The CODONS

The information in DNA (i.e. in the form of base pairing) is present in the form of codes. These codes are unidentified by the cell until it is encoded by the RNA system. The information on DNA is present in the form of nitrogenous bases i.e. adenine (A), guanine (G), cytosine (C), and thymine (T). The sequence of these nitrogenous bases is very specific but it does not have any meaning or does not directly form any protein or any other product that the cell needs. That’s why they are called codes of DNA or codons. The codons are uncoded by a system of RNA called transcription (DNA - mRNA) and translation (mRNA - protein). Transcription takes place in the nucleus while translation occurs in the cytoplasm of the cell. This RNA system also contains the codes in the form of nitrogenous bases but it varies from DNA’s codes like thymine (T) is replaced by uracil (U) in RNA.

Different types of RNA

Type of RNA	Short form	Function
Messenger RNA	mRNA	Act as a template for protein synthesis OR Carries the information from DNA.
Ribosomal RNA	rRNA	Act as a catalytic machinery that is used to translate mRNA.
Transfer RNA	tRNA	It transfers the amino acids according to the mRNA sequence, towards rRNA.
Small nuclear RNA	snRNA	Involved in the splicing of RNA (mostly in eukaryotes).
Small nucleolar RNA	snoRNA	rRNA processing.
Interference RNA	RNAi	Involved in the silencing of genes
Micro RNA	microRNA	Translation regulation.
Viral RNA (retrovirus)	Viral RNA	The genetic material of viruses.

Codons usually refer to the tri-nucleotide sequence of nitrogenous bases. These tri-nucleotides code for a single amino acid. 20 types of amino acids form different structures of proteins. These 20 different types of amino acids are coded by 64 codons, according to George Gamow, a sequence of three nucleotides codes for different amino acids which then form different functional proteins.

In 1961, Nirenberg and Matthaei elucidated the codon for the first time. They used a cell-free system and translated the sequence of poly-uracil (UUUUUU). They noticed that the chain of poly-uracil codes phenylalanine. Nirenberg identified the translation expression of 54 codons in his life. The remaining 10 codons were identified by Har Gobind Khorana.

Codons identified by Harbind Khorana

Amino acids	mRNA	Coding DNA
1. Serine (Ser)	AGC	AGC
2. Valentine (Val)	GUU	GTT
3. Threonine (Thr)	ACC	ACC
4. Isoleucine (Ile)	AUC	ATC
5. Serine (Ser)	UCA	TCA
6. Alanine (Ala)	GCG	GCG
7. Leucine (Leu)	UUA	TTA
8. Serine (Ser)	UCU	TCT
9. Proline (Pro)	CCA	CCA
10. Leucine (Leu)	CUC	CTC

All other codons were identified by Nirenberg.

Properties of genetic codes.

The code is a triplet:

Genetic codes are read by tRNA in the triplet form. Each unit of three nucleotides codes for an amino acid to form a functional protein.

Stop codons:

Three codons out of 64 usually did not code anything. They are called stop codons. These are UAA, UGA, UAG. They are called stop codons because they are the signals of the end of protein synthesis.

Codons are commaless:

The reading (or encoding) of codons is continuous. There is no gap between them, so they are commaless.

The codes are non-overlapping:

Codons are the triplet of nucleotides. If a triplet is read then the translation machine jumps on to another triplet (or the next unit of tri-nucleotides), and not a single nucleotide reads twice during the translation process. That’s why codes are non-overlapping.

Codes are nearly universal:

Genetic codes are nearly universal. It means the genetic code AAA always codes for lysine in every type of but or it is a universal code for lysine. However, some exceptions in genetic codes do not make them completely universal. Some of these are:

In animal and plant cells, AUG codes for methionine but in bacterial cells it codes for formyl-methionine.
Plant mitochondria follow the universal rule of genetic codes but in other organisms' mitochondria, some variations are seen in animal cell’s mitochondria AUA codes for methionine while according to the universal rule AUA codes for isolucine.
In many vertebrates, mitochondria translate AGA, and AGG as stop codons (did not code anything or signal for the end of translation) while these codons usually code for arginine.
In most cases, AUG (codes for methionine) acts as a start codon but in some cases, other start codons like GUG, and UUG are also seen.

Codons are unambiguous:

Each codon codes a specific amino acid only. For example, AGU codes serine and it is specific for serine only.

Degeneracy of codons:

Each amino acid is coded by multiple codons. However, codons are very specific for their amino acid but multiple codons can code for a single amino acid. For example, lysine is coded by two codons i.e. AAA, AAG. In the same way, serine is coded by six amino acids i.e. AGU, AGC, UCA, UCU, UCG, UCC. But any of two or six always codes lysine and serine.

Unambiguous of codons.

CODONS

(Coding DNA)

CODONS

(mRNA)

AMINO

ACID

1. AAA	AAA	Lysine
2. AAT	AAU	Asparagine
3. AAG	AAG	Lysine
4. AAC	AAC	Asparagine

5. ATA	AUA	Isoleucine
6. ATT	AUU	Isoleucine
7. ATG	AUG (Start codon)	Methionine
8. ATC	AUC	Isoleucine

9. AGA	AGA	Arginine
10. AGT	AGU	Serine
11. AGG	AGG	Arginine
12. AGC	AGC	Serine

13. ACA	ACA	Threonine
14. ACT	ACU	Threonine
15. ACG	ACG	Threonine
16. ACC	ACC	Threonine

17. TAA	UAA	Stop codon
18. TAT	UAU	Tyrosine
19. TAG	UAG	Stop codon
20. TAC	UAC	Tyrosine

21. TTA	UUA	Leucine
22. TTT	UUU	Phenylalanine
23. TTG	UUG	Leucine
24. TTC	UUC	Phenylalanine

25. TGA	UGA	Stop codon
26. TGT	UGU	Cysteine
27. TGG	UGG	Tryptophane
28. TGC	UGC	Cysteine

29. TCA	UCA	Serine
30. TCT	UCU	Serine
31. TCG	UCG	Serine
32. TCC	UCC	Serine

33. GAA	GAA	Glutamic acid
34. GAT	GAU	Aspartic acid
35. GAG	GAG	Glutamic acid
36. GAC	GAC	Aspartic acid

37. GTA	GUA	Valine
38. GTT	GUU	Valine
39. GTG	GUG	Valine
40. GTC	GUC	Valine

41. GGA	GGA	Glycine
42. GGT	GGU	Glycine
43. GGG	GGG	Glycine
44. GGC	GGC	Glycine

45. GCA	GCA	Alanine
46. GCT	GCU	Alanine
47. GCG	GCG	Alanine
48. GCC	GCC	Alanine

49. CAA	CAA	Glutamine
50. CAT	CAU	Histidine
51. CAG	CAG	Glutamine
52. CAC	CAC	Histidine

53. CTA	CUA	Leucine
54. CTT	CUU	Leucine
55. CTG	CUG	Leucine
56. CTC	CUC	Leucine

57. CGA	CGA	Arginine
58. CGT	CGU	Arginine
59. CGG	CGG	Arginine
60. CGC	CGC	Arginine

61. CCA	CCA	Proline
62. CCT	CCU	Proline
63. CCG	CCG	Proline
64. CCC	CCC	Proline

RNA polymerase enzyme reads the DNA strand which has a 3’ to 5’ end direction. So the resulting mRNA must be in the 5’ to 3’ end direction which is the same as the second strand of DNA (5’-3’). The second strand of DNA (which does not code the mRNA) but its sequence of nitrogenous bases is the same as the sequence of nitrogenous bases present on mRNA except thymine (T) and uracil (U), is called the coding strand of DNA. It is because thymine is the part of DNA while uracil is a part of RNA and during transcription, thymine is replaced by uracil.

Table of Degeneracy of codons.

1) Stop codons	TAA, TAG, TGA	UAA, UAG, UGA
2) Arginine (R)	AGA, AGG, CGA, CGT, CGG, CGC	AGA, AGG, CGA, CGT, CGG, CGC
3) Lysine (K)	AAA, AAG	AAA, AAG
4) Aspartic acid (D)	GAT, GAC	GAU, GAC
5) Glutamic acid (E)	GAA, GAG	GAA, GAG
6) Histidine (H)	CAT, CAC	CAU, CAC
7) Asparagine (N)	AAT, AAC	AAU, AAC
8) Glutamine (Q)	CAA, CAG	CAA, CAG
9) Tryptophan (W)	TGG	UGG
10) Tyrosine (Y)	TAT, TAC	UAU, UAC
11) Serine (S)	AGT, AGC, TCA, TCT, TCG, TCC	AGU, AGC, UCA, UCU, UCG, UCC
12) Threonine (T)	ACA, ACT, ACG, ACC	ACA, ACU, ACG, ACC
13) Proline (P)	CCA, CCT, CCG, CCC	CCA, CCU, CCG, CCC
14) Glycine (G)	GGA, GGT, GGG, GGC	GGA, GGU, GGG, GGC
15) Alanine (A)	GCA, GCT, GCG, GCC	GCA, GCU, GCG, GCC
16) Phenylalanine (F)	TTT, TTC	UUU, UUC
17) Cysteine (C)	TGT, TGC	UGU, UGC
18) Methionine (M)	ATG	AUG
19) Lucine (L)	TTA, TTG, CTA, CTT, CTG,CTC	UUA, UUG, CUA, CUU, CUG, CUC
20) Isoleucine (l)	ATA, ATT, ATC	AUA, AUU, AUC
21) Valine (V)	GTA, GTT, GTG, GTC	GUA, GUU, GUG, GUC