By Robert Hazen, George Mason University
All proteins are polymers, that is, they’re chains of relatively small molecules called amino acids, the building blocks. When it comes to understanding the structure of a protein, every amino acid can be thought of as having a central carbon atom, and then, having four attachments. What are those? Read on to find out.
Biological Molecules
The vast majority of life’s molecular building blocks obey four basic principles, they have four key characteristics. All of these molecules are based on carbon. Carbon wants to get four more electrons, and so it typically bonds to up to four additional elements.
The second principle of biological molecules is that they’re relatively simple in terms of their composition. They’re composed of just a few different elements: carbon, oxygen, hydrogen, and sometimes nitrogen. Phosphorus and sulfur may be thrown in, but relatively few elements. The third aspect is that they’re modular in design, that is, relatively small building blocks that link together to form larger structures. Finally, the shape of these molecules determines their function in physical systems, something we’ll certainly see when it comes to proteins.
There are two different kinds of biological molecules. First are the carbohydrates, which are composed of carbon, hydrogen, and oxygen. Carbohydrates are the most abundant biomolecules because they make up so much of the structure of plants. There are also sugar molecules: tiny, energy-rich molecules that play an important part in the metabolism of living things. Then there are lipids, a second class of biomolecules. Lipids have hydrocarbon backbones: they have carbon chains with hydrogens all around. Typical lipid molecules include the fatty acids, which store energy in fat cells.
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Proteins
Proteins follow the exact same trends. They serve numerous structural functions in living things. For example, structural proteins form supporting structures like skin and ligaments. They form cartilage; our hair is protein. Insect wings are made out of protein. We also have muscle protein. Muscles are not only formed from the structural material, but they also have the astonishing ability of being able to contract. These are molecules that actually can become shorter, through a change in shape.
Proteins also have numerous chemical functions in living things. They transport oxygen in the blood, for example, the protein hemoglobin. They regulate all sorts of chemical processes in the cell. Another example is insulin, which is a protein-like molecule that regulates various aspects of the body’s function.
Proteins can help defend against infection. They can store nutrients. They also catalyze many of the basic chemical reactions that go on in the body. Indeed, this is a principal function of proteins: acting as biological catalysts, which are also known as enzymes. Proteins also fulfill all of those four key characteristics of biomolecules.
Interestingly, proteins, more than any other kind of biomolecule, illustrate the astonishing complexity that can arise from the assembly of simple subunits, as is evident at this assembly process, the structure of proteins.
Amino Acids: The Building Blocks
All proteins are chains of somewhat small molecules called amino acids. When it comes to the structure of a protein, if we start going around the amino acid clockwise, the first attachment, at the top, is a hydrogen, a single H. The second attachment is a carboxyl group; that’s COOH [C=O-OH]. It’s a carbon attached to one oxygen with a double bond, and an OH with a single bond. That’s the second attachment. The third attachment is always an amine group; that’s an NH2 group. Every amino acid has those three building blocks, and then the fourth one is up for grabs.
The fourth is called the side group, and the side group can be almost anything. It can be a single hydrogen atom, as in the amino acid called glycine. It can also be a CH3 group, a methyl group, as in the amino acid alanine. One can build larger and larger amino acids, have rings, or have branching chains. One can also have groups that can include sulfur, groups that contain other nitrogen atoms. Almost anything we can imagine attaching to a carbon can be the side group, so there’s a huge variety of amino acids.
Because the central carbon atom has four distinct and different attachments, it turns out that one can have every amino acid in two distinct varieties: a clockwise variety and a counter clockwise variety, if you will. Scientists call these left- and right-handed amino acids.
While there are literally thousands of different possible amino acids, the variety you see is limited only by the nature of that side chain. The remarkable thing, in living systems, is that only 20 different amino acids are found commonly in living things. All amino acids in living things, it turns out, have the same handedness. In biological systems, we have virtually 100 percent of the left-handed type. How, in the history of life and in the origin of life, left-handed was selected over right-handed remains one of the great mysteries, one of the great puzzles that is still yet to be worked out.
Common Questions about Amino Acid and the Structure of Proteins
Carbohydrates are the most abundant biomolecules, because they make up so much of the structure of plants. There are also sugar molecules, tiny, energy-rich molecules that play an important part in the metabolism of living things.
Because the central carbon atom has four distinct and different attachments, it turns out that one can have every amino acid in two distinct varieties: a clockwise variety and a counter clockwise variety.
All amino acids in living things, it turns out, have the same handedness. In biological systems, we have virtually 100 percent of the left-handed type.
