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Basic Biochemical Roots

Dietrich H. Nies

Overview

How does life function? This chapter starts explaining the thermodynamics of life, shows that living entities are no exceptions from the important laws of thermodynamics, and derives the physical and chemical constraints of the life process from here. Moreover, the basics of energy transduction, the four most important classes of cellular macromolecules, the necessity of a semipermeable membrane, the chemical components and solvents of life are introduced.

s1.1 Chemistry and Physics of Life

s1.1.1 Thermodynamics of Life

Every year in spring the wonder happens. When the temperature turns milder, flowers explode from seeds or bulbs in the ground, and leafs appear on bushes and trees. On first glance, order seems to be spontaneous. However, this spontaneous appearance of order is against the laws of thermodynamics. Therefore, people thought in previous times that this appearance of order in living organisms was allowed by a special “life force.”

The word “thermodynamics” comes from Greek “thermós” = warm and “dynamis” = power. The principles of thermodynamics were formulated in the eighteenth century to improve the efficiency of steam engines, which were in fact already known as aeolipiles by the Greek engineer and mathematician Hero of Alexandria (about 10–70 AD). James Watt (1736–1819) pioneered a major improvement of the steam engine in the eighteenth century but many other scientists, such as Otto von Guericke, Robert Boyle, Robert Hooke, Joseph Black, Sadi Carnot, and William Rankine, also performed experimental work that led to the development of the principles of thermodynamics. This paved way for the industrial revolution in Europe and elsewhere, with all its social and political consequences.

The first law of thermodynamics states that energy cannot be created or destroyed. It is just that one form of energy can be transformed into another form of energy. This may be an unwelcome fact in times of high prizes for fuel; however, a spontaneous loss of energy would allow disappearance of matter such as this book or even its reader. Taking this aspect into account, the first law of thermodynamics makes our universe a much safer place.

The two other laws have to do with entropy, which means “disorder.” The second law states that a process occurs spontaneously only if the entropy of the respective system increases. A writing desk in an office is a good illustration of this principle, children's rooms are even better ones. The third law indicates that a system cannot be transferred into a state that does not contain any energy because it would have no entropy under these conditions. As a consequence, a temperature of 0 K cannot be reached. So, how do plants that sprout in spring especially cope with the second law of thermodynamics? A spontaneous appearance of order should not be allowed.

Box s01.1: The growth rate of a cell depends on its radius

The energy needed for growth Eg depends on the mass m of the cell, which is connected to its volume V by the density of living matter, ρ = m/V. For a sphere-like cell, its volume calculates from its radius V = 4/3 π·r3 and, therefore, is Eg proportional to ρ·4/3·π·r3. The flow of energy is a power (Energy/time) in terms of physics and depends on the surface of a cell (A = 4·π·r2). Some of the energy that is being transformed per time unit has to be continuously used for the maintenance energy, so some maintenance power Pm is always needed. The power available for growth is the power taken up Pup minus maintenance power Pm. Therefore, the growth rate of a living cell μ is directly proportional to (Pup–Pm)/Eg: μ = a·(Pup–Pm)/Eg = a(b·A–Pm)/(c·m) = a(b·4·π·r2–Pm)/(c·ρ·4/3·π·r3) = (a·b·4·π·r2–a·Pm)/(c·ρ·4/3·π·r3) = (a·b·4·π·r2)/(c·ρ·4/3·π·r3)–(a·Pm)/(c·ρ·4/3·π·r3) = (a·b·3)/(c·ρ·r)–(a·Pm)/(c·ρ·4/3·π·r3) = (a·b·3)/(c·ρ·r)–(a·Pm)/(c·ρ·4/3·π·r3) = 3ab/(cρ) r−1–3a/(4πcρ). Pm·r−3 = k1·r−1–k2·Pm·r−3 with k1 = 3ab/(cρ), k2 = 3a/(4πcρ), and unknown constants a,b,c. Because under most circumstances k1·r−1 k2·Pm·r−3 the result is μ = k1·r−1.

This contradiction was explained by Erwin Schrödinger (1887–1961) in his famous lecture “What is life?” delivered at Trinity College, Dublin, in February 1943 and published in 1944 for the first time. This lecture connects biology firmly to chemistry and physics by showing that life also obeys thermodynamics, and it was one of the theoretical foundations of modern molecular biology.

Life is a chemical process that is essentially connected to compartments separated from their environment, cells. These cells have to take up energy continuously to keep their state of order within, named “negentropy” by Schrödinger. To cope with the second law of thermodynamics, cells compensate the increase of order inside by a stronger decrease of order outside the cell. So, the decrease of the entropy inside is overcompensated by the increase of the entropy outside. Defined as one system, cells and their environment continuously enhance the entropy, following the second law of thermodynamics but allowing an increase of order inside the cell at the same time. This process can be driven by external energy or energy forms previously stored (Figure s1.1).

Figure s1.1 What is life? To build order inside an organism, cells continuously use energy to decrease the intracellular entropy (or increase the intracellular negentropy = order) and overcompensate this by increasing the entropy in the environment by the release of waste products and heat. Thus, in the total system composed of a cell and its environment, the entropy increases steadily during the chemical reactions in a cell, and the second law of thermodynamics is kept. Energy can be light energy or chemical energy (see Section S1.2). Intracellular order means macromolecules. (Earth photo: Courtesy of NASA.) (Graphics: D. Dobritzsch.)

Very important, these compartments, the cells, are needed to make a difference between the state of order inside and outside. The exact phrasing of this connection by Schrödinger was “Thus a living organism continually increases its entropy – or, as you may say, produces positive entropy – and thus tends to approach the dangerous state of maximum entropy, which is of death. It can only keep aloof from it, i.e. alive, by continually drawing from its environment negative entropy – which is something very positive as we shall immediately see. What an organism feeds upon is negative entropy.” Thus, during the chemical life process, energy is turned into negentropy and all cells are continuously extracting order from their environments (Figure s1.1).

s1.1.2 The Three Levels of Energy Transformation in Living Cells

The transformation of energy into negentropy by living cells happens on three different time levels. First and as quoted above, continuous transformation of energy from the outside or previously stored energy is essential to keep a cell from dying. The amount of energy needed to be kept alive is the maintenance energy, maintenance energy divided by time the maintenance power. The latter is the minimum energy flow needed by a cell to survive. Some organisms, such as autochthonous microorganism, are specialized to survive at a very low maintenance power.

Second, if more energy can be taken up from the environment than needed for maintenance, cells are allowed to grow and divide when they too are big. The growth rate of a cell depends on a constant divided by the radius (half of the diameter) of a cell (Box S1.1). Thus, a cell with a diameter of 1 µm can divide 10 times more rapidly than a cell with a diameter of 10...