Protein Structure and Metabolism

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Proteins are necessary for building the structural components of the human body, such as muscles and organs. You also need proteins to keep your immune system healthy, synthesize neurotransmitters, create and signal hormones, and much more.

Proteins tend to be large molecules made from building blocks called amino acids. The general structure of any amino acid molecule includes a carboxyl group of atoms, an amine group, and a side chain.

The carboxyl group contains one carbon, two oxygen, and one hydrogen atom. The amine group contains one nitrogen atom with two hydrogen atoms attached to it.

All 20 amino acids have different side chains, which vary in shape. There are straight chains of atoms, branched chains of atoms, and rings of atoms, plus the side chains may include carbon, hydrogen, sulfur, ​nitrogen, and oxygen atoms.

The configuration and molecules found in the side chain are what differentiates one amino acid from another. The branched-chain amino acids are isoleucine, leucine, and valine and are necessary for muscle structure. Tyrosine, phenylalanine, and tryptophan are called aromatic amino acids and each one contains a side chain with a ring-shaped formation. These three amino acids are needed for neurotransmitter production.

NonEssential and Essential Amino Acids

The 11 non-essential amino acids are not called "non-essential" because they are not important.

They are important, and your body requires them to perform several functions. These amino acids are called "non-essential" because you don't need to get them from your diet. Your body can build those 11 amino acids from chemicals already present in your body. The non-essential amino acids include:

  • Alanine
  • Arginine
  • Asparagine
  • Aspartic Acid
  • Cysteine
  • Glutamic Acid
  • Glutamine
  • Glycine
  • Proline
  • Serine
  • Tyrosine

The amino acids arginine, cysteine, glycine, and tyrosine are sometimes also considered to be "conditionally essential." That means most people manufacture them on their own, but individuals with certain illnesses or genetic abnormalities can't make them, so they need to get them through their diets.

The nine essential amino acids are called "essential" because you can't manufacture them; you have to eat proteins that contain those amino acids. They include:

  • Histidine
  • Isoleucine
  • Leucine
  • Lysine
  • Methionine
  • Phenylalanine
  • Threonine
  • Tryptophan
  • Valine

Do you need to worry about essential amino acids when you plan your daily meals? Not really. Animal sources of protein such as meat, eggs, and dairy products are "complete proteins." That means that each protein found in an animal product contains each of the nine essential amino acids. Vegetarians and vegans may need to pay a little more attention to the dietary proteins.

Plant proteins are called "incomplete proteins." Each plant protein is missing one or more of the nine essential amino acids. However, every amino acid is found in some plant, so you can combine different plant proteins to get all of the amino acids you need. Learn about vegan and vegetarian protein combinations.

There are many different proteins in your body, and they perform different functions. Proteins functions include:

  • Contributing to enzyme activity that promotes chemical reactions in the body
  • Signaling cells what to do and when to do it
  • Transporting substances around the body
  • Keeping fluids and pH balanced in the body
  • Serving as building blocks for hormone production
  • Helping blood clot
  • Promoting antibody activity that controls immune and allergy functions
  • Serving as structural components that give our body parts their shapes

How Protein Is Digested

The digestion of protein begins in the mouth with chewing, which makes food easier to swallow. It also helps with digestion by chopping food up into smaller bits. Remember that it's important to chew your food thoroughly; don't gulp your food down in huge bites.

Protein digestion continues in the stomach with the release of digestive juices that include hydrochloric acid and pepsinogen. Hydrochloric acid converts pepsinogen to pepsin, which begins to break down the bonds between the amino acids. This process takes place while the muscles surrounding the stomach squeeze and squish the foods and stomach fluids together.

The next step occurs in the small intestine where the hydrochloric acid is neutralized with bicarbonates released from the pancreas. The pancreas also releases an enzyme called trypsin. Trypsin continues to break apart the amino acids, which are then absorbed into the blood stream. Once in the bloodstream, the amino acids are carried to the cells in various parts of your body. Your body uses the individual amino acids to build the proteins needed for the different functions.

Proteins as Energy

You may not think of protein as an energy source, but proteins do contribute calories to your diet. Those calories need to be acknowledged if you are watching your weight. Each gram of protein you eat has four calories. The United States Department of Agriculture suggests that you get about 15 percent to 20 percent of your calories from protein. For someone who needs 2000 calories per day, that would equal 75 to 100 grams of protein.

Meats, fish, seafood, poultry, eggs, and dairy products are significant sources of protein, but you can also get protein from a variety of grains, legumes, nuts, and seeds. It isn't difficult to get enough protein in your diet. One chicken leg alone will provide you with about 30 grams of protein. One salmon fillet has about 40 grams of protein, a cup of oatmeal has six grams of protein, and a cup of asparagus even has two grams of protein. Since most people get enough protein from their diet, protein deficiency is rare in developed countries. 

In underdeveloped countries, malnutrition and protein deficiency is more prevalent. Severe protein deficiency is called kwashiorkor. Children with kwashiorkor tend to have very thin arms and legs and large, distended bellies. Lack of protein can cause growth failure, loss of muscle mass, depressed immune system function, lung problems, heart problems, and death.


Gropper SS, Smith JL, Groff JL. "Advanced Nutrition and Human Metabolism." Sixth Edition. Belmont, CA. Wadsworth Publishing Company, 2013.

Smolin LA, Grosvenor, MB. "Nutrition: Science and Applications." Third Edition. Wiley Publishing Company, 2013.

The National Academies of Sciences, Engineering and Medicine, Health and Medicine Division. "Dietary Reference Intakes Tables and Application."

United States Department of Agriculture United States Department of Agriculture Agricultural Research Service National Nutrient Database for Standard Reference Release 28.

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