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Transcript
Nucleotide and Pairing Universal Genetic Code Genetic Code Properties • Purine (A,G) is heavier than Pyrimidine (C,T) • Transition within a type (Purines or Pyrimidineㄴ) is more likely than Translation between types • All AAs have more than one codon, except for Met and Trp • Codons for an AA are clustered – Two codons for an AA – same in the first 2 positions and differ only by transition at the 3rd position – Four codons – differ only in the 3rd position – Six codons – form one four-codon box and one twocodon box Genetic Code X • Degeneracy is controlled by GC content of codons – G-C binding is stronger – First two bases (doublets) are GC – form four codon boxes (red X) – Doublets are AU – split boxes (blue X) – Doublets are mixed X X X X X X X Purine 2nd base is pyrimidine (C,T) – four codon boxes, split otherwise Larger purine at the 2nd position reduces binding at the 3rd position A doublet forms a four-codon box, its ‘conjugate’ forms a split box Conjugate – opposite size and opposite number of hydrogen bonds; A-C and G-U are conjugates Genetic Code Five most hydrophobic – Phe, Leu, Ile, Met, Val U at the 2nd position Three most similar – Leu, Ile, Val Single-base mutation at 1st position Six most hydrophilic – His,Gln,Asn,Lys,Asp, Glu A at the 2nd position (Tyr is hydrophobic and has A in 2nd position) Evolution of Genetic Code • From what the current Genetic Code became stable ? • Robin Knight – www.cs.uml.edu/~kim/580/99_knight.pdf Amino Acids General structure of amino acids an amino group a carboxyl group α-carbon bonded to a hydrogen and a side-chain group, R R determines the identity of particular amino acid • • • • • R: large white and gray C: black Nitrogen: blue Oxygen: red Hydrogen: white (Hydrophobic) (uncharged polar) (positively charged) (negatively charged) AA Groups Classification of R groups According to propensity to be in contact with polar solvent like water Nonpolar (Hydrophobic) – many carbons in R Polar Charged (hydrophilic) Acidic – negatively charged Basic – positively charged Uncharged polar Polar/nonpolar Polar share electron bonds unequally O-H bond is polar: O is more electro-negative and bonding electrons are closer to O C-H is nonpolar Element Electronegativty Oxygen 3.5 Nitrogen 3.0 Sulfur 2.6 Carbon 2.5 Phosphorus 2.2 Hydrogen 2.1 Group 1: Nonpolar (hydrophobic) Sometimes, Gly (G) is included because C-H bond is nonpolar Group 2: Polar Side chains are electronically neutral (uncharged) Ser (S), Thr (T), Cys (C), Asn (N), Gln (Q), Try (Y) Asn (N) and Gln (Q) are consider derivatives of group 3 Asp (D) and Glu (E) Group 3: Acidic Side chains have carboxyl group Asp (D) and Glu (E) Side chains are negatively charged Group 4: Basic • Side chain is positively charged – His (H), Lys (K), Arg (R) Vol. Physico-Chemical Properties • Physico-chemical properties of AA determine protein structures – bioinformatics can be used via a pattern recognition • Properties – (1) Size in volume Volume occupied by side groups is important (also for molecular evolution), and difficult to substitute a large AA for a small one Van der Waals radius (volume until atoms are pushed to repulsion) is used to measure the volume of the sphere (in Å3) W has 3.4 times the volume of G Alanine Ala A 67 Arginine Arg R 148 Asparagine Asn N 96 Aspartic Asp D 91 Cysteine Cys C 86 Glutamine Gln Q 114 Glycine Gly G 48 Histidine His H 118 Isoleucine Ile I 124 Leucine Leu L 124 Lysine Lys K 135 Methionine Met M 124 Phenyl. Phe F 135 Proline Prot P 90 Serine Ser S 73 Threonine Thr T 93 Tryptophan Trp W 163 Tyrosine Thr Y 141 Valine Val V 105 Mean 109 (2) Partial Vol. – • Measure expanded volume in solution when dissolved (3) Bulkiness – • • • The ratio of side chain volume to its length Measure of average cross-sectional area of the side chain Relevant to protein folding (4) Polarity index – • Electrostatic force acting on its surrounding at a distance of 10 Å (5) pH of isoelectric point of AA (pI) – • • • Acidic Asp and Glu have pI in 2-3: negatively charged at neutral pH due to ionization of COOH group to COO- -- need to put them in an acid solution to shift equilibrium and balance this charge (side chain is charged +) Basic (Arg, Lys and His) has pI >7 (charged -) All others have uncharged side chains (pl. in 5-6) – (6) Hydrophobicity • • • • • • – (7) Surface area • • – When molecules are dissolved in water, hydrogen-bonded structure is disrupted Polar AA residues can form hydrogen bonds with water –hydrophilic Non-polar that cannot form the bonds – hydrophobic Polar disrupts the structure less than non-polar Polar is usually at the exterior of a structure, non-polar, interior Hydrophobicity (hydropathy) scale: estimate of difference in free energy of AA when buried in hydrophobic environment of the interior of a protein in water solution (+ for hydrophobic – costs free energy to take residue out of protein and put it in water) Surface area of AA exposed (accessible) to water in an unfolded peptide chain and become buried when the chain folds Relevant to protein folding (8) Fraction of area • • Fraction of the accessible surface area that is buried in the interor in a set of known crystal structures Hydrophobic residues have a larger fraction Red: acidic Orange: basic Green: polar Yellow: nonpolar Vol. Bulk Pol. pI Hydro Surf2 Frac Alanine Ala A 67 11.5 0.0 6.0 1.8 113 0.74 Arginine Arg R 148 14.3 52.0 10.8 -4.5 241 0.64 Asparagine Asn N 96 12.3 3.4 5.4 -3.5 158 0.63 Aspartic Asp D 91 11.7 49.7 2.8 -3.5 151 0.62 Cysteine Cys C 86 13.5 1.5 5.1 2.5 140 0.91 Glutamine Gln Q 114 14.5 3.5 5.7 -3.5 189 0.62 Glu. Acid Glu E 109 13.6 49.9 3.2 -3.5 183 0.62 Glycine Gly G 48 3.4 0.0 6.0 -0.4 85 0.72 Histidine His H 118 13.7 51.6 7.6 -3.2 194 0.78 Isoleucine Ile I 124 21.4 0.1 6.0 4.5 182 0.88 Leucine Leu L 124 21.4 0.1 6.0 3.8 180 0.85 Lysine Lys K 135 13.7 49.5 9.7 -3.9 211 0.52 Methionine Met M 124 16.3 1.4 5.7 1.9 204 0.85 Phenyl. Phe F 135 10.8 0.4 5.5 2.9 218 0.88 Proline Prot P 90 17.4 1.6 6.3 -1.6 143 0.64 Serine Ser S 73 9.5 1.7 5.7 -0.8 122 0.66 Threonine Thr T 93 15.8 1.7 5.7 -0.7 146 0.70 Tryptophan Trp W 163 21.7 2.1 5.9 -0.9 259 0.85 Tyrosine Thr Y 141 18.0 1.6 5.7 -1.3 229 0.76 Valine Val V 105 21.6 0.1 6.0 4.2 160 0.86 109 15.4 13.6 6.0 -0.5 175 0.74 Mean