CHEM120 Week 7 LAB

Laboratory 10: Building models of Biological Macromolecules

Learning Objectives:

•         Gain a better understanding of the structure and composition of biological macromolecules such as proteins, lipids and carbohydrates

•         Gain an understanding of how structure impacts function

•         Learn to identify key functional groups present in biomolecules

The functions of our bodies depend on macromolecules such as proteins, carbohydrates, lipids and nucleic acids.  The structures of these macromolecules are crucial for their functions.  In this lab, we will use a molecular modeling kit to learn about composition and structural formulas of functional groups and biological macromolecules.

Note to Students:

Read the lab before coming to class.  The expectation at Chamberlain (CCN/CU) is that you come to class fully prepared for lab.

Materials: Molecular modeling kit

Exploration 1: Functional Groups

Functional groups are made of specific elements and have a specific arrangement of atoms in space. Functional groups modify chemical properties of the hydrocarbon they are attached to. For example, when a hydroxyl group is added to the hydrocarbon ethane, the resulting compound ethanol or ethyl alcohol is more polar than the parent molecule ethane (tastes better too).

Build the models of the following functional groups. Draw their extended structural formula. Show the models of functional groups to the instructor and obtain his/her signature before moving to the next section.

-OH (Alcohol)

-NH2 (Amine)

-COOH (Carboxylic acid)

-CHO (Aldehyde)

-Combine the amine and carboxyl group to show the resulting amide. Draw its extended structural formula in the space below.

What small molecule is produced as a byproduct of this reaction?

Signature of the Instructor: ____________________________

Exploration 2: Build the models of amino acids shown below.

Amino acids are named based upon the two key functional groups that they each contain: amine and carboxylic acid.  Each of these functional groups is connected to a carbon known as the alpha carbon.  Using an amide forming condensation reaction, amino acids link together with what are known as peptide bonds.  These linked amino acids are polypeptides.  Proteins are defined as long chains of polypeptides and serve numerous rolls in our bodies. 

To better understand these amino acids, we will build models of a few specific amino acids and explore peptide bond formation.  When modeling, be sure to always build each model individually before forming your product. 

Above: General Amino acid structure

Model:

Step 1:  In each of the following amino acids, the R has been replaced with the appropriate side chain.  Build a model of each of the amino acids below.  Note how they each contain both an amine and a carboxylic acid. 

Step 2: Using your models, perform the condensation reaction necessary to build the serine-alanine dipeptide.  The carboxylic acid on the serine will donate an OH and the amine of alanine will donate an H as seen in the reaction below.  Do not take apart the model until after step 4.

Step 3: Build a model of the amino acid glycine as seen below:

Step 4: Using your models, perform the condensation reaction necessary to add the glycine to the alanine end (C-terminal end) of your dipeptide structure from step 2.  Then draw the extended structural formula of the resulting tripeptide below and circle all the resulting amide groups you formed:

Signature of the Instructor: ____________________________

Questions:

1. What functional groups are responsible for the formation of the peptide bond?
2. When alanine (N-terminal) and glycine (C-terminal) are linked together by the amide forming condensation reaction, which functional group will glycine use for the peptide bond?
3. When serine is combined with alanine in the model you made (serine on the N-terminal end), which functional group will alanine use for peptide bond?
4. When alanine and glycine are linked together by the amide forming condensation reaction in the model you made (alanine on the N-terminal end), which functional group will alanine use for the peptide bond?

Exploration 3: Lipid modeling

Lipids are a class of biological macromolecule that are used primarily for energy storage.  Additionally, lipids are used for insulation, protection, and structure.  Lipids consist of many structurally and functionally diverse molecules. In this lab, we will focus on two major categories of lipids: fatty acids and fats.

Part 1: Fatty acids

Fatty acids are composed of a carboxylic acid group at the head of a long hydrocarbon chain.  Fatty acids can be either saturated or unsaturated.  Saturated fatty acids contain no carbon-carbon double bonds while unsaturated fats contain one or more carbon-carbon double bonds.

Model:

Step 1: Caproic acid (hexanoic acid) is a fatty acid that is a component of the fat in cow milk.  Build a model of this fatty acid based on the structure found below.

Step 2: A monounsaturated fat is a fat that contains only one C-C double bond.  Modify the fatty acid you modeled to make it into a monounsaturated fat and draw the extended structure below.  The site of the C – C double bond does not matter.

Step 3: A polyunsaturated fat is a fat that contains more than one c-c double bond.  Modify the fatty acid you modeled in part 2 to make it into a polyunsaturated fat with two carbon-carbon double bonds and draw the extended structure below.  The site of the C – C double bond does not matter.

Part 2: Fats

Fats are composed of triglycerides and are used for energy storage. In a triglyceride, three fatty acids link to one molecule of glycerol by forming ester bonds.  This occurs via a condensation reaction where the OH from the fatty acid and the H from one of the hydroxyl groups on the OH are removed and form a water byproduct. 

Model:

Step 1: Start by building a model of glycerol and two molecules of the fatty acid below.  Note the functional group at the end of the fatty acid chain.

Step 2: When only one fatty acid links to a glycerol, a monoglyceride is formed.  Model this by combining one of your molecules of butanoic acid with your glycerol in a condensation reaction.

Step 3: Create a diglyceride by adding the second molecule of butanoic acid via a condensation reaction and draw this structure below.

Step 4: Draw a structural formula of a triglyceride in the space given below.

Signature of the Instructor: ____________________________

Questions:

1. What small molecule is the byproduct produced from the ester linkage of a fatty acid to a glycerol?
2. Which functional group from the butyric acid is involved in the ester linkage to the glycerol?
3. Which functional group from the glycerol is involved in the ester linkage to the butyric acid?
4. Explain the structural differences between fatty acids found in fats vs. fatty acids found in oils.
5. Draw a triglyceride containing only unsaturated fatty acids.

Exploration 4: Build models of Carbohydrates.

Carbohydrates are a class of biological macromolecule that are used for quick energy, energy storage, and structure.  We will start our exploration of carbohydrates by looking at glucose, which is a major energy source in biology and is found in organisms ranging from bacteria, to plants, to humans. 

Model:

Step 1: Build the structure of glucose found below.

    Step 2: Two molecules of glucose can link together with what is known a glycosidic bond. Combine the molecule of glucose that you built with the glucose from another group or have each group build a model of the disaccharide maltose.  

Signature of the Instructor: ____________________________

Question:

1. In the formation of the glycosidic bond, what small molecule is released as a byproduct?
2. Complete the table below (Table 1).

Table 1:

Reflection: 

What did you learn from this lab?  Your response should be of sufficient length to answer all questions fully (Typically 10-14 sentences).