Friday, February 9, 2007

127)No. 7: Ayats(Signs) in the Universe series. How are proteins made inside living cells and what does this have to do with religion?

I have always been fascinated by proteins. Commonly called the workhorses of living cells, proteins exist and operate in every nook and cranny of living systems. Amazingly, the function of a protein is totally determined by its 3-dimensional shape and orientation in space. This 3-dimensional shape of a protein, in turn, is determined totally by the precise sequence of amino acids, the building blocks of a protein, that make up the protein. The unique set of electrostatic forces engendered by the unique sequence of amino acids making up a protein determine the ultimate shape and 3-dimensional structure of the protein. How does this precisely-determined linear sequence of amino acids come about?

It turns out that the sequence of amino acids that makes up a protein is determined from a coded sequence of information in a master molecule called DNA, the molecule of heredity. Linear sequences of code, themselves made up of unique molecules within the DNA macromolecule, which resides inside the nucleus of a living cell, are copied onto a molecule called messenger RNA, which then travels from the nucleus into the main part or cytoplasm of the cell. There it links up with a large molecular complex called a ribosome. Another type of RNA molecule, called transfer RNA, of which there are about 21 or so types, each ready and attached to its own specific amino acid, are then summoned to the messenger RNA-ribosome complex, and deposit their amino acids based solely on the coded information given to the single-stranded messenger RNA molecule by the DNA master molecule in the nucleus. This process is all the more remarkable by virtue of the fact that it is a submicroscopic process and therefore invisible to the naked eye. In a previous blog(no. 29 on my blogsite) I opined in mind-boggling fascination about how an entity as small as a living cell could have so many moving parts.

That proteins are called workhorses is no exaggeration. The sequence of protein synthesis as described above occurs ubiquitously in every type of cell in the human body, animals, plants and microorganisms like bacteria, but not in viruses. As I showed in blogpost no. 41 in talking about the HIV/AIDS virus, viruses have the genetic information to make more of themselves but lack the cellular machinery to carry out the process. They instead behave like pirates, breaking and entering into a human or other cell, commandeering its cellular apparatus to create more copies of themselves, then killing the hapless cell they just abused. As far as workhorsing goes, if a protein is made inside a stem red blood cell in the bone marrow, it becomes a hemoglobin molecule. 4 chains of these protein molecules link up with an iron atom in the center and this rapidly-moving bloodstream protein complex seizes oxygen from the air at an interface in the lungs and rapidly releases it to tissues all over the body, then takes carbon dioxide from the tissues back to the lungs to release into the air, then repeats the sequence. A protein from another blood stem cell becomes an antibody whose amino acid sequence creates a pincer-shaped molecule capable of neutralizing an invading bacteria, virus or other microorganism. Another protein, called an enzyme, made in a liver cell, can create or break down cholesterol molecules: how well it does this can determine whether or not we need to take the famous 'statin' tablets to lower our blood cholesterol. Other proteins like those made in the skin cells of our scalps end up being the hair we have on our heads; proteins and RNA made in brain cells are involved in creating and storing our memories; a structural protein can straddle the inside and outside of a cell membrane and serve a transportation function, where it pumps certain atoms or ions into and out of cells as part of their daily critical life processes. There are numerous and fascinating examples of the multiple functions that proteins perform. It is safe to say that life can absolutely not exist without proteins.

In putting an Ismaili Muslim spin on this crucial ayat or sign in nature I am reminded about the many rites and ceremonies carried out in Jamatkhana. Every one of these has a symbolic significance when performed, whether it is the sipping of holy water('niaz') or the eating of a morsel of substance prepared from specific ingredients('sukreet'), or the auctioning off of a food offering('nandi'). Likewise in the big Jamatkhana of the Universe, every object, event, ayat or sign has a symbolic significance as we have been told in farmans by our Imams, in ginans by our Pirs and in treatises by our cosmologist-philosopher-theologians of yesteryear. What, then, to make of the ubiquitous and enthralling ayat of protein synthesis?

A protein made up of a specific amino acid sequence initially lies flat on its back. Electrostatic forces then come into play and suddenly, like a phoenix, the protein stands up and assumes a unique 3-dimensional shape and structure based on its amino acid sequence. The protein as it stands represents microcosmically the multidimensional universe in which we live, move and have our being. We know and understand for sure that the protein is shaped the way it is only because of the unique sequence of its amino acid structure. However, in order to truly understand the protein, we have to look at the master molecule of DNA that exists at the geographical center(literally) of that protein's universe, the molecule solely responsible for giving that protein its structure and, therefore, its function. The master DNA macromolecule is, in a very real way, the celestial essence of that mutidimensional protein. In order to truly understand and gain knowledge about that protein, we need to search for, and find, its essence.


Islam, eminently logical, placing the greatest emphasis on knowledge, purports to understand God's creation:Aga Khan 4.
The God of the Quran is the One whose Ayats(Signs) are the Universe in which we live, move and have our being:Aga Khan 3