Biochemistry
Living things have physical bodies. They take up space and certainly
have mass. The physical bonding between atoms plays an important
role in living systems. From the function of proteins to the physical
structure of DNA, living things are impacted by atoms. In fact, they are
fundamentally made of atoms. This chapter will focus on atoms, ions,
the bonding of atoms, biological macromolecules and pH.
As we’ve just discussed, atoms are made up subatomic particles. The
three main subatomic particles are the proton, neutron and electron.
Protons and neutrons are located in the center area of the atom, called
a nucleus and account for almost all of the mass of an atom.
Electrons are located outside the nucleus. They are much tinier and
move very fast. They are so fast, in fact, that we can usually only
describe their location as a general area, instead of trying to pinpoint an
exact spot. This general area where an electron can be found is called
an electron cloud, but its proper name is an orbital.
Protons have a positive (+) charge, electrons have a negative (-) charge
and neutrons have no charge. The charge of an atom can be negative,
positive or neutral. In order to be unchanged (neutral), an atoms must
have the same umber of electrons and protons. When an atom is
charged, it is called an ion. If there are more electrons than protons, the
charge of the ion is negative. If there are fewer electrons than protons,
the charge if positive. Keep in mind that the number of protons does not
change under normal circumstances, but the number of electrons can
and does.
Ions and Biology
Atoms take on electrical charges when the number of electrons does not
equal the number of protons in the atom. Anions are atoms with
negative charges. An atom that has gained an electron takes on a
negative charge (it has more electrons than protons). Chlorine is one
common atom that easily becomes an anion. It is written Cl-. Cations
are atoms that have a positive charge. Cations “give up” or lose
electrons and have a positive charge (thus they have fewer electrons
than protons). Potassium and sodium are two common atoms that
become cations. They are written as K+ and Na+.
Atoms can gain or lose more than one electron. The amount of charge
on an ion is found by subtracting the number of protons from the
number of electrons. ( protons-electrons=charge of ion)
What exactly does this mean for living things? In living things, ions can
influence the amount of water in cells. They are also used to transmit
messages between cells. Inorganic metallic ions are even used by
organisms. The charge differential between cations and anions can be
used to transport molecules into or out of cells. Cells even use ions to
repel certain types of molecules from the cellular membrane. Toxins
from plants or bacteria and venoms from insects or reptiles also usi ions
to block cellular messages, inhibit muscular functions, and harm other
organisms. Animals rely on dissolved ions for muscle contractions,
digestion, and nerve function. Animals also use ions to eliminate
charged free radicals and detoxify the body. These are but a few simple
examples. We must remember that organisms are amazingly complex
and use ions in a wide variety of ways.
Bonding of Atoms
An element is a substance composed of identical atoms. A compound is
a substance composed of identical molecules. A molecule is the
product of two or more atoms joined by chemical bonds. Atoms of
different elements can combine chemically to form molecules by sharing
or by transferring valence electrons (their outermost electrons).
Valence electrons are either lost, gained or shared when bonds are
formed.
Ionic Bonds
An ion is an atom with a charge. It is formed by the transfer of
electrons. When on atom “takes” electrons from another atom, both are
left with a charge. The atom that took electrons has a negative charge.
(Recall that electrons have a negative charge). The atom that “gave”
electrons has a positive charge. The bond formed by this transfer is
called an ionic bond. Ionic bonds are vary strong. Ionic compounds
have high melting points and high boiling points. These compounds
tend to have ordered, crystalline structures and are usually solids at
room temperature. Ionic compounds will usually dissolve in water, and
they have the ability to conduct electricity when dissolved in water.
Special ionic salts dissolved in water are called electrolytes. Animals
use the types of solutions to transmit nerve signals within the body.
For example, table salt is an ionic compound, and its melting point is
around 800 degrees Celsius (over 1400 degrees Farenheit). Ionic solids
form geometric crystal or crystal lattices. Based on the arrangement of
positive and negative ions. These solids are usually soluble in water,
which means they will dissolve. When in a dissolved state, the ionic
compound separates into ions.
Covalent Bonds
Covalent bonds are formed when two or more elements share valence
electrons in such a way that their valence electron orbital is filled. The
sharing arrangement creates a more stable outer electron structure in
the bound elements than was present in their elemental state, In
general, there are two rules about which elements form covalent bonds.
Rule 1. Elements with similar electronegativities form covalent bonds.
Rule 2. Non-metals form covalent bonds.
The compounds that result from covalent bonding have low melting
points and low boiling points. They are usually liquids or gases; of solid,
they are brittle. In general, they do not conduct electricity well,
although there are some exceptions to that rule.
Water is one example of covalent bonding. Two hydrogen atoms and
one oxygen atom combine to form one molecules of water.
Polar Covalent and Hydrogen Bonds
The covalent bond will sometimes have an “ionic character” depending
on the identity of the atoms involved in the bonding. This means that
one of the two atoms participating in the bond “wants” electrons more
than the other, and thus pulls them closer, this atom has a partially
negative charge. The other atom, which as allowed its electrons to be
pulled away a bit, has a partially positive charge. These molecules are
called polar molecules, and water is an excellent example. The oxygen
atom in water pulls electrons toward it, the hydrogen atom is left with a
partially positive charge.
The presence of these partial charges creates an electrical attraction
between polar molecules the partially positive end (that is , the
Hydrogen) lines up in such a way that it is close to the partially negative
end (the oxygen) of another polar molecule. The resulting orientation is
highly stabilizing and powerful enough to be called a form of bonding :
Hydrogen bonding. Hydrogen bonds are not as powerful as covalent
bonds, but they represent a significant organizing force.
Review Questions
1. Define the following terms:
a. Compound
b. Ionic bond
c. Covalent bond
d. Polar molecule
e. Electrolyte
f. Molecule
g. Hydrogen bond
2. A covalent compound has which of the following characteristics?
a. High melting and high boiling points
b. Shared electrons
c. Conducts electricity
d. All of the above
3. Hydrogen bonding takes place between
a. Polar molecules containing hydrogen
b. Atoms of hydrogen
c. Ionic compounds
d. Valence electrons
4. What type of bond is formed when atoms transfer electrons?
a. Covalent
b. Hydrogen
c. Ionic
d. Polar
e.
5. Which of the following is a characteristic of an ionic bond?
a. Low melting point
b. Shared electrons
c. Dissolves in water
d. insoluble
6. Which of the following molecules is most likely to have a covalent
bond?
a. P2
b. NaCl
c. MgO
d. Al2O3
e.
7. Manganese (Mn2+) is an inorganic micronutrient used by all living
things. How would you best describe this micronutrient?
a. Cohesion
b. Cation
c. Anion
d. enzyme
8. Compare and contrast atoms and ions.