Hello Biologists!

Welcome to one of the most fundamental and fascinating topics in AS Level Biology: Nucleic Acids and Protein Synthesis. This is where we uncover the secrets of inheritance—how the instructions for life are stored, copied, and finally used to build the machinery (proteins) that keeps every cell running.

If you understand this chapter, you’ll unlock huge parts of genetics, cell biology, and biotechnology. Don’t worry if the names seem complicated; we’ll break down these tiny molecules step-by-step!

Section 1: The Structure of Nucleic Acids (DNA & RNA)

1.1 The Building Blocks: Nucleotides

Nucleic acids (like DNA and RNA) are large polymers (macromolecules). Their monomers (single units) are called nucleotides.

Structure of a Nucleotide

Every nucleotide has three components joined by condensation reactions:

  1. A Pentose Sugar: A 5-carbon sugar.
    • In DNA, this is deoxyribose.
    • In RNA, this is ribose.
  2. A Phosphate Group: The acidic part of the molecule.
  3. A Nitrogen-containing Base: The crucial part that carries genetic information.

Did you know? ATP (Adenosine Triphosphate), the universal energy currency, is actually a phosphorylated nucleotide! It consists of Adenine, Ribose, and three Phosphate groups.

The Nitrogenous Bases

The bases fall into two main categories, based on their ring structure:

1. Purines (Double Ring Structure)

  • Adenine (A)
  • Guanine (G)

2. Pyrimidines (Single Ring Structure)

  • Cytosine (C)
  • Thymine (T) (Found only in DNA)
  • Uracil (U) (Found only in RNA, replacing Thymine)

Memory Aid:

PURe as Gold (Purines = Adenine and Guanine)
Cut The PY (Cytosine, Thymine, Pyrimidines)

1.2 DNA: The Double Helix

DNA (Deoxyribonucleic acid) is the molecule of heredity. It stores all the genetic instructions necessary for building and operating an organism.

Key Features of DNA Structure
  1. Sugar-Phosphate Backbone: Nucleotides join together by forming strong covalent bonds called phosphodiester bonds between the phosphate group of one nucleotide and the sugar of the next. This forms the strong outer ladder rails.
  2. Double Helix: The molecule consists of two polynucleotide strands twisted around each other into a helix shape.
  3. Complementary Base Pairing: The two strands are held together by weak hydrogen bonds formed between specific base pairs (the steps of the ladder):
    • Adenine (A) always pairs with Thymine (T) (2 hydrogen bonds).
    • Guanine (G) always pairs with Cytosine (C) (3 hydrogen bonds).

    Note: The C-G bond (3 H-bonds) is stronger than the A-T bond (2 H-bonds).

  4. Antiparallel Strands: The two strands run in opposite directions. One strand runs from 5' to 3' (five prime to three prime), and the complementary strand runs 3' to 5'. This is crucial for replication and transcription!

Quick Review: Why is DNA stable? Its stability comes from the strong sugar-phosphate backbones and the vast number of weak hydrogen bonds (which add up to a strong overall structure) holding the complementary bases together.

Section 2: DNA Replication

2.1 Semi-Conservative Replication

During the S phase of the mitotic cell cycle, DNA must be copied accurately so that when the cell divides, each daughter cell receives a complete set of genetic instructions.

DNA replicates using the semi-conservative method. This means that each new DNA molecule consists of one original (template) strand and one newly synthesised strand.

Analogy: Think of copying a recipe. You don't scrap the original book; you use the original page as a guide to create a brand new copy.

The Process and Key Enzymes
  1. Unwinding and Separation: The enzyme DNA helicase unwinds the double helix and breaks the hydrogen bonds between the complementary base pairs, separating the two strands.
  2. Template Strands: Each original strand acts as a template for the formation of a new complementary strand.
  3. Complementary Pairing: Free nucleotides in the nucleus align themselves opposite their complementary partners (A to T, C to G) on the exposed template strands.
  4. Polymerisation: The enzyme DNA polymerase moves along the template strand, catalysing the formation of phosphodiester bonds, joining the aligned nucleotides to form the new strand.
  5. Ligation: The enzyme DNA ligase joins fragments of DNA together (especially important on the lagging strand).
The 5' to 3' Constraint

This is a critical AS detail! DNA polymerase can only add new nucleotides to the 3' end of the growing strand. It must move along the template strand in a 3' to 5' direction, meaning the new strand is synthesised in a 5' to 3' direction.

  • Leading Strand: This strand is synthesised continuously in the 5' to 3' direction (towards the replication fork).
  • Lagging Strand: This strand must be synthesised in short fragments (Okazaki fragments), moving away from the replication fork. DNA ligase then stitches these fragments together.

Key Takeaway for Replication: Replication is semi-conservative, ensuring genetic stability. The directionality (5' to 3' synthesis) creates leading and lagging strands.

Section 3: Genes and the Genetic Code

3.1 Genes and Polypeptides

The core function of DNA is to code for proteins. A gene is defined as a sequence of nucleotides (base pairs) that forms part of a DNA molecule and codes for a specific polypeptide (protein).

3.2 The Universal Genetic Code

The instructions for assembling amino acids into polypeptides are read using a code:

  • The code is read in groups of three bases, called a triplet on the DNA, or a codon on the mRNA.
  • Each codon codes for a specific amino acid (or a start/stop signal).
  • The code is universal, meaning that the same codon codes for the same amino acid in nearly all living organisms (from bacteria to humans). This universality is key evidence for evolution.

Don't worry if this seems tricky at first: The key concept is that the sequence of bases (A, T, C, G) dictates the sequence of amino acids, and that relationship is defined by the triplet codon rule.

Section 4: Protein Synthesis: Transcription

Protein synthesis has two main stages: Transcription (making the RNA copy) and Translation (reading the RNA copy to make protein).

4.1 RNA Structure

Before diving into transcription, let's look at RNA (Ribonucleic acid), using messenger RNA (mRNA) as the primary example:

  • It contains the pentose sugar ribose (instead of deoxyribose).
  • It contains the base Uracil (U) instead of Thymine (T).
  • It is usually single-stranded (DNA is double-stranded).
  • It is generally much shorter than DNA.

4.2 Transcription (DNA to mRNA)

Transcription takes place in the nucleus of eukaryotic cells (or the cytoplasm of prokaryotes). It is the process where the gene's DNA sequence is copied into a temporary mRNA molecule.

Step-by-step Process:

  1. Initiation: The enzyme RNA polymerase binds to the start of the gene sequence.
  2. Unwinding: RNA polymerase unwinds a small section of the DNA double helix.
  3. Synthesis: RNA polymerase moves along only one strand of the DNA—the transcribed strand (or template strand).
    • Free RNA nucleotides pair up with the exposed DNA bases (C pairs with G; G pairs with C; A pairs with U; T pairs with A).
  4. Elongation: RNA polymerase joins the RNA nucleotides together via phosphodiester bonds, forming the single-stranded primary transcript (pre-mRNA).
  5. Termination: When the enzyme reaches a stop signal, the primary transcript detaches, and the DNA strands rewind.

Important Distinction:

  • The strand used by RNA polymerase is the transcribed/template strand (3' to 5').
  • The strand not used is the non-transcribed strand (or coding strand).

Eukaryotic RNA Modification (Syllabus Specific)

In eukaryotes, the primary transcript made in the nucleus cannot be used immediately:

  • It contains both coding sequences (exons) and non-coding sequences (introns).
  • Modification occurs where the introns are removed (splicing), and the remaining exons are joined together.
  • This results in the production of a mature messenger RNA (mRNA) molecule, which then leaves the nucleus for the cytoplasm.

Key Takeaway for Transcription: Only the template strand is used by RNA polymerase to make a pre-mRNA copy, which must be edited (introns removed) in eukaryotes before translation.

Section 5: Protein Synthesis: Translation

Translation is the process by which the coded sequence in the mRNA is read to produce a specific sequence of amino acids (a polypeptide). This occurs at the ribosomes in the cytoplasm.

Key Roles of Components in Translation
  • Ribosomes: These are the binding sites and molecular machines for protein synthesis. They are composed of ribosomal RNA (rRNA) and protein.
  • mRNA (Messenger RNA): Carries the sequence of codons from the nucleus to the ribosome.
  • tRNA (Transfer RNA): Acts as an adapter molecule. Each tRNA molecule carries a specific amino acid and has an exposed base triplet called an anticodon.
  • Codon: The triplet sequence on the mRNA (e.g., AUG).
  • Anticodon: The complementary triplet sequence on the tRNA (e.g., UAC).
Step-by-step Translation
  1. mRNA Arrival: The mRNA molecule attaches to a ribosome.
  2. tRNA Alignment: A tRNA molecule carrying the starting amino acid enters the ribosome and its anticodon binds temporarily to the complementary mRNA start codon (e.g., AUG).
  3. Peptide Bond Formation: A second tRNA molecule aligns at the next codon. The ribosome catalyses the formation of a peptide bond between the two adjacent amino acids.
  4. Translocation: The ribosome moves along the mRNA (translocates) by one codon. The first tRNA detaches and leaves to collect another amino acid.
  5. Elongation: Steps 3 and 4 repeat, adding amino acids one by one, lengthening the polypeptide chain.
  6. Termination: The process stops when the ribosome reaches a stop codon on the mRNA, releasing the completed polypeptide chain.

Key Takeaway for Translation: The ribosome is the site where tRNA anticodons match mRNA codons, ensuring the correct amino acid sequence is assembled.

Section 6: Gene Mutations

A gene mutation is a change in the sequence of base pairs in a DNA molecule. Since the base sequence determines the amino acid sequence, a change in DNA often results in an altered polypeptide, which may affect the protein’s structure and function.

Types of Gene Mutation

We focus on three types of point mutations (changes affecting a single base pair):

1. Substitution

One base pair is replaced by another (e.g., CTT becomes CAT).

  • Effect on Polypeptide: This may result in a change in only one amino acid. Because the genetic code is redundant (several codons code for the same amino acid), sometimes a substitution has no effect (silent mutation). However, it might cause a significant change, such as in sickle cell anaemia (a substitution in the haemoglobin gene).
2. Deletion

One or more base pairs are removed from the DNA sequence.

  • Effect on Polypeptide: This is usually very serious. Since the code is read in triplets, deleting one base causes a frame shift—all subsequent bases are read in the wrong groupings. This changes every amino acid downstream of the mutation, leading to a non-functional or severely altered polypeptide.
3. Insertion

One or more extra base pairs are added into the DNA sequence.

  • Effect on Polypeptide: Like deletion, insertion causes a frame shift. All subsequent codons are misread, often leading to a premature stop codon or a highly altered, non-functional polypeptide.

Common Mistake to Avoid: A substitution only changes one codon. Deletion and Insertion change *all* codons after the mutation site (frame shift).

Chapter Summary: Key Takeaways

Nucleic acids (DNA/RNA) are polymers made of nucleotides.
DNA is the stable, antiparallel blueprint, replicated semi-conservatively by DNA polymerase (5' to 3').
A gene codes for a polypeptide using the universal genetic code (triplets/codons).
Transcription (nucleus) uses RNA polymerase to make mRNA (removing introns in eukaryotes).
Translation (ribosome) uses tRNA to match mRNA codons to amino acids.
Gene mutations like deletion and insertion cause catastrophic frame shifts.