1. Sections 14.9, 14.10, 14.11, and 14.12 Hannah Nowell and Jenny Sulouff

2. Secondary Structure of a Protein 14.9 Random coil Wheat α helix

3. Secondary structure  Repeating patterns created by folds  Two most common  α- helix  β-pleated  1940s -proposed by Linus Pauling and Robert Corey  Hydrogen bond between the backbone –C=O and N-H-  Distinguishes a secondary structure and a tertary structure

4. Secondary Structure (con.)  A R group can replace the hydrogen bonding  On side chains  Hydrogen bond between the backbone –C=O and N-H-  Distinguishes a secondary structure and a tertiary structure  A R group can replace the hydrogen bonding  On side chains

5. Random Coil  Does not show any signs of a repeating pattern  Main structure of a protein  Most proteins are not mainly α- helix or β-pleated  The remainder is a random coil  Especially common in globular proteins  Mostly soluble in water  Mainly only used for nonstructural purposes

6. α-helix  Resembles a right-handed spring  A helix  The twists are kept by intramolecular hydrogen bonds  Between the backbone –C=O and H-N-  Hydrogen bond between the –C=O and H-N-  Maintain the helical shape  -C=O point down  H-N-point up  All amino acid side chains point away from the helix

7. β- pleated sheet  The alignment of the protein chains are maintained by intermolecular or intramolecular hydrogen bonds  When peptide chains run parallel  N- terminal ends are on one side  Or when they are antiparallel  Neighboring N-terminal ends are alternating sides  Can occur when a hairpin structure is formed when a polypeptide makes a U-turn  Pleated sheet is antiparallel

8. β- pleated sheet (con.)  Microcrystals are deposited in the fiber axis, during the formation of β-pleated sheets  Can occur when a hairpin structure is formed when a polypeptide makes a U-turn  Pleated sheet is antiparallel  Microcrystals are deposited in the fiber axis, during the formation of β-pleated sheets  Microcrystals are found in Spider silk and silkworm silk  Allow the silk to be super strength and toughness  Unmatched by synthetics

9. Fibrous protein  β-pleated sheets  Keratin  Hair  Fingernails  Horns  Wool  Fibroin  Silk

10. Extended Helix  Made of collagen  Repeated units  The third amino acid is a glycine  Shortest of all the amino acid chains  Protein of connective tissues; bones, skin, tendons, etc.  Gives protein strength and elasticity  30% of the body’s protein

11. Tertiary Structure of a Protein 14.10

12. Tertiary Structures  3D arrangement of the atoms in a protein  Refers to the conformation or shape that is different for every protein molecule  Interactions between the amino acids side chains  There are five ways to stabilize a tertiary structure; covalent bonds, hydrogen bonding, salt bridges, hydrophobic interactions, metal ion coordination

13. Covalent bonds and hydrogen bonding  Covalent bonds  Most commonly used  Disulfide bond  Formation of a disulfide bond allows covalent linkage, which binds the two chains together  Hydrogen bonding  Between polar chains  On side chains  between side chains and a peptide backbone

14. Salt bridges  Salt bridges  Also called electrostatic attractions  Between a acidic amino acid (-COO - ) and a basic amino acid (-NH 3 + )  It is a simple ion-ion attraction

15. Hydrophobic Interactions  Hydrophobic Interactions  Aqueous solution  Polar groups turn outward, towards aqueous solvent; Non-polar turn inward, away from water molecules  Series of Hydrophobic interactions occur  The hydrophobic bond is weaker then the hydrogen bonding and salt bridges  Acts over large areas  Can stabilize a loop and other tertiary structures

16. Metal ion coordination  Same charge side chains linked by a metal ion  Ex:  Two glutamic acid side chains are attracted to magnesium ion  Forms a bridge  Human body needs selected trace minerals for components of proteins

17. Chaperones  Biologically active conformation is caused by a protein that helps other proteins  Helps stabilize polypeptide chains  prevents folds that would cause biologically inactive molecules

18. Quaternary Structure of a Protein 14.11

19. Quaternary structure  Spatial relationship along with the interactions of subunits in a protein that consists of multiple polypeptide chains  Determines how subunit are organized  One of the four levels of protein structures  Hydrogen bonds hold and pack the subunits together  Along with salt bridges and hydrophobic interactions hold and pack them together

20. Hemoglobin  Made of four chains, chains are called globin  Two identical α-chains which consist of 141 amino acid residues  Two identical β-chains which consist of 146 residues  Chains containing non-amino acids are called conjugated proteins  The non-amino acid part is called a prosthetic group

21. Collagen  High organization of subunits  Triple helix is called tropocallagen  Found in only fetal or young connective tissues  As it ages it organizes into fibrils cross link  Insoluble  Cross linking consist to covalent bonds  Link together in two lysine residues  Ex. Of tertiary structures

22. Integral membrane proteins  Traverse completely or partially into a membrane bilayer  1/3 rd of all proteins  The outer surface is nonpolar  Interacts with lipid bilayer  Two quaternary structures  6-10 α-helices that cross the membrane  Β-barrels consisting of 8, 12, 16, or 18 β-sheets that are antiparallel

23. How Proteins are Denatured 14.12

24. What is Denaturation? Any type of chemical or physical agent that can destroy the structure of a protein – The structure becomes a random shape protein – The agents do not break the peptide bonds so the sequence of amino acids remain the same. Only effects a secondary, tertiary, or quaternary structures not a primary structure – Denaturing a primary structure would cause a change in the arrangement of amino acids

26. Protein Denaturation Denaturing AgentAffected Regions HeatH bonds DetergentsHydrophobic regions Acids, basesSalt bridges, H bonds SaltsSalt bridges Reducing agents and Heavy metals Disulfide bonds AlcoholHydration layers

27. Reversible Denaturation  If the change in the protein is only minor than denaturizing can be reversed.  By chaperones  Not all denaturation can be reversed.  Ex.  A hard boiled egg can not be un boiled.