By Robert Hazen, George Mason University
The most common chemical reaction involving amino acids is called the formation of a peptide bond. A peptide bond occurs when two amino acids come close together. But, how does the reaction work? Read on to find out.
A Peptide Bond
A peptide bond occurs when the carboxyl group on one amino acid—that’s the COOH group—approaches and gets closer to the amine group on another amino acid—that’s the NH2 group. The amine group gives up a hydrogen; the carboxyl group gives up an OH, so you form an H2O molecule. That goes off into the solution, and what replaces it is a C-N bond, linking those two amino acids together. This is an example of a condensation polymerization reaction. In fact, a condensation polymerization reaction can result in a polymer that can be of any length. We can have two amino acids or even thousands. Indeed, the current record holder is a springy, fibrous muscle protein called titan, which is up to 27,000 amino acids long.
It is, however, its nomenclature that can get a bit confusing. In biological systems, a peptide, sometimes called a polypeptide, is a small group of amino acids that are bound together end to end, in a long chain. There are perhaps a few dozen; two to a few dozen would make a peptide or a polypeptide, and all of these amino acids are linked by peptide bonds.
For example, insulin is an important hormone that incorporates two peptide chains, one that’s 30 amino acids long, another that’s 21 amino acids long. Other hormones have fewer than 10 amino acids, so they’re quite short chains. Proteins are generally larger chains of amino acids, conceptually exactly the same, just longer—perhaps from 100 to several thousand of these units long. Still, this distinction is rather arbitrary. It only has to do with the relative length.
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Protein and Enzyme
Many proteins are also enzymes, and that’s a term that refers to the molecule’s role in chemical synthesis, in chemical processes. An enzyme is a catalyst; it’s a molecule that causes a chemical reaction to happen, but the molecule itself doesn’t change. Sometimes these words are used interchangeably; people use protein and enzyme in basically the same sense. That’s not quite true, as sometimes proteins are not enzymes, and sometimes enzymes are not proteins. But most enzymes are proteins, and most proteins are enzymes.
As with other biological molecules, in order to understand the role of proteins in living systems, one has to first understand their structure. In these complex molecules, function always follows form, so we need to understand structure.
Discovering a protein’s 3D structure is fiendishly difficult. It can take decades of work to discover just one protein structure. The first ‘simple’ step is to define the unique structure of the sequence of amino acids, because every protein is just a sequence: 1, 2, 3, 4, 5, 6, up to thousands of amino acids in a simple chain, like beads on a string. Remember, a protein chain can be anywhere from a dozen or so to tens of thousands of amino acids long. Usually they’re repeating patterns, though, in the larger proteins, which makes the job a little bit easier.
Structure of Amino Acids
But, in any case, all proteins begin with a single strand of amino acids, so this is the primary structure—a list, from one to as many amino acids. Each adjacent pair of amino acids forms a peptide bond. Think about it: there are 20 different amino acids to choose from, and there are a total of 20 plus 19 plus 18 plus 17, and so forth. The total number of possible combinations is 210; 210 different possible peptide bonds between 2 amino acids, if one starts with a group of 20. Each of these different peptide bonds forms a slightly different angle with its neighbor; it forms a slightly different character with its neighbor. One has a bunch of different building blocks to play with when they’re building up a protein.
As a result, the sequences of amino acids tend to adopt different secondary structures. Once we know what the beads on the string are like, sometimes they form spirals; those spirals can be quite open or they can be quite compact. Sometimes they form sheets that fold back on themselves and have very smooth layers; sometimes they form rather irregular, squiggly patterns. It all depends on which amino acids are linked to which ones. That’s the secondary structure. That’s the way the whole thing folds up.
Secondary Amino Acid Bonds
This, however, so far relates only to the adjacent amino acids. What can happen is that when we start folding up a protein, amino acids that are widely separated from each other start coming into contact with each other, and we start forming secondary bonds. We start forming, for example, hydrogen bonds between very diverse and remote parts of that protein, and we get a tertiary structure.
A tertiary structure is how the whole protein chain folds up and actually makes a 3D structure. That’s a third level of structure we have to solve; and as if that weren’t enough, there’s actually a fourth level of structure. That’s because we can take two or more chains of proteins and link them together to form an even larger structure, and it may be that larger structure that acts as the enzyme. So there we are; it’s a fairly complex business!
Common Questions about Amino Acids and the Formation of Peptide Bonds
A condensation polymerization reaction can result in a polymer that can be of any length. We can have two amino acids or even thousands. Indeed, the current record holder is a springy, fibrous muscle protein called titin, which is up to 27,000 amino acids long.
In biological systems, a peptide, sometimes called a polypeptide, is a small group of amino acids that are bound together end to end, in a long chain.
A protein chain can be anywhere from a dozen or so to tens of thousands of amino acids long. Usually they’re repeating patterns, though, in the larger proteins.