Gene Expression: From Gene to Protein – Pre-mRNA Processing and Translation

Gene Expression: From Gene to Protein

Pre-mRNA Processing

Before a eukaryotic mRNA can be translated into protein, it undergoes several modifications to ensure stability, export, and proper translation.

• 5' Cap: The 5' end of the pre-mRNA receives a modified nucleotide cap.

• Poly-A Tail: The 3' end gets a polyadenylated (poly-A) tail.

• These modifications serve several functions:

  • Facilitate export of mRNA from the nucleus to the cytoplasm

  • Protect mRNA from enzymatic degradation

  • Help ribosomes attach to the 5' end for translation

RNA Splicing

Eukaryotic genes contain noncoding regions called introns that interrupt coding sequences (exons).

• Introns: Noncoding stretches removed from the pre-mRNA by RNA splicing.

• Spliceosome: A complex of proteins and small RNAs that recognizes splice sites and catalyzes intron removal.

• Exons: Coding regions that remain in the mature mRNA and are expressed as protein.

The Functional and Evolutionary Importance of Introns

• Alternative Splicing: Some genes can encode more than one kind of polypeptide, depending on which exons are included during splicing.

• This increases protein diversity without increasing the number of genes.

Example: A single gene can produce different proteins in different tissues or developmental stages by alternative splicing.

Translation: mRNA to Protein

Codons: Triplets of Nucleotides

The genetic code is read in sets of three nucleotides called codons.

• Triplet Code: Each codon specifies one amino acid.

• Template Strand: One DNA strand serves as the template for RNA synthesis.

• During translation, codons are read in the 5' → 3' direction.

• The non-template (coding) strand has the same sequence as the mRNA (except T for U).

Cracking the Code

• There are 64 possible codons (43 combinations).

• 61 codons code for amino acids; 3 are stop signals for translation termination.

• The code is redundant (more than one codon may specify the same amino acid) but not ambiguous (each codon specifies only one amino acid).

Codon	Amino Acid	Type
UUU, UUC	Phe	Senses
AUG	Met (Start)	Start
UAA, UAG, UGA	Stop	Stop

Reading Frame

Codons must be read in the correct reading frame (groupings of three nucleotides) to produce the correct polypeptide.

Molecular Components of Translation

• tRNA (transfer RNA): Brings amino acids to the ribosome and matches them to the codons in mRNA via its anticodon.

• Ribosome: Composed of large and small subunits made of proteins and ribosomal RNAs (rRNAs). It is the site of protein synthesis.

The Structure and Function of Transfer RNA (tRNA)

• Each tRNA carries a specific amino acid at its 3' end.

• The anticodon region base-pairs with a complementary codon on mRNA.

• Hydrogen bonding creates a secondary structure (cloverleaf shape).

The Structure and Function of Ribosomes

• Ribosomes have three binding sites for tRNA:

  • A site: Holds the tRNA carrying the next amino acid to be added.

  • P site: Holds the tRNA carrying the growing polypeptide chain.

  • E site: Exit site for discharged tRNAs.

Building a Polypeptide

Translation occurs in three main stages, each requiring protein factors and energy (GTP):

• Initiation: Assembly of the translation machinery at the start codon.

• Elongation: Addition of amino acids one by one to the growing chain.

• Termination: Release of the completed polypeptide when a stop codon is reached.

Ribosome Association and Initiation of Translation

• The small ribosomal subunit binds to mRNA and scans for the start codon (AUG).

• The initiator tRNA carries methionine and binds to the start codon.

• Initiation factors help assemble the complete ribosome (initiation complex).

Elongation of the Polypeptide Chain

• Amino acids are added one by one to the C-terminus of the growing chain.

• Elongation involves three steps:

  1. Codon recognition

  2. Peptide bond formation

  3. Translocation

• Energy (GTP) is used in the second and third steps.

Termination of Translation

• Elongation continues until a stop codon is reached in the A site.

• A release factor protein binds to the stop codon, causing the addition of a water molecule instead of an amino acid.

• This reaction releases the polypeptide, and the translation complex disassembles.

Key Equations and Concepts

• Number of possible codons: $4^3 = 64$

• Direction of translation: mRNA is read 5' → 3'

Additional info: These processes are central to the flow of genetic information in the cell, described by the central dogma: DNA → RNA → Protein.