Cells, enzymes, and the secret of DNA

Posted on August 13th, 2008 in biology by paphinessorchids

Most people have a good idea of what a cell is.  If you need more background, you can look here.

Here’s my working definition: A cell is a self-contained unit filled with everything it needs to make a copy of itself and do a specific job (assuming it’s part of another organism).  Inside the cell are armies of what I’ll call “molecular machines” that perform various chemical reactions.

Biology is a bit like quantum mechanics, in a way.  In quantum mechanics, if you keep peering deep enough, you’ll find that your “real world” intuition falls apart.  Stuff gets weird and counter-intuitive, and all kinds of oddly named particles get involved.

In biology, an analogous strange situation holds.  A useful word to keep in mind here is “swarm”.  Each bee in a swarm chasing you is the same as every other bee and they have one unifying goal — driving their stingers into your flesh.  A cell is full of multitudes of different swarms, each composed of identical molecules(*).  Every molecule in a collective swarm seeks to do its specific job (usually some specific chemical reaction).  The way things get done in this dance of swarms is by, believe it or not, bumper car-like collision.  Yep, what we observe as the exquisite and astonishing organization of living things derives from intersecting swarms of molecules colliding and reacting with other swarms(**) of molecules.  Absolutely amazing.

So what is an enzyme?  I’ll probably cover this in more detail on some other slow news day, but for now, suffice to say that enzymes are biological molecules — molecular machines –  designed to do a specific job.  Slap a methyl group on here, chop a hydroxy group off there, string some nucleotides, shred RNA, make ATP; all of these and myriad others performed by specific enzymes at specific times and places.

Enzymes pretty much do the work of the cell.  They are the worker bees, the factory workers on the floor, the office drones in the giant bureaucracy.  And the work of the cell is chemistry: chemical bonds synthesized and broken, on and on, propelled forward by the light of the sun.

So how does the cell “know” how to make enzymes?  Ahh, that’s the secret.  Well, it’s no secret, really, just that most folks get confused and intimidated by all the scientific terminology.  Here it is:

The DNA is the blueprint/the software/the plans for making enzymes.

That’s pretty much DNA’s main job, acting as the cell’s how-to manual for making the molecular workers that do the jobs inside a cell.  In orchids (and all plants), there are enzymes that make pigments, enzymes that fix DNA, enzymes that make cellulose, enzymes that destroy other enzymes, and enzymes that monitor the passing of the seasons.

And that brings us back to my original subject: what happens when you let a plant “rest”.  That’s the subject for my next post…

(*) OK, so what’s a molecule?  I think of a molecule as a grouping of atoms that has unique characteristics.

(**) The swarm analogy breaks down when you notice that enzyme molecules, unlike bees, don’t have brains.  They simply collide with other molecules.

What happens when your plants “rest”

Posted on August 12th, 2008 in biology by paphinessorchids

If you’ve been growing orchids for awhile, you’ve probably heard that some plants need to rest from growing during the winter (or other season).

I’ve always found this to be puzzling advice. Plants, like all biological life(*), are made up of cells. Think of a cell as an autonomous factory capable of taking care of nearly all of its own needs. As long as the raw materials are present, and it is not irreparably damaged, and it is getting the green light from whatever other cell might be bossing it around(**), it can continue to grow, repair itself, and pretty much do whatever it was designed to do.

One thing that most cells like to do is replicate themselves. You’ve probably heard of cell division (a.k.a. mitosis). Cell division is how living things grow. You start with one cell, which divides into two, then into four, and so on, and so on, and so on. Of course, at some point, some cells stop dividing according to the organism’s genetic program.

But why should a plant need a seasonal “rest”? What is it resting from?

Take us humans, on the one hand… We get up, eat, drink, sleep, reproduce (or try to). Our cells churn away making energy for all of those important activities we engage in day to day. They also divide so that we grow and repair ourselves. But our bodies do wear out, and in our cells, after each cell replication, a small chunk of DNA gets lopped off the end; past a certain point, the cell just dies. It’s the cell’s way of marking time. Hopefully we get to reproduce before that genetic clock shuts us down.

On the other hand, an orchid plant’s job is pretty much to grow, and look attractive (whether to bug pollinators or society judges, both justifiably regarded as pests in certain circles). If the plant has light, water, carbon, nutrients, etc., it ought to be able to simply keep growing, pretty much forever.

So why do orchid plants need a rest? Why is it that many growers claim that you need to keep your plants from growing themselves to death?

Well, this post looks like it’s going to be much longer than I thought, since we’ll need to talk about cells and enzymes first…  And that will be the subject of my next post.

(*) I’m not entering the debate on whether viruses, either biological or digital, are “alive”. That idea has been argued to death elsewhere (no pun intended).

(**) Yes, even cells have bosses ordering them around. Sometimes many different bosses.

How orchid seeds germinate

Posted on August 11th, 2008 in biology by paphinessorchids

It’s quite easy to pollinate a slipper orchid. Obtain pollen from the pollinating plant on the flat end of a toothpick, and then spread on the pollinating surface behind the staminode.

Wait 6 - 12+ months until you obtain seed, and then plant the seeds in an appropriate place. If you’re in the jungle, probably just letting the wind blow the seed away will work well enough, since that’s exactly what happens in nature. One seed pod can produce many thousands of seeds on a good cross — the vast majority never make it, but enough do that the species can continue.

Before the development around 1920 of chemically defined, sterile laboratory based media (looks like white or black Jello) for orchid seed germination, orchid cultivators would sprinkle paph seeds onto the media surface around the base of the parent plant. A few seeds would germinate, and result in plants that would put out leaves, grow roots, and follow the natural cycle of plant development. I haven’t tried this myself yet, but it’s definitely on my list of experiments.

Seeds of other plants ranging from trees to carrots to beans all carry their own energy storage in the form of starch. Orchid seeds, on the other hand, do not carry their own energy storage resulting in extremely fine, dust-like seeds easily carried by the wind. While the orchid plant is still just a seed without leaves to photosynthesize for energy, the seed gets its energy from fungi called mycorrhizae. While mycorrhizae is not a household term, these microbes are probably one of the most important fungi on the planet (more on these in a future post) since they are intimately involved in plant growth just about everywhere.

Mycorrhizae provide the initial sugar the orchid seeds need to germinate. The fungi enters into a symbiotic relationship with the orchid seed, producing sugar for the orchid seed to grow leaves and roots. In exchange, the developing orchid plant produces substances which the mycorrhizae uses for its own growth. Once the plant puts out leaves, it can begin photosynthesis and produce its own energy although the mycorrhizae continue to play an important role. And that’s something we’ll look at in a future post.