Showing posts with label amino acid. Show all posts
Showing posts with label amino acid. Show all posts

Wednesday, January 29, 2014

Sweet, Salt, Bitter, Sour - They Ain't The Half Of It

Biology concepts – umami, taste, flavor, gustation, glutamate, chemoreception, CD36, fat taste, water receptor, calcium


Perhaps I was a little hasty when I said umami wasn’t the name
of a new band. Apparently “Umami” is the name of a band from
Minneapolis. They are described as an electro/psych band,
whatever that is. I like it when obscure science words are used
in culture – makes me think I’m in on some secret. Umami isn’t
that obscure a word, but I used to know a band made up of
statisticians called The Outliers.
Ever heard of umami? It’s not the name of a new band, or even a bad Robin Williams movie. It’s a taste; the fifth taste that humans can sense. Umami is the taste of savory; meats and other high protein foods. And what do we have to thank for umami? Seaweed.

Until 1908, science believed that most flavors were just combinations of the four traditional tastes - sweet, salty, sour, and bitter. But don’t get the idea that taste and flavor are the same - oh no. Taste is our gustatory sense, but that isn’t the same as flavor – flavor is something bigger than taste.

You know how having a head cold makes food bland? Well, that’s because smell is a big part of flavor; you don’t smell your food when you have a cold. Food stimulates all your senses - temperature, touch, smell, what it looks like and even how it sounds as you chew it. All these things add up to flavor.

This is why chefs say you eat with your eyes first, and why they try to incorporate different textures into a single dish. They’re trying to appeal to all your senses. Therefore, eat slowly to enjoy your food more. Give all your senses time to participate. And you might just eat less, since your satisfaction will come from the total experience, not just the craving for a particular taste.

But back to the origins of umami. The Japanese had an idea that there was another taste, mostly since their traditional cuisine used so much seaweed, and this flavor couldn’t be accounted for by the other four tastes.  Chemist Kikunae Ikeda wanted to identify the active molecule in seaweed, the one that gave it taste. He called it umami, from the Japanese words for delicious (umai), and taste (mi).

Ikeda’s biochemical studies led to the identification of glutamates as the molecules to which people reacted. And they aren’t just in seaweed, most living organisms contain truckloads of glutamates. When cooked, all glutamates convert to L-glutamate, the amino acid. Ikeda determined that this is what some of our gustatory (taste) receptors sense. Gustation is from Latin gustare = taste, and this is where the word gusto comes from; to taste life.


It turns out that umami taste is not produced by just L-glutamate.
Glutamate comes mostly from meat, as they are high in proteins,
but the nucleotides inosinate and guanylate also perceived as
savory tastes. Inosinates are also found in meats, but also in
seafood. Vegetables are a major source of guanylates, but so are
mushrooms – and we all know that mushrooms are fungi – right?
When you taste something, a chemical signal in the taste cells on
the tongue is converted to an electrical impulse. This is carried by
either the facial nerve or the glossophayrngeal nerve to the brain.
The most palatable form of glutamate that Ikeda could identify was monosodium glutamate (MSG), so he immediately set out to produce and sell it, starting in 1909. Made a pretty penny, he did. Now MSG is a common flavor enhancer in Japanese cooking, including soy sauce. World-class chefs are designing “U-bombs” (umami-filled dishes) to take advantage of the new official taste.

This is why identifying an umami taste receptor for L-glutamate makes sense. This is nature telling you that you need to eat protein, and by giving it a favorable neural response (it tastes good), it increases the chances that you will seek out protein sources for nutrition.

Glutamate has several functions, even beyond its role as one of twenty protein building blocks. Glutamate is the most common neurotransmitter in the central nervous system, and plays a crucial role in long-term potentiation (LTP) and learning. Glutamate is also an intermediate in synthesizing many of the molecules in glycolysis, gluconeogenesis, and the citric acid cycle. I’ve said it before and I hope it jumped into your mind just now – nature hates a unitasker.

So you sense L-glutamate through a gustatory receptor that is specific for that molecule, and the electrical impulse is converted to a specific taste – we call it savory. The cloning of the taste receptors in the late 1990’s (actually umami was the first) started people thinking about other possible tastes. Could there be a sixth taste sense – how about fats? Do we taste fats?


When in the insula of the brain, the input is sorted with other
input and interpreted as a taste. It is the perception that is
important. For the fatty acid receptors, they are receptors, they
are located in the taste cells, and they do carry information via
the same two nerves to the same part of the brain. But are they
then interpreted as a taste?
Much research has been performed in this area in the past few years and a couple of fatty acid receptors on the tongues of rodents and primates have been identified, specifically, CD36 and GPR120. But does this mean we “taste” fat? We said taste doesn't equal flavor – we should now add that sensation may not be the same as taste. Just because there are specific chemoreceptors on taste cells for different fatty acids doesn’t mean that we perceive the sensation as taste.

It has been shown that fatty acids in the oral cavity do have a threshold level for sensation, and that the fatty acid taste receptors do lead to specific changes in physiology. When subjects were given fatty acids on their tongues, they very quickly showed increased serum triglyceride levels, increased pancreatic hormone release, increased release of GI lipases (enzymes to breakdown fat) and a slowly of the GI tract (it takes more time to digest fats).

What is lacking here is a conscious perception of the discernable nature of the fatty acid (like how sugars are sweet or glutamates are savory). The 2009 studies by Mattes and colleagues controlled for the mouth feel, smell, and so forth of fats, so it was definitely the fatty acid receptor that was stimulating the responses, but no where did it say the subjects tasted something. However, his 2011 paper says that fat may very well be a basic taste.

This gives us a new way thinking about taste receptors. Taste is a type of chemoreception, but perhaps it’s only one subset of oral chemoreception. Gustatory chemoreception is a lot more than just tasting something. However, some researchers challenge this division, saying that participants do have a measurable psychophysical response when fatty acids on the tongue reach a threshold level – they do taste something.


Again I say, “nature hates a unitasker.” CD36 is the fatty receptor in
taste cells, but it also works in macrophage recognition of oxidized
fatty acids and the onset of atherosclerosis, and in the activation of
platelets by fatty acids. You can see in the cartoon that CD36 sticks
into the membrane at two places and loops out of the cell. If you
change the order of its amino acids, it’s shape will change. How well
it binds to fatty acids, or activates all those downstream signals will
also be affected. This is why people with different versions of CD36
may eat different amounts of fat. I wonder if people with poor CD36
versions also have more trouble with CD36 functions in other cells?
The CD36 glutamate receptor has been especially well studied in the past couple of years. It comes in several slightly different forms (polymorphisms – slight differences accounted for by single or few amino acid differences in the sequence of the protein), but these differences have a big effect.

When divided into groups based on which variant of CD36 they possessed, a couple of studies from 2012 (here and here) show that responses to fat and how much the subjects craved fats were different. Those who sensed fats most readily (at lowest concentrations) tended to eat less than those who needed more fat in order to trigger the responses.

The hypothesis of a 2013 review of fat taste and obesity says that those who sense less fat are more likely be tipped toward a hunger stimulating hormonal profile, while those who more readily sense the fatty acids in their food tip toward satiety (fullness). There are many hormones involved here and we could get bogged down very fast, so let’s leave it at that for now; undoubtedly someone is trying to make a diet pill based on it.

So, could there be more oral chemoreception events going on – a seventh taste? An eighth?  Let’s talk very briefly about two possibilities. Maybe we can taste calcium. Yes, you could taste your Tums. A 2008 study indicated that mice can perceive calcium as a specific taste. A single 2012 study extends this to humans as well. Calcium is sensed via a certain receptor (Tas1R3), which works with other proteins to sense sweet and umami. But here, it apparently works on its own (we will talk more about the receptors in the posts to come). I need to see more research before I buy calcium taste completely.

Taste number eight - do you think you can taste water? The common argument is that you can taste what is in the water, not the water itself. How or why would you taste water; you’re 65-70% water all the time! What good is it to taste the main ingredient of life? How about this – do you sense the water by taste receptor, not just by temperature, sound, smell, or mouth feel?


There are voluntary swallows an involuntary swallows. But even
in voluntary swallows there are involuntary parts. You don’t think
about closing off your trachea with your epiglottis, it just happens.
This closing is how you keep food and liquid from ending up in
your lungs. Water in your laryngeal pharynx is one stimulus to get
you to swallow and close off the wind pipe until the possible
problem is gone.
Yep, mammals have receptors in the oral cavity that specifically sense the presence of water. In some mammals, like dogs and rabbits, using salt water inhibits the firing of the laryngeal nerve fibers connected to the water receptors; not so in cats and rats. We’ll get to why in a second.

What is the purpose for water receptors in the oral cavity (really, they are in the entrance to the throat, the laryngeal pharynx)? It may be that this is an evolutionary protection from aspirating (breathing in) liquid to the lungs. Liquid in the lung is a bad idea, since it stops gas transfer and promotes bacterial growth. If acids or other liquids that could damage the lungs or throat get in their somehow, it would definitely be better to swallow them than to breathe them in.

When you were a fetus and a very young infant, stimulation of the water receptors in your throat caused you to swallow immediately. As you aged and gained more muscular control, the reflex was replaced by coughing – this is the hypothesis of a 2001 study on the reflex. But the water receptors are still there and still aid you as a stimulus for voluntary swallowing. Whether we taste water or not, I’m glad I have the chemoreceptors.

So, the dampening of the reflex by Cl- in salt might be helpful keeping you from constantly having the urge to swallow. This leads to another point – the power of suggestion. Can you do anything right now other than think about the saliva in your mouth and whether you should be swallowing? Creepy, isn’t it.

Don’t count out the idea of water as a basic tastant (something you can taste). A 2010 study showed by monitoring brain waves that people respond to water using the same pathways as taste, and the responses look the same. And a 2012 study indicates that rats have distinct portions of the gustatory cortex of the brain for identifying both salt and water. If we can taste umami to make sure we eat enough protein, and sweet to make sure we eat enough carbohydrate, why not water to make sure we keep hydrated?


The idea here is that everything seems better if you are in love.
With love, this is a fantastic summer day in a beautiful place.
Without love, it’s just sand in a whole lot of uncomfortable places.
Same with taste, water is water – unless you're in love.
One final point that reflects just how complex taste is – did you know that being in love makes water taste sweeter? Participants in a December 2013 experiment were asked to think or write about love, hate, or jealousy. Then they were asked to describe the taste of a new product (really just distilled water). Those who wrote or thought about love rated the water to be sweeter than those who contemplated hate or jealousy.

It seems that the brain pathways for rewarding feelings in love and in consuming sweet are the same. You can’t discern between the two, and one can stimulate the other. So when you say you love eating sweets, maybe you really do!

 Next week, we can go further into taste. Do people who are supertasters taste good or taste well?


Newman L, Haryono R, & Keast R (2013). Functionality of fatty acid chemoreception: a potential factor in the development of obesity? Nutrients, 5 (4), 1287-300 PMID: 23595136

Pepino MY, Love-Gregory L, Klein S, & Abumrad NA (2012). The fatty acid translocase gene CD36 and lingual lipase influence oral sensitivity to fat in obese subjects. Journal of lipid research, 53 (3), 561-6 PMID: 22210925

Keller KL, Liang LC, Sakimura J, May D, van Belle C, Breen C, Driggin E, Tepper BJ, Lanzano PC, Deng L, & Chung WK (2012). Common variants in the CD36 gene are associated with oral fat perception, fat preferences, and obesity in African Americans. Obesity (Silver Spring, Md.), 20 (5), 1066-73 PMID: 22240721

Chan KQ, Tong EM, Tan DH, & Koh AH (2013). What do love and jealousy taste like? Emotion (Washington, D.C.), 13 (6), 1142-9 PMID: 24040883

MacDonald CJ, Meck WH, & Simon SA (2012). Distinct neural ensembles in the rat gustatory cortex encode salt and water tastes. The Journal of physiology, 590 (Pt 13), 3169-84 PMID: 22570382



For more information or classroom activities, see:

Umami –

Fat taste –

Water receptor –

Wednesday, September 4, 2013

Three Lefts Make A Right

Biology concepts - chirality, homochiral, enantiomer, stereoisomer, racemic mixture, biofilm, antimicrobial peptide, protein, amino acid


Geordi was the chief engineer on Start Trek; The Next
Generation, but I was partial to Scotty on the original.
They both work on the matter-antimatter reactors that
powered everything from the warp drive to the phasers.
Don’t laugh – NASA is working on a warp drive as we
speak, and we have been able to produce antimatter for
years. Not sure how antimatter will solve our energy
problems though, it takes much more energy to produce
it than we get from a matter-antimatter reactor.
Today we’ll start with a story that may seem to have nothing to do with biology. Hopefully we can draw a parallel later.

For every type of every subatomic particle there is an opposite particle. There are protons and anti-protons, electrons and anti-electrons (positrons), neutrons and anti-neutrons. Together, they make up matter and antimatter – think Star Trek.

So why is our universe made of matter and not antimatter? It turns out that when matter meets antimatter, they obliterate one another. This is bad – Scotty was always trying to prevent a matter/antimatter catastrophe on the Enterprise.

When the universe was young, there was antimatter and matter; lots of annihilations. Scientists hypothesize that there were a few more molecules of matter than antimatter, so when the fireworks were over, only matter remained; so matter matters.

What’s this got to do with protein exceptions, our subject for last week and this? We’ll get to that, a little background first. Remember that the shape of the protein is important for its function, and its shape is dependent on the amino acid order and the structure of those amino acids.

Look at your hands. They’re mirror images of one another, but no matter how you try, you can’t make your left glove fit exactly on your right hand. Unlike a ball reflected in a mirror where the two images will be superimposable on one another, there is no way to do this with say….. your left and right shoes.


If you reflect your right hand in a mirror, you get an
image exactly like your left hand. But your right and
left hands can’t be superimposed – try it, turn one over,
turn the other over, turn them around the over
direction, detach one – you still can’t do it. It is the same
with chiral molecules. The different groups come at you
or away from you, and once you reflect them, no two can
be superimposed – try it, at least one group will be
pointing the wrong direction.
Molecules like this in chemistry are called chiral; the amino acid central carbon (chiral carbon) has four different groups, so no flipping will make the two mirror images look exactly the same. The two different amino acid variations are called stereoisomers, specifically, enantiomers.

The different enantiomers (enantio = opposite) have different chemical properties. Without getting into too much chemistry (nobody wants that), different enantiomers cause light waves to rotate in different directions.

One version of a molecule called gluteraldehyde rotates light to the right (dextrorotary or D, dextra = right), while the other is levorotary (levo = left). Amino acid enantiomers are comparable to the structure of gluteraldehyde, so amino acids that parallel the two gluteraldehydes are assigned a D- or L- label, ie. L-alanine has a structure similar to the gluteraldehyde enantiomer that rotates light to the left.

This is a bit of a misnomer because light rotation depends on many factors. In fact, many amino acids labeled L-type because of their similarity to L-gluteraldehyde actually rotate light to the right –that little factoid won’t be on anyone’s final exam.

Most proteins fold on their own, and they fold the same way every time. But what might happen if the protein sometimes used a certain L-amino acid and sometimes the D-version? The two resulting proteins would fold differently and therefore have different possible functions. Heaven forbid!

To avoid this, nature has devised an ingenious solution - only L-amino acids are used. This assures that all proteins of a specific type assume the same shape, and it turns out that proteins are most stable when they are made of all L- or all D-amino acids. This is the rule of homochirality.


Polarized light has practical implications. Your 3-D movie
glasses may be plane polarizers. The light from the screen
is a mix of right and left polarized light. One lens lets in
one, while the other lets in the opposite light. This splits
the image into two images, one for each eye, and they are
separated by a distance. This gives a stereoptic image, just
like your eyes seeing something in real space.
This is one of the best-known rules of biology, right behind the “form follows function” we talked about last week. But we saw that proteins were exceptions to that rule, so there must be exceptions to this one as well.

One question before the exceptions -just why did life opt for all L-proteins instead of all D-proteins? Do they annihilate one another when they come into contact, like matter and anti-matter? Thankfully, no.

Were there more L-amino acids available on the early Earth so life made a choice and stuck with it? Maybe – this is one of the hypotheses currently being investigated. It’s also possible that some life developed as D-protein makers, but they were out-competed somehow and we descended from the L-protein winners. It isn’t as easy a question as the physics matter/antimatter issue - more on this biology exception next week. There are so many more exceptions in biology as compared to physics – that’s why I love life more than physics itself.

The most mundane is exception to homochirality is the one amino acid that isn’t chiral. Glycine’s R group is just a hydrogen, so the central carbon has two bound hydrogens, and the mirror images can be superimposed. There’s no L-glycine or D-glycine, just glycine. Don’t worry, the rest of the exceptions are better.

It turns out that the rule of homochirality is more of a guideline - there are examples of important D-amino acids (D-aa) in plants, animals, and prokaryotes. We don’t have time or space to go into many of them, but I will highlight two exceptions that are simply amazing. Let’s start with the bacteria since they own the planet, and we probably inherited our D-amino acid uses from them.

Bacteria use D-amino acids in various ways. First, new research shows that as bacterial numbers go up and resources (food) go down, D-aa-containing proteins might prepare bacteria for the bad times ahead. A 2009 study shows that Bacillus subtilis and Vibro cholerae make large amounts of D-aa as they age, including D-tryptophan, D-tryosine, D-phenylalanine, and D-leucine. As the amounts increase, they start to have an effect on the bacterial cell wall.


A gram positive bacterium has a thick cell wall, which
includes peptidoglycan. The glycan parts are NAM and
NAG. The NAM has a tetrapeptide attached to it, and this
is where the D-aa can be used. This strengthens the cell
wall and makes it even thicker. The lipoteichoic acid in
the outer layer is where change to a D-aa prevents
defensins from sitting in the cell wall and disrupting
the buried plasma membrane.
The D-aa are incorporated into the growing peptidoglycan, the elastic and stress-bearing component of the cell wall, and they also regulate enzymes that control the thickness and structure of the peptidoglycan. By putting D-aa into the cell wall, the bacteria make themselves strong for the lean times ahead.

What is more, a 2010 study showed that in B. subtilis and S. aureus, the increasing numbers of bacteria and their increasing concentration of D-aa’s leads to a breakdown of the extracellular matrix that holds all the bacteria together (the biofilm). D-aa's were able to prevent biofilm formation and degrade existing biofilm, again preparing the bacteria to go off on their own as resources dwindle.

S. aureus also uses D-aa-proteins to avoid being killed. We have antimicrobial peptides (AMP) on our skin and mucosal surface that are always looking to kill bacteria. They often work by poking holes in the bacterial membrane. However, a 2013 study shows that by switching out L-alanine to D-alanine in its cell wall, S. aureus can render the AMP’s ineffective. The D-alanine gives the protein a different shape, so the AMP's can’t fit in and do their job. Smart bacteria.

Animals have gotten into the act, especially the gastropod mollusks, ie. some snails and sea hares (marine slugs). D-tryptophan is their exception of choice. The cone snails (genus Conus), the most predatory and venomous of the marine snails, use D-tryptophan in the active peptides of their venom, called contryphans. Large cone snails have been known to kill humans, but the role of the D-tryptophan in the venom activity is not yet known.


The cone snails use many peptide venoms to incapacitate
their faster prey; they move like snails don’t ya know. The
siphon has the black stripe and tests the water for prey.
Then the proboscis below (kind of pinkish orange at the
tip) sends out the radula that envenomates the victim.
The sea hare, Aplysia kurodai, also uses D-tryptophan in a cardioexcitatory neuropeptide called NdWFamide (it speeds up the slug’s heartbeat). This protein has also been found in terrestrial slugs, so it may be that many mollusks are D-aa users.

How about us? Do humans use D-amino acids? Sure we do. But there are tricksters here. D-alanine is found in all mammals, but we don’t know what it might be doing. Its levels change with the time of day (circadian cycling), so who know what it might be controlling. A 2013 study set out to determine what drove the circadian changes. They tested several things: changing diet or fasting didn’t matter; enzymes that degrade D-alanine didn’t change levels of function either. But when they studied germ-free mice, the D-alanine levels didn’t change.

The scientists determined that it’s our gut bacteria making D-alanine, and circadian changes in intestinal absorption rates is the reason that the D-alanine levels fluctuate. It doesn’t mean that D-alanine isn’t doing something, but it sure had us fooled for a while.

Mammals don't stop there; D-serine and D-aspartate are so important, we have special enzymes called racemases whose job it is to convert their L-forms to D-forms (racemic mixtures contain both D- and L-versions of a molecule). The most amazing exception must be D-serine. However, we will see that there is a Goldilocks effect to D-aa’s, you don’t want too much or too little.

A certain brain neuron receptor (called NMDAR, important for learning and memory) is activated by an amino acid called L-glutamate, but it needs help from either glycine or D-serine to set off the electrical impulse. It turns out that in Lou Gehrig’s disease (amyotrophic lateral sclerosis), lower motor neurons die because they undergo aberrant excitation. In genetic cases of ALS, patients have too much D-serine!


Most patients with ALS are diagnosed after age 50 and
live about five years. Stephen Hawking- the Nobel
winning cosmologist – was diagnosed at 21 and has
lived with the disease for 50 years! Hawking has round
the clock care, for the only muscles that work for him
are breathing, swallowing an eye movement. Lucky for
him, most people’s breathing and swallowing are not
spared and this is how they die. He uses his eye
movement to run his computer.
A 2012 study showed that D-amino acid oxidase (DAAO) is mutated in these patients and doesn’t do its job of breaking down D-serine. Mice with a mutated DAAO were shown to have decreased lower motor neurons and more ALS signs.

So too much D-Ser is bad, but how about too little? Many studies have shown that schizophrenia patients have low levels of D-Ser. It might be that DAAO is too active, or perhaps a D-Ser racemase is inactive, or maybe there is just too little L-Ser to make D-Ser from – we don’t know yet. 

A 2013 study has also implicated D-aspartic acid in schizophrenia. D-Asp can replace L-glutamate in activating NMDA receptors, and schizophrenic patients have low D-Asp levels in the brain and blood. The D-Ser and D-Asp data implicate glutamergic receptor activation in schizophrenia, so much work is underway to find ways to increase these D-aa’s in our brains - the very things that the rules say we shouldn’t be using in the first place. But let’s not raise them too much, no one wants ALS!

Next week, we switch our attention to carbohydrates, the energy sources in our cells. Every cell on Earth is designed to make ATP from glucose - except for those cells that ONLY use fructose.



Lam H, Oh DC, Cava F, Takacs CN, Clardy J, de Pedro MA, Waldor MK. (2009). D-amino Acids Govern Stationary Phase Cell Wall Re-Modeling in Bacteria Science, 18 (325), 1552-1555 DOI: 10.1126/science.1178123

Kolodkin-Gal I, Romero D, Cao S, Clardy J, Kolter R, Losick R. (2010). D-Amino Acids Trigger Biofilm Disassembly Science, 328 (5978), 627-629 DOI: 10.1126/science.1188628
Sasabe J, Miyoshi Y, Suzuki M, Mita M, Konno R, Matsuoka M, Hamase K, Aiso S. (2012). 

D-amino acid oxidase controls motoneuron degeneration through D-serine. Proc Natl Acad Sci U S A. , 109 (2), 627-32 DOI: 10.1073/pnas.1114639109  

Simanski M, Gläser R, Köten B, Meyer-Hoffert U, Wanner S, Weidenmaier C, Peschel A, & Harder J (2013). Staphylococcus aureus subverts cutaneous defense by d-alanylation of teichoic acids. Experimental dermatology, 22 (4), 294-6 PMID: 23528217

 Errico F, Napolitano F, Squillace M, Vitucci D, Blasi G, de Bartolomeis A, Bertolino A, D'Aniello A, & Usiello A (2013). Decreased levels of d-aspartate and NMDA in the prefrontal cortex and striatum of patients with schizophrenia. Journal of psychiatric research PMID: 23835041

For more information or classroom activities, see:

Chirality –

Bacterial cell wall –

Biofilm –

Antimicrobial peptides –

D-amino acids –

Amyotrophic lateral sclerosis –

Schizophrenia -



Wednesday, August 28, 2013

So Many From So Few

Biology concepts – protein, amino acids, non-standard amino acids, peptide bond


Severe dietary protein deficiency leads to distinct
symptoms, and if not resolved, death. Called kwashiorkor
(Ghanan word meaning “disease from second born”),
the deficiency leads to changes in osmotic potential in
the bodies cells as compared to their blood.
Hypoalbuminemia (low levels of the blood protein
albumin) lead to fluid leaving the vessels and accumulating
in the abdomen, called ascites. This often occurs when infants
stop nursing (like when a second child is born); they take in
enough calories but not enough protein.
Heterotrophic organisms, including us humans, must consume protein in order to survive. Meat is a great source, by far the best protein source per unit mass and the best for obtaining necessary protein subunits (amino acids). If you look at complete protein sources compared to caloric intake, four of the top five foods are: turkey/chicken; fish; pork chops; and lean beef.

Tofu comes in sixth and soybeans are seventh. This is why humans have sharp canine teeth – we're meat eaters. You can live happily (well, somewhat happily) as a vegetarian; you just have to work much harder at it.

So why is protein so important? How about, because it is one of the four major biomolecules and without it you die a horrible death? Sounds like a good reason to me.

Proteins reside in every cell of every living organism, from prokaryotes to your favorite uncle. There isn’t a job in a cell that proteins don’t have their hands in; proteins even perform numerous tasks at the extracellular level. Heck, that spider web hanging from your dusty Stairmaster is made of protein!

From prokaryotes to spiny echidnas to rosebushes, let’s look where proteins are involved in life. Proteins provide the structure from which cells hold their shape and onto which they build a membrane. Proteins do the talking, providing chemical signals and ways to sense chemical signals.

Proteins do the dirty work; as enzymes they put molecules together, cut them apart, and change their parts around. And most times, they make these reactions happen faster than they would otherwise and without being used up in the process.


Enzymes are specific for a very few molecules (called
substrates). Enzymes have a particular shape, and this
allows the correct substrate to bind and be acted on;
called the lock and key system. Notice that the
enzyme itself is not altered by the reaction, so it can
work again on another substrate molecule. However
there are exceptions – suicide enzymes are inactivated
by their own action, so they only work once.
Proteins allow for movement, like the contractile proteins in your muscles or the proteins that make up flagella and cilia. Proteins even act as defenders of the cell, as antibodies and myriad other immune molecules.

A typical cell may contain 10 billion protein molecules. However, not every cell has the same proteins. Many proteins are necessary for every cell, but others have specialized functions needed in only some cells. The exception is unicellular organisms. Their one cell must be able to produce every kind of protein they might ever need.

Space is at a premium, so cells can’t waste room on proteins that aren’t needed right now. Therefore, making protein must be efficient, tightly regulated, and fast. Over 2000 new protein molecules are made every second in most cells, while some proteins exist only to destroy unneeded or old proteins.

Humans can make about 2 million different proteins, but we only have about 25,000 genes that code for them. We accomplish this by having some genes produce many different proteins, just by changing the parts of the gene used. These alternative splice variant proteins may have different functions even though they come from the same gene. For example, the cSlo gene is required for hearing, and each one of the 576 different splice variants is responsible for sensing a different frequency. Biology is just so dang efficient.

Now that you know how important proteins are, let’s find out what they are. Proteins are polymers (poly = many, and mer= subunit) made up of bonded amino acid mers. Proteins come in many sizes; the TRP-Cage protein of gila monster spit is a polymer of only 20 amino acids, while the titin protein of your connective tissue is over 38,000 amino acids long.

Maybe we'll dig into the degeneracy of the genetic code when we talk about nucleic acids, but for now let’s just accept that DNA triplets code for different amino acids, and the order of the codons determines the order in which amino acids are linked to form a specific protein. The order of the different amino acids is the key. Why? I’m glad you asked.

Amino acids (or aa’s) are all small molecules made up of carbon, hydrogen, oxygen, nitrogen, and sometimes sulfur – five of last week’s “elements of life.” It’s the arrangement of these elements that makes an amino acid. Refer to the picture below for a visual aid. The central carbon is bound to four other things (often called moieities). One is simply a hydrogen. Another is an amino group (contains the nitrogen). The third is a carboxylic acid group. Get it? amino acid.


While not the most exciting images, these cartoons should
help you understand the structure of the amino acid (left)
and the building of the proteins (right). Each amino acid has
the same structure, except for whatever the R group might
be. The amino end of amino acid 2 is joined to the carboxylic
acid of amino acid 1. The next peptide bond would be between
the carboxy end of amino acid 2 and the amino end of amino
acid 3. Notice how water is created each time a peptide bond
is made.

The fourth group is what makes each aa different. Called an R group, this side chain can be small or big, neutral or charged, and gives the aa its properties. The R stands for something, but that story is just too long.

In glycine, the R group is merely another H, but in tryptophan it contains complex rings. We have talked about how tryptophan is the least used amino acid; it is bulky and introduces big bends in the peptide. We’ll show that bends, kinks and other interactions between aa’s are important for the protein function.

Most organisms can make all the amino acids they need, but mammals are the exception. We have abandoned (genetically) pathways for making some aa’s, so we must get them from our diet. These are the essential amino acids, of which there are nine if you are healthy. Tryptophan must acquired by all animals – good thing plants still have the recipe.

Ribosomes (made of proteins and nucleic acids) link the individual aa’s together in the order demanded by DNA via the mRNA. The bond that connects them is called a peptide bond, and is a “dehydration” or “condensation” reaction.

Look at the amino acid picture again; the peptide bonding process kicks out water, ie. dehydration (de = lose, and hydro – water). Water forms from seemingly nowhere, like condensation on your mirror. See how fitting the names are?

When in a protein chain (also called a peptide), the order of aa’s is called the protein’s primary (1˚) structure. The primary structure in turn dictates the secondary (2˚) structure, which is a folding of small regions of the protein based on the interactions of the side chains of closely associated amino acids.

In turn, the folding of small regions brings together aa’s from farther apart, and they fold up based on their interactions. This is the tertiary (3˚) structure of the protein. If a protein needs more than one peptide chain to be functional, the shape that those different chains form when they interact is called the quaternary (4˚) structure.

These cartoons can help you picture how an individual amino
acid can affect the structure of an entire protein. In the
secondary structure cartoon, there are two basic forms that
the nearby amino acids can form, helices and sheets, other
parts will form no patterned form at all. The tertiary and
quaternary cartoons are for hemoglobin, showing how non-
amino acids may be involved (heme), and how the
individual peptides fit together.

The hemoglobin that carries oxygen in our red blood cells is made up of four protein subunits. Why is this important – because what the protein does in life is completely dependent on its three dimensional shape. Lots of aa’s means lots of potential shapes. This is in itself one of the greatest exceptions, since one of the basic tenets of biology is “form follows function.” But with proteins, function follows form.

For the greatest number of possible combinations and shapes, it’s lucky that DNA codes for 20 aa’s. Or are there more? Proteinogenic aa’s are those that can be added into a growing peptide chain, and there are actually 22 of them. The two exceptions are selenocysteine (like cysteine with selenium substituting for sulfur) and pyrrolysine (like lysine with a ring structure added to the end).

We talked last week about the functions of selenocysteine and how it can be incorporated into a peptide even though there isn’t a normal mRNA codon dedicated to it. Pyrrolysine is similar in that it becomes coded for after the modification of what is usually a stop codon, in this case UAG (a signal to add pyrrolysine is located after the UAG codon).

Pyrrolysine is used by methanogenic (methane producing) archaea and bacteria. It's important in the active site of the enzymes that actually produce the methane. New research is showing that more organisms than previously believed use pyrrolysine. A 2011 study identified more than 16 archaea and bacteria with pyrrolysine coding mRNA modifications, but it looks like there may be more.

While the mammalian titin protein is the largest protein
known (38,136 amino acids), there is a close second in a
bacterium called Chlorobium chlorochromatii CaD3. The
gene has been found for a protein of 36,000 amino acids,
but we don’t know yet of the protein is actually made. In
archaea, the halomucin protein from the square prokaryote
Haloquadratum walsbyi is 9,200 amino acids but is exported
to protect the organism from its extreme environment.

A 2013 study indicates that the typical modification of the mRNA that occurs 100 bp downstream of the UAG stop codon isn't even there in some pyrrolysine-coding genes. One hypothesis is that in genes without the modification, the UAG sometimes acts as a stop codon and sometimes incorporates a pyrrolysine. Therefore, there are truncated (prematurely stopped) and full-length versions of the protein in the cell, and the relative number of each can be affected by local conditions and stressors.

In this paper, the authors have developed a different predictor, which doesn’t rely solely on the presence of the modification. Using it, they have identified many new candidate genes in archaea and bacteria that could be using pyrrolysines. Here’s my question – all organisms use selenocysteine, but it seems only arachaea and a few bacteria use pyrrolysine. Why did it go away in higher organisms? Can it only be used for methane production? Please, no methane production jokes.

Pyrrolysine and selenocysteine are coded for by mRNA and are added to proteins, so we definitely have 22 aa’s, but could there be more? You betcha. There are over 300 non-standard amino acids, but that isn’t such a big deal. Remember the definition of amino acid; a central carbon with a hydrogen, a carboxylic acid, an amino group, and something else attached. It isn’t a wonder there are many of them.


Bacteria kill bacteria all the time. They make their own
antibiotics, called bacteriocins, by modifying short peptides
so that they interfere with cell wall synthesis in other strains.
To do this, they modify amino acids in peptides to non-standard
amino acids, including lanthionine and 2-aminoisobutyric acid.
Those that contain lanthionine are called lantibiotics and are
hot commodities right now.
A few non-standard aa’s can be found in proteins, like carboxyglutamate which allows for better binding of calcium, and hydroxyproline, crucial in connective tissue function. These are formed by modifying the amino acids already added to the growing peptide chain.

Other non-standard aa’s are produced as intermediates in other pathways and are not used in proteins. The list of them is great and their functions are even greater, but some act as neurotransmitters, others are important in vitamin synthesis, especially in plants. Still think life uses just 20 amino acids?

Next week we can finish up proteins. Life is very selective with the form of its amino acids – except when it isn’t.


Theil Have C, Zambach S, & Christiansen H (2013). Effects of using coding potential, sequence conservation and mRNA structure conservation for predicting pyrrolysine containing genes. BMC bioinformatics, 14 PMID: 23557142

Gaston MA, Jiang R, & Krzycki JA (2011). Functional context, biosynthesis, and genetic encoding of pyrrolysine. Current opinion in microbiology, 14 (3), 342-9 PMID: 21550296


For more information or classroom activities, see:

Dietary proteins –

Functions of proteins –

Standard amino acids –

Peptide bond –

Protein structure –

Non-standard amino acids -