Intro to Proteins II Flashcards
Why do proteins have a finite number of conformations?
In an aqueous environment, proteins are driven to fold into their native conformation by the hydrophobic effect. Water and polar molecules in the environment want to associate with the polar AAs, whereas the hydrophobic AAs want to associate with each other and not the environment. This higher level of protein organization is energetically driven by the increasing disorder of water that results from proteins folding with polar groups on the outside and hydrophobic groups on the inside. Thus, one reason proteins have a finite number of conformations is that in order for protein folding to be energetically favorable, they must fold in this manner. Another reason is because as soon as one part of the protein starts to fold in this manner, other nearby sections of the protein will start to do the same and so there is a finite number of conformations that could result due to the interactions that occur between different segments of the protein.
What is a random coil?
Irregular arrangement of the polypeptide chain is called the random coil
Where do side chains point in alpha helix?
Outwards
Where do carbonyls point in alpha helix? What effect does this have on polarity of overall helix?
Down (or up) –> results in one end of helix being net negative and the other being net positive
In beta sheets, what features of peptide contribute to formation of pleated like structure?
Planarity of peptide bond and tetrahedral geometry of alpha carbon
What forces hold a beta pleated sheet together?
Hydrogen bonds between adjacent sheets
Which type of beta sheet, parallel or antiparallel, is stronger from an electrostatics perspective?
antiparallel - more h-bonds that are more regular in pattern and have shorter bond length
What are Beta turns? What two types are possible?
Beta turns are kinks in the backbone of the peptide that allow the peptide to turn to form a new sheet. Only two molecules can accomplish this turning effect:
Type 1 = proline
Type 2 = glycine
What is a fibrous protein?
Insoluble, typically consists of only a single secondary structure (i.e. all alpha helix or all beta pleated sheet)
What is a globular protein?
Water soluble or lipid soluble
What is a coiled-coil?
Coiled coils are built by two or more alpha-helices that wind around each other to form a supercoil. There can be two, three or four helices in the bundle and they might either run in the same (parallel) or in the opposite (antiparallel) directions. In essence coiled coils are built of sequence elements of three and four residues whose hydrophobicity pattern and residue composition is compatible with the structure of amphipathic alpha-helices
What role do coiled-coils have in producing protein fibrils?
What is an example of a protein that exhibits this structure?
2+ alpha helices –> coiled-coils –> protofilaments –> protofibrils –> fibrils
Example: Keratin
What is a peripheral membrane protein?
A protein that is on the interior or exterior of the cell and that is associated with components of the membrane
What is an integral membrane protein?
A protein that is imbedded in the lipid bilayer of the membrane
What is the function of membrane spanning alpha helices?
The alpha helix secondary structure is hydrophobic so proteins that are imbedded in the lipid bilayer often have one or multiple of these alpha helical structures that are approximately as long as the thickness of the lipid bilayer.
