We Underappreciate the Role of Proteins in Our Bodies
The word “protein” is quite familiar to all of us, and yet most of us have a very limited understanding of the role of proteins in our bodies. If you assume, as many people do, that the main role of proteins in your diet is to build and maintain strong muscles, then the following discussion will be full of surprises. You will find that there are thousands of different proteins in your body, located in every cell in your body, and that they greatly influence nearly everything that happens in your body.
The Essential Roles of Proteins in Your Body
Most of us think of protein as the material that muscles are made of. It is indeed true that your muscles are composed primarily of protein — not just the skeletal muscles that allow you to move around, but also the muscles associated with internal organs, such as the heart. However, there are actually many different kinds of proteins in the human body, which perform many different roles. To clarify this situation, let’s group these roles into six large buckets:
1. Contractile proteins
Contractile proteins allow living cells to change shape quickly, which enables motion. In particular, the contractile proteins in your muscle cells — primarily myosin and actin — give your muscles the ability to contract. Your skeletal muscles, most of which are anchored to the bones in your body, use this contracting action to move your body around — allowing you to walk, run, throw a ball, and so on. Additional proteins also play a role in muscle action. For example, the proteins troponin and tropomyosin hide and expose the binding sites where myosin molecules attach to actin molecules, thereby controlling when the muscle fibers contract.
2. Structural proteins
Although this second category of proteins is less familiar to most of us, it is present in large quantities throughout your body. Structural proteins comprise the matrix of the connective tissue that provides structure and support to cells and tissue throughout your body. These proteins — which include collagen and elastin — give shape to your bones, tendons, skin, cartilage, and other tissues, and quite literally hold your body together. Collagen alone constitutes about a quarter of the protein in your body. Another structural protein called keratin is the principal component of hair and fingernails.
3. Enzymes
An enzyme is any protein molecule that catalyzes a chemical reaction. In other words, an enzyme facilitates a chemical change without getting used up in the reaction. The enzymes in your body are incredibly important and amazingly diverse. Enzymes catalyze thousands of different processes in your body, producing many of the chemical compounds needed by your body. Enzymes mediate the cellular metabolism that keeps you alive, and they play a huge role in the development of a human body from a single-celled zygote to a fully formed adult.
Enzymes are essential for digesting your food — breaking down proteins into amino acids, starches into simple sugars, and fats into fatty acids. For example, pepsin is one of the enzymes that breaks down proteins in your food. Enzymes also break down spent molecules in your bloodstream and in your cells. However, only a small proportion of the enzymes in your body are dedicated to disassembling large molecules. Many of the enzymatic processes in your body involve the modification of existing molecules, with little impact on their size. These small changes are central to many of the metabolic processes that occur in your body, often involving a long chain of sequential steps, each mediated by a specific enzyme. Enzymes are also involved in the assembly of individual molecules into large complex structures — such as the construction of the plasma membrane that surrounds each of the trillions of cells in your body.
Most enzymes are named after the reactions they catalyze, with the suffix “-ase” at the end of the name. This is especially true of the enzymes that have long names — as in phenylalanine hydroxylase, an enzyme that changes phenylalanine (an amino acid) into tyrosine (another amino acid) via the process of hydroxylation. Because enzymes are not used up in the reactions they catalyze, small quantities can have a huge impact.
4. Signaling and sensory proteins
These two categories of proteins have related roles, so I’ve put them into a single bucket.
Signaling proteins carry signals between distant parts of the body, coordinating biological processes that involve multiple cells. Most of these proteins are classified as hormones. For example, the hormone insulin is a protein that tells the cells in your body when to absorb glucose from the blood, thereby regulating your blood sugar level. Hormones are produced by endocrine tissue — such as the pituitary gland, adrenal gland, pancreas, and gonads — and are carried by the bloodstream to interact with cells all over the body.
Sensory proteins are embedded in the plasma membrane that surrounds each cell in your body. The role of these proteins is to detect and react to signals and stimuli that arrive from outside the cell, triggering a response within the cell. These sensory proteins respond to specific molecules in the bloodstream — some of which are hormones, but many of which are non-protein molecules. Other proteins play important roles in specialized cells called receptors, which allow you to detect various physical phenomena. For example, the opsins in the cells of your retina respond to distinct wavelengths of light, the first step in the complicated process that results in vision.
5. Transport proteins
Transport proteins move small but vital molecules from one place to another, either within cells, across cell membranes, or between cells. A great example is hemoglobin, found in red blood cells, which carries molecules of oxygen from your lungs to all parts of your body. Transport proteins embedded in the plasma membrane of each cell help to move essential molecules from the bloodstream into the cell. If these proteins were absent, then the plasma membrane would present an impenetrable barrier to many essential nutrients. Other transport molecules help to remove excess molecules from the cell. Still others ferry molecules within the cell, moving them to locations where they are needed.
6. Defense proteins
Defense proteins help you fight infection and heal damaged tissue.
Antibodies, also called immunoglobulins, are proteins that attach to foreign material in your bloodstream — such as viruses and bacteria — a first step in destroying them. Your white blood cells are capable of creating an incredibly wide variety of antibodies, each of which is specialized to bind to a certain molecule or category of molecules. Vaccines train your immune system to recognize dangerous microbes and proteins, so that your body can quickly produce the appropriate antibodies if you should become infected.
Another protein called fibrin responds to wounds by forming blood clots and scabs to seal the wounds. Your body is able to respond quickly to such damage because the precursor protein fibrinogen always circulates in your blood. Physical and chemical changes at the site of a wound cause the enzyme thrombin to act on the soluble fibrinogen molecules, linking them together into an insoluble mesh of fibrin that binds to blood platelets to form a clot.
Where Do Proteins Come From?
People usually assume that the proteins in our bodies come from the proteins we eat. In one sense this is indeed correct, but in another sense it is quite wrong. In reality, all of the proteins in your body were built by your own body. However, most of the ingredients for building these proteins come from the proteins you eat. To make sense of this, we need to discuss the general structure of a protein.
So what exactly is a protein? A protein is a large molecule consisting of a long chain of amino acids, strung together in a linear sequence. Amino acids are rather small molecules, each containing between 10 and 27 atoms. Our bodies use 20 distinct amino acids — with names such as leucine, glutamine, and tryptophan — as the building blocks for assembling proteins. Each protein consists of a specific sequence of these amino acids — typically a chain of 250 to 500 amino acids, although some proteins can be shorter or much longer.
Most proteins fold up into a compact shape as soon as they are created, and the specific role the protein plays is often connected to the shape of the folded molecule, especially in the case of enzymes. So while a protein can be described as a chain of amino acids, the final shape of a protein is more likely to resemble a crumbled ball of paper than a necklace. However, the contractile proteins in your muscle fibers are exceptions, and do not fold up. These proteins maintain their linear shape, while forming temporary linkages with adjacent muscle proteins.
Whenever you eat any kind of protein, your digestive system breaks it into little bits, separating all the amino acids from one another. It is these individual amino acids, rather than entire proteins, that are absorbed into your bloodstream. Therefore your body builds every protein it needs from scratch, using the amino acids circulating in your blood as the raw components. This might make you wonder: How many kinds of proteins does your body actually make? Ten different proteins? A hundred different proteins? A thousand different proteins?
In fact, your body knows how to build tens of thousands of different protein molecules, probably at least 80,000. Some of these are contractile and structural proteins, which are typically needed in large quantities. But most of the proteins made by your body fall into the other categories — enzymes, hormones, antibodies, and so on. Even if these proteins are only manufactured in small quantities, they are essential to the proper functioning of your body. In fact, life would not be possible without them.
Each cell in your body manufactures its own proteins. The tiny factories where the protein molecules are assembled are called ribosomes. There are up to 10 million ribosomes in each of your cells. It has long been thought that nearly all the ribosomes in a cell are functionally identical. In other words, any ribosome is capable of building any protein. Recent studies have suggested that there might be some degree of specialization among ribosomes — but even if this is true, we can still say that any ribosome is capable of building multiple kinds of proteins. This raises two key questions:
1) What mechanism allows ribosomes to be so versatile?
2) After a ribosome has finished building a protein molecule, how does it know what protein to build next?
The short answer to both questions is that a ribosome builds a protein molecule whenever it receives a message from one of your genes. This message contains the entire recipe for building a specific protein, which means that the ribosome simply needs to follow the instructions contained in the message. This allows any ribosome to assemble any protein, simply by stringing together the exact sequence of amino acids specified by the message.
The Relationship Between Proteins and DNA
Your genes are composed of DNA, which contains the recipes for all the proteins that your ribosomes can make. Each recipe is stored as a coded message, which is why you hear references to the genetic code. In each gene, the coded message is stored as a sequence of four small molecules called nucleotides, which we traditionally designate as A, C, G, and T (which are the first letters of the four nucleotides — adenine, cytosine, guanine, and thymine). Because DNA is a linear molecule, we can read off these nucleotides as a sequence of letters, such as “GATCCTCCAT…”. Each set of three consecutive nucleotides is a code for a specific amino acid. For example, CAT represents the amino acid histidine.
Every form of life — plant, animal, fungus, or single-celled organism — uses essentially the same coding system in its DNA. Because each code represents a specific amino acid, this means that all living creatures use the same 20 amino acids to build the proteins they need, with a few rare exceptions. Furthermore, every form of life — even plants and fungi, which have no muscles — must assemble proteins in order to stay alive. At the very least, every living thing requires a diverse set of enzymes for its metabolism and to maintain the integrity of its cells.
In fact, the only information in your genes is a set of around 20,000 recipes for building proteins. Each gene is essentially a recipe for building a single protein — although in many cases several closely related proteins can be built from the same gene (by selectively reading only parts of the gene). When a gene is “expressed”, the coded message is copied onto a strand of messenger RNA (mRNA). This RNA molecule then travels to a ribosome located elsewhere in the same cell, which uses the information in the message to build the specified protein. After the protein has been built, enzymes might make modifications to it, further extending the number of proteins that your body can build.
So now we have reached a counter-intuitive point. On the one hand, your DNA is responsible for most of the details of your body, and for almost everything that happens within each cell of your body. On the other hand, nothing in your DNA directly specifies any of those details — except for what proteins your ribosomes should make. Everything that DNA does, it does indirectly by determining what proteins are built. It is these proteins that mediate all the biochemical processes that occur within your body. These processes not only keep you alive, they also direct your growth and development from a zygote to an adult human being.
The upshot is that proteins are far more than simply the stuff that muscles are made of. And just as all life depends upon DNA, all life also depends upon proteins.
Choose a Protein, Please
These days, when you visit a fast casual restaurant, it is not unusual to be asked to “choose a protein”. Perhaps you have ordered a burrito or a salad bowl, and now you must choose between chicken, beef, pork, fish, or tofu. A decade ago, you would have been asked to choose a meat. Because of the increased popularity and variety of meatless options, the language we use in this context has changed, even if most of options are still meat.
Many of us understand that “Choose a protein” is simply a verbal shortcut for “Choose a source of protein”. None of the available options is actually the name of a protein, and none of the options consist of 100% protein. But for the purpose of ordering a meal at a restaurant, the abbreviated wording simplifies the verbal transaction. This new use of the word “protein” has proven to be quite convenient. For example, the person taking your order might ask “Would you like to add a protein to your salad?” — and the intent of the question is perfectly clear.
I have no problem with the use of verbal shortcuts, and in fact I applaud linguistic changes that make our conversations more efficient. However, our understanding of science is often influenced by the words and phrases we commonly use. Therefore I wonder if this wording might affect how we think about protein in our foods. Do some people now assume that chicken consists of a single type of protein? Do some people now assume that tofu is 100% protein?
It is that latter question that most concerns me. By using the phrase “choose a protein”, we are implicitly dividing all foods into “proteins” and “not proteins”. This is a highly misleading mental model. Each source of protein in your diet includes molecules that aren’t proteins. Especially when it comes to plant products (such as tofu), it is better to think of these foods as consisting of a mix of nutrients, not just protein. Furthermore, there are foods that contain moderate amounts of protein — such as beans, brown rice, quinoa, buckwheat, potatoes, etc. — that we don’t even consider when we say “Choose a protein”.
Even wheat can be an important source of protein. The main protein in wheat is gluten — a word that has become familiar to everyone. It is ironic that we now demonize gluten while extolling the virtues of protein. If you seek out gluten-free baked goods, then in many cases you are choosing a product with a higher concentration of carbohydrates and a lower concentration of protein. But if you do your own baking, you can avoid this pitfall by carefully choosing what types of flour to use.
It’s Not the Proteins, It’s the Amino Acids
As mentioned above, any protein you eat is broken down into its constituent amino acids by your digestive system. These amino acids are absorbed into your bloodstream and transported across the plasma membranes into your cells, where they are available for the construction of new proteins by your ribosomes — based on recipes contained in mRNA that is transcribed from your DNA. But what happens if your diet is lacking in one or more of the 20 amino acids?
The answer to that question depends in part on which amino acids are lacking. Your body is able to synthesize 11 of the 20 amino acids. The other 9 amino acids are often called essential amino acids, due to the importance of including them in your diet. The upshot is that it is possible to eat adequate amounts of protein and still suffer from a nutritional deficiency disease due to a shortfall in one of the essential amino acids. Even some of the “non-essential” amino acids can be essential at times, especially when your body is rapidly growing.
Most sources of protein that originate from animals — such as meat, eggs, and dairy — include a complete mix of amino acids. If you obtain much of your protein from animal sources, then you don’t need to worry about a lack of essential amino acids. In contrast, many proteins that come from plants are lacking in certain essential amino acids. For example, a diet that consists mostly of rice will be lacking in lysine. A diet that consists mostly of beans will be lacking in tryptophan and methionine. But a diet that includes adequate amounts of beans and whole-grain rice will include all of the essential amino acids, eliminating the need for animal proteins. Certain other plant-based foods, such as quinoa, contain all of the essential amino acids, and therefore can be quite helpful in crafting a vegan diet.
Note: To craft a truly balanced diet — whether vegan or not — you should also consider the other critical nutrients, including fats, carbohydrates, vitamins, minerals, and fiber.
Conclusion
Imagine if this essay had begun by asking you to answer the following two questions:
1. Why is it important to include proteins in your diet?
2. Name three proteins.
What would your answers have been? Now that you have reached the end of this essay, would your answers be different? Perhaps you now have a deeper appreciation of the many roles that proteins play in your body — and of the crucial importance of these many roles. Furthermore, you may now better understand that all the consequences of your body’s DNA are realized through the manufacture of proteins in your cells.
Before reading this article, you might have been stumped by the question “Name three proteins”. Answering this question should be a little bit easier now. At the very least, you have now encountered the names of many different proteins — including gluten, insulin, hemoglobin, collagen, keratin, actin, opsin, pepsin, myosin, elastin, fibrin, thrombin, troponin — and when you encounter any of these words in the future, you may remember that it represents a protein. You also know that many important categories of molecules in your body — including enzymes, antibodies, and hormones — consist of proteins.
In the future, whenever you see the name of a biological molecule that ends with “-ase”, you are likely to realize that this is probably an enzyme. Some of these names will short (such as protease, lipase, amylase, and maltase), while other will have longer names (such as RNA polymerase, glycogen phosphorylase, and pyruvate carboxylase). You might not immediately recognize what these enzymes do, but you know that their role is to catalyze important chemical processes in your body (or in some other living thing).
In short, your appreciation for the role of proteins in your body might have significantly increased. If so, then I am delighted to have helped.
For a deeper examination of how DNA works, see the chapter “The Blueprint of Life” in my book The Stickler’s Guide to Science in the Age of Misinformation.
