14 January 2005
Lecture 3
Reading, Chapter 3
II. The Chemical Nature of Life, cont'd
You are a living organism. Your body is composed of organs, such as your heart and skin. These organs are in turn composed of tissues, which are groups of cells that function together, e.g. your blood is a tissue and is a component of your heart and skin. Tissues are composed of cells, which are the basic unit of living things. (Some organisms, in fact, are single cells). Cells consist of membranes and spaces that are in turn composed of molecules. Most of these molecules are much too small to be seen, even with a powerful microscope. Their properties exert an enormous influence on the living things that are made of them, however.
B. Chemistry
Understanding the molecules of living things is essential to understanding life. To know biology, you must know chemistry.
1. Atoms
Molecules consist of atoms stuck together by chemical bonds. In simple terms, atoms are particles of chemical elements that are made of three kinds of smaller particles: protons, neutrons, and electrons.
Protons are relatively large and have a positive electrical charge.
Neutrons are about the size of protons but have no charge.
Electrons are very small (1/2000 the mass of a proton) and have a negative electrical charge.
To understand chemical bonds between atoms in a molecule, you must know two properties of matter and the universe:
1) Particles with like charges, e.g. two electrons, repel each other. Particles with unlike charges, e.g. a proton and an electron, attract each other.2) Charged particles tend to move so as to create neutrality. One consequence of this is that atoms tend to have equal numbers of positive and negative charges, i.e. equal numbers of protons and electrons.
Some examples of atoms that are important in living things are:
Hydrogen (H) - 1 proton,1 electron, 0 neutrons
Oxygen (O) - 8 protons, 8 electrons, 8-10 neutrons
Carbon (C) - 6 protons, 6 electrons, 6-8 neutrons
Protons and neutrons are clumped together at the center of atoms in the atomic "nucleus". Electrons circle rapidly around the nucleus in orbits, forming a "cloud".
(Note that oxygen, carbon, and other atoms can sometimes have more neutrons than protons. These "heavy" forms of oxygen and carbon are called "isotopes". Isotopes are extremely useful in biology. For example, heavy carbon isotopes can be used to observe the flow of carbon atoms from the atmosphere into plants by photosynthesis, into animals when they eat the plants, and back into the atmosphere as the animals and plants die. Heavy isotopes of many atoms are used as "clocks" to determine the age of fossils and other materials.)
2. Electron shells
Electrons move rapidly through space and are drawn into orbits around atomic nuclei by their attraction to the protons there. The electrons orbiting around a nucleus have different amounts of energy. Low energy electrons orbit close to the nucleus while higher energy electrons orbit further away. Electron orbits are organized into "shells", each having room for a certain number of electrons. The first electron shell is where the lowest energy electrons are found and has room for 2 electrons. The second electron shell contains higher energy electrons than the first and has room for 8 electrons. The third electron shell contains higher energy electrons than the second and has room for 8 electrons. Large atoms, such as iron (Fe), have many electron shells but you need only think of these first three for now.
Two principles hold true about electrons in their shells:
1) The number of electrons is always equal or nearly equal to the number of protons in an atom.2) Atoms like to have their electron shells full and will even share electrons with other atoms to achieve this.
3. Chemical bonds
Molecules are formed when atoms stick together by chemical bonding. They stick together in several ways, i.e. there are several different kinds of chemical bonds.
a. Covalent bonds
These are the strongest type of chemical bond. They occur when two or more atoms share electrons in their outer shells so that all have their outer shells effectively full
For example, hydrogen (H) has 1 proton in its nucleus and 1 electron in the first shell. It would like to have another electron in its first shell to give it the full complement of 2. Oxygen (O) has 8 protons in its nucleus, 2 electrons in its first shell, and 6 electrons in its second shell. It would like to have 2 more electrons in its second shell to give it the full complement of 8
The happy ending to this story is that two hydrogens often share their single electron with an oxygen. This effectively gives the hydrogen atoms 2 electrons in their outermost shells and 8 electrons in the outermost shell of the oxygen atom. The result of these covalent bonds is water, H2O.
b. Ionic bonds
Ionic bonds between atoms are weaker than covalent bonds. They occur when an atom has one more or one less electron than it has protons in the nucleus, giving the atom a net positive or negative charge. Such charged atoms are called ions. Ions of opposite charge are attracted to each other and thereby form an ionic bond.
For example, sodium (Na) has 11 protons, 2 electrons in its first shell, 8 electrons in its second shell, but only 1 electron in its third shell. This single electron in the third shell is so "lonely" that it is easily taken away by other atoms, yielding a Na+ ion with a positive charge (11 protons, 10 electrons). Chlorine (Cl) has 17 protons in its nucleus, 2 electrons in its first shell, 8 electrons in it second shell, and 7 electrons in its third shell. Cl only needs one more electron in its third shell to be "happy" and often steals an electron from atoms like Na, yielding a Cl- ion with a negative charge (17 protons, 18 electrons).
Na+ and Cl- ions have opposite charge and form an ionic bond because of their attraction to each other. The result is sodium chloride (NaCl), also known as table salt.
c. Hydrogen bonds
Hydrogen bonds between atoms are weaker than ionic bonds. They occur when molecules are "polar". Polar means that the electrons of the molecule are not evenly distributed in their orbits but tend to hang around one end. For example, water (H2O) is polar. Its electrons tend to linger near the oxygen nucleus more than the two hydrogen nuclei. This gives the oxygen end of the molecule a small negative charge and the hydrogen ends small positive charges. Since opposite charges attract, the positive ends of water molecules stick loosely to the negative ends of other water molecules. These are hydrogen bonds. In a glass of water, hydrogen bonds between molecules cause the liquid to stick to itself.
Hydrogen bonding between water molecules gives water a relatively high boiling point because it takes a lot of energy to make the water molecules separate and form steam. Hydrogen bonding between water molecules also gives water a high heat capacity, meaning that it takes a lot of energy to raise the temperature of water. Both of these properties make water an ideal solvent for the chemistry of life. It remains a liquid over a realtively wide range of temperatures.
The polarity of water molecules also makes other polar or charged compounds dissolve in them. For example, NaCl separates into Na+ and Cl- ions in water (i.e. salt dissolves in water). This happens because the positive ends of water molecules crowd around the negatively charged Cl- ion and weaken its attraction to the Na+ ion. Similarly, the negatively charged ends of water molecules crowd around the positively charged Na+ ion and weaken its attraction to the Cl- ion. Non-polar compounds, e.g. oils, do not dissolve in water because they can't form hydrogen bonds with it.