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Chapter 2 Essential Chemistry for Biology

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Chapter 2 Two Lectures Wednesday Basic Chemistry Friday Biology of Water MasteringBiology Sunday night First MasteringBiology Assignment Due

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Outline for Essential Chemistry 1.Elements of Life a.Four most abundant elements in organisms b.Importance of trace elements 2.Structure of Atoms a.Subatomic Particles b.Atoms of Life c.Isotopes and ions 3.Chemical Bonds a.Covalent Bonds b.Hydrogen bonds c.Ionic bonds d.Hydrophobic interactions 4.Chemical Reactions 5.Water a.Four Properties b.pH and Buffers

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Structural Hierarchy

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Elements and Molecules Atoms - building blocks of molecules Elements types of atoms 92 natural elements Molecule composed of two or more atoms. Compounds molecules composed of more than one element. Emergent properties Sodium Chloride Sodium Chloride +

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Molecular Formulas Water H 2 0 Glucose C 6 H 12 O 6

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96% of living matter made of 4 elements. Oxygen O Carbon C Hydrogen H Nitrogen N Most of remaining 4% just 7 elements Remaining >0.1% are Trace Elements Oxygen (O): 65.0% Carbon (C): 18.5% Calcium (Ca): 1.5% Magnesium (Mg): 0.1% Chlorine (Cl): 0.2% Sodium (Na): 0.2% Sulfur (S): 0.3% Potassium (K): 0.4% Phosphorus (P): 1.0% Hydrogen (H): 9.5 % Nitrogen (N): 3.3% Trace elements: less than 0.01% Iron (Fe) Iodine (I) Fluorine (F) Copper (Cu) Cobalt (Co) Chromium (Cr) Boron (B) Zinc (Zn) Vanadium (V) Tin (Sn) Silicon (Si) Selenium (Se) Molybdenum (Mo) Manganese (Mn) 25 Elements Essential for Life

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Essential Trace Elements

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Nucleus 2e2e Electron cloud Nucleus Electrons Neutrons Protons 2 2 2 Atomic Structure Characteristics of Particles Location Atomic Number Atomic Mass Atomic Charge Atomic Volume (Size)

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Structure of Typical Atoms Rule 1 Neutral atoms have equal number of protons and electrons Rule 2 Typically, atoms have equal number of protons and neutrons Structure of typical Nitrogen Atom

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Exceptions to rules Exception to rule 1 Ions unequal protons and electrons (electric charge) Exception to rule 2 Variable Isotopes variable number of neutrons Nitrogen atom 7 proton and 7 electron Neutral Charge Nitrogen ion 7 proton and 6 electron Positive Charge C-12 6 proton and 6 neutron Common non radioactive isotope 6 n 6 p 6 n 8 p C-14 6 proton and 8 neutron Rare radioactive isotope

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Properties of Common Atoms ElementAbvAtomic #Mass #Valence # HydrogenH111 CarbonC6124 NitrogenN7143 OxygenO8162

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Four Chemical Bonds Strong Chemical Bonds Covalent Bonds Weak Chemical Bonds Ionic Bonds Hydrogen Bonds Other Interactions Hydrophobic Interactions

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Ionic Bonds Attraction between positive ions and negative ions

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Covalent Bonds

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Properties of Covalent Bonds Sharing of pair of electrons Strongest of chemical bonds Valence number Single, Double, and Triple bonds Important for Shape of Molecules Nonpolar/polar forms Ele- ment Valence # H1 C4 N3 O2

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Non-Polar and Polar Covalent Bonds Oxygen and Nitrogen have high electronegativity Hydrogen has low electronegativity

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Hydrogen Bonds Attraction between a hydrogen with a partial positive charge and an electronegative atom (linked to less electronegative atom.) Requires polar bonds. Weak Interaction

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Hydrophobic vs Hydrophobic Molecules Measure of hydrophobicity = # of non-polar minus # of polar

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Hydrophobic Interactions

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Chemical Reactions (Rearranging Chemical Bonds) 2H 2 + O 2 2H 2 O

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Water and Life Four special Properties Cohesion/Adhesion Temperature Moderation Significance of Floating Ice Solvent Properties Other issues pH

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Cohesion Surface Tension

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Temperature Moderation High Specific HeatEvaporative cooling

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Floating Ice

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Waters Solvent Properties Chloride ion in solution Sodium ion in solution Salt crystal Na Cl Na Cl

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H 2 O H + + OH - 55 M 10 -7 M 10 -7 M pH = -log [H + ] Conc [H+] pH 10 -2 M 2 10 -3 M 3 10 -4 M 4 10 -5 M 5 10 -6 M 6 10 -7 M 7 10 -8 M 8 10 -9 M 9 Disassociation of Water

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Buffers Carbonic Acid (buffer in our blood) In response to rise in pH H 2 CO 3 H + + HCO 3 - In response to a drop in pH