Chapter 2: The Chemical Basis of Life

Summary
This chapter mainly consists of basic chemistry which lays down a foundation for learning more intricate biology topics later on. All life-forms have matter, which is composed of atoms. Atoms are composed of subatomic particles (electrons, neutrons, and protons). Each specific type of atom is called an element, which are pure substances. The protons and neutrons of an atoms are confined to the center of the atom, at the atomic nucleus while the electrons are found in orbitals at varying distances from the nucleus. The number of neutrons and electrons in an atoms are equal, except for in the case of ions. Orbitals occupy "energy shells" that are numbered. The first energy can hold up to 2 electrons and each subsequent shell can hold up to 8 electrons. The electrons in the outermost electron shell level are called valence electrons. Atoms tend to be the most stable when the maximum number of valence electrons has been filled. Each elements has an atomic number, which is the number of protons it has. For example, helium has an atomic number of 2 and thus, it has 2 protons. The periodic table is arranged by atomic number and its groups or columns show the number of valence electrons the atoms in that group have. A Dalton is a unit of measure for atomic mass, and one dalton is equal to 1/12 of the mass of a carbon atom. A mole has an equal number of particles to the number of atoms in 12 g of carbon. Isotopes are forms of an element that differ in the number of neutrons they contain. For example, Oxygen-17 has 8 protons and 9 neutrons while Oxygen-16 has 8 protons and 8 neutrons. Hydrogen, oxygen, carbon, and nitrogen make up about 95% of the atoms in living organisms. Trace elements make up less than 0.001% of atoms, but are essential for normal bodily functions.


Molecules are formed when two or more atoms bond together and compounds are molecules composed of 2 or more elements. There are three types of bonds: covalent, ionic, and hydrogen. In a covalent bond, atoms share a pair of electrons. These are the strongest type of bond since the shared electrons acts as though it belongs to each atom. The octet rule states that most atoms are stable when the outer shell contains 8 electrons, with hydrogen being the exception. If the electron is more strongly attracted to one atom, that becomes slightly negative while the other becomes slightly positive, resulting in a polar covalent bond. Nonpolar covalent bonds have a relatively equal sharing of electrons. Hydrogen bonds are the weakest type, resulting from attraction between a polar molecule to an electronegative atom. Ionic bonds occur from the exchange of electrons, resulting in ions. A chemical reaction is when one or more substances are converted into other substances. The reactants become products. These reactions require an energy source, a catalyst, and a liquid environment in order to occur. They usually eventually lead to equilibrium.


A solution is made up of a solvent (liquid) and solutes (dissolved in the solvent). Water acts as the solvent in aqueous solutions, dissolving ions and molecules that have polar covalent bonds. Hydrophillic molecules readily dissolve in water while hydrophobic molecules do not dissolve in water. Water occurs in 3 states of matter: solid, liquid, and gas. Changes in the state of matter require an input of energy. The heat of vaporization is the amount of heat required in order to vaporize 1 mole of a substance, which is high in water. The heat of fusion is the amount of heat energy that has to be released from a substance to convert it from a liquid to a solid state, which is also high in water. Colligative properties are determined by the solutes, including the temperature at which a substance freezes or vaporizes. Water has various functions including: surface tension, cohesion, adhesion, participation in chemical reactions, providing force or support, evaporative cooling, and removing toxic wastes.


Acids are molecules that release H+ in solution while bases lower the H+ concentration, either by releasing OH- or binding H+. A pH of 7 is neutral, above 7 is is alkaline, and below 7 is acidic. A solutions's pH can affect how/if ions or molecules dissolve in water, the rate of chemical reactions, the shape and properties of molecules, and the capability of ions and molecules to bind to one another. Buffers help maintain a constant pH and buffer systems   can adjust pH by generating or releasing H+.


Helpful Links

This video explains the concept of a mole. While it is supposedly simple, I had trouble understanding it. So, this explains it pretty thoroughly. It's from Khan Academy and in case you didn't know, it pretty much has free tutorial videos or all sorts of subjects. Here's the link: Khan Academy.


Click here to see an animation of hydrogen bonds and water. You can scroll through by clicking on the bottom left. It basically tells you why water molecules have the properties that they do, such as why it is a polar molecule. There is also a pH animation to help you understand the different properties of acids and bases.


Article
http://www.ncbi.nlm.nih.gov/pubmed/21910123
This article talks about the desolvation of 2 hydrate solvates in a study on the compound finasteride, which is held together by water through hydrogen bonds in order to form channels for the solvent. When desolvation occurs, both the solvent and water simultaneously become obsolete, with no change in mobility of the water molecules. This is relevant because it involves the study of the affect of hydrogen bonds and solvents on a medication used to treat enlargement of the prostate gland.