Overview of Protein Secondary, Tertiary, and Quaternary Structures

1. Sections 14.9, 14.10, 14.11, and 14.12 Chapter 14 notes Hannah Nowell and Jenny Sulouff

2. Random coil Wheat Secondary Structure of a Protein14.9 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 Protein14.10

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 (-NH3+) • 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 Protein14.11

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 • 1/3rd 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 Denatured14.12

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

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.