Part 1: Exploring organic molecules with molecular model kits

BackgroundTypically chemistry is a prerequisite course for advanced biology courses. This is because all living things—from plants to bacteria to TBLS students—are made of atoms. A review of organic chemistry at the beginning of our advanced biology course will help you understand the molecular basis of life.

Physical models of molecules have played an important role in understanding chemistry throughout the history of science, both in the classroom and in research. The construction of physical models is often a creative act and has helped scientists elucidate the nature of complex molecules and formulate hypotheses. Famously, James Watson and Francis Crick used what they understood about nucleotide structure to construct a three-dimensional model of the double helix in 1953. By studying the structure of their model they formulated a hypothesis about the mechanism of DNA replication that was later proved accurate by experimentation.

The diagrams of molecules you are used to seeing in chemistry are also models. Lewis structures show the bonding between all the atoms of a molecule. Often in organic chemistry, when the structures are large, a simplified Lewis diagram known as a line drawing is used. Space-filling and ball-and-stick models are used to show more of the three-dimensional structure of atoms in a molecule.

In this activity, you will construct physical ball-and-stick models using the molecular model kits. You will: Build some common monomers of proteins, lipids, and carbohydrates Demonstrate condensation and hydrolysis in carbohydrates using the models Practice drawing molecular diagrams of molecules that are biologically important

Assessment

Answer all questions in this handout.

Materials Carbon (C): black orbs, at least 6 Hydrogen (H): yellow orbs, at least 12 Oxygen (O): red orbs, at least 6 Nitrogen (N): blue orbs, at least 1 C—C or C—O bonds: long wooden

sticks C-H bonds: short wooden sticks Double bonds: springs, at least 4

1

Macromolecules Reference Table

Common functional groups and their properties

In organic chemistry, functional groups are specific groups of atoms or bonds within molecules that are responsible for characteristic chemical properties or reactions.

2

Group Structural Formula Shorthand Properties of group Chemical reactivity

Hydrocarbon Chain

—(CH2)n— Nonpolar; the longer the chain the less polar

Usually not reactive

Methyl —CH3 Nonpolar Usually not reactive

Hydroxyl —OH Polar -H or -OH may be removed during condensation reactions

Carboxyl —COOH Polar

Acidic (releases H+ in solution, forming –COO-)

-H may be removed during condensation reaction

Amino —NH2 Polar

Basic (removes H+ from solution, forming NH3 +)

-H may be removed during condensation reactions

Phosphate —PO4 Very polar

Acidic (releases H+ into solution, forming PO3

-)

-H or -OH may be removed during condensation reactions

Examples of Amino Acids

Glycine Leucine Serine

Examples of Fatty Acids

Saturated fatty acids Unsaturated fatty acids

Examples of Monosaccharides

α-Glucose β-Glucose Ribose

Part 1: Amino acids (Protein subunits)

3

1. Perform a quick inventory of your model kit and make sure that you have everything listed in the materials section. If you are missing anything, report it to your instructor.

2. Use the molecular model kit to construct the amino acid glycine based on the structural formula given in the reference table.

a. Which functional groups are present in every amino acid? _______________________

b. What is the side chain (R-group) for glycine? ____________

3. Build the side chains for leucine and serine. Practice swapping out the side chain in your model amino acid to change between the different amino acids.

a. Examine the functional groups. Which amino acids are most likely polar? Nonpolar?

Polar: _____________________ Nonpolar: ___________________

4. Make sure that every person in your group can thoroughly answer these questions using the models. Write the answers in your notebook.

a. What are the identifying features of an amino acid?

b. What makes each type of amino acid unique?

Part 2: Fatty Acids (Lipid subunits)

5. Dismantle your amino acid and construct the lipid monomer heptanoic acid (C7H14O2).

6. What functional groups are present in every fatty acid? ________________________________

7. Heptanoic acid is considered a saturated fatty acid, because there are only single bonds between carbon atoms in the chain. Every carbon atoms is bonded to the maximum number of hydrogen atoms. Convert it to a monounsaturated fatty acid by creating a double bond between C-4 and C-5. Use the springs to model double bonds.

a. How many hydrogen atoms did you remove to form the double bond? _____________

8. Unsaturated fatty acids always have two isomers: a cis and a trans isomer. Based on the images in the reference table, practice converting the molecular model between cis and trans forms.

a. Describe two differences between the shape and bonding of cis and trans isomers.

________________________________________________________________________

________________________________________________________________________

4

Part 3: Monosaccharides (Carbohydrates)9. Deconstruct the fatty acid and build an alpha glucose molecule. This molecule is a little trickier

so carefully follow these instructions:

a. Connect the atoms that make up the ring structure first. Remember to use the long sticks for C—C and C—O bonds.

b. Add the additional hydrogen atoms and functional groups that are bonded to the atoms in the ring. Remember to preserve the “up” and “down” orientation around the ring. If you imagine the carbon ring like a crown sitting on your head, atoms in the “up” position would stick up like the points of the crown, and atoms in the “down” position would hang down into your eyes.

c. The molecular formula for glucose is C6H12O6. When you think you’ve finished your glucose, check that you’ve used the correct number of atoms.

10. Now, change the structure of your glucose molecule to represent beta glucose.a. Fill in this table showing the “up-down” pattern of the groups attached to each carbon:

Position of each functional group (up or down)C1 (OH) C2 (OH) C3 (OH) C4 (OH) C5 (CH3)

α-glucoseβ-glucose

11. CHECKPOINT 3: When you’re ready, bring your models and lab manual to your instructor. Make sure that every person in your group can thoroughly answer these questions using the models:

a. What are the identifying features of glucose?

b. What is the difference between alpha and beta glucose?

Part 4: Condensation and Hydrolysis1. Pair up with the other partner group at your table. You should each have one alpha glucose

molecule.

2. Condensation joins monomers into polymers. In monosaccharides, a condensation reaction often occurs between C1 and C4. Model a condensation reaction by performing the following steps:

a. Remove the hydroxyl group from C1 of one glucose molecule. Remove a hydrogen atom from the hydroxyl group on C4 of the second glucose molecule.

b. Attach the unbonded carbon to the unbonded oxygen. Congrats: You have a disaccharide!

c. Bond the hydroxyl group and hydrogen atom. Congrats: You have a molecule of water!

3. Hydrolysis forms monomers from polymers. Enact a hydrolysis reaction by reversing the steps you just took.

5

Part 2: Exploring organic molecules with molecular visualization software

BackgroundThere is a long tradition of constructing physical models of molecules in order to elucidate their molecular properties. However, because many biological molecules are large polymers, it is not always practical to construct ball-and-stick models such as the ones we constructed in the prior activity. In that activity, you constructed a single molecule of glucose and condensed it with a neighbor’s glucose model in order to form a disaccharide. If you wanted to construct glycogen (a glucose polymer synthesized in your liver), you would need 30,000 units of glucose! It would take thousands and thousands of balls and sticks to model even a partial structure.

Many software platforms have been developed for the visualization of virtual models of molecules. Physical models and computer models have complementary strengths and weaknesses. Though virtual models cannot readily show the flexibility and interchangeability of molecules like mechanical models can, they are valuable for representing large molecules that would take many months to build. Furthermore, while it would be impractical to mail a physical model, it is quite easy to upload a digital one. As the scientific community has become globalized, virtual models are a cheap and instantaneous method of communicating and sharing knowledge about molecular structures.

In this lab, you will analyze molecular models created in JSmol (a molecular modeling software) in order to better understand biological polymers. In particular, you will:

Review the structure of glucose Compare the structure of amylose, amylopectin, and glycogen Consider how the structure of cellulose influences its function

A useful collection of JSmol models relevant to the IB Biology course has been curated at the BioTopics website (http://www.biotopics.co.uk/jsmol/glucose.html). You’d be wise to bookmark this site as a study resource! In addition to the molecules we will study in this lab, you can find virtual models of many other molecules in the unit. During this lab, you may use any extra time for further exploration and revision.

Materials Computer with internet access Pencil for line drawings

Using JSmol software Rotation: Hold down the left mouse button and drag to turn the molecule. Zoom: Rotate the scroll wheel on the mouse. Alternatively, right click on the model and select

the “Zoom” menu. Highlight features: Each molecule is accompanied by text describing its features. If you click on

the hyperlinked (blue) text, it will highlight important features in the model.

Adapted from Paine, Chris. “BioKnowledgy 2.3 Carbohydrates and lipids.” Slideshare. Accessed June 2015. www.slideshare.net/diverzippy/bioknowledgy-23-carohydrates-and-lipids

6

Part 1: Comparing the Structure of Storage Carbohydrates 1 Glucose is the main primary energy storage molecule, and when it is in excess organisms may use it to form polysaccharides. Amylose and amylopectin are used in plants, and glycogen is used in mammals.

1. Navigate to the link given in the background. This will take you to a (hopefully familiar) model of glucose. Practice rotating, zooming, and highlighting features as you explore the glucose model.

a) Determine whether the glucose molecule shown is α or β, giving a reason.

________________________________________________________________________

2. Go to “3-D molecules” “Carbohydrates” “Amylose” in the menu at the top to observe a molecule of amylose. Examine the molecule and test yourself by answering the questions below.

a) Look at the amylose model and zoom out. Describe the overall shape of the molecule.

b) Zoom in on the amylose molecule. Each glucose sub-unit is bonded to how many other sub-units? Which carbon atoms (identified by number) are used to form the glycosidic linkages? Are there any exceptions to this rule?

3. Select the amylopectin model. You will notice that unlike amylose, amylopectin is branched. Zoom in on the branch point.

a) The glucose sub-unit at the branch point is bonded to how many others?

b) Which carbon atoms are used to form the glycosidic linkage that connects the branch?

c) According to the text, how many sub-units may a typical amylopectin molecule contain?

4. Use a similar approach to investigate glycogen and find its similarities and differences between it and both amylose and amylopectin. Summarize your findings in the table below.

Table 1: Comparing features of the storage polysaccharidesPolysaccharide Overall shape Types of linkages Approximate #

of sub-unitsAmylose

Amylopectin

Glycogen

1

7

Part 2: Understanding the structure of celluloseCellulose is a structural polysaccharide found in the cell walls of plants. Unlike the storage polysaccharides, structural polysaccharides are not used for energy storage, but rather for cell wall strength and stability. Like amylose, amylopectin, and glycogen, cellulose is composed of glucose subunits. However, in cellulose, these glucose subunits are bonded together very differently.

5. Select the cellobiose molecule. Cellobiose, a disaccharide, is the monomer of cellulose fiber. Read about cellobiose and rotate the virtual molecule until it matches the line drawing below.

a) Number all the carbons in both glucoses.b) Circle and label the 1-4 linkage.

c) Draw a box around C6 and its associated functional group in both glucoses. Note that these carbons are pointed in opposite directions.

d) Is cellubiose made of β-glucose, α-glucose, or a combination? How can you tell?

_______________________________________________________________________

_______________________________________________________________________

6. Select the cellulose molecule. a) How does the overall shape of cellulose differ from the storage polysaccharides?

_______________________________________________________________________b) Cellulose molecules vary in length. How many 1-4 linkages are present in this virtual

molecule? ________c) Highlight the hydrogen bonds within the cellulose molecule and zoom in on them. Use

dotted lines to indicate the H-bonds in the image below.

7. Considering your answers to 6, what structural features might make cellulose stronger and more rigid than the other polysaccharides?

______________________________________________________________________________

8

______________________________________________________________________________

Part 3: Practice with Lipids1. Based on the molecular models available at Biotopics and your knowledge of organic molecules,

make line drawings (review guidelines in 4a!) of all of the following molecules. USE PENCIL.

2. Alpha linolenic acid (ALA) is a fatty acid found in seeds, nuts, and vegetable oils. Using Biotopics, examine the virtual ALA molecule (Look under “Lipids”).

a) Add hydrogens to the appropriate sides of each double bond in the line drawing below. You do not need to draw all the hydrogens in the molecule.

b) Using arrows, indicate whether each double bond in ALA is cis or trans.

9

a. Glycerol (Look in “Lipids”)

b. Stearic acid (Look in “Lipids” “saturated & unsaturated fatty acids”)

c. Oleic acid (Look in “Lipids” “saturated & unsaturated fatty acids”)

3. Use Biotopics to draw an example of each of the molecules below.

d. Monoglyceride

e. Diglyceride

f. Triglyceride

4. From the examples in this lab, identify a lipid in each category:

a. Saturated fatty acid: _______________________________________________________

b. Monounsaturated fatty acid: ________________________________________________

c. Polyunsaturated fatty acid: _________________________________________________

5. Fatty acids can be condensed with glycerol to form mono-, di-, and tri-glycerides. Write a chemical equation for the condensation reaction (in the form of reactants products) for the formation of each molecule below. Use the names of the molecules rather than their chemical formulas. Make sure you indicate how many fatty acids are required and how many molecules of water are formed in each reaction.

a. Monoglyceride ___________________________________________________________

b. Diglyceride ______________________________________________________________

c. Triglyceride ______________________________________________________________

10

Additional Practice: Line DrawingsIn order to make structural drawings less crowded, organic chemists use an abbreviated drawing convention called “line structures.” The convention is quite simple and makes it easier to draw the structures, but it does take a little bit of getting used to. Here are the conventions:

Carbon atoms are depicted not by a capital C, but by a ‘corner’ between two bonds, or the end of a bond.

Straight chain molecules like a fatty acid are usually drawn in a ‘zig-zag’ shape to accentuate the corners where carbon atoms would be.

Hydrogens attached to carbons are generally not shown; rather, they are simply implied. Unless a positive formal charge is shown, all carbons are assumed to make 4 bonds and be saturated with hydrogen.

Hydrogens are shown if they are part of a functional group, as in a hydroxyl group (-OH).

As you can see, the pared-down line structure makes it much easier to see the basic shape and arrangement of the molecules. Line structures also make it easier to identify important functional groups without these groups getting lost amongst a sea of carbon and hydrogen atoms.Practice with line drawings

Based on the Lewis structures in the reference table and your knowledge of organic molecules, make line drawings of all of the following molecules. USE PENCIL.

a. Pentanoic acid (5 C) b. Heptanoic acid (6 C)

11

c. Cis-monunsaturated pentanoic acid (double bond located between C3 and C4)

d. Trans-monounsaturated pentanoic acid (double bond located between C3 and C4)

e. Alpha-glucose f. Beta-glucose

g. Ribose h. Maltose (1,4 linkage between two α-glucose)

12