Flashcards in Proteins Deck (45)
What interactions are involved in the protein native fold?
Hydrophic, hydrogen bonds, van der waals, and electrostatic interactions
Amino acid sequence. Structure is partially dictated by the properties of the peptide bond.
Angle around the alpha carbon and amide nitrogen bond.
Angle around the alpha carbon and carbonyl carbon.
What determines the secondary structure of the protein?
The organization around the peptide bond and the identity of the R groups. Refers to spatial arrangement of the polypeptide backbone.
2 arrangements of secondary structure
Alpha helix and beta sheet
Alpha helix is stabilized by...
Hydrogen bonds between near by residues.
Beta sheet is stabilized by...
Hydrogen bonds between adjacent segments that may not be near by.
Irregular arrangement of the polypeptide chain.
What is the helical backbone of a protein held together by?
Hydrogen bonds between the backbone amides of n and n+4 amino acids.
How many residues per turn?
Outside cell environment is...
Oxidizing, disulfide bonds form.
Inside cell environment is...
Protein with the lowest free energy =
Most stable, one with maximum weak interactions.
How are peptide bonds aligned with the helical axis?
Roughly parallel. So are H-bonds.
How are side chains aligned with the helical axis?
Which hydrophobic residues are strong helix formers?
Ones with small hydrophobic residues such as Ala and Leu.
Which amino acids act as helix breakers?
Proline, because rotation around N-C bond is impossible. Glycine because tiny R group supports other conformations.
How is the large dipole moment of the alpha helix enhanced?
By unpaird amides and carbonyls near the ends of the helix.
Where do negatively charged residues occurs in the helix?
Near the positive end of the helix dipole.
How do side chains sit in the beta sheet protein structure?
They stick out from the sheet, alternating up and down direction?
How are beta sheets held together?
By the hydrogen bonding of the amide and carbonyl groups of the peptide bond from opposite strands.
When do beta turns occur?
When beat sheets change direction. The 180 turn is accomplished over 4 amino acids.
How is the beta turn stabilized?
By hydrogen bonds from a carbonyl oxygen to amide proton 3 residues down the sequence.
Type I beta turn
Proline in position 2.
Type II beta turn
Glycine in position 3.
What is the typical connection of beta strands
What stabilizes protein secondary structure?
Numerous weak interactions between amino acid side chains. Mostly hydrophobic and polar interactions, can sometimes be disulfide bonds.
Form of protein teritary structure.