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1.   PUNCTUATION , DEGENERACY & WOBBLINESS BY GROP NO.15

2. INTRODUCTION What Is genetic code? Genetic code is defined as the sequence of nitrogen bases (nucleotides) in mRNA molecule which contains the information for the synthesis of protein molecules. There are four types of nucleotides in RNA, represented by the letters A ( adenine ), U ( uracil ), C ( cytosine ), and G ( guanine ). What are Codons? Codons are groups of three nucleotides combine to form a single amino acid. Each codon corresponds to a specific amino acid, which are the building blocks of proteins. For example, the codon AUG codes for the amino acid methionine .  

3. PUNCTUATION Punctuation refers to the specific sequences of nucleotides that signal the start and end of genetic code. Genetic code is punctuated , that means, it has the start and stop signals as shown in Table.1 below . The genetic code system has a codon that acts as a signal for the initiation of the synthesis of polypeptide chain. Just like punctuation in language helps clarify meaning, these sequences help us to understand how to read and interpret genetic information.  

4. The following are the types of genetic codons punctuations ( i ) Start Codons Start codons are specific sequences in the genetic code that signal the beginning of protein synthesis. The most common start codon is AUG , which codes for the amino acid methionine . When a ribosome encounters a start codon during translation, it knows to begin assembling the protein.

5. Genetic codons punctuations contd ….. ( ii) Stop Codons Stop codons are sequences that signal the end of protein synthesis. There are three main stop codons: UAA, UAG , and UGA , which does not code for any amino acid , acid because their primary function is to signal the end of the translation process. When the ribosome encounters a stop codon during translation, it does not add an amino acid to the growing polypeptide chain that’s why is known as nonsense codons , they have only one function which is to terminate only.

6.   Table 1. Genetic code table

7. Cont … During protein synthesis, stop codons cause the release of new polypeptide chain from the ribosome. This occur because there are no tRNAS with anticodons complementary to the stop codons. The stop codons (UAA, UAG, and UGA) are recognized by protein release factors , rather than by tRNA . Prokaryotes contain two release factors, RF-1 and RF-2 ; RF-1 terminates polypeptides in response to codons UAA and UAG, whereas RF-2 causes termination at UAA and UGA codons. Eukaryotes contain a single release factor ( RF-1 ) that recognizes all three termination codons.  

8. NOTE In the “ old view ” The names “ OCHRE ,” “ AMBER ,” and “ OPAL ” were derived from color names, reflecting a more informal and mnemonic approach to categorizing these codons.

9. OCHRE correspond to (UAA ): Represents the color “ ochre ”, which is a warm, earthy yellow-brown color . AMBER correspond to (UAG ): Represents the color “ amber ”, which is a yellowish-orange color . OPAL correspond to (UGA ): - Represents the color “ opal ”, which is typically a milky white or iridescent color, often with hints of blue, green, or pink .   These color names are used to help remember the corresponding stop codons in the genetic code.

10.   DEGENERACY Degeneracy in the genetic code refers to the phenomenon where multiple codons (sequences of three nucleotides) can code for the same amino acid. All amino acids except methionine (AUG) and tryptophan (UGG) are coded by several codons, that means some codons are synonyms. This fact is called degeneracy of the genetic code. For example, Threonine is coded by four codons ACU, ACC, ACA and ACG. Thus, for many amino acids, only the first two letters appear to be significant .

11. Cont ……. Degeneracy can be categorized into two main types: ( i )Synonymous Codons: These are different codons that code for the same amino acid. For example, the amino acid leucine can be encoded by six different codons: UUA, UUG, CUU, CUC, CUA, and CUG. ( ii) Non-synonymous Codons: These codons code for different amino acids. For instance, a change from a codon that codes for serine (UCU) to one that codes for proline (CCU) can lead to a completely different protein function.

12. Cont … The degeneracy is primarily of two forms. (1) Partial degeneracy occurs when the third base may be either of the two pyrimidines (U or C) or, alternatively, either of the two purines (A or G). With partial degeneracy, changing the third base from a purine to a pyrimidine, or vice versa, will change the amino acid specified by the codon. Example , a change from a codon that codes for serine (UCU) to one that codes for proline (CCU)

13. Cont …. (2 ) Complete degeneracy , any of the four bases may be present at the third position in the codon, and the codon will still specify the same amino acid. For example , valine is encoded by GUU, GUC, GUA, and GUG. Also arginine , which is encoded by six different codons: CGU, CGC, CGA, CGG, AGA, and AGG.

14. Table 2. Genetic code table

15.   WOBBLINESS Wobbliness in the genetic code refers to the flexibility in the pairing of nucleotides during the process of protein synthesis. Wobble base pairing refers to the ability of certain tRNA molecules to pair with more than one codon. This is particularly evident in the third position of a codon, where the pairing is less strict. For instance , the codons GAA and GAG both code for the amino acid glutamic acid. The tRNA that recognizes these codons can have a flexible pairing at the third position, allowing it to bind to both codons. This explained well by Wobble hypothesis

16. What is the Wobble Hypothesis ? The Wobble Hypothesis, proposed by Francis Crick in 1966, explains how the pairing between the codon on mRNA and the anticodon on tRNA is not always strict. According to this hypothesis, the first two nucleotides of the codon and the anticodon must pair perfectly, but the third nucleotide can be more flexible. This flexibility is what we call “ wobble .”

17. Wobble Hypothesis contd … For example, the anti-codon UCG of serine tRNA recognize the codon A GC in the mRNA. Here the third base G of tRNA pairs with C of mRNA. G-C pairing is the normal base pairing. The anti-codon can also pair with another codon CCU. Here the third base G of tRNA pairs with U of mRNA. The G-U is an unusual pairing and it is called wobble base-pairing.

18. Figure 1. wobble hypothesis 1

19. NOTE : Wobbliness of the third base helps the tRNA to carry more than one amino acid Watson-crick Base pairing : -A base pairing is a fundamental unit of double-stranded nucleic acids consisting of two nuclei bases bound to each other by hydrogen bonds.

20. Figure 2. Wobble base pairing

21. L REFERENCES   Alberts B, Johnson A, Lewis J, Rafi M ( 2015 ). Molecular biology of the cell 6 th edition . Garland Science . D. Peter Snustad , Michael J. Simmons.(2012). Principles of Genetics. 6th ed. United States of America . John Wiley & Sons, Inc . Karp G. (2013 ). Cell and Molecular Biology: Concepts and experiments. 7th Edition. John Wiley & Sons, Inc . Lodish , H. F. (2000 ). Molecular Cell Biology. United Kingdom : W.H. Freeman . Zubay GL., WW Parson and DE Vance (1995). Principles of Biochemistry . England. Wm. C.Brown Publisers .

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