Chapter 1
The basic principles of photosynthetic energy storage

1.1 What is photosynthesis?

Photosynthesis is a biological process whereby the Sun's energy is captured and stored by a series of events that convert the pure energy of light into the free energy needed to power life. This remarkable process provides the foundation for essentially all life and has over geologic time profoundly altered the Earth itself. It provides all our food and most of our energy resources.

Perhaps the best way to appreciate the importance of photosynthesis is to examine the consequences of its absence. The catastrophic event that caused the extinction of the dinosaurs and most other species 65 million years ago almost certainly exerted its major effect not from the force of the comet or asteroid impact itself, but from the massive quantities of dust ejected into the atmosphere. This dust blocked out the Sun and effectively shut down photosynthesis all over the Earth for a period of months or years. Even this relatively short interruption of photosynthesis, miniscule on the geological time scale, had catastrophic effects on the biosphere.

Photosynthesis literally means "synthesis with light." As such, it might be construed to include any process that involved synthesis of a new chemical compound under the action of light. However, that very broad definition might include a number of unrelated processes that we do not wish to include, so we will adopt a somewhat narrower definition of photosynthesis:

Photosynthesis is a process in which light energy is captured and stored by a living organism, and the stored energy is used to drive energy-requiring cellular processes.

This definition is still relatively broad and includes the familiar chlorophyll-based form of photosynthesis that is the subject of this book, but also includes the very different form of photosynthesis carried out by some micro organisms using proteins related to rhodopsin, which contain retinal as their light-absorbing pigment. Light-driven signaling processes, such as vision or phytochrome action, where light conveys information instead of energy, are excluded from our definition of photosynthesis, as well as all processes that do not normally take place in living organisms.

What constitutes a photosynthetic organism? Does the organism have to derive all its energy from light to be classified as photosynthetic? Here, we will adopt a relatively generous definition, including as photosynthetic any organism capable of deriving some of its cellular energy from light. Higher plants, the photosynthetic organisms that we are all most familiar with, derive essentially all their cellular energy from light. However, there are many organisms that use light as only part of their energy source and, under certain conditions, they may not derive any energy from light. Under other conditions, they may use light as a significant or sole source of cellular energy. We adopt this broad definition because our interest is primarily in understanding the energy storage process itself. Organisms that use photosynthesis only part of the time may still have important things to teach us about how the process works and therefore deserve our attention, even though a purist might not classify them as true photosynthetic organisms. We will also use both of the terms "photosynthetic" and "phototrophic" when describing organisms that can carry out photosynthesis. We will usually use photosynthetic to describe higher plants, algae, and cyanobacteria that derive most or all of their energy needs from light, and phototrophic to describe bacteria or archaea that can carry out photosynthesis but often derive much of their energy needs from other sources.

The most common form of photosynthesis involves chlorophyll-type pigments and operates using light-driven electron transfer processes. The organisms that we will discuss in detail in this book, including plants, algae, and cyanobacteria (collectively called oxygenic organisms because they produce oxygen during the course of doing photosynthesis) and several types of anoxygenic (non-oxygen-evolving) bacteria, all work in this same basic manner. All these organisms will be considered to carry out what we will term "chlorophyll-based photosynthesis." The retinal-based form of photosynthesis, while qualifying under our general definition, is mechanistically very different from chlorophyll-based photosynthesis, and will not be discussed in detail. It operates using cis-trans isomerization that is directly coupled to ion transport across a membrane (Ernst et al., 2014). The ions that are pumped as the result of the action of light can be either H+, Na+, or Cl- ions, depending on the class of the retinal-containing protein. The H+-pumping complexes are called bacteriorhodopsins, and the Cl--pumping complexes are known as halorhodopsins. No light-driven electron transfer processes are known thus far in these systems.

For many years, the retinal-based type of photosynthesis was known only in extremely halophilic Archaea (formerly called archaebacteria), which are found in a restricted number of high-salt environments. Therefore, this form of photosynthesis seemed to be of minor importance in terms of global photosynthesis. However, in recent years, several new classes of microbial rhodopsins, known as proteorhodopsin, heliorhodopsin, and others, have been discovered (Béjà et al., 2000; Pushkarev et al., 2018; Inoue et al., 2020). Proteorhodopsin pumps H+ and has an amino acid sequence and protein secondary structure that are generally similar to bacteriorhodopsin. The proteobacteria that contain proteorhodopsin are widely distributed in the world's oceans, so the rhodopsin-based form of photosynthesis may be of considerable importance. Recent evidence suggests that the proteorhodopsins are responsible for a significant amount of primary productivity in the ocean (Gómez-Consarnau et al., 2019).

As mankind pushes into space and searches for life on other worlds, we need to be able to recognize life that may be very different from what we know on Earth. Life always needs a source of energy, so it is reasonable to expect that some form of photosynthesis (using our general definition) will be found on most or possibly all worlds that harbor life. Photosynthesis on such a world need not necessarily contain chlorophylls and perform electron transfer. It might be based on isomerization such as bacteriorhodopsin, or possibly on some other light-driven process that we cannot yet imagine (Kiang et al., 2007a, b; Schweiterman et al., 2018).

1.2 Photosynthesis is a solar energy storage process

Photosynthesis uses light from the Sun to drive a series of chemical reactions. The Sun, like all stars, produces a broad spectrum of radiation output that ranges from gamma rays to radio waves. The solar output is shown in Fig. 1.1, along with absorption spectra of some photosynthetic organisms. Only some of the emitted solar radiation is visible to our eyes, consisting of light with wavelengths from about 400 to 700?nm. The entire visible range of light, and some wavelengths in the near infrared (700-1000?nm), are highly active in driving photosynthesis in certain organisms, although the most familiar chlorophyll a-containing organisms cannot use light with a wavelength longer than 700?nm. The spectral region from 400 to 700?nm is often called photosynthetically active radiation (PAR), although this is only strictly true for chlorophyll a-containing organisms. Recently, some oxygenic photosynthetic organisms that utilize radiation outside the PAR region have been discovered. These are discussed in detail in Chapters 2 and 7.

Figure 1.1 Solar irradiance spectra and absorption spectra of photosynthetic organisms. Solid curve: intensity profile of the extraterrestrial spectrum of the Sun; dotted line: intensity profile of the spectrum of sunlight at the surface of the Earth; dash-dot line: absorbance spectrum of Rhodobacter sphaeroides, an anoxygenic purple photosynthetic bacterium; dashed line: absorbance spectrum of Synechocystis PCC 6803, an oxygenic cyanobacterium. The spectra of the organisms are in absorbance units (scale not shown).

The sunlight that reaches the surface of the Earth is reduced by scattering and by the absorption of molecules in the atmosphere. Water vapor and other molecules such as carbon dioxide absorb strongly in the infrared region, and ozone absorbs in the ultraviolet region. The ultraviolet light is a relatively small fraction of the total solar output, but much of it is very damaging because of the high energy content of these photons (see Appendix for a discussion of photons and the relationship of wavelength and energy content of light). The most damaging ultraviolet light is screened out by the ozone layer in the upper atmosphere and does not reach the Earth's surface. Wavelengths less than 400?nm account for only about 8% of the total solar irradiance, while wavelengths less than 700?nm account for 47% of the solar irradiance (Thekaekara, 1973).

The infrared wavelength region includes a large amount of energy and would seem to be a good source of photons to drive photosynthesis....