Graphics Gallery

Gale Rhodes
Chemistry Department
University of Southern Maine

Revised 2006/08/02

Learn how to use Swiss-PdbViewer: Work through sections 1-4 of the Swiss-PdbViewer Tutorial.

Topic: Four Classes of Biomolecules

Examples: Four Major Classes of Biomolecules

NOTE: In some of these models, the hydrogens are not present. Assume that unfilled valences of carbon, nitrogen, oxygen, sulfur, and phosphorus are taken by hydrogen. Do you know why hydrogens are sometimes missing from models of macromolecules?

If these models exhibit extra, unrealistic bonds, set Deep View preferences as follows:

Prefs: General
Check "Reconnect atoms with unusual bond lengths" and set the bond threshold to 2.0 angstroms.

As you look at each biomolecular model, carry out the Exercises below.

Carbohydrates

• Trimannoside, a component of complex plant glycans (starches, more or less).

Lipids

• Phosphatidyl choline, a structural component of cell membranes.
• Cholesterol, a substance that modifies the fluidity of membranes.

Nucleic Acids

• A short piece of DNA, a nucleic acid, with five base pairs.

Proteins

• A short polypeptide, or protein segment, from a gene-regulating protein.

Others

Biomolecules include many cofactors and prosthetic groups that overlap or extend beyond these four categories. To obtain PDB files of many of these substances, go to HIC-Up.

Exercises

Carry out the following tasks with each of the models above. At this stage, these are quite challenging exercises. Don't be discouraged -- complex molecules will be revealing their secrets to you before you know it.

1. Predict whether each substance is more soluble in water or in hexane.
2. In the DNA and protein models, display hydrogen bonds (Tools: Compute H Bonds). Identify the atoms involved in each hydrogen bond.
3. Identify the functional groups present in each molecule.
4. Predict the products of acid- or base-catalyzed hydrolysis of each substance.
5. These hydrolysis products are the building blocks of biomolecules; use your organic-chemistry model kit to build models of some of these building blocks, and to link them together as they are linked in these models. Add hydrogens to complete the models.
6. What atoms must you delete in order to link the building blocks of your models (hint: the deleted atoms compose the main component of your favorite beverage).

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