Showing posts with label cell wall. Show all posts
Showing posts with label cell wall. Show all posts

Thursday, December 14, 2017

It’s A Plant World, We’re Just Living In It

Biology concepts – cell walls, chloroplasts, myco-heterotrophs, holoparasites,

Life on Earth is easy. It can be boiled down to three sentences. “The mitochondria and the chloroplasts are, in a fundamental sense, the most important things on Earth. Between them, they produce oxygen and arrange for its use. In effect, they run the place.” Lewis Thomas wrote this in his award winning book, The Lives Of The Cell: Notes Of A Biology Watcher, in 1975.


Nature’s carbon recycling center. The sun’s energy is used to 
polymerize carbon (CO2) into carbohydrates (CHO) and releases 
oxygen (O2). Then the mitochondria use the O2 to break down 
the CHO, resulting in chemical energy (ATP) and carbons (CO2) 
ready to be polymerized again.
He was so right - for the organisms that use them. I guess he didn't consider the exceptions. These two organelles mesh seamlessly in their functions. One produces carbohydrate and oxygen, while consuming carbon dioxide. The other consumes carbohydrate and oxygen and produces carbon dioxide. The ultimate recyclers.

If these two organelles are the most important things for life, then doesn’t that make plants the kings of life on Earth, since they have both chloroplasts and mitochondria? Makes you feel a bit more humble now about your place in world, doesn't it.

However, this brings up an essential question – and the main focus of today’s topic and exceptions. What makes a plant cell a plant cell? Green algae have chloroplasts and mitochondria, but they aren’t plants, they belong to the kingdom Protista. We have discussed the sea slug, E. chlorotica, and its ability to photosynthesize – it is certainly not a plant. So what makes a cell a plant cell?

Leaving the chloroplast out of the equation for a minute, you could argue that a plant cell is one with a cell wall and cell membrane. That surely separates them from animal cells, since animal cells only have the cell membrane. But many bacteria, archaea, fungi, and algae have cell walls. If the argument is refined to define a plant as having a certain kind of cell wall, then we must look a little closer. Many cell walls are made of sugars, but are plant cell walls unique in their constituents?


True bacteria have two large groupings, Gram+ and Gram -,
based on their cell wall structures. The gram stain sticks to
the peptidoglycan layer, so the thick layer on G+ bacteria make
them stain deeply. The lipopolysaccharide (LPS) layer of the G-
species keeps them from staining, and is highly toxic.
Endotoxin (LPS) and causes about 70% of septic shock cases.
Bacteria cell walls are made of peptioglycan (peptido = amino acid containing, and glycan = polymer of two sugars). One of the two components is always N-acetylmuramic acid, and the other is often poly-N-acetylglucosamine, but other things can be included as well. The exception is the Mycoplasma, a group of small bacteria that don’t have a cell wall at all. Since many antibiotics function by disabling the bacterial cell wall or preventing its formation, they don’t work against mycoplasma infections like M. genitalium, which a 2011 study linked to pelvic inflammatory disease in women.

Fungal cell walls are also made of a polysaccharide (poly = many, and saccharide = sugar), in a polymer called chitin. Chitin is also the rigid polymer that makes so many insects crunch when you step on them. Chitin cell walls are defining for fungi, as many cellulose containing cell wall fungi have been moved out of the kingdom of Fungi. But this still doesn’t tell us what is unique to plant cell walls.

Plant cell walls contain cellulose, and is complex. Plant cell walls can contain up to three layers, with different sugars involved, including cellulose, hemicellulose, and pectin, and lignin. Lignin is a more rigid polysaccharide that gives strength. It is what makes bark hard, protective, and water resistant.


If the hydrogens (H) bound to the #1 and #4 carbons
up on the same side, the polymer is starch. If they
are on different sides, the polymer is cellulose.
We can digest starch: we can’t digest cellulose.
Plants make both – the part we can’t digest we call
dietary fiber.
Cellulose is made of a chain of glucoses, yet we can’t digest it. The number one carbon in glucose has an –H that is sticking up or down. If the –H sticks “down”, then it is an alpha glucose. If it sticks “up”, then it is a beta-glucose. Cellulose is linked chains of beta-glucose. Starch is linked chains and branches of alpha-glucose. Just that difference in –H position determines if it is food for us or not. Herbivores have the enzymes (and bacteria) to digest cellulose, but not us.

So is it the inclusion of cellulose that makes a plant cell wall unique? Well, no. Algal cells also use cellulose in their cell walls. You might try to argue that algae are plants, since many of them also have chloroplasts and are primary producers – but you would be wrong. Algae can be unicellular (although they can also be multicellular) while plants are all multicellular. Algae don’t have specialized reproductive cells or parts like plants do; algae reproduce by spore or from broken parts of themselves. Finally, DNA analysis shows that while plants and algae are monophyletic (one ancestor), they diverged from one another long ago.

Then there is the issue that not every plant cell has a cell wall. In angiosperms (angio = chest or vessel, and sperm = seed; plants with enclosed seeds and flowers), the gamete (sex) cells of the male in the pollen and the gamete cells of the female in the ovary do not have cell walls, at least not on all sides. The ovary contains the ovules (latin for small egg), and the pollen contains the sperm cells and the tube cell, that forms the pollen tube and delivers the sperms cells to the ovules.

After the ovules are fertilized by the sperm cells of the pollen, the ovules form the seeds, and the ovary forms the fruit. From here on in, all the daughter cells will have cell walls. For fertilization, it would make sense that the involved cells would not have a cell wall that would just get in the way of love.


The Sago Palm isn’t a palm, but is one of the most
primitive plants that reproduces with seeds. It
presents a problem to pet owners because every part
is toxic to pets, but it tastes good to them. They don’t
know not to eat it; then they bleed to death.
And even weirder, not all plants use just this strategy. Cycads (like the sago palm, which isn’t really a palm at all), and gingko biloba plants have sperm cells with flagella, long projections that whip and move them along, hopefully toward an egg cell. They don’t use a tube cell or pollen tube; these plant cells without cell walls swim. Plant cells that move, now there is an exception worth noting! Some more primitive bryophyte plants (liverworts, mosses) also have motile sperm, but the cycads and gingko are the only examples of seed plants with motile cells.

So cell walls aren’t a defining characteristic of plant cells either. Maybe it is the chloroplast that defines a plant cell --- maybe not.

As you can guess, there are exceptions going both ways. There are organisms that have chloroplasts that aren’t plants, namely the algae. But a more interesting exception are many of the protozoan Euglenids. Euglena gracilis is a prototypical euglenid that can produce carbohydrate by photosynthesis. However, most euglenids can also eat things, which makes them both autotrophic and heterotrophic.

As for the other direction, there are many plants that don’t have chloroplasts. Of the roughly 350,000 different species of plants on earth, almost 3000 of them are non-photosynthetic. Therefore, the most common characteristic that people use to tell a plant from a non-plant (photosynthesis by chlorolplasts) isn’t true for almost 1% of the species on Earth. That is a pretty big exception. That would be like saying 1% of people on earth don’t have a brain! O.K., maybe that's a bad example.


Indian Pipe is Monotropa Uniflora. Monotropa means
one turn, and uniflora means one flower. The plant is
called the ghost plant – obvious, or the corpse plant –
because it turns black as it matures. This naming thing
is easy!
Indian pipe (Montropa uniflora, or ghost plant) is one such plant. Related to the blueberry of all things, the ghost plant has gone its own way and become parasitic. It garners its nutrients and energy from the tissue of another plant. The roots of the Indian pipe penetrate the rhizoids (root-like projections) of certain types of fungi and sponge off their hard work. In fact, the fungi themselves are symbiotic, having invaded the roots of certain pine tree species.

The fungus and tree live together in a mutualistic relationship, making the fungus a mycorrhizal (myco = fungus and rrhizal = root) variety. The tree supplies the fungus with carbohydrate, and fungus supplies the tree with mineral nutrients. However, Indian pipe does not respect this mutualism and is a parasite of the fungus, taking some of the carbohydrate supplied by the tree. This makes the Indian pipe a myco-heterotrophic parasite.

Other plants without chloroplasts are holoparasitic (gain nutrients only by parasitism).  These would include the rafflesia species of the Indonesian rainforests. These plants are know for having the largest single flowers in the world, some the size of car tires! The plant doesn’t have a stem or root or leaf, it is a vine that grows inside another type of vine. Only when it is ready to flower does it bud out from the bark of the host. The flower takes nine moths to develop, and then smells like rotting flesh in order to attract fly pollinators.


Rafflesia is also known as the corpse flower, as opposed
to the corpse plant (Indian pipe). This is because it
smells like a corpse in order to attract the flies that
pollinate it. This young man is either holding his breath,
has no sense of smell, or is just really odd.
In addition to holoparasitic plants, plant cells without chloroplasts would include those same gamete cells we discussed above as not having cell walls. And neither to do most root cells. However, there are exceptions, like many of the orchids. The ghost orchid has photosynthetic roots, which is a good idea, since they grow directly on other plants; their roots are not buried in the dirt.

Maybe it is not a single characteristic that makes a plant cell a plant cell, or a plant a plant. Maybe it is the combination of cells with cell walls, central vacuoles and in most cases, chloroplasts that make it a plant. I guess it is like beauty; you can’t define it, but you know it when you see it.

Next week we will take another shot at finding a defining characteristic of plant cells, namely the plastid, the mother of all chloroplasts – might there be an exception?



Mizukami I, & Gall J (1966). Centriole replication. II. Sperm formation in the fern, Marsilea, and the cycad, Zamia. The Journal of cell biology, 29 (1), 97-111 PMID: 5950730

Nikolov LA, Tomlinson PB, Manickam S, Endress PK, Kramer EM, & Davis CC (2014). Holoparasitic Rafflesiaceae possess the most reduced endophytes and yet give rise to the world's largest flowers. Annals of botany, 114 (2), 233-42 PMID: 24942001


For more information and classroom activities on cell walls or parasitic plants, see:

Cell walls –

Parasitic plants -
http://www.gardenbuildingsdirect.co.uk/Article/parasitic-plants 

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 -