Biology (9610) | Protein synthesis

🧬 Protein Synthesis: Turning Genes into Functional Organisms

Welcome to one of the most exciting topics in Biology! Protein synthesis is the fundamental process by which the genetic instructions stored in your DNA are used to build proteins. These proteins are the molecular machines—the enzymes, hormones, and structural components—that determine the characteristics and functions of every living organism. In short, this is how you become you!

This chapter bridges the gap between the genetic information we’ve stored in nucleic acids (DNA/RNA) and the functional molecules (proteins) that create the incredible diversity of life we see around us.

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1. The Genetic Code: The Language of Life (3.1.8.1)

Your DNA holds the instructions, but how does the cell read them? It uses a universal language called the Genetic Code.

What is a Base Triplet?

Proteins are made of long chains of amino acids. There are 20 different common amino acids. To specify which one to use, the cell uses a sequence of three nucleotide bases in the mRNA molecule. This sequence is called a codon (or a base triplet).

Analogy: Think of the genetic code as a dictionary where every three-letter word (codon) corresponds to one specific meaning (amino acid).

Key Properties of the Genetic Code

The code isn't just a simple list; it has four critical properties that make life possible:

1. Universal: The code is virtually the same in all organisms.

Did you know? Because the code is universal, scientists can take a human gene (like the one for insulin) and put it into a bacterium, and the bacterium can correctly produce the human protein! This is crucial for genetic engineering.



2. Non-overlapping: Each base in the sequence is read only once as part of a single triplet.

If an mRNA sequence is ABC-DEF-GHI, it is read as ABC, then DEF, then GHI. It is not read as ABC, BCD, CDE, etc.



3. Degenerate: Most amino acids are coded for by more than one base triplet.

There are 64 possible codons (4x4x4), but only 20 amino acids. This redundancy is great for us! If a random mutation changes one base, it might still code for the correct amino acid, protecting the cell from harmful changes.



4. Start and Stop Codons: Specific codons signal the start of synthesis (usually AUG) and the end of synthesis (UAA, UAG, or UGA).

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2. Polypeptide Synthesis: From Gene to Chain (3.1.8.2)

Protein synthesis is a two-step process:

1. Transcription: Copying the gene sequence from DNA into messenger RNA (mRNA).
2. Translation: Using the mRNA sequence to assemble the amino acids into a polypeptide chain.

2.1. Transcription (DNA → mRNA)

Transcription takes place in the nucleus of eukaryotic cells (or the cytoplasm of prokaryotic cells).

Step-by-Step Transcription Process:

1. Unwinding: The DNA double helix unwinds at the position of the gene to be copied.
2. Template Identification: Only one strand of the DNA acts as the template strand.
3. Synthesis by RNA Polymerase: The enzyme RNA polymerase moves along the DNA template strand. It links free RNA nucleotides together to form a complementary mRNA chain.

(Remember the base pairing rules: DNA A pairs with RNA U; DNA T pairs with RNA A; C pairs with G).

4. Separation: Once the gene is fully copied, the mRNA molecule detaches, and the DNA strands rewind back into a double helix.

Key Takeaway: The mRNA molecule is a portable copy of the gene, ready to leave the nucleus and travel to the ribosome.

Eukaryotes vs. Prokaryotes: The Splicing Stage

This is a crucial difference to remember, especially for complex eukaryotic cells:

• Prokaryotes (Bacteria): Transcription results directly in the production of functional mRNA. They have no nucleus, so translation can start immediately while transcription is still finishing!


• Eukaryotes (Animals, Plants, Fungi): Transcription first produces a large precursor molecule called pre-mRNA.

Why pre-mRNA? The Mystery of Introns and Exons

In eukaryotic genes, the DNA sequence contains two types of segments:

• Exons: Sequences that code for the amino acid sequence (these are 'expressed' regions).
• Introns: Non-coding sequences that interrupt the exons.

The pre-mRNA contains both introns and exons. Before the mRNA can leave the nucleus, the non-coding introns must be removed. This editing process is called splicing, which forms the final, shorter, functional mRNA molecule ready for translation.

Common Mistake Alert: Students often forget that prokaryotes do not do splicing because their genes generally lack introns!

2.2. Translation (mRNA → Polypeptide)

Translation is the process of building the polypeptide chain using the mRNA code. This takes place on the ribosomes in the cytoplasm.

The Three Key Players in Translation:

1. Ribosomes: (The cellular workbench). These are organelles made of protein and ribosomal RNA (rRNA). They bind to the mRNA and facilitate the formation of peptide bonds between amino acids. They act as the "assembly line."
2. Transfer RNA (tRNA): (The delivery trucks). These are short, single polynucleotide chains folded into a specific shape. One end carries a specific amino acid, and the other end carries a three-base sequence called an anticodon.
3. ATP: Provides the necessary energy for various steps, especially the attachment of the amino acid to the tRNA molecule.

Step-by-Step Translation Process:

1. Initiation: The ribosome attaches to the start codon (AUG) on the mRNA. The first tRNA, carrying its corresponding amino acid, moves into place.
2. Elongation: A second tRNA, whose anticodon is complementary to the next mRNA codon, moves into the ribosome.
3. Peptide Bond Formation: An enzyme within the ribosome catalyses the formation of a peptide bond between the amino acid carried by the first tRNA and the amino acid carried by the second tRNA.
4. Translocation: The ribosome moves along the mRNA by one codon (three bases). The first tRNA detaches (now empty), and the process repeats. The polypeptide chain grows rapidly.
5. Termination: The process continues until the ribosome reaches a stop codon. No tRNA matches a stop codon, so the ribosome releases the mRNA and the completed polypeptide chain.

Key Takeaway: Translation is the decoding step, where the ribosome reads the mRNA codons and uses tRNA molecules to link the corresponding amino acids together in the correct sequence.

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3. Protein Folding: Shaping the Final Product (3.1.8.3)

A newly synthesized polypeptide chain is just a string of amino acids—this is its primary structure. For the protein to be functional (e.g., an enzyme, or a structural component like keratin), it must fold into a precise three-dimensional shape.

The Role of Amino Acid Sequence

The final, characteristic 3D structure of a protein (its tertiary structure) is entirely determined by its primary structure (the exact sequence of amino acids). This sequence dictates where weak bonds (like hydrogen bonds, ionic bonds, or disulfide bridges) will form, forcing the chain to coil and fold.

If even one amino acid is wrong (due to a mutation), the protein may fold incorrectly, leading to a dysfunctional protein (a classic example is sickle cell haemoglobin).

Chaperone Proteins

Don't worry if this seems tricky at first! Cells have help!

The folding process can be complicated and prone to error, especially in a crowded cellular environment. Specialised proteins called chaperones (or chaperonins) assist in the folding of other proteins. They provide a protective environment to ensure the polypeptide folds correctly and efficiently into its stable tertiary structure.

Key Takeaway: The DNA determines the amino acid sequence (primary structure), which automatically dictates the final 3D shape (tertiary structure), often with assistance from chaperones.

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Putting it all Together: The Central Dogma (Quick Review)

The flow of genetic information is often summarised as the Central Dogma of molecular biology:

DNA (Gene)
(Instructions)

↓ Transcription (in nucleus/cytoplasm)

mRNA
(Disposable copy)

↓ Translation (on ribosome)

Polypeptide Chain
(The product)

↓ Folding (assisted by chaperones)

Functional Protein
(The molecular machine)

Student Skill Check: You must be able to use a provided piece of information (like a codon table or an amino acid sequence) to relate a base sequence to the amino acid sequence of a polypeptide. You do not need to memorise the specific codons or the amino acids they code for.