What are Amino Acid Functional Groups?

What is an amino acid functional group? This article will answer that question with information on amino acid classification and how proteins (and possibly all life on Earth) are formed.

What are Amino Acid Functional Groups?

So you’ve heard of amino acid functional groups and you want to understand them better. This article will help to clarify the structure of amino acids, their functional groups, and what it all has to do with the creation of protein.

Some Basic Reference Definitions

Below are the names of the 20 common amino acids in the body, nine of which are essential amino acids, meaning humans must eat or otherwise consume them to get what we need to function. The essential aminos are designated with an asterisk (*). There are their names, their three-letter codes, their one-letter codes (as used in drawing models of molecular bonds), plus their bond type and properties. Polar vs. nonpolar bond types refers to their covalent bonds. We will start with those definitions for the bond type category—get ready for some high school clique metaphors to help you visualize all this organic chemistry.

Covalent Bonds

Covalent bonds form the base of the chemical reactions between atoms of different elements. The bonds form in only one way: when an electron becomes shared by two elements. That creates the connection that then results in a new substance. Covalent bonds can exist as polar or nonpolar compounds, and all bonds that are polar or nonpolar in nature are by definition covalent.

To visualize: think of these bonds like the bonds of friendship. Two students (atoms) come close to one another and share their lunch (electrons). This sharing means there is a bond of friendship (the covalent bond). Whereas before they had been two separate elements, strangers, now a new substance has formed: a friendship.

Polar Bonds

Polar bonds are bonds where the electrons are not shared equally between two atoms. These types of bonds are what designates polar molecules from nonpolar ones. This occurs when the two atoms bonding are from two different elements; atoms from the same element do not form polar bonds.

Just as bigger planets can hold bigger moons in their orbits, so it is with atoms: they pull electrons to the best of their ability, but when they come into the orbit of a better puller (a bigger planet), that atom will pull more electrons into its orbit (and steal the lesser planet’s moons).

When two atoms of the same element meet, neither is stronger than the other, and thus neither one is more attractive than the other regarding electrons, and so neither side exhibits the polar pull, and the bond is considered nonpolar. The negative charge end of the bond is the more attractive atom, because it can draw more negative (-) electrons.

To put this back into the context of our high school friends, let’s say the two atoms meeting and bonding are a vivacious theater student and a more reserved math student. In sharing lunch, somehow the theater student always gets more to eat because the math student is so transfixed and feels the need to be overly generous. This is true whenever the theater student meets someone with less personal magnetism, which means the theater student gets an overabundance of food (electrons), which is negative because the increased calories may cause the theater student to gain weight, or get a bad complexion from eating too much processed lunch food. Eventually the theater student will fill up to the brim with extra food, and won’t be able to accept any more.

Nonpolar Bonds

A nonpolar bond is formed when two atoms from the same element meet and share electrons equally and evenly with one another. Neither atom is a better electron puller than the other, and so there is no one side more polar than the other.

In our friendship metaphor, this is a bond between two theater students, or two math students, who pool all of their lunch food together in the middle of the table, and pull from the pile equally and in unison.

Hydrophobic vs. Hydrophilic

For the properties category, hydrophobic and hydrophilic refer to molecules and their reactions to water. Molecules that repel water, or are phobic of hydration, are hydrophobic. The molecules that can form an ionic or hydrogen bond with a water molecule are hydrophilic, they have a philia for water, they like the feel of it.

If atoms are students once again, the hydrophilic ones are either on the swim team itself, or part of a group that likes to swim and heads out to the beach or the lake every weekend. The hydrophobic ones either can’t swim or simply do not like it. Hydrophobic students will tell you that their friends and the community pool go together like oil and water: they don’t mix.

Your Amino Acids: Names and Designations

Amino-acid name: Alanine Amino-acid name: Arginine
Three-letter code: Ala

One-letter code: A

Bond type: Nonpolar

Properties: Hydrophobic

Three-letter code: Arg

One-letter code: R

Bond type: Polar, positively charged

Properties: Hydrophilic

Amino-acid name: Asparagine Amino-acid name: Aspartate
Three-letter code: Asn

One-letter code: N

Bond type: Polar, no charge

Properties: Hydrophilic

Three-letter code: Asp

One-letter code: D

Bond type: Polar, negatively charged

Properties: Hydrophilic

Amino-acid name: Cysteine Amino-acid name: Glutamate
Three-letter code: Cys

One-letter code: C

Bond type: Nonpolar, no charge

Properties: Hydrophilic

Three-letter code: Glu

One-letter code: E

Bond type: Polar, negatively charged

Properties: Hydrophilic

Amino-acid name: Glutamine Amino-acid name: Glycine
Three-letter code: Gln

One-letter code: Q

Bond type: Polar, no charge

Properties: Hydrophilic

Three-letter code: Gly

One-letter code: G

Bond type: Nonpolar, no charge

Properties: Hydrophilic

Amino-acid name: Histidine* Amino-acid name: Isoleucine*
Three-letter code: His

One-letter code: H

Bond type: Polar, positively charged

Properties: Hydrophilic

Three-letter code: Ile

One-letter code: I

Bond type: Nonpolar

Properties: Hydrophobic

Amino-acid name: Leucine* Amino-acid name: Lysine*
Three-letter code: Leu

One-letter code: L

Bond type: Nonpolar

Properties: Hydrophobic

Three-letter code: Lys

One-letter code: K

Bond type: Polar, positively charged

Properties: Hydrophilic

Amino-acid name: Methionine* Amino-acid name: Phenylalanine
Three-letter code: Met

One-letter code: M

Bond type: Nonpolar

Properties: Hydrophobic

Three-letter code: Phe

One-letter code: F

Bond type: Nonpolar

Properties: Hydrophobic

Amino-acid name: Proline Amino-acid name: Serine
Three-letter code: Pro

One-letter code: P

Bond type: Nonpolar

Properties: Hydrophobic

Three-letter code: Ser

One-letter code: S

Bond type: Polar, no charge

Properties: Hydrophilic

Amino-acid name: Threonine* Amino-acid name: Tryptophan*
Three-letter code: Thr

One-letter code: T

Bond type: Polar, no charge

Properties: Hydrophilic

Three-letter code: Trp

One-letter code: W

Bond type: Nonpolar, no charge

Properties: Hydrophobic

Amino-acid name: Tyrosine Amino-acid name: Valine*
Three-letter code: Tyr

One-letter code: Y

Bond type: Polar, no charge
Properties: Hydrophilic

Three-letter code: Val

One-letter code: V

Bond type: Nonpolar

Properties: Hydrophobic

It’s a lot of information, to be sure, but it’s provided as a reference point to help facilitate the following explanations.

What Are Amino Acid Functional Groups?

Amino acids are all made up of groups of atoms, and the functional groups are the important ones in each amino, it’s what makes them different and unique, deciding whether the amino overall is polar or nonpolar, acidic or basic.

Each of the above standard 20 aminos have one hydrogen atom, and two groups attached to its alpha carbon atom: an amino or amine group (~NH3+) and a carboxyl group (~COOH). They are each then distinguished from other types of amino acids by their third attached functional group: side chains referred to as R groups. When you ask what are amino acid functional groups, here they are, with the R group being the one with the most diversity. When you think of R groups, think R for radical, as it’s the variable part that makes each amino acid different from the rest.

What is the amino acid functional group?

About R Groups

Of the 20 standard amino acids that make up the building blocks of protein:

  • 6 of them have hydrocarbon R groups
  • 7 of them have neutral R groups
  • 6 of them have acid or base R groups

The simplest of the amino acids is glycine, which has just one hydrogen atom in the position of the side chain group (no R group at all, just an attached loner).

Some Quite Interesting Relevant Facts

  • In chemistry, organic compounds are generally thought of as any chemical compound that contains carbon, which includes amino acids.
  • All amino acids are soluble in an aqueous solution (water), even the hydrophobic ones (counterintuitive but true).
  • All naturally occurring amino acids are in the L-form; L for levorotatory, referring to the way you’d turn the amino acid to read the order of its attached groups (the opposite of is dextrorotatory or D-form).
  • As you can see in the above list, 50% of the amino acids have nonpolar side chains. The other half is designated polar, five of which have side chains that are not only polar, but charged.
  • Because the carboxyl group is an acid, it can form peptide bonds with the base amino groups of other amino acids, causing chemical reactions that create polypeptide chains and amino acid residues.
  • When two amino acids react and form a peptide bond, and that process goes on to be repeated, many amino acids may string together, which forms a protein structure.
  • This protein synthesis (though a little more complicated than just linking acid to base over and over again like links of a chain) is among the most fundamental of biological processes, an invaluable component of every cell. Proteins make our nails and hair, protein builds and repairs our tissues, protein is needed to make our hormones, our enzymes, and many other chemicals in the human body.
  • In 1953, Stanley Miller and Harold Urey conducted a simulation, to test a hypothesis about how life originally formed on Earth. They built a closed system that contained a heated pool of water under a mixture of gases that were thought to be present in the early atmosphere of Earth. They delivered an electric current to simulate lightning, and after a week analyzed the contents of the liquid pool. In there they discovered that several organic amino acids had spontaneously formed from inorganic raw materials. This leant support to the theory that the first life on Earth arose out of the primordial ooze through naturally occurring chemical reactions like a little flash of lightning.

Conclusion

The functional or R groups of amino acids are the groups that define the chemistry of proteins. They are the basis on which amino acids are classified, and according to the Miller-Urey experiment, possibly the start of all organic life on Earth. Not only is “What are amino acid functional groups?” a stimulating question to ask, but the answer to that question comes awfully close to revealing the true answers behind life, the universe, and…well…everything.

What Are Nonpolar Amino Acids?

What are nonpolar amino acids? This article will help explain how these amino acids are designated and what purpose they serve in the body.

Of the 20 common amino acids in the human body that build protein structures, 9 of them are essential (meaning we must eat or otherwise consume them to get them), and half of them are nonpolar. What are nonpolar amino acids? Which are they, and what does “nonpolar” mean? The review of the topic in this article will help explain.

The Definition of a Nonpolar Molecule

The nonpolar molecules we’ll be talking about are hydrophobic amino acids, meaning “water fearing” because they don’t mix with water molecules. You know how oil and water don’t mix? That’s because oil is hydrophobic.

The opposite of a nonpolar molecule is, as you might guess, polar. Polar molecules are hydrophilic, meaning “water loving.” If you’d like to visualize: polar molecules are like puppy dogs who love water so much that they’ll go barreling straight into muddy or smelly water after a tennis ball, with no hesitation at all. That would make nonpolar molecules like cats, better known for avoiding water, no thank you, and cleaning themselves without it.

Molecules are classified this way based on the charges on the atoms bonded together to form the molecule. If you remember your first taste of high school chemistry, you may remember that atoms have a nucleus of neutral neutrons and positive protons in the middle, and negative electrons swirling all around. Protons have a positive charge that draws electrons to it, like how opposites attract.

When two atoms bond together, they share electrons. Two atoms of the same element have equal positivity, so don’t have the power to steal electrons from the other. These molecules are nonpolar because they have no resulting charge. When atoms of two different elements connect together, invariably one of them will have the higher charge and attract the most electrons to its end of the joint molecule. That means the molecule is polar, or charged, and that charge will then be identified as either a positive or negative charge.

Examples of Nonpolar Molecules

Methane gas is an example of a nonpolar molecule that is created during the breakdown of food and released as a gas (or more colloquially, a fart). Methane is made up of one carbon atom that is bound to four hydrogen atoms: this hydrogen bonding allows the atoms to all share electrons equally, so this smelly molecule has no charge and is nonpolar.

Inside our body, we have both polar and nonpolar molecules, which includes those 20 amino acids mentioned above.

Nonpolar Amino Acids

The chemical properties of amino acids are largely determined by one group of molecules, what’s known as the R group: a side chain that differs on each amino acid. To visualize the amino acid groups, picture a pizza with four toppings, and a little support table in the middle that’s there to keep the cheese from sticking to the lid. That table is the alpha carbon to which all the groups or toppings are attached.

Every amino acid has three groups/toppings in common: the amino group (-NH2), the carboxyl group (COOH), and a hydrogen atom, which in pizza terms would be three standard toppings, say pepperoni, sausage, and cheese (cheese is hydrogen, which is just one atom and not a group of them, and so it gets the plainest topping). That fourth quarter of the pizza? That is the R group, the functional group that identifies and characterizes different amino acids—when you think of the R group, think R for Radical, because that is a completely different and unique topping, and every R group amino acid side chain has a distinct flavor of its own. To get up to 20 it would have to be pineapple, spinach, olives, Canadian bacon, jalapeño, garlic, anchovies, bell pepper, salami, feta cheese, beef, oregano, bacon, barbecue sauce, chicken, pesto, chorizo, broccoli, eggplant, and mushroom. Some are weirder than others.

The nonpolar amino acids have R groups mostly made up of hydrocarbons, though the amino acids methionine and cysteine also each feature a sulphur atom. The nonpolar amino acids are as follows, with more information on each one.

Glycine

  • Three letter code: gly
  • One letter code: G

The body needs glycine to make compounds like as glutathione, creatine, and collagen, which is the most abundant protein in your body. Collagen is a vital part of your muscles, blood, skin, cartilage, ligaments, and bones. Glycine may also protect your liver from alcohol damage, contribute to heart health, and improve your sleep quality. Glycine might also protect those with type 2 diabetes from muscle-wasting. You can gain more glycine by eating certain meat products or by taking a collagen supplement.

Alanine

  • Three letter code: ala
  • One letter code: A

Alanine is an amino acid that helps convert glucose into energy and helps eliminate excess toxins from your liver. Alanine keeps muscle protein from being cannibalized by the body during intense aerobic exercise or activity, and it’s needed to balance nitrogen and glucose levels in the body, which it does via the alanine cycle.

Alanine is a nonessential amino acid, which means that usually your body can make the substance on its own and doesn’t need you to ingest it from outside. However, people with eating disorders, extremely low-protein diets, diabetes, liver disease, or certain genetic conditions that cause UCDs (urea cycle disorders), may need to take a supplement or adjust their diet to gain this amino acid.

Good sources of alanine are meat, fish, poultry, eggs, and dairy products, as well as some protein-rich plant foods, like avocado. There are supplements containing alanine on the market, however, taking any one amino acid alone could upset the balance of nitrogen in the body, putting stress on the liver and kidneys as they try to eliminate waste. It is advisable that those with liver or kidney disease should consult a trusted medical professional before taking any amino acid supplement.

Proline

  • Three letter code: pro
  • One letter code: P

Proline is needed for the manufacture of cartilage and collagen, which helps heal cartilage and cushion our joints and vertebrae. It keeps joints flexible, and skin supple when it is affected by sun damage or signs of normal aging. Proline breaks down proteins for cell creation, and is essential at sites of injury where the tissue must be rebuilt to heal. Proline supplementation is sometimes valuable to people with chronic back pain or osteoarthritis.

Proline is also needed for the maintenance of muscle tissue, and is sometimes found low in long-distance runners and other serious athletes. Proline is usually nonessential, as the body naturally derives proline from its supplies of glutamic acid. However, if necessary, proline can be found in natural sources like dairy, meat, and eggs, or can be gained from amino acid supplementation.

Valine

  • Three letter code: val
  • One letter code: V

Valine is a branched-chain amino acid (BCAA) that works with the other two BCAAs (isoleucine and leucine) to regulate blood sugar, repair tissues, and provide the body with energy. Valine assists in stimulating the central nervous system and is necessary for mental functioning. Valine helps provide muscles with extra glucose energy during intense physical activity, which prevents muscle breakdown, and helps remove toxic excess nitrogen from the liver. Valine may help the liver and gallbladder recover from damage due to alcoholism or drug abuse, as well as help possibly reverse alcohol-related brain damage, or hepatic encephalopathy.

Valine is an essential amino acid, and must be obtained through a diet including meats, mushrooms, dairy products, peanuts, and/or soy protein. Most people have no problem getting enough valine, however maple syrup urine disease or MSUD is caused by an inability to metabolize leucine, isoleucine, and valine. Supplementation is sometimes warranted in those with low-protein diets or who are trying to build muscle mass, but be advised that too much valine intake will make one’s skin feel like it is crawling, and may cause hallucinations. Supplements should always be taken responsibly.

Leucine

  • Three letter code: leu
  • One letter code: L

Leucine helps with blood sugar regulation, muscle repair, and energy production. It also helps burn fat located deep inside the body that is hard to reach through diet and exercise alone.

Leucine is a branched-chain amino acid (BCAA) along with valine and isoleucine, all of which help to promote post-exercise muscle recovery, leucine being particularly effective, as it converts to glucose the fastest of the three. That is also why leucine is closely linked with the regulation of blood sugar, and why a leucine deficiency causes symptoms like hypoglycemia: headaches, fatigue, dizziness, confusion, depression, and irritability.

Leucine promotes the recovery of skin, bones, and muscle tissue after injury or surgery. Natural sources of this essential amino acid are meat, nuts, soy flour, brown rice, beans, and whole wheat.

Isoleucine

  • Three letter code: ile
  • One letter code: I

An isolated form of leucine, isoleucine is prized by bodybuilders for its ability to increase endurance, help repair muscle tissue, and encourage clotting at sites of injury. Isoleucine is broken down for energy inside muscle tissue, and helps stabilize energy levels by aiding in blood sugar regulation. An isoleucine deficiency also produces symptoms that mimic hypoglycemia.

Isoleucine is an essential amino acid, and food sources include high-protein options like nuts, peas, lentils, seeds, meat, eggs, fish, and soy protein.

Methionine

  • Three letter code: met
  • One letter code: M

An essential amino acid that helps the body process and eliminate fat, methionine contains sulfur, a substance required for the production of the body’s natural antioxidant, glutathione. The body also needs methionine to produce two other sulfur-containing amino acids, cysteine and taurine, which help the body eliminate toxins, build tissues, and promote cardiovascular health.

Methionine helps the liver process fats (lipids), preventing accumulation of too much fat in the liver, which is essential for the elimination of toxins to stay functional. Methionine is needed to make creatine, a nutrient found mainly in muscle tissue and often taken as a supplement to boost athletic performance. Methionine is also needed for collagen formation, which is then used to make skin, nails, and connective tissue. One study suggested that taking 6 grams of methionine a day can improve memory recall in AIDS patients who otherwise show a marked methionine deficiency. Methionine may also help treat symptoms of Parkinson’s disease.

Methionine is an essential amino acid, and can be gained from eating garlic, beans, seeds, eggs, fish, lentils (in lower levels), meat, onions, soybeans, and yogurt.

Tryptophan

  • Three letter code: trp
  • One letter code: W

Tryptophan is an essential amino acid that helps balance nitrogen in adults and growth in infants. It also creates niacin, which is needed to create the “happy” neurotransmitter serotonin. In this way, tryptophan helps influence relief from depression and anxiety, managing pain tolerance and increased emotional well-being. Tryptophan is also associated with promoting deeper sleep.

You can get tryptophan through certain foods or a supplement in powder form. Natural food sources include cheese, milk, fish, turkey (famously), chicken, eggs, pumpkin and sesame seeds, chocolate, as well as tofu and soy.

Phenylalanine

  • Three letter code: phe
  • One letter code: F

Phenylalanine is an essential amino acid that is needed for the functioning of the central nervous system. It has been successfully used to help control feelings of depression and chronic pain, and other diseases linked to a malfunctioning central nervous system. Especially effective for treating brain disorders, phenylalanine is able to penetrate the blood-brain barrier, and only chemicals that are able to cross that barrier can directly influence brain function.

Phenylalanine is used to make epinephrine, dopamine, and norepinephrine, neurotransmitters that control how you perceive and interact with the world around you. Phenylalanine supplementation can help you feel happier and more alert, and it also has been used to treat chronic pain and improve cognitive function. An essential amino acid, phenylalanine is normally obtained from high-protein foods like meat, fish, chicken, eggs, milk, dairy products, beans, and nuts.

Cysteine

  • Three letter code: cys
  • One letter code: C

Cysteine is an amino acid containing a sulfur atom, and is used to form healthy bones, skin, hair, and connective tissue. It is also needed to make glutathione, one of the body’s natural antioxidants that fight free-radical damage. Cysteine and glutathione work together to remove toxins from the liver, and cysteine is often used in emergency rooms to treat acetaminophen overdoses before they can cause liver damage. It also protects the brain and liver against toxins from alcohol and cigarettes, and may be useful in preventing hangovers.

Cysteine is a nonessential amino acid, which means the body manufactures it in-house, but foods such as meat, eggs, dairy products, and whole grains are also good sources of cysteine.

Nonpolar Knowledge

There you have the rundown of the amino acid nonpolar side chains, the nonpolar aminos that variously help form protein molecules in our bodies, and do so much to keep us alive and functioning at top form.