Sunday, April 22, 2018

The Demeaning of Life...Chapter 8. Brief Detour Into the World of "What Makes Cells Go"

We have learned to appreciate the complexity and perfection of the cellular mechanisms, miniaturized to the utmost at the molecular level, which reveal within the cell an unparalleled knowledge of the laws of physics and chemistry…. If we examine the accomplishments of man in his most advanced endeavours, in theory and in practice, we find that the cell has done all this long before him, with greater resourcefulness and much greater efficiency.
                          Albert Claude, from his 1974 Nobel Prize lecture[1]

Another installment of “Things We All Should Know About Life,” this one another brief synopsis of the methods cells employ to make life-sustaining energy available in usable forms. Respiration, phosphorylation…photosynthesis, chemiosmosis. These matters are so technical, so abstruse, that to even attempt such an abbreviated picture might well be counterproductive. But these most basic of metabolic processes are not merely representative of how living things work: they are the stuff of life’s true essence. This chapter’s aim is not an attempt to describe or explain these arcane inner workings so much as to lend a sense of the means and methods, the thrifty efficiency and harmonious balancing acts. I have attempted to distill this narrative down to its bare rudiments. This is rich food—the terminology and details will bewilder those unfamiliar with such matters. (For others, those with a semester of organic chemistry or advanced biology some-where in their past, this will perhaps dredge up some painful memories.) Let this account serve as another illustration of the remarkably effective ways and means that life has devised to cope with the bare necessities of subsistence. There is a profound beauty here…an exhibition of nature’s innate genius.[2]
Plants, some algae, and certain kinds of single-celled organisms manufacture their own energy sources using sunlight through the process of photosynthesis and are thus known as photoautotrophs. Their ability to harness “free” solar energy is the backbone that upholds all biological activity.
A much rarer life form produces its own nutrients without benefit of light, carbon, or oxygen. These ancient microbial organisms—called chemoautotrophs—use energy extracted from substances such as hydrogen sulfide, ammonia, or methane by way of anaerobic reactions (that is, in the absence of oxygen). These inorganic geochemical reactions originated with early life forms but are still widely employed by various types of bacteria and primitive bacteria-like microorganisms belonging to a group known as the Archaea, which live in hot springs and even within solid rock. All other organisms—the heterotrophs—are either directly or indirectly dependent on substances produced by photoautotrophs for their sustenance. 
There are two distinct approaches heterotrophs use to derive the energy needed for all their metabolic requirements. Both are based on the transference of electrons during chemical reactions. (In point of fact, all life processes at all levels—cell, organism, ecosystem, biosphere—are driven by the exchange of electrons.) What follows describes metabolic pathways used by eukaryotic organisms.
One of the approaches, employed by the majority of living things, is a form of oxidative metabolism called cellular respiration. In short, cellular respiration consists of exploiting oxygen (a powerful reactant) to break down organic substances, converting them into forms the cell can use. The complete process takes place in three interconnected stages: glycolysis, the citric acid cycle,[3] and the electron transport chain. Each is carried out in a series of enzyme-assisted intermediate steps. This measured strategy ensures that energy is released in small increments in a form that can be stored for later use. (Were the organic fuels oxidized in an unregulated fashion, most of the released energy would be lost to the environment as heat. This is what metabolism is: controlled combustion.) 
A second method—not nearly as effective as respiration—is fermentation, which consists of the partial breakdown of sugars in the absence of oxygen. Fermentation was the principal form of metabolism before the rise of oxygen in the atmosphere. As a means of extracting energy from food, cellular respiration is up to sixteen times more efficient. The energy efficiency of oxidative metabolism is what made multicellularity feasible and, along with the advent of nucleated cells, led to the complexification of life. 
The central figure in bioenergetics is adenosine triphosphate (ATP), a chemically stable substance unequaled in its facility to hold in store energy for future use, much like a minuscule battery.[4] ATP is frequently called the universal energy currency since all known types of life use it to power their metabolic functions. In fact, every recognized variety of cell has been found to contain ATP. Eukaryotic cells make the most of its energy storage capacity, producing large quantities when a rich food source like glucose is available. ATP’s stored potential is liberated by the removal of a single phosphate group, which releases energy and temporarily converts the molecule to adenosine diphosphate (ADP). This form, akin to a depleted battery, is then sent back to the mitochondria for “recharging.” Once there, another phosphate group is added, making it ready for re-use. One molecule of glucose can be converted to between 30 and 32 molecules of ATP. It is produced at astonishing rates: by one estimate, a single cell uses somewhere around ten million (10) molecules per second. At any given moment, our bodies contain only about 60 grams of ATP but the quantity produced, consumed, and replenished in one day’s time amounts to between sixty and a hundred kilograms (132–220 lbs).

Cells get their energy needs through byproducts of the breakdown of organic  matter including proteins, fats, starches…even indigestible substances like cellulose. Many of these substances must first be converted to one or another of the numerous forms of fatty acids and sugars.[5] Foremost among the latter is the six-carbon sugar glucose, a major energy source for most cells. Glucose (CH₁₂O) is a key ingredient in the chemistry of living things. It enters the cell by way of membrane-spanning transport proteins called glucose ports whose binding sites, upon making contact with a molecule of glucose, alter the shape of the protein such that it bodily pivots downward, in effect dragging the glucose through the cell membrane and releasing it into the cytosol.

During glycolysis (the initial stage of respiration), freshly delivered glucose is reduced to two molecules of the three-carbon compound pyruvate. As a preliminary stage, glycolysis liberates less than 25% of the glucose’s potential energy in its reduction to pyruvate. This happens one molecule at a time in the cytosol, in ten separate steps, each of which is assisted by a specific enzyme. The first five steps require energy input (in the form of ATP) but the final five conclude with a significant net energy gain. Pyruvate then passes into the mitochondrial interior space (the matrix) by way of transport proteins similar to glucose ports.

Inside the matrix, pyruvate is reduced in three further steps to acetyl CoA,[6] where this two-carbon compound enters the citric acid cycle. In the course of the citric acid cycle’s eight steps (which are steered by 18 different enzymes and coenzymes), carbon and oxygen are removed as waste products while hydrogen atoms are stripped of electrons. Upon entering the rotation, acetyl CoA is joined to oxaloacetate (the result of the step 8) to produce citrate. Subsequent steps convert citrate back to oxaloacetate and it is oxaloacetate’s eventual regeneration that makes the entire, remarkably energy-efficient process a “cycle.”

During the course of cellular respiration, numerous enzymes (assisted by coenzymes) strip electrons and hydrogen ions[7] from glucose and several other organic intermediates. These are passed to the crucial “carrier molecules,” primarily nicotinamide adenine dinucleotide (NAD+), eventually to be used in the production of ATP. During key steps in both glycolysis and the citric acid cycle, each molecule of NAD+ receives two electrons and one H ion from enzymes. It is this reduced form of NAD+, called NADH, that shuttles its ionic cargo to a series of elaborate catalytic “complexes” embedded in the surface of a mitochondrion’s inner membrane. The entire collection of coordinated nano-scale machinery comprises an electron transport chain. Nick Lane offers further perspective on this remarkable assemblage:

[T]he respiratory chain is organized into four gigantic molecular complexes…. Each complex is millions of times the size of a carbon atom, but even so they are barely visible down the electron microscope. The individual complexes are composed of numerous proteins, coenzymes, and cytochromes…. Curiously, mitochondrial genes encode some of the proteins, while nuclear genes encode others, so the complexes are an amalgam encoded by two separate genomes. There are tens of thousands of complete respiratory chains embedded in the inner membrane of a single mitochondrion.


The protein complexes pass through the membrane but are not physically connected. (Nor are the individual elements of each chain.) Electrons are dispatched from one to the next in line by other types of carrier molecules such that the chains act as minuscule wires. Through a sequence of redox reactions, each step oscillates between a  reduced state and an oxidized state. This scenario is typically represented in terms of a vertical drop: energy being gradually passed on in a downhill “cascade” to successive constituents, each of which has a greater electrochemical affinity for electrons. The exchanges occur spontaneously. At certain junctures, Hions are ejected into the intermembrane space (the area between a mitochondrion’s inner and outer membranes). In the electron transport chain’s final step, an oxygen molecule (O) receives a pair of electrons and also picks up two Hions from the aqueous solution, forming a single molecule of water. Water, along with COproduced during glycolysis and the citric acid cycle, are cellular respiration’s waste byproducts.

Useful energy is released at several steps in the respiratory chain but cells need energy in a stable, transportable form that can be redistributed to various locations, to be used for a wide variety of tasks. Here is where ATP enters my abbreviated portrayal.

A further independent element in the respiratory chain is another membrane-embedded complex called ATP synthase (ATPase for short). Recall that the energy released at each step in the respiratory chain is accompanied at several points by the physical expulsion of H ions across the mitochondrial inner membrane into the intermembrane space. This results in a concentration gradient across the membrane “dam.” Since hydrogen ions bear a positive charge, an electric gradient (in the form of electrochemical potential energy) results as well. The pressure created by this potential is called the proton-motive force; this is what lends ATPase its ability to manufacture ATP. This absolutely vital process is known as chemiosmosis.

Hydrogen ions held within the intermembrane space enter the ATPase complex. The almost beyond-belief sophistication of this matchless nanomachine is sometimes cited by creationists as proof of the existence of God. Nick Lane describes how it works:

ATPase is a marvelous example of nature’s nanotechnology: it works as a rotary motor, and as such is the smallest known machine, constructed from tiny moving protein parts. It has two main components, a drive shaft, which is plugged straight through the membrane from one side to the other, and a rotating head, which is attached to the drive shaft…. The pressure of the proton reservoir on the outside of the membrane forces protons through the drive shaft to rotate the head; for each three protons that pass through the drive shaft, the head cranks by 120°…. There are three binding sites on the head, and these are where the ATP is assembled. Each time the head rotates, the tensions exerted force chemical bonds to form or break. The first site binds ADP; the next crank of the head attaches the phosphate onto the ADP to form ATP; and the third releases the ATP.

The regeneration of ATP through chemiosmosis concludes the process of oxidative phosphorylation (so called because the addition of phosphate to ADP is the final result of a transfer of electrons to oxygen). The enzyme ATP-ADP translocase, abundantly implanted throughout the inner mitochondrial membrane, is responsible for catalyzing the shuttling of those molecules into and out of the matrix. Their flows are said to be coupled (in that ATP does not exit unless ADP enters—and vice versa). ATP, once released into the cytosol, is available for immediate use.

And there you have it. The entirety of the process of respiration, vastly more complex than this brief sketch suggests, is what powers almost all living things. (Prokaryotes, lacking mitochondria to manufacture energy-bearing ATP, follow a somewhat different path: respiration takes place within the cytoplasm, where suites of enzymes and carrier molecules are on hand at all times.) As a metabolic system, cellular respiration is unrivaled, and—from all indications—has undergone but slight modification since its establishment. To draw a parallel: it is as if one of the very first iterations of the internal combustion engine was still in use today, because the original design worked so flawlessly and with such reliability that the Model T engine was never improved upon. But this analogy is faulty in the sense that cars and trucks have been around for little over a century—not for hundreds of millions of years. (Not to mention that they break down with annoying regularity.)


Photosynthesis is an impeccably matched counterpart to oxidative metabolism—each process making use of the other’s waste products to produce energy via an elaborate series of redox reactions. Photosynthesis uses the energy of captured sunlight to make energy-rich sugars. This is made possible by that remarkable substance, chlorophyll, which has the ability to transform solar photons into energized electrons.[8] Chlorophyll is a medium-sized molecule centered around a single atom of magnesium and possessing a long hydrocarbon tail. Once “excited” by photons, grouped chlorophyll atoms initiate a series of enzyme-mediated reactions. These take place via an electron transport chain similar to the one found in cellular respiration, ultimately resulting in the production of sugars. More to the point: photosynthesis converts water and CO (one end-product of respiration) to oxygen and reduced carbon compounds—both of which happen to be required for respiration to proceed. In turn, respiration consumes reduced carbon compounds—mostly sugars—converting them to CO (essential for photosynthesis) and water. Photosynthesis, then, is essentially the reverse of cellular respiration and it is these two entwined processes that together turned a dead planet green. And once greened, Earth’s surface was soon teeming with life.
 By one estimate, each year more than 100 billion metric tons of carbon are incorporated into living organisms through photosynthetic activity. The amount of energy thus sequestered equals around six times the power consumed annually by humanity. Most prokaryotes and virtually all animals live off the products of photosynthesis, either directly or indirectly (as in the case of carnivorous animals that prey on herbivores.) Even chemoautotrophs living around deep-ocean vents are obliquely dependent on sunlight since some of them make use of photosynthetically derived oxygen dissolved in seawater or bits of organic material drifting down from the surface. The exquisite balance of this relationship powers all living things in a mutually beneficial association; it epitomizes the way life always finds ways to satisfy its needs. As is so often the case in nature, there is a paradoxical quality to life’s ways: convoluted and circuitous, they are at the same time artfully straightforward in their thrifty efficiency. 
Photosynthesis takes place inside organelles called chloroplasts. Indicative of their once-independent origins, chloroplasts (like mitochondria) have their own DNA and ribosomes. And, similar to mitochondria, their membranes are studded with ATP synthase complexes that pump protons across an inner membrane to manufacture ATP.
 Photosynthetic prokaryotes, chief among them being the cyanobacteria (formerly known as blue-green algae), have chloroplasts embedded in their plasma membrane. Chloroplasts are born primarily in the leaves of green plants but also in the tissues of stems and unripened fruit. There are around 500,000 chloroplasts contained in a bit of leaf tissue with a surface area of one square millimeter. Chloroplasts are capable of movement: in low light conditions, they orient themselves in sheets to maximize surface area but, under intense light, will seek shelter or align themselves edge-on to the Sun to avoid photooxidative damage. Like mitochondria, chloroplasts are bound by both an inner and outer membrane. Their fluid-filled interior is called the stroma. Suspended in the stroma are interconnected stacks of flattened disks called thylakoids whose outer casing, the thylakoid membrane, holds chlorophyll and various protein complexes and is the actual site of photosynthesis. The individual disk-shaped structures have a fluid-filled interior called the thylakoid space where H ions are kept in reserve. 
Photosynthesis happens in two stages: the light reactions and the Calvin cycle. 

The initial phase revolves around a pair of elaborate molecular light-harvesting elements known as photosystems I and II.[9] The process begins in clusters of up to several hundred individual chlorophyll molecules embedded in a protein complex. When excited by photons, this assemblage functions as an energy-focusing “antenna.” A discrete region in each complex—the reaction center—delivers photoexcited electrons to a specialized molecule called the primary electron acceptor. This is the first step in a photosynthetic version of cellular respiration’s electron transport chain. The first photosystem shunts electrons to the second via this redox reaction chain, providing energy for the chemiosmotic synthesis of ATP during its course. The next photosystem, which gathers energy from light of a slightly longer wavelength, repeats the process: photoexcited electrons are driven from a second reaction center to another primary electron acceptor, which then passes them on via the iron-containing protein ferredoxin to a final enzyme complex. In this terminal reaction, the carrier molecule NADP+ is converted to its reduced form, NADPH.[10]

During an early phase of the light reactions, water molecules were split, releasing H ions into the thylakoid space and O to the atmosphere (as waste). This same water-splitting reaction was the source of two electrons and one proton later used to reduce each molecule of NADP+ to NADPH. Note that energized electrons carried by NADPH, the main reducing agent in chloroplasts, supply the  energy needed to power the second stage of photosynthesis—not sunlight.

This second stage—the Calvin cycle—takes place in the stroma and is similar to the citric acid cycle in that participating components are regenerated after molecules enter and leave the rotation. In the conversion of CO into sugars, the Calvin cycle draws on both ATP and energy from electrons held by NADPH (each produced during the light-dependent reactions). NADP+ is fed back into the photosystems where, as a contributor to the electron transport chain, it is converted back to NADPH. Most of the electron carrying molecules and protein complexes are very similar to those involved in cellular respiration. Chemiosmosis proceeds along similar lines: protons from the electron transport chain are released into the thylakoid space, where there can be a thousand-fold difference in proton concentration on either side of the membrane. This proton concentration gradient drives Hions through ATPase complexes into the stroma. By using the mechanical energy provided by the rotating ATPase shaft to add phosphates to ADP, fresh supplies of ATP are generated.

Photosynthesis is considered to be the single most complex biological process, yet is known to have been fully operative in DNA-bearing, self-replicating organisms at least 3.5 billion years ago—very early in life’s history. This well-established fact is one of the most powerful bits of evidence supporting the Natural Design construct. Biology students, throughout their educations, are taught that this utterly indispensable system, including its seamlessly intertwined association with cellular respiration, is in effect a fortunate “accident” of chemical interactions. Students are repeatedly assured that “somehow” (no one really knows how), the photosynthetic process, along with all its extraordinarily sophisticated molecular machinery, simply “came together,” “one step at a time.” This is the position espoused in virtually all biological literature. As I have asserted more than once, a time will come when young students will be astonished to learn that, as late as the 21st century, such antiquated ideas were still believed.

More to the point: from a position that recognizes life’s innate capacity to craft ingenious, energetically frugal solutions to each of its needs, the notion that these sophisticated solutions arose in some providential (but in the end chance) fashion seems positively ludicrous. Metabolism entails a number of discrete, integrated systems—all acting in unison with neat efficiency, each one subject to elaborate regulatory schemes. Even in their most primitive states, the various systems would have been unable to function below a certain level of complexity. It is difficult to envision how these wonderful biological solutions could have originated. No one has yet seriously attempted to recreate likely pathways in anything more than rough outline; earnest attempts by leading experts are openly admitted to be based on pure surmise. And all such conjectures tend to set aside the thorniest obstacles, relying instead on high-octane optimism.

Given the scientific climate of our time, it is much to ask of any well-educated non-creationist that they stand aside, take in a view of life in all its totality, and see that ultra-complex processes such as photosynthesis and respiration did not simply “come about” through gradual selection over the course of eons. And as I have repeatedly emphasized, we have not yet plumbed how it is that all these things function so flawlessly, nor, in some cases, even precisely how they work. Some of the most ornate processes are understood down to the finest details while their origins remain a complete mystery. So, yes, it is folly to assert that these processes arose in stepwise fashion through the selection of chance alterations to amino acid sequences—something more was driving the courses of development. It is folly, particularly in light of the fact that hundreds of millions of years ago microbes employed many of the same processes that they use today. In other words, most of the bugs and kinks had already been worked out when life was still in its infancy. Some organizing principle was assisting in the coordination of endless mutually-dependent associations. With its assistance, subtle lawful influences helped craft the endless array of protein machines with their myriad specialized capabilities.

 I call this organizing principle Natural Design. It is an inherent and irreducible feature of nature. But it has no name…is certainly not a “thing.” It is not a force, nor is it a process. While scientifically inappropriate, the words that come closest to encapsulating the spirit of what Natural Design represents might be “ineffable influence.” The picture I have been painting all along shows a vibrant, living world that exists by virtue of an exquisite capacity to organize layers upon layers of complexity into one colossal network called the biosphere. (This topic will be the focus of Chapters 10 and 11.) But first, a look at the way Earth, and all the matter and materials that makes up its countless environments, has been found to be an absolutely ideal medium for life.   

 

©2018 by Tim Forsell     draft                        23 Feb 2018

 






[1]From his Nobel Prize lecture, Stockholm, 12 Dec. Quoted in “Cell Traffic,” Calder, 122–23. Albert Claude (1899–1983) was a Belgian medical doctor and cell biologist who discovered the process of cell fractionation, which involved grinding up cells and using a centrifuge to isolate their contents. This led to his discovery of the ribosome and several major organelles.
[2] A little basic chemistry to help illuminate some key details: Bonds between atoms carry an innate potential energy. The potential energy held within chemical bonds, and their resistance to being broken, vary depending upon which elements are involved. The energy released when bonds are broken in the course of chemical reactions can be captured and stored by living things, then put to use to perform work. (In physics, “work” refers to the performance of some task requiring an input of energy.) For this reason, biologists typically do not speak of energy being “generated.” Properly speaking, once liberated by a reaction, energy is conserved by being transferred to special molecules that can release this stored energy on demand. In any reaction, however, energy is lost in the form of heat due to entropy. Many important chemical reactions are based on the exchange of electrons when bonds are broken. These are known as redox (or oxidation-reduction reactions) because they occur in tandem. In a redox reaction, the substance that gives up electrons is said to have been oxidized while the substance receiving those electrons has been reduced. Another way of expressing these roles is to say that the electron “donor” is the reducing agent  while the electron “acceptor” is the oxidizing agent. For example, oxygen is one of the most potent oxidizing agents because, chemically speaking, it has a powerful “hunger” for electrons.
[3] Currently the favored name for the Krebs Cycle (feared by biology students everywhere, such is its daunting complexity).
[4] So named because a single molecule has three phosphate groups attached in line. Energetically, ATP is likened to a “coiled spring;” its phosphate groups (PO₄ˉ), being of like charge, repel one another. This makes it relatively difficult to make ATP but easy to break it apart. This is accomplished in a process that removes one of the phosphates—an energy releasing reaction.
[5] A component of lipids, fatty acids are long-chain hydrocarbons capped on one end by a carboxyl group (COOH). Sugars, rich in high energy bonds, are compounds which typically have chemical formulas based on some multiple of CH₂O.
[6] CoA stands for coenzyme A. Coenzymes are electron-carrying molecules required for the proper functioning of enzymes involved in cellular respiration.
[7] A hydrogen atom consists of a single proton and an electron. Hydrogen ions are solitary protons (designated H⁺).
[8] Chlorophyll is a type of pigment. By definition, pigments are substances that absorb visible light. Different kinds absorb light of differing frequencies; those frequencies not absorbed are reflected. Chlorophyll absorbs light in the red and blue parts of the visible light spectrum and reflects light with wavelengths in the green range, hence its apparent color.
[9] The light reactions actually commence with photosystem II. (This is so because photosystem I was still unknown when photosystem II was discovered.)
[10] NADP+ is similar to NAD+ (the energy-bearing molecule from cellular respiration) but with the addition of a phosphate group.

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