ANAPHY CHAPTER 2: Basic chemistry
carbon atoms, and the element oxygen is composed of
CHEMISTRY
Chemistry is the scientific discipline concerned with the atomic
composition and structure of substances and the reactions they
undergo during chemical reaction.
Chemistry's fundamental units or components are the atom and
the molecule. Chemists are always interested in identifying and
explaining how chemical transformations take place.
MATTER
Matter is anything that occupies space and has mass. Matter may
neither be living or nonliving, has an odor or no odor. It can be
detected using our senses – sight, hearing, taste, touch and smell.
Matter is what the world made of. The three main states of
matter are solid, liquid, and gas.
Solids are particles that are securely bound to one another and
do not have enough freedom to move freely. (The solids have
definite volume and definite shape)
Liquids are particles that are close together yet have the ability
to move about. (They have a definite volume but no definite
shape and they take the shape of the container.)
Gases are particles that move rapidly and effortlessly apart from
one another. (It has neither a defined volume nor a defined
shape)
The matter only moves from one phase to another by the
physical means. One can create a physical change if energy is
added which means the temperature is increased or energy is
taken away stating something is frozen.
MASS
Mass is the amount of matter in an object. Mass measures the
quantity of matter regardless of both its location in the universe
and the gravitational force applied to it. An object's mass is
constant in all circumstances; contrast this with its weight, a
force that depends on gravity.
o The international unit for mass is the kilogram (kg),
which is the mass of a platinum-iridium cylinder kept
at the International Bureau of Weights and
Measurements in France.
WEIGHT
Weight is a gravitational force acting on an object of a given
mass. Weight is a measure of the effect of gravity (or other
acceleration) upon an object. The international weight
measurement is kilogram.
ELEMENTS
Elements are the simplest type of matter having unique chemical
properties. This are substances that are made up of only one type
of atom. They cannot be further separated into simpler
substances.
o About 96% of the body’s weight results from the
elements oxygen, carbon, hydrogen, and nitrogen.
o Other elements such as calcium helps form bones and
sodium ions are essential for neuroelectric activity.
o An element, or an atom of that element, is often
represented by a symbol. Usually the symbol is the
first letter or letters of the element’s name—for
example, C for carbon, H for hydrogen, and Ca for
calcium. Occasionally, the symbol is taken from the
Latin, Greek, or Arabic name for the element; for
example, the symbol for sodium is Na, from the Latin
word natrium.
ATOM
Atom is the smallest particle of an element that has the chemical
characteristics of that element. An element is composed of
atoms of only one kind.
 For example, the element carbon is composed of only
only oxygen atoms
Atomic structure - the characteristics of matter result from the
structure, organization, and behavior of atoms.
Subatomic particles – the three major types of subatomic
particles are neutrons, protons, and electrons. Neutrons have no
electrical charge, protons have positive charges, and electrons
have negative charges.
 The positive charge of a proton is equal in magnitude
to the negative charge of an electron.
 The number of protons and number of electrons in
each atom are equal, each atom is electrically neutral.
 Protons and neutrons form the nucleus at the center of
the atom and electrons move around the nucleus.
 Protons and neutrons are in the nucleus and electrons
can be represented by an electron cloud around the
nucleus.
Model of an atom:
Each element
is uniquely defined by the number of protons in the atoms of that
element. For example, only hydrogen atoms have one proton,
only carbon atoms have six protons and only oxygen atoms have
8
protons.
Positively charge atom: when an atom loses electron, it has one
more proton than it has electrons.
Negatively charged atom: when an atom gains an electron, it has
one more electron than it has protons.
ELECTRONS AND CHEMICAL BONDING
Chemical bond – interaction between atoms to form molecules
by either sharing or transferring their outermost electrons.
 The chemical behavior of an atom is dependent on its
electrons.
Electron cloud – around an atom’s nucleus is organized into
different energy level depending on the distance of an electron
from the nucleus.
Electron shells – the energy level that are often drawn as
concentric rings and is around the nucleus. There is a maximum
number of electrons that each shell can hold.
 Outer shells do not contain electrons until the inner
shells have reached their maximum.
Atoms with strong electronegativity are those with 6 or 7
electrons in the valence shell – these are farther away from
achieving an octet.
Atoms with a weak electronegativity are those with only 1 or
2 electrons in the valence shell – these are farther away from
achieving an octet.
 Notable exceptions to this generation is hydrogen
because hydrogen only has 1 proton in its nucleus, its
 electronegativity is lower than that of other, larger
atoms lack only valence electron.
 The innermost shell (the shell closest to the nucleus)
holds a maximum of 2 electrons and the remaining
shells hold a maximum of 8 electrons.
Valence shell – outermost shell.
 The number of electrons in the valence shell
determines an atom’s chemical behavior. If an atom’s
valence shell is not at its maximum, it will form bonds
with other atoms to achieve a full valence shell called
octet. Thus, most atoms follow the octet rule.
OCTET RULE
Rule that refers to the tendency of atoms to combine with
another atoms until each has 8 electrons in its valence shell.
Two ways an atom achieves an octet:
1. Transferring electrons between atoms.
2. Sharing electrons between atoms
Shared or transferred electrons determines the type of chemical
bond – ionic bond and covalent bond.
 Whether an electron is transferred or shared between
two atoms is determined by the relative
electronegativities of the two atoms.
ELECTRONEGATIVITY
Electronegativity is the ability of the atom’s nucleus to pull
electrons towards it.
o When the electronegativity between atoms are very
different, the atoms tend to transfer electrons from one
atom to the other. However, when the
electronegativities are similar, the atoms are likely to
share the electrons.
o The strong atom can steal the valence electron from
the weak atom, resulting in a transfer of electrons.
o Two major types of chemical bond are ionic and
covalent bonds.
ION
Ion is a charged particle; it is formed when the number of
protons and electrons are no longer equal.
CHEMICAL BONDING
Chemical bonding occurs when the outermost electrons are
transferred or shared between atoms.
Two major types of chemical bonding:
1. Ionic bonding - results when an electron is transferred
from an atom with a weaker electronegativity to an atom
with a stronger electronegativity.
o Occurs when electrons are transferred between
atoms, creating oppositely charged ions.
o Sodium atom lose an electron to become a
positively charged sodium ion (Na+)
o After an atom gains electron, it has one more
electron that is has protons and is negatively
charge. For example, chlorine atoms (Cl) can
accept an electron to become negatively
charge chlorine ion (Cl-)
o Oppositely charge ions are attracted to each
other, positively charged ions tend to remain
close to negatively charges ions.
2. Covalent bonding - forms when atoms share one or
more pairs of electrons, the sharing of electrons, rather
than the transfer of electrons, occurs because the
atoms have similar electronegativity.
o The resulting combination of atoms is called
a molecule. An example is the covalent bond
between two hydrogen atoms to form a
hydrogen molecule.
Single
covalent
bond – a
result from
the sharing
of one pair of
electrons by
2 atoms.
 For
example, a single line between the symbols of the
atoms involved represents a sing covalent bon (H-H);
(H-H covalent bond between two Hydrogen (H)
atoms, the two hydrogen atoms are now held together
by a covalent bond)
Double covalent bond – results when two atoms share two pairs
of electrons.
 For example, a carbon atom combines with 2 oxygen
to form carbon dioxide, two double covalent bonds are
formed. Double covalent bons are indicated by a
double line between the atoms. (O=C=O)
Polar covalent bond – the unequal, asymmetrical sharing of
electrons; occurs because one atom has a slightly stronger
electronegativity than the other atom. The unequal sharing
results in one end or pole of the molecule having a partial
electrical change opposite to that of the other end.
 For example, two hydrogen atoms can share their
electrons with an oxygen atom to form a water
molecule.
 Non-polar covalent bond: there is an equal sharing of
electrons between atoms because their
electronegativities are the same.
 Non-polar molecules: molecules with symmetrical
electrical charge.
HYDROGEN BOND
Hydrogen bond, it is not a chemical bond because electrons are
not transferred or shared between the atoms of the different
polar molecules.
o The positive end of one polar molecule can be weakly
attracted to the negative end of another polar molecule.
o The attraction between molecules
resulting from hydrogen bonds is
much weaker than in ionic or
covalent bonds. For example, the
positively charged hydrogen of
one water molecule is weakly
 attracted to a negatively charged oxygen of another
water molecule. Thus, the water molecules are held
together by hydrogen bonds.
MOLECULES
A molecule is formed when two or more atoms chemically
combine to form a structure that behaves as an independent unit.
o Sometimes the atoms that combine are of the same
type, as when two hydrogen atoms combine to form a
hydrogen molecule.
o a molecule consists of two or more different types of
atoms, such as two hydrogen atoms and an oxygen
atom combining to form water. Thus, a glass of water
consists of a collection of individual water molecules
positioned next to one another.
COMPOUND
Compound is a substance resulting from the chemical
combination of two or more different types of atoms.
o Water is an example of a substance that is a compound
and a molecule. Not all molecules are compounds. For
example, a hydrogen molecule is not a compound
because it does not consist of different types of atoms
o Sodium Chloride is an example of substance that is a
compound but not a molecule. A piece of NaCl does
not consists of individual sodium chloride molecules
positioned next to one another.
Molecules and compounds can be represented by the symbols of
the atoms forming the molecule or compound plus subscripts
denoting the quantity of each type of atom present. For example,
glucose (a sugar) can be represented as C6 H12O6, indicating
that glucose is composed of 6 carbon, 12 hydrogen, and 6
oxygen atoms.
DISSOCIATION
It is the separation of ions in an ionic compound by polar water
molecules.
o When ionic compounds dissolve in water, their ions
dissociate or separate, from each other because the
positively charged ions are attracted to the negative
ends of the water molecules, and the negatively
charged ions are attracted to the positive ends of the
water molecules.
Electrolytes – dissociated ions; they have the capacity to
conduct an electrical current – the flow of charge particles.
 When molecules dissolve in water, the molecules
usually remain intact even though they are surrounded
by water molecules. Thus, in a glucose solution,
glucose molecules are surrounded by water molecules.
 Glucose is the most abundant monosaccharide (simple
sugar)
SYNTHESIS REACTION
A combination of reactants to form a new, larger product.
Symbolically represented as: A + B → AB
o Synthesis of adenosine triphosphate (ATP); Synthesis
reaction = A-P-P (ADP) + P (phosphate group) A-P-P-
P (ATP)
o ATP is synthesized when adenosine diphosphate
(ADP), which has two (di-) phosphate groups,
combines with a phosphate group to form the larger
ATP molecule. The phosphate group that reacts with
ADP is often denoted as Pi , where the i indicates that
the phosphate group is associated with an inorganic
substance
o For example, Anabolism; all of the synthesis reaction
that occur in the body. The linking block to form
proteins, which may result in water formation.
o Growth. Maintenance, and repair of the body could
take place without anabolic reaction.
DECOMPOSITION REACTION
Breakdown of larger reactants into smaller products.
o Example of decomposition = A-P-P-P (ATP) +Pi
(Phosphate group)
o The decomposition reactions that occur in the body are
collectively called catabolism.
o For example, breakdown of foods into individual
nutrients, which uses water in the process (hydrolysis
reaction or water breakdown) which includes the
digestion of food molecules in the intestine and within
cells, the breakdown of fat stores and breakdown of
foreign matter and microorganisms in certain blood
cells that protect the body.
o All of the anabolic and catabolic reactions in the body
is called metabolism.
EXCHANGE REACTION
An exchange reaction is a combination of a decomposition
reaction in which reactants are broken down and a synthesis
reaction, in which the products of the decomposition reaction are
combined
o The symbolic representation of an exchange reaction
is: AB + CD → AC + BD
o An example of an exchange reaction is the reaction of
hydrochloric acid (HCl) with sodium hydroxide
(NaOH) to form table salt (NaCl) and water (H2 O):
HCl + NaOH → NaCl + H2O
REVERSIBLE REACTIONS
A reversible reaction is a chemical reaction that can proceed
from reactants to products and from products to reactants.
o The reaction can run in the opposite direction, so that
the products are converted back to the original
reactions.
o When the rate of product formation is equal to the rate
of reactant formation, the reaction is to be at
equilibrium.
o At equilibrium, the amount of reactant relative to the
amount of product is constant.
o At equilibrium, the amount of reactant relative to the
amount of product in each compartment is always the
same because the partition allows water to pass
between the two compartments until the level of water
is the same in both compartments.
o For example, an important reversible reaction in the
human body occurs when carbon dioxide (CO2) and
water (H2O) form hydrogen ions (H+) and bicarbonate
ions (HCO3 −). The reversibility of the reaction is
indicated by two arrows pointing in opposite
directions: CO2 + H2O H+ + HCO3 –
 If CO2 is added to H2 O, the amount of CO2
relative to the amount of H+ increases.
However, the reaction of CO2 with H2 O
produces more H+, and the amount of CO2
relative to the amount of H+ returns to
equilibrium. Conversely, adding H+ results
in the formation of more CO2, and the
equilibrium is restored.
o Maintaining a constant level of H+ in body fluids is
necessary for the nervous system to function properly.
This level can be maintained, in part, by controlling
blood CO2 levels.
o For example, slowing the respiration rate causes blood
CO2 levels to increase, which causes an increase in
H+ concentration in the blood.
ENERGY AND CHEMICAL REACTIONS
Energy is defined as the capacity to do work—that is, to move
matter. Energy can be subdivided into potential energy and
kinetic energy.
o Potential energy is stored energy that could do work
but is not doing so.
 For example, a coiled spring has potential
energy. It could push against an object and
move the object, but as long as the spring
does not uncoil, no work is accomplished.
o Kinetic energy is energy caused by the movement of
an object and is the form of energy that actually does
work.
  For example, an uncoiling spring pushing an
object and causing it to move. Kinetic
energy dies work by causing the movement
of an object.
o Potential and kinetic energy exist in many different
forms: chemical energy, mechanical energy, heat
energy, electrical energy, and electromagnetic
(radiant) energy.
o The chemical energy of a substance is a form of
potential energy stored in chemical bonds.
o Chemical bonding is a form of potential energy
because of the charges and positions of the subatomic
particles bound together.
o Chemical reactions are important because of the
products they form and the energy changes that result
as the relative positions of subatomic particles change.
o If the products of a chemical reaction contain less
potential energy than the reactants, energy is released.
The energy can be lost as heat, used to synthesize
molecules or used to do work.
o An example of a reaction that releases energy is the
breakdown of ATP to ADP and a phosphate group. In
the two reaction, the “larger sunburst” represents
greater potential energy and the smaller “sunburst”
represents less potential energy.
A. Energy is released as a result of the breakdown of
ATP.
B. The input of energy is required for the synthesis
of ATP.
o According to the law of conservation of energy, the
total energy of the universe is constant. Therefore,
energy is neither created nor destroyed. However, one
type of energy can be changed into another. Potential
energy is converted into kinetic energy.
o For example, as a spring is released, its potential
energy is converted to mechanical energy and heat
energy.
o Mechanical energy is energy resulting from the
position or movement of objects. Many of the
activities of the human body, such as moving a limb,
breathing, or circulating blood, involve mechanical
energy.
ATP → ADP + Pi + Energy (used by cells)
o If the products of a chemical reaction contain more
energy than the reactants, energy must be added from
another source. The energy released during the
breakdown of food molecules is the source of energy
for this kind of reaction in the body. The energy from
food molecules is used to synthesize molecules such
as ATP, fats, and proteins:
ADP + Pi + Energy (from food molecules) → ATP
RATES OF CHEMICAL REACTION
The rate at which a chemical reaction proceeds is influenced by
several factors, including how easily the substances react with
one another, their concentrations, the temperature, and the
presence of a catalyst.
o The rate of a chemical reaction increases when the
chemical reactants increases, the temperature
increases, or a catalyst is presented.
o A catalyst (enzyme) increases the rate of a chemical
reaction without being altered permanently.
o Reactants are substances initially present in a
chemical reaction that are consumed during the
reaction to make products. It differs from one another
in their ability to undergo chemical reactions.
o Concentration are components of a mixture or
solution. Within limits, the greater the concentration of
the reactants, the greater the rate at which a chemical
reaction will occur because, as the concentration
increases, the reacting molecules are more likely to
come in contact with one another.
 For example, the normal concentration of
oxygen inside cells enables it to come in
contact with other molecules, producing the
chemical reactions necessary for life. If the
oxygen concentration decreases, the rate of
chemical reactions decreases. A decrease in
oxygen in cells can impair cell function and
even result in cell death.
ACID AND BASES
The body has many molecules and compounds, called acids and
bases.
o An acid is a proton donor. Because a hydrogen atom
without its electron is a proton, any substance that
releases hydrogen ions (H+) in water is an acid. For
example, hydrochloric acid (HCl) in the stomach
forms H+ and chloride ions (Cl−): HCl → H+ + Cl−
pH
The letters pH stands for potential of hydrogen, since pH is
effectively a measure of the concentration of hydrogen ions (that
is, protons) in a substance. The pH scale was devised in 1923 by
Danish biochemist Søren Peter Lauritz Sørensen 1868 – 1969)
pH SCALE
A measure of the H+ concentration of a solution. The scale
ranges from 0-14.
o A neutral solution has an equal number of H+ and
OH− and thus a pH of 7.0.
o An acidic solution has a greater concentration of H+
than of OH− and thus a pH less than 7.0.
o A basic (alkaline) solution has fewer H+ than OH−
and thus a pH greater than 7.0
 Acids are proton (H+) donors while the
bases are proton receptors.
o As the pH value becomes smaller, the solution
becomes more acidic; as the pH value becomes larger,
the solution becomes more basic.
Refers to the
Hydrogen
ion
concentration in a solution.
Neutral: pH of 7 or equal hydrogen and hydroxide ions.
Acidic: a greater concentration of hydrogen ions.
Alkaline or basic: a greater concentration of hydroxide ions.
A change of one unit on the pH scale represents a 10-fold SALT
change in the H+ concentration, for example, a pH of 6.0 has A salt is a compound consisting of a positive ion other than H+
100 times more H+ than a solution with pH of 8.0. thus, small and a negative ion other than OH− (hydroxide ion)
changes in pH represent large changes in the H+ concentration. o Salts are formed by the reaction of an acid and a base.
o The normal pH range for human blood is 7.35 to For example, hydrochloric acid (HCl) combines with
7.45. If blood pH drops below 7.35, a condition is sodium hydroxide (NaOH) to form the salt sodium
called acidosis results. If blood pH rises above 7.45, a chloride (NaCl): HCl + NaOH → NaCl + H2O (Acid)
condition is called alkalosis results. Both acidosis and (Base) (Salt) (Water)
alkalosis can result in death.
o A base is a proton acceptor. For example, sodium
hydroxide (NaOH) forms sodium ions (Na+) and
hydroxide ions (OH−). It is a base because the OH− is
a proton acceptor that binds with a H+ to form water.
NaOH → Na+ + OH− H2O H+

SALT
A salt is a compound consisting of a positive ion other than H+
and a negative ion other than OH− (hydroxide ion)
o Salts are formed by the reaction of an acid and a base.
For example, hydrochloric acid (HCl) combines with
sodium hydroxide (NaOH) to form the salt sodium
chloride (NaCl): HCl + NaOH → NaCl + H2O (Acid)
(Base) (Salt) (Water)

BUFFERS
A buffer is a chemical that resists changes in pH when acids or
bases are added to a solution containing the buffer.
o The chemical behavior of many molecules changes as
the pH of the solution in which they are dissolved
changes.
o The survival of an organism depends on its ability to
maintain homeostasis by keeping body fluid pH within
a narrow range. One-way normal body fluid pH is
maintained is through the use of buffers.
o When an acid is added to a buffered solution, the
buffer binds to the H+, preventing these ions from
causing a decrease in the pH of the solution.
Illustration below:

ACID-BASE-BUFFER PHYSIOLOGY
o The most important way that the pH of the blood is
kept relatively constant is by buffers dissolved in the
blood. Other organs help enhance the homeostatic of
the buffers.
o The kidney help remove excess chemicals from the
blood. It is the kidney that ultimately remove (from
the body) H+ ions and other components of the pH
buffers that build up in excess.
o Acidosis is the results from failure of the kidney to
perform this excretory function is known as metabolic
acidosis. However, excretion by the kidney is a
relatively slow process, and may take too long to
prevent acute acidosis resulting from a sudden
decrease in pH (e.g., during exercise).
o The lung provides a faster way to help the pH of the
bloods. The increased breathing response to exercise
helps to counteract the pH- lowering the effects of
exercise by removing CO2, a component of the
principal pH buffer in the blood. Acidosis that results
from failure of the lungs to eliminate co2 as fast as it
is produced is known as respiratory system.