PROTEIN SECONDARY STRUCTURE
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ALPHA HELIX -
    Ball and Stick Model

1. How many Amino Acids are found in this structure?
Can you identify them based on the CPK color code (see "Color Schemes" at the bottom of this frame)?

ALPHA HELIX -
    Side Chains Space Filled

2. Some of the side chains are missing in this display, can you determine where they should be attached to the backbone structure?
Click on the MDL logo to get a menu that includes the heading "color". Use this display to distinguish the individual amino acids within the helix.
Does this sequence agree with the sequence of Amino Acids you determined above?
3. What are the single letter codes for each and to which group do each of these amino acids belong?

ALPHA HELIX -
    Backbone Only
4. Which is the amino end and which is the carboxyl end of this helix?
5. Does this change your answer to question 2?

ALPHA HELIX -
    Ribbon Model

ALPHA HELIX -
    Hydrogen Bonds Indicated

6. Look at the single hydrogen bonds that stabilize this alpha helix, these bonds are between every amino group nitrogen and the _______ atom situated ___ amino acid residues away.

BETA SHEET CONFORMATION -
    Stick Model

BETA SHEET CONFORMATION -
    Ribbon Model

7. The amino acid chains in this beta sheet are in an (parallel / antiparallel ) arrangement.

BETA SHEET CONFORMATION -
    Beta Conformation in Yellow
    Beta Turns in Blue

BETA SHEET CONFORMATION -
    Side Chains Highlighted
8. What are the interactions that stabilize the INTERMOLECULAR associations in these beta sheets?

BETA SHEET CONFORMATION -
    Hydrogen Bonds Indicated

9. What atoms are involved in forming the INTRAMOLECULAR non-covalent interactions that stabilize each beta sheet?  (Hint: you can click on the MDL logo in the bottom right corner and selest "color" to change the way the molecules are displayed)

(Go to Tertiary Structure for more questions)

PROTEIN TERTIARY STRUCTURE