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AP Biology
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MACROMOLECULE INVESTIGATION
Molecular shape is extremely important in living systems. Slight shifts in configuration
or re-arrangement of groups of atoms can determine whether or not the molecule can
function normally. In some cases, this can mean life or death for the organism.
The purpose of this lab is to get you familiar with the 3-dimensional characteristics of
different organic molecules. You will construct several models of various organic
molecules. You will be asked to simulate a common reaction used in the building of
larger molecules (polymers) from smaller ones (monomers). Upon completion of the lab,
I hope you will gain some appreciation of the enormous variety of biological molecules
that makes the amazing diversity of living things on our planet possible.
Materials:
(Per lab pair/group)
6 carbon atoms (black)
12 hydrogen atoms (yellow)
6 oxygen atoms (red)
2 nitrogen atoms (blue)
Gray links
Long gray flexible links, used to make double covalent bonds
Introduction to Organic Chemistry
A. Hydrocarbons - Use your modeling kit to build each of the following molecules.
Write the molecular formula and draw the structural formula for each of them.
1. Methane
2.
Butene
B. Isomers - For each of the following formulas, construct as many different molecules
as you can. Draw the possible structural formulas below.
1. C3H7OH
2. C5H12
3. Define isomer. Which would a biologist be more interested in, molecular
formulas or structural formulas? Why?
C. Functional Groups - Identify the following functional groups.
D. Synthesis and Breakdown of Polymers
1. What is the relationship between monomers and polymers?
2. The chemical mechanisms by which cells make and break down polymers are
basically the same for all large biological molecules. Monomers are connected by
a covalent bond that is formed after the loss of a water molecule. This is known
as a dehydration reaction or dehydration synthesis (which is a specific type of
condensation reaction).
Use your molecular modeling kit, to build two ethanol molecules. Ethanol is a
simple alcohol with the formula: C2H5OH. Simulate a dehydration synthesis
reaction and bond the two ethanol molecules together. Keep this new molecule
intact.
3. Polymers are disassembled by hydrolysis, which is basically the opposite of
dehydration synthesis. The covalent bond between two monomers is broken with
the addition of a water molecule.
Use your molecule modeling kit to perform a hydrolysis reaction, breaking your
two ethanol molecules apart.
Structure and Function of Large Biological Molecules
A. Proteins – Read Concept 5.4 (pg. 77 – 86).
1. Describe several of the functions of proteins.
2. The monomer of a protein is an amino acid. All amino acids have the same basic
structure. They possess both a carboxyl group and an amino group.
Note the R group in the structure above. This group is different for the 20 amino
acids. The physical and chemical properties of the R group (also known as the
side chain) determines the characteristics of a particular amino acid, which then
affects the functional role of the polypeptide.
What are the general categories that the side chains fall into?
3. Use your molecular modeling kit to build 2 amino acids – glycine and alanine.
The formula for glycine is NH2CH2COOH and the formula for alanine is
NH2C2H4COOH.
4. Amino acids are attached to one another through dehydration synthesis. Bind
your molecules of glycine and alanine together using dehydration synthesis.
Draw the structural formula of this polypeptide. What is the resulting covalent
bond called?
5. The specific activities of proteins result from their specific three-dimensional
shape. Therefore the folding of protein into a particular shape is extremely
important. There are several levels of protein structure. Review pg. 82-83. Click
on the following link:
http://www.learner.org/channel/courses/biology/units/proteo/images.html Click on
the video – The Three Dimensional Structure of a Protein. Summarize the four
levels of protein structure.
6. Explain the term denaturation. Under what conditions can a protein denature?
B. Carbohydrates – Read Concept 5.2 (pg. 69 – 74).
1. What are the primary functions of carbohydrates?
2. Distinguish between monosaccharides, disaccharides, and polysaccharides. Give
an example of each.
3. Monosaccharides generally have molecular formulas that are some multiple of the
unit CH2O. Glucose has a molecular formula of C6H12O6. What functional
groups are found in sugars?
4. In an aqueous solution, glucose assumes a _______________ shape. Click on the
following link:
http://www.stolaf.edu/people/giannini/flashanimat/carbohydrates/glucose.swf and
watch the video. Glucose can assume 2 forms: ________________ and
________________. What is the difference between the 2 forms?
5. Using your molecular modeling kit, make 2 α glucose molecules. You will need
to use 2 kits for this. Please make sure that the appropriate number of atoms gets
back into each kit. Simulate dehydration synthesis to connect these 2
monosaccharides. In your lab notebook, draw the chemical reaction you just
modeled.
6. What functional groups are involved in dehydration synthesis of
monosaccharides? To which carbon are they attached? What disaccharide have
you constructed? What term is given to the bond linking these 2 monomers?
What molecule have you removed?
7. Discuss the similarities and differences between starch, glycogen, and cellulose.
C. Lipids – Read Concept 5.3 (pg. 74 – 77)
1. Lipids are the one class of large biological molecules that does not include true
polymers. They do generally share one important trait. What property do all
lipids have in common?
2. Although fats are not polymers, they are large molecules that are assembled from
smaller molecules by dehydration reactions. A fat is made from glycerol and fatty
acids. Using your molecular modeling kit, construct a glycerol molecule. Draw
the structural formula of glycerol.
3. Fatty acids have a long carbon skeleton, usually 16 to 18 carbon atoms in length.
The carbon at one end as a carboxyl. Use the molecular modeling kit, construct 3
fatty acids. These fatty acids will be much shorter than normal fatty acids. Use
the following formulas: (1) COOHC2H5, (2) COOHCH3, and (3) COOHCH3.
4. In making a fat, 3 fatty acid molecules join to glycerol through dehydration
synthesis. Using your molecular modeling kit, join the 3 fatty acids to glycerol.
Draw the structural formula representing this fat. What is the resulting covalent
bond called?
5. What is the structural difference between a saturated fatty acid and an unsaturated
fatty acid? How and why does this structural difference affect the solidification at
room temperature?
6. Draw and label/describe a phospholipid. What important role do they serve in the
cell?
7. What are steroids characterized by? What is an example of a steroid?
D. Nucleic Acids – Read Concept 5.5 (pg. 86 – 89).
1. Relate the terms nucleotide and polynucleotide using monomer and polymer in
your description.
2. Summarize the role of DNA and RNA.
3. Identify the parts of a nucleotide.
4. Distinguish between pyrimidines and purines. Include which nitrogenous bases
fall into each category.
5. Describe the differences and similarities between DNA and RNA.
6. Using the following strand of DNA, write the complementary strand of DNA:
5’-TAACGGTCCT-3’
7. Using the following strand of DNA, write the complementary strand of RNA:
5’-GATCCGTGGA-3’
8. Describe the structure of DNA using the terms double helix and antiparallel.