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Bonds, Molecules, and pH
Part I. Molecules and Chemical Reactions
with ionic bonds often break apart or dissociate
since the bond is of intermediate strength.
Definition of a Molecule
Molecules are groups of two or more
atoms linked together by chemicals bonds. The
simplest molecules are diatomic, or two-part
molecules, such as oxygen gas (O2) and iodine
(I2). In the chemical formula for a molecule,
each different element within the molecule is
listed alphabetically from left to right. A
subscript following the element symbol indicates
how many atoms of this type are linked within
the molecule. For example, in the formula for
water, H2O, there are two atoms of hydrogen
and one atom of oxygen.
Bonding in Molecules
Figure 1. A crystal of sodium chloride (table salt) in
which the basic molecule, NaCl, is repeated over and over
to form a large solid.
Ionic compounds are called salts. Such
compounds are composed of a positively
charged metal ion (such as Li+, Ca+2, Al+3, Cu+1)
and a non-metal ion (such as Cl-, Br-, SO4-2, or
NO3-1).
Ionic Bonds
Chemical reactions are the processes by
which atoms lose or gain electrons so that they
can adjust the number of electrons in their
outermost shell. When electrons are gained or
lost, however, the atom becomes unbalanced
electrically. The outermost shell may be
complete, but the number of protons may not
now equal the number of electrons, and so the
atom has a net positive or negative charge.
Such electrically unbalanced atoms are
called ions, where positive ions are cations and
negative ions are anions. Ions of opposite
charge attract each other, just as the north pole
of a magnet is attracted to the south pole of
another.
When positive and negative ions associate
together through ionic attraction, they form a
molecule. Two ions (electrically unbalanced
atoms) of opposite charge are said to be held
together through an ionic bond. Sodium
chloride (NaCl), a molecule formed from the
association of a positive sodium atom and a
negative chloride is held together by an ionic
bond. When dissolved in water, compounds
ACTIVITY A. – Viewing a model of a
sodium chloride crystal
1. Locate a model of a sodium chloride crystal
and answer the questions on the report
worksheet as you examine it. Answer the
questions posed under Part A on the report
worksheet.
Covalent Bonds
Two electrically balanced atoms which
have unfilled outer shells may react together to
form a very strong bond called a covalent bond.
This means that the outer shells of the two atoms
get very close together and that electrons are
shared. Covalent bonds are almost always made
between non-metals like O, H, N, P, Cl, etc.
found on the far upper right of the Periodic
Table. Covalent bonds are the strongest types of
chemical bonds.
The nifty thing about sharing electrons is
that the electrical balance of each atom is not
disturbed. An electrically balanced
Science 214 Lab Manual pg. 1
atom therefore retains electrical balance while
also fulfilling the need to fill the outer shell.
Covalent bonds can be single, double, or triple
(nitrogen gas).
H
H
H C
C
H
H
H
N
C
OH
2. Using the foregoing as an example,
complete the addition of hydrogen atoms to
the molecule in Part B on the worksheet.
Hydrogen Bonds
Figure 2. A cartoon representation of two atoms sharing
two electrons in a covalent bond and an atomic diagram of
C2H6 showing seven covalent bonds. This is a relatively
strong bond.
The number of bonds that any non-metal
atom can make depends upon the number of
electrons in the outermost shell of that atom.
Atoms will seek to fill their outermost shells to
the maximum capacity. In this way, H forms 1
bond, O forms 2 bonds, N forms 3 bonds, and C
forms 4 bonds.
Polar covalent bonds are formed when
atoms differ in electronegativity or electron pull.
This asymmetrical pull causes the molecule to
be partially charged at two ends. Non-polar
covalent bonds are usually between atoms of the
same kind like H2, O2, and N2.
When two different molecules contain
polar covalent bonds, parts of these two
molecules become partially charged. An
example of this is found in the water molecule
where polar covalent bonds extend between the
oxygen and the two hydrogen atoms.
The partially positive or partially
negatively charged portions of these molecules
can be attracted to each other, if they are of
opposite charge. In the case of water, the
partially negatively charged oxygen of one water
molecule can be attracted to the partially
positive charge on a hydrogen of another
molecule. Such an attraction forms a fairly
weak link known as a hydrogen bond.
 ACTIVITY B – Completing a molecule
formed of covalent bonds
1. If you are given a partially completed
molecule lacking, say, hydrogen atoms, it is
possible to fill out the rest of the molecule
based on the rules of how many hydrogen
bonds the atoms of H, O, N, and C normally
form. For example, in the molecule below,
C – C – N=C – O
one can add hydrogen atoms to the molecule
based on how many bonds each atom
already has. This produces the molecule:
Figure 3. A hydrogen bond formed between two different
water molecules. The Greek letter sigma () is used to
indicate a partial charge, not a full charge as seen in an ion.
This is a relatively weak bond.
ACTIVITY C – Examining the hydrogen
bonds in a model of frozen water (ice).
1. Describe the arrangement of individual
water molecules (red oxygen with two white
hydrogens) in a model of ice. What atoms
are involved in making a hydrogen bond
from one water molecule to the next?
Answer these questions under Part C on the
report worksheet.
Science 214 Lab Manual pg. 2
 ACTIVITY D – Naming the type of bond
found within a molecule.
1. In Part D on the worksheet, write in the type
of bond seen between the indicated atoms
(i.e. is it an ionic, covalent, or hydrogen
bond)?
 ACTIVITY E- Writing out simple
chemical reactions
Chemical Reactions
Chemical reactions (interactions between
atoms) are usually a subtraction, addition or
exchange of outer shell electrons. Atoms that
have incompletely filled outer shells have a
tendency to want to fill the shell up to its
capacity ( 2 or eight) through the stealing or
giving away of electrons.
Sulfur (S), for example, is lacking two
electrons in its outer shell. What does this
mean? This means that sulfur wants to form
chemical bonds with other atoms in order to
gain 2 more electrons, even if the sulfur atoms
has to share those two electrons in a covalent
bond with another atom.
In the course of a chemical reaction where
sulfur acquires two new electrons, chemists
show the progress of the reaction using an arrow
between the beginning substances, or reactants,
and the ending substances, the products.
Chemical reactions also tend to occur so the
reactants change from high energy to lower
energy products. This is explained by the
Second Law of Thermodynamics which says all
matter will tend to become more disordered (or
lower in energy).
In the case of sulfur borrowing two electrons
from oxygen gas to form a covalent bond, we
write:
S + O2
(oxidation-reduction reactions); the trading of
ionic partners (exchange reactions); the
breakdown of carbon-hydrogen molecules with
oxygen to produce heat, carbon dioxide, and
water (combustion); the breakdown of molecules
using water (hydrolysis); and the synthesis of
chains of units with the loss of water
(condensation).
O-S=O (or just SO2)
In the chemical reaction equation shown
above, the sulfur dioxide product can be written
either using a structural formula or a simple
molecular formula. The structural formula (OS=O) shows in more detail how the atoms are
connected to each other.
Some common chemical reactions found in
nature involve the transfer of electrons
1. Complete the chemical reactions shown in
Part E of the report worksheet. Note that some
reactions are very simple, such as the association
of two oppositely charged ions to form an ionic
bond.
Biomolecules
Living things are largely composed of
molecules that are quite large. These
macromolecules are known as biomolecules.
The four different types of biomolecules are
carbohydrates, lipids, proteins, and nucleic
acids.
Carbohydrates (the sugars) are used as
direct sources of energy in their simple forms
and as energy storage molecules or rigid support
molecules when in long chains. The most
common simple forms are glucose, fructose,
sucrose and lactose. The complex or long-chain
forms include starch and cellulose.
Lipids are water-fearing molecules that
serve in a number of roles in living things.
Some lipids store energy and provide insulation
(fats and oils, like corn oil), others form a barrier
envelope around cells (phospholipids) in a
structure called the plasma membrane. Still
other lipids capture light in photosynthesis
(pigments like chlorophyll)or serve as chemical
messengers (hormones like estrogen) in a
multicellular organism.
Proteins also have a wide variety of
functions. In simple form, called amino acids,
they act as a building blocks for larger
molecules. When found in long chains, proteins
act to speed up chemical reactions (enzymes),
provide insulation (fur and feathers), send
Science 214 Lab Manual pg. 3
chemical messages (hormones), carry other
molecules around (transport proteins), defend
the body from attack (antibodies), hold a
multicellular organism together (structural
proteins), and act as identification labels on cells
(membrane proteins).
Nucleic acids are found mostly in their
long chain forms where they function to store or
transport genetic information. Living things use
deoxyribonucleic acid (DNA) to store hereditary
information while ribonucleic acid (RNA)
allows a cell to utilize the hereditary
information. DNA is usually found in the
nucleus or nucleoid of a cell, while RNA is
found in the nucleus and the cytoplasm.
 ACTIVITY F. Using molecular models to
follow a heat-producing reaction.
1. Get a molecular modeling kit for you and
your team. Open it up and study the color
coding of the atoms (black for carbon, red
for oxygen, blue for nitrogen, white for
hydrogen). Note also the medium length
connectors which serve as covalent bonds
between atoms and the long connectors
which are used when double bonds lie
between two atoms. We won’t be using the
short white connectors.
2. Build the following molecules using
medium length bonds for carbon-hydrogen
bonds and the longest connectors in forming
the double bonds between the oxygen atoms:
(CH4) molecule. You should be able to
rearrange and rebond the atoms of the three
reactant molecules to produce one carbon
dioxide (CO2) and two water molecules
(H2O).
CH4 + 2O2
4. The reactants of this equation (CH4 and O2)
have a lot of energy stored in the covalent
bonds of these molecules. The products
have much less energy in their bonds. Since
energy can neither be created or destroyed
(First Law of Thermodynamics), some of
the energy of the reactants must be released
when the products form. Answer the
questions about this reaction under part F on
the report worksheet.
5. Please take apart the atoms and bonds of
your models and return them to the kit when
you are finished with this activity.
 ACTIVITY G. Using molecular models to
follow a protein breakdown reaction.
1. Use the model kit to form the following twopart protein molecule made of two amino
acids linked together, glycine and alanine.
You’ll need to use the longer bond
connectors to form the double bonds
between the Cs and the Os.
H
H
H
N
and
O
O
and
O
O
H C
O
H
H C H
O=C=O + 2 H-O-H
H
C
H
C
H
O
N
C
H
H
C
H
O
H
or (in 3D):
Your model should look something like
this:
3. Now you will take these three molecules and
perform the following chemical reaction.
Note that according to the reaction, two
molecules of oxygen react with one methane
Science 214 Lab Manual pg. 4
2. The dark bold line at the end of the arrow in
the structural formula of the protein shown
above is the covalent bond (called a peptide
bond) connecting the two amino acids
together. The chemical reaction you are
about to perform involves the breakage of
this bond and the addition of a hydrogen
atom to the nitrogen on the right and an
OH combination to the carbon atom on the
left. This will produce two separated amino
acids.
3. Make a molecule of water for use in this
reaction (H-O-H).
4. Now perform this “water cutting” or
hydrolysis reaction by separating the two
amino acids at the peptide bond between
them. Break your water molecule apart and
add the pieces to the two amino acids as
described in Step 2. You should now have
two product molecules that look like this:
5. Answer the questions under part G on the
report worksheet
6. Please take apart the atoms and bonds of
your models and return them to the kit.
pH, Acidity and Alkalinity
Water is made of molecules each with two
hydrogen atoms and an oxygen atom (H2O). A
water molecule occasionally breaks down into
charged molecules called the hydrogen ion (H+)
and the hydroxide ion (OH-). The amount of
hydrogen ions and hydroxide ions in pure water
and human blood is approximately equal.
If the amount of H+ is greater than the
amount of OH-, the water is said to be acidic. If
the amount of OH-is greater than the amount of
H+, the water is said to be alkaline, or basic.
A system of measuring the
concentration of OH- or H+ in water was
invented; it is called the pH scale. The pH scale
has values between 0-14, with pH 7 being the
value where the concentration of H+ equals the
concentration of OH- in a water sample. This is
called neutral pH. See the pH scale below.
and
pH
OH->H+
Alkaline
Neutral
H+>OHAcidic
14
13
12
11
10
9
8
7
6
5
4
3
2
1
Substance
Draino, lye
household bleach, oven cleaner
household ammonia, fertilizer
milk of magnesia, soap
baking soda, Tums
seawater
deionized, distilled water; blood
rainwater, cow’s milk, urine
black coffee
tomato juice
Coca cola, beer, wine, orange juice, vinegar
lemon juice, acid rain
stomach acid, battery acid
Figure 1. The pH scale and some pH values for common substances
Science 214 Lab Manual pg. 5
Most living things require a pH of about 7
to function properly. When the pH drops below
7 (acidic conditions) or rises above 7 (alkaline
conditions), a living thing will begin to die
because the environmental conditions block or
destroy a cell’s important metabolic reactions.
Specifically, the enzymes in cells are ruined by
high or low pHs. In humans, a variation of just a
few tenths of a pH in the blood can be fatal.
For this reason, our blood contains
bicarbonate buffer, a substance which absorbs
extra hydrogen or hydroxide ions. This means
that bicarbonate buffer helps to prevent the pH
change in our bodies, keeping the pH fairly
constant, even if we eat or drink acidic or basic
foods.
 ACTIVITY H. Measuring pH
1. Complete the pH chart on your lab report
sheet.
2. pH or phydrion paper allows you to determine
the pH of a liquid by dipping the paper briefly
into the liquid. To see how this works, dip
separate sticks of pH paper into the beakers
labeled H2O, HCl and NaOH. Record your data
on the lab report sheet.
blood cells. Use a graduated cylinder to
accurately measure 10 ml. Label this tube “B”.
2. Pour exactly 10 ml of “Pure water” into
another beaker. Use a graduated cylinder to
accurately measure out this volume. Label this
tube “W”.
3. Add 5 drops of Methyl Red solution to both
the “B” and “W” tubes. Methyl Red is a
substance called a pH indicator. After adding
Methyl Red, the liquid should be yellowish in
color. If the liquid in the test tube becomes acid,
the color will change to red.
4. This step involves working with acid, which
can burn your skin and make holes in your
clothes. Wash your hands or sleeves
immediately if you spill it on yourself.
Using the Acid/HCl solution, carefully add
drops to the “W” tube, counting the drops as you
go. Stop and SWIRL THE WATER in the tube
AFTER ADDING EACH DROP to provide
constant mixing. Stop adding drops when the
liquid turns red. Record the number of drops it
took to make pure water acidic in the table on
page 10.
3. Locate the set of test tubes containing various
mystery liquids. Measure the pH of each liquid
using pH paper. Then use the pH chart at the
beginning of this lab exercise, other
observations, and your own experience to
identify each liquid. Do not attempt to taste
these liquids and use caution if you try to smell
them.
6. Next, use the Acid/HCl solution to make the
“B” water acidic. Carefully add drops to the “B”
tube, counting the drops as you go. Stop and
SWIRL THE WATER in the tube AFTER
ADDING EACH DROP to provide constant
mixing. Stop adding drops when the water turns
red. Record the number of drops it took to make
blood plasma acidic in the table on page 10.
4. Record a description, the pH, and the identity
of each solution on the lab report sheet.
7. Wash out your B and W tubes and remove
any labels from them. Place them upside down
in the rack. Please wipe up any spills.
5. Be sure to clean up any spilled liquids and
pieces of pH paper.
 ACTIVITY I. Testing the Buffering
Capacity of Blood
1. Pour exactly 10 ml of “Blood Plasma” into a
50 ml beaker. Blood plasma is the clearish
liquid in your bloodstream that surrounds the red
Science 214 Lab Manual pg 6
Lab Report
Bonds, Molecules and pH
Name
A. Describe the arrangement of the individual ions (green is sodium, silver is chloride) and their spacing
in this model of NaCl (sodium chloride). What is the ratio of sodiums to chlorides? Describe the spacing
between two sodiums as well as between a sodium and a chloride.
B. Describe the arrangement of individual water molecules (red oxygen with two white hydrogens) in a
model of ice. What atoms are involved in making a hydrogen bond from one water molecule to the next?
C. Complete the following molecule by adding covalent bonds to hydrogen atoms according to the rules
of how many bonds each of the different atom types make.
C = C—N—O—C—N = C
D. Name the type of bond found between the atoms indicated by the arrow.
(Ca+2)(SO4-2)
(K+) (Br -)
H_Cl
-CH2-O-H+
H-N- - CH2-
_
H OH
E. Complete the following chemical reactions by showing what the products of the reaction will be.
Ca+2 + CO3-2
forms an ionic bond
Science 214 Lab Manual pg 7
(Ag+)(NO3-) + (Na+)(Cl-)
Silver (Ag) changes places with sodium (Na) t produce
silver chloride and sodium nitrate (an exchange reaction)
Li + Br
(loses) (gains)
Each atom steals or give up a single electron
to become ions and then an ionic bond is formed
(an oxidation-reduction reaction)
F. Concerning the reaction where methane and oxygen react to form carbon dioxide and water as
described under Activity F in the text:
i. Rewrite this reaction (using chemical formulas) but include heat (written as 890 Calories of
heat) as another one of the products of the reaction.
ii. Given that this reaction features a carbon-hydrogen molecule breaking down in the presence
of oxygen to form carbon dioxide, water, and heat, what type of chemical reaction is this? See
the end of the Chemical Reactions section in the foregoing text for this lab.
G. Concerning the reaction where a two-part protein (alanine-glycine) was broken apart (with the
addition of water) to form two free amino acids:
i. What type of chemical reaction is this? See the end of the Chemical Reactions section in the
foregoing text for this lab.
ii. Given that meats are nearly all protein, describe where in your body you might find this
particular reaction taking place.
Science 214 Lab Manual pg 8
 Measuring pH
1. Complete the following chart. Write in the location of pH 0, 7, and 14 in the appropriate places
on the pH line scale below. Also indicate with arrows where a strong acid and a weak base would be.
Acidic
Neutral
Basic
2. Complete the chart below with the pH and type of solution for the three solutions shown.
Table 1. The pH of three different solutions.
H2O
CH3COH
NaOH
(vinegar)
(Draino)
pH
Acid, Base, or
Neutral?
3. Complete the description, the pH, and the probable identity of each of the mystery liquids.
Solution A
Description:
pH=
Solution B
Description:
pH=
Solution C
Identity of liquid:
Description:
pH=
Solution D
Identity of liquid:
Identity of liquid:
Description:
pH=
Identity of liquid:
Science 214 Lab Manual pg 9
Solution E
Description:
pH=
Solution F
Description:
pH=
Solution G
Identity of liquid:
Description:
pH=
Solution K
Identity of liquid:
Description:
pH=
Solution J
Identity of liquid:
Description:
pH=
Solution I
Identity of liquid:
Description:
pH=
Solution H
Identity of liquid:
Identity of liquid:
Description:
pH=
Identity of liquid:
Science 214 Lab Manual pg 10
 Buffering Capacity of the Blood
Number of drops required to turn
acidic (red)
Pure water
Blood plasma
1. Which solution turned acidic with the fewest drops?
2. Which solution is buffered?
3. What specific chemical do we have in our blood that prevents our blood from becoming acidic
whenever we drink vinegar (salad dressing) or Coca Cola?
4. How is the pH change (or lack thereof) of blood an advantage to living things?
Science 214 Lab Manual pg 11