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Lecture 4

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Biochemistry 2280A
Christopher Brandl

Translation: mRNA to Protein Genetic Code ● The genetic code spells out the amino acid sequence in 3 “letter” “words” called codons ● Each codon represents an amino acid thus cells technically only need 20 or 21 different codons as there are 20 or 21 amino acids ● There are 64 different ways to put together a codon as there are 4 different bases for each 3 “letter” codon therefore 4 = 64 ○ a two letter code would provide 4 = 16 codons ○ This large number of possibilities in codons results in redundancy in the code ● Akey feature of the genetic code is that it is universal and that the code has evolved once; every organism uses the same code ● Another key feature is that code is non overlapping; the problem with an overlapping code is that it would place significant restrictions of what amino acid residues could follow each other ○ an nonoverlapping code can have any amino acid in any order ● Also, there are no gaps in the code, it is directly continuous and consecutive ● Redundancy often occurs at the third position of the codon; the difference occurs on the third position but this does not always hold ○ some codons can have differences at the second or first codon ● Generally amino acids found less frequently in proteins have fewer codons ○ Met -AUG ○ Trp - UGG ● There are 3 stop codons and 1 start codon: ○ Stop: ■ UAA, UAG, UGA ○ Start: ■ AUG ● Functionally related amino acids have similar codons ○ AsparticAcid can be: GAC or GAU ○ GlutamicAcid: GAG and GAA ○ The two acid residues have the same first two bases but differ in the last position ○ Gln can be: CAG OR CAAwhich are similar in the last two positions to Glu but differ in the first codon ● Functionally related amino acids have similar codons because it increases the chance of a functional protein in the case of a single base substitution mutation Types of Mutations ● Missense mutation in single base is substituted and results in a single amino acid change; good chance that the protein will still be functional due to redundancy ● Frameshift mutation in where there is an insertion or deletion of bases resulting in changes of the reading frame of the protein from the point of the mutation onwards ○ has a major consequence on the protein and is very detrimental ○ if there are 3 insertions/deletions, that would reset the reading frame and are less detrimental ● Nonsense mutations prematurely terminates the protein due to a substitution resulting in an premature stop codon tRNA  ● Function is to bring the amino acid to the growing polypeptide chain ● Tend to be ~80 bases in length and all have very similar structure ● Stem-loop structures occur due to internal base pairing in tRNAs ○ 4 stems, 3 loops resulting in a typical tRNAstructure ● tRNAs all tend to have nonconventional bases which are important in post-transcriptional modifications ● tRNAs all have very crucial single stranded regions which are added post- transcriptionally ○ 3’acceptor site (ACC sequence) ○ Anticodon site (is antiparallel and complementary to the binding site) ● In 3D, the trNAs the shape tends to be L-shaped ○ ● Wobble: ○ Most organisms have fewer than 45 different tRNAs ○ how can all 61 codons be used? ○ Some tRAspecies mst pair with more than one codon ○ for some tRNAs, base pairing between the anticodon and the codon only requires matching at two positions rather than the full three ● For example, Phe has two codons for it and a single tRNAcan bind to it ○ for one of its codons, the tRNAbinds to all three whereas for the other codon, the tRNAbinds to only the second two bases (the first base would be wobble) Aminoacyl tRNA synthetases ● Function is to couple the 3’end of a specific tRNAto its correct amino acid; puts the two together ○ process of this is often called charging of the tRNAs ○ There has to be at least one for each amino acid ● The aminoacyl tRNA has to recognize the tRNA and the amino acid, both correctly ○ requires extreme precision ● Storing energy fromATP, it creates a high energy ester linkage between the 3’end of the tRNAand the amino acid ● It also has proofreading functions as the process requires the correct amino acid bound to the tRNAas otherwise, the protein will have an incorrect amino acid attached ○ once it creates the bond, it looks back an
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