Download 01•Building Models of Macromolecules

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2014-2015 ERHS
MYP H Biology
01Building Models of Macromolecules
UNIT I: SCALE
Introduction
Carbohydrates, along with proteins, fats and nucleic acids are the major groups of
organic chemicals, which make up cells. Carbohydrates are primarily responsible for the
storage of energy within a cell system, but also aid in the structural support of tissues. They
are commonly referred to as sugars, starches or fiber.
The term carbohydrate is derived from the elements that make up the molecule:
“carbo-“ from carbon, and “hydrate” (meaning water) from the combination of hydrogen and
oxygen. The ratio of two hydrogen atoms to one oxygen in a water molecule is duplicated in
carbohydrates, giving more credence to the term meaning “watered” carbon.
The smallest unit of the carbohydrate family is called monosaccharide (also known as
“simple sugar”). Though occasionally found in a chain form, the monosaccharide normally
exists as a ring consisting of five carbon atoms and one oxygen. The molecular formula is
C6H12O6 giving an empirical formula ratio of one carbon to two hydrogen to one oxygen. Figure
1 shows a two-dimensional drawing of a typical monosaccharide known as galactose.
galactose
glucose
fructose
Two monosaccharides combine via dehydration synthesis to form a disaccharide,
molecular formula C12H22O11. Common disaccarides include lactose (milk sugar) and sucrose
(cane sugar). Disaccharides combine further, to form polysaccharides starch and cellulose.
Note: many carbohydrate names end in –ose.
Starch is produced in plants, and its decomposition shows the importance of
carbohydrates. When starch is consumed by an animal or by the plant itself, the
polysaccharide undergoes hydrolysis (addition of water to break apart bonds). Eventually the
polysaccharide is divided into its individual glucose molecules. In turn, glucose disintegrates
at its carbon hydrogen bonding sites. Each time a hydrocarbon bond is broken, energy is
released which can be used for various cell processes.
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2014-2015 ERHS
MYP H Biology
Cellulose is produced by plants, but it cannot by hydrolyzed by most organisms
(exceptions include some protozoa, bacteria and insects: can you guess which one?) Because
the cellulose structure is so stable, it provides support to plant tissue (fiber, wood).
Objective
Models will be used to visualize simple sugars, emphasizing the characteristic carbonhydrogen-oxygen bonds and the aromatic structure in solution. The monosaccharides will be
joined to create a disaccharide, the disaccharides bonded to show polypeptides.
Materials
1 molecular models set:
2 blue nitrogen atoms
48 white hydrogen atoms
12 black carbon atoms
48 single bonds (short tubes)
12 red oxygen atoms
6 double bonds (long tubes)
Procedure
Part I-Building a simple sugar (Monosaccharide)
1. The ring
A. Obtain five carbon atoms, one oxygen atom and six pieces of bonding tubes from
your kit. Join the five carbons in a chain, with only one bond between each atom. Place
one of the remaining bonding tubes on a bonding site of the first carbon in your chain;
place the other bonding tube on a bonding site of the last carbon in your chain.
Without bending the bonding tubes, attach them to the two bonding sites of the
oxygen atom. You should now see a ring of atoms.
B. Each carbon atom should have two of its four bonding sites open, while the oxygen is
full. Eventually all of the carbon sites will be filled by bonds to other atoms.
C. Note that all six atoms are not in the same plane, which allows the ring to bend
upward or downwards. This structure is the most stable arrangement for the atoms.
2. Filling the bonding sites and making a simple sugar
A. Place the ring on the table in front of you with the lone oxygen atom at the “twelve
o’clock” position. Moving clockwise, place one hydrogen atom on each of the five
carbons in the ring. At this point there should be one open bonding site on each carbon.
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2014-2015 ERHS
MYP H Biology
B. Moving clockwise, place one oxygen atom on the first four carbons in the ring. Add a
hydrogen atom to each of the four carbons in the ring. Add a hydrogen atom to each
of the four oxygen’s remaining bonding sites. At this point, the only bonding site not
filled should be the one on the final carbon of the ring.
C. Bond another carbon atom to the final ring carbon.
D. Bond an oxygen atom to one of the bonding sites open on the new carbon.
E. Using three hydrogen atoms, fill all remaining bonding sites on the new carbon and
oxygen atoms. The simple sugar you have made is called glucose. Check with your
instructor to see if your model is constructed properly.
3. Another monosaccharide.
A. Put your glucose molecule to the side, saving it for later use in the lab.
B. Observe the diagram of the monosaccharide fructose below. (Figure 2)
Figure 2. Fructose
C. Construct a fructose molecule using the remaining atoms from your molecular model
packet. Use the structure diagram above as a guideline for your model.
4. Variance within the monosaccharide family
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2014-2015 ERHS
MYP H Biology
A. Note the structural inconsistencies between the two monosaccharides you have built.
Even though each contains the same number of carbon, hydrogen, and oxygen atoms, glucose
and fructose are arranged differently.
5. Energy storage
A. Carbohydrates provide organisms with energy in the form of hydrogen-carbon bonds.
Whenever a hydrogen atom separates from a carbon, energy is released which can be used to
perform work within the organism. Do your models show many sites where hydrogen could
separate from carbon? Are the bonds on the exterior of the molecule, making them easier to
break?
Part II-Building a disaccharide
6. Combining monosaccharides
A. Place the two models in front of you with glucose on the left, and the ring oxygens at the
“twelve o’clock” position. Can you guess where and how these two monosaccharides will join?
B. On the glucose molecule, locate the first carbon next to the oxygen in the ring. This
carbon has a hydrogen and an oxygen-hydrogen section branching off of it. Now locate the
oxygen-hydrogen section bonded off this carbon. Remove this hydrogen (with bonding tube)
from the fructose).
C. On the fructose molecule, locate the first carbon next to the oxygen in the ring. This
arbon has another carbon branching offof it. Now locate the oxygen-hydrogen section
bonded off this carbon. Remove this oxygen-hydrogen combination (without bonding tube)
from the fructose.
D. Joining the two monosaccharides to create a disaccharide. The disaccharide you have
made is called sucrose (also known as table sugar). The 2-dimensional representation of
sucrose is shown below.
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2014-2015 ERHS
MYP H Biology
Figure 3. Sucrose
7. Dehydration synthesis
Note what pieces are left over from the glycosidic bond in step six. Can these pieces bond
together? Because water (H2O) is formed during the making of a disaccharide, the reaction
is called dehydration synthesis.
Part III-Building a polysaccharide
8. Joining disaccharides
A. Select another lab group to work with, and join your disaccharides together.
Following a procedure similar to the previous Step 6, combine the two disaccharides. Four
simple sugars are now bonded together, forming a polysaccharide. Any time three or more
monosaccharides combine, the term polysaccharide is used to describe the product.
B. Note that each time a new connection between sugars is made, another water
molecule is released.
C. Two common groups of polysaccharides are starch and cellulose. Each contains
hundreds, if not thousands, of glucose molecules linked together.
Questions
1. How many carbons, hydrogens, and oxygens are in your completed simple sugar model?
C_______
H_______ O________
Use these numbers to write the molecular formula for glucose: C H O
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2014-2015 ERHS
MYP H Biology
2. Make a drawing of your glucose molecule:
3. How many carbons, hydrogens, and oxygens are in your completed fructose?
C______
H _______ O________
Use these numbers to write the molecular formula for fructose: C H O
4. How many carbons, hydrogens, and oxygens are in your completed sucrose?
C______
H_______ O________
Use the numbers to write the molecular formula for sucrose:
C H O
5. Based on the information gathered during this laboratory, why are carbohydrates
excellent sources of energy for organisms?
Part III-Structure of a protein
9. General structure of an amino acid
A. Obtain one carbon atom from your packet. Your amino acid will be centered around
this carbon.
B. All amino acids must have a hydrogen atom bonded to the central carbon. Single
bond a hydrogen to your carbon.
C. All amino acids must have an amine (-NH2) group bonded to the central carbon.
Construct an amine by connecting a hydrogen with a plastic tube to two of the
bonding sites on a nitrogen atom. Using the third bonding site on the nitrogen,
connect this amine to the central carbon. The fourth bonding site on nitrogen
represents an unshared pair of electrons and will not be used in this lab.
D. All amino acids must have a carboxylic acid group (-COOH) bonded to the central
carbon. Construct one carboxylic acid following the same procedure used for lipids
in Step 9. Use the further bonding site on the carboxylic acid carbon to connect it
to the central carbon.
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2014-2015 ERHS
MYP H Biology
E. The model in front of your is the general structure of every amino acid found in
nature. Note the remaining bonding site on your central carbon. What connects
here, called the radical (R), determines which amino acid is formed. Each of the
twenty amino acids that make up proteins has a different radical.
10. Building an actual amino acid-glycine
A. Glycine is the simplest amino acid, since its radical is only a hydrogen atom.
Construct glycine by adding a hydrogen atom to the remaining bonding site on the
general amino acid model from Step 14. Save the model for later use.
11. A second amino acid-alanine
Figure 4. Glycine
A. Build a second general amino acid structure by following Step 9.
B. Add the radical –CH3 (a carbon with three hydrogens bonded to it) to the fourth
central carbon bonding-site. This amino acid is called “alanine”.
C. Compare glycine to alanine. Note any similarities and differences
Figure 5. Alanine
12. The peptide bond
A. Place the glycine model created in Step 15 next to the alanine model made in Step 16.
Remove the –OH end (with bonding tube) from the carboxylic acid group of the glycine
model. Remove a hydrogen atom (without bonding tube) from the amine group of the
alanine. Bond the glycine to the alanine at these locations.
B. Whenever two amino acids combine, the bond is called a peptide bond, and the larger
molecule is generally called a dipeptide.
C. Note what pieces are left over from the peptide bond. Can these pieces bond
together? Because water (H2O) is formed during the making of a dipeptide, the
reaction is called dehydration synthesis.
Gallegos/Brombach/Miller/Bare
2014-2015 ERHS
MYP H Biology
13. Starting a protein
A. Form a peptide bond between your dipeptide model and a model from another group.
Another water molecule will be given off when you are finished.
B. This model is a small polypeptide chain, and the beginning of a protein. It is however,
only the start, because you have combined only 4 amino acids. Most proteins have
hundreds of amino acids linked together, while some have thousands.
Questions
6. What two functional groups are contained in all amino acids? Include the structure of
each group.
7. With respect to amino acids, what does the term radical mean?
8. Arrange the following terms in order of least to greatest representative size:
dipeptide
amine
protein
amino acid
carboxylic acid
9. State the similarities that exist between proteins and polysaccharides in these areas:
a. elements that make up the molecules
b. Type of reaction involved in forming the substance & secondary product given
off in each instance.