CODONS AND GENETIC CODE (Part 2)

 

CODONS AND GENETIC CODE (Part 2)

Introduction

A codon is a sequence of three nucleotides on messenger RNA (mRNA) that specifies an amino acid or a termination signal. Since RNA contains four nitrogenous bases (A, U, G, C), all possible triplet combinations produce: [4³ = 64]

Thus, there are 64 possible codons in the universal genetic code. These codons direct the synthesis of proteins in almost all living organisms.

Total Number of Codons

Each codon consists of three nucleotides. Possible combinations:

Number of Bases	Possible Combinations
1	4
2	16
3	64

Therefore, Total codons = 64

These are divided into:

Category	Number
Sense Codons	61
Stop Codons	3
Total	64

Types of Codons

The genetic code contains two major categories.

1. Sense Codons

Sense codons specify amino acids. There are: 61 Sense Codons.  Every amino acid is encoded by one or more sense codons.

2. Stop Codons

Three codons terminate protein synthesis. These are:

• UAA
• UAG
• UGA

They do not code for any amino acid.

The Start Codon

Protein synthesis begins with a special codon.

Universal Start Codon

AUG

Functions:

• Signals the start of translation.
• Codes for Methionine (Met) in eukaryotes.
• Codes for N-formylmethionine (fMet) during initiation in most bacteria.

AUG is both:

• A start codon
• A sense codon

Biological Significance of the Start Codon

The start codon:

• Determines the correct reading frame.
• Ensures accurate protein synthesis.
• Recruits the initiator tRNA.
• Marks the beginning of the Open Reading Frame (ORF).

Without AUG, translation usually cannot initiate correctly.

Stop Codons (Termination Codons)

Translation ends when a ribosome encounters one of three stop codons.

Codon	Traditional Name
UAA	Ochre
UAG	Amber
UGA	Opal (Umber)

Functions of Stop Codons

• Signal termination of translation.
• Recruit release factors (not tRNA).
• Release the completed polypeptide chain.
• Cause ribosomal subunits to dissociate.

Important Fact

There is no tRNA corresponding to stop codons. Instead, release factors recognize them and terminate protein synthesis.

Complete Genetic Code Table

Standard Genetic Code (mRNA Codons)

First Base	Second Base	Third Base	Amino Acid
UUU, UUC			Phenylalanine (Phe)
UUA, UUG			Leucine (Leu)
CUU, CUC, CUA, CUG			Leucine (Leu)
AUU, AUC, AUA			Isoleucine (Ile)
AUG			Methionine (Met) – Start Codon
GUU, GUC, GUA, GUG			Valine (Val)
UCU, UCC, UCA, UCG			Serine (Ser)
CCU, CCC, CCA, CCG			Proline (Pro)
ACU, ACC, ACA, ACG			Threonine (Thr)
GCU, GCC, GCA, GCG			Alanine (Ala)
UAU, UAC			Tyrosine (Tyr)
UAA, UAG			Stop
CAU, CAC			Histidine (His)
CAA, CAG			Glutamine (Gln)
AAU, AAC			Asparagine (Asn)
AAA, AAG			Lysine (Lys)
GAU, GAC			Aspartic acid (Asp)
GAA, GAG			Glutamic acid (Glu)
UGU, UGC			Cysteine (Cys)
UGA			Stop
UGG			Tryptophan (Trp)
CGU, CGC, CGA, CGG			Arginine (Arg)
AGU, AGC			Serine (Ser)
AGA, AGG			Arginine (Arg)
GGU, GGC, GGA, GGG			Glycine (Gly)

Codons for Each Amino Acid

Amino Acid	Number of Codons
Methionine	1
Tryptophan	1
Phenylalanine	2
Tyrosine	2
Histidine	2
Glutamine	2
Asparagine	2
Lysine	2
Aspartic acid	2
Glutamic acid	2
Cysteine	2
Isoleucine	3
Valine	4
Alanine	4
Glycine	4
Proline	4
Threonine	4
Serine	6
Leucine	6
Arginine	6

Codon Families

Codons can be grouped according to the number of codons specifying an amino acid.

One-Codon Amino Acids

Only two amino acids are encoded by a single codon.

Amino Acid	Codon
Methionine	AUG
Tryptophan	UGG

Important Point

Methionine and Tryptophan have only one codon each.

Two-Codon Amino Acids

• Phenylalanine
• Tyrosine
• Histidine
• Glutamine
• Asparagine
• Lysine
• Aspartic acid
• Glutamic acid
• Cysteine

Three-Codon Amino Acid

Only one amino acid:

Isoleucine

Codons: AUU,  AUC,  AUA

Four-Codon Amino Acids

• Alanine
• Glycine
• Proline
• Threonine
• Valine

Six-Codon Amino Acids

Three amino acids possess six codons.

• Leucine
• Serine
• Arginine

Degeneracy of the Genetic Code

Definition

The ability of more than one codon to specify the same amino acid is called degeneracy (or redundancy) of the genetic code.

Examples

Leucine:

• UUA
• UUG
• CUU
• CUC
• CUA
• CUG

All encode leucine.

Glycine:

• GGU
• GGC
• GGA
• GGG

All encode glycine.

Why is the Genetic Code Degenerate?

There are:

• 64 codons
• 20 amino acids

Since 64 is greater than 20, many amino acids are encoded by multiple codons.

Biological Advantages of Degeneracy

Degeneracy:

• Minimizes the harmful effects of mutations.
• Improves accuracy of protein synthesis.
• Provides evolutionary stability.
• Allows wobble base pairing during translation.

Silent (Synonymous) Mutations

Because of degeneracy, a mutation may not change the amino acid.

Example: GAA → GAG

Both encode: Glutamic acid. Protein remains unchanged. Such mutations are called silent (synonymous) mutations.

Codon Usage Bias

Although multiple codons encode the same amino acid, organisms often prefer certain synonymous codons over others. This phenomenon is known as codon usage bias.

Biological significance includes:

• Increased efficiency of protein synthesis.
• Regulation of gene expression.
• Applications in recombinant DNA technology and gene optimization.

Start Vs Stop Codons

Feature	Start Codon	Stop Codon
Codon	AUG	UAA, UAG, UGA
Amino Acid	Methionine (or fMet in bacteria)	None
Function	Initiates translation	Terminates translation
Recognized by	Initiator tRNA	Release factors

Complete Flow of Protein Synthesis

DNA

│

▼

Transcription

│

▼

mRNA

│

▼

Start Codon (AUG)

│

▼

Sense Codons

│

▼

Stop Codon

│

▼

Protein

High-Yield Facts

·       Total codons = 64

·       Sense codons = 61

·       Stop codons = 3

·       Start codon = AUG

·       Methionine is encoded only by AUG.

·       Tryptophan is encoded only by UGG.

·       Leucine, Serine, and Arginine each have 6 codons.

·       Isoleucine has 3 codons.

·       No tRNA recognizes stop codons.

·       Release factors terminate translation.

Summary

• The genetic code consists of 64 codons, of which 61 code for amino acids and three function as stop codons.
• AUG serves as both the initiation codon and the codon for methionine.
• The genetic code is degenerate because most amino acids are encoded by more than one codon.
• Stop codons do not specify amino acids but signal the end of protein synthesis.

Memory Tricks

Stop Codons

"U Are Away, U Are Gone, U Go Away"

• UAA
• UAG
• UGA

Single-Codon Amino Acids

"My Trip"

• Methionine → AUG
• Trp (Tryptophan) → UGG

Six-Codon Amino Acids

"Leu–Ser–Arg: The Big Three"

• Leucine
• Serine
• Arginine

Four-Codon Amino Acids

"GAP TV"

• Glycine
• Alanine
• Proline
• Threonine
• Valine

Exam Summary

Topic	Key Point
Total Codons	64
Sense Codons	61
Stop Codons	3 (UAA, UAG, UGA)
Start Codon	AUG
One-Codon Amino Acids	Methionine, Tryptophan
Degeneracy	Multiple codons specify the same amino acid
Six-Codon Amino Acids	Leucine, Serine, Arginine
Translation Stops	At stop codons via release factors