Energy and Matter
Energy is roughly defined as the ability
to do work (i.e. movement, cause chemical or physical changes, etc.).
Energy exists as two forms, kinetic energy, which is the energy
of motion and activity, and potential energy, which is stored or
at rest. Matter is defined as anything which has mass and
occupies space. The building blocks of matter are called elements.
Ninety-two elements occur naturally, and these, plus eighteen which have
been artificially produced, are classified in the Periodic Table
of Elements, according to size, number of particles, and mass.
The smallest complete component of an element is called the atom,
and the number of atoms which compose a substance is the mass of
that substance. The atom is composed of three basic types of particles;
protons, which carry a net positive electrical charge, electrons,
which carry a net negative electrical charge approximately equal to that
of the proton, and neutrons, which have no electrical charge.
The smallest atom, hydrogen, is composed of a single proton which resides
in a region called the nucleus, and a single electron which moves or orbits
around the proton. The electron carries a great deal of energy which
is released to produce movement approaching the speed of light, but since
it is attracted to the positively charged proton, it orbits along a path
around the nucleus. The space between the electron and the nucleus
of the atom is called its energy level, since it takes a certain amount
of energy to maintain a specific distance. The greater the amount
of energy carried by an electron, the farther away from the nucleus of
an atom it will orbit. Electrons arrange themselves into pathways
called orbitals, and each orbital can hold a specific number of
electrons. The first orbital, which is closest to the nucleus of
the atom, can hold only two electrons. The second can hold eight,
and so on. If an atom has more or less electrons in its outermost
orbital than eight or some multiple of eight, it is chemically active,
since it can either lose, gain, or share those electrons with other atoms,
forming a molecule. The outermost orbital is called the valence
(bonding) orbital. Atoms which have valence orbitals containing
the maximum number of electrons, such as helium, neon, argon, xenon, and
radon are chemically inert, since they do not need to gain or lose electrons
to fill or remove an orbital. Since these elements exist in a gaseous
state, they are often called noble gasses.
The number of protons in the nucleus of an
atom is called the atomic number, and this is generally also equivalent
to the number of electrons orbiting the nucleus. Hydrogen is said
to have an atomic number of 1, since there is only one proton in its nucleus
and only one orbiting electron. The atomic mass of an atom
is the sum of the number of protons and neutrons in the nucleus.
Hydrogen has an atomic number of 1, since its nucleus only contains a single
proton. Helium has an atomic number of 2, and an atomic mass of 4,
since its nucleus is composed of two protons and two neutrons. Neutrons
act as a type of "nuclear glue" since they carry no charge. In the
absence of the two shielding neutrons, helium's protons would repel one
another and the atom would disintegrate. This is also true of the
atoms of other elements, which have increasingly larger atomic numbers
Isotopes and Ions
If an atom has more or less neutrons in its nucleus
than protons, it is called an isotope. Isotopes can be of
great interest to scientists, since many of them have a tendency to lose
the excess neutrons and energy. For example, the carbon atom, which
has an atomic number of 6 and an atomic mass of 12, can exist as several
isotopes. Carbon 14 (14C) contains two more neutrons and
has a known rate of decay which is measured according to its half-life,
or the amount of time necessary for the atom to lose approximately one-half
of its mass, of about 5600 years. By measuring the amount of 14C
in a sample such as a fossilized bone, scientists are able to estimate
how old the sample is.
Ions are elements which have either
more or less than the normal number of electrons filling their valence
orbital. This excess or lack of electrons gives a normally neutral
atom an electrical charge which is either positive or negative. For
example, sodium normally has eleven electrons, so there is only one electron
in its valence orbital. Chlorine has seventeen electrons, seven of
which compose its valence orbital. Sodium serves as an electron donor,
releasing its extra electron to chlorine, the electron recipient.
This changes sodium into a cation (Na+), or positively charged
atom, and chlorine into an anion (Cl-), or negatively charged
atom, and forms an ionic bond between the two atoms, producing sodium chloride
(table salt). Ionically bonded compounds are very hard to break physically,
but can be dissociated (pulled apart) by charged solvents such as water.
Another means by which chemically reactive elements
can fill their outermost valence orbitals is through the formation of covalent
(sharing) bonds. In this type of chemical bond, electrons
are shared between the valence orbitals of two or more atoms. This
sharing of electrons can either be equal, such that there is no residual
electrical charge, or unequal, resulting in weak residual charges on opposite
ends of the molecule. Molecules which carry no charge are called
nonpolar, while those which have charges are said to be polar.
Covalent bonds can be single, when only one pair of electrons is shared,
double, when two pairs are shared, or multiple, when more than two pairs
are shared. The strength of the bond depends on how many pairs are
A molecule of water (H2O) is composed
two hydrogens and one oxygen atom. Each hydrogen gains an electron
from oxygen, filling its valence orbital, while oxygen receives two electrons,
one from each hydrogen, raising the number of electrons in its valence
orbital from six to eight, thus satisfying the rule of octets for that
atom. The resulting molecule takes on a bent shape, wherein the two
hydrogen atoms lie at an angle to one another of about 104.5o
owing to the unequal affinity for electrons by the nucleus of the larger
oxygen and two small hydrogens and the repulsive forces exerted by the
protons in each of the three atoms. The sharing is thus unequal,
since at any time there could be as many as ten electrons surrounding the
oxygen, but only two surrounding each of the hydrogens. This establishes
polarity, with the oxygen end of the molecule more negative and the hydrogen
end more positive. The water molecule is thus analogous to a bar
magnet having negative and positive poles. It tends to be attracted
by the more negative oxygen end to positive charges, and to negative charges
by the more positive hydrogens. When the hydrogen end is attracted
to the partially negative end of another polar molecule, a hydrogen bond
can be formed which only lasts for milliseconds. Alone, a single
hydrogen bond is very weak, but many of these can form at any one time
and the net bond can be very strong. This explains the ability of
water to dissociate ionic compounds and pull other polar molecules apart
from one another when substances are dissolved, such as when sugar is placed
in water. It also explains the biologically important aspects of
water such as cohesion of water molecules allowing them to cling together
to produce surface tension and adhesion of water molecules to other polar
compounds, high specific heat caused by the release of heat when hydrogen
bonds form and absorption of heat when they break, and high heat of vaporization,
or the amount of heat necessary to initiate the physical change of water
from a liquid to a gas.
The interaction of water with ionic, polar
and nonpolar compounds is of great biological significance. When
a charged molecule, such as an ionically bonded compound like salt is dissociated,
water molecules quickly surround the cationic sodium and anionic chlorine
atoms, forming hydration shells which prevent the ions from forming new
associations with one another. When nonpolar compounds which do not
form hydrogen bonds are placed in water, they are pushed aside by water
molecules which tend to form hydrogen bonds with one another. Nonpolar
compounds are thus referred to as hydrophobic (water fearing).
Conversely, polar molecules are pulled apart from one another as hydration
shells form due to the tendency of the water molecules to form hydrogen
bonds with the molecules rather than one another. These compounds
are thus said to be hydrophyllic (water loving). The movement
of water molecules across structures such as the plasma membrane of a cell
is influenced by this interaction, since cell membranes are composed of
both hydrophobic and hydrophyllic components.
Acids and Bases
In liquid form, water is composed of molecules
which interact with one another owing to their dipolar structure.
Water molecules do not, however, remain joined together as H2O,
rather the relatively weak bonds between single hydrogen atoms in water
molecules are continuously breaking and reforming. This means that
at any time, there could be free hydrogen protons (H+) called
hydronium ions, as well as an equal number of OH- molecules
called hydroxide ions present in the solution. If the number
of hydroxide and hydronium ions present in a solution is equal, as is the
case for pure, deionized water, the solution is essentially neutral
with respect to its electrical charge. Alternatively, if a substance
dissociates in water such that the concentration of H+ ions is greater
than that of the OH- ions present, the solution has a net positive
charge and is said to be acidic. If the reverse is true, with
more OH- than H+, the solution is said to be basic. A measure
of the number of hydrogen ions present in a solution can be provided by
the pH scale, which represents pH as the negative logarithm of molar
H+ concentration. The number of H+ ions is
equal to an exponent of log base 10, but on the scale the exponent is written
as a positive number. Pure water has an H+ concentration
of 10-7 ions, meaning that at any one time there are as many
OH- as H+ present, therefore its pH value is 7.
The pH scale ranges from about 14 (10-14 H+ moles
per liter; strongly basic), to 0 (10-1 moles per liter; strongly
acidic). Most living cells can only operate properly across a narrow
range of pH values close to a neutral pH since overly acidic or basic environments
alter the shape of proteins necessary for essential life activities.
To balance alterations in external and internal pH balance, cells rely
on buffers, compounds which freely donate H+ ions when pH is
too high or take away excess H+ ions when the pH is too low.
States of Matter
The physical states of matter include liquids,
solids, gasses, and plasma. Individual atoms
and molecules are in constant motion, and the amount of motion is directly
associated with the amount of free energy (usually in the form of heat)
present in the system. While the basic chemical makeup of a substance
can change, the matter from which it is composed does not. Changes
in the state in which matter exists can either be physical, owing to the
spacing of atoms and/or molecules as a consequence of the amount of energy
present, or chemical, wherein the interactions between atoms or molecules
change. In a physical change the amount of energy which each
atom or molecule has is either increased or decreased and the spacing between
these changes. For example, if liquid water is cooled, the amount
of free energy decreases, and water molecules begin to slow down.
In time, enough free energy can be removed from the system to cause the
molecules to lie very close together and express little movement.
As a consequence, the water changes in its physical state from a liquid
to a solid called ice. Keep in mind, however, that the chemical structure
of the water (H2O) is not altered in any way, only the amount
of the free energy of movement expressed by the water molecules.
By giving ice more free heat energy, the water molecules begin to move
more rapidly and will eventually return to the liquid state. Giving
liquid water even more energy, raising the temperature to 100o C,
will make the molecules move so rapidly that they will leave the liquid
state and enter the gaseous state as water vapor.
Chemical changes occur when the actual
atomic makeup of molecules is altered. Such changes occur as chemical
reactions, wherein existing bonds between atoms are broken, or new bonds
are formed. Reactions which break bonds between atoms or molecules
release energy, generally in the form of heat. These are called exergonic
reactions. Conversely, endergonic reactions store energy
in the form of new chemical bonds. The storing and releasing of energy
in small, manageable amounts is vital to the proper metabolic functioning
Chemical reactions which occur within living
cells generally occur as one or more of three basic types. Exchange
reactions occur when atoms or parts of molecules are exchanged between
two molecules. For example, when sodium hydroxide (NaOH) is mixed
with hydrochloric acid (HCl), there is an exchange of atoms between the
two reactants, resulting in the formation of two products, water (H2O)
and sodium chloride (NaCl). Written in chemical notation, this how
the reaction appears:
NaOH + HCl --------> NaCl + H2O
Note that the number of atoms in the products
of the exchange reaction are exactly the same as the number in both of
the reactants. Condensation (dehydration) reactions occur
when two or more molecules are linked together through the removal of water
molecules. This type of reaction is necessary in living cells to
build new molecules for structure and as storage products. Hydrolysis
reactions are the opposite of condensation reactions, because they involve
the addition of water to break large biological molecules apart, releasing
the energy store within the bonds of their component parts. Both
condensation and hydrolysis are reactions which usually do not occur spontaneously
in living cells, but must be stimulated by a group of very specialized
protein compounds called enzymes.
All living things are composed of compounds which
contain carbon (C), hydrogen (H), oxygen (O) and nitrogen (N). These
are referred to as organic compounds. The carbon atom has
four valence electrons in its outmost shell, and can form single, double,
or triple covalent bonds either with other carbon atoms, or with other
elements, forming a complex skeleton. The structures which can be
formed by these associations can be quite complex, ranging from linear
to ring-shaped. Structure is important, because it conveys upon the
organic compound characteristics which allow it to interact with others
in ways which give rise to important cell components and metabolic activity.
Organic compounds are generally composed of subunits called monomers, which
can be joined together by condensation, or split apart by hydrolysis.
When two or more monomers are linked together, they form polymers which
can be quite large. There are four basic categories of organic compounds;
carbohydrates, lipids, proteins, and nucleic acids.
This category of organic compounds is composed
of carbon, hydrogen, and oxygen atoms bonded together in a ratio of 1:2:1
(carbon:hydrogen:oxygen). Carbohydrates serve as a source of energy,
serve to store energy, and as structural components for cells. The
smallest complete subunit of a carbohydrate is called a monosaccharide,
which may have a minimum of three carbon atoms, or a maximum of six.
Glucose and fructose are examples of six-carbon monosaccharide (sugar
monomer) compounds which are important to cells. They are called
isomers, since both have the same chemical formula (C6H12O6),
but have different three-dimensional arrangements of atoms. By enzymatically
removing and -OH group from glucose and an H+ from fructose,
the two can be linked to form a disaccharide (a type of polymer;
polysaccharide) called sucrose, which is common table sugar.
Mono- and disaccharide compounds can be broken
down relatively easily by cells to release energy stored between chemical
bonds. Larger polysaccharides are generally used as storage compounds
or structural components of cells, based on their shapes. For example,
starch is a complex polysaccharide composed of long chains of glucose
molecules linked together by condensation. Starch is used as an energy
storage compound by organisms such as plants. Many living things,
including humans, have the enzymes necessary for the hydrolysis of starch
into glucose, but do not have the enzymes necessary for the hydrolysis
of another compound called cellulose, which plants and algaes use as structural
components of their cell walls. Cellulose is chemically identical
to starch, but its individual glucose monomers are linked together differently.
Thus cellulose is an isomer of starch, chemically the same, but structurally
different. Some protists and bacteria have the necessary enzymes
to break cellulose down, and many of these have evolved symbiotic relationships
with animals. For example, termites and large herbivores such as
cows rely upon their stomach microflora such as the ciliate protist Trichonympha
to break down the cellulose into glucose, which can then be used by the
host organism as a source of energy. If the microflora are excluded
from the digestive process, both hosts would be unable to break cellulose
down, and would starve.
Lipids are also composed of carbon, hydrogen,
and oxygen, but not in the exact ratio of 1:2:1. The most common
forms of lipids are fats, waxes, and oils. These compounds have carbon
backbones which are either linear or ring-shaped. Lipids provide
energy storage (one molecule of a fat can store twice as much energy between
its chemical bonds than a molecule of glucose), structural components of
cells, insulation in multicellular organisms, lubrication, and protection.
Some lipid-containing compounds such as mucus and cerumin (ear wax) are
bacteriostatic, since they inhibit the growth of many bacterial species
and trap the organisms so that they cannot colonize the host. Lipids
can also serve as chemical messengers which elicit changes in cell activity.
Many hormones, such as testosterone, are lipid compounds.
Fats and oils are examples of triglycerides,
lipids composed of fatty acid monomers bonded to glycerol. Fats are
solids at room temperature since they are composed of fatty acids which
have hydrogens single-bonded to most of the carbon atoms composing the
backbone. Such fatty acids are said to be saturated.
Saturated lipids are very hard to hydrolyze, and can build up in the blood
vessels of humans, leading to the formation of plaques which block the
flow of blood. Conversely, oils are liquids which are generally unsaturated,
since some of the carbon atoms form double bonds with one another, leaving
no valence electrons available for forming bonds with hydrogen atoms.
Sterols are ring-shaped lipids.
These can serve as the basic components of hormones, and can act as units
to maintain the structural integrity of the cell membrane. Animal
cells contain the sterol cholesterol, while fungal cells contain
ergosterol. This distinction is important clinically, since
it can be used to produce antimicrobial compounds which are selectively
toxic (i.e. will attack pathogenic fungi while causing no toxic side-effects
to the host).
Phospholipids are composed of two fatty
acid "tails" bonded to a phosphate (-PO4) group "head".
These are key components of the cell membrane of plants, animals, protists,
and bacteria, but not of the archaebacteria, whose membranes are composed
of fatty acids bonded to hydrocarbon compounds rather than glycerol.
The polar/nonpolar nature of the phospholipid molecule facilitates an orientation
wherein the phosphate head faces water either outside of the cell or inward
toward the cytoplasm, while the nonpolar fatty acid tails face inward toward
one another in a double-layered structure. Though each phospholipid
subunit is independent of the other, this interaction with water helps
maintain the integrity of the cell membrane.
Proteins are long-chain polymers or polypeptides,
which are composed of monomer subunits called amino acids.
Each amino acid has two ends, a carboxyl group composed of carbon,
hydrogen, and oxygen, and an amino group composed of nitrogen and
hydrogen. When two amino acids are joined by condensation, hydroxide
is removed from the carboxyl group of one, and a hydrogen ion from the
amino group of the other. A carbon- nitrogen peptide bond
is then formed which links the two together. Since each amino acid
has its own specific three-dimensional architecture, peptide bonding results
in folding or bending of the growing polypeptide chain. The sequence
of amino acids, called the primary structure (1o) of
the protein, is important since it determines the shape and ultimately
the function of the protein. The secondary structure (2o)
is the way the protein arranges itself into folds or pleated sheets.
The tertiary structure (3o) refers to the three-dimensional
appearence the protein assumes, and the quartenary structure (4o)
refers to how each protein interacts with others in the formation of very
complex molecular structures.
Proteins form many major structural components
of the cell, often forming complexes with other organic molecules such
as lipids and carbohydrates. They serve in the production of components
for cellular recognition, movement, and transport of substances into and
out of the cytoplasm of the cell. Many also are vital to metabolism
as enzymes which catalyze chemical reactions both for the building and
breaking down of molecules in and outside of the cell. Without
the activity of enzymes, the cell would be incapable of living processes.
Another group of molecules essential for life
to occur are called nucleic acids. These are large, long-chain molecules
composed of carbon, oxygen, nitrogen, hydrogen, and phosphorus. Nucleic
acids function in the storage, transport, and processing of cellular information
by maintaining a molecular code for the production of polypeptides which
ultimately become structural proteins and enzymes. Each nucleic acids
is composed of a five carbon sugar, bonded to a phosphate group. Also bonded
to the sugar is a molecule called a nitrogenous base, which is one of five
types: adenine, thymine, cytosine, guanine, or uracil. The combination
of phosphate, sugar, and nitrogenous base is called a nucleotide, which
is the basic monomer of the nucleic acid.
Each nucleotide is joined to another by a 3'-5'
glycosidic covalent bond. These bonds form when the phosphate
group from one nucleotide is bonded by condensation to either the third
or the fifth carbon atom on the sugar molecule. Unless the nucleic
acid is circular, as in prokaryotes, this leaves unbonded portions on each
side of the sugar-phosphate backbone referred to as the 3' (-OH)
and the 5' (P) ends. This conveys directionality to
the molecule, which is important to the way it interacts chemically
with other molecules when it is replicated, and during the process which
gives rise to new polypeptides called protein synthesis.
The two categories of nucleic acids found in
cells are deoxyribonucleic acid (DNA), and ribonucleic acid
(RNA). DNA generally occurs as a double-stranded molecule, composed
of chains of nucleotides bonded by 3'-5' glycosidic bonds to form nucleosides.
The nucleosides are joined together by hydrogen bonding which forms between
the nitrogenous bases adenine, thymine, guanine, and cytosine on each strand.
Adenine and guanine are double-ringed bases called purines, while
thymine and cytosine are single-ringed bases called pyrimidines.
Adenine and thymine can form two hydrogen bonds, while guanine and cytosine
can form three, so these pairs bond to one another specifically in a complementary
fashion. The order in which nucleotide bases align themselves on
a nucleoside confers information ultimately about how amino acids are linked
together to form polypeptides. Each individual sequence of nitrogenous
bases which carries this information is called a gene, and all of
these combined compose the genetic code carried by each living cell.
RNA generally occurs as a single nucleoside
with a sugar-phosphate backbone linked by 3'-5' glycosidic bonds.
Its five-carbon sugar, ribose, contains an additional oxygen atom
not found in the sugar deoxyribose found in DNA. Additionally, RNA
is composed of the bases adenine, guanine, and cytosine, but does not contain
the pyrimidine thymine. Replacing thymine is the nitrogenous base
uracil, which can also form two hydrogen bonds when linked to adenine.
RNA can be found in three forms, messenger RNA (mRNA) which carries
the information concerning the sequence of amino acids contained within
a gene to the site of cellular protein synthesis, transfer RNA (tRNA)
which carries amino acids to the site, and ribosomal RNA (rRNA),
which acts with protein in structures called ribosomes to enzymatically
combine amino acids into polypeptides. In order for the cell to survive,
both RNA and DNA must act together to produce new proteins which enable
growth, repair, and metabolism to occur properly.
I. Test Yourself: Use this link to quiz yourself
about basic chemistry.
II. Diagram - Phosphorus has an atomic number of 15, and
an atomic mass of 30. Draw a diagram to represent this atom, including
the components of the nucleus.