Bioinformatics and genome biology by Paul G Higgs; et al

By Paul G Higgs; et al

Preface.Chapter Plan.Chapter 1. creation: The Revolution in organic Information.Chapter 2. Nucleic Acids, Proteins, and Amino Acids.Chapter three. Molecular Evolution and inhabitants Genetics.Chapter four. types of series Evolution.Chapter five. info assets for Genes and Proteins.Chapter 6. series Alignment Algorithms.Chapter 7. looking out series Databases.Chapter eight. Phylogenetic Methods.Chapter nine. styles in Protein Families.Chapter 10. Probabilistic equipment and desktop Learning.Chapter eleven. additional themes in Molecular Evolution and Phylogenetics.Chapter 12. Genome Evolution.Chapter thirteen. DNA Microarrays and the 'omes.Mathematical Appendix.List of internet address.Glossary.Index

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1. The table is divided into blocks that have the same bases in the first two positions. For example, codons of the form UCN (where N is any of the four bases) all code for Ser. There are many groups of four codons where all four code for the same amino acid and the base at the third position does not make any difference. , CAY codes for His and CAR codes for Gln (Y indicates a pyrimidine, C or U; and R indicates a purine, A or G). There are only two amino acids that have a single codon: UGG = Trp, and AUG = Met.

This means that these amino acids would be negatively charged at neutral pH due to ionization of the COOH group to COO−. We need to put them in an acid solution in order to shift the equilibrium and balance this charge. The basic amino acids (Arg, Lys, and His) have pI greater than 7. All the others usually have uncharged side chains in real proteins. They have pI in the range 5–6. Thus, pI is a useful measure of acidity of amino acids that distinguishes clearly between positive, negative, and uncharged side chains.

Many tRNAs can pair with more than one codon due to the flexibility of the pairing rules that occurs at the third position in the codon – this is known as wobble. For example, most bacteria have two types of tRNA-Ala. One type, with anticodon UGC, decodes the codons GCA and GCG, while the other type, with anticodon GGC, decodes the codons GCU and GCC. The actual number of tRNAs varies considerably between organisms. For example, the E. coli K12 genome has 86 tRNA genes, of which three have UGC and two have GGC anticodons.

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