Genetic Code

XII  BIOLOGY

CH-4  Molecular  Basis  of Inheritance

PART-III- Genetic Code

Genetic Code:

1)It is already known that DNA is a master molecule of a cell that initiates, guides, regulates and controls the process of protein synthesis.

2)To perform this complicated function, it must carry the requisite information for the synthesis of proteins.

3)Obviously, this information has to be verily located in the DNA itself.

4)The site for storing this information lies in the sequence ofnucleotides (i.e. nitrogen bases), as evidenced by Yanofski and Sarabhai (1964).

5)About, 20 different types of amino acids are involved in the process of synthesis of proteins.

6)DNA molecule has 4 types of nitrogen bases to identify these 20 different types of amino acids. .

7)According to F.H.C. Crick, this information is stored in the form of coded language (cryptogram) called genetic code, that contains code words (codons) each one specifying (representing) specific amino acid.

8)Genetic code, therefore, is a collection of base sequences that correspond to each amino acid.

9)A single nitrogen base in a codon (singlet codon) will encode for only four different types of amino acids. .

10)A combination of two nitrogen bases (doublet codon) will specify only 16 different types of amino acids.

11)A combination of three nitrogen bases (triplet codon) will specify 64 different types of amino acids.

12)Hence G. Gamov (1954) suggested that in a codon, there must be combination of three consecutive nitrogen bases that will be sufficient to specify 20 different types of amino acids.

13)Thus, there would be 64 different codons (code words) in the dictionary of genetic code and that each code word has to be a triplet codon. .

14)Every three consecutive nucleotides in DNA will constitute a triplet codon. .

15)Genetic code is a triplet code, was evidenced first by Crick (1961) using "frame- shift mutation".

16)However, M. Nirenberg and Matthaei were able to synthesize artificial m-RNA which contained only one type nitrogenous base i.e. Uracil (Homopolymer). .

17)This synthetic poly-U sequence was transferred to protein synthesizing enzymes. .

18)A small polypeptide molecule was produced/ formed by the linking of phenylalanine molecules.

19)This explains that UUU codes for phenyl alanine.

20)Later different homopolymer codons were deciphered.

21)Codons formed by two or more bases were also tried.

22)Dr. Har Gobind Khorana: He devised a technique for artificially synthesizing m-RNA with repeated sequences of known nucleotides.

23)By using synthetic DNA, Dr. Khorana prepared chains of polyribonucleotides  with known repeated sequences of two or three nucleotides. e.g. CUC UCU CUC UCU                             

29)This resulted in formation of polypeptide chain having two . ifferent amino acids placed alternately (Leucine and Serine). .

30)Similarly, polynucleotide chain with three- nitrogen base repeats gave  polypeptide chain with only one amino acid. E.g. CUA CUA CUA CUA (leucine).

31)Later, Severo Ochoa established that the enzyme 0 ynucleotide phosphorylase) was also helpful in polymerising RNA with defined sequences in a template-l ,,-ependent manner (i.e. enzymatic synthesis of RNA). .

32)Finally, Nirenberg, Matthaei and Ochoa deciphered all the 64 codons  in the dictionary of genetic code.

1. •     During replication and transcription, a nucleic acid is copied to form another nucleic acid. These two processes are based on complementarity principle.
2. •      During translation, genetic information is transferred from a polymer of nucleotides to a polymer of amino acids.
3.          Here, complementarity principle does not exist.
4. •        It is evident that change in nucleic acid (genetic material) results in the change in amino acids of proteins.
5. •        This clearly explains that genetic code directs the sequence of amino acids during synthesis of proteins.

Characteristic of Genetic code:

• Genetic code of DNA has certain fundamental characteristics   
• i)Genetic code is a triplet code: Sequence of three consecutive bases constitute codon, which specifies one particular amino acid. Base sequence in a codon is always in 5' 3' direction. In every living organism genetic code is a triplet code.
• ii)Genetic code has distinct polarity:  Genetic code shows definite polarity i.e. direction. It, therefore, is always read in 5' 3' direction and not in 3' 5' direction. Otherwise message will change e.g. 5' AUG 3'.
• iii)Genetic code is non-overlapping:Code is non overlapping i.e. each single base is a part of only one codon. Adjacent codons do not overlap. Ifnon-overlapping, then with 6 consecutive bases only two amino acid molecules will be in the chain. Had it been overlapping type, with 6 bases, there would be 4 amino acid molecules in a chain.
• iv)Genetic code is commaless:  There is no gap or punctuation mark between s ccessive/ consecutive codons.
• v)Genetic code has degeneracy:   Usually single amino acid is encoded b single codon. However, some amino acids are encoded by more than one codon. e.g. Cysteine has tw cbdons, while isoleucin has three codons. This is called degeneracy of the code. Degeneracy of the C0 is explained by Wobble hypothesis. Here, the first two bases in different codons are identical but the hir one, varies.
• vi)Genetic code is universal: By and large in all living organis the specific codon specifies same amino acid. e.g. codon AUG always specifies amino acid methionin m all organisms from bacteria up to humans.
• vii)Genetic code is non-ambiguous:  Specific amino acid i en oded by a particular codon. Alternatively, two different amino acids will never be encoded by the  same codon.
• viii)Initiation codon and termination codon:  AUG i always an initiation codon in any and every mRNA. AUG codes for amino acid methionine. Out  of 64 codons,.three codons viz. UAA, UAG and UGA are termination codons which terminate/ stop the  process  of elongation of polypeptide chain, as they do not code for any amino acid.
• ix)Universal: Usually in all organisms t  specific codon specifies same amino acid.
• x)Codon and anticodon:Codon ar a! art of DNA e.g. AUG is codon. It is always represented as 5' AUG 3'. Anticodon is a part of tRNA. is always represented as  3 'UAC 5'.                                                                                                   

Mutations and Genetic Code:

1)Mutation is a phenomenon which sudden change in the DNA sequence takes place. It results in the chan ,of genotype (i.e. character).

2)Along with recombination, mutation is raw material for evolution as it also results in variations.

3)During mutation, possibility of loss (deletion) or gain (insertion! duplication) of a segment of DNA results in alteration in the chromosome.

4)Mutation can also occur due to change in a single base pair ofDNAs. This is known as point mutation.

5)E.g. Sickle cell anaemia (Refer to earlier chapter).

6)Deletion or insertion of base pairs of DNA causes frame - shift mutations or deletion mutation.

7)Insertion or deletion of one or two bases changes the reading frame from the point of insertion or deletion.

8)Insertion or deletion of three or multiples of three bases (insert or delete) results in insertion or deletion of amino acids and reading frame remains unaltered from that point onwards.

t-RNA- the adapter molecule:

Scientists considered that there has to be a mechanism in which t-RNA will read the codon and also simultaneously binds with the amino acid as amino acid does not have any special capacity to read the codon. So, t-RNA is considered as an adapter molecule. This role of tRNA was understood much later.

1. •Clover leaf structure (2 dimensional) of t-RNA possess an anticodn oop that has bases complementary to the codon. It is called anticodon.  
2. • It shows amino acid acceptor end (3' end) having unpaired CCA bases (i.e. amino acid binding site) to which amino acid binds.          
3. • For every amino acid, there is specific t- RNA.
4. •  Initiator t-RNA is specific for methionine .
5. • There are no t-RNA's for stop codons.         
6. • In the actual structure, the t-RNA molecule like inverted L (3-dimensional structure).                  B. Translation - protein synthesis:

Translation is the mechanism in whiGIt odons of mRNA are translated and specific amino acids in a sequence form a polypeptide ID ibosomes. .

All types of proteins are synthesized by the cell, within itself (i.e. intracellularly)

Process of translation require  amino acids, mRNA, tRNA, ribosomes, ATP, Mg⁺⁺   ions, enzymes, elongation, translocation  and release factors.

i)Amino acids form raw material for protein synthesis. About 20 different types of amino acids are known to proteins. These are available in the cytoplasm.

ii)DNA control synthesis of proteins having amino acids in specific sequence. This control is possible through transcription of m-RNA. Genetic code is specific for particular amino acid.

iii)RNA'  serve as intermediate molecules between DNA and protein.

iv)Ribosomes serve as site for protein synthesis. Each ribosome consists of large and small subunits. These subunits occur separately in cytoplasm. Only during protein synthesis, these two subunits get associated together due to Mg⁺⁺  ions

•A ribosome has one binding site for m-RNA and 3 binding sites for t-RNA. They are P site (peptidy t-RNA site), A site (aminoacyl- t-RNA site) and E site (exit site). Only first t- RNA­amino acid complex, directly enters P site of ribosome.

•In Eukaryotes, a groove is present between two subunits of ribosomes. It protects the Polypeptide chain from the action of cellular enzymes and also protects mRNA from the action of nucleases.

Mechanism of translation 

 (i.e. synthesis of polypeptide chain)-

It involves three steps:   i. Initiation, ii. Elongation iii. Termination

1)Initiation of Polypeptide chain:

a)Activation of amino acids is essential before translation initiates for which ATP is essential. Small subunit of ribosome binds (attaches) to the m-RNA at 5' end. Initiator codon, AUG is present on m-RNA which initiates the process of protein synthesis (translation).

Initiator t- RNA binds with initiation codon (AUG) by its anticodon (UAC) through hydrogen bonds. It carries activated amino acid methionine (in Eukaryotes) or formyl methionine (in prokaryotes). .

b)Now the large subunit of ribosome joins with the smaller subunit, that requires Mg-. ions.

c)Initiator charged t-RNA (with activated amino acid methionine) occupies the P- site of ribosome and A- site is vacant.

2)Elongations of polypeptide chain:

During this process, activated amino acids are added one by one to first amino acid (methionine). .

Amino acid is activated by utilizing energy form ATP molecule. .

This amino acid binds with amino acid binding site oft-RNA- This results in formation oft-RNA- amino acid complex.

Addition of Amino acid occurs in 3 Step cycle -

a)Condon recognition- Amino acyl t- RNA molecule enters the ribosome at A-site. Anticodon binds with the codon by hydrogen bonds.

b) Amino acid on the first initiator t-RNA at P-site and amino ac'8, on t-RNA at A-site join by peptide bond. Here enzyme Ribozyme acts as a catalyst. At thise time first tRNA at 'P' site is kicked off.

c) Translocation- The t- RNA at A-site carrying a dipeptide at A-site moves to the P-site. This process is called translocation. 

In translocation, both the subunits of ribosome move also relation to tRNA and mRNA. Hence, tRNA carrying dipeptide now gets positioned at 'P' site of.rib some, making 'A' site vacant.

At this site, then next charged tRNA molecule carrying amino acid will be received. 

During this process, first uncharged tRNA is discharged from E-sitet.

This process is repeated as amino acids are added to Polypeptide. It takes less than 0.1 second for formation of peptide bond.

Third charged t-RNA with its amino aci , arrives at A-site of ribosome.

Anticodon and codon bind by hydrogen bond. Polypeptide bond is formed. 

 Second t-RNA is discharged from P-site to E-site and leaves the ribosome.So, the events like arrival of t-RNA- amino acid complex, formation of peptide bond, ribosomal translocation and removal  previous tRNA, are repeated. 

  As ribosome move over the m- RNA, all the codons on mRNA are exposed one by one for translation.

3)Termination and release of polypeptide:

1)At the end of m-RNA, there is a stop codon (UAA/UAGI UGA). It is exposed at the A-site. It is not read and joined by anticodon of any  t-RNA.

2)The release factor binds to the stop codon, thereby terminating the translation process. The Polypeptide is now released in the cytoplasm.

3)Two subunits of Ribosome dissociate and last tRNA is set free in the cytoplasm. .

4)m-RNA also has some additional sequences that are not translated and are referred as untranslated regions (UTR).

5)The UTRs are present at both 5'-end (before start codon) and at 3'-end (after stop codon). They are required for efficient translation process.

6)Finally, mRNA is also released in the cytoplasm. It gets denatured by nucleases immediately. Hence mRNA is short -lived

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