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1. Chapter 2
THE CHEMISTRY OF BIOLOGY—ATOMS,
MOLECULES, AND HOW THEY SUPPORT LIFE
Chapter 2
Learning Objectives
• Relate major principles of chemistry to the study of biology.
o What is Chemistry?
▪ Chemistry is one of the natural sciences concerned with
the study of matter and how it interacts with each other,
what it is composed of and what properties this
composition yields.
o Answer and Explanation:
▪ Biological systems - life - is composed of matter so it is
governed by chemical processes. These include a huge
variety of reactions, many of which can be observed at
the cellular level. It can be found that all the
manifestations of life visible with the naked eye are
effects of chemical reactions occurring at the microscopic
level.
• Describe atomic structure.
o Atomic structure refers to the structure of an atom
comprising a nucleus (center) in which the protons
(positively charged) and neutrons (neutral) are present. The
negatively charged particles called electrons revolve around the
center of the nucleus.
• Explain how an atom’s electrons determine whether and how the
atom will bond with other atoms.
o When one atom loses an electron and another atom gains that
electron, the process is called electron transfer.

2. o Sodium (Na) only has one electron in its outer electron shell, so
it is easier (more energetically favorable) for sodium to donate
that one electron than to find seven more electrons to fill the
outer shell. Because of this, sodium tends to lose its one
electron, forming Na^++start superscript, plus, end superscript.
• Compare and contrast the major chemical bonds (there are 3
major types) involved in important molecules and compounds.
o Chemical bond:
▪ A chemical bond is a lasting attraction between atoms,
ions, or molecules of the same type or of different types.
The aim is to fill the valency of the outermost shell and be
more stable. Chemical bonds result in the formation of
chemical compounds.
o Answer and Explanation:
▪ The three major types of chemical bonds are ionic bonds,
covalent bonds, and metallic bonds. In ionic bonds
oppositely charged ions are attracted to each other. One
or more electrons are donated from one atom to another.
▫ For example, in sodium chloride (NaCl) the sodium
atom donates an electron to the chloride atom. Now
sodium has a positive charge and chloride has a
negative charge. An ionic bond forms between
atoms of opposite charge and it is moderately
strong. In contrast, a covalent bond is a very strong
bond in which electrons are shared between two
atoms. In a nonpolar covalent bond, the electrons
are shared equally between the two atoms. For
example, sharing of one pair of electrons between
two hydrogen atoms form a single bond in hydrogen
gas. Polar covalent bonds are created by unequal
sharing of electrons between two atoms. The more
electromagnetic atom has a greater pull on the
shared electrons. An example is water where the
oxygen atom is slightly negative, and the two
hydrogen atoms are slightly positive. Both ionic and
covalent bonds occur between two discrete atoms.

3. In contrast, in metallic bonding, electrons are
shared between many atoms of a metal element.
The electrons act as a glue giving the metal a
definite structure, for example in iron, silver, and
gold.
• Explain how the cohesive properties of water are relevant to the
study of biology.
o The cohesion of water molecules helps plants take up water at
their roots. Cohesion also contributes to water’s high boiling point,
which helps animals regulate body temperature.
• Describe four properties of water that contribute to its crucial
role in the biology of all organisms.
o Water:
▪ Water is a unique molecule in that it is integral to life. The
unique properties of water are uncharacteristic of a
molecule of such a small size. Similar molecules of the
same size are often a gas at room temperature. The
properties of water contribute to why water is a liquid at
room temperature.
o Answer and Explanation:
▪ The four unique properties of water that make it unique
are high specific heat, high polarity, adhesion cohesion,
and a lower density as a solid. Water having a high
specific heat allows it to absorb heat energy without a
subsequent change in temperature. This allows water to
be used as an intermediary and disperses heat energy
without a subsequent change in temperature. Water being
highly polarity allows it to be a universal solvent. This
allows water to dissolve many substances for life to
utilize. This high polarity also contributes to the ability to
form adhesion - cohesion networks. This allows water to
form hydrogen bonds with itself and serve as cohesion
networks with other substances. This property allows
plants to transport water up the entire mass of the plant
body. Finally, water having a lower density as a solid
allows frozen water to float atop liquid water. In lake

4. environments that are frozen, the top layer is frozen which
protects the bottom layer from the cold temperature
above. This allows life to continue below the lake.
• Explain what pH is and what the pH scale is.
o 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.
o The scale used for measuring the acidity or alkalinity of a
substance. The scale is numbered 1 - 14. A pH value of 7.0 is
considered Neutral. Highly Acidic is 1.0 and highly alkaline is
14.0.
Unit 4: The Chemistry of Biology
Chapter 2: The Chemistry of Biology
I. Atoms, Subatomic Particles and the Periodic Table
A. Atoms, Isotopes, Ions, and Molecules: The Building Blocks
1. Matter is any substance that occupies space and has mass.
B. Atom
1. What is an atom?
a. An atom is the smallest unit (of matter) that retains all of the
element's chemical properties.
b. An element is something that cannot be broken down any further
into something else. They are unique forms of matter with specific chemical
and physical properties that cannot break down into smaller substances by
ordinary chemical reactions.
2. The Periodic Table
a. The atomic number is the whole number (number of protons) of an
element in the periodic table.
b. The atomic mass (number of protons and neutrons) is not a whole
number and twice that of the atomic number and is shown below the
element name.

5. c. The chemical symbol is the abbreviation or letters shown to
represent the element name. A single capital letter or when the first letter is
already “taken,” by another element, a combination of two letters.
3. Anatomy of the Atom
a. The nucleus is the atom’s center and contains protons and neutrons.
b. Protons and neutrons have approximately the same mass, about
1.67x10^-24 grams. Scientists define this mass as one atomic mass unit
(amu) or one Dalton. The number of neutrons contributes significantly to
the atom’s mass, but not to its charge.
c. Atoms contain protons, electrons, and neutrons among other
subatomic particles with the exception of hydrogen, which is made up of
one proton, and one electron, but no neutrons.
d. Protons are positively charged, neutrons are unchanged, and
electrons are negatively charged.
e. Protons and neutrons have the same atomic mass but differ in their
electric charge.
f. The number of protons and electrons are equal in an atom.
g. The electron's mass is only 9.11x10^-28 grams or 1/1800 of an
atomic mass unit and contributes greatly to the atom’s charge, but not in
mass. Therefore, only consider protons and neutrons when calculating an
atom’s mass.
h. Atoms are electrically NEUTRAL.
i. The VALENCE shell is the outermost electron shell of an atom which
is involved in atomic bonding. The first shell can hold up to two electrons,
the next shell can hold up to eight electrons, the next shell can hold up to
eight electrons, and then the numbers vary after getting into bigger atoms.
II. Electron Shells
A. Electron Shells and Anatomy Stability
1. Electron Shells

6. a. Electrons move around the nucleus in designated areas called
electron shells.
2. Atom Stability
a. Atoms become stable when their outermost shell is filled to capacity.
Stable atoms tend not to react or combine with other atoms.
b. When the valence shell is not full of electrons, that’s when we get
into atomic bonding.
B. Atoms of the Atmosphere, Lithosphere, Biosphere
1. Atmosphere
a. 78% Nitrogen
b. 21% Oxygen
c. 0.9% Argon
d. 0.04% Oxygen
e. 0.2-4% Water Vapor
2. Lithosphere
a. 46.6% Oxygen
b. 27.7% Silicon
c. 8.1% Aluminum
d. 5% Iron
e. Phosphorous comes from rocks that are weathered and taken up by
plants into the Biosphere.
e1. Phosphorous comes from the mineral apatite, the mineral
responsible for weathering from the atmosphere, rain, streams, and waves.
We weather rocks from apatite, and it introduces phosphorous into the soil
which gets taken up by plants and then into the Biosphere.
3. Biosphere
a. Most of your body is made up of Oxygen (65%), Carbon (18.5%),
Hydrogen (9.5%), and Nitrogen (3%).

7. III. Atomic Bonding
A. Atom Stability
1. Atoms become stable when their outermost shell is filled to capacity.
2. Stable atoms tend not to react or combine with other atoms. These
are called inert or noble gases.
3. Atoms are electrically neutral. They have the same amount of positive
protons and same amount of negative electrons.
B. Electron Shells and Atom Stability
1. Electrons move around the nucleus in designated areas called electron
shells.
C. Atoms versus Ions: In the Name of Stability
1. A Sodium atom is unstable with one valence electron.
2. By getting rid of the lone valence electron (loses a negative charge).
3. Go from 11 protons and 11 electrons (neutral) to 11 protons and 10
electrons.
4. Net charge is +1
5. CATION Na+1
6. A Chlorine atom has 17 protons and electrons.
7. Valence electrons is 7, vacancy 1.
8. It can add one electron to fill that vacancy producing a full valence
shell.
9 Net charge is –1.
10. Cl-1 Anion because it now has 17 protons and 18 electrons.
11. Now you have a positive Cation (Sodium), it has a full valence shell,
but it is charged; and you have a negatively charged Anion (Chlorine) with
a full valence shell and it is charged –1. These are polar. The positive
charge and the negative charge attract to one another with electrical glue.
These are referred to as ionic bonds.

8. 12. An ionic bond forms between ions with opposite charges.
13. NaCl is an ionically bound mineral known as halite (table salt).
14. A covalent bond is two different atoms sharing an electron, which is
another way to satisfy the octet rule.
15. Covalent bonding occurs when you have overlapping valence shells
where electrons are free to migrate two or more valence shells.
16. When you form covalent bonds there is no change in charge and they
are much more difficult to break than ionic bonds because they are sharing
and overlapping.
17. Carbon usually bonds with other Carbon atoms or Hydrogen atoms.
D. Polar and Non-polar Covalent Bonds
1. There are two types of covalent bonds:
a. Polar Covalent Bonds form as a result of unequal electron sharing,
resulting in creating slightly positive and negative charged molecule
regions.
b. Non-polar Covalent bonds that form between atoms when electrons
are shared equally between them.
2. The attraction of an atom for the shared electrons of a covalent bond is
called electronegativity.
a. Strongly electronegative atoms pull the shared electrons toward
themselves.
IV. Water Has the Properties of Life
A. Water is Special
1. Water is a polar molecule.
2. Water is cohesive
3. Water has a high specific heat
4. Water is less dense as a solid than a liquid
5. Water is a universal solvent

9. B. Water is Polar
1. Two hydrogen atoms covalently bound to one oxygen atom
2. Neutral charge for the molecule
3. Oxygen is a larger atom and has more protons + in the nucleus so it
attracts the electrons towards the oxygen atom (instead of towards the H
sides with only 1 proton)
4. Electrons are pulled towards oxygen making it “slightly” negative
rendering the H sides “slightly” positive.
5. Water is electrically lopsided.
6. Delta – and Delta + are used when the atom is slightly positive or
slightly negative.
C. Polar Molecules from Hydrogen Bonds
1. Hydrogen bonds are electric interactions between “slightly” positive
Hydrogen ends with the “slightly” negative oxygen ends of adjacent water
molecules.
2. Hydrogen bonds form when a hydrogen atom that is already in a polar
bond is attracted to another atom with a partial negative charge.
3. They are magnetically attracted to each other.
4. Water is attracted to itself.
D. Water is Polar Rendering it Cohesive
1. Cohesion is “stickiness” due to hydrogen bonding between adjacent
water molecules.
2. Surface water molecules adhere strongly to neighboring water
molecules because it is not surrounded on all sides by water (surface
tension).
E. Life Depends on Cohesion
1. How does water travel UP a plant against gravity?
a. Water is released by leaves via photosynthesis.

10. b. Water enters root systems and is pulled UP the plant.
c. Water molecules in the “plumbing” of the plant are attracted to one
another.
d. Evaporation at the leaf pulls water molecules up from the roots.
e. Losing one at the leaf draws another one from the root (chain of
water).
F. Water Has High Specific Heat (heat capacity)
1. When substances are heated, molecules move faster and spread
further (I.e., solid, liquid, gas).
2. Specific heat is defined by the amount of heat needed to raise the
temperature of 1 gram of a substance 1-degree Celsius.
3. Water has a high specific heat capacity which we will refer to as “heat
capacity,” meaning it takes more energy to increase the heat of water
compared to other substances.
4. Hydrogen bonding inhibits this expansion during heating allowing water
to ABSORB more energy without expanding.
5. Stickiness of H bonds requires more heat to “break” them.
6. This is why water is valuable to industries (coolant in nuclear power
plants) or your car’s radiator to keep the engine cool.
G. Water Expands when Frozen
1. 9% volumetric expansion
2. Water is DENSEST at 4% Celsius.
H. Water is Less Dense as a Solid
1. Water molecules are arranged in a specific pattern when frozen (in a
solid state) --which takes up more space.
2. Liquid water molecules are attracted to one another and pack closely
(taking up less space, more dense).
I. Water is a Universal Solvent
1. Polarity of water molecules can aid in dissolving substances.

11. 2. Recall NaCl and the ionic bonds.
3. Positively charged Sodium cations are attracted to the slightly
negatively charged sides of the water (and Chlorine to the hydrogens).
4. Water is not ‘charged’ and therefore several slightly negative oxygen
ends must ‘gang up’ on one fully charged sodium ion to be strong enough
to PULL Na away from the Cl.
5. Many substances are polar like water and therefore can readily dissolve
in it –materials can be transported to all the parts of your body and all
within your cells.
6. Non-polar substances (I.e., oils, fats, etc.) are NOT soluble in water
(there is nothing for the water to attract to).
7. This is good for cells.
8. A liquid with dissolved substances is called a solution.
Ex. A sugar cube in a glass of water dissolves to form a solution of sugar
and water. The dissolving agent is the solvent, and the substance that is
dissolved is the solute. In our example, water is the solvent and sugar is the
solute. In biology, water is almost always the solvent.
9. Water is an effective solvent because it readily forms hydrogen bonds
with charged and polar covalent molecules.
Ex. when a crystal of salt (NaCl) is placed in water, the Na+
cations (ions of
positive charge) interact with the partial negative charges of the oxygen
regions of water molecules. The Cl−
anions (ions of negative charge) interact
with the partial positive charges of the hydrogen regions of water
molecules. Eventually, water dissolves all the ions, resulting in a solution
with two solutes: sodium and chloride ions.
10. Polar molecules are soluble in water because they form hydrogen bonds
with water.
11. Things that dissolve in water are called hydrophilic (water-loving).
Ex. paper is hydrophilic because plant fibers have lots of polar covalent
bonds. However, its giant fiber molecules are too large to dissolve in water.
When water molecules form hydrogen bonds with the cellulose fibers of

12. paper, the water actually gets stuck to the fiber! This is why, when you wipe
up a spill with a paper towel, the water is pulled into the towel.
12. Substances that have no affinity for water are hydrophobic (water-
fearing).
Ex. Have you noticed that paper towels don't absorb oil very well? Oils
such as vegetable oil are hydrophobic because the dominant bonds, i.e.,
carbon-carbon and carbon-hydrogen, are nonpolar. As a result, they are not
sticking to the plant fibers very well.
V. pH, Acids, and Bases
A. Molecules are Picky
1. All molecules in a living system have different chemistries, so they are
sensitive to changes in:
a. Temperature
b. Salinity
c. pH
2. pH is how basic or acidic a liquid is.
3. Molecules have a specific SHAPE that they are recognized by. Without
the proper SHAPE it cannot do its JOB.
4. pH can alter the shape of some molecules.
B. Water can break up via Hydrolysis
1. Hydrolysis means to “split” water
2. One H2O molecule can split into a positively charged hydrogen ion and
a negatively charged hydroxide ion.
3. When the number of both are equal in solution, the solution is
NEUTRAL and balanced.
C. The lower the pH the more acidic
1. The pH of a solution us dependent on the number of Hydrogen ions in
solution H+ compared to OH- ions.

13. 2. Acids are fluids that have a greater proportion of H+ ions to OH- ions.
a. H+ ions are very reactive.
b. Strong acids are corrosive to metals.
c. Acids break down food in your digestive tract.
d. Acids are generally sour in taste.
3. Bases are fluids that have a greater proportion of OH- ions to H+ ions.
a. OH- ions bind with H+ ions, neutralizing acids.
b. Strong bases are caustic to your skin.
c. Bases can be found in many household cleaners.
d. Bases are generally bitter in taste and slippery.
D. What is a Hydrogen Ion?
1. Hydrogen atom is one proton, one electron, and zero neutrons.
2. Donate an electron, the H+ ion is just a proton.
3. Chemicals in solution continuously accept and lose H+ ions so the
acidity of a solution can continuously change.
Ex. HCl dissolves in water producing H+ ions increasing the acidity
(dropping in pH).
4. Basic substances like bicarbonate (alka seltzer) excess OH- to bind with
H+ removing them from the solution forming water.
5. Reducing the H+ increases the pH (HCl = (H+) + (Cl-)
E. Can acid rain have negative impacts on microbes and streams and plants
and living organisms on Earth?
1. Acids
a. Atmospheric CO2 combines with water vapor forming carbonic acid.
b. Carbonic acid dissociates into carbonate and hydrogen ions (making the
solution acidic).

14. 2. Is acid rain likely to have any impact on microbes living in lakes,
streams, or soil?
a. Depends on the rock type.
3. Seawater that is absorbing carbon dioxide from the atmosphere:
a. CO2 (Carbon dioxide in atmosphere) + H2O (Water) => H2CO3
(Carbonic acid is created first; it dissociates further) => (H+) +HCO3
(Bicarbonate ions)
4. Carbonation: Dissolution of carbonate minerals specifically (calcite in
limestones and marble). Requires the solution to be acidic. The acid splits
into H+ ions and Bicarbonate ions. The more H+ ions in the solution, the
more acidic the solution, the lower the pH.
5. Hydrogen ions in solution contribute to pH. The more H ions the lower
the pH, the more acidic the solution.
6. After dissolving limestone rocks (made of calcite) with acid, the H+ ions
are no longer dissolved in the solution rendering the solution no longer
ACIDIC.
7. Calcite + carbonic acid (dissociated) -> dissolved Calcium ions +
bicarbonate ions.
8. Sodium bicarbonate is in tums.
F. Buffers
1. All the chemical reactions going on in your body will produce or
utilize H+ ions.
2. Your cells do not operate well in swings of pH 0.5 point in either
direction.
3. Buffers are molecules that ABSORB H+ ions to prevent them from
becoming too acidic or release H+ ions if it is becoming too basic.