Biology 12

Appendix 5 • MHR 559

Part A: Protein Shape

The function of a protein is directly related to
the specific shape of the protein. Ultimately, the
shape of a protein depends on the sequence of
amino acids that make up the protein.
Amino acids are biologically significant
molecules, essential to life. As shown in Figure
A5.1, an amino acid contains two reactive
groups of atoms: an amine group, and a
carboxyl group, joined by a central carbon
atom. The central carbon atom is also bonded
to a side chain, usually represented by the
letter R. There are twenty common amino acids,
each with a different side chain, or R-group.

Primary Structure

The amine group on one amino acid can react
with the carboxyl group on another amino acid
to form a peptide bond. In this way, many amino
acids can be joined by peptide bonds to form
a long, linear chain of amino acids called a
polypeptide, as shown in Figure A5.2. A
proteinis made of one or more polypeptides.
The specific sequence of amino acids in a
polypeptide is known as the primary structure.
Part A of Figure A5.3, on the next page,
illustrates the primary structure of a polypeptide.

Figure A5.2 A short polypeptide chain with three amino
acids, each with a different R-group

Secondary Structure

As you can see in Figure A5.2, the backbone of
a polypeptide chain contains both N–H groups
and C=O groups. These two groups can form
hydrogen bonds with each other. This interaction
causes polypeptide chains to fold into specific

shapes, with hydrogen bonds holding the shape

in place. These shapes are known as the

secondary structure. Part B of Figure A5.3,

on the next page, illustrates the secondary

structure of a polypeptide.

Linear polypeptides spontaneously form

one of two structures: the alpha-helix, and the

beta-sheet, or pleated sheet. The alpha-helix is

a right-handed spiral structure. In an alpha-

helix, the hydrogen bonds are between the

hydrogen and oxygen atoms of amino acids

within the same polypeptide. The beta-sheet

is formed by hydrogen bonding of amino acids

between different polypeptides. These two

structures are shown in Figure A5.4 on page 561.

When a beta-sheet is formed from polypeptides

that run in the same direction, the resultant

shape is called a parallel beta-sheet. If the

polypeptides run in opposite directions, the

beta-sheet is antiparallel. This antiparallel

structure is often the result of a chain that loops

back on itself.

Tertiary Structure

When amino acids are joined together in a

polypeptide, the R-group of each amino acid

sticks out from the chain. These R-groups

interact with each other and with the

surroundings. Each R-group can be categorized

as either hydrophilic (“water-loving”) or

hydrophobic (“water-hating”). The hydrophobic

R-groups are non-polar, so they orient inward,

away from water. The hydrophilic R-groups are

attracted and oriented to water. As a result,

when a protein is placed in water, it arranges

itself so that the hydrophobic R-groups are

protected within the protein, while the

hydrophilic R-groups are on the outside of the

structure. This organization makes proteins

soluble in water.

As mentioned earlier, R-groups can interact

with each other, as shown in Figure A5.4 on

page 561. Some R-groups containing nitrogen

and oxygen atoms can form hydrogen bonds.

Other R-groups containing sulfur atoms can

form disulphide bonds between different areas

of a protein. As shown in Figure A5.4, these

R OH

O

C

H H O H

H

N C C N

H

C

R

O

CN

H H

C

R

Figure A5.1Amino acids have a

standard form. An R-group is

bonded to a carbon atom that is

connected to a reactive amine

group on one side and a reactive

carboxyl group on the other side.

H H

H OH

O

C

R

N C

5

APPENDIX

Shapes of Selected Macromolecules