Cell Biology

I. Overview

II. Membranes: How Matter Get in and Out of Cells

III. Cellular Respiration

IV. Photosynthesis

 

Overview:

Although all organisms can harvest energy by breaking down organic molecules (Cellular Respiration), some have evolved a mechanism for transforming radiant energy in chemical bond energy. Photosynthesis is that process of energy transformation. Again, although energy can neither be created nor destroyed, it can be transformed. In the "Light Dependent Reaction" radiant energy ('carried' by photons in light) is transformed into chemical energy ('carried' by electrons). It requires an electron DONOR to provide electrons that will 'carry' this energy. The energy 'carried' by this electron is used to form a bond between ADP and P, creating ATP. Through this transfer, the electron loses this energy. As we have discussed before, the phosphate bonds in ATP are easily made and easily broken - that's why energy in this form of chemical bond can be 'used' by all enzymes in the cell. However, ATP is readily hydrolyzed in water...so it is difficult for a cell to build up a large amount of ATP before it 'dissolves' to ADP and P again. To store large amounts of energy for a longer time, the energy in ATP can be converted to a more stable molecule. In most photosynthetic organisms, the catabolism of ATP is coupled to anabolic reactions that bind carbon dioxide molecules together into stable molecules of glucose, for longer term E storage. This also provides the cell with organic carbon that it can use to make the other biologically important molecules. These are the "Light Independent Reactions" of photosynthesis.

When we think of photosynthesis, most of us think "plants". This is generally correct, but very incomplete. First, there are some plants like Indian Pipe (Monotropa uniflora) that do not photosynthesize. Although they evolved from photosynthetic ancestors, they have adopted a parasitic lifestyle and no longer harvest their own energy from sunlight. In addition, there are photosynthetic protists (algae and Euglenozoans), and photosynthetic archaeans and eubacteria. In fact, there are several animals that harbor photosynthetic symbionts, too. Many corals (corals are animals) ingest algal cells and distribute them to their tentacles. The algae photosynthesize, and excess sugars are passed to the coral animal. These symbiotic algae give corals their spectacular colors. When stressed by water polution or high water temperatures, the corals release their symbionts and lose their color ("a phenomenon called "coral bleaching"). Long periods without their symbionts results in coral death.

Photosynthesis in prokaryotes occurs on the double-membrane system of these organisms. In eukaryotes, photosynthesis occurs in organelles called chloroplasts. Chloroplasts have a bacteria-like double membrane, and they have their own DNA. This DNA is more similar in most respects to the DNA in free-living bacteria than to the DNA in the nucleus of the eukaryotic cells they 'inhabit'. For these reasons, most scientists accept the 'endosymbiotic theory' of chloroplast origins. This theory states that chloroplasts in the cells of photosynthetic eukaryotes are descendants of free-living photosynthetic bacteria. At some point in the early evolution of protists, these photosynthetic bacteria were engulfed by not digested. Rather, the host cells fed on the excess sugars produced by the internalized bacteria. Eventually, as the result of gene exchange between the host and proto-chloroplasts, the eukaryotic host and the prokaryotic symbiont became dependent on one another. But chloroplasts can still live outside of cells for several days. Plants, evolving from green algae ancestors, inherited these bacteria-like chloroplasts, too.

Photosynthesis is a critically important process in the evolution and diversity of life. Prior to the evolution of photosynthesis, life was dependent on absorbing spontaneously generated organic molecules, or preying on other cells. Neither of these sources of energy was probably all that common and easy to find. Evolving the ability to use sunlight as an energy source, which IS abundant and IS easy to find, meant that life could grow, prosper, and radiate dramatically - almost anywhere there was a light source. Indeed, it looks like photosynthesis evolved very early in the history of life; the earliest fossils (stromatolites and filamentous microfossils dating to ~3.5 by) look very similar to photosynthetic bacteria that are alive today. When photosynthetic organisms became abundant, they provided a food supply for a wider variety of heterotrophic cells. Heterotrophs could then live anywhere phototrophs lived; they were not limited to those rare places where biological molecules were forming spontaneously. So, complex bacterial food webs evolved. These early photosynthetic organisms used a primitive form of photosynthesis that did not produce oxygen as a waste product. So, even though they flourished for a billion years, no oxygen was added to the atmosphere. About 2.0 billion years ago, a 'modern' type of photosynthesis evolved that used water as the electron donor and produced oxygen gas as a waste product. The production of oxygen gas transformed the oceans (precipitating iron), and eventually changed the atmosphere, as well. Although oxygen was probably a highly toxic gas at first (because it is so reactive), life eventually evolved to tolerate it and then to USE it in oxidative respiration. The evolution of aerobic respiration allowed for more energy to be harvested from the catabolism of complex organic molecules, and may have allowed for the evolution of more energy-demanding eukaryotes and multicellular organisms. As you know, almost all food webs are ultimately dependent on the photosynthetic organisms at the base of the "food chain" (hydrothermal vent communities are a possible exception). We use this energy to stick amino acids together to make our proteins, etc. Even the gas and oil that powers our industrial societies was initally stored as glucose produced by photosynthesis. Coal, gas, and oil are just fossilized plants - and we "burn" that energy millions of years after it was converted from sunlight. We are powering our societies with sunlight that hit the Earth millions of years ago. But not only are you (and every other heterotroph) energetically dependant on photosynthetic organisms for food, you are also indebted to them for changing the planet and stimulating the evolution of eukaryotic and multicellular life. In short, there are few processes more important to the history and current function of living systems (and our petroleum-based economy) than photosynthesis.

A. Step 1: The Light Dependent Reaction

AGAIN, the purpose of the light-dependent reaction is to convert radiant energy to chemical energy. Obviously, light must be present; so this reaction "depends" on sunlight.  There is one group of Archaeans that performs photosynthesis (Halobacteria), but their process of harvesting light energy seems quite different from the process in eubacteria and chloroplasts in eukarya and probably evolved independently. Within the eubacteria, there are also a wide variety of photosynthetic processes. We will focus on a couple major types and make reference to others as we go.

1. PRIMITIVE SYSTEMS:

a. cyclic phosphorylation in "purple non-sulphur" and "green non-sulpher" bacteria:Like all bacteria, they have a double membrane (two bilayers). Proteins nested within the inner membrane form "reaction centers (also called "photosystems") and "electron transport chains" (ETC's) used in photosynthesis. This inner membrane is often highly convoluted, increasing the surface area and the number of reaction centers and ETC's that can be imbedded. Each reaction center contains proteins arrayed around molecules of bacteriochlorophyll, which contain atoms of Magnesium. In the presence of light, the photons transfer energy to these electrons. The electrons are raised to a higher energy state, lost from the atom, and transferred to an 'electron acceptor molecule' in the inner membrane of the bacterium, which transfers the electron the the electron transport chain. When a high-energy electron is transferred down the chain, protons (H+) follow ('electrostatically') and are pumped across the inner membrane into the intramembrane space. This build-up of H+ ions in the intermembrane space creates an electrostatic charge differential across the membrane. There are closed protein channels that, when opened, allow the H+ to flood through in response to the charge gradient. This electric discharge energy is used by the enzyme ATP-synthetase to add a phosphate group to ADP, making ATP. This is called 'chemiosmotic synthesis' or 'chemiosmosis'. So, what has happened is that the passage of an electron -excited by light energy - has been used to 'pump protons' into the intermembrane space, establishing an H+ ion charge gradient. The flow of H+ ions through protein channels transforms this electric energy to chemical bond energy in the form of a bond between ADP and P--> ATP. The high-energy electron is then passed down the electron transport chain. and ATP is produced. The electron, having lost its energy, can be recycled back to the Mg atom. This cyclic production of ATP, powered by sunlight, is called cyclic phosphorylation. As discussed below, these odd bacteria do not perform the light independent pathways. In other words, they do not use the energy in ATP to make glucose. This has two interesting consequences. First, it means they can't rely on photosynthesis, alone, for energy harvest, because ATP isn't stable enough to last over the course of an evening. So, they must also 'eat' - they are heterotrophs, and can harvest energy from the food they ingest. The other consequence is discussed below.

b. "green sulphur" and "purple sulphur" bacteria that use sulphides as the electron donors:

When the excited electron is recieved by the 'electron acceptor',something else can happen. Instead of the Electron Acceptor giving the electron to the ETC, it can give the electron to NADP... another 'energy transport molecule' like ADP. When this happens, the NADP gains energy and a negative charge and is NADP-. It reacts with free H+ ions that are always present in aqueous solutions (you should know why...), to make the high energy transport molecule, NADPH. In this case, the electron isn't returned to the Magnesium.... photosynthesis would stop, unless the photosystem can strip electrons from other molecules in solution. There are several groups of primitive eubacteria ("green sulphur bacteria" and "purple sulphur bacteria") that use sulfides (like hydrogen sulfide - H2S) as the electron donor.

Sulphur bacteria have photosystems that strip electrons from Hydrogen Sulphide (H2S). This releases 2H+ ions and S as a waste product. So, sulphur bacteria that are still present today photosynthesize in sulphur springs and do not produce oxygen as a waste product. This explains an interesting geological pattern: The oldest fossil life on record are photosynthetic bacteria that date to 3.8 billion years old. However, the first evidence of oxygen in the Earth's atmosphere occurs at about 2 billion years ago. So, how can you now explain how there were photosynthetic bacteria present for 1.8 billion years, without any oxygen being produced? Sulphur bacteria. And they have another interesting characteristic - they are anaerobic organisms poisoned by oxygen gas. So, not only don't they produce oxygen, but they can only survive in its absence. All these factors suggest that they may be similar to the first photosynthetic life forms that thrive in the anaerobic environment of the early earth. There is a problem for them, however. These bacteria can only survive in places where H2S is abundant - like sulphur springs. These places are rare. If something evolved a system that could strip electrons from a more abundant source, like water (H2O), then these new organisms could exploit almost the whole planet - as 75% of the planet is covered by H2O.

 

2. ADVANCED SYSTEM: most other photosynthetic bacteria (cyanobacteria), and photosynthetic eukaryotes.

       - In photosynthetic Eukaryotes(photosynthetic protists and plants), these reactions occur on the inner membrane of the Chloroplast - a specific membrane-bound organelle very much like a bacterium within the larger eukaryotic cell. Indeed, as described above, eukaryotic chloroplasts are probably the deescendants of free-living cyanobacteria - with whom they share basic membrane structure and DNA similarity.
       - In cyanobacteria and chloroplasts, there are two types of reaction centers called "photosystems". The second photosystem (PSII) has a lower electronegativity than the first, so it can exert a 'stronger' pull and can strip electrons from WATER (which holds the electrons more strongly than H2S does.) The splitting of water releases oxygen gas as a waste product, so this type of photosynthesis is also called "oxygenic photosynthesis".
        - Here's how it works: Light strikes the phosystems nested in the inner membrane (called the 'thylakoid' membrane in chloroplasts). An electron in each photosystem is excited and lost from the Mg in the chlorophyll molecule. The electrons are accepted by partcular electron acceptor molecules. The electron lost from PS I is ultimately passed to NADP, which accepts a H+ to balance the charge, making the high energy molecule, NADPH. The electron lost from PSII is passed to an electron acceptor, and then to molecules in the electron transport chain. As the electron is passed down the chain, ATP is produced by chemiosmosis (as described above). When this electron has lost it's energy, it replaces the electron lost from PS I. So, PS I is all set, and need not strip electrons from an electron donor. However, PS II has lost an electron, and must replace this electron for photosynthesis to continue. PSII strips electrons from H2O. Water is split into oxygen, 2 H+, and 2 electrons. The electrons are passed to the cholorophyll in PS II, excited by light, and energized. The oxygen reacts with another oxygen atom to produce oxygen gas, which is released as a waste product. The propose of photosynthesis is not "to produce oxygen". The purpose of the light reaction of photosynthesis is to transform radiant energy into chemcial energy, and produce ATP and NADPH. The two molecules, ATP and NADPH, are the useful products. Again, oxygen gas is produced as a waste product when electrons are stripped from water. The presence of oxygen in the oceans 2.5-2 billion years ago, indicated by the presence of sedimentary deposits with oxidized iron (banded iron formations), indicates the evolution of this more advanced type of photosynthesis that evolved in ancient photosynthetic bacteria.

3. SUMMARY OF LIGHT REACTIONS:

B. Step 2: The Light Independent Reactions:

The purpose of the "Light Independent Reactions" is to convert the chemical energy in fragile ATP and NADPH molecules into a more stable energy form by building covalent bonds between carbon atoms to make glucose. In prokaryotes, these reactions occur in the cytoplasm of the cell; in eukaryotes, these reactions occur in the stroma - or cytoplasm - of the chloroplasts. It is important to appreciate that organisms using both primitive and advanced light reactions perform the light independent reactions.

The primary reaction is called the Calvin-Benson Cycle, and it works like this:
        - 6 CO2 molecules bind to 6 C5 molecules of Ribulose Biphosphate (RuBP), making 6 C6 molecules.  (ATP is broken and the energy that is released is used to link CO2 to RUBP).
        - These energized C6 molecules are unstable; the split into 12 C3 molecules. So, since the first stable product is a C3 molecule, this type of reaction is called the C3 pathway.
        - 2 C3 molecules are used to form 1 glucose (C6) molecule. More ATP is used, and NADPH is used, too, and H is transferred to put the 'hydrogen' in 'carbohydrate'.
        - the 10 remaining C3 molecules (30 C total) are rearranged, using ATP and NADPH, and 6 C5 molecules are generated (30 C total).

The reaction can be summarized like this: Six CO2 molecules are used to make one molecule of glucose. Six RuBP molecules are involved, and are recycled through the process. The ATP and NADPH formed in the light reaction are used to power this reaction; the energy in these molecules is used top make bonds between the CO2, and the H from NADPH is used to reduce the CO2 to form glucose (C6H12O6). As such, the radiant energy initially trapped in chemical bonds in ATP and NADPH is transferred to form bonds between carbon atoms in glucose. The energy intially trapped in fragile molecules has been stored in a more stable form.

When cells build glucose from CO2, they have not only stored energy in a stable form - they have also harvested carbon from the environment and transformed it into a usable organic molecule. Since all biologically important molecules (except water) are carbon-based organic molecules, all life forms needs a source of carbon to build amino acids, nucleotides, sugars, and lipids. "Heterotrophs" get organic carbon in the 'food' they eat. "Autotrophs" get their carbon through the light independent reaction, which also stores energy.       

The first group of bacteria discussed above - the green non-sulphur bacteria and purple non-sulphur bacteria - perform the Light Dependent Reaction and make ATP using sunlight, but they do not perform the light indepedent reactions. So, they do not absorb CO2 to make their organic molecules. Instead, they must consume organic molecules to acquire their carbon. These organisms are "photoheterotrophs". They may represent the first step in the evolution of photosynthesis: the evolution of light-trapping reactions by heterotrophic cells. They use cyclic phosphorylation to make ATP in the presence of light, but they use organic molecules as electron donors.

C. Photorespiration - Problem and Solutions:

1. PROBLEM:

RuBP will bind to BOTH CO2 and O2.  And when RuBP binds to O2, it is split and transformed to the amino acid serine, with the production of CO2 as waste.  Essentially, it is digested. These reactions use the ATP and NADPH produced in the light reaction, too. So, when RuBP binds O2, it does the exact opposite of photosynthesis - it IS RESPIRED - the energy of the light reaction is used to BREAK DOWN a carbohydrate (RuBP) and RELEASE CO2. This happens when the relative concentrations of O2 and CO2 cross a critical threshold,  If O2 is super-abundant and CO2 is scarce, then photorespiration will ocur. Oxygen levels can rise to these levels on HOT, DRY days, when there is a lot of sun for photosynthesis to proceed (so O2 concentrations rise in the leaf and CO2 concentrations fall), and it is DRY so the stomates are closed and gases can't be exchanged with the environment (so O2 builds up in the leaf). It may seem curious that such a critical molecule has such a debilitating characteristic. However, because
the light independent reaction probably evolved long before oxygenic light reactions, it was already incorporated into the process before the accumulation of oxygen in the oceans and atmosphere revealed its weakness.

2. SOLUTIONS:

a. C4 metabolism:

"C3 plants" (as described above - called C3 because the first STABLE product of carbon fixation is a C3 molecule) have chloroplasts in their mesophyll and not their bundle shealth. They suffer from photorespiration on hot dry days. "C4 plants" have chloroplasts in both cells; the bundle shealth has RuBP, but the mesophyll has a different binding molecule (PEP) with a higher affinity for CO2.  So, PEP (a C3 molecule) can bind CO2 at low concentrations, and then the product (a C4 product) is passed to the bundle shealth. In the bundle shealth the CO2 is dissociated from PEP, and PEP is returned to the mesophyll. This keeps the concentration of CO2 in the bundle shealth high enough for RuBP to keep fixing CO2, even though the leaf may be closed.  So, PEP "pumps" CO2 into the bundle shealth, keeping the concentration of CO2 high enough that photosynthesis (and not photorespiration) will occur. This allows C4 plants to maintain glucose production even on hot dry days when their stomates are closed.  Grasses are classic C4 plants, and they have adapted physiologically (and morphologically) to their environment.

b. Crassulacean Acid Metabolism (CAM)

"CAM plants" (for crassulacean acid metabolism) fix CO2 at night and bind it to a C# molecule to form malate (C4).  Then, in the day when stomates are closed but light is available, they harvest energy and split the malate to release the CO2 to RUBP, allowing both reactions to proceed.

Study Questions:

1. Draw what happens in the primitive light reaction of sulphur bacteria, and explain the events that occur.

2. What is the electron donor for sulphur bacteria? What type of limitation does this impose on where these organisms can live?

3. Draw and explain what happens in the more advanced light dependent reaction. Why can we call this an 'adaptation'? (Why is this an improvement over the the more primitive system, considering the habitats available on Earth?)

4. Describe the correlations between these observations:

- the oldest fossils are 3.8 billion years old and look like photosynthetic organisms

- eukaryotic photosynthetic organisms about 2 billion years ago

- 'red beds', the oldest sedimentary deposits that include oxidized minerals, date to about 2 billion years

- previous to these red beds, minerals in sedimentary deposits are in their reduced state, suggesting that they were not exposed to an oxidizing atmosphere during their erosion and deposition, suggesting that the atmosphere contained no oxygen gas.

5. Draw the Light Indepedent reaction and describe the events that occur.

6. Explain photorespiration and describe two different adaptations of plants that live in hot, dry, environments.

7. When, where, and why is oxygen produced by photosynthesis?  What is the primary function of photosynthesis?