Name_______________________________

Laboratory 1: Organic Molecules

Prelab: Due at the start of lab.

Read the entire lab to answer the following questions.

1. Draw the Amino Acid Glycine. Label the R group, the amine group and the carboxylic acid
group (2pts).

2. How many bonds can a carbon atom form? (1pt)

3. Draw a single nucleotide of Adenine. Label the sugar, the base and the phosphate group. (3pts)

4. Draw the structure of glucose molecule.(2pts)

5. What three main elements are lipids primarily composed of? (2pts)
Laboratory 1: Organic Molecules

Part I – Structure of Some Organic Molecules

Written by Dr. R.A. Donahue (CWU), with modifications.

Introduction: (work in pairs)

Carbon is often referred to as the backbone element for biological macromolecules or
organic compounds. Because carbon can form 4 covalent bonds with either carbon or other
atoms or functional groups it can be used to create an incredibly diverse array of molecules in
biological systems. In this lab you will use molecular models to create and investigate simple
carbon molecules and some simple examples of each of the 4 types of organic macromolecules,
i.e. carbohydrates, lipids, proteins, and nucleic acids. Each of these four major classes of
macromolecules has particular chemical and structural traits that influence its behavior, and
therefore its role(s) in organisms.

Materials:
You will be using a flexible molecular model kit to make carbon molecules and
monomers of each of the types of organic macromolecules. Initially, familiarize yourself with
the models and how they work. Basically you will snap 2 of the model pieces together to make
an atom; e.g. carbon with a tetrahedron shape, which can form bonds with 4 other atoms.

Try to be consistent with the color designations for the different atom types as follows:
carbon = black (or grey)
oxygen = red
nitrogen = blue
phosphorous = pink (or use 2 grey with 3 bonds each)
The small spheres can be attached to the ends of the bonds to represent functional groups and the
bonds can be left unattached to represent covalently bound hydrogen atoms.
Make 3 carbon atoms. Experiment with different atoms to which C can bond.

Answer questions 1 and 2 on the Organic Molecules Worksheet.

Attach the 3 carbon atoms together in a chain. Experiment with single, double and triple bonds.
You will need different parts for these. Do your best to figure it out, but PLEASE ask if you have
questions. We are here to help!

Answer question 3 on the Organic Molecules Worksheet.

Assembling molecules and macromolecules:
If you have enough model material try to make enough monomers (2 or more) to form the basis
of a polymer of the type of macromolecule you are investigating. You might need to combine
your monomers with those from another lab group to create the beginning of a polymer.

Lipids:

1. Use the 3 carbons you have and 3 single red pieces (oxygen): to build a glycerol
molecule.

2. Assemble 3 fatty acids. For simplicity, make the “tails” ~6-7 carbons long, and use only one
carbon piece to represent a carbon atom and assume the other electron orbitals are present with
attached hydrogen atoms.

3. Assemble a fat molecule (a triglyceride) from these 'monomers'.

Answer questions 4 and 5 on the Organic Molecules Worksheet.

3. Make an unsaturated fatty acid. Create a double bond between 2 of the carbon atoms in one
of the fatty acids to see how it affects the structure of the fatty acid and the fat molecule.

Answer question 6 on the Organic Molecules Worksheet.

4. Make a phospholipid: Remove one of the saturated fatty acids, and add a phosphate group to
the glycerol backbone of the molecule. Work with other groups to place two phospholipids side
by side to envision a mono-layer. Also position phospholipids together as they would be in a
lipid bi-layer.

Answer question 7 on the Organic Molecules Worksheet.

Carbohydrates:
1. Collect 10 carbon pieces and assemble them into 5 carbon atoms. Make one carbon with 2
grey pieces.

2. Assemble the 6 carbons with the grey carbon on the 5th position.

3. Place a single red piece { } on the 5th (grey) carbon.

4. Cyclize the ring structure of the 6 carbon sugar using the oxygen on the 5th carbon and the 1st
carbon.

5. Using the diagram below, make glucose by adding oxygens to the appropriate sides of the ring
structure. {For clarity, you may place white balls (hydrogen) on the oxygens to complete the
hydroxyl functional groups.}

6. Practice linearizing and cyclizing the sugar, keeping the oxygen on carbon #5 attached to that
5th carbon atom.

Answer question 8 on the Organic Molecules Worksheet.

7. Make either another cyclic glucose molecule or with some cleverness, make a cyclic fructose
(only 4 carbons in the cyclic part). OR: If the other two students at your table have a
monosaccharide, the four of you can work together on this step. Combine the two
monosaccharides to make either mannose or sucrose (disaccharides):

Answer questions 9 and 10 on the Organic Molecules Worksheet.

8. Break down the disaccharide by hydrolysis.

Answer question 11 on the Organic Molecules Worksheet.

Proteins:
1. Amino acid monomers. Use the models to create one non-polar; one polar; and one charged
amino acid. Use the structural models of amino acids as a guide to construct the molecules.
2. Assemble the amino acids into a tri-peptide (a short polypeptide) by forming peptide bonds.

Peptide Bond

H R H R

H N C C N C C OH
H
H O H O
Dipeptide

Answer questions 12 and 13 on the Organic Molecules Worksheet.

3. Work with another group to see how two polypeptides might interact. Use the R-groups to
form non-covalent hydrogen bonds, ionic bonds, hydrophobic interactions, and covalent
disulfide bonds. Realize that these two short tri-peptides could be two parts of a larger protein
that are interacting.
Nucleic Acids
Answer question 14 on the Organic Molecules Worksheet.

1. Discuss with another group before starting, so that one group makes a purine and one group a
pyrimidine.

2. Assemble a single nucleotide. {You might have to review the carbohydrate section.}
Focus specifically on which atoms contribute to forming a polymer from this monomer:
the -OH group on the 3’ carbon of the ribose
and the -PO4 group on the 5’ carbon of the ribose

3. Working with the other group, join the two nucleotides together in the correct orientation.

Answer question 15 on the Organic Molecules Worksheet.

4. Disassemble the nucleic acid back into single nucleotides. Attempt to align the two as if each
were part of separate strands of nucleic acid polymers. {Again, the DNA model is helpful.}

Answer question 16 on the Organic Molecules Worksheet.

 Name: _________________________________________

Laboratory 1 Worksheet: Organic Molecules

Turn in these last two pages for grading by your Teaching Assistant.

Introduction:

1. How many single bonds can a carbon atom make with other atoms? (1pt)

2. Do the bonds a carbon atom makes lie in a flat plane or have a 3-D shape? Describe.
(1.5pts)

3. Do carbon chains with double or triple bonds have as much rotational flexibility as
those with only single bonds? Explain. (1.5pts)

Lipids:

4. Which atom(s) is (are) lost during this dehydration (or condensation) reaction? (1pt)

5. What else is formed during this dehydration reaction? (1pt)

6. How does this double bond affect the overall structure of the macromolecule? (1pt)

7. Draw a lipid bilayer of phospholipids indicating the charged phosphate “heads” and the
fatty-acid “tails”. {You don’t need to show every atom of each macromolecule.}
(2pts)
Carbohydrates:
8. Is there a net change in the number of atoms during the cyclization reaction? (1pt)

9. Which atom(s) is (are) lost during this dehydration (or condensation) reaction? (1pt)

10. What else is formed during this dehydration reaction? (1pt)

11. What does each part of the word, “hydrolysis” refer to? (2pts)

hydro- refers to ________________________________________

-lysis refers to __________________________________________

Proteins:

12. Which atom(s) is (are) lost during this reaction? (1pt)

13. What else is formed during this reaction? (1pt)

{Is this sounding familiar?}

Nucleic Acids
14. A nucleotide is a monomer for larger nucleic acid polymers. What are the 3 separate
components of a nucleotide? (2pts)

15. What would be the orientation of the two bases relative to each other if your nucleic
acid was part of a long strand of DNA? {Observe the models of DNA for a clue.}
(1pt)

16. What forces now hold the two polynucleotides together? {i.e.: What forces hold two
strands of double stranded DNA together?} (1pt)