AP Biology Study Guide

1 AP Biology Study Guide *. UNIT I. CHEMISTRY/BIOCHEMISTRY. I. CHEMISTRY: THE BASIS FOR LIFE. A. ELEMENTS. Almost everything around us can be broken down into simpler substances. These substances can be further broken down into other simpler substances. There is a point where substances can no longer be broken down into other substances while keeping their characteristic properties. These substances are called elements. There are currently 106 named elements (92 naturally occurring), but this number is increasing because more man made elements are being created in laboratories. From these 92 naturally occurring elements, only 20 are necessary for life. Of these 20 life elements, 6. make up 99% of all living matter: Sulfur, Phosphorous, Oxygen, Nitrogen, Carbon and Hydrogen (SPONCH, mnemonic device). Living organisms still need the other 14 elements, but in smaller amounts.

2 An atom is the smallest indivisible unit of an element that still has the characteristic of the element. Two or more atoms can combine chemically and form a molecule. A compound is any pure substance that contains two or more different atoms. Atom = H Molecule = H2 Compound = H2O. B. FORMS OF MATTER. Atoms, elements, and compounds are forms of matter. Matter can come in one of three states on the earth: 1. Solid Has definite shape and has a definite volume 2. Liquid Has no definite shape but has a definite volume 3. Gas Has no definite shape and has no definite volume C. SUBATOMIC PARTICLES. Atoms can be broken down into smaller components called subatomic particles: protons, neutrons, and electrons. Protons and neutrons make up the nucleus of an atom. They are roughly equal in mass, one atomic mass unit (amu) or Dalton. Protons are positively charged and neutrons are not changed.

3 Electrons are negatively charged, have relatively small mass. An atom can be described as having a small, very dense nucleus with a very low-density electron cloud surrounding it. Therefore, most of the mass of the universe is made up of protons and neutrons. Strong nuclear forces hold the protons and neutrons together, while the electrons are attracted to the positive charge of the protons. Protons and neutrons can be broken down into smaller particles called quarks. All atoms of the same element have the same number of protons. The number of protons is the atomic number (written in subscript to the left of the atomic symbol). Unless otherwise noted, the number of protons equals the number of electrons. An atom is usually neutral in charge since the positive and negative charges are equal. We can determine the number of neutrons by using the mass number which is the sum of the protons and neutrons (written as a superscript to the left of the atomic symbol).

4 The number of protons is fixed, but the number of neutrons can vary within the same element. Thus, the same element may have different atomic masses. Atoms of the same element that have different atomic masses are called isotopes: Hydrogen: 1p, 1e- Deuterium:1p, 1n, 1e- Tritium: 1p, 2n, 1e- 1 amu 2 amu 3 amu *. Some combinations of protons and neutrons are stable, but other combinations are internally unstable and break down spontaneously. When this happens, the atom releases various subatomic particles and radiation. These isotopes are called radioactive isotopes. D. ELECTRON ORBITALS. Electrons move in undefined paths in regions around the nucleus, called orbitals (orbitals are merely a volume in which the electron is probably moving). Only two electrons can occupy the same orbital. Electrons move to the orbital that is lowest in energy, usually closet to the nucleus.

5 There are other regions called energy levels that contain orbitals. The energy level closet to the nucleus contains one orbital. The second energy level holds four orbitals and the third level also contains four orbitals. The first energy level can hold up to two electrons. (1s). The second energy level can hold up to eight electrons. (2s, 2p). The third energy level can hold up to eight electrons. (3s, 3p). There are more than three energy levels, but biologists are concerned with 18 total electrons. Atoms are most stable when their outer energy level is filled with electrons. Of the three atomic particles, only the electrons are directly involved in the chemical reactions between atoms. Not every electron has the same amount of energy (the ability to do work). There are two types of energy: Potential energy and Kinetic energy. Potential energy, the amount of energy that matter stores, is due to the position or location of the matter.

6 Electrons have potential energy in relation to the nucleus. The potential energy that an electron has is determined by its distance from the nucleus. The more energy the electron contains, the further it will be from the nucleus; an electron with low energy will be closer to the nucleus. Electrons can move to a higher energy level by having added to it (sunlight and light energy). Once the electron moves to the higher level, it contains that added energy. When this electron moves back to its original position, the same amount of energy that it took to move the electron is released. E. HOW ATOMS FILL THEIR OUTER SHELL. An atom with its outer shell filled with electrons is a stable atom. Atoms react with other atoms chemically by filling their outer shells. Atoms can fill their outer shell in one of three ways. 1. Ionic Bonds a. Gain electrons from another atom.

7 B. Lose electrons from its outer shell to another atom. 2. Covalent Bond a. Share one or more pairs of electrons with another atom. F. BONDS. There are two types of bonds between atoms, and these correspond to how the atom attains a stable electron configuration. 1. Ionic Bonds and Ions Look at Sodium and Chlorine. Sodium has 11 electrons: 1s2, 2s2, 2p6, 3s5. Sodium needs to gain seven more electrons or lose one electron. Chlorine has 17 electrons: 1s2, 2s2, sp6, 3p5. Chlorine has to lose seven electrons or gain one electron. Sodium donates one electron to Chlorine. These two atoms combine to form a compound, sodium chloride salt. An ion is any charged atom. Sodium donates an electron, which is negatively charged and becomes a positively charged ion. The Chlorine receives an electron and becomes a negatively charged ion. The two ions are Sodium+ and Chlorine.

8 When two atoms give and receive electrons, they form ions and ionic bonds. These bonds are approximately as strong as covalent bonds. Cation: Positively Charged Ion. Anion: Negatively Charged Ion. 2. Covalent Bonds Covalent bonds form through the process of sharing of electrons. Two atoms can fill their outer shells by sharing electrons. In fact, atoms give up little by sharing. For example, 2 Hydrogen atoms share their electron to have two electrons in their shell. Oxygen (1s2, 2s2, 2p4) shares two electrons to form O2. Methane is another example. Carbon has six electrons: 1s2, 2s2, 2p2. The carbon shares its four electrons of its outer shell with 4 Hydrogen atoms to get CH4 = Methane. If atoms share one pair of electrons, one electron from each atom, then they form one covalent bond (single bond). If two atoms share two pairs of atoms, two from each atom, they form two covalent bonds (double bond).

9 If two atoms share three pairs of electrons, three from each atom, they form three covalent bonds (triple bond). a. Nonpolar 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 there are two atoms of the same element or the same electronegativity, the pull of the electron is equal and the bond is a nonpolar covalent bond. covalent bonds If one atom is more electronegative than another atom, 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- due to the fact that a negative electron spends more time around its nucleus. The other atom has a slightly positive charge. This bond is called a polar covalent bond. c. Hydrogen bond Hydrogen bonds happen between molecules.

10 The electrons between hydrogen and the other atoms are shared unequally. (Hydrogen forms a polar covalent bond with an atom with greater electronegativity.) This unequal sharing causes the hydrogen to have a partial positive charge. The hydrogen is attracted to another atom or molecule, (not the one that it is covalently bonded to) with a slightly negative charge. G. Dissociation and pH scale Many substances come apart (dissociate) in water. Some dissociate completely, while others dissociate only partly. In a solution, some molecules are intact while others are ionized (gain or lose electrons). Water dissociates into H+ and OH- equally (hydrogen and hydroxide)(10 -7 Keq). 1. Acids Substances that yield H+ when they dissociate in water are called acids (by Arrherrius definition). Acids add H+ to the solution, increasing the H+ concentration.