Amino Acids - PDF

Amino acids Dr Thomas Hoefken  Overview General properties of amino acids Structures and characteristics of amino acids found in proteins Formation of peptide bonds Major classes of biomolecules Amino acids and proteins Nucleotides and nucleic acids (DNA and RNA)...

Amino acids Dr Thomas Hoefken  Overview General properties of amino acids Structures and characteristics of amino acids found in proteins Formation of peptide bonds Major classes of biomolecules Amino acids and proteins Nucleotides and nucleic acids (DNA and RNA) Carbohydrates Lipids  Amino acids and proteins 20 different amino acids protein (most 50-2,000 amino acids) Amino acids Possible combinations 2 202 = 400 3 203 = 8,000 100 20100 = 10130 1,000 201,000 = ? Proteins have a wide range of functions Hormones Antibodies Muscle fibres Oxygen transport Ion channels Enzymes … General structure of amino acids Variable side chain Amino group Carboxyl group Hydrogen atom Amino acids in proteins are -amino acids Naming carbon atoms in carboxylic acids β γ α GABA, a γ-amino acid General structure of amino acids Variable side chain Amino group Carboxyl group Hydrogen atom Amino acids in proteins are -amino acids Amino acids have a negative and a positive charge  General structure of amino acids The -carbon always has four substituents and is tetrahedral All have: – an acidic carboxyl group – a basic amino group – a hydrogen connected to the -carbon The fourth substituent (R) is unique  Stereoisomers of amino acids C4H10 Isomers: same molecular formula but different chemical structure  Stereoisomers of amino acids Stereoisomers: same molecular formula and the same bonding but different three-dimensional orientation of atoms Enantiomers: stereoisomers that are non-superimposable mirror images Chiral carbon atom: carbon atom that has four different groups Amino acids are chiral Fischer projection Proteins contain only L amino acid Abbreviations for amino acids Amino acid sequence of a protein: Met-Tyr-Ala-Gly-Gly-Trp-Leu-…. MYAGGWL…  Amino acid classification Amino acids can be placed in five basic groups depending on their R substituents: Nonpolar, aliphatic Aromatic Polar, uncharged Positively charged Negatively charged  Nonpolar, aliphatic R groups What does that mean? Covalent bonds can be polar and nonpolar  Electronegativity - Electronegativity: a measure of the ability of an atom to attract electrons in a chemical bond - Elements with high electronegativity have a greater ability to attract electrons than do elements with low electronegativity - The greater the difference in electronegativity between two atoms, the greater the polarity of their bond Hydrogen and carbon: low electronegativity Oxygen and nitrogen: high electronegativity Nonpolar, aliphatic R groups C C C O C H H O C N H N  Why is that important? - Water makes up 70% of the weight of most organisms - Water is polar - Polar and charged compounds are soluble in water (hydrophilic) - Unpolar compounds are not soluble in water (hydrophobic) - These interaction are important for structure and function of biomolec  Nonpolar, aliphatic R groups Aromatic compounds are organic compounds that contain the benzene ring or a derivative of the benzene ring. Aliphatic compounds are organic compounds that do NOT contain the benzene ring or a derivative of it. Nonpolar, aliphatic R groups  Nonpolar, aliphatic R groups There is no D and L form for glycine The central carbon is not chiral (four different groups/atoms bonded to Nonpolar, aliphatic R groups Nonpolar, aliphatic R groups Nonpolar, aliphatic R groups Aromatic R groups Positively charged R groups Negatively charged R groups Polar, uncharged R groups Glutamate, glutamic acid, glutamine What’s the difference? Glutamic acid Glutamate Glutamate, glutamic acid, glutamine What’s the difference? Aspartate, aspartic acid and asparagine  Alternative amino acid classifications Amino acids containing a hydroxyl group Alternative amino acid classifications Amino acids containing sulfur  Are glycine and alanine really hydrophobic? Solubility in water: 250 g/l 167 g/l  Hydrophobicity of amino acids Highly hydrophobic Highly hydrophilic Isoleucine Lysine Leucine Arginine Valine Histidine Phenylalanine Glutamate Aspartate Glutamine Asparagine N and O in the side chain only C and H in the side chain Amino acids are linked by peptide bonds to form polypeptide chains Peptide bond  Peptide ends are not the same N-terminal C-terminal Ser-Gly-Tyr-Ala-Leu SGYAL  Amino acids, peptides and proteins Peptides are small condensation products of amino acids They are “small” compared to proteins (Mw < 10 kDa) Kilodalton (kDa) A unit of mass equal to 1,000 Da Dalton (Da) A unit of mass equal to that of a hydrogen atom Glycine: 75 Da Tryptophan: 204 Da Peptide/protein size varies greatly  Summary Proteins are built from a set of 20 different amino acids In amino acids the central carbon is linked to an amino group, a carboxyl group, a hydrogen atom and a side chain These side chains vary greatly in size, shape and functional groups Amino acids are linked by peptide bonds to form polypeptide chains