amino acids and proteins, Study notes of Biochemistry

Download amino acids and proteins and more Study notes Biochemistry in PDF only on Docsity! AMINO ACIDS AND PROTEINS cea Proteins and Amino Acids (Amino Acids as Acids and Bases)  SFJINDIIOWOYOVW , ions, small a molecules (4%) phospholipids (2%) DNA (1%) RNA (6%) proteins (15%) polysaccharides (2%) Protei . & roteins @ Protein Diversity o a> Catalase Wysgicbin ve &| Deoxyribonuclease Cytochrome ¢ Proteins are molecular tools *They are a diverse and complex group of macromolecules From McKee and McKee, Biochemistry, Sth Edition, ©2011 by Oxford University Press Types of Amino Acids a Amino acids are classified as Nonpolar Polar * Nonpolar (hydrophobic) ws to HN 7" H with hydrocarbon side chains. * Polar (hydrophilic) with — ease polar or ionic side chains. Acidic Basic * Acidic (hydrophilic) with acidic side chains. * Basic (hydrophilic) with : : -NH,side chains. fo fo Aspartic acid (Asp) Lysine (Lys) ‘Copyright © 2007 by Pearson Education, inc. Publishing as Benjamin Cummings Amino Acids Classification Table ——— AMINO ACID SIDE CHAIN AMINO ACID SIDE CHAIN Aspartic acid Asp D negative Glutamic acid = Glu E negative POLAR AMINO ACIDS. ~—————/ |——_ NONPOLAR AMINO ACIDS. )=9§ Nonpolar Amino Acids ——————————— Anonpolar amino acid has * An R group that is H, an alkyl group, or aromatic. Polar Amino Acids Sass A polar amino acid has * An R group that is an alcohol, thiol, or amide. Polar Amino Acids (Neutral) Hi8—C—coo™ fin —C—coo" Hk-C—coo- Hi8—C—coo" HyN—C—COO™ HX—C—COo" " i u " mie womans (th Tyronine Tye conan Asparagine Asn) Chwamine (Gi we 1 ‘y 2 Copyright © 2007 by Pearson Education, Inc. Publishing as Benjamin Cummings Acidic and Basic Amino Acids An amino acid is * Acidic with a carboxyl R group (COO’). «# Basic with an amino R group (NH;*). Aodic Amino Rod Basic Amino Acids a H.N—C—Coo™ rr 48—c—coo™ ' D E 4 Copyright © 2007 by Pearson Education, Inc. 13 Publishing as Benjamin Cummings Optical Activity —— Amino acids * Are chiral except for glycine. #* Have Fischer projections that are stereoisomers. #* That are L are used in proteins. COOH COOH COOH COOH Han HN, HaN—H r Hp CH CH CH SH CH,SH L-alanine D-alanine L-cysteine D-cysteine Fischer Projections of Amino Acids 15 pH and Ionization (« H+ OH- + + H,N-CH,-COOH H,N-CH,-COO- ~—-H,N-CH,-COO- positive ion zwitterion negative ion (at low pH) (at pl) (at high pH) Acid-base Properties AA have multiple pK,’s due to multiple ionizable groups oO pK, ~ 2.2 \| rotonated below 2.2 E - HO—C pK,~ 9.4 | (NH; below 9.4) > H2N—C—H pK, bP—> R (when applicable Abbreviation/ 9x ox, ok, Amino acid symbol M, (—COOH) (—NHJ) (R grou) Table 3-1 triste R groups Giycine Gy 6 7s (234 9.60 Aanine Aa & 89234 9.69 Proline PoP 115 = 199 10.96 Valine Vi Vo «MMT 232 9.62 Leucine teu t 131-236 9.60 Isoleucine te 31236 9.68 Methionine Met M = 149228 9.21 Aromatic R groups Pheryiaianine Phe F 165 1.83 9.13 - Tosine wy 1812.20 911 1007 Note 3-letter and Tryptophan mW 208 238 939 ‘letter Pour, uncharged abbreviations R groups Serine SeS 105 = 221 9.15 Threonine Tw T 92a 9.62 Cysterne Osc 12 196 10.28 818 Asparagine AsnN = 1322.02 8.80 Giutamine GnQ 146247 9.13 Positively charged R groups Amino acid organization chart — sine ls K 146 218 895 10.53 Histidine Ws H 1551.82 9.17 6.00 Argrine agR 17427 904 = 1248 Negatively charged R groups Aspartate AspD 1331.88 9.60 3.65 Giutamate Gu E 147 219 9.67 425 Electrophoresis: Separation of Amino Acids Sass In electrophoresis, an electric current is used to separate a mixture of amino acids, and * The positively charged amino acids move toward the negative electrode. * The negatively charged amino acids move toward the positive electrode. * An amino acid at its pl does not migrate. * The amino acids are identified as separate bands on the filter paper or thinlayer plate. Electrophoresis With an electric current, a mixture of lysine, aspartate, and valine are separated. Mix of Lys, Asp, Val Tereerine, Garerat Orgure: ans Baamgeat Chart Copy © Paarnon Eaucatian ne pubtrng as Benen Commer Copyright © 2007 by Pearson Education, Inc. Publishing as Benjamin Cummings Essential Amino Acids Essential amino acids * Must be obtained Arginine (Arg) Methionine (Met) from the diet. Histidine (His) Phenylalanine (Phe) * Are the ten amino Isoleucine (Ile) Threonine (Thr) acids not Leucine (Leu) Tryptophan (Trp) synthesized by the Lysine (Lys) Valine (Val) body. ee * Are in meat and Copyright © 2007 by Pearson Education, Inc Publishing as Benjamin Cummings diary products. * Are missing (one or more) in grains and vegetables. 24 Amino Acids and Proteins Protein Structure: Primary and Secondary Levels me ‘Amide group, Peptide Gtycylalanine (Gly-Ala) ‘Copyright © 2007 by Pearson Education, inc Publishing as Benjamin Cummings Proteins Protein Diversity @ Phosphocarrier protein HPr Lysozyme @ Catalase Hemoglobin Deoxyribonuciease Collagen From McKee and McKee, Biochemistry, Sth Edition, ©2011 by Oxford University Press Primary Structure of Proteins ——————————— The primary structure of a protein is * The particular sequence of amino acids. * The backbone of a peptide chain or protein. gr CH, s e ¢H_CH, SH CH ian CHO CHO ¢HO ¢H,0 HoH EN GH- En GH On bHb-o 1 Hh Hh Copyright © 2007 by Pearson Education, Inc Ala—Leu-Cys-Met Publahing as Benjamin Cummings Primary Structures Sass The nanopeptides oxytocin and vasopressin * Have similar primary structures. * Differ only in the amino acids at positions 3 and 8. Copyright © 2007 by Pearson Education, inc Publishing as Benjamin Cummings ai Primary Structure of Insulin Insulin oe * Was the first protein to " have its primary structure determined. * Has a primary structure of two polypeptide chains @® linked by disulfide bonds. * Has a chain Awith 21 amino acids and a chainB with 30 amino acids. ‘Copyright © 2007 by Pearson Education, Inc Publishing as Benjamin Cummings Secondary Structure — Alpha Helix The secondary structures of proteins indicate the three-dimensional spatial arrangements of the polypeptide chains. An alpha helix has * Acoiled shape held in place by hydrogen bonds between the amide groups and the carbony| groups of the amino acids along the chain. * Hydrogen bonds between the H of a -N-H group and the O of C=O of the fourth amino acid down the chain. Amino Acids and Proteins Protein Structure: Tertiary and Quaternary Levels ‘Amide group, Peptide bond Glycylalanine (Giy-Ala) Copyright © 2007 by Pearson Education, Inc Publishing as Benjamin Cummings 39 Tertiary Structure as The tertiary structure of a protein * Gives a specific three dimensional shape to the polypeptide chain. * Involves interactions and cross links between different parts of the peptide chain. * Is stabilized by Hydrophobic and hydrophilic interactions. Salt bridges. Hydrogen bonds. Disulfide bonds. Tertiary Structure * The interactions of the R groups give a protein its specific three- dimensional tertiary structure. Copyright © 2007 by Pearson Education, Inc Publishing as Benjamin Cummings Tertiary Structure “TABLE 19.5. notre of Bonding Sangh Hydrophobic Attractions between —CcH, interactions: nonpolar alkyl and cH,— ‘aromatic groups form a 2 nonpolarcenterthatis = _CH OH O—H repelled by water Hydrogen ‘Occur between polar side Seo Ho — % Disulfide bonds Strong covalent links —SH + HS— —* —S—S— | os - oO H a a2 Globular Proteins Globular proteins * Have compact, spherical shapes. * Carry out synthesis, transport, and metabolism in the cells. * Such as myoglobin store and transport oxygen in muscle. 87 Copyright © 2007 by Pearson Education, Ine Publishing as Benjamin Cummings Fibrous Proteins Fibrous proteins * Consist of long, fiber-like shapes. * Such as alpha keratins make up hair, wool, skin, and nails. * Such as feathers contain beta keratins with large amounts of beta-pleated sheet structures. a. helix Alpha keratin Copyright © 2007 By Peaisor Edlication, The PUBISHING SS BEAjmin Cummings 58 Protein Hydrolysis Protein hydrolysis * Splits the peptide bonds to give smaller peptides and amino acids. * Occurs in the digestion of proteins. * Occurs in cells when amino acids are needed to synthesize new proteins and repair tissues. 49 Hydrolysis of a Dipeptide * In the lab, the hydrolysis of a peptide requires acid or base, water and heat. * In the body, enzymes catalyze the hydrolysis of proteins. OH CH; O CH 0 het Pay ru 120, H* H3N—CH-C—N-—CH-C-—OH = ——> | H oH , CH; 0 CH, O *- J i wN—CH-UOH + HWN-CH-C_OH 80 Denaturation Denaturation involves * The disruption of bonds in the secondary, tertiary and quaternary protein structures. # Heat and organic compounds that break apart H bonds and disrupt hydrophobic interactions. * Acids and bases that break H bonds between polar R groups and disrupt ionic bonds. # Heavy metal ions that react with S-S bonds to form solids. # Agitation such as whipping that stretches peptide chains until bonds break. 51 Applications of Denaturation Denaturation of protein occurs when * An egg is cooked. # The skin is wiped with alcohol. * Heat is used to cauterize blood vessels. ; bike Fea * Instruments are sterilized in saleane autoclaves. > Actve proton erated poten Copyright © 2007 by Pearson Education, inc Publishing as Benjamin Cummings  Ribonuclease Refolding Experiment Ribonuclease is a small protein that contains 8 cysteins linked via four disulfide bonds Urea in the presence of 2- mercaptoethanol fully denatures ribonuclease When urea and 2-mercaptoethanol are removed, the protein spontaneously refolds, and the correct disulfide bonds are reformed The sequence alone determines the native conformation Quite “simple” experiment, but so important it earned Chris Anfinsen Native state; catalytically active. a [occ 65 fo \8B Unfolded state; inactive. Disulfide 26 cross-links reduced to yield Cys residues. by removal of urea and mercaptoethanol Native, active state. a correctly re-formed. Figure 4-26 ‘Pramipie of Blochemetry. FAND Lion Lehanger ©2008 W Ht Freeman and Comer