IM13. Drawing biological macromolecules
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- 4077
Line structures will be the most common type of structural drawing you see in these pages. You will also see some others used for specific purposes, and those representations are explained here. Sometimes even drawing a line structure is too much. Proteins often contain thousands of atoms. Presenting all that information about bonding could make the drawing hard to read, especially in a three-dimensional shape.
As we have seen before, a three-dimensional shape can be presented in several ways. A space-filling model gives a good idea of the real shape of the structure. An example of a space-filling drawing of a protein, bovine low molecular weight protein tyrosyl phosphate, binding to inorganic phosphate, is shown below.
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Animation IM13.1. A space-filling drawing of a protein, bovine low molecular weight protein tyrosyl phosphate, binding to inorganic phosphate.
One abbreviation used in biochemistry is sometimes called a wireframe structure. In a wireframe structure, none of the atoms are labeled and all of the hydrogens are omitted. That means it is difficult to tell a carbon from a nitrogen. However, biological macromolecules like DNA and proteins are made of a few simple building blocks. A very experienced reader would remember the structures of these building blocks. She would be able to tell what atoms go in which place based on the shapes of the building blocks.
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Animation IM13.2. A wireframe drawing of bovine low molecular weight protein tyrosyl phosphate with bound inorganic phosphate.
A protein is made of amino acids strung together in a chain. The chain does not hang out in a long, straight line. It folds up into a coil, and the shape of that coil influences its biological activity. Sometimes a biochemist may be interested in how the chain of amino acids coils up. A backbone structure only shows the atoms that are connected directly in a row from one end of the chain to the next. Any atoms that hang out along the sides of the chain are left off.
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Animation IM13.3. A backbone drawing of bovine low molecular weight protein tyrosyl phosphate with bound inorganic phosphate.
The order in which a chain of amino acids is connected together is called the primary structure of a protein. For example, the amino acids glycine, alanine, tyrosone and arginine could be connected in the order gly-ala-tyr-arg, or ala-gly-arg-tyr, or tyr-gly-ala-arg, and so on. These compounds are isomers of each other. Knowing which isomer we have tells us something about the protein.
The way that chain arranges itself is called the secondary structure. Very often, proteins coil up into spirals or helices. This helical structure is similar to that of DNA. Another possible secondary structure is a beta-sheet, which is sort of wavy, a bit like a sheet of corrugated steel. These secondary structures are held in place by hydrogen bonds between different amino acids. (You can see the structure-property relationship chapter to review hydrogen bonding).
Usually, the entire protein does not adopt the same secondary structure. There may be a section that coils into a helix and another section that forms a beta-sheet. The helical domain and the beta-sheet domain then arrange themselves and pack together somehow. The arrangement of domains in the protein is called tertiary structure.
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Animation IM13.4. A cartoon drawing of bovine low molecular weight protein tyrosyl phosphate with bound inorganic phosphate.
Seeing the tertiary structure in a protein can be difficult even with a backbone structure. Instead, ribbon drawings or cartoon structures are used to convey how beta-sheets and helices are arranged in a protein. Sometimes a protein is made of more than one chain of amino acids. The arrangement of different coils of amino acids all stuck together is called quaternary structure.