Lecture 3: Protein Structure & Function
Lecture 3: Protein Structure & Function 200001
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This 8 page Class Notes was uploaded by Olivia Sutton on Friday February 19, 2016. The Class Notes belongs to 200001 at Boston College taught by Danielle Taghian in Spring 2016. Since its upload, it has received 14 views. For similar materials see Molecules and Cells in Biology at Boston College.
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Date Created: 02/19/16
Lecture 3: Protein Structure and Function January 27, 2016 Structure of Amino Acids Non ionized form is the most common form H2N (amino group) COOH (carboxyl group) H – hydrogen atom R – side chain In water (pH 7) Amino groups ionize to NH3+ and Carboxyl group ionizes to COO The higher the pH, the more protons you lose o pKa increases; not good if it goes past 9.0 Some acids completely ionize completely in water Carbon atoms are designated alpha and beta o Alpha carbon: C that always bonds to amino and carboxyl groups o Beta carbon: first carbon on attached R group In pH 7, Lysine (NH3+ R group) could form a hydrogen bond or an ionic bond (salt bridge) ▯ ▯ ▯ ▯ ▯ ▯ ▯ ▯ ▯ ▯ Amino acid Rgroups differ in electronegativity When atoms of different electronegativity are bonded, they form polar, water soluble molecules Nonpolar when electronegativity of Hydrogen and Carbon are the same In organic chemistry, electrons can be spread past their electron cloud Lysine is positively charged while Aspartate is negatively charged The 20 major amino acids differ only in the variable side chain or Rgroup attached to the central carbon o Groups differ in their size, shape, reactivity, and interactions with water and other molecules ▯ ▯ ▯ ▯ ▯ The Nature of Side Chains If given a structural formula for an amino acid, determine the amino acid type by asking three questions 1. Does the side chain have a NEGATIVE charge? a. If yes, it has lost a proton, so its acidic 2. Does the side chain have a POSITIVE charge? a. If yes, it gains a proton, so its basic 3. If the side chain has no charge, does it have an OXYGEN atom? a. If yes, the highly electronegative oxygen or nitrogen will result in a polar covalent bond, so it ends up being uncharged and polar If the answer to all 3 questions are no, then you’re looking for a nonpolar amino acid! ▯ ▯ Why these 20 Amino Acids? The set of 20 amino acids found within the standard genetic code is the result of considerable natural selection. May represent a largely global optimum, such that any aqueous biochemistry would use a very similar set 20 is the minimum number that provides enough specificity in the Rgroups that we need ▯ ▯ Condensation/Hydrolysis Reactions Monomers polymerize through condensation reactions, which releases a water molecule Hydrolysis is when water reacts with a polymer to release a monomer ▯ ▯ The Peptide Bond Condensation reactions bond the carboxyl group of one amino acid to the amino group of another Has double bond characteristics where electrons can switch places (amide bond) o Electrons shared between carbonyl group ad peptide bond offer some char The two groups that flank the amide bond can create hydrogen bonds There is some rotation of bonds around alpha carbon: Why alpha acids vs. beta acids? o Only alpha amino acids can form secondary structures o Must posses a hydrogen atom in the alpha position to avoid steric hindrance when folding Why amide bonds? o Amide bonds are planar, which allows intrastrand Hbonding o Are also chemically stable ▯ ▯ ▯ ▯ ▯ ▯ ▯ ▯ ▯ ▯ ▯ ▯ (Carboxyl Group + Amino Group = Peptide Bond) ▯ ▯ ▯ ▯ Protein structure Primarily built up based on domains Has four levels of structures ▯ ▯ Primary Structure Is the protein’s unique sequence Essential to elucidating the protein’s function (e.g catalytic, structural) Amino acid sequence is the link between the digital code within genes and the structure of the proteins Polypeptide: flexible and has directionality, and its side chains extend from peptide backbone ▯ ▯ ▯ ▯ The Power of One Because amino acid Rgroups affect a polypeptide’s size, shape, chemical reactivity, and interactions with water, just ONE amino acid change can radically alter protein function Example: Sickle Cell o Hemoglobin tends to crystallize when Glutamate is changes to Valine ▯ ▯ Secondary Structure The secondary structure is the local conformation of the polypeptide chain Depends on the primary structure Is formed by hydrogen bonds o Occurs between the carbonyl group of one amino acid and the amino group of another The most common location of the alpha helix is along side the outside of the protein In the alpha helix, the CO group of residue n forms a hydrogen bond with the NH group of the residue n + 4 Each 360 turn = 3.6 aa. The peptide bond of every 4 aa interacts via Hbonds The Hbonds are parallel to the axis of the alpha helix, whereas the aa side chains are perpendicular ▯ ▯ Beta Turns Allows the peptide chain to reverse direction Carbonyl C of one residue is Hbonded to the amide proton of a residue three residues away Proline and Glycine are prevalent in beta turns Beta Turn Tertiary Structure Results from between Rgroups or Rgroups and the peptide backbone o Caused the backbone to bend and fold o Bending and folding contributes to the distinctive threedimensional shape of the polypeptide Rgroup interactions include o Hydrogen bonds o Hydrophobic interactions o Van der Waals interactions o Covalent disulfide bonds o Ionic bonds Quaternary Structure Some proteins contain several polypeptide subunits Bonding of two or more subunits produces the quaternary structure ▯ ▯
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