Biochemistry Lo: Protein Structure--Primary, Secondary, Tertiary, Quaternary

Front 1

Learn the different levels of protein structure

Back 1

1* primary: amino acid sequence of the polypeptide

2* secondary: local folding (helices, sheets, turns)

3* tertiary: arrangement of 2* structure into a globally fold

4* quaternary: complex of several folded polypeptides

Front 2

Relate the properties of the different amino acids to intermolecular forces

Back 2

--Nonpolar, aliphatic R groups: hydrophobic side chains

--Aromatic R groups: hydrophobic

--Positively charged R groups: basic

--Negatively charged R groups: acidic

--Polar, uncharged R groups: Cysteine can form covalent bonds through sulfide bonds; hydrophobic

Front 3

Qualitatively understand the constraints on protein flexibility imposed by peptide bonds

Back 3

Peptide bonds always have the main chains trans to one another because of steric reasons and because it is energetically more favorable.

--Proline is the exception and can be in cis form

Front 4

Describe the interactions required to form the 4 major classes of secondary structure

Back 4

--Hydrogen bonding stabilizes the a-helix within the strand

--B-conformation: anti-parallel B-sheet is stronger because the hydrogen bonds are linearly aligned, and this accumulation of H-bonds creates a strong interaction

--Proline and glycine are found in turns (B-turns) because they disrupt the a-B secondary structure.

Front 5

Describe at least three examples of quaternary structure, and relate quaternary structure to function

Back 5

1. Fibrous: having polypeptide chains arranged in long strands or sheets

2. Globular: having polypeptide chains folded into a spherical or globular shape. [tend to be functional: enzymes and regulatory proteins]. The folding provides the structural diversity necessary for proteins to carry out a wide array of biological functions.

--Symmetrical: protimer interacts with itself

Cyclic symmetry: involves rotation about a single axis. Hemoglobin is an example and the structure allows it to keep the heme groups relatively far apart.

Dihedral symmetry: rotational in which a two fold rotational axis intersects an n-fold axis at right angles. Protein with dihedral symmetry has 2n protomers. Example is hemoglobin.

Icosahedral symmetry: regular 12- cornered polyhedron having 20 equilateral triangular faces. Each face can be brought to coincidence with another by rotation about one of the 3 axis. Common for virus coats and an example is the polio virus; structure helps with fxn by allowing it to use small amount of its genome to cover a large volume.

--Asymmetrical: protimer interacts with others