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Chapter 32 The Genetic Code to accompany Biochemistry, 2/e by Reginald Garrett and Charles Grisham All rights reserved. Requests for permission to make copies of any part of the work should be mailed to: Permissions Department, Harcourt Brace & Company, 6277 Sea Harbor Drive, Orlando, Florida 32887-6777
The Collinearity of Gene and Protein Structures
Watson and Crick's structure for DNA, together with Sanger's demonstration that protein sequences were unique and specific, made it seem likely that DNA sequence specified protein sequence
Yanofsky provided better evidence in 1964: he showed that the relative distances between mutations in DNA were proportional to the distances between amino acid sunstitutions in E. coli tryptophan synthase
Elucidating the Genetic Code
A triplet code is required: 4 3 = 64, but 4 2 = 16 - not enough for 20 amino acids
But is the code overlapping ?
See Figure 32.2
And is the code punctuated ?
The Nature of the Genetic Code
A group of three bases codes for one amino acid
The code is not overlapping
The base sequence is read from a fixed starting point, with no punctuation
The code is degenerate (in most cases, each amino acid can be designated by any of several triplets
Biochemists Break the Code
Assignment of "codons" to their respective amino acids was achieved by in vitro biochemistry
Marshall Nirenberg and Heinrich Matthaei showed that poly-U produced polyphenylalanine in a cell-free solution from E. coli
Poly-A gave polylysine
Poly-C gave polyproline
Poly-G gave polyglycine
But what of others?
Getting at the Rest of the Code
Work with nucleotide copolymers (poly (A,C), etc.), revealed some of the codes
But Marshall Nirenberg and Philip Leder cracked the entire code in 1964
They showed that trinucleotides bound to ribosomes could direct the binding of specific aminoacyl-tRNAs (See Figure 31.6)
By using C-14 labelled amino acids with all the possible trinucleotide codes, they elucidated all 64 correspondences in the code (Table 32.3)
Read also about Khorana's experiment
Features of the Genetic Code
All the codons have meaning : 61 specify amino acids, and the other 3 are "nonsense" or "stop" codons
The code is unambiguous - only one amino acid is indicated by each of the 61 codons
The code is degenerate - except for Trp and Met , each amino acid is coded by two or more codons
Codons representing the same or similar amino acids are similar in sequence
2nd base pyrimidine: usually nonpolar amino acid
2nd base purine: usually polar or charged aa
AA Activation for Prot. Synth.
The Aminoacyl-tRNA Synthetases
Codons are recognized by aminoacyl-tRNAs
Base pairing must allow the tRNA to bring its particular amino acid to the ribosome
But aminoacyl-tRNAs do something else: activate the amino acid for transfer to peptide
Aminoacyl-tRNA synthetases do the critical job - linking the right amino acid with "cognate" tRNA
Two levels of specificity - one in forming the aminoacyl adenylate and one in linking to tRNA
Mechanism and specificity
Deacylase activity "edits" and hydrolyzes misacylated aminoacyl-tRNAs
Despite common function, the synthetases are a diverse collection of enzymes
Four different quaternary structures: , 2 , 4 and 2 2
Subunits from 334 to more than 1000 residues
Two different mechanisms (See Figure 32.5)
Recognition of tRNAs
by the aminoacyl-tRNA synthetases
Anticodon region is not the only recognition site
The "inside of the L" and other regions of the tRNA molecule are also important
Read pages 1080-1082 on specificity of several aminoacyl-tRNA synthetases
and the Wobble Hypothesis
Codon-anticodon pairing is the crucial feature of the "reading of the code"
But what accounts for "degeneracy": are there 61 different anticodons, or can you get by with fewer than 61, due to lack of specificity at the third position?
Crick's Wobble Hypothesis argues for the second possibility - the first base of the anticodon (which matches the 3rd base of the codon) is referred to as the "wobble position"
The Wobble Hypothesis
The first two bases of the codon make normal (canonical) H-bond pairs with the 2nd and 3rd bases of the anticodon
At the remaining position, less stringent rules apply and non-canonical pairing may occur
The rules: first base U can recognize A or G, first base G can recognize U or C, and first base I can recognize U, C or A (I comes from deamination of A)
Advantage of wobble: dissociation of tRNA from mRNA is faster and protein synthesis too