Anatomy & Physiology
(c) The McGraw-Hill Companies, Inc.
Basic Chemistry for Physiology
It is assumed that the students are familiar with basic
chemistry. They should already be familiar with:
Atoms and Molecules
1. Structure of an atom: the subatomic particles are the
nucleus consisting of proton (+), neutrons (0), and
clouds of electrons (-).
2. Atomic number: the number of protons in an atom.
3. Chemical elements: the atoms with the same atomic
4. Atomic Weight: roughly equals to the sum of the
number of protons and neutrons.
5. Isotopes: atoms with the same atomic number, but their
nuclei contain different number of neutrons. Also known
as radioisotope. Thus a different atomic weight and
6. Electrons and Electron Orbital/shells: neutral atoms
have an equal number of electrons and protons. A pair
of electrons occupy each electron orbital and the
orbital of similar energy form the shells K, L, M,
etc…. These shells can occupy 2, 8, 10, electrons,
respectively. The rule of 8 applies.
The electrons in the outermost shell determine the
activities of the atom. If they are completely filled. The
atom will be in active I.e, He, Ne etc….
Electrons and Chemical Bonding
Chemical bonding occurs when the outermost electrons
are transferred or shared between atoms.
Two types of chemical bonds, Ionic bonds and covalent
bonds (require a large amount of energy to break them
up – around 100 Kcal/mole).
Then, there are other forms of bonds, often termed noncovalent bonds. They are hydrogen bonds, ionic
attraction, hydrophobic attractions, which have much less
energies than covalent or ionic bonds. ( 2-3 Kcal/mole)
• An atom is electrically neutral because it has an equal
number of protons and electrons. If an atom loses or
gains electrons, the number of protons and electrons are
no longer equal and a charged particle called an Ion is
Thus, they form anions (-) and cations (+).
How do neutral atoms become ionized atoms? After an
atom loses an electron, it has one more proton than it
has electrons and is positively charged. i.e.,
A neutral Na atom has 11 electrons, only one electron
on its outermost shell, which tends to be lost and makes
Na positive or electro-positive and if….
Neutral Cl atom has 17 electrons and 7 electrons in its
outermost shell. It can accept one electron and become
negatively charge, an Cl- anion or electro-negative
Thus, when sodium atoms and chlorine atoms are close
to each other, Na gives an electron to Cl and both
become ionized atoms, establishing an ionic bond and
will be held together with ionic bonds. This is what is
seen in a solid sodium chloride crystal.
• They are formed when atoms share one or more pairs of
electrons. One pair of electrons form a single bond, two
pairs forms a double bond, three pair form a triple bond.
• In covalent bonds, usually electrons are shared evenly
between the two bonding atoms, called polar bonds. But
in some molecules the electrons are not equally shared.
In other words, the electrons tend to stay longer with one
atom than the other. Then the atoms become slightly
ionized and the ionization becomes added energy for the
holding the atoms together forming a polar-covalent
• A molecule is formed when two or more atoms chemically combine
to form a structure that behaves as an independent unit.
• A compound is a substance composed of two or more different types
of atoms that are chemically combined.
Intermolecular Forces ( non-covalent bonds)
• They result from the weak electrostatic attractions between the
oppositely charged parts of different molecules, or between ions and
• The amount of energy found in these bond are small compared to the
covalent or ionic bonds. The mere large large number found in
biological macromolecules, makes them important
• Hydrogen Bonds – these are one of the most popular non-covalent
bonds and are found every where in life. Usually they require the
presence of hydrogen atom between two relatively small
electronegative atoms, O, N, F, etc….
NH+ ····O¯= C
• Ionic Interactions – they are interactions between ions with much
less energy than that of ionic bonds.
• Hydrophobic Interactions – these are forces that are found within
the oily molecules which are excluded from water. It is the force
that keep s oil droplets held together.
• Review the following terms:
• The making and breaking of chemical bonds are the chemical
reactions. In the body it is metabolism.
• Synthesis Reaction – occurs when two or more reactions
chemically combine to form a new and larger product. i.e., the
combination of two amino acids to form a dipeptide (anabolism).
– Dehydration reaction- removal of water from a reaction.
• Decomposition Reaction – a larger reactant is chemically broken
down into two or more smaller products (catabolism)
– Hydrolysis reactions – reactions that add water to a reaction.
Work, Energy, and Heat
• Work – is the change in physical status, such as,
pushing a car ( the car must move to be recognized as
energy being exerted)
• Energy and Heat - is the capacity to do work.
• Energy can be subdivided into two forms, Kinetic and
• Kinetic Energy – is the energy of motion. Moving
atoms and molecules, as well as a moving car.
• Potential Energy – is the stored energy within a object
placed high (I.e. force of gravity), a compressed spring,
and in chemical potential when a solution is more
concentrated than the other.
• These two energies could be interchangeable, as the
kinetic energy brings up an object to a higher place.
• The conversion between the two could be wasted energy
in the form of heat. Heat arises from the random motion
of matter and when in increases, the temperature goes
Classes of Reactions
There are two types of chemical reactions: Exothermic
(exergonic) and Endothermic (endergonic). The former releases
heat during the reaction, I.e. get hot. The latter consumes heat
during the reaction, i.e. gets cold.
The reaction may also be classified as :
Exchange reaction (swapping)
Reversible reactions and equilibrium
Acids and Bases
• An acid releases hydrogen ions (protons) into a solution.
HCl H+ + Cl¯
• A base removes hydrogen ions or releases hydroxide ions
into a solution
NaOH Na+ + OH¯
• Weak acids only partially dissociate in water.
Hac H+ + Ac¯
• The concentration of hydrogen ions is very important in blood and
other fluids since hydrogen is very reactive. Thus, people define a
special concentration scale for this ion.
• The concentration of hydrogen ion is expressed in its negative
pH = ¯log [H+]
• Thus, the smaller the number of pH, the higher the concentration of
• Furthermore, the change of one unit of pH equals to a factor of 10.
• Buffers are compounds that resist the change of pH. Antacids,
sodium bicarbonate, and body fluids are buffers.
• Inorganic compounds are void of carbon, except carbon
• The most important inorganic compound in life is water,
which amount ups to 70% of human body.
• Bonding of two hydrogen atoms with oxygen
(electronegative atom) has made the molecule slightly
Some features of water are:
1. Water is a good solvent.
2. Water is involved in many biochemical reactions for
hydration or condensation of molecules.
3. Water has a very high heat of capacity and heat of
vaporization contributing to homeostasis of the body.
4. Water increases it volume upon freezing.
Inorganic Acids and Bases
• is a compound consisting of a cation other than a
hydrogen and an anion other than a hydroxide ion. Salts
are formed by the interaction of an acid and a base in
which the hydrogen ions of the acid are replaced by the
positive ions of the base.
• Solid in dry form and are held together with ionic
bonds. They completely dissolve in water as ions.
(NaCl, KCl, MgCl2)
• Salts are electrolytes, since their ionic form contributes
to the flow of electrical currents. Abnormal
concentrations of electrolytes in the body effect vital
functions of the body. i.e cofactors such as Fe++, Zn++,
Cu++, enzymes and vitamins.
• Organic compounds contain carbon, except CO2, in
addition to H, and O are commonly found.
• Less frequently found but equally important atoms
found in organic compounds are P, N, S, Fe, and metal
• Consist of C, H, and O in a ratio of 1:2:1., such as
cellulose (plants) and glycogen (humans).
• Monosaccharides – are important source of energy in
metabolism and starches are excellent energy storage. A
monosaccharide is a simple sugar and has up to 6
carbons. ( glucose, fructose, galactose)
• Disaccharides – have two sugars and breakdown to
monosaccharides by hydration process., i.e. (glucose +
• Polysaccharides – are chain of monosaccharides. Long
chains of starches that are glucose based, while animal
polysaccharide –glycogen are a branched form of
polymeric glucose. They are water insoluble. After
being enzymatically digested to monosaccharides , then
they will enter the metabolic cycles.
• Some plant starches may not be digested within human
digested system, makes them a good diet food.
• Some carbohydrates makes a complex with protein and
become a glycoprotein. These are often found in the
• Carbohydrates are also found as (in):
– Ribose of DNA, RNA
– Energy source
– Structural support in plants, cell wall
– Glycoproteins of membranes
• Like carbohydrates, lipids consist of C, H, and O, but
their ratio is that of having less Oxygen.
• They also contain small amounts of P, N and S.
• Example of lipids are: Fats, Oils, & Waxes.
• Lipids are water insoluble, but may be solubilized by
binding without other molecules.
• When metabolized, lipids generate nearly twice as much
energy as carbohydrates do. (low fat diet)
• Lipids constitute about 12% of body weight.
• Lipids function in various ways such as, protection,
insulation, regulation as hormones, vitamins, membrane
structure, energy source, etc……..
• Are long chains of carbons surrounded with hydrogen atoms
except for a carboxylic acid (COO¯ )at the end.
• Saturated F.A’s have all their there C-C bonds are single bonds.
This type is found in butter, fatty meats, and ice cream.
• For unsaturated F.A.’s some C-C bonds are double bonds, such as
those found in vegetable oils.
• The ratio of saturated to unsaturated F.A.’s are known to be
important in relation to the risk of heart disease and other
• Are a conjugated form of fatty acids and is only
possible through the presence of another compound,
such as glycerol. Glycerol is a three carbon compound
is bound to three F.A’s by dehydration, thus
synthesizing a substance called a triglycerides.
• Triglycerides, neutral fats, are common fats in the body
serving as an energy reserve, fat droplets for heat
insulation and protection.
• Saturated triglycerides are solid at room temp, while
unsaturated triglycerides are usually liquid at room
• Phospholipids, are important lipids in the formation of
the double layer of the cell membrane.
• Phospholipids, important in cell membrane, consist of a
di-glyceride attached to a molecule containing a
• Thus, a phospholipids consists of a water soluble head
group and a water insoluble tails.
• Steroids are made of several carbon containing ring
structures and linear carbon chains.
• Cholesterol is one of the best known steroids.
• Cholesterol is a precursor for chemical messengers,
hormones, such as testosterone and estrogen.
• Cholesterol comes from:
– Diet, such as meat, cream, and egg yolks
– Manufactured in the body in the liver. Thus making
it difficult to control the level of cholesterol in the
blood with diet alone.
• There are about 100,000 different kinds of proteins, amounting to
20% of the total body weight.
• Basically, proteins are single chain amino acids consisting of
primarily of C, N, O, H and small quantities of S and metal ions.
So, proteins are different from carbohydrates in the amount of N.
Functions of Proteins:
– Metabolic regulation with enzymes
– Coordination of hormones
– Defense (antibodies)
• Protein structure – they are made of amino acids brought together
with peptide bonds into a non-branched molecule also called a
• There are about 20 AA’s in nature and human proteins use most of
them, but not all.
• The sequence of AA’s determines the nature of the protein.
• The basic structure of an amino acid includes:amino group,
hydrogen atom, carboxyl group, and a variable R side chain group.
• AA’s are bonded through peptide bonds to become polypeptides
• The AA sequence determines their primary structure.
• Their secondary structure, alpha, beta, pleated sheet,
and beta bends are the manner in which the
polypeptides are held together firmly.
• The tertiary structure is how the secondary and
random structures are folded together.
• The quaternary structure is the arrangement of
• The number of AA’s used in protein vary, i.e. insulin –
51, ribonuclease – 124, cytochrome C –104, myoglobin153 et…….
• The overall structure of proteins are:
• Proteins are sensitive to changes of temperature, at
43°C, many proteins will denature (no longer active)
and will cause the death of the organism.
Enzymes and Chemical Reactions
• In order for a chemical reaction to take place, two
atoms or molecules must first collide. Usually, the
kinetic energy of collision, especially after raising the
temperature, may be sufficient to initiate the reaction.
This energy is the activation energy.
• In the biologically systems, increasing the temperature
is not always possible and in viscous solutions the
energy of collision will not be really that great.
• Thus, enzymes reduce the activation energy
• A substrate fits into the active site of the enzyme. The
enzyme and substrate interaction can be visualized
conceptually by “lock and key” model and the
“induced fit” concept.
• Each enzyme has it’s optimal pH and temperature
• In addition to high content of C, H, O and N, the
concentration of P is high in nucleic acids.
• The sequence of nucleotides in a nucleic acid is the
source of metabolic and genetic information.
• There are two types of nucleic acids: Deoxyribonucleic
acids (DNA) and Ribonucleic acids (RNA).
• DNA is the primary source of genetic information
which will determine what kinds of proteins will be
made, hence genetically determined appearances.
• Since most enzymes are proteins, the regulation of
synthesis of proteins will also affect the rates of many
• There are several forms of RNS, which will be
Structure of Nucleic Acids
• Nucleic acids are made of a pair of poly-nucleotides.
• Each nucleotide consist of: 5- carbon sugar, phosphate
group, and a nitrogenous base.
• The sugar for DNA is Deoxyribose and for RNA is
• The bases for DNA are adenine (A), guanine(G),
cytosine ©, and Thymine (T). How they are sequenced
in the chain of nucleic acid determines the information
• The base for RNA is uracil (U) and it replaces Thymine
• For humans, DNA comes in a pair of coiling nucleotide
strands (double helix), bases pairing A-T and C-G, form
the complementary base pairs.
• Structure of RNA – RNA remains as a single chain. It
however may partially base pair on itself.
• ATP forms a high energy source.