Chapter
2: Chemical Principles
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The structure of the atom is a difficult thing to grasp at first. In many ways it is the ultimate in abstraction, something so small yet we see them everyday. A good exercise to do is to try and make the electron diagrams for the first two rows of the periodic table on your own. I am sure you can find them somewhere, but try it alone first... maybe later I'll post them. The key to making the jump from looking a bunch of diagrams and actually doing chemistry is in realizing that it is all about pushing electrons around. Pushing these electrons around results in the three types of chemical bonds.
Ionic bonds are the easiest to understand in that they have the simplest structure. In an ionic bond one atom has a very high attraction for electrons, while the other has a very weak ability to retain its few outer shell electrons. It is important to remember that we are only concerned with the outer shell in these atoms, any filled shells are considered stable and out of play. Ionic bonds occur between atoms with a large vertical separation on the periodic table, typically between atoms from column IA or IIA and those in VIIA (such as Na and Cl). The VIIA atoms have a very strong pull on electrons, a property called electronegativity, while those in IA and IIA have only one or two weakly attached outer shell electrons. The ionic bond results from the strong attraction of the VIIA atom pulling one of the weakly held electrons of a IA or IIA atom away, resulting in ions. The VIIA atom becomes a negatively charged ion and the IA or IIA atom becomes a positively charged ion. These opposite charges attract each other (similar to putting two magnets next to each other with opposite poles) and this attraction is the ionic bond.
Covalent bonds are about sharing electrons. The most important concept to get here is that electrons enter the shells in a specific order, forming first single electrons, and then pairs. Pairs of electrons are more stable than singles. A covalent bond is when two atoms contribute one electron each to form a pair, they share the two electrons between them. To add a wrinkle to this nice easy picture we have to introduce the concept of polar and nonpolar bonds. If the atoms involved in the bond are the same element, they will both exert the same pull on the shared electrons, resulting in an equal sharing. This equal sharing results in an equal distribution of the charges involved and is called a nonpolar covalent bond. However, if the elements involved are different, they will exert an unequal force on the electrons and produce a lopsided sharing arrangement. This lopsided sharing of electrons results in an unequal charge separation that is referred to as a polar covalent bond. Covalent bonds are on a continuum between very polar covalent bonds (high charge separation, though NOT ionic) and completely nonpolar bonds (between two identical elements). The degree of polar nature can be determined by how separated elements are on the periodic table, the more separated the more polar the bond between them as a general rule.
Hydrogen bonds are the result of polar covalent bonds. Highly polar bonds (such as O-H or N-H) result in a partial charge forming on each side of the bond. These are not true ions, rather a mild charge we refer to as a partial charge (denoted either as δ+ or δ-). These partial charges are attracted to their opposite charge and result in very weak, transient bonds between adjacent O-H and N-H bonds. Individual hydrogen bonds are very weak, but in mass are one of the strongest forces in biology. This importance is because all of biology is based on water, which is nothing but O-H bonds. In a quantity of water even if a million transient hydrogen bonds break a million more can instantly form.
I. The structure of atoms
A. Atomic structure
1. The smallest unit of matter is the atom
2. Atoms are composed of three particles
1. Protons – positively charged particles that are in the nucleus
2. Neutrons – neutral particles that are in the nucleus
3. Electrons – negatively charged particles that orbit the atomic nucleus in fixed energy level shells.
3. Atoms interact in certain combinations to form molecules.
4. The number of protons determines the type of atom and gives its atomic number.
5. The number of protons plus the number of neutrons gives an atoms approximate atomic weight.
B. Chemical Elements
1. All atoms with the same atomic number have the same physical properties and are classified as the same chemical element.
2. Atoms of the same chemical element can have differing atomic weights due to variations in the number of neutrons. These differing atoms are called isotopes.
C. Electronic configurations
1. Electrons orbit the nucleus in discrete electron shells.
2. Each shell is a discrete energy level.
3. Shells fill from lowest energy to highest energy
4. A stable atom has as many electrons as there are protons
5. Atoms whose electron shells are completely filled are very unreactive and considered inert.
II. How atoms form molecules: chemical bonds
A. The valence of an atom is the number of missing or extra electrons in its outer shell, and a measure of its combining potential.
B. Molecules hold together by forming attractive forces between valence electrons.
C. Ionic Bond
1. When an atom has the same number of protons and electrons it is electrically neutral. However sometimes they lose or gain electrons, becoming either positively (protons>electrons) or negatively (electrons>protons) charged. These are called ions.
2. When oppositely charged ions form an electrostatic bond, it is called and ionic bond.
D. Covalent Bond – A bond formed by two neutral atoms sharing valence electrons.
E. Hydrogen Bond – A bond where a hydrogen atom that is covalently bound to an oxygen or nitrogen forms a weak electrostatic interaction with another oxygen or nitrogen atom.
F. Molecular weight – The sum of the atomic weights for all atoms in a molecule.
G. Molar weight – The molecular weight of a molecule in grams
III. Chemical Reactions
A. Endergonic reaction – a chemical reaction that requires energy.
B. Exergonic reaction – a chemical reaction that releases energy.
C. Synthesis reaction – a chemical reaction that forms more complex and larger molecules.
D. Decomposition reaction – a chemical reaction that forms simpler and smaller molecules.
E. Exchange reaction – part synthesis / part decomposition
F. In theory all chemical reactions are reversible, though the energy requirements to go one way may be steep.
IV. Important Inorganic Molecules
A. Water
B. Acids – substances that dissolve into one or more hydrogen ions and a negative ion.
C. Bases – substances that dissolve into one or more hydroxide ions and a positive ion.
D. Salt – substance that dissolves into positive and negative ions, neither of which is a hydrogen or hydroxide ion.
E. pH – A measure of the acidity in a solution, designating the amount of hydrogen ions present. A pH of 7 is neutral, greater than 7 is basic, and lower than 7 is acidic.
V. Organic Molecules
A. Organic molecules are those that are made from carbon.
B. Functional group – are specific groups of atoms that are most commonly involved in chemical reactions and are responsible for the properties of the molecule (i.e. –OH or -NH2)
C. Carbohydrates
1. Complex molecules composed of hydrogen, oxygen, and carbon
2. Sugars and starches
3. Three types
a. Monosaccharides – 3 to 7 carbon atom simple sugar (i.e Glucose)
b. Disacchrides – a combination of two simple sugars
c. Polysaccharides – tens to hundreds of simple sugars combined into complex patterns (chitin, cellulose, and glycogen are examples)
D. Lipids
1. Nonpolar molecules (lacking significant electrostatic separation of charge) composed of hydrogen, oxygen, and carbon.
2. Three types
a. Simple lipids – contain an alcohol glycerol group and fatty acids. These are your oils and triglycerides.
b. Complex Lipids – lipids that contains elements such nitrogen, sulpher, and phosphorus; some have a polar (electrostatic separation of charge) side and a nonpolar side (i.e. phospholipids).
c. Steroids – an interconnected four carbon ring structure whose prime example is cholesterol.
E. Proteins
1. Proteins are organic macromolecules that contain carbon, hydrogen, oxygen and nitrogen.
2. Proteins are composed of monomers called amino acids, which have carboxyl and amino functional groups.
3. The linkage between amino acids is called a peptide bond.
4. There are twenty naturally encoded amino acids that have a wide variety of third functional groups. These functional groups give each amino acid a distinct chemical property.
5. Protein structure is divided into four levels.
a. Primary – the sequence of amino acids
b. Secondary – the local interactions between neighboring amino acids.
c. Tertiary – the long distance interactions and folding of the chain.
d. Quaternary – the interaction of multiple protein chains.
6. Denaturation is the unraveling of higher protein structure.
F. Nucleic Acid - The macromolecule that contains genetic information
1. Two types of nucleic acids
a. DNA - Deoxyribonucleic acid (contains deoxyribose as the base sugar), utilized
for the transfer and replication of genetic information in all living organisms.
b. RNA - Ribonucleic acid (conatins ribose as the base sugar), utilized to process
the genetic information into proteins, and is used in replication of some viruses.