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The Chemistry of Villin Gary Benz and Claudia Winkler The Chemistry of Villin • Villin is a protein • Proteins are macromolecules (polymers) formed by a defined sequence of small similar molecules (monomers) of amino acids • Amino acids are organic compounds containing at least one amino group (NH3) and one carboxyl group (-COOH). • 20 different amino acids make up all proteins The amino-acid alphabet • Biologists represent each amino acid with a capital letter • For instance: – D=Aspartic Acid, E=Glutamic Acid, F=Phenylalanine, K=Lysine, A=Alanine, V=Valine, F=Phenylalanine • All amino acids are made of 4 elements: Carbon, Hydrogen, Oxygen, Nitrogen. Two also contain Sulfur. Villin’s Single Chain • Biologists describe the sequence of amino acids that make villin as: – DEDFKAVFGMTRSAFANLPLWKQQNLKK EKGLFMLS – Although villin is made of a chain of 36 letters, only 16 different letters are needed to describe villin – In the next slides we shall look at the individual amino acids that make up villin D – Aspartic Acid Name Aspartic acid, Letter: D Abbreviation: Asp Info 4 4 6 1 oxygen carbon hydrogen nitrogen Looks E – Glutamic Acid Name Info Glutamic acid Letter: E Abbreviation: Glu 5 8 4 1 carbon hydrogen oxygen nitrogen Looks F – Phenylalanine Name Info Phenylalanine Letter: F Abbreviation: Phe 9 carbon 11 hydrogen 1 nitrogen 2 oxygen Looks K – Lysine Name Info Lysine Letter: K Abbreviation: Lys 6 carbon 14 hydrogen 2 nitrogen 2 oxygen Looks A – Alanine Name Info Alanine Letter: A Abbreviation: Ala 3 7 1 2 carbon hydrogen nitrogen oxygen Looks V – Valine Name Info Valine Letter: V Abbreviation: Val 5 carbon 11 hydrogen 1 nitrogen 2 oxygen Looks G – Glycine Name Info Glycine Letter: G Abbreviation: Gly 5 carbon 11 hydrogen 1 nitrogen 2 oxygen Looks M – Methionine Name Info Methionine Letter: M Abbreviation: Met 5 carbon 11 hydrogen 1 nitrogen 2 oxygen 1 suphur Looks T – Threonine Name Info Threonine Letter: T Abbreviation: Thr 4 9 1 3 carbon hydrogen nitrogen oxygen Looks R – Arginine Name Info Arginine Letter: R Abbreviation: Arg 6 carbon 14 hydrogen 4 nitrogen 2 oxygen Looks S – Serine Name Info Serine Letter: S Abbreviation: Ser 3 7 1 3 carbon hydrogen nitrogen oxygen Looks N – Asparagine Name Info Asparagine Letter: N Abbreviation: Asn 4 8 2 3 carbon hydrogen nitrogen oxygen Looks L – Leucine Name Info Leucine Letter: L Abbreviation: Leu 6 carbon 13 hydrogen 1 nitrogen 2 oxygen Looks P – Proline Name Info Proline Letter: P Abbreviation: Pro 5 9 1 2 carbon hydrogen nitrogen oxygen Looks W – Tryptophan Name Info Tryptophan Letter: W Abbreviation: Trp 11 carbon 12 hydrogen 2 nitrogen 2 oxygen Looks Q – Glutamine Name Info Glutamine Letter: Q Abbreviation: Gln 5 carbon 10 hydrogen 2 nitrogen 3 oxygen Looks Elements • Carbon (C), Hydrogen (H), Oxygen (O), Nitrogen (N) and Sulfur (S) are the only chemical elements that make up all villin’s amino acids. • We shall review some of their properties in the next pages. Carbon • (Latin: carbo, charcoal) Carbon, an element of prehistoric discovery, is very widely distributed in nature. It is found in abundance in the sun, stars, comets, and atmospheres of most planets. • Carbon is the source of energy for life through carbohydrates, just like a burning log is a source of energy to a cold room. Atomic number 6 Atomic Symbol C Atomic mass 12.011 u Electron Configuration [He]2s22p2 Hydrogen • (Greek: hydro, water, and genes, forming) Hydrogen is the most abundant of all elements in the universe. • The heavier elements were originally made from Hydrogen or from other elements that were originally made from Hydrogen. • Used in rocket fuel. Atomic number 1 Atomic symbol H Atomic mass 1.0070 u Electron Configuration 1s1 Oxygen • Greek: oxys, sharp, acid, and genes, forming; acid former) Oxygen is the third most abundant element found in the sun. Oxygen is vital to the respiration of living organisms. • Oxygen is responsible for the bright red and yellowgreen colors of the Aurora. • Essential element for combustion (i.e. burning). Atomic number 8 Atomic symbol O Atomic mass 15.9994 u Electron Configuration [He]2s22p4 Nitrogen • (Latin Nitrum, Greek. Nitron, native soda; genes, forming). • Nitrogen gas (N2) makes up 78.1% of the Earth’s air, by volume. • Nitrogen is found in all living systems as part of the makeup of biological compounds. • Ammonia (NH3) is the most important commercial compound of nitrogen, with a very pungent smell, used in cleaning supplies. Atomic number 7 Atomic symbol N Atomic mass 14.00674 Electron Configuration [He]2s22p3 Sulfur • (Sanskrit, sulvere; Latin sulpur) Known to the ancients; referred to in Genesis as brimstone. • Sulfur occurs native in the vicinity of volcanoes and hot springs. • It is widely distributed in nature in various minerals (iron pyrites, galena, sphalerite, cinnabar, stibnite, gypsum, epsom salts, celestite, barite, etc.) • Sulfur is found in meteorites. Atomic number 16 Atomic symbol S Atomic mass 32.6 Electron Configuration [Ne]3s23p4 Yellowstone hot springs Molecules, Bonds • Atoms are bonded together to form molecules and molecules are bonded together to form macromolecules. • The next slides shows some characteristics of chemical bonds. Chemical Bonds Peptide Bond • Amino acids join together via a special bond called “peptide bond”. • In a peptide bond, two molecules (amino acid 1 and amino acid 2) are joined together with the accompanying removal of a molecule of water. Activity • Knowing that villin is made of the following sequence of amino acids – DEDFKAVFGMTRSAFANLPLWKQQNLKKEKGLFMLS • Compute the molar mass of villin. • Compute the percentage by number of each atom component. • Compute the percentage by mass of each atom component. • (Remember that amino acids are joined together through peptide bonds….) • Lesson Plan