REVIEW Biochemistry Protein structure

3D structures

chemical or structural functions relate to unique ___

conformations

thermodynamically the most stable, lowest Gibbs free energy 3D structures

native

protein in any functional, folded conformations

stability

tendency of a protein to maintain a native conformation

• unfolded proteins have low ___ and high entropy

• __ provided by multiple weak, noncovalent interactions

hydrophobic effect

predominating weak interaction stabilizing protein by forming solvation layer

solvation layer

highly structured shell of H2O around a hydrophobic molecule

• decreases nonpolar groups cluster

hydrogen bonding

repeating secondary structures (beta sheets and alpha helices) optimize ___

salt bridges

polar groups interacting with others of opposite charges form ion pairs and thus ___

van der Waals

___ interactions apply only on short distance and only contribute to protein stability in high numbers

dipole

peptide bond is rigid and planar and has a small ___

• 3 covalent bonds separate alpha carbons of adjacent amino acids

• resonance between carbonyl oxygen and amide nitrogen create partial + and - charges thus creating a small electric ___

peptide bond

___ links the C-terminal of one amino acid to the N-terminal of another, thus linking 6 atoms in a single plane, meaning that the ___ CANNOT ROTATE FREELY.

dihedral angles

angles defining peptide conformation

• phi (usually between -180 and +180 degrees)

• psi (usually between -180 and +180 degrees)

• omega

many phi and psi conformations cannot happen due to steric interferences (cannot both be 0 degrees for example)

secondary structure

describes the spatial arrangement of the main-chain atoms in a segment of polypeptide chain

• alpha helix

• beta sheets

• beta turn

• coils

alpha helix

simplest arrangement with the maximum number of hydrogen bonds

• each helical turn is ~3.6 residues

• R groups protrude from imaginary longitudinal backbone

• most of them are right-handed

• H bond between nitrogen atom of residue n and carbonyl oxygen atom of residue n+4 (both atoms end up stacked on top of each other)

3 to 4

interactions between R chains spaced ___ residues apart significantly affect helix stability

• ion pair and hydrophobic effect stabilize

• charge, size, and shape can destabilize

proline, glycine

__ & __ occur infrequently in alpha helices

• ___ causes destabilizing kinks due to rigid ring

• __ causes high conformational flexibility and creates coiled structure

positively, negatively

in alpha helices, ___ charged amino acid found near COO- terminus & ___ charged amino acids found near NH3+ terminus

• balance everything out

Beta strand

single protein segment whose backbone extends into zigzogs

beta sheets

several strands in beta conformation side by side forming zigzag pattern