Chemistry and Introductory Biochemistry from Unicamillus

Biochemistry Instructors

Prof. M.Gabriella De Martino (B) mariagabriella.demartino@unicamillus.org Prof. Luca Federici (A) luca.federici@unicamillus.org Prof. Barbara Tavazzi (C) barbara.tavazzi@unicamillus.org

Lectures

• Theory
• Practicals (preparation for the written test)

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General Chemistry

Introduction Remarks

Periodic table of elements and inorganic nomenclature. Atom: atom models, atomic particles: proton, neutron, electron. Isotopes. Electrons and atom electronic configuration. The quantum- mechanical model of the atom. Quantum numbers and orbitals. Auf-bau. Chemical bonds.

Matter States

Gas: ideal gas law. Absolute temperature and its relationship with mean molecular speed. Mixture of gases; Dalton law.

Liquids

Vapor pressure of a liquid. Solids: structural characteristics of covalent, ionic, molecular and metallic solids.

Thermodynamics

Thermodynamic potentials; enthalpy, entropy. Free energy: relationship with enthalpy and entropy.

Solutions

Concentrations of solutions: dilution and mixing of solutions. Vapor pressure of a solution (Raoult's law). Solubility of gases in liquids: Henry law.

Chemical Equilibrium

Expression of equilibrium constant. Equilibrium influencing factors. Homogeneous and heterogeneous equilibrium.

Solutions of Electrolytes

Strong and weak electrolytes: dissociation grade. Colligative properties of electrolyte solutions. Van't Hoff binomial. Acids and bases following Arrhenius, Bronsted and Lowry, Lewis definitions. Strong and weak acid and bases. pH in strong and weak acid and base solutions. Buffers.

Heterogeneous Systems

Equilibria of slightly soluble ionic compounds. The solubility-product constant. The effect of a common ion.

Kinetics

Introduction to kinetics, activated complex theory, activation energy. Kinetic equations and reaction order. Relationship between kinetic constants and equilibrium constants.

Electrochemistry

Redox reactions. Oxidation number. Redox reactions and their balance. Redox standard potentials. Nerst equation. Electromotive force potential of a cell. Half-cells. Chemical and concentration cells.

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Introductory Biochemistry

HYBRIDIZATION OF THE CARBON ATOM - sp3, sp2, sp hybridizations and their geometry. HYDROCARBONS - Saturated hydrocarbons: alkanes and cycloalkanes. Nomenclature. Unsaturated hydrocarbons: alkenes and alkynes. Nomenclature. Conformational isomerism and geometric isomerism (cis-trans). AROMATIC COMPOUNDS - Structure of benzene: the resonance model. Nomenclature of aromatic compounds. Polycyclic aromatic hydrocarbons (outline). ALCOHOLS, PHENOLS, THIOLS - Nomenclature. Acidity and basicity of alcohols and phenols. Thiols, analogues of alcohols and phenols. ALDEHYDES AND KETONES - Nomenclature. Preparations of aldehydes and ketones. The carbonyl group. The nucleophilic addition to the carbonyl groups; formation of semiacetals and acetals. The aldol condensation (outline). CARBOXYLIC ACIDS AND THEIR DERIVATIVES - Nomenclature of acids. Derivatives of carboxylic acids: esters, amides. Mechanism of esterification; triesters of glycerol. AMINES AND OTHER NITROGEN COMPOUNDS - Classification of amines and nomenclature. Basicity of amines. Comparison between the basicity of amines and amides. STEREOISOMERY - Chirality. Enantiomers. Polarized light; the polarimeter (hints). Diastereomers. CARBOHYDRATES - Definitions and classification. The monosaccharides. Chirality in monosaccharides; Fischer's projections. Cyclic structures of monosaccharides. Anomers. Phenomenon of mutarotation. Pyranosic and furanotic structures. AMINO ACIDS, PROTEINS - Properties of amino acids. Peptide bond LIPIDS: Structure, nomenclature, properties NITROGEN BASES AND NUCLEOTIDES - Structure, nomenclature.

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Suggested Textbooks

Wiley Loose-Leaf Print Edition FOUNDATIONS OF COLLEGE CHEMISTRY 15€ Morris Hein Susan Arena . Cary Willard WILEY Seventh Edition Chemical Principles The Quest for Insight Peter Atkins Loretta Jones Leroy Laverman PRINCIPLES OF Fourth Edition BIOCHEMISTRY VOET . VOET . PRATT International Student Version General chemistry Biochemistry Any text of general chemistry is suitable !!!

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Chemistry: Science That Studies Matter

CHEMISTRY: SCIENCE THAT STUDIES MATTER (everything that has a mass and occupies a volume) Properties Structure Transformations Physical or Chemical Aggregation state (macroscopic level) Chemical structure (atomic-molecular level) Atomic structure (atomic-nuclear level) · Physical transfomations (change of a physical property, the chemical composition of matter does not change) . Chemical transformations (change in chemical composition) · Nuclear reactions (radioactive decays)

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Pure Substances

ELEMENT: substance that cannot be divided into other components through ordinary chemical reactions (O, C, H, N, Au, Cu, Zn, Fe ... ) periodic table Compound: substance formed by two or more atoms from the same or different elements combined in fixed and constant proportions. A compound presents different properties from its constituents. (O2, H2O, C6H1206, NH3 ... ) (NaCl, Na2SO4 ... ) - - molecules salts, ionic compounds

Mixtures

Made by two or more substances combined in not defined proportions. Properties of costituents remain unaltered. Homogeneous mixtures Heterogeneous mixtures

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Atoms and Compounds

Atoms element 1 Atoms element 2 Compound formed by elements 1 and 2 Mixture of elements 1 and 2

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Elements in Living Organisms

Carbon (C) Hydrogen (H) Nitrogen(N) Oxygen (O) Most abundant Calcium (Ca) They are present in small Chlorine (Cl) Magnesium (Mg) quantities and are essential to life Phosphrous (P) Potassium (K) Sodium (Na) Sulfur (S) Aluminum (Al) Arsenic (Ar) Boron (B) Bromine (Br) Chrome (Cr) Fluorine (F) Iodine (I) Molybdenum (Mo) necessary in traces Cobalt (Co) Copper (Cu) Iron (Fe) Manganese (Mn) Zinc (Zn) Transition metals. Less abundant but present in all organism

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Atoms, Molecules, Ions and Chemical Reactions

Common Language

Table salt dissolves in water + CI- Na+

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Chemical Language

H2O NaCl (s) Na+(aq) + Cl-(aq) + CI- Na+

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Atoms, Molecules, Ions and Chemical Reactions: Water

H2O NaCl (s) Na+(aq) + Cl-(aq) Atom Cl Atom Na lon CI" Ion Na+ 104,45° O 8 + 95,84 pm Water molecule

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Atoms, Molecules, Ions and Chemical Reactions: Sodium Chloride

Na· + 0 00 CI : 00 Na + + O o O * ** Na X * + Cl 1s2 2s2 2p6 3s 1s2 2s2 2p6 3s2 3p5 1 . Na * d Legame ionico 1 s2 2s2 2p6 3s2 3p6 = [Ar]

OF H INTERNA NCES Ain Lumine Tuo Videbimus Lumen UNICAMILLUS 12 1s2 2s2 2p6 + X CI = [Ne] 0 .

Properties of Matter: Physical and Chemical

PROPERTIES OF THE MATTER: Physical Chemical Cl2 is a toxic gas, yellow-green, with a density equal to 3.21 g/l. It turns to a liquid (condensation) if it is cooled down to -34.6 º C. (these are all physical properties and transformations). Gasous Cl2 reacts with metallic Na. The reaction is extremely exothermic and the product is NaCl. 2Na + Cl2 > 2NaCl This is a chemical transformation. Life of a cell, and of organisms, depends on the timely and spontaneous occurrence of thousands of reactions

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Periodic Table of the Elements

Group 1 1A 18 8A 1 11 -- Atomic number Alkaline earth metals Metalloids 1 Na Element symbol Lanthanides Other nonmetals 13 3A 14 4A 15 5A 16 6A 17 7A 2 Li Lithium 6.938 Be Beryllium 9.0122 Boron 10.806 Carbon 12.009 Nitrogen 14.006 O Oxygen 15.999 Fluorine 18.998 11 12 13 14 16 17 18 3 Na Sodium 22.990 Mg Magnesium 24.305 3 3B 4 4B 5 5B 6 6B 7 7B 8 10 11 1B 12 2B Aluminum 26.982 Si Silicon 28.084 Phosphorus 30.974 Sulfur 32.059 CL Chlorine 35.446 Ar Argon 39.948 19 20 23 24 25 27 31 32 Ga Gallium 69.723 Ge Germanium 72.63 33 As Arsenic 74.922 34 Se Selenium 78.96 35 4 Potassium 39.098 Ca Calcium 40.078 21 Sc Scandium 44.956 22 Ti V Cr Mn 26 Fe Iron 55.845 Co Cobalt 58.933 28 Ni Nickel 58.693 29 Cu Copper 63.546 30 Zn Zinc 65.38 37 38 39 40 42 43 Tc 44 Ru 45 Rh Pd Ag Silver 107.87 Cd Cadmium 112.41 In Indium 114.82 Sn Tin 118.71 Sb Antimony 121.76 Tellurium 127.60 Lodine 126.90 Xe Xenon 131.29 55 72 73 74 77 79 80 81 83 85 86 6 Cs Cesium 132.91 Hf Hafnium 178.49 Ta Tantalum 180.95 W Tungsten 183.84 75 Re Rhenium 186.21 76 Os Osmium 190.23 Ir Iridium 192.22 78 Pt Platinum 195.08 Au Gold 196.97 Hg Mercury 200.59 Thallium 204.38 82 Pb Lead 207.2 Bi Bismuth 208.98 84 Po Polonium (209) At Astatine (210) Rn Radon (222) 87 104 Rf 105 Db 106 Sg 107 Bh Bohrium (264) 108 Hs Hassium (269) 109 Mt 110 Ds 111 Rg 112 Cn Uut FL 115 Uup Lv 117 Uus 118 7 Fr Francium (223) 88 Ra Radium (226) Rutherfordium Dubnium (261) (262) Seaborgium (266) Meitnerium Damstadtium Roentgenium Copernicium Ununtrium Flerovium Ununpentium Livermorium Ununseptium Ununoctium (268) (268) (268) (268) (268) (268) (268) (268) (268) (268) Actinides Lanthanides 89 Ac Actinium (227) 90 Th Thorium 232.04 91 Pa 92 U 93 Np Neptunium (237) 94 Pu Plutonium (244) 95 Am Americium (243) 96 Cm Curium (247) 97 Bk 98 99 Cf Es 100 Fm Fermium (257) 101 Md Mendelevium (258) Nobelium (259) Lawrencium (262) SITY OF HE INTERNATIO NCES In Lumine Tuo Videbimus Lumen UNICAMILLUS 14 5 7 8 9 10 Transition metals Noble gases B N F 2 He Helium 4.0026 Hydrogen 1.0078 2 2A Sodium- 22.990- Element name Actinides Halogens 3 4 Atomic weight Ne Neon 20.180 AL 15 P S K Titanium 47.867 Vanadium 50.942 Chromium Manganese 51.996 54.938 46 47 48 49 50 51 52 Te 54 5 Rb Rubidium 85.468 Y Yttrium 88.906 Zirconium 91.224 41 Nb Niobium 92.906 Mo Molybdenum Technetium Ruthenium 95.96 98.9062 101.07 Rhodium 102.91 Palladium 106.42 63 Eu Europium 151.96 64 Gd Gadolinium 157.25 65 Tb Terbium 158.93 66 Dy Dysprosium 162.50 67 Ho Holmium 164.93 68 Er Erbium 167.26 69 Tm Thulium 168.93 70 Yb 71 Lu Lutetium 174.97 57 La Lanthanum 138.91 58 Ce Cerium 140.12 59 Pr 60 Nd 61 Pm Promethium (145) 62 Sm Samarium 150.36 Ytterbium 173.04 102 No 103 Lr Berkelium |Californium Einsteinium (251) (247) (252) 113 114 116 Br Bromine 79.904 53 36 Kr Krypton 83.798 Zr Sr Strontium 87.62 56 Ba Barium 137.33 Praseodymium Neodymium 140.91 144.24 Protactinium 231.04 Uranium 238.03 Alkalai metals Post-transition metals H 6 C Unknown properties 9 88 Uuo TL