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From RNA to Proteins

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John Coleman

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Chapter 6: From RNA to Protein (Reading 366-390) - Even though the final product of some genes is the RNA itself, most genes in a cell produce mRNA molecules that serve as intermediaries on the pathway to proteins - How does the cell concert the information carried in the mRNA into a protein molecule? - Coding problem: how is the information in the linear sequence of RNA translated into a linear sequence of a chemically different set of units, the amino acids? - Since the question has been posed, the process of translation has been cracked step by step and the structure of the elaborate machinery by which cells read out this code, the ribosome has been revealed in atomic detail 1. An mRNA sequence is decoded in sets of three nucleotides - Once an mRNA is made, its nucleotide sequence can be used to synthesize proteins - Transcription is simple to understand as the means of information transfer, RNA and DNA are chemically and structurally similar and the DNA can ace as a direct template for synthesis of RNAs by complementary base-pairing - During transcription, the language and the form of the message does not change - The conversion of information in mRNA to PRs represents translation of information into another language - Translation is the process by which the sequence of nucleotides in a mRNA molecule directs the incorporation of AAs into PR; occurs in a ribosome - Translation cannot be accounted for direct one to one correspondence, as there are 4 nucleotides in RNA and 20 AAs - The translation of mRNA into PRs by rules which are called the genetic code - Genetic code is the set of rules specifying the correspondence between nucleotide triplets in DNA or RNA and amino acids in PRs - The nucleotides are read out is sets of three - The code is redundant and some AAs are specified by more than on triplet - Each triplet is called a codon, and each codon specifies and AA or a stop to translation - Codon is the sequence of three nucleotides in a DNA or mRNA molecule that represents the instruction for incorporation of a specific AA into a growing PR chain - The genetic code is almost universal to all organisms, however few differences were found in the mitochondria o Mitochondria have their own transcription and PR synthesis process, thus their small genomes have been able to accommodate small changes to the code www.notesolution.com - Reading frame phase in which nucleotides are read in sets of three to encode a PR; a mRNA molecule can be read in any one of three protein reading frames, only one of which will the required protein - Small punctuation signal at the beginning of each RNA message sets the correct reading frame at the start of protein synthesis 2. tRNA molecules match amino acids to codons in mRNAs - The codons in mRNA can not recognize or bind to the amino acids they specify - Translation depends on an adaptor molecule, which binds to the codon and the amino acid on different sites of its surface, these molecules are small RNA molecules called transfer RNAs - tRNAs can fold into precise 3D structures, four short segments of tRNA are double helical, producing a molecule that looks like a clover leaf when drawn schematically this leaf undergoes additional folding patterns, forming a compact L-shaped structure that is held together by additional hydrogen bonds between different regions of the molecule - For example, 5-GCUC-3 can form a relatively strong association with a 5-GAGC-3 in another region of the same molecule - Two regions of the unpaired nucleates are crucial to the function of tRNA, one from the anticodon, a set of three nucleotides that pairs with complementary codon in mRNA and the other is a short single stranded regions at the 3 end of the molecule were the amino acid that matches the codon is attached - The genetic redundancy (several different codons can specify a single AA) implies that there is more than one tRNA for many AAs or that some tRNA molecules can base-pair with more than one codon o Both are true, some tRNAs are constructed in such a way that they require accurate base pairing only at the first two position and can tolerate a wobble at the third o Wobble base-pairing explains why so many of the altering codons for AA differ only in their third nucleotide o The number of different tRNAs differs between organisms, humans have 500 tRNA genes, but only 48 different anticodons are represented 3. tRNAs are covalently modified before they exit from the nucleus - Like other eucaryotic RNAs, tRNAs are covalently modified before they are allowed to leave the nucleus - Polymerase III synthesizes tRNAs - In both bacteria and eucaryotes, tRNA are typically synthesized as larger precursor tRNAs, which then are tripped to produce mature tRNAs - Some tRNA precursors contain introns which must be spliced out, tRNA splicing is different from pre-mRNA splicing, it uses a cut-and-paste mechanism that is catalyzed by proteins - Trimming and splicing requires that precursor tRNAs to be correctly folded in its covalent cloverleaf configuration www.notesolution.com - Because misfolded tRNA precursors will not be processed property, the trimming and splicing are though to act as quality control steps in generating tRNAs - All tRNAs are modified chemically, nearly 1 in 10 nucleotides in a mature tRNA molecule is an altered version of a standard G, U, C, or A ribonucleotide - Some of the modified nucleotides (esp inosine, produced by deamination of adenosine) affect the conformation and base pairing of the anticodon and thereby facilitate correct recognition of the mRNA codon by the tRNA molecule - Other modifications affect the accuracy with which the tRNA is attached to the correct amino acid 4. Specific enzymes couple each amino acid to its appropriate tRNA molecule - In order to read the genetic code, cells make different tRNAs - Attachment of correct amino acids depends on the enzyme called aminoacyl-tRNA synthetase, which covalently couple each amino acid to its correct set of tRNA molecules - Aminoacyl-tRNA synthetase is an enzyme that attached the correct amino acid to a tRNA molecule to form an aminoacyl-tRNA - Most cells have different aminoacyl-tRNA synthetase for each amino acid - Many bacteria have fewer than 20 synthetases, and the same synthetase is responsible for coupling more than one AA to its correct tRNA o In such cases, a single synthetase places identical AAs on different tRNAs, only one that has an anticodon that matches the AA o A second enzyme then chemically modifies each incorrectly attached AA, so that is corresponds to the anticodon of the tRNA - The synthetase-catalyzed reaction which attached the AA to the 3 end of the tRNA is one of many reactions coupled to the energy-releasing hydrolysis of ATP, and it produces a high energy bond between the tRNA and the AA o The energy of this reaction is later used in PR synthesis to covalently link the AA to the growing PR chain - Both aminoacyl-tRNA synthetase and tRNAs are equally important for the decoding process o Genetic code is translated by two sets of adaptors that act sequentially o Each matched one molecular surface to another with great specificity o Their combined action of both is what that associates each codon with the correct AA 5. Editing by tRNA synthetases ensures accuracy - Several mechanism ensure that the tRNA synthetases links the correct amino acid to each tRNA - Synthetase must select the correct amino acid, most synthetases do this by a 2-step mechanism www.notesolution.com o (1) The correct amino acid has the highest affinity for the active-site pocket on its synthetase Larger than correct AAs are easily excluded Discrimination between alike AA is difficult to get with one step o (2) This occurs after an AA has been covalently linked to AMP tRNA tried to force the AA into a second pocket in the synthetase, the precise dimensions of which exclude the correct AA, but allow the incorrect one in Once an AA enters the pocket it hydrolyzed from AMP and is released from the enzyme o Hydrolytic editing is analogous to exonucleolytic proofreading by DNA polymerase, raises overall accuracy to 1 mistake per 40, 000 couplings - Extensive structural and chemical complementariness between the correct tRNA synthetase and tRNA or tRNAs o Most tRNA synthetases directly recognize the matching tRNA anticodon These tRNA synthetase contain three adjacent nucleotide binding pockets, each of which is complementary in shape and charge to the nucleotide in the anticodon o For other tRNA synthetase, the nucleotide sequence on of the acceptor step is the key recognition determinant o In most cases tRNA synthetase reads the nucleotides at several different positions on the rRNA 6. Amino acids are added to the C-terminal end of the growing polypeptide chain - Mechanisms that join AA together to form proteins - The fundamental reaction of protein synthesis is the formation of the peptide bond between the carboxyl group at the end of a growing peptide chai
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