The structure and function of all living things are governed by the laws fo chemistry. By understanding the fundamental principles of chemistry, we will have a better understanding of living things and how they function.

To understand living organisms and how they function, we must know something about how they are made up chemically.  To understand diseases and how to cure them we have to know their chemical makeup so we know how to destroy or alter their ability to take control or our lives.
    The chemistry begins with the Atom which all living and non living things are made of
1) Nucleus
  a) Protons- which have a positive charge
  b) Neutrons- which have a neutral or no charge
2) Electrons - which revolve around the nucleus of the atom and have a negative charge. Basically in most all atoms there are equal numbers of protons and electrons so therefore atoms basically have no charge. Sometimes atoms may react with other atoms which produce atoms with unequal numbers of electrons or protons, which produces atoms called Ions.
 When atoms in a sample of matter are all alike, we call this sample an element which cannot be broken down to any other substance by ordinary chemical means. We have 109 known elements which are denoted with 1,2,or 3 letter symbols in a chart called the Periodic Table of Elements. The number of protons an atom has is used as the atomic number in this table.
 Atoms are held together by chemical bonds which is called a compound. There are 3 kinds of bonds which are important to biological systems.

1) Covalent Bonds- (pg 33 of text) are formed when two or more atoms join together by sharing electrons. These are the strongest bonds and most of the compounds in our bodies are held together by covalent bonds. Atoms which are held together by covalent bonds are called molecules. There are two key properties of covalent bonds.
1) Very Strong
2) Very Directional- which means they can form bonds in more than one direction.

2) Ionic Bonds- These bonds are formed between two or more atoms in which one or more electrons are loss or gained which leaves us with a positively or negatively charged atom. Substances that form ionic bonds break apart when placed  in water, producing free ions. (pg 34 of your text)

3) Hydrogen Bonds- play key rolls in living organisms. The bond is very weak due to the fact atoms are not linked together here, but molecules are what is bonded together.  Water is a polar molecule which means as H, & O combine, the molecule has areas of unequal charge. As two polar molecules come together and form a bond, it is known as a hydrogen bond.

 Water is one of the most important molecules we have on our planet. We see its importance considering that 3/4 of our earths surface is covered by water and over 60% of our body is composed of water. Water has many functions within the biological processes of living organisms.

1) Heat Storage- Water heats slowly and retains its heat longer than other substances.
2) Water clings to itself & other molecules-
 a) Cohesion- is when water clings to itself, this is why water is a liquid at room temp.
 b) Adhesion- is when water clings to something other than itself.
3) Water Ionizes- as covalent bonds are put into water they break apart, producing ions. As water breaks apart , it produces H+ ions and OH- ions.
4) Water is a powerful solvent- Many compounds break up when put in water due to waters polar nature which pulls against compounds. When non polar molecules are placed in water ( like oil) it causes oil to crowd together, this is why oil and water do not mix

Section 2-2

Energy

Energy is defined as the ability to do work or cause change.
 
Forms of energy that are important to biological systems are explained below.

Chemical Energy- the energy found in molecules of matter.

Thermal Energy- The energy given off with heat that is used to do work or as a result of work.

Electrical Energy- Provided through electrical currents in positive and negative fields.

Mechanical Energy- the energy coming from the mechanical operation of something

Free energy- is the energy in a system that is available for work. Biologist refer to this type of energy when discussing living systems.

States of Matter

As we usually don't see it, all the atoms of molecules are in constant motion. The rate at

which these atoms or molecules of a substance move determines the following states of matter.

Solid- particles of a solid are tightly packed in a definite shape where they vibrate in place and maintain a fixed volumn or shape.

Liquid- are not as tightly packed as solids and the particles move more freely and will conform to the shape of the container they are held in.

Gas- these particles move most rapidly and have little or no attraction to each other as they fill the volumn of the container they are in.

Thermal energy is used to change the particle structure from one state to another.

The Chemical Reaction

The chemical reaction in fig. 2-7 on page 36 of the text shows a simple chemical reactions that takes place in the blood.

Reactants (compounds on the left side of the reactionary arrow) are components that are going to react together to produce a product. The Product (shown on the right side of the arrow) is the result of the reactants combining together. The double arrow means that the reaction can go either way. (Products converting into reactants or reactants converting into products)

Exergonic Reactions- are reactions which produce a net release of free energy, like when sugar is broken down into CO2 & H2O and energy is released for the cell to use.

Endergonic Reactions- is where there is a net absorption of free energy as during the photosynthesis chemical reaction where energy is stored in a glucose molecule.

Often times energy is required to start either endergonic or exergonic reactions. The energy required to do this is called Activation Energy.

Catalyst are chemicals which are used to reduce the amount of activitation energy needed to begin a chemical reaction. In living things these catalyst are called enzymes, and each enzyme is especially suited to bring about a specific chemical reaction.

Reduction-Oxygenation Reactions or Redox Reactions

The chemical reactions involving free energy in living organims often involve the transfer of electrons between atoms.

When a reactant loses one or more electrons thus having a positive charge, it is termed as a oxidation reaction.

When a reactant gains one or more electrons thus having a negative charge it is termed as a reduction reaction.

The chemical reaction in the formation of NaCl involves redox reactions

2-3 Solutions

Solution- is a mixture in which one or more substances are uniformly distributed in another substance, which can be liquids, solids or gases. Ex. blood plasma has all three states of matter making it up.

Solute- is the substance being dissolved in a solution and may be ions, atoms or molecules.

Solvent- is the substance in which a solute is being dissolved, ex is when water a solvent dissolves sugar which is a solute to form sugar water.

Concentration- is the measurement of the amount of solute dissolved in a fixed abount of the solution. This can change according to the amount of solute you add to a solution. The more solute the higher the concentration of a solution.

Saturated- is a term used to describe a solution in which no more solute can be dissolved in a solution. Ex. when we drink tea in the summer, if we add too much sugar, it will not dissolve in the tea, and will settle to the bottom of a glass.

Aqueous Solution- is one in which water is the solvent. This is universally important to living things.

Acids & Bases

Many of you are already familiar with the terms Acidity or Alkalinity of materials in biology or living organisms, at least you have probably heard of them. What causes a solution be be acidic or basic?

Dissociation of Water

Water is a polar molecule as we discussed earlier in lecture, meaning that each end of a water molecule, has a slightly negative end while the other end is slightly positive. This opposite polarity can cause a water molecule to split apart into an H+ hydrogen ion and an OH- hydroxide ion which is dissociation. After water dissociates, the free hydrogen ion can be picked up by another water molecule forming H3O+ which is a hydronium ion. Acidity or Alkalinity of a solution is based upon the amount of hydronium ions in a solution.

Acids- are solutions in which the number of hydronium ions are greater than the number of hydroxide ions. Acids tend to have a sour taste and can be corrosive.

Bases- are solutions in which the number of hydroxide ions are greater than the number of hydronium ions. Bases tend to have a bitter taste and tend to feel slippery when mixed with the oil of our skin.

pH scale- is a scale scientist use to compare the amounts of hydronium or hydroxide ions in a solution. This scale ranges from 0-14. A pH of 0 is very acidic and a solution of 14 is very basic. This scale is a logarithmic scale which means a change of one pH unit is tenfold change in the acidity or alkalinity. Litmus paper is a instrument used to detect this level by changing colors at various pH levels.

Example of logarithmic scale

a pH of 4 has 10 times more hydronium ions than a pH of 5 and the 4 has a 100 times more hydronium ions than a pH of 6.

Neutral- is when there are equal number of hydronium and hydroxide ions in a solution and is represented by the number 7 on the pH scale.

Buffers- are chemical substances that neutralize small amounts of either an acid or a base added to a solution.

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