Codons and Amono Acids:

Amono acid is a group of organic molecules composed of a basic amino group (-NH2), an acidic carboxyl group (-COOH), and an organic R group (or side chain), which is unique to each amino acid. Among more than 100 amino acids that occur naturally, 20 are commonly used in protein synthesis in all living organisms on earth (all plants and animals).

Every 3 adjacent nucleotide bases along the RNA sequence are combined to form in total $4\times 4 \times 4=4^3=64$ possible codons, among which 61 code for 20 different types of amino acids. In particular, one of these 20 amino acids Methionine (M met) also serves as the start codon indicating the beginning of a code sequence. The remaining 3 codons (TAA, TAG, TGA) are stop codons, indicating the end of an amino acid sequence.

There are three ways to divide a sequence of nucleotide bases into a sequence of trinucleotide codons (by shifting the boundary between two codons by one base). Each one of these three ways is called a reading frame. However, all actual reading frames used, called the open reading frames (ORF) are determined by the start and stop codons. Most genes code for proteins that are hundreds of amino acids long, although the average distance between two stop codons in a ``random'' DNA is $64/3=21$.

$$\begin{tabular}{l\vert c\vert c\vert\vert l} \hline Amino Aci... ...s & Stop & termination & TAA, TAG, TGA \hline \end{tabular}$$

The 20 amino acids are coded by 61 codons by a degenrate (many-to-one) mapping. Many of the amino acids are coded by multiple codons called synonyms. Due to such redundency allowing an amino acid to be coded by more than one codon, the effect of mutation in gene on the resulting protein will be much reduced.

However, single nucleotide mutations can still have serious effects. For example, human beta-globin is a protein of about 150 amino acids. A single mutation of A to T in the 6th codon results in the replacement of Glu (coded here by GAG) by Val (GTG) and results in a form of haemoglobin leading to the disease sickle-cell anemia.

Proteins:

The 20 different types of amino acids (letters), and their different linear combinations (a chain of a few to a few thousand amino acids) form various proteins (words), which are the building blocks of the organism. (For example, insulin is a small protein consisting of 51 amino acids.)