CHAPTER 14 NOTESSections 14.9, 14.10, 14.11, and 14.12

Hannah Nowell and Jenny Sulouff

Secondary Structure of a Protein14.9

Random coilWheat

α helix

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

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

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

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

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

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

Fibrous protein

β-pleated sheets

Keratin Hair Fingernails Horns Wool

Fibroin Silk

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

Tertiary Structure of a Protein14.10

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

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

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

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

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

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

Quaternary Structure of a Protein14.11

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

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

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

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

How Proteins are Denatured14.12

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

Protein Denaturation

Denaturing Agent Affected RegionsHeat H bondsDetergents Hydrophobic regionsAcids, bases Salt bridges, H bondsSalts Salt bridgesReducing agents and Heavy metals

Disulfide bonds

Alcohol Hydration layers

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.