Dr. Steven Griffiths Monthly Column, published in the Times & Transcript

Examining the building blocks of life

Tuesday April 15, 2008

Early in life, my intrigue in a community of microscopic pond monsters eventually led to the realization that each was made of smaller communities, communities of cells. I had no idea I was only on the outermost edge of a downward spiral into an education in the fundamental pieces of life. For now, let's start with something I know a particle about and work our way down as far as we can without getting a nose bleed.

Inside each cell there is yet another layer of complexity: proteins. The proteins are made up of 20 different building blocks called amino acids. The order in which these building blocks are put together is inscribed on a spaghetti shaped instruction manual called DNA. The entire manual is found in all cells of a single creature and has the recipes for every single protein that any cell might need. Each recipe is presented as code for the order of amino acids that need to be stuck together to make an individual protein.

If unraveled this cellular taffy would be six feet long -- not bad for something loosely bundled into one millionth of a millimeter.

DNA has a basic shape like one-sided barbed wire with four different types of saucers sticking out where the pointy bits should be. It is the order of the four different saucers along the barbed wire that determines which building blocks are incorporated into the protein.

The DNA might be thought of as a very long recipe book written on ticker tape in braille. The braille of DNA, however, is multi-dimensional and only allows other molecules of a certain shape, static charge or magnetism to interact and "read" specific recipes. Depending on which part of the body the cell is in, only some of the recipes will be read by the proteins.

Some proteins are whipped up from the DNA recipe book in all cells (individually or combined). These universally required proteins maintain the shape of the cell by acting as rigid nanoscopic girders and scaffolding. Other common proteins generate energy by the stock piling and release of bits of hydrogen atoms called protons (not proteins).

Other more specialized proteins shift and wobble on the surfaces of the cell on a lipid membrane, what one might imagine as a shimmering, humming sea of tiny oil droplets. If we were able to see them, these surface proteins might remind us of half-submerged jelly fish assuming the shapes of catcher's mitts and spiky cacti. These are the receptor proteins that receive signals released by other cells. The signals might consist of single proteins that fit into the pocket of the mitt or get caught on the spines of the cacti. Alternatively, similar proteins might coat miniature bubbles known as microvesicles.

The microvesicles are continuously being pinched off from all cells and are carried away in the fluid of a body cavity or a blood vessel. The proteins on the surface of this “bubble-mail” determine which cellular address get the mail by selecting the complementary combination of mitts and cacti on the surface of all possible recipients: it could be a private message or it could be bulk depending on the types of interlocking cacti and jelly fish that recognise them. Once the right mailbox is identified, the bubble mail can be adsorbed inside the recipient cell, bearing news from other parts of the body, details on the microscopic weather and suggestions for looking up new protein recipes where necessary.

This method of communication and interaction also ensures appropriate bits developed either in the babies of my little pond monsters or my own (shown in the accompanying picture taking after his old man).

In a manner similar to the bubble mail concept, surface proteins and protein signals permit jack-of-all trade stem cells to shuffle over one another until they're in the right position. In this instance, instead of catcher's mitt-cacti-jelly fish we might think of such surface proteins as 101 types of molecular Velcro that can schlep and schlopp around until everything is in the right place. The cell community becomes a body and it's time to move around to get some nosh and some nookie.

Yes, nookie. The prime objective of all this malarkey is the protein-driven cell communities must ensure as many copies of it are left behind as possible, albeit with a soupçon of variety. The variety arises from subtle, generally innocuous, biological typos that the proteins make copying the DNA instruction book that gets passed onto the nippers. The typos overlooked by the copying, proofreading and buffering proteins leave an element of chance to simmer away -- barely perceptible kinks and bumps in the shape of one or more proteins that generally don't have any noticeable effect.

Under certain conditions, however, a certain collection of stealthily hoarded new shapes might allow a better way of getting around, consume more or different nosh, get better at nookie or be more able to withstand the weather (from drizzle to that caused by Moncton-sized meteors).

How this happens, and how this process may be sped up and ultimately explain the existence of cancer, we'll deal with later. For now we'll accept that, in the end, from the perspective of the universe, success means leaving more copies behind and in more places. While on paper, our species may have reached the point of where we won't grow beaks, gills or develop any other appendages or spectacular X-Men type abilities, our current level of protein interactions are getting us to the point where we can co-exist as tribes of cell communities. Not beaks and gills then, but increasing the capabilities those proteins have already endowed us with: reason, wisdom and communication.

Notwithstanding the beauty of the other collections of proteins that surround us or the creative legacy left by our species, our development is more often marked by attrition than spiritual evolution. You know this by reading of the constant and monumentally cretinous sources of misery reported in the media if not the stupefaction that we need to know that Ashton Kutchner is not yet ready to be domesticated. Once we’ve figured this all out, then we can get down to the business of leaving more copies of ourselves on places other than the apple skin of our planet, inward or outward. It is inevitable. The way we’re going to figure that out though will involve the topic that I’ve been desperately trying to avoid and will tip toe over in the next column: that every thing that you sense or create an impression upon, every thing, whether it is gravity, moonlight, a Heineken, the beach or indeed Ashton Kutchner, will ultimately be based on a single bit of something. See you soon.

Article as published:
http://timestranscript.canadaeast.com/news/article/268316

n Dr. Steve Griffiths is a researcher at the Atlantic Cancer Research Institute in Moncton. His column, the Science of Life, appears in this section on the third Tuesday of each month.

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(Published in Times & Transcript)