8/20/2012 H C OH H R. Proteins

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1 Proteins Rubisco monomer = amino acids 20 different amino acids polymer = polypeptide protein can be one or more polypeptide chains folded & bonded together large & complex 3-D shape hemoglobin Amino acids Structure central carbon amino group carboxyl group (acid) R group (side chain) variable group confers unique chemical properties to each amino acid H O H N C C OH H R amino = NH 2 acid = COOH Effect of different R groups: Nonpolar amino acids nonpolar & hydrophobic 1

2 Effect of different R groups: polar amino acids polar or charged & hydrophilic Building proteins Peptide bonds covalent bond between NH 2 (amine) of one amino acid & COOH (carboxyl) of another C N bond dehydration synthesis H 2 O peptide bond Building proteins Polypeptide chains have direction N-terminus = NH 2 end C-terminus = COOH end repeated sequence (N-C-C) is the polypeptide backbone 2

3 Sulfur containing amino acids form disulfide bridges covalent cross links betweens sulfhydryls stabilizes 3-D structure H-S S-H Primary (1 ) structure Order of amino acids in chain amino acid sequence determined by gene (DNA) slight change in amino acid sequence can affect protein s structure & its function Secondary (2 ) structure Local folding folding along short sections of polypeptide interactions between adjacent amino acids H bonds weak bonds between R groups forms sections of 3-D structure -helix -pleated sheet 3

4 Tertiary (3 ) structure Whole molecule folding interactions between distant amino acids hydrophobic interactions cytoplasm is water based, nonpolar amino acids cluster away from water H bonds & ionic bonds disulfide bridges covalent bonds between sulfurs in sulfhydryls (S H) anchors 3-D shape Quaternary (4 ) structure More than one polypeptide chain bonded together only then does polypeptide become functional protein hydrophobic interactions collagen hemoglobin Conjugated proteins - Proteins that have a nonproteinaceous prosthetic group attached ex. Hemoglobin contains iron which alters the properties of the protein (increases affinity for O 2 ) 4

5 Protein structure 1 amino acid sequence peptide bonds determined by DNA 2 R groups H bonds R groups hydrophobic interactions disulfide bridges (H & ionic bonds) 3 multiple polypeptides hydrophobic interactions 4 Protein denaturation Unfolding a protein conditions that disrupt H bonds, ionic bonds, disulfide bridges temperature ph salinity alter 2 & 3 structure alter 3-D shape destroys functionality some proteins can return to their functional shape after denaturation, many cannot Metabolism Chemical reactions of life forming bonds between molecules dehydration synthesis synthesis anabolic reactions breaking bonds between molecules hydrolysis digestion catabolic reactions 5

6 Energy & life Organisms require energy to live where does that energy come from? coupling exergonic reactions (releasing energy) with endergonic reactions (needing energy) digestion + + energy synthesis + + energy Endergonic vs. exergonic reactions exergonic endergonic - energy released - energy invested - digestion -synthesis +G -G G = change in free energy = ability to do work Reducing Activation energy Catalysts reducing the amount of energy to start a reaction uncatalyzed reaction catalyzed reaction NEW activation energy reactant product 6

7 Lock and Key model Simplistic model of action substrate fits into 3-D structure of s active site like key fits into lock substrate active site products Induced fit model More accurate model of action 3-D structure of fits substrate substrate binding cause to change shape leading to a tighter fit conformational change bring chemical groups in position to catalyze reaction Factors Affecting Enzyme Function Enzyme concentration Substrate concentration Temperature ph Salinity Activators Inhibitors 7

8 Compounds which help s Activators cofactors non-protein, small inorganic compounds & ions Mg, K, Ca, Zn, Fe, Cu bound within molecule cos non-protein, organic molecules bind temporarily or permanently to near active site many vitamins NAD (niacin; B3) FAD (riboflavin; B2) Co A Fe in hemoglobin Mg in chlorophyll Cooperativity Substrate acts as an activator substrate causes conformational change in induced fit favors binding of substrate at 2 nd site makes more active & effective hemoglobin Hemoglobin 4 polypeptide chains can bind 4 O 2 ; 1 st O 2 binds now easier for other 3 O 2 to bind a. Competitive inhibitors inhibitors that resemble the shape of the normal substrate and compete for the active site and block it a. Noncompetitive inhibitors inhibitors that do not directly compete with substrate at active site bind to another part of causing it to change shape so active site cannot bind substrate 8

9 Allosteric regulation Conformational changes by regulatory molecules inhibitors keeps in inactive form activators keeps in active form Conformational changes Allosteric regulation Feedback Inhibition Regulation & coordination of production product is used by next step in pathway final product is inhibitor of earlier step allosteric inhibitor of earlier feedback inhibition no unnecessary accumulation of product A B C D E F G X allosteric inhibitor of 1 Feedback inhibition threonine Example synthesis of amino acid, isoleucine from amino acid, threonine isoleucine becomes the allosteric inhibitor of the first step in the pathway as product accumulates it collides with more often than substrate does isoleucin e 9

10 Industrial Uses of Enzymes Enzymes have long been used for industrial purposes Leather tanning proteases are used to soften hides and remove hair Brewing s in barley grains at germination are used to convert stored starch to sugars that can be fermented by yeast Biotechnology restriction s are frequently used in genetic engineering Lactose-free milk some people are lactoseintolerant (do not produce lactase in pancreatic juices) cannot digest milk and milk products Lactase is obtained from bacteria Milk and milk products are treated with lactase before consumption to remove lactose 10

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