Chapter 6 Flashcards
What is conformation?
Every functional 3D structure from the same organism is exactly the same.
Why do proteins assume a certain conformation?
Because it’s thermodynamically favorable (lowest Gibbs free energy).
What are the four levels of protein organization?
A protein’s primary structure is defined as the amino acid sequence of its polypeptide chain; the secondary structure is the local spatial arrangement of a polypeptide’s backbone (main chain) atoms; tertiary structure refers to the three-dimensional structure of an entire polypeptide chain; and quaternary structure is the three-dimensional arrangement of the subunits in a multisubunit protein.
What are the two principles to remember?
1)Hydrophobic residues are buried within a protein’s core.
2)The number of hydrogen bonds and ionic interactions within a protein is maximized.
The stability of a protein’s structure is maintained through what?
Weak interactions (hydrogen bonds, hydrophobic/hydrophilic interactions, ionic interactions, van der Waals interactions, disulfide bonds).
What is the primary structure of proteins?
Amino acids joined together in a linear way by peptide bond; with no folding.
The primary covalent bond in proteins is the peptide bond, which constrains the conformation of the polypeptide.
What configuration do almost all peptide bonds in proteins occur in?
Trans configuration.
What are the three dihedral angles peptide conformations are defined by?
phi, psi, omega
What bonds does phi involve?
C-N-C(alpha)-C bonds, with rotation occurring about the N-C(alpha) bond.
What bonds does psi involve?
The N-C(alpha)-C-N bonds
What bonds does omega involve?
The peptide bond C(alpha)-C-N-C(alpha), where rotation is constrained.
Which dihedral angle is not often considered? Also, think about what happens to it regarding trans and cis configurations.
The omega angle, because peptide bonds are almost always trans, which constrains omega to be + or - 180 degrees. When the peptide bond is cis, omega = 0 degrees.
What degree are phi and psi when the first and fourth atoms are furthest apart and the peptide is fully extended and all the peptide groups are in the same plane?
180 or -180 degrees
When omega is 0 degrees, what configuration is it? What about 180 degrees?
0- cis
180- trans
What is the secondary structure of proteins?
The simplest secondary structure that a peptide can assume is the alpha helix. With the “R” group protruding from the helical structure of the peptide.
How many protein structures are alpha helices?
1/4th of all protein structures.
Why is there a predominance of alpha helices as secondary structures?
Due to their stability from extensive internal hydrogen bonding.
What conformation do alpha helices have in nature?
The right-handed conformation. The left-handed conformation has never been observed in nature.
What types of amino acids can form right-handed alpha helices, and how do they have to do it?
D-amino acids and L-amino acids. In order to do so, the alpha helix must be a homogenous mix of either stereoisomer.
Because of the shape of an alpha helix, the R group of amino acids 3 or 4 residues apart must be what?
Compatible.
What does Proline cause in alpha helices?
A kink
What is flexible, and a major component of alpha helices, though by themselves, don’t form an alpha helices?
Glycine
Every alpha helix has what on the N and C - terminals?
A dipole.
In beta-pleated sheets, what conformation are the peptide bonds in and what amino acid do they involve?
Cis conformation and proline.
