Chapter 2 Chemistry of Life Dr. R.M. Moody

Matter Matter is anything that occupies space and has mass (e.g., solids, liquids and gases). Atoms are the building blocks of all matter. Elements are pure substances that contain only one type of atom. An atom is the smallest unit of matter that retains the properties of a particular element. Dr. R.M. Moody

States of Matter

Structure of Atoms Atoms consist of a nucleus (“core”), which is orbited by electrons. Subatomic particles of the nucleus: Protons – Positively charged particles Neutrons – Particles with a neutral charge Electrons have a negative charge Electrons move around the nucleus in an orbital. Number of electrons is equal to the number of protons. Only the outermost electrons take part in chemical reactions. Dr. R.M. Moody

Atoms are mostly empty space Atoms are mostly empty space. If you scaled a hydrogen atom to the size of a football stadium, the nucleus would be the size of a pea! Dr. R.M. Moody

Structure of Atoms All atoms of a given element have the same number of protons in the nucleus. This is called the atomic number. The atomic number determines the identity and chemical properties of an element. The mass number is the number of protons plus the number of neutrons. Helium Atom Atomic number: 2 Protons: 2 Neutrons: 2 Electrons: 2 Mass number: 4 Dr. R.M. Moody

He was even able to predict the existence of undiscovered elements! In 1869, Dmitry Mendeleyev arranged elements known at the time by their chemical properties. He was even able to predict the existence of undiscovered elements! Dr. R.M. Moody

Chemical Composition of Organisms Four elements make up ~96% of all organisms: Oxygen: 65% Carbon: 18.5% Hydrogen: 9.5% Nitrogen: 3.3% Other important elements include: calcium, phosphorous, potassium, and sulfur. Dr. R.M. Moody

Isotopes Atoms that have the same number of protons but different numbers of neutrons are called isotopes. Isotopes are defined by their mass number (protons + neutrons). Example: Carbon isotopes Dr. R.M. Moody

Notice that the number of protons remain the same—they are what make carbon, carbon! Dr. R.M. Moody

From Atoms to Molecules A chemical bond is an attractive force between atoms. They form when atoms: Give away or gain electrons (ionic bonds) Share electrons (covalent bonds) A molecule is formed when two or more (same or different) atoms bond together. Compounds are molecules containing atoms of two or more elements in fixed proportions. All compounds are molecules, but not all molecules are compounds. Dr. R.M. Moody

Ionic Bonds Ionic bonds: A chemical bond that forms between an atom that gains an electron and an atom that loses an electron. An atom with a charge is called an ion. Ions with opposite charges (+ or -) attract one another, forming an ionic bond. Dr. R.M. Moody

Sodium Chloride (table salt) Note that the number of protons does not change!!

Covalent Bonds Covalent bonds: Atoms share one or more pairs of electrons. Strongest type of chemical bond Dr. R.M. Moody

Polar and Nonpolar Covalent Bonds In a nonpolar covalent bond, atoms share electrons equally. Atomic charges are equally distributed. In a polar covalent bonds, atoms share electrons unequally. Partial positive and negative charges form on each end of molecule. Dr. R.M. Moody

Two hydrogen atoms share two electrons in a single, nonpolar covalent bond. (H-H)

molecular oxygen (O2) O=O Two oxygen atoms share four electrons in a double, nonpolar covalent bond. molecular oxygen (O2) O=O

(δ+) (δ-) Water (H2O) H-O-H In water, two hydrogen atoms share electrons with an oxygen atom in two polar covalent bonds. The oxygen exerts a greater pull on the shared electrons, so it has a slight negative charge. Each hydrogen has a slight positive charge. (δ+) (δ-) Water (H2O) H-O-H

Chemical Bookkeeping Use symbols for elements when writing formulas Formula for glucose is C6H12O6 6 carbons 12 hydrogens 6 oxygens Dr. R.M. Moody

Chemical Reactions Chemical Reaction: Process by which the atoms of one or more substance are rearranged to form different substances. Example: LIGHT ENERGY 12H2O + 6CO2 6O2 + C6 H12O6 + 6H2O REACTANTS PRODUCTS Dr. R.M. Moody

Activation Energy Most reactions require energy to begin. This energy is called activation energy. Chemicals that help speed up reactions are called catalysts. Enzymes are used as catalysts in organisms: Proteins RNA Dr. R.M. Moody

Oxidation-Reduction Reactions Many reactions that transfer energy in living things involve the transfer of electrons. Redox reactions involve the loss or gain of electrons: Reduction: Gain electrons  Becomes (-) Oxidation: Lose electrons  Becomes (+) Remember: OIL RIG Dr. R.M. Moody

Emergent Properties of Water (water drop activity) Dr. R.M. Moody

Hydrogen Bonding Recall that water is a polar molecule. Hydrogen has a partial (+) charge Oxygen has a partial (-) charge A hydrogen bond is the force of attraction between a partially charged hydrogen and an atom or molecule with a partial or full negative charge. Dr. R.M. Moody

Hydrogen Bonding H-bonds impart structure to liquid water and stabilize nucleic acids and other large molecules. (δ+) (δ-)

Emergent Properties of Water (1) Water is a great solvent because ions and polar molecules dissolve in it. Polar substances are hydrophilic (“water- loving”); nonpolar ones are hydrophobic (“water-fearing”) and are repelled by water (e.g., oil has nonpolar bonds). Solutes dissolved in a solvent form a solution. Concentration refers to the amount of solute in a solution. Dr. R.M. Moody

Emergent Properties of Water (2) Water tends to stabilize temperature because it can absorb considerable heat before its temperature changes. (3) Hydrogen bonding of water molecules provides cohesion and adhesion. Dr. R.M. Moody

Emergent Properties of Water (4) Water expands when it freezes (10% less dense). If water didn’t float, much of life wouldn’t exist--ice would sink to the bottom of bodies or water and would not provide insulation. Figure 2.11 Antarctic bottom water; gaseous water Dr. R.M. Moody

Acids and Bases Water molecules spontaneously separate into hydrogen ions (H+) and hydroxide ions (OH-) ions. Hydrogen ions can then bond with water to form hydronium ions (H3O+). H3O+ Hydronium ions H2O Water Dr. R.M. Moody

Acids and Bases pH is a measure of the concentration of H3O+ ions in a solution. When [H3O+] ions = [OH-] ions, a solution is said to be neutral and has a pH of 7. Acidic: [H3O+] ions > [OH-] ions Basic: [H3O+] ions < [OH-] ions Dr. R.M. Moody

Acids and Bases A one-unit increase or decrease on the pH scale represents a 10-fold increase or decrease in H3O+ ions. Acids give up H3O+ ions when dissolved in water (add them) and lower pH. Bases accept H3O+ ions when dissolved in water and raise pH. Pure water has a pH of 7. Rain water has a pH <7 and seawater has a pH >7 Dr. R.M. Moody

Buffer Systems Buffer systems control pH in living systems. Enzymes only work in a narrow range of pHs. Buffers are chemicals that neutralize small amounts of acid or base in solutions to maintain a neutral pH in the body. Dr. R.M. Moody

Acids and Bases: Buffers Carbonic acid and bicarbonate constitute a buffer system (e.g., your blood and seawater) ACID BASE