overall physical appearance and how it contributes to the diversity of living organisms.

Don't worry if this chapter seems dense; we will break down the structure and processes (like replication and protein synthesis) into easy, manageable steps. Let's get started!

3.1.7 The Structure of Nucleic Acids

What are Nucleic Acids?

Nucleic acids (DNA and RNA) are massive biological molecules (polymers) built from small repeating units called nucleotides (monomers).

The Structure of a Nucleotide

Every single nucleotide follows the same basic structural formula, composed of three parts joined together:

  1. Pentose Sugar: A sugar containing five carbon atoms.
  2. Phosphate Group: A negatively charged chemical group.
  3. Nitrogen-Containing Organic Base: This is the component that varies and carries the genetic information.

Analogy: Think of a nucleotide as a three-piece puzzle: Sugar + Phosphate form the backbone (the frame), and the Base sticks out like the specific code on the piece.

DNA vs. RNA: The Key Differences

The type of nucleic acid depends on its specific components:

Deoxyribonucleic Acid (DNA)

  • Sugar: Deoxyribose (a pentose sugar).
  • Bases: Adenine (A), Cytosine (C), Guanine (G), and Thymine (T).
  • Structure: A double helix consisting of two long polynucleotide chains wound around each other.

Ribonucleic Acid (RNA)

  • Sugar: Ribose (a pentose sugar).
  • Bases: Adenine (A), Cytosine (C), Guanine (G), and Uracil (U) (Uracil replaces Thymine).
  • Structure: A relatively short polynucleotide chain (usually single-stranded).
The DNA Double Helix

The two polynucleotide chains in DNA are held together by hydrogen bonds formed between the complementary bases.

  • Complementary Base Pairing: Bases pair up specifically across the helix:
    • Adenine (A) always pairs with Thymine (T) (2 hydrogen bonds).
    • Cytosine (C) always pairs with Guanine (G) (3 hydrogen bonds).

Memory Aid: The curvy letters (C and G) pair together; the straight letters (A and T) pair together.

Specialised RNA Structures

Two important types of RNA we need to know for protein synthesis:

  • mRNA (Messenger RNA): A short, single chain molecule that carries the genetic information copied from DNA in the nucleus out to the ribosome in the cytoplasm.
  • tRNA (Transfer RNA): A small, cloverleaf-shaped molecule that transports specific amino acids to the ribosome during protein synthesis.

Key Takeaway 1: Nucleic acids are polymers of nucleotides. DNA uses deoxyribose and T; RNA uses ribose and U. The double helix of DNA is stabilized by complementary A-T and C-G base pairs.

3.1.7.2 DNA, Genes, and Chromosomes

The Concept of the Gene and Loci

A gene is defined as a specific section of DNA that codes for the amino acid sequence of one or more polypeptides. These polypeptides ultimately determine the nature and development of an organism.

Genes occupy specific, fixed positions on a DNA molecule, known as a locus (plural: loci).

The Genome

The genome is the complete set of genes (genetic material) present in a cell or organism. It is the entire instruction manual.

DNA Packaging (Eukaryotes vs. Prokaryotes)

The way DNA is stored in the cell depends on whether the cell is eukaryotic or prokaryotic.

Eukaryotic DNA (Plants, Animals, Fungi)
  • Structure: DNA is linear (straight).
  • Association: It is tightly wound and packaged by associating with specialised proteins called histones.
  • Organisation: The DNA-protein complex coils up to form the dense structures we call chromosomes.
  • Location: Primarily found within the nucleus. (Smaller amounts are also found in mitochondria and chloroplasts).
Prokaryotic DNA (Bacteria)
  • Structure: DNA is shorter in length and circular.
  • Association: It is not associated with histone proteins.
  • Location: Free in the cytoplasm.

Did you know? The DNA in mitochondria and chloroplasts (which are organelles in eukaryotes) is structured similarly to prokaryotic DNA—it is short, circular, and not associated with histones. This is key evidence for the endosymbiotic theory!

Coding and Non-Coding DNA in Eukaryotes

The vast majority of DNA in eukaryotic cells does not code for polypeptides.

  1. Non-Coding Multiple Repeats: These are long sections of base sequences found between genes. We often call this 'junk DNA', but it may have regulatory functions.
  2. Introns and Exons: Even within a single gene, the sequence is interrupted:
    • Exons: The coding sequences (they are expressed). These are the parts that contain the instructions for the amino acid sequence.
    • Introns: The non-coding sequences (they interrupt the coding sequence). These must be removed before the gene can be translated.

Analogy: If a gene is a recipe book, the Exons are the actual ingredients list and instructions. The Introns are advertisements or blank pages scattered in between the steps—they must be cut out (spliced) before you can actually cook the meal!

Key Takeaway 2: A gene is a DNA section coding for a polypeptide. Eukaryotic DNA is linear, packaged by histones into chromosomes; prokaryotic DNA is circular and histone-free. Eukaryotic genes contain coding segments (exons) separated by non-coding segments (introns).

3.1.7.3 DNA Replication: Copying the Blueprint

When a cell divides, it needs an exact copy of its genetic material. This process is called DNA replication and it is semi-conservative—meaning each new DNA molecule conserves one old strand and one newly synthesised strand.

The Semi-Conservative Replication Process (Step-by-Step)

This process relies on the precise pairing of complementary bases (A with T, C with G).

Step 1: Unwinding and Unzipping
The double helix unwinds, and the enzyme DNA helicase moves along the molecule, breaking the weak hydrogen bonds between the complementary base pairs. This separates the two strands, exposing the bases.

Step 2: Template Function
Each original strand now acts as a template (a guide) for the creation of a new, complementary strand.

Step 3: Attraction and Base Pairing
Free-floating DNA nucleotides floating in the nucleus are attracted to the exposed bases on the template strands. Due to complementary base pairing, only the correct nucleotide fits into place (e.g., a G template attracts a C nucleotide).

Step 4: Polymerisation
The enzyme DNA polymerase moves along the template strands, catalyzing the condensation reaction that joins the phosphate group and deoxyribose sugar of the adjacent new nucleotides together, forming the sugar-phosphate backbone.

Result: Two new DNA molecules are formed, each containing one old (template) strand and one newly synthesised strand. The genetic information is preserved exactly.

Quick Review: The Key Enzymes

  • DNA Helicase: Unwinds helix and breaks H-bonds (the 'unzipper').
  • DNA Polymerase: Joins new nucleotides to form the new backbone (the 'builder').

3.1.8 Protein Synthesis: From Gene to Polypeptide

Genes carry the instructions, but how are those instructions read and converted into functional proteins? This happens in two main stages: Transcription and Translation.

3.1.8.1 The Genetic Code

The instructions encoded in DNA are read in groups of three bases, called a base triplet on DNA, or a codon on mRNA. Each base triplet codes for one specific amino acid.

Key Properties of the Genetic Code:

  1. Universal: The same triplet codes for the same amino acid in almost all organisms (from bacteria to humans). This universality is crucial, as it allows recombinant DNA technology (3.4.10) to work!
  2. Non-overlapping: Each base in the sequence is read only once, as part of one triplet. The triplets are read sequentially (e.g., CAT | GAT | TAC).
  3. Degenerate: Most amino acids are coded for by more than one codon (base triplet). This redundancy protects against some mutations.

3.1.8.2 Polypeptide Synthesis

Stage 1: Transcription (DNA to mRNA)

Transcription is the process where a gene sequence on DNA is copied into a molecule of mRNA. This happens in the nucleus (for eukaryotes).

Steps:

  1. The enzyme RNA polymerase attaches to the DNA near the start of a gene.
  2. The DNA helix unwinds and separates at that section.
  3. RNA polymerase moves along the DNA template strand, synthesizing a new RNA strand by linking complementary RNA nucleotides. (Remember U pairs with A, not T).

Crucial Difference (Eukaryotes Only): Pre-mRNA Splicing
In eukaryotes, the initial RNA transcript is called pre-mRNA and it contains both coding (exons) and non-coding (introns) sequences. Before leaving the nucleus, the introns are cut out, and the exons are joined back together (this is called splicing) to form the final, mature mRNA molecule.

In prokaryotes (which lack introns), transcription results directly in the production of functional mRNA.

Stage 2: Translation (mRNA to Polypeptide)

Translation is the process where the sequence of codons on the mRNA is used to assemble a sequence of amino acids into a polypeptide chain. This happens at the ribosome (in the cytoplasm).

The Main Players:

  • Ribosome: The cellular machinery (the ‘factory’) where translation occurs. It holds the mRNA in place.
  • tRNA (Transfer RNA): Small molecules (the ‘delivery trucks’) that carry a specific amino acid to the ribosome. They have an anticodon sequence that complements the mRNA codon.
  • ATP: Provides the immediate source of energy (the ‘fuel’) required for translation.

Steps:

  1. The mRNA attaches to a ribosome.
  2. A tRNA molecule carrying the correct amino acid (whose anticodon is complementary to the start codon on the mRNA) moves into position.
  3. The ribosome moves along the mRNA, reading the next codon. The next tRNA arrives, bringing its amino acid.
  4. A peptide bond is formed between the two amino acids.
  5. The first tRNA detaches and leaves to collect another amino acid.
  6. This process repeats, linking amino acids in sequence until a stop codon is reached, releasing the complete polypeptide chain.

3.1.8.3 Protein Folding

Once the long chain of amino acids (the polypeptide) is synthesized, it is not yet a functional protein. It must fold into its characteristic three-dimensional structure (its secondary, tertiary, and sometimes quaternary structure).

  • The final folded shape is determined entirely by the sequence of amino acids (the primary structure).
  • Specialized proteins called chaperones (or chaperonin proteins) often assist polypeptides in folding correctly, especially complex or unstable ones, preventing them from forming incorrect bonds prematurely.

Key Takeaway 3: Protein synthesis involves transcription (DNA to mRNA, catalyzed by RNA polymerase) and translation (mRNA to polypeptide, involving ribosomes, tRNA, and ATP). In eukaryotes, pre-mRNA must be spliced to remove introns. The final polypeptide folds into a functional 3D shape, often assisted by chaperones.