From Genes to Proteins: Transcription and Translation

From Genes to Proteins

Overview

This section explores how genetic information encoded in DNA is used to synthesize proteins, a process involving two main stages: transcription and translation. These processes are fundamental to gene expression and are central topics in molecular biology.

Key Definitions

• Genotype: The sequence of nucleotide bases in an organism's DNA. A gene is defined as a specific sequence of these bases.

• Phenotype: Observable traits of an organism that result from the expression of proteins encoded by genes.

• Example: A specific DNA sequence (genotype) encodes proteins that determine eye color (phenotype).

What is RNA?

• RNA (Ribonucleic Acid): A nucleic acid similar to DNA but with key differences:

  • Sugar is ribose instead of deoxyribose.

  • Contains the base uracil (U) instead of thymine (T). U pairs with A.

  • Usually single-stranded, not a double helix.

  • Three main types: mRNA (messenger RNA), tRNA (transfer RNA), rRNA (ribosomal RNA).

The Central Dogma: The Big Picture

• Genetic information flows from DNA → RNA → Protein.

• In prokaryotes, transcription and translation occur in the cytoplasm.

• In eukaryotes, transcription occurs in the nucleus, and translation occurs in the cytoplasm after RNA processing.

Transcription (DNA → RNA)

• Occurs in the nucleus (in eukaryotes).

• Only one DNA strand serves as the template for RNA synthesis.

• RNA polymerase is the enzyme that links RNA nucleotides together.

• Uracil (U) replaces thymine (T) in RNA.

• Direction: RNA polymerase reads the DNA template strand from 3' to 5'.

RNA Splicing

• Genes contain introns (non-coding regions) and exons (coding regions).

• During RNA processing, introns are removed, and exons are joined to form mature mRNA.

• This process occurs before mRNA leaves the nucleus in eukaryotes.

Diagram of RNA Splicing

Pre-mRNA	mRNA
5' Cap - Intron - Exon - Intron - Poly-A tail	5' Cap - Exon (coding segment) - Poly-A tail
Contains both introns and exons	Only exons (introns removed)

Codons and the Triplet Code

• Codon: A sequence of three RNA bases (e.g., AAG, CCU) that codes for a specific amino acid.

• Several codons in sequence form a "sentence" that specifies a polypeptide chain.

• Example mRNA sequence: AAGCCUAGGUCAUACGGA

Discovery of the Triplet Code

• Marshall Nirenberg (1961) demonstrated that UUU codes for phenylalanine (Phe).

• "Start" codon: AUG (codes for methionine; signals the start of translation).

• "Stop" codons: UAA, UAG, UGA (do not code for any amino acid; signal the end of translation).

• The genetic code is universal—shared by almost all organisms.

Translation (RNA → Protein)

• Occurs in the cytoplasm at the ribosome.

• tRNA molecules match codons in mRNA with the correct amino acids.

• Each tRNA has an anticodon that pairs with a codon on the mRNA.

• Amino acids are linked together to form a polypeptide chain (protein).

Ribosomes

• Composed of two subunits (large and small).

• Made of proteins and rRNA.

• Coordinate the interaction of mRNA and tRNA during translation.

• Three binding sites for tRNA:

  • A site (Aminoacyl-tRNA binding site)

  • P site (Peptidyl-tRNA binding site)

  • E site (Exit site)

Summary Table: Key Steps in Gene Expression

Step	Location	Main Molecules Involved	Key Events
Transcription	Nucleus (eukaryotes)	DNA, RNA polymerase, mRNA	DNA template used to synthesize mRNA
RNA Splicing	Nucleus (eukaryotes)	Pre-mRNA, spliceosome	Introns removed, exons joined
Translation	Cytoplasm (ribosome)	mRNA, tRNA, rRNA, amino acids	mRNA codons translated into amino acid sequence

Important Equations and Concepts

• Central Dogma:

  • $\text{DNA} \rightarrow \text{RNA} \rightarrow \text{Protein}$

• Direction of Synthesis:

  • RNA polymerase reads DNA template strand from $3' \rightarrow 5'$

  • mRNA is synthesized in the $5' \rightarrow 3'$ direction

Additional info:

• Alternative splicing can produce different proteins from the same gene by including or excluding certain exons.

• Mutations in DNA can alter the amino acid sequence of proteins, potentially affecting phenotype.