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Light Energy and Pigments
The sun emits an enormous amount of electromagnetic radiation (solar energy) that spans a broad swath of the electromagnetic spectrum, the range of all radiation frequencies. When solar radiation reaches Earth, a fraction of this energy interacts with and may transfer to the matter on the planet. In BIS2A, we
First, however we need to refresh a few key properties of light:
- Light in a vacuum travels at a constant speed of 299,792,458
m/s. We often abbreviate the speed of light with the variable " c".
- Light has properties of waves. A specific "color" of light has a characteristic wavelength.
We refer to the distance between peaks in a wave as the wavelength and abbreviate it with the Greek letter lambda (Ⲗ). Attribution:
The inverse proportionality of frequency and wavelength. Wave 1 has a wavelength that is 2x that of wave 2 (Ⲗ1 > Ⲗ2). If the two waves are traveling at the same speed (c)—imagine that both of the whole lines that are dragged past the fixed vertical line at the same speed—then the number of times a wave peak passes a fixed point is greater for wave 2 than wave 1 (f2 > f1). Attribution: Marc T. Facciotti (original work)
3. Finally, each frequency (or wavelength) of light is associated with a specific energy. We'll call energy "E". The relationship between frequency and energy is:
[E = h imes f]
where h is a constant called the Planck constant (~6.626x10-34 Joule•second when frequency is expressed in cycles per second). Given the relationship between frequency and wavelength, you can also write E = h*c/Ⲗ. Therefore, the larger the frequency (or shorter the wavelength), the more energy is associated with a specific "color". Wave 2 in the figure above is associated with greater energy than wave 1.
The sun emits energy in the form of electromagnetic radiation. All electromagnetic radiation, including visible light, is characterized by its wavelength. The longer the wavelength, the less energy it carries. The shorter the wavelength, the more energy is associated with that band of the electromagnetic spectrum.
The Light We See
The visible light seen by humans as white light is composed of a rainbow of colors, each with a characteristic wavelength. Certain objects, such as a prism or a drop of water, disperse white light to reveal the colors to the human eye. In the visible spectrum, violet and blue light have shorter (higher energy) wavelengths while the orange and red light have a longer (lower energy) wavelengths.
The colors of visible light do not carry the same amount of energy. Violet has the shortest wavelength and therefore carries the most energy, whereas red has the longest wavelength and carries the least amount of energy. Credit: modification of work by NASA
Absorption by Pigments
The interaction between light and biological systems occurs through several mechanisms, some of which you may learn about in upper division courses in cellular physiology or biophysical chemistry. In BIS2A, we concern ourselves mostly with the interaction between light and biological pigments. These interactions can start a variety of light-dependent biological processes that can be grossly grouped into two functional categories: cellular signaling and energy harvesting. Signaling molecules perceive changes in the environment (in this case, changes in light). An example of a signaling interaction might be the interaction between light and the pigments expressed in an eye. Light/pigment interactions that are involved in energy harvesting are used for—not surprisingly—capturing the energy in the light and transferring it to the cell to fuel biological processes. Photophosphorylation, which we will learn more about soon, is one example of an energy harvesting interaction.
Possible NB Discussion Point
Photophosphorylation is a process involving an electron transport chain that allows organisms to harvest energy from light. Some of you may already be familiar with this process. Many of you are learning about this for the first time. Given your current knowledge base, offer your best explanation or hypothesis as to how light interacts with the ETC. You will have a chance to revisit this topic very soon.
At the center of the biological interactions with light are groups of molecules we call organic pigments. Whether in the human retina, chloroplast thylakoid, or microbial membrane, organic pigments often have specific ranges of energy or wavelengths that they can absorb. The sensitivity of these molecules for different wavelengths of light is due to their unique chemical makeups and structures. A range of the electromagnetic spectrum is given a couple of special names because of the sensitivity of some key biological pigments: The retinal pigment in our eyes, when coupled with an opsin sensor protein, “sees” (absorbs) light predominantly between the wavelengths between of 700 nm and 400 nm. Because this range defines the physical limits of the electromagnetic spectrum that we can actually see with our eyes, we refer to this wavelength range as the “visible range”. For similar reasons, as plants pigment molecules tend to absorb wavelengths of light mostly between 700 nm and 400 nm, plant physiologists refer to this range of wavelengths as "photosynthetically active radiation".
Three Key Types of Pigments Commonly Discussed in General Biology
Chlorophylls (including bacteriochlorophylls) are part of a large family of pigment molecules. There are five major chlorophyll pigments named: a, b, c, d, and f. Chlorophyll a is related to a class of more ancient molecules found in bacteria called bacteriochlorophylls. Chlorophylls are structurally characterized by ring-like porphyrin group that coordinates a metal ion. This ring structure is chemically related to the structure of heme compounds that also coordinate a metal and are involved in oxygen binding and/or transport in many organisms. We distinguish different chlorophylls from one another by different "decorations"/chemical groups on the porphyrin ring.
The structure of heme and chlorophyll a molecules. The common porphyrin ring is colored in red. Facciotti (original work)
Carotenoids are the red/orange/yellow pigments found in nature. They are found in fruit—the red of tomato (lycopene), the yellow of corn seeds (zeaxanthin), or the orange of an orange peel (β-carotene)—which serve as biological "advertisements" to attract seed dispersers (animals or insects that may carry seeds elsewhere). In photosynthesis, carotenoids function as photosynthetic pigments. In addition, when a leaf is exposed to full sun, that surface is required to process an enormous amount of energy; If that energy is not managed properly, it can do significant damage. Therefore, many carotenoids help absorb excess energy in light and safely dissipate that energy as heat.
Flavonoids are a very broad class of compounds that are found in great diversity in plants. These molecules come in many forms but all share a common core structure shown below. The diversity of flavonoids comes from the many combinations of functional groups that can "decorate" the core flavone.
The core ring structure of flavans.
Each type of pigment can be identified by the specific pattern of wavelengths it absorbs from visible light. We define this characteristic as the pigment's absorption spectrum. The graph in the figure below shows the absorption spectra for chlorophyll a, chlorophyll b, and a type of carotenoid pigment called β-carotene (which absorbs blue and green light). Notice how each pigment has a distinct set of peaks and troughs, revealing a highly specific pattern of absorption. These differences in absorbance are because of differences in chemical structure (some of these are highlighted in the figure). Chlorophyll a absorbs wavelengths from either end of the visible spectrum (blue and red), but not green. Because chlorophyll reflects green light and absorbs other wavelengths of light, things containing this pigment appear green. Carotenoids absorb in the short-wavelength blue region and reflect the longer yellow, red, and orange wavelengths.
(a) Chlorophyll a, (b) chlorophyll b, and (c) β-carotene are hydrophobic organic pigments found in the thylakoid membrane. Chlorophyll a and b, which are identical except for the part indicated in the red box, are responsible for the green color of leaves. Note how the small amount of difference in chemical composition between different chlorophylls leads to different absorption spectra. β-carotene is responsible for the orange color in carrots. Each pigment has a unique absorbance spectrum (d).
Importance of having multiple different pigments
Not all photosynthetic organisms have full access to sunlight. Some organisms grow underwater where light intensity and the number of wavelengths decrease and change, respectively, with depth. Other organisms grow in competition for light. For instance, plants on the rainforest floor must be able to absorb any bit of light that comes through because the taller trees absorb most of the sunlight and scatter the remaining solar radiation. To account for these variable light conditions, many photosynthetic organisms have a mixture of pigments whose expression they can tune to improve the organism's ability to absorb energy from a wider range of wavelengths than would be possible with one pigment alone.
Photophosphorylation an overview
transferring the energy from light into chemicals, particularly ATP. The evolutionary roots of photophosphorylation are likely in the anaerobic world, between 3 billion and 1.5 billion years ago, when life was abundant in the absence of molecular oxygen. Photophosphorylation probably evolved relatively shortly after electron transport chains (ETC) and anaerobic respiration provided metabolic diversity. The first step of the process involves the absorption of a photon by a pigment molecule. Light energy transfers to the pigment and promotes electrons (
-) into a higher quantum energy state—something biologists term an "excited state". Note the use of anthropomorphism here; the electrons are not "excited" in the classic sense and aren't suddenly hopping all over or celebrating their promotion. They are
in a higher energy quantum state. In this state, the electrons are colloquially said to
". While in the "excited" state, the pigment now has a much lower reduction potential and can donate the "excited" electrons to other carriers with greater reduction potentials. These electron acceptors may become donors to other molecules with greater reduction potentials and, in doing so, form an electron transport chain.
As electrons pass from one electron carrier to another via red/ox reactions, enzymes can couple these exergonic electron transfers to the endergonic transport (or pumping) of protons across a membrane to create an electrochemical gradient. This electrochemical gradient generates a proton motive force (PMF). Enzymes can couple the exergonic drive of these protons to reach equilibrium to the endergonic production of ATP, via ATP synthase. As we will see in more detail, the electrons involved in this electron transport chain can have one of two fates: (1) they may return to their initial source in a process called cyclic photophosphorylation; or (2) they can transfer onto a close relative of NAD+ called NADP+. If electrons return to the original pigment in a cyclic process, the whole process can start over. If, however, the electron transfers onto NADP+ to form NADPH (**shortcut note—we didn't explicitly mention any protons but assume that they
**), the original pigment must regain an electron from somewhere else. This electron must come from a source with a smaller reduction potential than the oxidized pigment and depending on the system there are different sources, including H2O, reduced sulfur compounds such as SH2 and even elemental S0.
What happens when a compound absorbs a photon of light?
When a compound absorbs a photon of light, the compound is said to leave its ground state and become "excited".
What are the fates of the "excited" electron? There are four
e- can relax to a lower quantum state, transferring energy as heat.
e- can relax to a lower quantum state and transfer energy into a photon of light—a process known as fluorescence. The energy can be transferred by resonanceto a neighboring molecule as the e- returns to a lower quantum state.
- The energy can change the reduction potential such that the molecule can become an
e- donor. Linking this excited e- donor to a proper e- acceptor can lead to an exergonic electron transfer. The excited state can be involvedin red/ox reactions.
As the excited electron decays back to its lower energy state, it can transfer its energy in a variety of ways. While many so-called antenna or auxiliary pigments absorb light energy and transfer it to something known as a reaction center (by mechanisms depicted in option III in Figure 2), it is what happens at the reaction center that we are most concerned with (option IV in the figure above). Here a chlorophyll or bacteriochlorophyll molecule absorbs a photon's energy, and an electron is excited. This energy transfer suffices to allow the reaction center to donate the electron in a red/ox reaction to a second molecule. This starts the electron transport reactions. The result is an oxidized reaction center that must now
Simple photophosphorylation systems:anoxygenicphotophosphorylation
Early in the evolution of photophosphorylation, these reactions evolved in anaerobic environments where there was very little molecular oxygen available. Two sets of reactions evolved under these conditions, both directly from anaerobic respiratory chains as described previously. We know these as the light reactions because they require the activation of an electron (an "excited" electron) from the absorption of a photon of light by a reaction center pigment, such as bacteriochlorophyll. We classify the light reactions either as cyclic or as noncyclic photophosphorylation, depending upon the final state of the electron
ferredoxin (ox) version 1
ferredoxin (red) version 1
ferredoxin (ox) version 2
ferredoxin (red) version 2
-0.42 (at [H+] = 10-7;
NAD+ + 2H+
NADH + H+
NADP+ + 2H+
NADPH + H+
FMN (enzyme bound)
FAD+ (free) + 2H+
Pyruvate + 2H+
FAD+ + 2H+ (bound)
CoQ (Ubiquinone - UQ + H+)
UQ + 2H+
Complex III Cytochrome b2; Fe3
Cytochrome b2; Fe2
Complex III Cytochrome c1; Fe3
Cytochrome c1; Fe2
Cytochrome c; Fe3
Cytochrome c; Fe2
Complex IV Cytochrome
1/2 O2 + H2O
Complex IV Cytochrome a3; Fe3
Cytochrome a3; Fe2
Cytochrome f; Fe3
Cytochrome f; Fe2
1/2 O2 + 2H+
* Excited State, after absorbing a photon of light
GS Ground State,
PS1: Oxygenic photosystem I
P840: Bacterial reaction center containing bacteriochlorophyll (
PSII: Oxygenic photosystem II
In cyclic photophosphorylation the
Figure 4. Cyclic electron flow. The reaction center P840 absorbs light energy and becomes excited, denoted with an *. The excited electron
Possible NB Discussion Point
The figure of cyclic photophosphorylation above depicts the flow of electrons in a respiratory chain. How does this process help generate ATP? Why might running the process in a cyclical fashion be advantageous for a cell?
In cyclic photophosphorylation, electrons cycle from bacteriochlorophyll (or chlorophyll) to a series of electron carriers and eventually back to bacteriochlorophyll (or chlorophyll); there is theoretically no net loss of electrons and they stay in the system. In noncyclic photophosphorylation, electrons leave from the photosystem and red/ox chain and eventually end up on NADPH. That means there needs to be a source of electrons, a source that has a smaller reduction potential than bacteriochlorophyll (or chlorophyll) that can donate electrons to
Noncyclic electron flow
Figure 5. Noncyclic electron flow. In this example, the P840 reaction center absorbs light energy and becomes energized; the emitted electron reduces a
We note that for bacterial photophosphorylation pathways, for each electron donated from a reaction center [remember only one electron is actually donated to the reaction center (or chlorophyl molecule)], the resulting output from that electron transport chain is either the formation of NADPH (requires two electrons) or ATP can be made but NOT not both. The path the electrons take in the ETC can have one or two outcomes. This puts limits on the versatility of the bacterial anoxygenic photosynthetic systems. But what would happen if a process evolved that used both systems? More precicely, a cyclic and noncyclic photosynthetic pathway which could form both ATP and NADPH from a single input of electrons? A second limitation is that these bacterial systems require compounds such as reduced sulfur to act as electron donors to reduce the oxidized reaction centers, but they are not necessarily widely found compounds. What would happen if a chlorophyll
Generation of NADPH and ATP
The overall function of light-dependent reactions is to transfer solar energy into chemical compounds, largely the molecules NADPH and ATP. This energy supports the light-independent reactions and fuels the assembly of sugar molecules. We depict the light-dependent reactions in Figures 6 and 7. Protein complexes and pigment molecules work together to produce NADPH and ATP.
The actual step that transfers light energy into a biomolecule takes place in a
Both photosystems have the same basic structure; several antenna proteins to which the chlorophyll molecules bind surround the reaction center in which the photochemistry takes place. Each photosystem associates with the light-harvesting complex, which passes energy captured from sunlight to the reaction center; it comprises multiple antenna proteins that contain a mixture of 300–400 chlorophyll
The reaction center contains a pair of chlorophyll
PSII and PSI are two major components of the photosynthetic electron transport chain, which also include the cytochrome complex. The reaction center of PSII (called P680) delivers its high-energy electrons, one at a time, to a primary electron acceptor called pheophytin (Ph), and then sequentially to two bound plastoquinones QA and QB. Electrons then transfer off of PSII onto a pool of mobile plastoquinones (Q pool) which then transfer the electrons to a protein complex called Cytochromeb6f. The cytochrome complex uses the red/ox transfers to pump proton across the thylakoyd membrane establishing a proton-motive force that can
As electrons move through the proteins that live between PSII and PSI, they take part in exergonic red/ox transfers. The free energy associated with the exergonic red/ox reaction
Figure 3. A diagram depicting the flow of electrons and the red/ox potentials of their carriers in oxygenic photosynthetic systems expressing both photosystem I (boxed in blue) and photosystem II (boxed in green). Ph = pheophytin; QA = bound plastoquinone, QB = more loosely associated plastoquinone; Q pool = mobile plastoquinone pool;
Light IndependentReactions and Carbon Fixation
A short introduction
The general principle of carbon fixation is that some cells under certain conditions can take inorganic carbon, CO2 (also referred to as mineralized carbon), and reduce it to a usable cellular form. Most of us know that green plants can take up CO2 and produce O2 in a process known as photosynthesis. We have already discussed photophosphorylation, the ability of a cell to transfer light energy onto chemicals and ultimately to produce the energy carriers ATP and NADPH in a process known as the light reactions. In photosynthesis, the plant cells use the ATP and NADPH formed during photophosphorylation to reduce CO2 to sugar, (as we will see, specifically G3P) in what we call the dark reactions. While we appreciate that this process happens in green plants, photosynthesis had its evolutionary origins in the bacterial world. In this module we will go over the general reactions of the Calvin Cycle, a reductive pathway that incorporates CO2 into cellular material.
In photosynthetic bacteria, such as Cyanobacteria and purple non-sulfur bacteria, as well plants, the energy (ATP) and reducing power (NADPH) - a term used to describe electron carriers in their reduced state -
The Calvin Cycle: the reduction of CO2 to Glyceraldehyde 3-Phosphate
Figure 1. Light reactions harness energy from the sun to produce chemical bonds, ATP, and NADPH.
In plant cells,
Stage 1: Carbon Fixation
In the stroma of plant chloroplasts, besides CO2, two other components are present to start the light-independent reactions: an enzyme called ribulose-1,5-
RuBisCO catalyzes a reaction between CO2 and RuBP. For each CO2 molecule that reacts with one RuBP, two molecules of another compound (3-PGA) form. PGA has three carbons and one phosphate. Each turn of the cycle involves only one RuBP and one carbon dioxide and forms two molecules of 3-PGA. The number of carbon atoms remains the same, as the atoms move to form new bonds during the reactions (3 atoms from 3CO2 + 15 atoms from 3RuBP = 18 atoms in 3 atoms of 3-PGA). We call this process carbon fixation, because CO2 is “fixed” from an inorganic form into an organic molecule.
Stage 2: Reduction
ATP and NADPH are used to convert the six molecules of 3-PGA into six molecules of a chemical called glyceraldehyde 3-phosphate (G3P) - a carbon compound also found in glycolysis. The process uses six molecules of both ATP and NADPH. The exergonic process of ATP hydrolysis is in effect driving the endergonic redox reactions, creating ADP and NADP+. Both "spent" molecules (ADP and NADP+) return to the nearby light-dependent reactions to be recycled back into ATP and NADPH.
Stage 3: Regeneration
Interestingly, at this point, only one of the G3P molecules leaves the Calvin cycle to contribute to the formation of other compounds needed by the organism. In plants, because the G3P exported from the Calvin cycle has three carbon atoms, it takes three “turns” of the Calvin cycle to fix enough net carbon to export one G3P. But each turn makes two G3Ps, thus three turns make six G3Ps. One is exported while the remaining five G3P molecules remain in the cycle and are used to regenerate RuBP, which enables the system to prepare for more CO2 to be fixed. These regeneration reactions use three more molecules of ATP.
Possible NB Discussion Point
Have you ever heard anyone accidentally refer to the Amazon rainforest as the "lungs of the Earth"? In reality, the majority of our planet's oxygen is produced by marine organisms, such as microscopic phytoplankton -- which, by the way, also take up appreciable amounts of carbon dioxide from the environment. The family of phytoplankton include organisms like cyanobacteria and diatoms (a visually stunning type of algae -- look it up!) that are able to survive and aggregate close to the water's surface, where sun exposure is higher. Try to approach phytoplankton from a BIS 2A lens... What biochemical processes had to happen in order for these phytoplankton to produce oxygen? What exactly are the phytoplankton doing with the carbon dioxide they take up from the atmosphere? What large-scale global effects would you expect if phytoplankton health were to be severely compromised?