Our focus this week is to understand the variety of biological molecules: lipids, carbohydrates, and proteins. You should strive to develop a good working familiarity with each of these. What are their uses? What do they look like? How are they named? What are some common examples? What are the monomers, and how do they differ from their corresponding polymers? NOTE: we will postpone details of nucleic acid structure for a few weeks, until we study the functions of DNA and RNA.

See links at bottom of lecture note web pages.

Ch. 4:

Activity 4A: Diversity of Carbon-based molecules. (Note that there are 2 pages to this activity – use the “next” button above the text to advance)

Activity 4B: Isomers. (4 pages)

Activity 4C: Functional Groups. (2 pages)

Ch. 5

Activity 5A: Making and breaking polymers (1 page)

Activity 5C: Carbohydrates (5 pages)

Activity 5D: Lipids (6 pages). Be sure to build a tryglyceride (page 6)

Activity 5E: Protein functions (1 page). Click different proteins to see what they do.

Activity 5F: Protein structure (5 pages). Be sure to explore the magnifying glasses.

CHIME activity: If you are using your own computer and have installed the CHIME plug-in, or are using another computer with this plug-in installed, it is strongly recommended that you explore the interactive “Explore Insulin” Tutorial at this URL:

You should see an instruction box on the left, and a display of the insulin protein on the right. If you put your mouse over the right image and drag, you can move the molecule and experience its 3-dimensional structure.

There are 3 panels on the left that you should explore: Introduction, Disulfide Bonds, and Alpha Helices. Read the text and be sure to click each box labeled with an “x” – this will change the representation of the image to illustrate the point. Once you have worked through and played with this image, you should have a much better appreciation of protein structure!

Chapter 4. This short chapter introduces properties of Carbon and the basic "rules" for building organic molecules. It also describes the handful of important functional groups found in biological molecules. These groups are like molecular "signatures" -- once you know them, you can look at a molecular structure and actually guess some of its properties and where it might be found in a cell. Learn them!

Chapter 5. There's a lot of information in Chapter 5, and it will take us at least two lectures to cover this material.

Polypeptides consist of amino acids linked together by peptide bonds, as indicated in the following diagram:

The sequence of amino acids is indicated by either a 3-letter code or a 1-letter code. For example:

3-letter code: Met-ser-leu-val-...

1-letter code: MSLV

The table at the end of this guide indicates the names and code symbols for the 20 amino acids found in proteins.

Exercise 1: Refer to the diagram on page 72-73 of your text (Figure 5.15), which shows the chemical structure of all 20 amino acids. Compare the two peptides shown below. Which one has significantly more non-polar amino acids? (Hint: in Fig. 5.15, notice how the amino acids are grouped in 3 different groups).

Peptide A: MLVICAAVRGGP

Peptide B: MDVSEGHGSSGP

Exercise 2: Here is a diagram of a peptide:

Identify the amino acids present, using Figure 5.15. Write the 3-letter and 1-letter sequence of this peptide. Note: by convention, the Amino-terminus (NH₂-) end of the peptide is always written on the left, and the Carboxy-terminus (-COOH) is always written on the right. Your answer should take the form:

N-asp-ser-glu-gly-C (these are not the correct amino acids)

Exercise 3: Here is the beginning of the actual amino acid sequence for a polypeptide:

LNEHSLIEIEGLNKT.................

Using the amino acid representations in Figure 5.15 of your text, draw the first five amino acids, illustrating the peptide bonds that join them. Use the diagram in Exercise 2 as a guide to what your drawing should look like.