Biology (9700) | Protein synthesis

🧬 Protein Synthesis: The Recipe for Life

Welcome to one of the most fundamental processes in biology! Protein synthesis is how your cells read the genetic instructions stored in your DNA to build the thousands of different proteins that keep you alive, from enzymes that speed up reactions to hormones that send messages.

Think of your DNA as the master cookbook stored safely in the vault (the nucleus). Proteins are the delicious dishes you need to make (e.g., insulin, haemoglobin). Protein synthesis involves two main stages:

1. Transcription: Copying the recipe from the DNA vault onto a small, portable note (mRNA).
2. Translation: Taking that note out to the kitchen (ribosome) and assembling the ingredients (amino acids) according to the instructions.

1. The Genetic Code: Reading the Instructions (Syllabus 6.2.1, 6.2.2)

Before we start, we need to understand the language used in the recipe.

What is a Gene?

A gene is a sequence of nucleotides that forms part of a DNA molecule and codes for a single polypeptide.

Understanding Codons (The Triplets)

The genetic instructions are read in sets of three bases, called a triplet on the DNA, or a codon on the mRNA.

• Each codon codes for one specific amino acid (or a start/stop signal).
• Since there are 4 different bases (A, U, C, G in RNA), \(4^3 = 64\) possible codons. This is more than enough for the 20 common amino acids.

This leads to two key features of the code:

1. The Code is Universal: With minor exceptions, the same codons code for the same amino acids in almost all organisms, from bacteria to humans. (This is why genetic engineering works!)
2. The Code is Degenerate: Most amino acids are coded for by more than one codon. (Example: both UUU and UUC code for Phenylalanine).

2. Step 1: Transcription (In the Nucleus) (Syllabus 6.2.3, 6.2.4)

Transcription is the process of synthesizing a strand of messenger RNA (mRNA) from a section of DNA.

Role of Key Players:

• DNA: Contains the gene blueprint.
• RNA Polymerase: The enzyme responsible for unwinding the DNA helix and joining the complementary RNA nucleotides together.

The Process of Transcription (Step-by-Step)

1. Initiation: The enzyme RNA polymerase binds to a specific sequence on the DNA near the start of the gene.
2. Unwinding and Separation: RNA polymerase separates the two DNA strands over a short length.
3. Elongation (Base Pairing): RNA polymerase moves along the DNA, synthesizing the pre-mRNA strand using complementary base pairing.
   • Cytosine (C) pairs with Guanine (G).
   • Adenine (A) pairs with Uracil (U) (Remember, RNA uses U instead of DNA's T!).
4. Termination: RNA polymerase reaches a termination sequence, detaches, and the pre-mRNA strand is released. The DNA strands rejoin into a double helix.

Important DNA Strand Distinction (Syllabus 6.2.4):

• Template Strand (Transcribed Strand): This is the DNA strand used by RNA polymerase to synthesize the complementary RNA molecule. The mRNA sequence is built directly complementary to this strand.
• Non-transcribed Strand (Non-coding Strand): This is the DNA strand not used in transcription. Its base sequence is the same as the resulting mRNA (except T is replaced by U).

3. mRNA Modification (Eukaryotes Only) (Syllabus 6.2.5)

In eukaryotic cells (like ours), the RNA molecule formed immediately after transcription is called the primary transcript (or pre-mRNA). This molecule is not ready to leave the nucleus yet! It contains large non-coding regions that must be removed.

Introns and Exons

• Introns: These are the non-coding sequences within a gene. They are *removed* during modification. (Think of them as junk DNA that needs to be cut out.)
• Exons: These are the coding sequences that contain the instructions for the polypeptide. They are *kept* and joined together.

The process of removing introns and joining the exons is called splicing. After splicing, the molecule is known as mature mRNA. This mature mRNA is finally ready to leave the nucleus and travel to the cytoplasm for translation.

4. Step 2: Translation (In the Cytoplasm) (Syllabus 6.2.3)

Translation is the process where the sequence of codons on the mRNA is used to assemble a sequence of amino acids to form a polypeptide.

Role of Key Players:

• Ribosomes: The site of translation. These organelle 'factories' read the mRNA and catalyze the formation of peptide bonds. (80S in the cytoplasm of eukaryotes).
• mRNA (Codons): Provides the sequence of codons (the instructional tape).
• Transfer RNA (tRNA): Acts as the 'adapter' molecule. Each tRNA carries a specific amino acid and has a three-base sequence called an anticodon.
• tRNA (Anticodons): The anticodon sequence is complementary to the codon on the mRNA.

The Process of Translation (Step-by-Step)

1. Initiation: The mRNA binds to a ribosome. The ribosome locates the 'start' codon (usually AUG). A tRNA molecule carrying the first amino acid (usually methionine) binds its complementary anticodon to the start codon.
2. Elongation:
   • A second tRNA molecule, carrying its specific amino acid, binds to the next codon on the mRNA.
   • The ribosome catalyzes the formation of a peptide bond between the first and second amino acids.
   • The ribosome moves along the mRNA (translocates) by one codon.
3. Translocation and Release: The first, now 'empty' tRNA molecule detaches and leaves the ribosome to pick up another amino acid. The process repeats, adding amino acids one by one, elongating the polypeptide chain.
4. Termination: The ribosome reaches a 'stop' codon (e.g., UAA, UAG, UGA). Since there are no tRNA molecules with anticodons complementary to the stop codons, the synthesis halts. The ribosome complex disassembles, and the completed polypeptide is released.

5. Gene Mutations: Errors in the Recipe (Syllabus 6.2.6, 6.2.7)

A gene mutation is a change in the sequence of base pairs in a DNA molecule. This can result in the wrong amino acid sequence, leading to an altered polypeptide (a faulty protein).

Don't worry if this seems tricky at first; visualizing how the triplet code is read is the key here!

Types of Gene Mutations

1. Substitution:

One base is replaced by another base.

• Example: C-G is replaced by T-A.
• Effect: This mutation may change only one codon, which might result in a different amino acid being incorporated (a missense mutation). However, due to the degenerate nature of the code, it might still code for the original amino acid (a silent mutation). It could also change an amino acid codon into a stop codon (a nonsense mutation), resulting in a drastically shortened, non-functional polypeptide.

2. Deletion or Insertion:

A base is either removed (deletion) or added (insertion) to the DNA sequence.

• Example: Inserting an extra A into the sequence.
• Effect: These are usually much more serious because they cause a frameshift. Since the ribosome reads the code in sets of three, adding or removing a single base shifts the entire reading frame for every subsequent codon. This drastically changes the entire amino acid sequence, almost always leading to a non-functional or severely altered polypeptide.

Comprehensive Summary: Roles in Protein Synthesis

Here’s a final quick-reference table of the key molecules and their roles:

• DNA Template Strand: Contains the blueprint sequence (triplets) for the gene.
• RNA Polymerase: Synthesizes pre-mRNA during transcription.
• mRNA (Codons): Carries the code from the nucleus to the ribosome.
• tRNA (Anticodons): Transfers specific amino acids to the ribosome; pairs its anticodon with the mRNA codon.
• Ribosomes: The site of translation; forms peptide bonds between amino acids.
• Introns (Eukaryotes): Non-coding sequences removed from the primary transcript.
• Exons (Eukaryotes): Coding sequences spliced together to form mature mRNA.