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Concept 5.4: Proteins have many structures, resulting in a wide range of functions • Proteins account for more than 50% of the dry mass of most cells • Protein functions include structural support, storage, transport, cellular communications, movement, and defense against foreign substances Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Table 5-1 Polypeptides • Polypeptides are polymers built from the same set of 20 amino acids • A protein consists of one or more polypeptides Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Amino Acid Monomers • Amino acids are organic molecules with carboxyl and amino groups • Amino acids differ in their properties due to differing side chains, called R groups Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 5-UN1 carbon Amino group Carboxyl group Fig. 5-19 Protein Structure and Function Groove Groove (a) A ribbon model of lysozyme (b) A space-filling model of lysozyme • A functional protein consists of one or more polypeptides twisted, folded, and coiled into a unique shape • The sequence of amino acids determines a protein’s three-dimensional structure • A protein’s structure determines its function Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 5-20 Antibody protein Protein from flu virus Four Levels of Protein Structure • The primary structure of a protein is its unique sequence of amino acids • Secondary structure, found in most proteins, consists of coils and folds in the polypeptide chain • Tertiary structure is determined by interactions among various side chains (R groups) • Quaternary structure results when a protein consists of multiple polypeptide chains Animation: Protein Structure Introduction Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 5-21 Primary Structure Secondary Structure pleated sheet +H N 3 Amino end Examples of amino acid subunits helix Tertiary Structure Quaternary Structure • Enzymes are a type of protein that acts as a catalyst to speed up chemical reactions • Enzymes can perform their functions repeatedly, functioning as workhorses that carry out the processes of life Animation: Enzymes Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 5-16 Substrate (sucrose) Glucose OH Fructose HO Enzyme (sucrase) H2O Fig. 5-17 See book chapter 5 Nonpolar Glycine (Gly or G) Valine (Val or V) Alanine (Ala or A) Methionine (Met or M) Leucine (Leu or L) Trypotphan (Trp or W) Phenylalanine (Phe or F) Isoleucine (Ile or I) Proline (Pro or P) Polar Serine (Ser or S) Threonine (Thr or T) Cysteine (Cys or C) Tyrosine (Tyr or Y) Asparagine Glutamine (Asn or N) (Gln or Q) Electrically charged Acidic Aspartic acid Glutamic acid (Glu or E) (Asp or D) Basic Lysine (Lys or K) Arginine (Arg or R) Histidine (His or H) Amino Acid Polymers • Amino acids are linked by peptide bonds • A polypeptide is a polymer of amino acids • Polypeptides range in length from a few to more than a thousand monomers • Each polypeptide has a unique linear sequence of amino acids Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 5-18 Peptide bond (a) Side chains Peptide bond Backbone (b) Amino end (N-terminus) Carboxyl end (C-terminus) Four Levels of Protein Structure • Primary structure, the sequence of amino acids in a protein, is like the order of letters in a long word • Primary structure is determined by inherited genetic information Animation: Primary Protein Structure Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 5-21a Primary Structure 20 127 ways to make a chain 127 amino acids long -Primary structure all determined by genetics 1 +H 5 3N Amino end 10 Amino acid subunits 15 20 25 • The coils and folds of secondary structure result from hydrogen bonds between repeating constituents of the polypeptide backbone • Typical secondary structures are a coil called an helix and a folded structure called a pleated sheet Animation: Secondary Protein Structure Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 5-21c Silk protein in spider’s web Secondary Structure β pleated sheet Examples of amino acid subunits α helix Structural protein in hair H, O, N all have an affinity for each other -Each hydrogen bond is weak, but together very strong Fig. 5-21d Hydrogen bonds makes each fiber stronger than a steel strand of same weight Abdominal glands of the spider secrete silk fibers made of a structural protein containing pleated sheets. The radiating strands, made of dry silk fibers, maintain the shape of the web. The spiral strands (capture strands) are elastic, stretching in response to wind, rain, and the touch of insects. • Tertiary structure is determined by interactions between R groups, rather than interactions between backbone constituents • These interactions between R groups include hydrogen bonds, ionic bonds, hydrophobic interactions (hide side chains away from water at core of protein), and van der Waals interactions • Strong covalent bonds called disulfide bridges may reinforce the protein’s structure Animation: Tertiary Protein Structure Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 5-21f Hydrophobic interactions and van der Waals interactions Polypeptide backbone Hydrogen bond Disulfide bridge Ionic bond Fig. 5-21e All caused by R-group interactions Tertiary Structure Quaternary Structure • Quaternary structure results when two or more polypeptide chains form one macromolecule • Collagen is a fibrous protein consisting of three polypeptides coiled like a rope (40% of protein in humans, connect skin tissue, bone, tendons, and ligaments) • Hemoglobin is a globular protein consisting of four polypeptides: two alpha and two beta chains (each having heme which binds to oxygen) Animation: Quaternary Protein Structure Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Fig. 5-21g Polypeptide chain Chains Iron Heme Chains Hemoglobin Collagen