Chemical Basis of Life
Before we can explore the world of biology we must first take a look at chemistry.
Organisms are essentially bags of chemicals. The way these chemicals are
arranged, the compounds and molecules they form make up cells and ultimately
entire organisms. In order to understand how organisms and parts of those
organisms function we must look at the composition of the chemicals that
comprise the organism. As you will learn structure determines function.
Living things are made of matter-anything that occupies space and has mass.
Matter exists in 3 physical states: gas or vapor, liquid and solid. All matter is
composed of elements. 92 occur naturally; 25 of which are used in the human
body. 96% of the body is composed of only 4 elements: O (oxygen), C (carbon), H
(hydrogen) and N (nitrogen). Ca (calcium), P (phosphorous), K (potassium) and S
(sulfur) make up most of the remaining 4%. Trace elements such as Fe (iron), Mg
(magnesium), Mn (manganese) and I (iodine) are some of the more important trace
elements. They are also called essential because humans cannot live without them.
As an example we need 0.15mg of I/day. If not the result is goiter.
Elements are substances which cannot be decomposed into simpler substances by
ordinary chemical means. They are the basic substances out of which all matter is
composed. Elements combine to form molecules and compounds by chemical
bonds. Each element consists of one kind of atom which is different from all other
elements. Atom comes from the Greek word: atomos meaning indivisible or
invisible. Dalton's Atomic Theory of 1803 tells us that each element is composed
of extremely small particles called atoms.
Atoms are the basic building blocks of matter. They are the smallest units of an
element that retains the properties of that element. The structure of an atom
determines how the element it comprises can combine to form compounds and
molecules. Dividing an atom yields sub-atomic particles and destroys the
element's unique properties. There are over 100 sub-atomic particles known but
only three are important for us: proton, electron & neutron.
The proton has one positive electrical charge +1. Electrons possess one negative
electrical charge. Neutrons have no charge and are electrically neutral. Neutrons
and protons are found in the nucleus of an atom while electrons orbit about the
nucleus at about the speed of light. Unlike charges attract; therefore the positive
charge of the proton and the negative charge of the electron keep the particles close
together.
Elements differ in the number of the three sub-atomic particles that they possess.
All atoms of an element have a unique number of protons. The number of protons
in an atom is the atomic number of an element. The number of protons equals the
numbers of electrons so that there is no net electrical charge.
A He (helium) atom has 2 neutrons and 2 protons in the nucleus. The atomic
number of helium is therefore 2. The mass number of an element can be found by
adding the number of neutrons and the number of protons; so in the case of He the
mass number is equal to 4. The mass of a proton and the mass of a neutron are
nearly identical. Electrons have only 1/2000 the mass of a proton; so the mass
number is equal to the total number of protons and neutrons without considering
the mass of the electrons. Variant forms of elements can exist. Some atoms of an
element may have different mass numbers. These elements are called isotopes.
Isotopes have the same number of protons and electrons but differ in the number
of neutrons.
Since the net charge on an atom is 0, an atom must have the same number of
electrons as protons therefore an atom of helium has 2 electrons. The arrangement
of electrons determines the chemical properties of an atom. Electrons play a major
role in chemical reactions. They have different amounts of energy; the farther from
the nucleusthe greater their energy. Electrons in an atom are found at different
energy levels called shells. Each shell accommodates a specific number of
electrons. The innermost shell holds 2 electrons; the 2nd and 3rd hold 8. It is the
number of electrons in the outermost shell that determines the chemical properties
of an atom. Those whose shells are not full will interact with other atoms and
therefore participate in chemical reactions. H (hydrogen) has only one electron in
its outer most shell and therefore is very reactive. C, N, & O are also highly
reactive since their outer shells are incomplete. He is inert or nonreactive because
its outer shell is full.
When two atoms with incomplete outer shells react with another atom they can
either share, donate or receive electrons so both partners can have a completed
outer shell. These interactions usually result in atoms staying close together held
by attractions called chemical bonds.
Chemical Bonds
Chemical bonding results in the formation of molecules. Molecules are substances
containing two or more elements combined in a fixed ratio held together by
energy. NaCl is a molecule which you know as table salt. It is composed of one
Na+ and one Cl- held together by a chemical bond between electrons in the outer
shell of the Na atom and the outer shell of the Cl atom.
There are two basic types of chemical bonds: ionic and covalent. In ionic bonds
electrons are transferred from one atom to another and ions are formed. Atoms
can gain or lose electrons. When electrons are lost or gained by a neutral atom, the
result is a charged particle called an ion. Na has 11 protons and 11 electrons so it
can easily lose 1 electron. By losing an electron the sodium atom has 11 protons
and 10 electrons; now there is an excess positive charge. The sodium atom is called
a cation and is designated as Na+ to show it has one positive charge. The ionic
state is represented by a superscript to the right of the chemical formula: Na +,
Mg2+.
The Cl (chloride) atom easily gains 1 electron. It now has 17 protons and 18
electrons; an excess negative charge and therefore is designated Cl-. It is called an
anion. When Na and Cl meet they will react. Na donates 1 electron to Cl so that
now both have complete outer shells. NaCl forms. NaCl is electrically neutral.
Na+ and Cl- are simple ions, in contrast to polyatomic ions such as NO3- (nitrate
ion) and SO42- (sulfate ion) which we will discuss later in the course. Polyatomic
ions are compounds made of chemically bonded atoms, but with net positive or
negative charges.
Covalent bonds form when 2 atoms share one or more pairs of electrons. Many
elements are found in nature in their molecular form where 2 or more atoms of the
same element are bonded together. Oxygen is most commonly found in its
molecular form O2 (2 oxygen atoms covalently bonded together). 7 elements
commonly occur as diatomic molecules-H, N, O, F, Cl, Br, I. The number of
covalent bonds an atom can form equals the number of electrons needed to fill its
outer shell. H-can form one; O-2 and C-4.
Chemical Reactions
Chemical reactions refer to changes in the chemical composition of matter due to
rearrangement of molecules by breaking and reforming chemical bonds. Atoms
combine to make molecules. 2 H2 + O2  2H2O. 2 molecules of H react with one
molecule of O (reactants) to form 2 molecules of water (product). The arrow
indicates the direction of the reaction. Chemical reactions cannot create nor destroy
matter-only rearrange it. The two sides of an equation on either side of the arrow
must balance.
Water and Life
One inorganic molecule, water has important effects on all biological systems. It is
the single most important constituent of the body. Life on Earth depends on the
unusual structure and anomalous nature of liquid water. Organisms consist mostly
of water. Water comprises 2/3rds the total body weight of humans. Biochemistry is
a wet chemistry meaning that biological molecules do not react chemically unless
in solution. Water is an important reactant. In fact nearly all chemical reactions in
the body occur in water.
Foods are digested to their building blocks by decomposition reactions called
hydrolysis which involves the addition of water. When large molecules form from
smaller ones, water is removed in dehydration synthesis or condensation reactions.
Water seems like a very simple molecule consisting of 2 H atoms attached
covalently to one O2 molecule-few molecules are smaller. Water’s size belies its
complexity.
In molecules, the two atoms involved in the bond have an equal pull on electrons
involved in the bond. The bond is said to be nonpolar. In water, oxygen pulls
more on the electrons than does the hydrogen atom so the shared electrons spend
more time near the oxygen molecule than near the hydrogen. This unequal sharing
produces a polar bond.
Because O2 attracts electrons more strongly than H water has an asymmetrical
distribution of charge; resulting in a V-shape. The 2 Hs are located at one end of
the molecule and the O2 at the opposite end. The H end has a positive charge and
the O end has a negative charge. Since water has 2 poles it is called polar. This
polarity results in weak electrical attractions between neighboring water
molecules. The slightly positive Hs in one water molecule attract the slightly
negatively charged O2 in another water molecule. Opposite electrical charges
attract, water molecules attract each other, making water kind of sticky. The side
with H (positive charge) attracts the O2 side (negative charge) of different water
molecules. These weak attractions are much weaker than covalent or ionic bonds
and are called hydrogen bonds. Polarity and H bonding are important to most of
water’s life supporting properties. Which include: a cohesive nature, ability to
moderate temperature, ice floating and universal solvent properties.
Water molecules possess a cohesive nature that is they attract each other and
clump together; this clinging or sticking together forms a film giving water surface
tension. This property causes water to bead into spheres when placed on hard
surfaces and is important in the living world. Trees depend on the cohesive nature
of water to help transport water from its roots to its leaves.
Water also has the ability to absorb and retain heat and therefore has the ability to
moderate temperature. H bonding allows water to resist temperature changes.
Temperature and heat are related and yet different. Heat is the amount of energy
associated with movement of atoms and molecules in a body of matter.
Temperature is a measure of the intensity of heat. It refers to the average speed of
molecules rather than to the total amount of heat energy in a body of matter. For
example: a swimmer in a large body of water may have a higher temperature than
the water; water has more heat because of its immense volume. When heat is
applied to water, the heat energy first disrupts the H bonds making molecules
move faster. Because heat is used to break bonds first and not to raise temperature
water can absorb a large amount of heat while only warming a few degrees. Water
has a high specific heat index meaning it can absorb a great deal of heat before it
begins to get hot. This property makes water valuable to industry and in car
radiators as coolant.
Water also has a high heat of vaporization. Temperatures must be quite high
before individual molecules have enough energy to break free and become water
vapor. Water vapor carries heat away with it as it is transformed from liquid to gas.
This gives water a cooling effect and accounts for the cooing of perspiration via
evaporative cooling. When water cools, it remains a liquid over a wide range of
temperatures. The freezing and boiling points of water are far apart. It freezes at
32o F and boils at 212o F. An unusually large amount of heat energy is needed to
change the temperature of 1 gram of water by 1oC. Once an amount of water has
reached a particular temperature, it changes temperatures very slowly. This
thermal inertia helps stabilize body temperatures. A large body of water can store
a huge amount of heat from the sun. In cold temperatures the heat given off from
the gradually cooling water can warm the air. This property helps stabilize ocean
temperatures.
Ice Floating is another important property of water. When most liquids cool, the
molecules get closer and closer & if cold enough the liquid becomes solid. When
water molecules cool, they move apart to form ice. Ice has fewer molecules than
an equal volume of liquid water, making it less dense and so it floats. This property
is due to H bonding. Ice is a spacious crystal and promotes life because if water
behaved as other liquidsall water would freeze solid. When warming only the
upper few inches would thaw. When a deep body of water cools, the floating ice
insulates the liquid water beneath and life persists.
Water is the universal solvent. If a substance dissolves in water it is said to be
soluble and forms a solution, a uniform mixture of 2 or more substances. The
solvent is the medium in which other atoms, molecules or ions are dispersed. The
dispersed substances are called solutes. Water is a powerful solvent. It is termed
universal because it dissolves more substances than any other liquid. Molecules
that dissolve in water are hydrophilic or water loving. Those that do not readily
react with water are hydrophobic and have few if any polar, covalent bonds. These
substances are termed non polar.
Being soluble in water means that wherever water goes, through the ground or
through the body, it takes along with it chemicals, minerals, and nutrients that are
dissolved in it. Water is useful as a transport mechanism. Because of its polar
nature, water molecules orient themselves with their slightly negative ends towards
the positive side of solutes and vice versa; first attracting and then surrounding
them.
Compounds formed by ionic bonds will ionize or dissociate in water; that is they
will break down into their individual ions by interacting with either the positive or
negative end of water. This dissociation produces cations (+) and anions (-)
surrounded by water molecules forming hydration spheres. An aqueous solution
containing anions and cations will conduct electrical currents. Cations move to the
negative side having a + change and anions move to the positive side having a –
charge. Soluble inorganic molecules whose ions will conduct an electrical current
in solution are called electrolytes. NaCl is an electrolyte. NaCl + H2ONa+ + Cl-.
Acids & Bases
Most water molecules remain intact in solution so water is essentially neutral.
Some water molecules break apart or dissociate into H2O H+ + OH- hydroxyl
ions. H+ (hydrogen ions) and OH- (hydroxyl ions) are extremely reactive. In
excessive they can break chemical bonds, change the shape of complex molecules
and disrupt cell and tissue functions. Their concentrations must be precisely
regulated.
H+ & OH- are in solutions at all times. H2O <-------> H+ + OH- is a reversible
reaction. Some compounds add more hydrogen ions and others remove them. A
compound that donates a hydrogen ion is called an acid. Strong acids dissociate
completely in solution. The reaction goes only in one direction. HClH+ + Cl-. An
acidic solution is one that has more H+ than OH-.
A compound that accepts or removes a hydrogen ion from solution is termed a
base. Strong bases dissociate completely in solution. NaOHNa+ +OH-. The
released OH- combines with H+water, thus removing the hydrogen ion from
solution. A basic solution is one that has more OH- than H+.
A pH scale (pH = potential hydrogen) developed in 1909 by Dane Soren
Sorensen, a beer brewer who was looking for a way to check the acidity of beer is
used to describe how acidic or basic a solution is. The pH scale ranges from 0-14.
0 = most acidic, 14 = most basic and 7=neutral. Each unit represents a tenfold
change in the concentration of hydrogen ion.
At a neutral pH the H+ = OH-. A pH < 7 is acidic and a pH > than 7 is more basic
or alkaline. In pure water: [H+] = [OH-] = 1 x 10-7 mol/l. pH is calculated as:
-log[H+] in moles/liter; therefore water has a pH of 7.
The pH of blood ranges between 7.35-7.45. This value must be maintained in a
narrow range since even a small change can lead to severe metabolic
consequences. Biological fluids contain buffers, substances that resist changes in
pH by accepting H+ when in excess and donating H+ when depleted.