Amino Acids & Proteins - PDF

Amino Acids & Proteins  The Protein Hierarchy Protein = A macromolecule made of 1 or more polypeptide chains Polypeptide chain = polymers of amino acids (more than 30 up to 4,000 amino acids) that are arranged in a specific order and linked by peptide bonds Peptide = short chain of am...

Amino Acids & Proteins  The Protein Hierarchy Protein = A macromolecule made of 1 or more polypeptide chains Polypeptide chain = polymers of amino acids (more than 30 up to 4,000 amino acids) that are arranged in a specific order and linked by peptide bonds Peptide = short chain of amino acids liked by peptide bonds having a defined sequence (fewer than 20-30 amino acids) Amino Acid = building block molecule of a protein Amino Acids ? ?  Amino Acid Structure 1. Hydrogen atom 2. Carboxyl group 3. Amino group 4. R group (side chain) - Physical properties of this group determine the uniqueness of the amino acid – size, shape, charge, hydrophobicity, reactivity α-carbon D- or L-configurations Levorotatory Dextrorotatory (Left) (Right) Form inserted into proteins Bacteria can use D-amino acids Classification of Amino Acids  Classification of Amino Acids Aliphatic amino acids: contain hydrocarbon chains Valine Alanine Leucine Isoleucine  Classification of Amino Acids Aromatic amino acids: contain ring structures Tyrosine Phenylalanine Tryptophan Aromatic Amino Acids Absorb UV Light 280 nm Spectrophotometer can Measure UV Absorption Beer-Lambert law: A = εlc A = absorbance ε = absorption coefficient (M-1cm-1) l = path length (cm) c = concentration (M)  Classification of Amino Acids Acidic amino acids: negatively-charged at pH 7 Aspartic acid Aspartate - Neutral pH Glutamic acid Glutamate - Neutral pH  Classification of Amino Acids Basic amino acids: positively-charged at pH 7 Lysine Arginine Histidine + + + 3 3  Classification of Amino Acids Polar side chains: Have a slight negative charge and are thus hydrophilic  Classification of Amino Acids Sulfur amino acids: contain sulfur atom Cysteine Methionine Disulfide bond formation Classification of Amino Acids Proline: side group is bound to amide group and α-carbon Amino Acids are Amphoteric Molecules Water acts as both a base and an acid. Henderson-Hasselbalch Equation Conjugate Amino acid H+ ion base [H +][A-] HA H + A- Ka = [HA]  All Amino Acids have at Least 2 Ionizable Groups Basic Acidic Low pH High pH (Protonated) (Deprotonated) Alanine and pKa Values Aspartic Acid and pKa Values  Amino Acids and Buffers Buffers are solutions that minimize changes in pH Best buffering at pKa values. Least buffering at pI Buffer Range Question  Protein Structure Primary o (1 ): Amino acid residues in peptide chain  Protein Structure Amino acid residues determine properties of proteins including shape and function  Protein Structure Peptide bond formation Peptide bond  Protein Structure Secondary (2o): Hydrogen bonds between amino acids hold secondary structure together  Protein Structure α-helix Hydrogen bond between every 4 amino acids resulting in ~ 3.6 amino acids per turn. Protein Structure β-pleated sheet  Protein Structure Tertiary o (3 ): Functional groups interact with one another to hold protein shape Denaturation: Disruption of the proteins 3D structure, many times not reversible. Heat, pH, salt Domains and Motifs  Protein Structure Quaternary o (4 ): More then one peptide chains held together in 3-dimensional structure  Ocular Proteins Ocular cells have thousands of different kinds of proteins with varied functions Buffers Photo-sensation Photo-transduction Osmotic pressure (corneal deturgenscence)  Crystallins Abundant and long lived protein of the fiber cells in the lens (90% of all proteins) 3 major forms- α, β, γ Structural – Maintain elongated fiber cell shape and lens structure – Affects light refraction that passes through lens Molecular chaperones Moreau and King 2012  Crystallins Role in cataracts Insoluble protein increases with age Unfolded crystallins oxidize Moreau and King 2012 and aggregate – disulfide bonds Yellowing in nuclear cataracts is caused by tryptophan oxidation (UV light) Xia et.al 2013  Rhodopsin and Cone Pigment Proteins An intrinsic membrane protein (Opsin) and cofactor (Retinal) It is a G-protein coupled receptor Retinal is in 11-cis configuration = most energetically favorable to fit in α-helices Covalently attached to protein (Lys 296) via Aldehyde end as a protonated Schiff’s base  Rhodopsin and Cone Pigment Proteins Light causes change from cis to all-trans configuration and thus breaks covalent interaction between protein and retinal via deprotonation of Schiff’s base This change stimulates activation of the G- protein transducin  Rhodopsin and Cone Pigment Proteins Cone pigment proteins are very similar They also use retinal = differences in wave lengths of light absorbed is the result of varied amino acid environments around the retinal  Collagen 80-90%of the bulk of the eye Extracellular, insoluble complex Roles – Form support fibers – Scaffolding for basement membranes – Anchoring point for cells – In the eye, makes the semiliquid gel of the vitreous  Collagen All collagens have some form of tropocollagen – triple helix formed by three polypeptide chains The three peptides are highly hydroxylated The main portions of the chains contain a lot of glycine, proline and hydroxyproline Triple helix-Fibrils-Fibers  Collagen 29 types of collagen – 12 found in the eye Corneal stroma – – Type I = form sheets (lamellae) – Type V = Limits Type I diameter – Type VI = stabilizing molecule for proteoglycans and keratocytes  Collagen Vitreous – Runs parallel orientation anteriorly to posteriorly – A few random joining fibers – Type II – vitrosin – Type IX – Link type II to proteoglycans – Type V-XI hybrid – control type II diameter  Collagen Basement membranes – Type IV – forms a spider web Descemet's Membrane – Type VIII = forms a box spring arrangement  Collagen Anchoring Attach basal cells to basement membrane Bowman’s membrane – Type VII – From hemidesmosome to anchoring plaque