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.
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 (C₆H₁₂O₆) 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, H⁺ ions
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 (O₂) receives a pair of electrons and also picks up
two H⁺ ions from the aqueous solution, forming a single
molecule of water. Water, along with CO₂ produced 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 CO₂ (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 CO₂ (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.
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.
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 O₂ 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 CO₂ 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 H⁺ ions
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.
