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Lab No. _______________
Date __________________
Name_________________________
Biology Section _________________
THREE DIMENSIONAL MODELS OF CHEMICAL COMPONENTS
AND REACTIONS IN LIVING THINGS
ATOMS AND CHEMICAL BONDS
Wooden balls of different colors represent different kinds of atoms according to the following key:
carbon
hydrogen
oxygen
nitrogen
(C)
(H)
(O)
(N)
-----
black
yellow
red
light blue
For this exercise use springs and pegs as chemical bonds according to the following scheme:
C–C
C–O–C
C–N
use long wooden pegs
C–H
C–O–H
N–H
use short pegs
C=O
--
use springs
The models of the atoms are drilled with one or more holes. Each hole represents an electron that may
be shared with other atoms. The valence or combining power of an atom is represented by the number
of holes.
What is the valence of a hydrogen (H) atom?
Oxygen (O)?
2. _____________________
1. ___________________________
Carbon (C)? 3. ________________
Short, wooden pegs, long wooden pegs, and springs are used to connect the atoms in the formation of
molecules of compounds and represent chemical bonds. Each chemical bond in the models represents a
pair of electrons shared by two bonded atoms. This type of chemical bond is called a covalent bond.
MODELS OF SIMPLE MOLECULES
Using short pegs combine two hydrogen atoms to form a molecule of hydrogen (H2). A structural
formula of a molecule is made by using chemical symbols for the atoms and a dash (-) for the
connecting chemical bonds. Draw the structural formula for a molecule of hydrogen (H2). (4)
Using springs (to help form double bonds) make a model of the oxygen molecule (O2). Draw the
structural formula of a molecule of oxygen. (5)
I-M
5/09
-2How many electrons are shared by the two oxygen atoms? (6) __________________________
Using short pegs make a model of a water (H2O) molecule and draw its structural formula. (7)
Similarly make a model of carbon dioxide (CO2) using springs for chemical bonds. Draw the structural
formula for carbon dioxide. (8)
GROUPS AND SIMPLE ORGANIC MOLECULES
Living things are composed of molecules that contain carbon atoms. Such molecules are said to be
organic molecules as opposed to inorganic molecules that do not contain carbon.
Construct a model of methane (CH4), the simplest organic compound. Write the structural formula for
methane. (9)
Remove a hydrogen from methane along with the bond to make a methyl (CH3) group. What is the
valence of this group? (10)
___________________________
Now make an alcohol (OH) group. What is the valence of this group?
(11)________________________
Combine the CH3 group with the OH group. The compound formed is methyl alcohol. Draw the
structural formula for methyl alcohol and circle and label the alcohol group. (12)
Make another CH3 group. Construct an amino (NH2) group (use only the holes in nitrogen that do not
go clear through). Combine the methyl and the amino group for form methylamine. Draw the structural
formula for methylamine and circle and label the amino group. (13)
-3Construct an organic acid group (COOH). It should look like this:
Connect the organic acid group to a CH3 group forming acetic acid.
Draw the structural formula for acetic acid and circle and label the
organic acid group. (Sometimes called the carboxyl group). (14)
Construct an aldehyde group that looks like this:
C-O-H
O
C–H
O
Connect the aldehyde group to a CH3 group forming acetaldehyde. Draw the structural formula for
acetaldehyde and circle and label the aldehyde group. (15)
CARBOHYDRATES
Carbohydrates are composed of carbon, hydrogen and oxygen. The general formula for a carbohydrate is
CnH2nOn. Note that the hydrogen to oxygen ratio is 2:1 as in water. There are twice as many hydrogens
as carbons.
A. MONOSACCHARIDES
The simplest carbohydrates are the simple sugars called monosaccharides with the formula
C6H12O6. The most commonly occurring simple sugar is glucose.
Make a molecule of glucose as follows:
C1
A. Assemble a chain of six carbon atoms as shown.
C2
B. Make carbon #1 part of an aldehyde group.
C3
C. Add an alcohol group to each of the other carbons.
C4
D. Fill in any unsatisfied carbon valences with hydrogen.
C5
E. Complete the linear diagram of glucose shown on the left. (16)
C6
-4Put this molecule into a ring form (see diagram below) by twisting it to bring carbon #1 and carbon #5
close together. Remove one of the double bonds at carbon #1. In its places put an OH group which is
taken from carbon #5. Complete bonding of oxygen by joining it to carbon #5. Complete the ring
structure of glucose below. Recall that the formula for glucose is C6H12O6. (17)
C6
C5
O
C4
C1
C3
C2
B. DISACCHARIDES
Cooperate with your neighbor and bring two models of glucose close together so that the OH group
of carbon #1 of one molecule and the OH group of carbon #4 of the second molecule are next to one
another. Remove one OH of one molecule and an H of the OH group of the second molecule. Join
the H and the OH that have been removed. What molecule consists of an H join to an OH?
(18) _________________
Now bond the carbon of one molecule (where the OH has been removed) to the O of the second model
(where the H has been removed). The two remains of the glucose molecules have now been bonded
together and form a new compound, a double sugar (disaccharide) known as maltose.
Count the atoms in your model of maltose and write the molecular formula below. (19)
Explain why this reaction that you simulated is called dehydration synthesis of two glucose molecules
to form maltose. (20)
The digestion of maltose is called hydrolysis. Simulate this reaction by splitting the water molecule
into OH and H groups, breaking the bond that holds the two parts of maltose together, and adding the H
and OH groups to reform the two molecules of glucose.
The suffix “lysis” means to “break up”. Explain why the process of breaking up maltose is called
hydrolysis. (21)
-5Complete the equation below for dehydration synthesis and hydrolysis of maltose. (22)
C6H12O6 + C6H12O6
dehydration synthesis
hydrolysis
C. POLYSACCHARIDES
If we similarly joined all of the models of glucose prepared by this class, removing a molecule of
water from between each molecule in the long chain, we would have a polysaccharide. Starch is
such a molecule several thousand units long. Cellulose from which cell walls of plant cells are
made is another long carbohydrate molecule. Both starch and cellulose can be hydrolyzed to
glucose by the use of suitable enzymes.
PROTEINS
Proteins are made from small molecules called amino acids.
Make a model of an amino acid as follows:
A. Make a two carbon chain (C-C)
B. Make one carbon an organic acid group:
C-O-H
O
C. Add an amino group
to the second C.
N–H
H
Use only holes in the N that do not go all the way through the ball.
D. Bond an H to the second carbon (the same one that is bonded to the amino group).
The structure you have made is the fundamental part of any amino acid. Note that it has one remaining
valence on the carbon atom to which the amino group is attached. There are 20 different kinds of amino
acids each having a different group called the R group bonded to this remaining valence of carbon.
Now construct a second model just like the first.
-6Convert one of these models to the amino acid glycine by bonding an H to the empty carbon valence.
The H is the R group of glycine.
Convert the second model to alanine by bonding a CH3 to the empty carbon valence. The CH3 group is
the R group for alanine.
Complete the structural formula for each of the models of amino acids that you have made. (23)
After you have completed the formula, circle and label the R group, organic acid group (carboxyl
group), and the amino group. (24)
Lay the two amino acids down so that the amino groups of one is next to the organic acid group of the
other as below.
Remove an OH group from the organic acid group of one amino acid and an H from the amino group of
the other amino acid. Join the H and OH. What model have you made? (25)
-7Bond the remains of the two amino acids by joining the carbon of one to the N of the other. This C-N
bond is called a peptide bond. Circle this bond in the diagram below. The new molecule formed is a
dipeptide. Complete the structure below. (26)
N–C–C–N–C–C
If you joined many amino acids together, a polypeptide would be formed.
Join your dipeptide to your neighbors’ forming a polypeptide with four units. Most proteins are long
polypeptide chains consisting of several hundred amino acids.
If you separated the units of the chain by adding water in the proper places, you would reform the amino
acids. When you do this, you are simulating the process of hydrolysis or digestion of proteins.
LIPIDS
Lipids are the group of organic compounds that include: fats, oils, waxes and sterols. Fats are large
molecules that contain carbon, hydrogen and oxygen although in different ratios than carbohydrates. All
fats contain three fatty acid molecules combined with a molecule of glycerol.
H
H
H
H–C –C – C–H
OH – OH – OH
glycerol
H
H
H
O
H – C – C ….... C – C – O – H
H–H
a fatty acid
H
-8What type of compound is glycerol? (Hint: What group do you recognize?) (27)
What makes the fatty acid shown above an acid? (28)
In the synthesis of a “fat”, glycerol and three fatty acids react in the following way:
How many water molecules are formed in the above reaction? (29)
What reaction would occur when this fat molecule is digested back into glycerol and fatty acids? (30)