# AP Biology/The Nature of Molecules

Study Time | X minutes. (explanation.)

## Subatomic Particles

Subatomic particles are the particles that make up atoms: protons, neutrons, and electrons. Protons and neutrons cluster in a dense core called the nucleus, while electrons orbit the nucleus in shells. The number of protons in a nucleus determines the name of the atom: one proton is hydrogen, two is helium, etc. See the periodic table for a full listing of all the atoms.

## Molecules

Molecules are groupings of atoms that bond together to form one building block of a substance. For example, water is H2O. A single molecules of H2O would be 2 hydrogen atoms and a lone oxygen atom.
Molecules are held together by three different bonds: ionic, polar covalent, and nonpolar covalent. An ionic bond is a bond between a metal and a non-metal. Generally the metal takes electrons from the non-metal, creating a very strong bond. A polar covalent bond is between two non-metals. A covalent bond is formed when valence electrons (electrons in the outer shell) are shared between the two atoms. Each atom wants to have eight valence electrons, and achieves this by sharing electrons and forming bonds. A polar covalent bond is when the electrons are shared unequally, because one of the atoms has a higher electronegativity (pull on electrons). A nonpolar covalent bond has electrons shared equally.
(Needs info on polar and nonpolar molecules, also on isomers, enantiomers, etc.)

## Compounds

ionic bonds covalent (polar/nonpolar) bonds isomers polymers

## Reactions

Any process in which chemicals change properties or identities (i.e. transform into other substances) is called a reaction. The substances that participate (enter) in a reaction are called the reactants; substances that form once the reactants react are called the products. For instance, consider the production of water (H$_2$O):
$2{\hbox{H}}_{2(g)}+{\hbox{0}}_{2(g)}\to 2{\hbox{H}}_{2}{\hbox{0}}_{(l)}$
The reaction dictates that for every two parts hydrogen (H$_2$) and one part oxygen(O$_2$) reacting together, two parts water will form as a product.

### Energy in Reactions

The problem, however, is that not all reactions - including this one - will occur unless energy is added to fuel the reaction. The energy needed for such a reaction to occur is called the activation energy, or threshold energy. In the water reaction above, we would have to combust (burn) both gases (when mixed together) to produce water, the end result. The combustion, in this case, provides the activation energy needed to fuel the reaction.
Reactions can also be classified and categorized based on their relationships with the energy involved. Endergonic reactions absorb energy in the process; exergonic reactions release energy in the process. The general form for an endergonic reaction is:
${\hbox{energy}}+{\hbox{A}}\to {\hbox{B}}$
and the general form for an exergonic reaction is:
${\hbox{A}}\to {\hbox{B}}+{\hbox{energy}}$

### Enzymes

Some reactions can be catalyzed - sped up - to overcome the 'barrier' set by activation energy. To do so, a catalyst is introduced - a substance that lowers the activation energy of a reaction but does not chemically affect either the reactants or the products. In biology, catalysis is usually carried out by specialized proteins called enzymes. Enzymes contain a region called an active site; when the reactants (also referred to as substrates) interact with the active site, they bind to the site (this is called the enzyme-substrate complex) and undergo an alternate reaction that requires less energy. The enzyme then releases the substrates, which have combined to form the product.

## Water

The wonderful properties of water.
Cohesion Cohesion is an intermolecular attraction between like molecules, and is useful in describing why certain liquids (such as water) have peculiar properties like surface tension (which create a skin like barrier between the air and the water.)
Adhesion Adhesion is the attraction of liquid molecules to other surfaces, this can be contrasted to cohesion which is the intermolecular attraction.
Capillary Action When adhesive forces are stronger than cohesive force, liquids can actually travel against the force of gravity, this is particularly useful when describing xylem in plant tissues and blood vessels. What aides in having adhesive forces stronger than cohesive forces is the fact that the path the liquid travels is very narrow, this creates a proportional lessening of cohesion (intermolecular bonds) to adhesion, attraction to the conduit of the liquid.
Heat capacity Also known as thermal capacity is the ability of matter to store heat, it is usually measured as the heat energy (joules) used to create a 1 Kelvin increase in a particular object.

## Acid/Base

Acids are substances that have a higher concentration of $H+$ ions relative to the concentration of OH- ions (example: acetic acid - $CH_{3}COOH$). Conversely, bases are substances that have a higher concentration of $OH^{-}$ ions relative to the concentration of $H+$ ions (example: sodium hydroxide). The strength of acids and bases is determined by how much they dissociate in water. Neutral pH water has a H+ concentration of $10^{-7}$. The addition of an acid would actually increase the hydrogen ion concentration even though the pH would become $<10^{7}$. This can be explained by the fact that the smaller the exponent, the larger the value. Thus, if the pH of a substance changes by 1, then it becomes 10 times more acidic or basic. There are three definitions of acids and bases (will be explained in the section below).
Acid Base / pH
The letters pH stand for "power of hydrogen"
One can measure pH using either litmus paper (which changes color using reduction/oxidation reactions) or a metal probe (where the substance will make electrons move toward or away from the probe).
The common Silver-Silver Chloride reference electrode used with most combination pH electrodes has a Potassium Chloride salt-bridge which is saturated with Silver Chloride.