بسم الله الرحمن الرحيمUMM AL-QURQ UNIVERSITYFaculty of MedicineDep. Of BIOCHEMISTRY PROTEINS AND AMINO ACIDS 
WHAT ARE PROTEINS ?: • Proteins are polymers of the bifunctional monomer, amino acids. • The amino group from one amino acid attached to the carboxylic group of the adjacent amino acid, the resulting link between them is an amide link called (peptide bond). • The resulting structure is called (Dipeptide). • Similarly we can have Tri, Tetra, Penta … Peptides. • Many amino acids joined in this fashion is called (Polypeptide). • In this reaction, water is released. In a reverse reaction, the peptide bond can be cleaved by water (hydrolysis). • Peptide bonds can be hydrolyzed by boiling with strong acids and bases, and by certain enzymes (e.g. trypsin, chymotrypsin).
OO ║ ║ H2NC------HNCOH CC R1 R2 Peptide bond H2O
Dipeptide: • A peptide is named from the free amine (NH3+) using -yl endings for the names of the amino acids. • The last amino acid with the free carboxyl group (COO-) uses its amino acid name. • Example: Glycine + Alanine Glycylalanine + H2O
Primary Structure: • A polypeptide containing 50 or more amino acids is called a protein. • The primary structure of a protein is the sequence of amino acids in the peptide chain. • Even a slight change in primary structure can affect a protein’s conformation and ability to function. • Insulin: Was the first protein to have its primary structure determined.
Secondary Structure Alpha Helix • The secondary structures of proteins indicate the arrangement of the polypeptide chains in space. • The alpha helix is a three-dimensional arrangement of the polypeptide chain that gives a shape like a coiled telephone cord. • The coiled shape of the alpha helix is held in place by hydrogen bondsbetween the amide groups and the carbonyl groups of the a.as. along the chain. Pleated Sheet • Holds proteins in a parallel arrangement with hydrogen bonds. • Has R groups that extend above and below the sheet. • Is typical of fibrous proteins such as silk. Triple Helix • Consists of three alpha helix chains. • Contains large amounts glycine, proline, hydroxyproline and hydroxylysine that contain –OH groups for hydrogen bonding. • Is found in collagen, connective tissue, skin, tendons, and cartilage.
Tertiary Structure • Gives a specific overall shape to a protein. • Involves interactions and cross links between different parts of the peptide chain. • Is stabilized by • Hydrophobic and hydrophilic interactions • Salt bridges • Hydrogen bonds • Disulfide bonds
the folding of residues 10-55 of Staphylococcus aureus protein A which form a 3-helix bundle structure.
Quaternary Structure • The quaternary structure contains two or more tertiary subunits. • Hemoglobin contains two alpha chains and two beta chains. • The heme group in each subunit picks up oxygen for transport in the blood to the tissues. Qaternary structure of the multisubunit protein (Hb)
Fibrous Proteins • Fibrous proteins have high a-helix or b-sheet content. Most are structural proteins. • Examples include: Collagen: • Principal component of connective tissue (tendons, cartilage, bones, teeth). • Proline content is unusually high • Proline and HydroxyProline together make 30% of residues. Elastin: • Abundant in ligaments, lungs, artery walls, skin. • Provides tissues with ability to stretch in all directions without tearing. Keratin: Found in hair, fingernails, claws, horns and beaks.
Globular proteins:A large number of atoms rolled into relative small volumes through folding • Water-soluble • Most proteins which occur in the plasma are of globular nature. • they are approximately spherical in shape, or consist of several different lobes (domains). • Hemoglobin is an example of a tetramer Globular protein.
Isoelectric point of proteins • Is the pH-value of a solution at which the total net charge of a protein equals zero. The charge is positive below pI, while the charge is negative above pI
Protein Hydrolysis • Splits the peptide bonds to give smaller peptides and amino acids. • Occurs in the digestion of proteins. • Occurs in cells when amino acids are needed to synthesize new proteins and repair tissues.
Denaturation • Denaturation involves the disruption of bonds in the secondary, tertiary and quaternary protein structures. • Denaturation of protein will not affect the primary structure. • Denatured proteins are functionally inactive. • Heat and organic compounds break apart H bonds and disrupt hydrophobic interactions. • Acids and bases break H bonds between polar R groups and disrupt ionic bonds. • Heavy metal ions react with S-S bonds to form solids. • Agitation such as whipping stretches chains until bonds break.
ABDULLATIF TAHA ABDULLAMSc. BIOCHEMISTRY سبحانك لا علم لنا إلا ما علمتنا * إنك أنت العليم الحكيم 0