14.9-14.10

By Kaitlin Kodack

14.9- What is the secondary structure of a protein?

• Three kinds of secondary structure: α-helix, β-pleated sheet & random coil

• Repeating patterns in a protein backbone• Most common are α-helix and β-pleated sheet• Don’t have a repeating pattern, they are

called random coils.• Helix is a protein chain that is twisted into a

right handed coiled spring.• Shape of the helix is maintained by many

intramolecular hydrogen bonds between the backbone.

• β- sheet structures can occur between molecules when polypeptide chains run parallel or antiparallel.

• Hydrogen bonding occurs between –C=O and H-N- groups & between R groups on side chains.

• Most proteins, like globular ones, consist of certain portions of their molecules. The rest have a random coil.

• Globular proteins contain all three secondary structures in different parts of their molecules.

• Keratin is a fibrous protein found in hair, nails, horns and wool. Is the one protein that has mainly an α-helix structure.

• Silk is made from fibroin, another fibrous protein.

• Repeating pattern classified as a secondary structure is the extended helix of collagen.

• Collagen is the structural protein of connective tissue in which it provides support and elasticity– Bone, cartilage, tendon, blood vessel, skin

• The collagen is the most abundant protein in humans. – Makes up about 30% by weight of all the body’s

protein.• Primary structure of collagen helped make

the extended helix possible.• Each strand repeats the pattern, Gly-X-Y;

every third amino acid in the chain is glycine.• Glycine has the shortest side chain of all

amino acids.• 1/3 of the X amino acid is proline and Y is

often hydroxyproline.

14.10- What is the tertiary structure of a protein?

• Three-dimensional arrangement of atoms in a protein.

• Includes interactions of the side chains.• Tertiary structures are stabilized in 5

ways– Covalent bonds– Hydrogen bonding– Salt bridges– Hydrophobic Interactions– Metal Ion Coordination

Covalent Bonding• Most often used is the disulfide bond.• Amino acid cysteine is converted to

dimer cystine.• When cysteine residue is in one chain

and another cysteine residue is in another chain, disulfide bond makes a covalent bond and binds the chains together.

Hydrogen Bonding

• Between backbone -C=O and -N-H groups.

• Between polar groups on or between side chains and peptide backbone.

Salt Bridges• Also called electrostatic attractions.• Occurs between two amino acids

with ionized side chains- between a acidic amino acid and a basic amino acid chain.

• Held together by simple ion-ion attraction

Hydrophobic Interactions• Polar groups turn outward (toward

aqueous solution) and nonpolar turns inward ( away from water molecules)

• Nonpolar interact with each other, not in water regions.

• Weaker than hydrogen bonding or salt bridges.

• Acts over large surface areas and can stabilize a loop or some other tertiary structure.

Metal Ion Coordination• Two chains with same charge can

repel each other, but they can also be linked by a via metal ion.

• Ex: two glutamic acid side chains would attract magnesium ion forming a bridge.

• Human body requires certain trace minerals- necessary component of proteins.

• Side chains of some proteins can fold one way.

• Long polypeptides can fold numerous ways.

• Chaperone is a protein that helps other proteins to fold in to biologically active conformation and enables partially denatured proteins to regain their biologically active conformation.

The End