Exploring the Chemistry of Life: Atoms, Molecules, and Bonds

1. The Chemistry of Life Atoms and molecules

2. Basic definitions • Matter: anything that has mass and takes up space • Atoms: particles that make up matter • Atomic structure: dense nucleus and orbiting electrons • Atomic number: number of protons in the nucleus; defines the element • Element: can’t be broken down into another substance by any natural means

3. Atomic structure

4. Particles and their charges • In the nucleus: • Protons- positive charge • Neutrons- no charge • Orbiting the nucleus: • Electrons- no charge • Total number of protons and electrons determines the net charge on the atom

5. Isotopes • Atomic mass: sum of masses of protons and neutrons • Number of neutrons can vary (isotopes) • Some isotopes are unstable and decay • Radioactive “half-life” is consistent

6. Atoms interact with each other through electrons • Electrons arranged around nucleus in orbitals • Each orbital is “filled” with two electrons (paired electrons) • If an orbital is unfilled, the atoms can interact with another atom • Energy of the electron depends on its distance from the nucleus

7. Chemical bonds and energy • Energy is stored in chemical bonds, and released when chemical bonds are broken • Oxidation –reduction reaction: • One reactant loses an electron (is oxidized) • The other reactant gains an electron (is reduced) • These reactions are often coupled in the cell (one item is oxidized and the other is reduced)

8. Ninety natural elements

9. Types of chemical bonds

10. Ionic bonds form crystals (salts) • One atom “donates” an electron to another • Ions are now electrostatically attracted to each other • Aggregate forces hold crystal together • If water is present…

11. Electrons are shared in covalent bonds • Atoms come close enough together for electron orbitals to overlap • Valence shell is filled • “Bonding capacity”: number of electrons needed to fill the shell (valence) • Molecules are formed

12. Many compounds are composed of more than two atoms • A carbon atom can form bonds with up to four other atoms • “Backbone” for very large molecules

13. Covalent bonds can be polar or nonpolar • Electronegativity: affinity for electrons • Atoms with same electronegativity will share electrons equally • Electrons are drawn toward more electronegative atom

14. A polar molecule

15. Weak bonds play important roles within cells • Hold large molecules together • Hydrogen bonds • Van der Walls interactions • Allow interactions to occur and break apart • Water molecules are involved in many of these bonds • The shape of a molecule helps define its function

16. Chemical reactions make and break bonds • Reactants form products (under favorable conditions) • Environment is right • Concentration of reactants is sufficient • Catalysts are present • Many specific chemical reactions are essential to life

17. Summary • Matter consists of elements and compounds • An element’s properties depends on the properties of its atoms • Molecules are formed by chemical bonding between atoms • In chemical reactions, bonds are made and broken