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Exam 2 Book Notes CHAPTER 22: PROTEIN SYNTHESIS-Clear there was a genetic code that had to be used to translate a nucleotide sequence into a sequence of amino acids...messenger RNA is one of the key intermediate in the flow of information from DNA to protein-I. THE GENETIC CODE A. DNA alphabet consists of 4 letters (A, T, C, and G) they encode 20 amino acids, and contain codons (three letter “words”)B. Transfer RNA (tRNA) plays an important role in interpreting the genetic code and translating a nucleotide sequence into an amino acid sequence. They are the adapters between mRNA and proteins. C. One region of tRNA is covalently linked to a specific amino acid, anther region interacts directly with an mRNA codon by complementary base pairingD. Genetic code made up of 3 letters can be overlapping or nonoverlapping. If they overlap each letter is a part of more than one word, a mutation would result in several changes. Nonoverlapping each letter is part of only one word, mutation would only affect one codon. 1. All living organisms have nonoverlapping genetic code E. Each potential translation initiation point defines a unique sequence of three letter words known as a reading frame in the mRNA, correct translation depends on selecting the correct reading frame F. All nucleotide sequences are written in the 5’-->3’ direction G. The standard genetic code main features are:1. The genetic code in unambiguous: each codon corresponds to ONE amino acid2. There are multiple codons for most amino acids: because many codons correspond for several amino acids, the genetic code is known as a degenerate. Different codons for one amino acid are synonymous codons. a) Degeneracy limits the effects of mutations3. First two nucleotides are enough to specify a given amino acid4. Codons with similar sequences specify chemically similar amino acids 5. Only 61 of the 64 codons specify amino acids: the three remaining are termination/stop codons (UAA, UGA, UAG). They are not recognized by mRNA, recognized by specific proteins that cause the release of newly synthesized peptides. a) Methionine codon (AUG) specifies the initiation site and I known as initiation codonII. TRANSFER RNAA. tRNA molecules are the interpreters of the genetic code. They are the link between the sequence of nucleotides in mRNA and the sequence of amino acids (AA) in a polypeptide.B. At least 20 different tRNA species, one for every AA, each tRNA recognizes at least one codonC. THE 3-D STRUCTURE OF TRNA1. 5’ end and the region near the 3’ end are base-paired forming the acceptor stem, (AA stem) the AA is covalently attached to tRNA at the 3’ end of this stem. 2. All tRNA molecules have a phosphorylated nucleotide at the 5’ end3. Loop opposite to the acceptor stem is the anticodon loop. Contains the anticodon that binds to a complementary codon in mRNA 4. tRNA molecule is bend into an L shape, the structure is compact, stable (due to hydrogen bonds between the nucleotides in the D and T†U and variable arms D. TRNA ANTICODON BASE-PAIR WITH MRNA CODONS1. tRNA and mRNA molecules interact via base pairing between anticodons and codons2. Anticodon of tRNA determines where the AA attaches to its acceptor stem is added to the a polypeptide chain 3. tRNA molecules are named for the AA they carry4. Watson-Crick base pairing: A with U, G with C. The 5’ position is conformationally flexible and is called the “wobble” position. I (inosinate) can hydrogen bonds with A, C, or U5. Wobble allows some tRNA molecules to recognize more than one codon, several different tRNA molecules need to recognize all synonymous codons. RancanoBCH3023C6. Different tRNA molecules that can attach to the same AA are called isoacceptor tRNA molecules also applies to tRNA molecules with the same anticodons but different primary structures III. AMINOACYL-TRNA SYTHETASESA. Protein synthesis can be divided into: initiation, elongation, and termination stages. B. Activation of AA is considered part of the overall translation process. C. In aminoacylation a particular AA is covalently attached to the 3” end of each tRNA molecule resulting in aminoacyl-tRNA (energy rich molecule therefore the AA is considered activated for transfer to a growing polypeptide chain). Reaction is catalyzed by aminoacyl-tRNA synthetases D. Synthetases can recognized many isoacceptor tRNA molecules E. Accuracy of protein synthesis depends on aminoacyl-tRNA synthetase to catalyze attachment of the appropriate AA to the correct tRNA F. THE AMINOACYL-tRNA SYNTHETASE REACTION1. Requires ATP2. Amino Acid + tRNA + ATP → Aminoacyl-tRNA + AMP + PPi 3. Amino acid is attached to tRNA molecule by the formation of an ester linkage between the carboxylate group amino acid and a hydroxyl group of the ribose at the 3’ end of the tRNA molecule a) Since all tRNAs end in -CCA the attachment site is always an adenylate residue. 4. Aminoacylation takes place in two steps: a) 1. The AA is activated by the formation of a reactive aminoacyl-adenylate intermediate. The intermediate is non-covalently bound to the aminoacyl-tRNA synthetase. Hydrolysis of the pyrophosphate makes the reactions IRREVERSIBLEb) 2. Aminoacyl-group transfer from the intermediate group to tRNA molecule. The AA must be attached to the 3’ position in order to serve as a substrate in protein synthesis 5. The energy stored in the aminoacyl-tRNA is used in the formation of a peptide bond during protein synthesis. 2 ATP equivalents are consumed during each aminoacyl reaction. G. SPECIFICITY OF AMINOACYL-tRNA SYNTHETASES1. Each aminoacyl-tRNA synthetase binds ATP and selects the correct AA based on its charge, size, and hydrophobicity (this eliminates most of the other AA that are not specific to the enzyme) 2. Synthetase binds a specific tRNA molecule (distinguished by features unique to its structure)3. In some cases the synthetase recognizes both the anticodon as well as the acceptor stem of the tRNA 4. Net effect between tRNA and synthetase: to position the 3’ end of the tRNA molecule in the active site of the enzyme H. PROOFREADING ACTIVITY OF AMINOACYL-tRNA SYNTHETASES1. In some cases chemically similar amino acids can be accommodated in the active site of isoleucyl-tRNA synthetase. (isoleucine and valine)2. Some aminoacyl-tRNA synthetases do not need proofreading: phenylalanine and tyrosine only differ by one hydroxyl group however are effectively distinguished from one another IV. RIBOSOMESA. Four components are

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