CHAPTER 2
CHEMICAL LEVEL OF ORGANIZATION
Our
bodies are made of chemicals and our life processes involve chemical reactions.
A special name for chemistry that relates to living beings is biochemistry.
All
living and nonliving things consist of matter.
Matter--anything
that occupies space and has mass (weight).
Comes in 3 forms:
Solid
Liquid
Gaseous
All
forms of matter are composed of chemical elements. Elements are described as
the building blocks of matter. There are 112 elements, 92 of which occur in
nature. All matter is made up of either 1 pure element or a combination of
elements. Definition of an element: a substance that cannot be split into
simpler substances by ordinary chemical reactions.
Elements
have names and also are represented by abbreviations called chemical symbols:
Carbon C
Nitrogen N
Hydrogen H
Calcium Ca
If 2
letters are used, the first is a capital and the second is not
Chlorine Cl
Sodium Na
Our
bodies contain 26 elements: (See Table 2.1 P. 29)
Oxygen
Carbon
These first 4 on the list make up 96% of the body
Hydrogen
Nitrogen
Lesser
elements:
Calcium Sulfur
Magnesium
Phosphorus
Sodium
Iron
Potassium
Chlorine
These
8 make up 3.8% of the body.
The
remaining 14 are present only in tiny quantities (0.2% all together) and are called
trace elements.
Atoms--smallest
units of matter having the characteristics of
1. Proton--positively
charged and found within the nucleus. Have a mass of 1 dalton
(a dalton is a very tiny unit used to measure mass of
subatomic particles).
2. Neutron--neutral
charge and also within the nucleus--mass of 1 dalton.
(All
except hydrogen have neutrons.)
3. Electron--has a
negative electrical charge and orbits around the nucleus. The mass is so tiny
we will consider them weightless for A & P purposes.
IMPORTANT
FACTS ABOUT ATOMS:
1. The number of
electrons and the number of protons in an atom is normally the same, giving a
neutral charge
2. The number of
protons in the nucleus is what makes the atoms of one element different from
another. For example, a hydrogen atom always contains 1 proton--if it had 2 it
would be a helium atom. An oxygen atom always contains 8 protons--7 would make
it nitrogen; 9 would make it fluorine. There is a chart called the periodic
table that shows how many protons are always present in the atoms of each
element (appendix B in your text).
3. The number of
protons is the atomic number of the element, so each element has its own atomic
number from 1 – 112.
4. Since both protons
and neutrons have a mass of approx. 1 dalton each,
the number of protons plus the number of neutrons equals the mass of the atom,
which is called the mass number.
5. Atoms of each
element have their own characteristic number of neutrons
Carbon 6 protons
atomic number = 6
6 neutrons
mass number = 12
Sodium 11 protons
atomic
number = 11
12 neutrons
mass number = 23
6. Under unusual
conditions, the number of neutrons in certain atoms of some elements may vary
(remember protons MUST remain constant). Atoms having a variation in neutron
number are called isotopes of the element. They behave the same as normal atoms
in chemical reactions, but their mass has changed.
Normal oxygen atom: 8
protons
atomic number = 8
8 neutrons
mass number
= 16
Occasional
atoms may have 9 or 10 neutrons, giving mass numbers of 17 or 18.
7. Although most
isotopes are stable, certain isotopes of certain elements are radioactive
because their nuclear structure seeks to change (decay) to a simpler and more
stable form. As the change takes place, radiation (waves of energy with special
properties) are emitted. If exposed to this energy, normal cells are damaged or
destroyed by having their molecules broken apart. This is what makes atomic
bombs so dangerous, but we also make use of radiation in medicine in the form
of x-rays and by administering radioactive substances for special tests and
treatments:
Radioactive iodine to
thyroid gland Brain
scans
Thallium imaging of
heart
Cancer treatment
Bone scans
More
on the structure of atoms:
Shell
#1 2 spaces
Shell
#2 8 spaces
N
Nucleus
P
Shell #3 8
spaces OR
18 spaces
Electrons
orbit around the nucleus. They were once believed to follow set paths called
electron shells around the nucleus. We now know the motion is more random, but
for A & P we will stick to the paths. (See Fig. 2-1 p. 30).
Each
shell has space for a set number of electrons. Every space will not always be
filled, but shell #1 will fill completely before any electrons go to shell #2;
#2 will fill completely before #3 begins to fill.
The outermost shell that contains any electrons in
For
stability, atoms are always seeking to achieve a completely filled outer shell
by giving up, gaining or sharing electrons with other atoms. This
giving up, gaining or sharing of electrons results in chemical reactions.
OXYGEN
SODIUM
8 P
11 P
8 N
12 N
8 electrons with 2
11
electrons with only
empty spaces in
1 in outermost shell
outermost shell
(7 empty spaces)
What
if the outermost shell is naturally full? In that case (helium, neon, etc.) the
element generally does not participate in chemical reactions and is said to be
inert. Only those elements whose atoms have incompletely filled outermost
shells tend to participate in chemical reactions.
For practice, see Fig. 2-2 P. 31
When
2 or more atoms combine, a molecule is formed. A molecule is held together by
interaction among electrons.
A
molecule may be formed by 2 atoms of the same element combining (H2,
O2) or by 2 or more atoms of different elements (H2O, NaCl). If the molecules contain 2 or more different
elements, the resulting substance is called a compound. Since compounds are
formed by chemical reactions they can also be broken down by chemical reactions
(different from elements).
A free
radical is an electrically charged atom or group of atoms with an unpaired
electron in its outermost shell. Free radicals are formed by exposure to UV
light, X-ryas, and normal metabolism. A common
example is superoxide---an oxygen molecule that has gained 1 electron. Free
radicals seek to either give up the unpaired electron or to take an electron
from a normal cellular molecule. Free radicals are destructive and are
currently believed to play a role in a number of diseases as well as in aging.
Antioxidants appear to lessen the damage caused by free radicals. Figure 2.3
P. 32
CHEMICAL
BONDS
These
are the forces of attraction that hold molecules together. They happen as atoms
try to achieve completely filled outermost shells. 3 major types:
1.
IONIC BONDS--an atom normally has an equal number of protons and electrons and
therefore a neutral charge. If it gains electrons it becomes negatively charged
(anion); if it gives up electrons it becomes positively charged (cation). Table 2.2 P. 35
lists common ions in the body.
Sodium tends to give up 1 electron and become positively charged
Chlorine tends to gain 1 electron and become negatively charged
These
charged atoms are called ions. When ions are in solution the solution will conduct
an electric current, so ions are also called electrolytes.
As
these positive and negative ions are formed they tend to be attracted to each
other and this attraction is an ionic bond. (Fig. 2.4
P. 33)
In
general:
If the outer electron
shell is less than half filled, the atom loses electrons and forms
If the outer electron
shell is more than half filled, the atom gains electrons and forms a negative
ion (anion)
What if the outer
shell is exactly half filled? Mostly these elements do not participate in ionic
bonds but are more likely to enter covalent bonds. Hydrogen is one
exception--it has 1 electron, so its outer shell (#1) is half filled. Even so,
it has a tendency to give up its electron in some cases and become H+, a cation.
2. COVALENT
BONDS--these involve a sharing of electrons (1,2, or 3
pairs) and are the most common chemical bonds in the body. One example of this
type of bond is the formation of hydrogen molecules, which also show the other
way H can behave.
(See Fig. 2.5 P. 34)
The
electrons alternate--travel around first one nucleus and then the other, so
each has a filled outermost shell half of the time. This can occur between 2
atoms of the same element or between atoms of different elements.
In a
kind of shorthand, the sharing of one pair of electrons is represented:
H H
If 2
pairs of electrons are shared:
H
H
O O
C
If 3
pairs are shared:
H
H
N N
METHANE
Sometimes
in a covalent bond, one atom attracts the shared electrons more strongly than
the other. This is called
WATER (H2O)
Electrons are more strongly attracted
to the oxygen, to this end of the
molecule becomes somewhat negative
O
H
H
Electrons spend less time traveling around the H, so
this end becomes somewhat positive
3.
HYDROGEN BONDS--2 other atoms (O or N) associate with a hydrogen atom. The H
atom is covalently bonded to one O or N atom and is also attracted to the
negative area of another O or N atom involved in
Even
though these bonds are relatively weak, they are still extremely important in
biochemistry. Hydrogen bonds do not actually bind atoms into molecules and no
electrons are shared or exchanged. However, they do act as bridges between
molecules or different parts of the same molecule. In some large complex
molecules a 3-dimensional shape is a necessary part of the structure and
hydrogen bonds are what maintains this shape.
3
TYPES OF BONDS:
|
IONIC |
COVALENT |
HYDROGEN |
|
GAIN
OR LOSS OF ELECTRONS |
SHARING
OF ELECTRONS |
NO
ELECTRONS ARE GAINED, LOST OR SHARED, BUT AN ATTRACTION BETWEEN CERTAIN AREAS
OF THE MOLECULE(S) INVOLVED HOLDS THOSE AREAS TOGETHER |
|
MOSTLY
IN INORGANIC COMPOUNDS |
MOSTLY
IN ORGANIC COMPOUNDS (WATER IS AN EXCEPTION) |
ORGANIC
COMPOUNDS AND WATER |
|
MEDIUM
STRENGTH |
STRONGEST
TYPE |
WEAK |
CHEMICAL
REACTIONS
Chemical
reactions involve the making or breaking of bonds between atoms. They occur as
atoms, ions and molecules collide. After a chemical reaction, the total number
of atoms is the same, but new molecules with different properties have been
formed.
Chemical
reactions involve energy changes. Energy is the capacity to do work. Forms of
energy:
1. Potential energy is stored
energy
2. Kinetic energy is associated
with matter in motion
3. Chemical energy is stored in
chemical bonds (a form of potential energy)
Energy
can be converted from one form to another. In the process, heat is often
released.
When
atoms or molecules are joined by a chemical bond, energy is required to form
the bond and the energy is stored in the bond. This type of reaction absorbs
energy and is said to be endergonic. When the bond is
broken, that energy is released. This reaction is described as exergonic.
Chemical
reactions are described by chemical equations. A chemical equation looks like
this:
Mg + H2O
à
MgO + H2
The atoms, ions, or molecules
on the
The arrow
The atoms, ions, or molecules on
left side of the arrow are
what you
represents
the right side of the arrow
are
have BEFORE the reaction
takes place.
the reaction.
what you have AFTER the
These are called the
REACTANTS.
reaction takes place. These are
called the PRODUCTS.
In a chemistry course, you will spend a lot of time balancing
equations. We don’t worry much about this in here, but what it means is
that to properly represent a
chemical reaction, every
atom shown on the left side of the arrow (the before side) must also appear in
some form on the right side of the arrow ( the after side).
Atoms, ions, and molecules are continuously moving and
colliding with each other. If the collision is forceful enough, an existing
chemical bond may break or a new one may form. Activation energy is the minimum
amount of energy required for a chemical reaction to occur. Two things make
chemical reactions more likely:
1.
Concentration—increasing the concentration increases chances of a
collision
2.
Temperature—speeds up movement
Catalysts speed up chemical reactions by lowering the
activation energy required for the reaction to start. At the end of the
reaction, the catalyst is unchanged. Catalysts are essential for chemical
reactions in the body, since temperature, pressure and concentration are
generally too low for reactions to occur at a speed that would sustain life.
Raising these would kill the cells, so the solution is biological catalysts in the
form of enzymes.
In
all living things, large numbers of chemical reactions are constantly taking
place. Metabolism is the sum of all chemical reactions occurring in a living
organism. Types of chemical reactions:
1. SYNTHESIS
REACTIONS--joining of 2 or more ions, atoms or molecules to form new and larger
molecules. In order to do this, new chemical bonds are formed and energy is
absorbed (endergonic reaction). This phase of
metabolism is called anabolism. In our bodies, an example is the linkage of
amino acids to form proteins.
A + B à
AB
C + O2 à CO2
Reactants
Product
2.
DECOMPOSITION REACTIONS--bonds are broken--larger molecules are broken down
into smaller molecules, atoms or ions. As bonds are broken, energy is released
(exergonic reaction).
AB à A + B
CH4
à C + 2H2
This
phase of metabolism is catabolism. An example in the body is digestion of food
molecules. As bonds are broken, energy is released for use by cells.
3. EXCHANGE
REACTIONS--this type of reaction combines the first 2 types:
AB + CD à AD + BC
Bonds
forming molecule AB and bonds forming molecule CD are broken (decomposition).
Then new bonds are formed (synthesis) and molecules AD and BC result. In the
body buffer reactions are exchange reactions.
4. REVERSIBLE
REACTIONS--some reactions can go either way depending on conditions. Under one set of conditions:
A + B à AB
Under another set of conditions:
AB à A + B
All this can also be expressed as:
A + B → AB
←
Conditions
that might determine which direction the reaction will proceed include:
A. Temperature
B. pH
C. Relative amount of
reactants or products present
D. Amount of energy
available
E. Presence or absence
of catalysts (catalysts are atoms or molecules that can speed up the rate of a
reaction without themselves being consumed or changed in the reaction). In
reactions occurring in living cells, the catalysts are enzymes.
A
great many biochemical reactions are reversible.
BIOCHEMISTRY—chemical
reactions in living cells
Most
of our chemicals are in the form of compounds. There are 2 types:
1.
Inorganic
Usually held
together by ionic bonds
Small molecules
Usually LACK
carbon
Examples:
Water
CO2
Salts
Acids
Bases
2.
Organic
Held together by
covalent bonds (many)
Large molecules
ALWAYS have C ; almost always also have H
Carbon atoms tend to
form chains or rings
Examples:
Proteins
Carbohydrates
Lipids
INORGANIC
COMPOUNDS
WATER
Water--most
abundant substance of the body--around 55-60%; the only tissues low in water are bones and teeth. It is the most important
inorganic compound in living things.
Terms
to help explain the role of water in the body:
Mixture—combination
of elements or compounds that are physically blended together but not held by
chemical bonds. 3 types of mixtures:
1. Solution--solvent + solute
Solvent--liquid or gas in which other materials dissolve
Solute--thing that dissolves
2. Colloid—particles are
larger and the mixture looks cloudy, but will not settle out
3. Suspension--material mixes with
medium but will settle out
Properties
of water:
1. Water is an excellent solvent and suspending medium. It is the
solvent in our body fluids. Many substances (but not all) will dissolve in
water. This is mostly due to its polar covalent bonds.
O More negative
H H More positive
NaCl
dissolves in water because:
O end is attracted to the Na+ portion
H2 end is attracted to the Cl- portion
This
pull takes the NaCl molecule apart (dissolves it).
Hydrophilic—substance
will dissolve—solutes usually charged or contain polar covalent bonds
Hydrophobic—will
not dissolve—usually contain nonpolar covalent
bonds
As a
solvent in the body, water:
a.Dissolves and suspends many substances, allowing metabolic
reactions to occur between dissolved substances
b.Dissolves certain waste products so
they can be removed from the body
2.
Water participates in chemical reactions, both synthesis and decomposition.
3.
Water absorbs and releases heat slowly--helps maintain homeostasis as
surrounding temperature
changes
4.
Water cools the body by evaporation of perspiration--water requires a large
amount of heat to change from a liquid to a gas
5.
Water serves as a lubricant--mucus, fluid in joints, fluid in ventral body
cavity, food passing through digestive system
INORGANIC
ACIDS, BASES AND SALTS
When
molecules of these dissolve in water, they undergo ionization or
dissociation---separate into + and - ions.
Acid—substance
that when dissolved in water dissociates into 1 or more H+ ions and 1 or more
anions (negative ions)
HCl à H+ + Cl-
Base—dissociates
into 1 or more hydroxyl ions (
NaOH à Na+ +
Salt—when
dissolved in water dissociates into cations other
than H+ and anions other than
NaCl à Na+ + Cl-
Salts
are formed when acids and bases react together:
HCl + KOH à KCl + H2O
Acid
Base
Salt
Salts
are present in intracellular and extracellular fluid.
This makes the fluids able to conduct electrical currents, so the ions of salts
are sometimes called electrolytes. Ions of salts also provide many essential
chemical elements, and solid forms of calcium salts give strength to bones and
teeth.
ACID-BASE
BALANCE