The Calvin Cycle

Overview

The Calvin cycle is a series of enzymatic reactions that synthesize carbohydrates from carbon dioxide.
These reactions are divided into three distinct phases:
  1. Carboxylation - Carbon dioxide (CO₂) is added to a 5-carbon molecule.
  2. Reduction - Energy and electrons are transferred.
  3. Regeneration - The 5-carbon molecule needed for the first phase is regenerated (Reference: Fig. 8.14).
Light dependant and light independant reactions

Input and Output

Input: Carbon dioxide (CO₂)
Output: Triose phosphate (sugar molecules)

Phase 1: Carboxylation

In the first phase, CO₂ is added to a 5-carbon compound known as ribulose 1,5-bisphosphate (RuBP).
Catalyzing Enzyme: Ribulose bisphosphate carboxylase/oxygenase (rubisco).
- The term carboxylase indicates that rubisco adds CO₂ to another molecule.
The reaction requires both RuBP and CO₂ to diffuse into the active site of rubisco.
The resulting product is a 6-carbon compound that immediately splits into two molecules of 3-phosphoglycerate (3-PGA).

Phase 2: Reduction

The reduction of 3-PGA involves two key reactions:
1. ATP Donation: ATP donates a phosphate group to 3-PGA.
2. NADPH Transfer: NADPH transfers two electrons and one proton (H+), resulting in the release of one phosphate group (P) from the reaction.
Notably, for each CO₂ molecule that rubisco incorporates, two ATP and two NADPH are needed due to the production of two molecules of 3-PGA.
Energy Source: NADPH provides the majority of the energy stored in the newly formed carbohydrate bonds, while ATP prepares 3-PGA for further transformation.
The final products of this phase are two types of sugar molecules:
  - Glyceraldehyde 3-phosphate (G3P)
  - Dihydroxyacetone phosphate (DHAP)
  - Collectively, these are referred to as triose phosphates.

Output of the Calvin Cycle

Triose phosphates are the primary products of the Calvin cycle and serve as the principal export from the chloroplast during photosynthesis.

Phase 3: Regeneration

For the Calvin cycle to continue, RuBP must be regenerated from triose phosphates.
Energy Requirement: ATP is essential for the regeneration of RuBP.
The regeneration of RuBP occurs in a series of reactions rearranging carbon atoms from five 3-carbon triose phosphate molecules into three 5-carbon RuBP molecules.
For each CO₂ molecule incorporated by rubisco:
- Energy Consumption: A total of two NADPH and three ATP molecules are required (2:3 ratio of NADPH to ATP).

Redox Reactions

Redox reactions are a type of chemical reaction in which electrons are transferred from one reactant to another. Where a substance gains an electron (and thus energy), this is called a reduction reaction, while oxidation reactions are those where a substance loses an electron and the energy that electron carries

This can be a little confusing – how is something that is being reduced be a gain in electrons? This is because by adding negatively charged electrons to an atom reduces the amount of positive charge on that atom. Two French scientists coined the term oxidation in the late 1700s to signify the reaction of a substance with oxygen. However, its meaning now includes other reactions in which electrons are lost, regardless of whether oxygen was involved.

OIL - oxidation is loss of electrons

RIG - reduction is gain of electrons

Oxidation number rules

free elements are zero
for ions its the charge
oxygen is always -2 (peroxides -1)
hydrogen is +1 (w non-metals) -1 (w metal)
in neutral compounds the sum is zero (or charge) in ions

Carbohydrate Storage

Carbohydrates are typically stored in the form of starch within cells, allowing for excess carbohydrates to be managed without causing osmotic damage from soluble sugars.
Starch granules, formed in chloroplasts during the daytime, provide a carbohydrate reservoir for consumption during the night (Reference: Fig. 8.16).

Relation to Cellular Respiration

Cellular respiration contrasts with photosynthesis as it breaks down carbohydrates in the presence of oxygen to produce energy and generates carbon dioxide and water as by-products.
Photosynthesis, conversely, utilizes carbon dioxide and water, facilitated by sunlight, to build carbohydrates while releasing oxygen.
Diagrams illustrating the interconnection of these metabolic processes can be found in Visual Synthesis 2 following this chapter.

8.1 An Overview of Photosynthesis

Photosynthesis is the primary entry point for energy into biological systems.
  - It is the source of all food, both directly from plant consumption and indirectly through animal consumption.
  - It produces all the oxygen we breathe.
  - It is the origin of fuels used for heating, electricity generation, and transportation.
  - Fossil Fuels:
    - Oil originates from marine algae and organisms that fed on them.
    - Coal represents the geological remains of terrestrial plants.
Distribution and Categories of Photosynthesis:
  - Photosynthesis occurs widely across different organisms.
    - Most visible photosynthetic activity occurs in land plants (trees, grasses, shrubs).
    - Both prokaryotic and eukaryotic organisms perform photosynthesis.
  - Approximately 60% of global photosynthesis is executed by terrestrial organisms.
  - 40% occurs in oceanic environments:
    - Majority executed by unicellular organisms categorized as phytoplankton (single-celled marine eukaryotes and photosynthetic bacteria).
Conditions for Photosynthesis:
  - Photosynthesis occurs where sunlight is available:
    - In oceans, it is limited to a surface layer of about 100 meters.
    - On land, most productive in warm, moist environments (e.g., tropical rainforests, temperate grasslands).
  - Organisms have adapted to extreme environments:
    - Desert crust: a layer formed by photosynthetic bacteria and unicellular algae (e.g., Colorado Plateau).
    - Hot springs: presence of photosynthetic bacteria in extreme heat (e.g., Yellowstone National Park).
    - Glaciers: unicellular algae can cause red snow coloration.

Photosynthesis Processes

Stages of Photosynthesis:
  - Photosynthesis consists of two stages:
    1. Light Capture:
       - Involves absorption of sunlight into usable chemical energy forms.
    2. Carbon Fixation:
       - Uses energy from the light stage to synthesize carbohydrates from carbon dioxide (CO₂).
Carbon Fixation:
  - Fixation transforms inorganic molecules into organic molecules.
  - Carbohydrates are primary products serving as fuel for energy in cellular respiration.
  - Example:
    - When consuming sugar, the energy initially derived from sunlight through photosynthesis.
Light Capture Mechanism:
  - Involves pigments that absorb sunlight (mainly chlorophyll).
  - Light energy causes electron movement through the photosynthetic electron transport chain:
    - Involves redox reactions where chlorophyll-powered electrons are transported.
    - Electrons originate from water, producing oxygen gas as a byproduct.
  - Results in production of NADPH and ATP, known as light reactions.
Comparative Process:
  - Similar to electron transport in cellular respiration but:
    - Electron donors are different (water vs. organic molecules).
    - Final electron acceptor changes (NADP⁺ reduced to NADPH vs. O₂ reduced to H₂O).

The Calvin Cycle

Chloroplasts and Photosynthesis in Eukaryotes

Photosynthesis Location:
- Occurs in chloroplasts within eukaryotic cells.
- Chloroplasts fulfill a similar role as mitochondria in cellular respiration.
Chloroplast Structure:
  - Surrounded by two membranes with an interior membrane known as the thylakoid.
  - The lumen is the fluid-filled space enclosed by thylakoids, which are folded into structures called grana.
  - Thylakoid membranes contain the photosynthetic electron transport chain.
  - The stroma, the space between the inner and thylakoid membranes, is where carbon fixation takes place.
  - Autotrophs: Photosynthetic organisms are termed autotrophs as they can form carbohydrates from CO₂.
  - While chloroplasts generate ATP, they export carbohydrates needed for energy, hence necessity for both chloroplasts (to synthesize energy) and mitochondria (to extract it).

8.2 Capturing Sunlight into Chemical Forms

For sunlight to power the Calvin cycle, cells must utilize light energy to produce both NADPH and ATP.
The process of photosynthesis is driven by light energy absorbed by pigment molecules, leading to the flow of electrons through the photosynthetic electron transport chain which results in the formation of NADPH and ATP.

Understanding Light in Photosynthesis

Chlorophyll:
- Major entry point for light energy in photosynthesis, critical for energy capture.
Electromagnetic Spectrum:
  - The sun produces a broad spectrum of electromagnetic radiation, including gamma rays to radio waves.
  - Different energy levels and corresponding wavelengths are represented across the electromagnetic spectrum.
  - Visible Light:
    - The visible range, which can be perceived by the human eye, encompasses wavelengths between 400 nm and 700 nm.
    - Approximately 40% of the sun's energy that reaches Earth falls within this range.
Pigments:
- Molecules that absorb specific wavelengths of visible light.
- Apparent color is due to the reflection of light wavelengths that are not absorbed.
Chlorophyll Characteristics:
  - Chlorophyll has a light-absorbing region containing a magnesium atom and a long hydrocarbon side chain.
  - Alternating single and double bonds around the magnesium create overlapping electron orbitals, enabling chlorophyll to absorb visible light.
  - Chlorophyll is integrated into integral membrane proteins and is organized into photosystems, which are essential for absorbing light and driving electron transport.

Types of Chlorophyll

Chlorophyll a:
- Universally present in all photosynthetic eukaryotes and cyanobacteria.
Chlorophyll b:
- Found in green algae and land plants.
Accessory Pigments:
- Pigments other than chlorophyll that assist in light absorption, such as carotenoids (orange-yellow pigments).
- These allow photosynthetic cells to absorb a wider range of wavelengths than chlorophyll alone provides and protect against damage to the photosynthetic electron transport chain.

Energy Transfer Mechanism in Chlorophyll

When chlorophyll absorbs light:
  1. An electron is elevated to a higher energy state.
  2. The fate of the energy depends on the chlorophyll's arrangement within the chloroplast:
     - In Solution: Absorbed light energy is lost as heat and/or fluorescence (Fig. 8.8a).
     - In a Plant Cell: The energy is transferred to an adjacent chlorophyll, minimizing heat loss (Fig. 8.8b).
  - Antenna Chlorophyll: This chlorophyll serves to capture incoming energy and funnel it to the reaction center.

Reaction Center Mechanism

Function of the Reaction Center:
  - Comprised of specially configured pairs of chlorophylls, it allows energy transfer to an adjacent electron-acceptor molecule.
  - This transfer oxidizes the reaction center and reduces the electron-acceptor molecule (Fig. 8.9a).
  - Once the reaction center loses an electron, it must acquire a new one to continue functioning (Fig. 8.9b).
  - Replacement electrons come from water, illustrating the division of labor among chlorophyll molecules.
Historical Experiment by Emerson and Arnold (1940s):
- Investigated how many chlorophyll molecules contribute to electron transport in photosynthesis.
- Resulted in the conclusion that many chlorophylls are involved for producing one molecule of NADPH, leading to the understanding of the photochemical unit.

Photosynthetic Electron Transport Chain (PETC)

Two Photosystems:
- Photosystem I (PSI) and Photosystem II (PSII) are arranged in series in the PETC, with PSI characterized as needing input of light after PSII.
- Electrons flow from PSII to PSI to convert NADP+ to NADPH.
Role of Water:
- Water acts as an ideal electron donor—abundant but requires significant energy to extract electrons.
Energy Flow in PETC:
- Energy from light absorbed by PSII pulls electrons from water.
- The flow of electrons increases energy at two photosystems, forming a Z scheme due to the up-down energy pattern.
Components of the PETC:
  - Major proteins include PSII, PSI, cytochrome complex, and mobile compounds such as plastoquinone (Pq) and plastocyanin (Pc) (Fig. 8.12).
  - Electrons flow from water through PSII, to the cytochrome complex, then to PSI, culminating in NADPH formation (Fig. 8.12b).
  - Water is oxidized, releasing O2 and H+, while NADP+ is reduced by adding electrons and protons from the stroma.

ATP Production in Photosynthesis

Photophosphorylation:
- The process of synthesizing ATP powered by the accumulation of protons in the thylakoid lumen.
- Similar to ATP generation in mitochondria, ATP synthase in chloroplasts uses proton gradients to generate ATP.
Proton Accumulation:
  - Two mechanisms contribute to this concentration difference:
    1. The oxidation of water releases protons in the lumen.
    2. Protein complexes (Pq and Cyt-) function as proton pumps, akin to cellular respiration mechanisms.
  - At full capacity, the proton concentration can exceed 1000 times that of the stroma, creating a 3 pH unit difference.

Cyclic Electron Transport

Cyclic Electron Transport:
  - Additional ATP production occurs as electrons from PSI are redirected back into the PETC, enhancing proton pumping (Fig. 8.13).
  - Enables more protons to accumulate in the lumen, driving the synthesis of ATP through ATP synthase due to the increased proton concentration in the lumen.
  - This pathway is distinct from the linear movement of electrons from water to NADPH and serves to balance the energy requirements needed for efficient photosynthesis.

The Evolution of Photosynthesis

Introduction

The evolution of photosynthesis significantly altered the trajectory of life on Earth.
Provided organisms with a new energy source.
Released oxygen into the atmosphere, which transformed environmental conditions.

Stepwise Evolution of Photosynthesis

Evolution generally progresses incrementally, building upon pre-existing biological structures and processes.
Photosynthetic pathways likely evolved in a similar stepwise fashion.

Initial Interactions with Sunlight

Sunlight is an excellent energy source but poses potential harm due to ultraviolet (UV) radiation.
Early life forms may have developed UV-absorbing compounds as protective measures against sunlight's damaging effects.

Development of Photosynthetic Mechanisms

Random mutations over time produced variants of UV-absorbing molecules that could possibly harness sunlight's energy.
One hypothesis includes the early evolution of light-driven electron transport mechanisms.
- This may have involved the synthesis of ATP (adenosine triphosphate) without requiring an electron donor.
- Alternatively, early reaction centers possibly facilitated electron movement from an extracellular electron donor to an intracellular electron-acceptor.

Electron Donors in Early Photosynthesis

Early organisms could have used soluble inorganic ions, such as reduced iron, as electron donors due to their abundance in early oceans.
Initial photosynthetic organisms likely did not utilize chlorophyll due to its complex biosynthetic pathway, requiring at least 17 enzymatic steps.

Intermediate Compounds and Selection

Compounds leading to chlorophyll may have served as pigments for early photosynthetic organisms.
The biosynthetic pathways likely gained complexity through random mutations that enhanced efficiency or absorption of broader light spectra.

Evolution of Water as an Electron Donor

The capability of using water as an electron donor emerged in cyanobacteria, marking a significant evolutionary advancement.
Ancient photosynthetic forms primarily possessed a single photosystem in their electron transport chains.
    - A single photosystem lacks the capacity to oxidize water and elevate the energy levels of electrons sufficiently to meet metabolic needs.
    - Consequently, these organisms relied on more easily oxidized substances like hydrogen sulfide as electron donors, exclusively inhabiting environments rich in such compounds.
    - These organisms did not produce oxygen during photosynthesis.

The Emergence of Oxygenic Photosynthesis

A pivotal advancement was the development of electron transport chains employing water as an electron donor, first achieved by cyanobacteria.
Cyanobacteria incorporated two distinctive photosystems into a unified electron transport chain:
- One photosystem for extracting electrons from water molecules.
- A second for elevating electron energy levels to facilitate reductions of other molecules.

Mechanisms of Genetic Diversity in Cyanobacteria

Hypotheses explore how cyanobacteria developed dual photosystems:
- Genetic Transfer Hypothesis: Genetic components from one photosystem could have been transferred to a bacterium with an existing photosystem, resulting in a bacterium endowed with both.
- Duplication and Divergence Hypothesis: Genetic duplication of one photosystem could produce variations through mutations, subsequently evolving into two related photosystems.

Implications of Water Utilization in Photosynthesis

The usage of water as an electron donor facilitated:
1. Photosynthetic processes in diverse environments where sunlight and water were present.
2. Oxygen production as a byproduct of water oxidation, drastically altering Earth’s atmosphere.
Post-evolution, free oxygen became available, originating solely from photosynthesis by organisms with dual photosystems.

Endosymbiotic Theory in Eukaryotes

Eukaryotic organisms are believed to have acquired photosynthesis via endosymbiosis, in which a free-living cyanobacterium established a symbiotic relationship with a eukaryotic cell.
Over time, the cyanobacterium lost independent survival capabilities, evolving into modern chloroplasts:
    - The outer chloroplast membrane likely originates from the host eukaryotic cell's membrane.
    - The inner chloroplast membrane corresponds to the original cyanobacterium’s cell membrane.
    - The thylakoid membrane mirrors the internal photosynthetic membrane of cyanobacteria.
    - The stroma is believed to correspond to the cytoplasm of the ancestral cyanobacterium.

Endosymbiotic Hypothesis

This theory posits that chloroplasts and mitochondria arose through the process of endosymbiosis, indicating a crucial evolutionary step for eukaryotic life forms.