Lecture_5 - Models of protein and rRNA evolution Fredrik...

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Models of protein and rRNA evolution Fredrik Ronquist September 14, 2005 In this lecture, we will be covering models for the evolution of two important gene expression products, proteins and ribosomal RNA. 1 Protein models [JF:14] DNA sequences (genes) that code for proteins are first transcribed into messenger RNA (mRNA) which is translated with the help of transfer RNA (tRNA) into polypeptides (sequences of amino acids). The polypeptides are then folded to form proteins; often there are several polypeptide units in a single protein. The basic flow of information is affected by several additional processes, includ- ing so-called splicing of messenger RNA in higher organisms to remove introns (non-coding DNA segments) from exons (protein-coding segments). There is also some post-translational processing of the polypeptides before they are assembled into functioning proteins. Much of this complexity is ignored here even though it can, in principle, be accommodated in stochastic models of protein evolution. Polypeptide chains are constructed from twenty amino-acid building blocks, which differ consider- ably in size, hydrophobicity, and chemical properties (Table 1). These features are all significant in the evolution of protein-coding sequences. For instance, transmembrane proteins usually have regions of hydrophobic amino acids where they are embedded in the cell membrane and regions of hydrophilic amino acids where they interact with the aqueous solution inside or outside the membrane. Most cytosol proteins (proteins that float around in the interior of the cell) have in- terior regions that consist mainly of hydrophobic amino acids and an exterior dominated by more hydrophilic amino acids. The translation of RNA into polypeptides is governed by the genetic code . Each tRNA molecule 1
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BSC5936-Fall 2005-PB,FR Computational Evolutionary Biology Table 1: The amino acids (sorted alphabetically on their three-letter code) Trivial name Three-letter code One-letter code Volume 1 Hydrophobicity 2 Properties Alanine Ala A 88.6 1.8 hydrophobic Arginine Arg R 173.4 -4.5 basic Asparagine Asn N 114.1 -3.5 hydrophilic Aspartic acid Asp D 111.1 -3.5 acidic Cysteine Cys C 108.5 2.5 hydrophilic Glutamine Gln Q 143.8 -3.5 hydrophilic Glutamic acid Glu E 138.4 -3.5 acidic Glycine Gly G 60.1 -0.4 hydrophilic Histidine His H 153.2 -3.2 basic Isoleucine Ile I 166.7 4.5 hydrophobic Leucine Leu L 166.7 3.8 hydrophobic Lysine Lys K 168.6 -3.9 basic Methionine Met M 162.9 1.9 hydrophobic Phenylalanine Phe F 189.9 2.8 hydrophobic Proline Pro P 112.7 -1.6 hydrophobic Serine Ser S 89.0 -0.8 hydrophilic Threonine Thr T 116.1 -0.7 hydrophilic Tryptophan Trp W 227.8 -0.9 hydrophobic Tyrosine Tyr Y 193.6 -1.3 hydrophilic Valine Val V 140.0 4.2 hydrophobic has three nucleotides coding for a particular amino acid. These three tRNA nucleotides are called a codon . There are 4 3 = 64 different codons and one different kind of tRNA molecule for each. The codon corresponds to three nucleotides in the sense strand of the DNA, except that the tRNA
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This note was uploaded on 11/27/2011 for the course BSC 5936 taught by Professor Staff during the Spring '08 term at FSU.

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Lecture_5 - Models of protein and rRNA evolution Fredrik...

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