CHEMISTRY REVIEW

SUMMER 2007

ELEMENTS - These are the pure substances that make up everything on earth. They cannot be broken down into simpler
substances by chemical means. There are a variety of elements which make up our bodies and are essential to us, such as C,
O, H, N, S, Ca, P, K, Na, Mg, Fe, etc. The first 4 of these make up 96% of body weight.

ATOMS - these are the smallest possible units of the elements. They retain the unique properties of the elements and are
made up of a nucleus and orbiting electrons.
NUCLEUS - this is made up of protons and neutrons.
protons - which carry a positive charge and a relative large mass

neutrons - which carry no charge and have the same mass as protons
electrons - carry a negative charge, and their mass is so small that it is not figured in with the mass of the protons and
neutrons
An atom carries a neutral charge, and since protons are positive and electrons are negative, their should be as many
electrons as protons

atomic number – the number of protons. This number is written as a subscript in front of the chemical symbol, 1H, 2He

mass number - number of protons + the number of neutrons. This number is written as a superscript, 1H, 4He.

From these two numbers, you can figure out the number of protons, the electrons (atomic #), and the neutrons (mass#-
atomic#)

Atomic weight - all atoms of an element have the same number of electrons and protons, but atoms may have a different
number of neutrons. Remember that this will not effect the charge of an atom, but will effect its weight. This leads to what is
known as isotopes. Thus, we can have different mass numbers for an atom. The average of the mass numbers, or the
relative weights, of all the isotopes would be the atomic weight. This is very close to the mass number of the most abundant
isotope. The atomic weight of hydrogen is 1.008; the most abundant isotope of hydrogen would have a mass number of 1.
Many of the heavier isotopes are unstable, and emit energy from the nucleus as they move to more stable forms. These
isotopes are known as radioisotopes, because they emit radioactivity. This energy can be detected by scanners, etc. so that
they can be used as diagnostic medicine, i.e. iodine-131 used in checking out the thyroid. They can also be used in
treatment, since the energy they emit is harmful, to destroy cancer cells.

Atoms are usually joined together to form molecules. If two (or more) of the same atoms are joined together, they will be
molecules of an element. If they are different atoms, they are then molecules of a compound.
Mixtures are combinations of 2 or more components and are classified as either solutions, colloids or suspensions. Mixtures
can be separated by physical means (filtering, evaporation), can be either homogeneous(the same throughout) or
heterogeneous(different in different places).

solutions - homogeneous mixtures and may be gases, liquids or solids. The solvent in the mixture is that which is in the
greatest quantity, that which the rest of the substances, or solutes, are dissolved in.
colloids - heterogeneous mixtures, and are usually translucent(milky), that is they scatter light, due to the larger size of the
solutes. These substances undergo sol-gel transformations, going from a fluid(sol) to a more solid(gel) state.(cytosol)
suspensions - heterogeneous mixtures and their solutes are large and usually very visible, such as sand mixed in water.
(blood)

There have been several theories put forth to explain the structure and the way that atoms interact with each other. It is
clear that the nucleus of an atom contain the protons and the neutrons, with the electrons moving around the nucleus in
some fashion.
orbital model - This theory states that electrons are thought to circulate around the nucleus in a cloud, and that you
cannot be certain exactly where the electron will be at any given time, but there is a high probability that it will be in a
certain place.

planetary model - said that electrons moved around the nucleus in discreet orbits, much like the planets move around the
sun, and would always be found in those orbits. While we know this is not true, it is still useful to use the planetary model in
explanations, because it is easier to demonstrate.

The electrons in the shells contain different energies and the shells themselves are sometimes referred to as energy
levels. Electrons farthest from the nucleus have the greatest potential energy.

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Valence shell – The outermost shell of electrons of any atom is known as the valence shell. The activity of an atom will
depend on how many electrons there are in this shell, if it is filled up or if it has room for more electrons or wants to get rid
of some that it has.
The shells follow the OCTET RULE or rule of eights- a valance shell needs 8 electrons to be stable, with the exception
of the first shell, which only needs 2
if a valance shell has 8 electrons in it, it will not react with another atom- it is inert
if a valance shell is not filled, then it will react with other atoms to try and fill itself.

BONDING OF ATOMS

atoms form bonds in order to stabilize their valence shell- they will either give up an electron, add an electron or share
electrons-
ionic bond - this is the type formed when they give up or accept an electron the atom that gives up an electron becomes
positively charged, and is called a CATION, and the atom that gains an electron becomes negatively charged and is called an
ANION-- example of NaCl - Na(atomic # 11) has one electron in it's valence shell, if it loses it, it drops down to the previous
shell which has eight electrons and is balanced, but becomes positive - Cl(atomic # 17) has 7 electrons in valence shell, and
if it attracts one will have 8, and will become negative. The two will be attracted to each other and form an ionic bond-- ionic
compounds form crystals because of the charged particles

non-polar covalent bond/molecule- this is the type formed when they share- most common atom is carbon, which has 4
electrons in it's valence shell--the basis of organic chemistry and life-- easier to share than to give up or accept more

Bonding is not black and white, there are degrees to how much one atom may attract an electron, and when they share one
may have possession more often than the other
electronegative - when an atom "hogs" the electron it is sharing, an attraction for electrons.
electropositive - when an atom lends it's electrons freely.

polar covalent bond/molecule - where one side of the molecule is positive, the other is negative--water is like this, and is
the reason why salts dissolve easily in water- the negative side is attracted to the positive side of the salt, and visa versa

hydrogen bonds - these are weak bonds between H which is slightly positive, due to the fact that it shares an electron, and
an electronegative atom also bonded to something else- it useful in forming structures of proteins and surface tension in
water

TYPES OF CHEMICAL REACTIONS

There are several types of equations that can occur when elements get together. First, the materials involved would be the
reactants, those things being acted on, and the products, the end result.

Anabolic, synthesis, combination reactions - combine to form larger, more complex molecules. anabolic means
constructive. This involves the formation of a bond, the use of energy to form that bond. It is endergonic.

Catabolic, decomposition reactions – breaking down into smaller parts. a degradative reaction. In this reaction, energy is
released. They are exergonic.

Exchange, displacement reactions - where an atom takes the place of another atom in a molecule. Bonds are made and
broken in this reaction. We will not know if we gain or lose energy in this reaction until we look at the details.

All of these reactions are reversible, meaning they can go in either direction. When they do go back and forth they are in
equilibrium. However, this is really only in theory. The reactions have a tendency to go in one direction, due to the fact that
whatever it is they are making is being used up and needs to be replaced.
Factors that influence chemical reactions deal with the fact that atoms and molecules must collide to interact. Small particles
move faster and therefore collide more frequently and with more force. The higher the temperature, the more the elements
move. The higher the concentration of the elements, the more likely they are to collide. And if catalysts are available, they
help to join the elements that have to react.

When two or more different atoms join together, they form a molecule of a compound (a molecule is two or more atoms held
together by a bond)

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There are two different kinds of compounds, inorganic and organic
inorganic- compounds that do not contain carbon, such as water, salts and acids
organic- compounds that contain carbon- have covalent bonds

INORGANIC CHEMISTRY

WATER
1. high heat capacity - which means it can absorb or release a lot of heat before it changes it's temperature

2. high heat of vaporization - which means it takes a lot of heat for it to turn to a vapor-- when you sweat, the moisture
on your skin has to absorb a lot of heat(from you skin) before it vaporizes

3. polar molecule - and therefore it will dissolve most other molecules-the universal solvent

4. reactant – breaks down a lot of material. Involved with hydrolysis and dehydration synthesis reactions

5. cushions

SALTS
These are ionic compounds that do not contain a H+ or an OH- ion- they are useful in helping to conduct electrical charges in
the body (electrolytes- NaCl, KCl) and are also used for strength in bones

ACIDS AND BASES

Acids –have a sour taste. Defined as proton donors (a proton is the same as a hydrogen atom w/o an electron)- some acids
dissociate completely, donating all their protons- these are the strong acids- whereas others will dissociate incompletely and
are weak acids-- this concept comes into play when we discuss buffers.

Bases – bitter taste, slippery. Proton acceptors, and often do this by donating an OH- ion, or the hydroxyl ion

pH - the measurement of the number of H+ or OH- ions in solution- a pH of 7 is neutral, which means there are equal
numbers of H+ and OH-, which is the case with water (H2O).

BUFFERS
Buffer system - helps to maintain the pH of a solution (the body's internal environment) within a certain pH. It does this by
replacing a strong acid with a weak acid, or a strong base with a weak base. A strong acid is one that will dissociate
completely, donating a lot of hydrogen ions to a solution (the acidity of a solution depends on the number of hydrogen ions
in solution). A weak acid will donate only a few hydrogen ions to a solution, it will not dissociate completely

STRONG ACID
10HCl > 10 H+ + 10Cl-

WEAK ACID
10HAc > 8 HAc + 8H+ + 8Ac-

these equations work in both ways, establishing an equilibrium between the molecules and the ions. If a strong acid is added
to a solution, the weak acid will be created by adding the hydrogen ions to the Ac-.

EXAMPLES OF BUFFER SYSTEMS

Bicarbonate- has carbonic acid(H2CO3) as it's weak acid, and sodium bicarbonate(NaHCO3) as it's weak base

HCl + NaHCO3 > H2CO3 + NaCl

NaOH + H2CO3 NaHCO3 + H2O

Proteins can also work as a buffer, which we will see when we look at them in more detail.

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ORGANIC COMPOUNDS

These are carbon containing compounds and are considered electroneutral. They share electrons and often form double
bonds or more. They have a set of functional groups which allow them to be identified by name and also give them certain
qualities in chemical reactions. Of the functional groups included in the table below, alcohols, esters, and ketones all act in a
polar nature with other compounds. The amine group can act as a base, accepting hydrogen ions, and the carboxyl group
can act as an acid, by donating hydrogen ions to a solution. The methane group is nonpolar. The phosphate group is ionic,
and is found in high energy molecules, like ATP. The sulfhydryl group, as part of an amino acid, helps in the structure of
proteins.

Functional groups
alcohol – OH

amine – NH2

carboxyl – COOH

ester – COO

aldehyde – COH

ketone - CO

methyl – CH3

phosphate – OPO3H2

sulfhydral – SH

CARBOHYDRATES- "Carbon hydrated"- contains the formula C(H2O)n, where the n is the number of carbon atoms. They are
classified by the number of sugar groups they contain. Their major function is energy.
monosaccharides- contain one sugar, simple ring structures of 5 or 6 carbons- glucose- the one involved in the body, blood
sugar.

disaccharides - contain 2 sugars and are formed through dehydration synthesis, where two sugars lose a water molecule
between them and form a bond

These sugars are too large to fit through a membrane and have to undergo hydration or hydrolysis, where they are broken
down to monosaccharides by the addition of water.
sucrose - table sugar- glucose + fructose

lactose - milk sugar- glucose + galactose

maltose - malt sugar- glucose + glucose

polysaccharides - long chains of simple sugars

Starch- the storage form found in plants

Glycogen - the storage form found in animals

both of the above storage forms store glucose

LIPIDS
These are molecules that are insoluble in water. Neutral fats(triglycerides) contain a glycerol molecule and three
fatty acids, which contain the -COOH group at one end. These are joined by dehydration synthesis. These can be either solids
or liquids, and are the type of fats known as saturated if they have only single covalent bonds, or unsaturated if they contain
double or triple bonds. Unsaturated are most often liquids, such as oils.

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 Lipids also include cholesterol, which is used to make hormones, and phospholipids, which are important structural
components of cell membranes. Phospholipids have a phosphorous head which is hydrophilic, and a lipid tail which is
hydrophobic

PROTEINS
These are long chains of amino acids, which contain and amine group and an acidic group. Amino acids are also
joined through dehydration synthesis. There is an interaction between the amine group and the carboxyl group that forms a
peptide bond, leaving the carboxyl group free to form another peptide bond.
There are 20 different amino acids to make up all the proteins in the body; they constitute the "alphabet of proteins"

Proteins have several structural levels

Primary- the string of amino acids

Secondary- joined by H bonds. This will be in the form of an alpha helix or a beta pleated sheet.

Tertiary- joined by H and covalent bonds

Quaternary - when two or more chains join together

While the primary structure of a protein is held together by peptide bonds, the other structures are held by hydrogen
bonds, which are weak. It is the upper level structures that determine the functioning of a protein. If we do not have this
structure, the protein may maintain its amino acid sequence, but no longer have its function. This can be caused by
chemicals, heat or other conditions, and is known as denaturing a protein.
This can play an important role in the activity of enzymes. Enzymes are materials in the body that act as catalysts,
that is they speed up reactions by lowering the energy required of the reaction or by bringing materials together. They are
generally protein in nature.

There are two different classes of proteins- Fibrous/Structural, which are stable, insoluble and are often found in tissues, and
Globular/Functional, which are mobile, active molecules, such as hormones, antibodies, enzymes or catalysts.

Proteins can act as a buffer, donating a H+ ion to solution, acting as an acid and bringing pH down by tying up hydroxyl ions.
Or it can act as a base by accepting hydrogen ions.
R-COOH > R-COO + H+ acid
R-NH2 + H+ > R-NH3+ Base

NUCLEIC ACIDS
These consist of Deoxyribonucleic acid(DNA) and Ribonucleic acid(RNA). These are made up of nucleotides, which
consist of a nitrogen containing base, a phosphate and a pentose sugar group.
DNA is a double helix structure where bases pair up with each other to form a chain. The base Adenine teams up
with the base Thymine, and the base Guanine pairs up with Cytosine. In RNA, the base Uracil takes the place of Thymine
Adenosine Triphosphate(ATP) is used as energy in the body. It is made up of an adenine molecule, a ribose sugar
and 3 phosphate groups, attached to each other by high energy bonds. When one of these bonds is broken, energy is
released. This molecule allows us to store energy in the body.