1. Genetic code and Post translational modifications
Dr Shumaila Asim
Lecture #10

2. Flow of genetic information
The central dogma of molecular biology describes the two-step process, transcription and translation, by which the information in genes flows into proteins: DNA → RNA → protein.

3. Introduction
The pathway of protein synthesis is called Translation because the language of nucleotide sequence on mRNA is translated in to the language of an amino acid sequence. The process of Translation requires a Genetic code, through which the information contained in nucleic acid sequence is expressed to produce a specific sequence of amino acids.

4. Introduction – Genetic Code
The letters A, G, T and C correspond to the nucleotides found in DNA. They are organized into codons. The collection of codons is called Genetic code. For 20 amino acids there should be 20 codons. Each codon should have 3 nucleotides to impart specificity to each of the amino acid for a specific codon 1 Nucleotide- 4 combinations 2 Nucleotides 16 combinations 3 Nucleotides- 64 combinations ( Most suited for 20 amino acids)

5. Genetic Code
Genetic code is a dictionary that corresponds with sequence of nucleotides and sequence of Amino Acids.
Words in dictionary are in the form of codons
Each codon is a triplet of nucleotides
64 codons in total and three out of these are Non Sense codons.
61 codons for 20 amino acids

6. Genetic Code- Table

7. Six features of the genetic code
Triplet code
Specificity
Degeneracy
Universality
Non-overlapping
Punctuated

8. The code is a triplet code
The DNA code for a protein is first copied into messenger RNA (mRNA) before a protein is made
mRNA is complementary to the DNA
DNA
mRNA

9. Genetic Code-Characteristics
Specificity- Genetic code is specific (Unambiguous)
A specific codon always codes for the same amino acid.
e.g. UUU codes for Phenyl Alanine, it can not code for any other amino acid.

10. Genetic Code-Universal
Universal- In all living organism Genetic code is the same.
The exception to universality is found in mitochondrial codons where AUA codes for methionine and UGA for tryptophan, instead of isoleucine and termination codon respectively of cytoplasmic protein synthesizing machinery.
AGA and AGG code for Arginine in cytoplasm but in mitochondria they are termination codons.

11. The universality of the genetic code is among the strongest evidence that all living things share a common evolutionary heritage

12. Genetic Code-Redundant
Redundant- Genetic code is Redundant, also called Degenerate.
Although each codon corresponds to a single amino acid but a single amino acid can have multiple codons. Except Tryptophan and Methionine each amino acid has multiple codons.

13. Genetic Code- Non Overlapping and Non Punctuated
All codons are independent sets of 3 bases.
There is no overlapping ,
Codon is read from a fixed starting point as a continuous sequence of bases, taken three at a time.
The starting point is extremely important and this is called Reading frame.

14. Non Sense Codons
There are 3 codons out of 64 in genetic code which do not encode for any Amino Acid.
These are called termination codons or stop codons or nonsense codons. The stop codons are UAA, UAG, and UGA. They encode no amino acid. The ribosome pauses and falls off the mRNA.

15. Initiator codon AUG is the initiator codon in majority of proteins-
In a few cases GUG may be the initiator codon
Methionine is the only amino acid specified by just one codon, AUG.

16. Wobbling phenomenon
The rules of base pairing are relaxed at the third position, so that a base can pair with more than one complementary base. 
Some tRNA anticodons have Inosine at the third position. 
Inosine can pair with U, C, or A.  This means that we don't need 61 different tRNA molecules, only  half as many are required.

17. Wobbling phenomenon
First two bases in Codon in m RNA(5’-3’) base pair traditionally with the 2 nd and 3rd base of the Anticodon in t RNA(5’-3’)
Non traditional base pairing is observed between the third base of the codon and 1st base of anticodon.
The reduced specificity between the third base of the codon and the complementary nucleotide in anticodon is responsible for wobbling.

18. Wobbling phenomenon t RNA (first base) m RNA (Third base) Base pairingC G
Traditional A U
Nontraditional I

19. Wobbling phenomenon Proline has 4 codons(5’-3’) CCU CCC CCA CCG
The first three codons can be recognized by a single t RNA having Inosine at the first place.(IGG- 5’-3’)

20. Genetic code- Summary
Genetic code is unambiguous, universal, degenerate, commaless and non overlapping.
UAG, UGA and UAA are termination codons .
AUG is the start codon

22. Translation is the synthesis of protein from an mRNA template.
This process involves several key molecules including:
mRNA
Ribosome
tRNA
Release Factor

23. Initiation
Elongation
Termination

24. Peptide chain undergoes folding
Some amino acids might be changed
Carbohydrates or lipids can be added
Peptide can be activated by addition or removal of some residue (acetate, phosphate, methyl etc.)

25. Changes in the Hydrogen bond proclivity which results in secondary and tertiary structures
Some of the proteins might remain in cytosol while others are transported across the membrane or even imported into cellular organelles (mitochondria or chloroplasts) to accomplish their functions

26. The chemical modification of a protein after its translation is known as Post-Translational Modification.

27. Play a crucial role in generating the heterogeneity in proteins.
Help in utilizing identical proteins for different cellular functions in different cell types.
Regulation of particular protein sequence behavior in most of the eukaryotic organisms.

28. Play an important part in modifying the end product of expression.
Contribute towards biological processes and diseased conditions.
Translocation of proteins across biological membranes.

29. Trimming
Covalent Modification
Ubiquitination

31. Removal of a part of the translated sequence.
Proteases Protein activation.

32. In vivo conversion of preproinsulin to Insulin
(51 amino acid)
(103 amino acids)

33. Phosphorylation
Glycosylation
Hydroxylation
Carboxylation
Biotinylation
Acetylation

35. Methylation
Alkylation
Glutamylation
Lipoylation
Sulfation

36. Phosphorylation
The addition of a phosphate (PO4) group to a protein or a small molecule.
Can occur on Serine, Threonine, Tyrosine.

37. Glycosylation
The addition of saccharide to a protein or a lipid molecule.
N-Linked Glycosylation
Amide nitrogen of Asparagine
O-Linked Glycosylation
Hydroxyl oxygen of Serine and Therionine.

39. Hydroxylation Carboxylation
The addition of hydroxyl group to proline of protein.
Carboxylation
The addition of carboxyl group to glutamate.

40. Biotinylation Acetylation
The addition of biotin to protein or nucleic acid.
Acetylation
The addition of an acetyl group, usually at the N- terminus of the protein.

41. Methylation Alkylation
The addition of a methyl group, usually at lysine or arginine residues.
Alkylation
The addition of an alkyl group (e.g. methyl, ethyl).

42. The addition of a sulfate group to a tyrosine.
Glutamylation
Covalent linkage of glutamic acid residues to tubulin and some other
Lipoylation
The attachment of a lipoate functionality
Sulfation
The addition of a sulfate group to a tyrosine.

43. Highly specific degradation of protein can be achieved through the addition of one to several ubiquitin molecules to a target protein. The process is called Ubiquitination.

44. These are particularly important for the study of heart disease, cancer, neurodegenerative diseases and diabetes.
These are key mechanisms to increase proteomic diversity.