Biology: Semester I

Sections:

Introduction | Section 1 | Section 2

Section Two:

Part 1 | Part 2 | Part 3 | Part 4 | Part 5 | Part 6

Biology: Chemistry of Life: Part Two Atoms, Elements, and Compounds What does all matter have in common? Matter consists of atoms. An atom is the smallest unit of matter that cannot be broken down by chemical means. The exact structure of an atom is difficult to determine because atoms are so small. The universe consists of matter and energy. Energy is the capacity to do work. Matter has mass and occupies space. The atom is composed of smaller units called subatomic particles that were discovered during the 1800s. Descriptions of these particles appear in the table below. Table—Some Basic Subatomic Particles. Particle Name Location in Atom Electrostatic Charge Mass (in atomic mass units) Proton In the nucleus +1 1 Neutron In the nucleus 0 *1+ Electron Orbital surrounding the nucleus -1 1/1800 *The mass of the neutron is slightly greater than the mass of a proton. The proton is located in the nucleus of the atom, which is the center. Every atom has at least one proton. A proton has a charge of +1 and a mass of approximately 1 atomic mass unit (amu.). One atomic mass unit is defined as one-twelfth the mass of a carbon-12 atom. Using the atomic mass unit allows us to refer to atomic masses using whole numbers instead of decimal values (one amu is approximately 10-27 kilograms or 0.00000000000000000000000001 kilograms)! Atoms of different elements have different numbers of protons. For example, a hydrogen atom has one proton; a helium atom has two protons. The neutron also is located in the atom’s nucleus. The neutron has no charge and has a mass of slightly over 1 amu. The only exception to this rule is hydrogen, which has no neutron. The electron is a very small particle located outside the nucleus. Because electron movement has been recorded at near the speed of light (about 186,000 miles per second), the precise location of electrons is hard to pin down. Most of the time they are located around the atomic nucleus. The charge of an electron is -1. Its mass is negligible (approximately 1800 electrons are needed to equal the mass of one proton). An element is a pure substance made of only one kind of atom. For example, pure, 24-karat gold is composed of only gold atoms. Each element is identified by the number of protons in the nucleus. More than 100 elements are known. Most occur naturally, but others are human-made. Every element is represented by a one- or two-letter symbol. For example, H is the symbol for hydrogen. Atoms are the smallest particles into which an element can be divided and still have the properties of that element. Although ancient Greek philosophers developed the idea of the atom, they did not know that the atom, as we understand it today, is divisible. Scientists such as Enrico Fermi showed that sub-atomic particles (protons and neutrons) can react to release tremendous energies. This is evident in nuclear explosions or thermonuclear power plants. A compound is a substance made of one or more elements whose atoms have joined.For example, NaCl, sodium chloride (ordinary table salt), is created when sodium (Na) atoms and chlorine (Cl) atoms react and link together. Several types of chemical bonds and attractions are important to the study of biology. Ionic bonds form when neutral atoms gain or lose electrons to become charged particles called ions. A chlorine atom tends to gain one electron, acquiring a charge of -1, when it contacts a metal like sodium. The chlorine atom (Cl) is now a chloride ion (Cl-). A sodium atom tends to lose one electron, acquiring a charge of +1, when it comes in contact with a nonmetal like chlorine. The sodium atom (Na) is now a sodium ion (Na+). Oppositely charged ions are attracted to each other. Thus, Cl- and Na+ form an ionic bond, becoming the compound sodium chloride (NaCl). Not all atoms bond in this manner. Covalent bonds form when atoms neither gain nor lose, but instead share their electrons. In a covalent bond, the electron clouds surrounding two atomic nuclei overlap, as shown in the representation of the hydrogen molecule (H2) below. The shared electrons spend most of their time in the space between the two bonded nuclei. A carbon atom (C) has four electrons it can share with other atoms. The molecule methane, chemical formula CH4, has four covalent bonds. These bonds occur between the one central carbon atom and each of the four hydrogen atoms. To form each covalent bond, carbon contributes an electron and hydrogen contributes an electron. The sharing of a single electron pair is a covalent bond. When two pairs of electrons are shared between two atoms, a double bond results, like in carbon dioxide. Sometimes, instead of being shared equally, electrons in a covalent bond tend to spend more time near one of the two bonded atoms. In these cases, a polar covalent bond develops. Each H-O bond in a water molecule is an example. Since the electrons spend more time with the oxygen atom, that end of the bond takes on a slightly negative charge. The movement of the bonded electrons away from the hydrogen end leaves a slightly positive charge. Since the water molecule has a bent shape, the entire molecule has one slightly negative side and one slightly positive side. Water is one example of a polar molecule. Polar molecules are neutral overall but that have areas of slightly positive and slightly negative charge. The shapes of molecules are often key to their functioning. Can you think of any toys or models you have played with in the past that might help you understand atoms and chemical bonds? A hydrogen bond is an electrical attraction that forms between the positive end of one water molecule and the negative end of another. A single hydrogen bond between water molecules is weak. In large enough quantities, however, the result is strong enough to hold molecules together in a three-dimensional shape. Now go on to the next part.

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