Lecture 13 Flashcards
What is the Secondary Structures of Proteins?
The local folding of the polypeptide backbone
What does the Secondary Structure of polypeptides allow for?
Hydrogen bonding of the group in the polypeptide backbone (N-H and C=O)
When do Regular Secondary structures occur?
When every amino acid in a segment of the polypeptide adopts the same geometry
What are the two regular patterns of secondary structure?
Alpha-helix
Beta-sheets
What are the two important consideration when looking at the structures that polypeptide chains might adopt?
- Minimize steric conflicts
* Maximize hydrogen bonds
Does secondary structure break bonds or form bonds?
No, it is just rotating bonds
What do both the alpha-helix and the beta-sheets satisfy?
The hydrogen bonding potential and the steric restraints
What are the H-bonds like in Alpha-helices?
The carbonyl oxygen of each residue forms an H-bond with the backbone - NH group four residues downstream
What is an Alpha helix?
A portion of a polypeptide that forms a right handed helical structure
Which amino acid residues do not form hydrogen bonds in the alpha helix structure?
Those at the ends of the backbone
What is the helix axis?
The axis that all the hydrogen bonds in a alpha helix is parallel to
What is the proximity of side chains to each other in the alpha helix?
The side chains are close to each other in alpha helices
What is the core of an alpha helix entirely made up of?
The backbone
What is the arrangement of the amino acid side chains in the alpha helix?
They are projecting away from the helix core
How does the orientation of the side chains of amino acids change when going from the primary structure to the alpha helix secondary structure?
The amino acid side chains that are 3-4 chains apart from each other in the primary structure become a lot closer in the secondary structure
What are the different ways the projecting side chains in alpha helices can interact favorably?
- Positive and negative charges
- H bond donors and acceptors
- Hydrophobic groups near each other
What are the different ways the projecting side chains in alpha helices can interact unfavorably?
- Multiple negative or positive charges as part of their amino acid side chains
- Too many bulky side chains
What can unfavorable interactions between projecting side chains in alpha helices do?
They destabilize the structure
What is the function of the major groove in B-form DNA?
It is the appropriate size to interact and bind to proteins (specifically an alpha helices)
What is the similarity between the alpha helix and the major groove of B-form DNA?
They are the same diameter
What is proline not common in the middle of a double helix?
Because the nitrogen is bonded to three carbons and is missing an H to form hydrogen bond interactions and proline is big
What is the consequence of a proline being in the middle of an alpha helix?
It will cause a kink in the bonds
Where is Prolin usually found in an alpha helix?
At the end terminal of an alpha helix so it doesn’t have to participate in H-bonds
What are Beta-Sheets
Multiple beta strands arranged side by side and strands are joined by loops or other structures
