Amino Acids and Proteins: Structure, Classification, Ionization, and Function - Prof. Jiax, Study notes of Biology

Download Amino Acids and Proteins: Structure, Classification, Ionization, and Function - Prof. Jiax and more Study notes Biology in PDF only on Docsity! Outline of Today's Lecture Amino!acids Structure Classification Ionization Proteins Peptide!bond Polypeptide Structure Function Homework:!!HW5a!and!HW5b!(chapter!5,!Sapling!Learning)! Amino Acids Aspartate (Asp, D) and Glutamate (Glu, E) are dicarboxylic acids, and are negatively charged at neutral pH These amino acids can form ionic interactions and hydrogen bonds Negatively Charged (Acidic) Amino Acids Side chains are nitrogenous bases which are positively charged at neutral pH These amino acids frequently form ionic interactions as well as hydrogen bonds Lysine (Lys, K): alkylamino group Arginine (Arg, R): guanidinium group Histidine (His, H): imidazole Positively Charged (Basic) Amino Acids This nitrogen has a relatively weak affinity for an H+ and is partly positive at neutral pH Formation of Disulfide Bonds Two!cysteine!side!chains!can!be!cross"linked!by!forming!a! disulfide!bond ("CH2"S"S"CH2")!– the!cysteine!dimer!joined!by!a! disulfide!bond.!is!called!cystine Disulfide!bonds!act!as!atomic!staples!to!stabilize!the!three" dimensional!structures!of!proteins! Oxidation Reduction Cystine Titration Curve for Alanine • Because amino acid is a weak acid, most of it will exist in the protonated form at the beginning of the titration • When concentrations of acid and its conjugate base are equal, the pKa of the species has been reached When = pK1 = 2.3 When = pK2 = 9.7 [+NH3CRHCOOH] [ +NH3CRHCOO-] pI!(isoelectric!point)!=!(pK1 +!pK2)!/2! =!(2.3!+!9.7)!/2!=!6.0 At!pI,!there!exists!only!+NH3CRHCOO" [+NH3CRHCOO-] [NH2CRHCOO-] R R R zwitterion +1 -10 Isoelectric Point (pI) of Amino Acids • Amino!acids!are!always!ionized!in!aqueous!solutions • However,!depending!on!the!pH,!the!net!charge!on!the!molecule! may!be!zero • The!pH!at!which!the!net!charge!on!a!molecule!is!zero!is!called!the! isoelectric!point for!the!molecule!or!the!pI • An!amino!acid!will!have!net!negative!charge if!the!pH!of!the! solution!is!above!its!pI;!it!will!have!net!positive!charge if!the!pH! of!the!solution!is!below!pI Calculation of Isoelectric Point (pI) 1) For free amino acids with nonionizable side chains, the pI is the arithmetic mean of the pKa of its carboxyl group and that of its amino group e.g. for alanine, the pI is 6.0, the average of the pKa of its carboxyl group, 2.3, and the pKa of its amino group, 9.7 2) For free amino acids with charged side chains, the pI is the arithmetic mean of the pKa of the side chain group and the pKa of the !-carbon group with the same charge e.g. for lysine, the pI is 9.8, the average the pKa of the side- chain, 10.54, and the pKa of the !-amino group, 9.06 Peptides, Polypeptides, and Proteins Peptide bond • Peptide bond is the amide bond between two amino acids • Formed by condensation of the !-carboxyl group of one amino acid with the !-amino group of another amino acid (loss of H2O molecule) Peptide Bonds Peptide!bonds!link!amino!acids!in!proteins Polypeptide Chain • Peptide bonds can connect multiple amino acids to make an amino acid polymer (polypeptide chain) • Residue: an amino acid unit in a peptide – the part left over after losing a H from its amino group and an OH from its carboxyl group • Amino (N) terminal end – the end of a peptide with a free !-amino group Carboxyl (C) terminal end – the end of a peptide with a free !-carboxyl group • When an amino acid sequence of a peptide (protein) is displayed, the N terminal end is placed on the left and the C-terminal end on the right e.g. (N) Ser-Gly-Tyr-Ala-Leu (C) Much!of!our!body!is!constructed!from!protein!molecules.!Muscle,! cartilage,!ligaments,!skin!and!hair!" these!are!all!mainly!protein! materials! In!addition!to!these!large!scale!structures!that!hold!us!together,! smaller!protein!molecules!play!a!vital!role!in!keeping!our!body!working! properly! e.g.!hemoglobin,!hormones!(such!as!insulin),!antibodies,!and!enzymes Why are Proteins Important to Us Four Levels of Protein Structure • Primary structure - amino acid linear sequence • Secondary structure - regions of regularly repeating conformations of the peptide chain, such as alpha-helices and beta-sheets • Tertiary structure - the shape of the fully folded polypeptide chain • Quaternary structure - arrangement of two or more polypeptide chains into multisubunit molecule The primary Structure of Proteins The primary structure of a protein represents the linear arrangement of amino acids via peptide bonds. By convention, the sequence is read from N-terminus to C- terminus Primary structure, the amino acid sequence, is specified by genetic information In general, the primary sequence of a protein will dictate its higher order structures–such as secondary, tertiary, and quaternary structures–as well as its function Figure 3-8 Molecular Biology of the Cell (© Garland Science 2008) Antiparallel beta sheets A polypeptide chain that fold back and forth upon itself, with each section of the chain running in the direction opposite to that of its immediate neighbors i.e. strands run in opposite N- to C- terminal directions Parallel beta sheets A polypeptide chain that fold back and forth upon itself, with sections of the chain running in the same direction i.e. strands run in the same N- to C- terminal direction Parallel and Antiparallel beta-Sheets N C N C Tertiary Structure of Proteins • Tertiary structure results from the folding of a polypeptide chain into a closely-packed three-dimensional structure • Amino acids far apart in the primary structure may be brought together • Stabilized primarily by noncovalent interactions (e.g. hydrophobic interactions) between side chains • Disulfide bridges (-S-S-) also part of tertiary structure Adenylate kinase Space"filling!model shows!the!overall! shape!of!a!protein Ribbon!model:!Easy!way!to! visualize!secondary!structures Quaternary Structure • Refers to the organization of subunits in a protein with multiple subunits (polypeptides) • Subunits (may be identical or different) have a defined stoichiometry and arrangement • Subunits are held together by many weak, noncovalent interactions (hydrophobic, electrostatic) Hemoglobin Figure 3-4 Molecular Biology of the Cell (© Garland Science 2008) Noncovalent Bonds Help Proteins Fold Two Classes of Proteins with Respect to Shape Globular!Proteins • Have!polypeptide!chains!that!are!folded!in!a spherical or! rounded!shape • Hydrophobic!interior,!hydrophilic!surface!(usually!water! soluble) • Include!enzymes,!regulatory!proteins,!and!carrier!proteins,!e.g.! hemoglobin • Are!usually!water!soluble Fibrous!Proteins • Have!polypeptide!chains!arranged!in!long!strands! • Provide!mechanical!support! e.g.!keratins:!major!components!of!hair!and!nails collagen:!major!component!of!tendons,!skin,!bones • Are!insoluble!in!water Protein Denaturation • A!protein’s!function!is!intricately!linked!to!its!three"dimensional! structure • Denaturation " disruption!of!native!conformation!of!a!protein,!with! loss!of!biological!activity!by!chemical!or!physical!means • Proteins!can!be!denatured!by!a!variety!of!means,!including!heat,!pH! extremes,!organic!solvents,!chaotropic!agents!(urea,!guanidine! hydrochloride),!and!detergents.!In!each!case,!no!covalent!bonds!are! broken • Denaturing!agents!disrupt!noncovalent!bonding,!resulting!in!loss!of! tertiary!and!quaternary!structure!(sometimes!secondary!structure) Protection: blood!clotting!involves!the!protein!fibrinogen;!the! body!uses!proteins!called!antibodies!to!fight!disease Storage: casein!in!milk!and!ovalbumin!in!eggs!store!nutrients!for! newborn!infants!and!birds;!ferritin,!a!protein!in!the!liver,!stores! iron Regulation: certain!proteins!not!only!control!the!expression!of! genes,!but!also!control!when!gene!expression!takes!place Protein Functions Amino!acids! Classification!of!amino!acids Ionization!of!amino!acids,!!Isoelectric!point!(pI),!!Peptide!bond Protein!structure Primary!structure Secondary!structure Tertiary!structure Quaternary!structure Fibrous!proteins!and!globular!proteins Protein!function Summary of Today’s Lecture