Overview: Building Blocks of Proteins - Amino Acid Composition, Functional Groups, and Polymer Formation

1. Overview Building blocks of proteins (i) amino acid - composition/functional groups (ii) different amino acids polymer formation of amino acids proteins Function of proteins Classification/ structure (i) primary/ secondary/ tertiary Proteins function as an enzyme Hemoglobin and myglobin

2. What are Proteins? • relatively large organic compounds made of amino acids • Perform variety of functions • The blueprint of cells (genes) defines the a particular protein and its function. • Amino Acids • Building block of proteins • Contains: Amino and carboxyl group – functional groups • > contributes to the behavior of the molecule • R group attached to alpha carbon • > determines chemical properties (hydrophilic, hydrophobic) • 300 aa occur in nature, only 20 occur in proteins

3. most biochemistry occurs in the physiological pH range near neutrality. At this pH most amino acids exist as Zwitterions

4. Amino acids are classified according to their capacity to interact with water. > 4 classes

5. Neutral Non-polar> contain hydrocarbon R group > neutral - R group does not bear +ve or –ve charge > non polar – poorly react with water; hence have a role in maintaining the 3-D structure Neutral Polar > hydrophilic- hydroxyl group enables hydrogen bonding that easily interacts with water.

6. 3. Acidic Amino Acid (eg. aspartate, glutamate) > Have side chains with carboxylate groups which are –vely charged at physiological pH 4. Basic Amino Acids (eg. lysine, arginine, histidine > Bears a +ve charge at physiological pH.

7. Peptide Bond Formation Amino acid molecules link > peptides form - dipeptide, tripeptide …. Facilitated by peptide bonds - occurs b/w amino group of one amino acid and carbonly carbon of another Reaction is called dehydration (a water molecule removed is removed Amino acid polymers longer than 50 aa > PROTEINS

8. A peptide bond is a chemical bond formed between two molecules : when the carboxyl group of one amino acid reacts with the amino group of the other amino acid >>>>>>>releasing a molecule of water (H2O).

9. Function of proteins Catalysis: acts as enzymes and regulate chemical reaction in biological systems. Nearly all known enzymes are proteins Transport & Storage: carriers of molecules or ions across membranes or between cells. E.g- hemoglobin carries O2 to tissues from lungs Immune Protection- antibodies

10. Coordinated motion muscle-major component is proteins (myosin and actin. Structural forms structural network of various part of the body. Eg. Collagen (fibrous) bones & keratin in skin, hair, nail. Regulatory- hormones regulate physiological process, growth, development & response to nervous system

11. Protein Classification 2 major groups based on their shape (i) Fibrous long rod shaped molecules; insoluble in water - serve structural roles e.g Keratin- hair, nails, skin (ii) Globular compact spherical molecules; water soluble - function as enzymes Protein can also be classified as: Simple- contain only amino acids e.g. keratin and serum albumin conjugated- simple + non protein component - Non protein component is called the prosthetic group

12. Protein Structure Primary The specific sequence of aa which also determines the ultimate conformation Sequence not random and specified by inherited genetic information Slight change can affect conformation; hence its function

13. 2. Secondary Refers to the spatial arrangements of aa that are near one another in a liner sequence Are repeated twisting and folding of these aa. Occurs because of H-bonding (b/w CO &NH groups) at regular intervals (along the polypeptide backbone) Weak H-bond repeated several times support/stabilize a particular shape. E.g. alpha helix and beta sheet

14. Common 2º encountered in globular class • Formation is spontaneous and stabilized by H-bond b/w amide N and carbonyl C of peptide bonds spaced 4 residues apart • Rod like structure –tightly coiled polypeptide main chain forms the inner part of the core and side chains extended outward like a helix • 3.6 residues per turn Alpha helix

16. (ii) ß-sheet • Is a sheet (not a rod) • Polypeptide chain is fully extended • Stabilized by H-bond between CO and NH groups in different polypeptide chains

18. Tertiary Interaction b/w side chains (R groups) 2º structure- 3-D structure (distinct domains) H-bond, ionic bonds and van der Waals interactions stabilize the 3º structure -all weak but cumulative effect Further strengthening-strong covalent bond > Disulphide bridges

19. Quaternary Two or more polypeptides aggregate into one functional molecule. E.g. Collagen, a fibrous protein-triple helix Hemoglobin, globular protein -4 polypeptides (of 2 kinds)

20. Protein folding assisted my proteins called Chaperonins > Physical and chemical factors important to maintain the 3-D structure: pH Salt concentration Temperature

21. Study Questions • What are proteins? • Draw and label an amino acid? • What are the 4 classes of proteins classified into? • Distinguish between proteins and peptides? • Illustrate how an amino acid is joined together? • Explain why peptide bond is rigid and planar? • Distinguish between primary, secondary, tertiary and quarternary structures? • Compare and contrast alpha helix and beta sheet? • Differentiate between the following: • Fibrous and globular? • Simple and conjugate proteins • Apoproteins and holoproteins