Essential Chemistry for Biology Chapter 2 Essential Chemistry for Biology

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

Outline for Essential Chemistry Elements of Life Four most abundant elements in organisms Importance of trace elements Structure of Atoms Subatomic Particles Atoms of Life Isotopes and ions Chemical Bonds Covalent Bonds Hydrogen bonds Ionic bonds Hydrophobic interactions Chemical Reactions Water Four Properties pH and Buffers

Structural Hierarchy

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 +

Molecular Formulas Water H20 Glucose C6H12O6

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

Essential Trace Elements

Atomic Structure Characteristics of Particles 2 Protons Nucleus 2 Location Atomic Number Atomic Mass Atomic Charge Atomic Volume (Size) 2 Protons Nucleus 2 Neutrons 2 Electrons Nucleus 2e– Figure 2.4 Two simplified models of a helium atom Electron cloud 9

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

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 6 n 6 p 6 n 8 p C-12 6 proton and 6 neutron Common non radioactive isotope C-14 6 proton and 8 neutron Rare radioactive isotope

Properties of Common Atoms Element Abv Atomic # Mass # Valence # Hydrogen H 1 Carbon C 6 12 4 Nitrogen N 7 14 3 Oxygen O 8 16 2

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

Ionic Bonds Attraction between positive ions and negative ions

Covalent Bonds

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 # H 1 C 4 N 3 O 2

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

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

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

Hydrophobic Interactions

Chemical Reactions (Rearranging Chemical Bonds) 2H2 + O2 2H2O

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

Cohesion Surface Tension

Temperature Moderation High Specific Heat Evaporative cooling

Floating Ice

Water’s Solvent Properties Sodium ion in solution Chloride ion in solution Cl– Na Na Cl– Salt crystal

Disassociation of Water H2O 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

Buffers Carbonic Acid (buffer in our blood) H2CO3 H+ + HCO3- In response to rise in pH H2CO3 H+ + HCO3- a drop in pH