The Structure of Proteins Has Four Levels of Organization

For a protein to be functional, the polypeptide chains must be folded into their correct 3-D structures. The structures of biological polymers, both protein and nucleic acid, are often divided into levels of organization (Fig. 3.26). The first level, or primary structure, is the linear order of the monomers—i.e., the sequence of the amino acids for a protein, or of the nucleotides in the case of DNA or RNA. Secondary structure is the folding or coiling of the original polymer chains by means of hydrogen bonding. Although DNA is not a protein, hydrogen bonding between base pairs forms the famous double helix. In proteins, hydrogen bonding between peptide groups results in several possible helical or wrinkled sheet-like structures (see Ch. 7 for details).

The next level is the tertiary structure. The polypeptide chain, with its preformed regions of secondary structure, is then folded to give the final 3-D structure. This level of folding depends on the side chains of the individual amino acids. In certain cases, proteins known as chaperonins help other proteins to fold correctly (see Ch. 7). As there are 20 different amino acids, a great variety of final 3-D conformations is possible. Nonetheless, many proteins are roughly spherical. Lastly, quaternary structure is the assembly of several individual polypeptide chains to give the final structure. Not amino- or N-terminus The end of a polypeptide chain that is made first and that has a free amino group carboxy- or C-terminus The end of a polypeptide chain that is made last and has a free carboxy-group cofactor Extra chemical group non-covalently attached to a protein that is not part of the polypeptide chain primary structure The linear order in which the subunits of a polymer are arranged prosthetic group Extra chemical group covalently attached to a protein that is not part of the polypeptide chain quaternary structure Aggregation of more than one polymer chain in final structure secondary structure Initial folding up of a polymer due to hydrogen bonding tertiary structure Final 3-D folding of a polymer chain

— Ala— Val— Gly— Val — Glu— Tyr-Phe — Leu- His--

(a) Primary structure

a helix b sheet

(b) Secondary structures

(c) Tertiary structure

FIGURE 3.26 Four Levels of Protein Structure

The final protein structure is best understood by following the folding process from simple to complex. The primary structure is the specific order of the amino acids (a). The secondary structure is due to regular folding of the polypeptide chain due to hydrogen bonding (b). The tertiary structure results from further folding of the polypeptide due to interactions between the amino acid side chains (c). Finally, the quaternary structure is the assembly of multiple polypeptide chains (d).

(c) Tertiary structure

(d) Quaternary structure

Proteins Vary in Their Biological Roles 73

Functional active site components

Functional active site components

Polypeptide chain

Polypeptide chain

Folding

FIGURE 3.27 Polypeptide Forms an Active Site after Folding

Folding of the protein brings together several regions of the polypeptide chain that are needed to perform its biological role. The active site forms a pocket for binding the substrate. Some of the amino acid residues at the active site are also involved in chemical reactions with the substrate.

Pocket formed by active site residues

all proteins have more than one polypeptide chain; some just have one, so they have no quaternary structure.

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