Genetic Code PDF

# 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...

# 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) # 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 # 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. # GENETIC CODE - **Salient features of genetic code.** - Universal - the codons code for any amino acid in any organism, be it a bacterium or a human being. - Non ambiguous - each codon codes for only one amino acid, so the genetic code is unambiguous and specific. - Comma less - the codons are read in 5'3' direction and no punctuation. - Degenerate - some amino acids are coded by more than one codon, the genetic code is said to be degenerate. - Non overlapping - 3 successive nitrogen bases code for only one amino acid. - Nonsense codon (UAA, UAG, UGA)- do not code for any amino acids, but act as terminating/stop codons of protein synthesis. - Linear - the sequence of amino acids present in a polypeptide chain corresponds to sequence of nitrogen bases of DNA with 3 successive nitrogen bases forming a single codon. - Triplet - there are 64(4x4x4) codons, 61 codons code for 20 amino acids. - Initiation Codon AUG # Genetic Code Table | First base | Second base | U | C | A | G | Third base | | ---------- | ------------ | ----- | ----- | ----- | ----- | ----------- | | **U** | **U** | UUU Phe | UCU Ser | UAU Tyr | UGU Cys | **U** | | | **C** | UUC Phe | UCC Ser | UAC Tyr | UGC Cys | **C** | | | **A** | UUA Leu | UCA Ser | UAA Stop | UGA Stop | **A** | | | **G** | UUG Leu | UCG Ser | UAG Stop | UGG Trp | **G** | | **C** | **U** | CUU Leu | CCU Pro | CAU His | CGU Arg | **U** | | | **C** | CUC Leu | CCC Pro | CAC His | CGC Arg | **C** | | | **A** | CUA Leu | CCA Pro | CAA Gln | CGA Arg | **A** | | | **G** | CUG Leu | CCG Pro | CAG Gln | CGG Arg | **G** | | **A** | **U** | AUU Ile | ACU Thr | AAU Asn | AGUSer | **U** | | | **C** | AUC Ile | ACC Thr | AAC Asn | AGC Ser | **C** | | | **A** | AUA lle | ACA Thr | AAA Lys | AGA Arg | **A** | | | **G** | AUG Met | ACG Thr | AAG Lys | AGG Arg | **G** | | **G** | **U** | GUU Val | GCU Ala | GAU Asp | GGU Gly | **U** | | | **C** | GUC Val | GCC Ala | GAC Asp | GGC Gly | **C** | | | **A** | GUA Val | GCA Ala | GAA Glu | GGA Gly | **A** | | | **G** | GUG Val | GCG Ala | GAG Glu | GGG Gly | **G** | # Important features of the genetic code - Each codon consists of three bases (triplet). There are 64 codons. They are all written in the 5' to 3' direction. - 61 codons code for amino acids. The other three (UAA, UGA, UAG) are stop codons (or nonsense codons) that terminate translation. - There is one start codon (initiation codon), AUG, coding for methionine. Protein synthesis begins with methionine (Met) in eukaryotes, and formylmethionine (fmet) in prokaryotes. - The code is unambiguous. Each codon specifies no more than one amino acid. # Describe the characteristics of Genetic code - Written in linear form - Each word consists of 3 ribonucleotide letters - The code is unambiguous - The code is degenerate - The code contains 1 start and 3 stop codons - The code is commaless - The code is non-overlapping - The code is (nearly) universal # Characteristic of the genetic code 1. Triplet code 2. Comma less 3. Nonoverlapping code 4. The coding dictionary 5. Degenerate code 6. Universality of code 7. Non ambiguous code 8. Chain inition code 9. Chain termination codons # Salient features of genetic code - **1. Triplet codons:** Each codon is a consecutive sequence of three bases on the mRNA, e.g. UUU codes for phenylalanine. - **2. Non overlapping:** The codes are consecutive. Therefore, the starting points is extremely important. The codes are read one after another in a continuous manner, e.g. AUG, CAU, CAU, GCA, etc. - **3. Non punctuated:** There is no punctuation between the codons. It is consecutive or continuous. - **4. Degenerate:** When an amino acid has more than codon, this called degeneracy of the code. E.g. serine has 6 codons while glycine has 4 codons. - **5. Unambiguous:** Through the codons are degenerate, they are unambiguous or without any doubtful meaning. That is, one codon codes only one amino acid. # Redundancy of the Genetic Code Another term for this is degenerate There are many situations where different codons specify the same amino acid But no codon will ever specify for two different amino acids The codons encoding for one amino acid will usually differ in the third or second position This makes it more difficult for mutations to cause serious issues # Complementary base pairing *Diagram of tRNA molecule with complimentary base pairing to AUG.* # The Wobble Hypothesis UCC and UCU both code for serine *Diagram of tRNA anticodon loop illustrating the wobble phenomenon* <start_of_image>-*Wobble* *When several codons encode same amino acid, the difference is usually in the third position* *If an anticodon recognize a codon as a triplet, there should be tRNAs for each codon* *But some anticodons of tRNAs contain inosinate (I)* *It forms rather weak bonds than Watson-Crick base pairs* *Table of codon-anticodon base pairing illustrating wobble* *Diagram of two tRNA molecules illustrating the wobble phenomenon* # Universal The codons are the same for the same amino acid in all species, the same for "Elephant and E.coli". The genetic code has been highly preserved during evolution. # Terminator codons There are three codons which do not code for any particular amino acids. They are "nonsense codons", more correctly termed as punctuator codons or terminator codons. They put "full stop" to the protein synthesis. These three codons are UAA, UAG, and UGA. # Initiator codon In most of the cases, AUG acts as the initiator codon. # Genetic Code-Universal - Universal - in all living organism Genetic code is the same. - The exception to universality is found in mitochondrial codons where, - AUA - methionine and - UGA - tryptophan, - In Cytoplasmic codons - AUA - isoleucine and - UGA - termination codon, - AGA and AGG code for Arginine in cytoplasm but in mitochondria they are termination codons. # Marshall Nirenberg and Heinrich Matthaei experiments - The 2nd experiments AAAAAA..... Result: Peptide of lysine - The 3rd experiments CCCCCC.... Result: Peptide for Proline. - GGGGGGG.... was unstable, so this part of the experiment could not be done. - Next to prove other codon-amino acid pairs hence researchers synthesized chains of alternating bases # Genetic Code Cracking Phase 1 - Nirenberg & Matthaei Take bacterial cell extract containing ribosomes and other stuff needed to make proteins - but not the instructions *Diagram of test tube with all amino acids and ribosomes* Include a mix of amino acids, where 1 at a time is radiolabeled. *Diagram of test tube with all amino acids, ribosomes, and RNA sequences. Some of the RNA sequences are highlighted* Stick in different RNA sequences to act as instructions *Diagram of a test tube with ribosomes, RNAs, and amino acids. There are three RNA sequences in the test tube: UUUUUUUUUUUUUUU, CCCCCCCCCCCCC, AAAAAAAAAAAAAAAA* Let protein be made Measure radioactivity compared to amount of protein made. It'll only be high when the amino acid spelled by the sequence is labeled. # Experiment - What amino acids are specified by codons composed of only one type of base? *Diagram illustrating the experiment using radioactive phenylalanine* # Ribosome *Diagram of a ribosome showing the small and large subunits and the sites where mRNA and tRNA bind* # Experiment - With the use of tRNAs, what other matches between codon and amino acid could be determined? *Diagram illustrating the experimental method* # Experiment - With the use of tRNAs, what other matches between codon and amino acid could be determined? *Diagram illustrating the experimental method and showing the results* # Nirenberg-Leder experiment using a filter-binding assay *Diagram illustrating the Nirenberg-Leder filter-binding assay* # THANK YOU # Protein Synthesis Termination 1. Termination of translation occurs when the ribosome encounters *stop codons*. *Diagram showing a ribosome bound to mRNA and tRNA* 2. Release factors (RF-1, RF-2 or RF-3) bind to the stop codons and cause the polypeptide chain to be released from the ribosome. *Diagram showing the release factors, RF-1 and RF-3, binding to the stop codon* 3. When a release factor *binds to the A site*, the polypeptide chain is released from the tRNA in the P site. *Diagram showing the polypeptide chain being released from the tRNA* 4. Hydrolysis of GTP releases the release factors and the tRNA from the ribosome. *Diagram showing the polypeptide and tRNA detaching from the ribosome* # Initiation of translation 1. The ribosome is composed of two *subunits*. *Diagram showing the ribosome and its two subunits* 2. *Initiation factor 3 (IF-3)* binds to the small subunit which prevents the large subunit from associating with it, ensuring that the small subunit can first bind to the mRNA. *Diagram illustrating the IF-3 binding to the small subunit* 3. The *small subunit binds to the mRNA*. *Diagram showing the small subunit of the ribosome binding to the mRNA* 4. *A tRNA charged with N-formylmethionine* forms a complex with initiation factor 2 (IF-2) and GTP. *Diagram showing a tRNA charged with N-formylmethionine bound to IF-2 and GTP* 5. As the tRNA/IF-2/GTP complex moves along the mRNA, this complex *binds to the initiation codon on the mRNA*. *Diagram showing the tRNA, IF-2 and GTP moving along the mRNA and binding to the initiation codon* 6. *IF-1 binds to the small subunit*. *Diagram showing the IF-1 binding to the small subunit* 7. When the mRNA is bound to the small subunit and the initiation codon is bound by a tRNA and IF-1 and IF-2 have bound to the complex, the *GTP is hydrolyzed to GDP and Pi*. *Diagram showing the IF-3 dissociating from the small subunit, the GTP being hydrolyzed to GDP and Pi, and the IF-1 and IF-2 remaining bound* 8. *The large subunit binds* to the complex formed by the small subunit, the mRNA, the initiator tRNA and IF-1 and IF-2. This creates a complete 70S initiation complex. *Diagram showing the large subunit binding to the small subunit and the rest of the complex* 9. The *initiation factors dissociate* from the complex which leads to the initiation of translation. *Diagram showing the initiation factors dissociating from the complex and leaving the mRNA bound to the ribosome* # Nirenberg-Leder Experiment *Diagram illustrating the experiment*