Biomolecules and the Chemistry of Life
Topics in Depth
The Theme of Proteins in Biomolecules and the Chemistry of Life
Now that we have left Lipid Town, we move on to the big city, Proteinopolis. Proteins do all sorts of nifty things. For instance, they may provide structure, increase the speed of chemical reactions, or allow movement of molecules. They may also transport other substances from place to place, facilitate cellular communication (probably better than your local cell phone company), or help to defend against harmful invaders. You’ll learn about all of these kinds of proteins eventually, but for now, you must be wondering, "If proteins are incredibly diverse in function, what makes them all proteins?" Glad you asked.
Proteins are all made of monomers—we knew that word would come in handy—called amino acids. There are 22 different kinds of naturally occurring amino acids, and each one is made of four components:
- A central carbon with one hydrogen
- One carboxyl group (–COOH)
- One amino group (–NH2)
- One R group (–R; Mr. Anonymous is back!)
Carbon needs four bonds, which means that our central carbon needs an R group. Up until now, the R group has been rather anonymous, but it can be numerous things. In fact, the identity of the enigmatic R group is what gives each amino acid its identity. In the simplest case, the R group is a hydrogen, H, but sometimes, the R group can be a chain of hydrocarbons, or a complex ringed structure. The R group can be polar, nonpolar, or even charged, and knowing what you know about polarity and charged particles, you can imagine how much these differences affect the properties of amino acids. R, you crazy wild card, you.
Amino acids bind to each other by dehydration synthesis: the OH group on one amino acid’s carboxyl group (–COOH) combines with one of the hydrogen groups from another amino acid’s amino group (–NH2). We call the resulting covalent bond a peptide bond. When many amino acids bind together, it’s called a polypeptide.
Watch as we demonstrate the magic of how a peptide bond forms between two amino acids:
To understand how proteins function, we need to understand how they’re put together and what gives them their shape. Proteins actually have four levels of structure with each more complex than the last. As you will soon learn, proteins can either be simple as pie or so high maintenance that you are ready to pull your hair out, which, by the way, is also made of protein.
- Primary structure
- Secondary structure
- Tertiary structure
- Quaternary structure
The first level, the primary structure, is a long string, or sequence, of amino acids linked together (aka, a polypeptide chain). If we think of each amino acid as a letter in the alphabet, polypeptides would then be the words. The word "star" has four letters, and when we see this word, we think of a shiny speck in the night sky. Rearrange those letters and you can get "rats." Rats and stars are not at all the same thing even though the letters are in fact exactly the same. Now, we can modify that word further, and replace the letter "r" in rat with a "b". Bats and rats are also not the same even if both are undesirable to have in your attic. The bottom line is that primary structures of proteins vary because the kinds of amino acids, and/or the sequence of those amino acids, vary.
Secondary structure in proteins results from hydrogen bonds that form between parts of the polypeptide chain that are not variable. By variable, we mean the parts that are not part of the infamous R group. These repeating, nonvariable parts include nitrogens that were originally part of amino groups, now called amides, and the remaining oxygens that are part of carboxyl groups. Both nitrogen and oxygen are somewhat bad at sharing electrons, so they create polar regions. The end result is that the polypeptide has several possible structures: the helix, the sheet, the coil, the loop, and the turn.
While all of this bonding is going on, those R groups aren’t just sitting there twiddling their imaginary thumbs and waiting for something to happen like they were a Redshirt in Star Trek. They are interacting with other R groups, and these interactions give polypeptides their tertiary structure. See what we did there? In reality, secondary and tertiary structure together give a protein it’s three-dimensional (3D) shape. To use a food analogy (since we know how much you love those), a straight line of peas is a good way to think of a polypeptide chain with only primary structure, and a rotini noodle is a good way to think about a polypeptide once it has secondary and tertiary structure. Never mind the fact that both of those foods actually contain mostly carbohydrates.
Some proteins join together in order to carry out their function. The quaternary structure is the overall shape that results once all the interacting subunits of the protein have clumped together. Collagen and hemoglobin are two good examples of proteins with quaternary structure. Read more about their function in our theme on structure and function.
You eat lots of proteins in your diet. Do you ever wonder how they get digested? Special enzymes (read more here) in your gut, called proteases, are able to break down those bonds we just discussed.
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