Exploring Biomolecules in the PDB
Exploring Atoms, Bonds and Biomolecules
Activity:
Exploring three dimensional structures in atomic detail will require you to recognize atoms and the various types of bonds they make to form molecules and interact with other molecules. In Part I of this lesson, we will explore the atoms and bonds in molecules (including a polymer building block and biopolymer) molecules. In Part II we will explore the types of biomolecules found in the PDB to appreciate the contents of the archive.
Part I: Exploring Atoms and Bonds
Directions: Examine a molecule of Vitamin C also known as Ascorbic acid, (chemical component ID ASC) and answer the following questions.
Questions (4 points each)
1. What type of molecule is it?
2. How many atoms are present in this molecule?
3. What types of atoms are present in this molecule?
4. How many bonds are there in the molecule?
5. Based on your knowledge of bonds and noncovalent interactions seen in biological molecules, list at least two types of bonds it could form when this molecule is interacting with a water molecule?
Directions: Click on the link listing the number of entries that have ASC bound to it – e.g., the link “41 entries” at the time of this writing.
Graphical user interface, text, application Description automatically generated
Once the results are listed, sort them by Oldest to Newest.
Graphical user interface, text, application Description automatically generated
Question (2 points):
6. What are the two oldest PDB entries that have ASC in the structure?
Part II: Exploring Biomolecules in the PDB
Directions: Although the archive is called Protein Data Bank, it also includes structures of nucleic acids, carbohydrates, lipids, inhibitors, drugs, cofactors and much more. This section explores the contents of the archive.
Question (16 points total–4 points per molecule)
Complete the table listing the types of bonds these building blocks make to form their respective polymers. Follow the example completed in the first row.
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