The Chemical Context of Life Chapter 2

The Structure of Atoms An atom is the smallest unit of matter that is unique to a particular element. Atoms are composed of three particles: protons (positive charge, nucleus, amount gives atomic number); neutrons (no charge, nucleus, these added to protons yields atomic mass); electrons (negative charge, orbitals, amount is equal to protons, mass is negligible). Atomic numbers and mass numbers give idea of how substances will react.

Isotopes Atoms with the same number of protons but a different number of neutrons are called isotopes (Ex. Carbon can exist as C-12, C-13, C-14) Some radioactive isotopes are unstable and tend to decay spontaneously giving off particles and energy. This decay into more stable atoms occurs AT A PREDICTABLE RATE. These characteristics makes isotopes good to use for radioactive dating, for use as tracers to follow the path of an atom in a series of reactions and for use in diagnosing disease. see pages 30-31 for scintillation counters, autoradiography, and PET scans

Electrons & Energy Levels If outer orbital (valence shell) is not full of electrons, an atom has 3 choices: give up extra ones to fall down to the next level, gain more to fill up the current level, share what they have with another atom. Loss or gain results in ions (charged atoms) – opposite charges attract and give ionic bonds Sharing of electrons results in covalent bonds Electrons differ in their amounts of energy – the closer to the nucleus, the less potential energy that it has Electrons can move to a higher energy level, but will move back to original position; releases energy gained when this occurs.

Energy Levels of an Atom’s Electrons

Energy ENERGY IS THE ABILITY TO DO WORK. Potential energy is the energy that matter stores because of its position or location. Kinetic energy is energy of motion. Need activation energy to convert potential energy to kinetic energy.

Molecules Molecules are formed when two or more atoms bond together; may be either one element or different elements If consist of two or more different elements in proportions that never vary, then is referred to as a COMPOUND (Ex. Water) If two or more elements are simply intermingling in proportions that CAN vary, then it is called a MIXTURE. (Ex. Water and sucrose)

Bonds Any atom that has lost or gained electrons is called an ion – if lost electrons, will be positive (cation); if gained, will be negative (anion). When a cation and an anion are attracted, they form an ionic bond. Covalent bonds are formed when electrons are shared between atoms; one pair shared gives a single bond, two pairs gives a double bond, three pairs, a triple bond.

Ionic Bonds

Sodium Chloride Crystal

Covalent Bonds The attraction of electrons to an atom is called electronegativity. The more electronegative an atom, the more a shared electron is pulled towards its nucleus. If two atoms are of the same element or of the same electronegativity, the pull of the electron is equal and the bond is a NONPOLAR covalent bond. POLAR covalent bonds form when one atom is more electronegative than another; thus, the electron is pulled closer to the atom and the electron is not shared equally. The atom with the greater electronegativity will be slightly negative because the electron spends more time around its nucleus. The other atom has a slightly positive charge.

Covalent Bonding

Water – POLAR COVALENT BONDING

The Importance of Weak Chemical Bonds Examples: Ionic bonds Hydrogen bonds – pg 36 Van der Waals Interactions – pg 36 All of these are weak, but the advantage is that the contact between molecules can be brief; the molecules come together, respond, then separate.

Hydrogen Bonds These occur between molecules (or even in different parts of the same molecule). They are weak attractions between an electronegative atom and a hydrogen taking part in a second polar covalent bond. Individually, hydrogen bonds break easily; collectively, they work to stabilize structure. Ex. DNA molecule, water

A Hydrogen Bond

Van der Waals Interactions Occur when atoms and molecules are very close together. Due to movement of electrons and productions of “hot spots” within a molecule that make it stick to another molecule or atom.

Molecular Shape & Function Molecules have characteristic sizes and shapes. Shape determines recognition and response to other molecules.

Molecular Mimics Morphine affects pain perception and emotional state by mimicking the brain’s natural endorphins. The boxed portion of the endorphin molecule is recognized by receptor molecules on target cells in the brain. The boxed portion of the morphine is a close match.

Chemical Reactions – Reaching Equilibrium