Info

FIGURE 7.04 The L- and D-Forms of an Amino Acid

The four groups are arranged around the alpha carbon differently in the L-form and the D-form of an amino acid. Although they share the same molecular formula, one is the mirror image of the other.

FIGURE 7.04 The L- and D-Forms of an Amino Acid

The four groups are arranged around the alpha carbon differently in the L-form and the D-form of an amino acid. Although they share the same molecular formula, one is the mirror image of the other.

Linear polypeptide chains are folded up to give the final 3D structures.

D-amino acids and several peptide antibiotics, also made by prokaryotes (e.g., bacitracin, polymixin B, actinomycin D), contain D- amino acids.

The Structure of Proteins Reflects Four Levels of Organization

The linear polypeptide chains must be folded into the correct 3-D structure to function properly. Furthermore, many proteins are assembled from more than one polypeptide chain and many also have cofactors or prosthetic groups—associated molecules that are not made of amino acids. The final shape of a protein is determined by its amino acid sequence, so proteins with similar sequences have similar 3-D conformations.

Typical polypeptides are 300-400 amino acids long. Polypeptides much smaller or much larger are less common. However, many hormones and growth factors, such as insulin, do consist of relatively short polypeptide chains. Individual polypeptides with more than a thousand amino acids are very rare and very large proteins tend to consist of several separate polypeptide chains rather than a single long chain.

The structures of biological polymers, both proteins and nucleic acids, are often divided into four levels of organization:

1. Primary structure is the 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.

2. Secondary structure is the folding or coiling of the original polymer chains by means of hydrogen bonding. In the case of proteins, the hydrogen bonds are between the atoms of the polypeptide backbone.

3. Tertiary structure is the further folding that gives the final 3-D structure of a single polymer chain. In the case of proteins, this involves interactions between the R groups of the amino acids.

4. Quaternary structure is the assembly of several separate polymer chains.

The Secondary Structure of Proteins Relies on Hydrogen Bonds

By definition, the secondary structure is folding that depends solely on hydrogen bonding. In DNA, hydrogen bonding occurs between base pairs and is the basis of the double helix. In proteins, hydrogen bonding occurs between the peptide groups that form the backbone of the polypeptide (Fig. 7.05). The polypeptide chain must be folded around to bring two peptide groups alongside each other. The hydrogen on the nitrogen of one peptide group is then bound to the oxygen of the other. [Note that hydrogen bonds also contribute to tertiary structure, but here they are not the only or even the major forces involved.]

Most of the secondary structure found in proteins is due to one of two common secondary structures, known as the a- (alpha) helix and the b- (beta) sheet. Both structures allow formation of the maximum possible number of hydrogen bonds and are therefore highly stable.

alpha- (a-) helix A helical secondary structure found in proteins b- (beta-) sheet A flat sheet-like secondary structure found in proteins cofactor Extra chemical group bound (often temporarily) to a protein but which 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 bound (often covalently) to a protein but which is not part of the polypeptide chain quaternary structure Aggregation of more than one polymer chain to form a final structure secondary structure Initial folding up of a polymer into a regular, repeating structure, due to hydrogen bonding tertiary structure Final 3-D folding of a polymer chain

The Secondary Structure of Proteins Relies on Hydrogen Bonds 161

Folded protein

FIGURE 7.05 Hydrogen Bonding between Peptide Groups

Two peptide bonds of a polypeptide chain may be aligned to form a hydrogen bond by looping the polypeptide chain around.

Folded protein

C = OIIIIIIIIIIIH—N

Was this article helpful?

0 0

Post a comment