4-2 PROTEIN STRUCTURE
Levels of Protein Structure

Primary structure: The linear _______________ of amino acids from the ___-terminus to
the ___-terminus.

Secondary structure: Regulated by local conformations maintained by _______________
bonds across the backbone.

Tertiary structure: Describes the completely _______________ and _______________
polypeptide chain.

Quaternary structure: Involves the association of two or more polypeptide chains into a
multisubunit, or _______________, protein.
Methods for Determining Protein Structure

Amino acid sequence can be determined directly by _______________ degradation or
indirectly from the sequence of the _______________.

The usual technique for determining the 3D conformation of a protein is ___-_____
_______________.
o Figure A:

A beam of collimated (_______________) X-rays is aimed at a crystal of
protein molecules.

Electrons in the crystal _______________ the X-rays, which are then
recorded on film or by an electronic detector.
o Figure B:

_______________ analysis of the diffraction pattern produces an image of
the electron clouds of the atoms in the crystal.

This electron density map reveals the overall _______________ of the
molecule and the _______________ of each of the atoms in 3D space.

Combining the X-ray data and chemical bonding principles reveals the
location of all the _______________ in a molecule, hence its overall
structure.
Figure A
Figure B
History of Protein Structure Determination
o Read page 88 to learn about the development of using X-ray crystallography to
determine protein structure.
Methods of Showing 3D Protein Structure

Space–filling models
-
Depicts each atom as a __________
-
Reveals __________, closely packed
nature

-
Illustrates the overall __________
-
Emphasizes the _______________
-
Clarifies __-__ structure
-
Can see _______________
-
Can recognize common __________ and
Cartoon models
__________

Space Filling-Cartoon hybrid models
-
Most detailed, showing structures of
amino acid __________ __________
-
Emphasizes the site being __________
(active site, for example)

Backbone models
-
Shows _______________ only
-
Reveals _______________ bonds