Amino Acids and Proteins

1. Principles of Biochemistry (BCH 3000) Amino Acids and Proteins Dr. Syahida Ahmad Department of Biochemistry Faculty of Biotechnology & Biomolecular Sciences UPM

3. Amino Acids • An organic molecule with carboxyl(-COOH) and amino (-NH2) group • Present in plant and animal cells • 20 -amino acids • Genetically coded for incorporation into proteins • Carbon center (the alpha carbon), surrounded by a H, a carboxyl group, an amino group and side chain (R) • carboxylgroup (-COOH) • Acidic – capable of donating a proton to solution • amino group (-NH2) • Basic – accept proton • R side chains • Have functional groups that are acidic or basic – may donate or accept protons • Only the L-isomers of amino acids are used in building blocks for proteins

7. Ionic forms of Amino Acids • Pure form of 20 -amino acids are white, crystalline and high-melting solids • Additionally, there are two additional amino acids which are incorporated by overriding stop codons. • Selenocysteine (Sec, U) • Pyrrolysine (Pyl, O) • Sarcosine - an unusual amino acid that occurs in nature occasionally. • They are soluble in water and insoluble in organic solvents (e.g. acetone, chloroform and ether) • Amino acids exist as dipolarionic species • They have a positive and negative charge on the same molecule (zwitterions) • Aqueous solutions of amino acids conduct and electric current • Isoelectric point • The pH at which the molecular structure of amino acid has no net charge

8. Sarcosine • Also known as N-methylglycine, is an intermediate and byproduct in glycine synthesis and degradation. • Sarcosine is metabolized to glycine by the enzyme sarcosine dehydrogenase, while glycine-N-methyl transferase generates sarcosine from glycine. • Sarcosine is a natural amino acid found in muscles and other body tissues. • In the laboratory, it may be synthesized from chloroacetic acid and methylamine. • Sarcosine is found naturally as an intermediate in the metabolism of choline to glycine. • Sarcosine is sweet to the taste and dissolves in water. • It is used in manufacturing biodegradable surfactants and toothpastes as well as in other applications.

14. Classification of Amino Acids • The R side chain makes each amino acid chemically and biologically distinct • The R groups vary in size, polarity, charge and chemical reactivity • Thus, amino acids can be divided into classes based on polarity of the side chain • Group I • Amino Acids with Nonpolar, Hydrophobic Side Chains • Group II • Amino Acids with Polar, Uncharged Side Chains • Group III • Amino Acids with Polar, Charged Side Chains

17. Amino Acids Online Games http://www.wiley.com/legacy/college/boyer/0470003790/animations/acideroids/acideroids.htm

18. Monosodium Glutamate - The Tase of Umami • Umami (Japan) – delicious or savory • How “glutamate” is in our food? • MSG • Accent (US), Aji-No-Moto (Japan) • Flavour enhancer in soups, stews, sauces and snacks • Also contained in common foods like canned soups, frozen dinners, junk foods and instant meals • Chinese restaurant syndrome • Individual allergic to MSG • Weakness, facial flushing & pressure, sweating, headache, numbness around the mouth, and rapid heart rate with skipping beats • Alternative: Inosine 5’-monophosphate (IMP) and guanosine 5’-monophosphate (GMP)

20. Polypeptides and Proteins • Two amino acids can be link together by formation of an amide or peptide bond • Link at carboxyl group (C-terminus) of one amino acid with the amino group (N-terminus) of the other to yield dipeptide (condensation) • Peptides • Di-, tri-, tetra-, penta-, hexa-, hepta-, octa-, nona-, deca • Polypeptides • 10-100 amino acids • Proteins • >100 amino acids

22. Protein Functions • Enzymes • Amylase and DNA polymerase • Structural Proteins • Collagen and keratin • Immune Proteins • Antibodies • Transport and Storage Proteins • Lipoprotein • Regulatory and Receptor Proteins • G proteins • Muscle Contraction and Mobility Proteins • Actin and myosin – components of contractile system of skeletal muscle • Dynein – components of microtubules of flagella and cilia

25. Structural Properties of Proteins • Molecular Mass • Daltons • Protein Composition and Behavior • Monomeric, oligomeric and multisubunit • Simple proteins • Conjugate proteins – have a prosthetic group • Globular proteins • Water soluble, more dynamic and flexible – presents in biological fluids (blood) or cytoplasm • play a role in transport, immune protection and catalysis • Amino acids residues with polar and charged R groups • Fibrous proteins • Water insoluble, rigid conformation and have high tensile strength – structural proteins collagen and keratin • Amino acids residues with nonpolar R groups • Silk

30. Proteins Structure • Functional activity of a protein is depends on its folding into 3-D structure – native conformation • Primary structure • Sequence of amino acid residues in a protein • Secondary structure • Localized regions of primary sequence fold into regular and repeated structure – e.g. -helix and -helix sheets • Tertiary structure • Secondary structure of a protein interact and pack into a compact globular unit • Quaternary structure • Association of two or more polypeptide chains to form a multisubunit protein molecule