Fasil Ahmed (MSc)

February 2024
α–ketoacid: Alpha-ketoacids are organic compounds that have a keto group (C=O) at the alpha (α) position,
meaning the carbonyl group is adjacent to a carboxyl group. These compounds are often intermediates in
various metabolic pathways, especially in the catabolism (breakdown) of amino acids.

α-ketoglutarate: It is a key intermediate in the Krebs cycle. α-ketoglutarate is formed in the citric acid cycle
through the decarboxylation of isocitrate. The enzyme isocitrate dehydrogenase catalyzes this reaction, leading
to the release of carbon dioxide and the formation of α-ketoglutarate.

1,3-bisphosphoglycerate: It is a key intermediate in the glycolytic pathway, an essential metabolic process

that breaks down glucose to produce energy. It is formed during the sixth step of glycolysis. In the preceding
steps, glucose is phosphorylated and cleaved, resulting in the production of two molecules of glyceraldehyde-
3-phosphate (G3P). In the subsequent steps, G3P is oxidized, and 1,3-BPG is formed.

2-phosphoglycerate: It is an intermediate in the glycolytic pathway, a central metabolic process that breaks
down glucose to produce energy. 2-Phosphoglycerate is formed during the eighth step of glycolysis. In the
preceding steps, glucose is phosphorylated and cleaved, leading to the production of glyceraldehyde-3-
phosphate (G3P). In the subsequent reactions, G3P is oxidized and phosphorylated to form 1,3-
bisphosphoglycerate (1,3-BPG), which is then converted to 3-phosphoglycerate (3-PG). Finally, 3-PG is
rearranged to form 2-phosphoglycerate.

3-phosphoglycerate (3-PGA): It is a three-carbon molecule (C3H7O6P) that plays a crucial role in the Calvin
cycle, which is part of the light-independent reactions of photosynthesis. It is produced during the initial phase
of carbon fixation when carbon dioxide (CO2) is incorporated into an existing five-carbon sugar molecule,
ribulose-1,5-bisphosphate (RuBP), catalyzed by the enzyme RuBisCO (ribulose-1,5-bisphosphate
carboxylase/oxygenase). During the reduction phase of the Calvin cycle, 3-PGA receives energy and electrons
from ATP and NADPH, leading to the formation of G3P. This step is essential for the synthesis of
carbohydrates.

Absorption spectrum: It is a graphical representation that shows the wavelengths of light absorbed by a
substance, revealing its unique pattern of absorption and providing insights into its molecular properties. In the
context of photosynthesis, it helps illustrate the specific wavelengths at which photosynthetic pigments, such as
chlorophyll, absorb light most effectively.

Accessory pigments: They are additional pigments that complement the action of primary pigments by
capturing light energy at different wavelengths and transferring it to the primary pigments. Chlorophyll-b and

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carotenoids are accessory pigments. Chlorophyll-b assists chlorophyll-a by capturing light energy in
wavelengths not absorbed efficiently by chlorophyll-a. Carotenoids, in addition to aiding in light absorption,
also provide photoprotection by dissipating excess light energy as heat.

Acetaldehyde: It is an intermediate compound in the process of alcohol fermentation, particularly during the
conversion of glucose to ethanol by yeast, such as Saccharomyces cerevisiae.

Acetyl coenzyme A (Acetyl CoA): It is a key molecule in cellular metabolism, serving as a central
intermediate in various metabolic pathways. Acetyl-CoA is formed in the mitochondria through the process of
pyruvate oxidation, which occurs after glycolysis in the presence of oxygen. Pyruvate, the end product of
glycolysis, undergoes oxidative decarboxylation, resulting in the formation of acetyl-CoA. It serves as a carrier
of acetyl groups (two-carbon units) derived from various metabolic sources, including glucose, fatty acids, and
amino acids. It acts as a central hub that integrates carbon molecules from different nutrients into a common
metabolic pool. It is a critical substrate for the citric acid cycle, also known as the Krebs cycle or tricarboxylic
acid (TCA) cycle. In the citric acid cycle, acetyl-CoA combines with oxaloacetate to form citrate, initiating a
series of reactions that ultimately lead to the release of carbon dioxide and the production of reducing
equivalents (NADH and FADH2).

ADP (Adenosine Diphosphate): ADP is a nucleotide molecule formed by the removal of one phosphate
group from ATP. It consists of two phosphate groups, a ribose sugar, and an adenine base. ADP is an
intermediate in cellular energy transfer. When cells require energy, ADP can be converted back to ATP
through the addition of a phosphate group, a process that typically occurs during cellular respiration and
photosynthesis.

Aerobic respiration: It is a biological process that extracts energy from organic molecules, typically glucose,
in the presence of oxygen. This process involves the complete oxidation of glucose to produce carbon dioxide,
water, and a large amount of adenosine triphosphate (ATP), which is the primary energy currency of the cell.
Aerobic respiration consists of multiple stages, including glycolysis, the transition reaction, the citric acid
cycle (Krebs cycle), and oxidative phosphorylation. The final stage, oxidative phosphorylation, takes place in
the mitochondria and involves the electron transport chain and ATP synthase. Aerobic respiration is highly
efficient, producing a maximum yield of ATP per glucose molecule.

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Alcoholic Fermentation: It is a metabolic process in which certain microorganisms, such as yeast, convert
sugars into ethanol (alcohol) and carbon dioxide. This anaerobic process is commonly used in the production
of alcoholic beverages, such as beer and wine, and has been exploited by humans for thousands of years.

AMP (Adenosine Monophosphate): AMP is a nucleotide molecule consisting of a single phosphate group, a
ribose sugar, and an adenine base. AMP is an intermediate in cellular energy transfer. It can be further
phosphorylated to ADP and ATP. While AMP is not as prevalent as ATP or ADP in energy transfer reactions,
it plays a role in certain cellular processes and signaling pathways.

Anabolism: The set of metabolic pathways that involve the synthesis of complex molecules from simpler
ones. It requires energy input and it is associated with the storage of energy.

Anaerobic respiration: It is a type of cellular respiration that occurs in the absence of oxygen. It involves the
partial oxidation of organic molecules to generate energy. Unlike aerobic respiration, anaerobic respiration
does not completely oxidize the substrate molecules, leading to the production of fewer ATP molecules per
substrate molecule. In anaerobic conditions, various electron acceptors other than oxygen are used in the final
steps of the electron transport chain. Common electron acceptors in anaerobic respiration include nitrate,
sulfate, and certain organic molecules. One of the byproducts of anaerobic respiration is often a compound
other than carbon dioxide, such as lactate or ethanol, depending on the organism and specific metabolic
pathways. While anaerobic respiration is less efficient than aerobic respiration in terms of ATP production, it
allows cells to generate energy in environments lacking oxygen.

Antenna Complex: It consists of an array of chlorophyll and accessory pigments surrounding the reaction
center within a photosystem. The primary function of the antenna complex is to capture light energy from
photons. The various pigments within the antenna complex have different absorption spectra, allowing them to
absorb light at different wavelengths. This broadens the range of light that can be effectively captured for
photosynthesis. Once light energy is absorbed, it is transferred from pigment to pigment until it reaches the
reaction center, where the conversion of light energy into chemical energy occurs.

ATP (Adenosine Triphosphate): ATP is a nucleotide molecule that serves as the primary energy currency in
cells. It consists of three phosphate groups, a ribose sugar, and an adenine base. ATP stores and transfers
energy within cells. The energy is released when the terminal phosphate bond is hydrolyzed, converting ATP
to ADP and releasing energy that is used for various cellular processes, such as muscle contraction, active
transport, and biosynthesis.

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ATP synthase: It is a complex enzyme located in the inner mitochondrial membrane in eukaryotic cells and
the plasma membrane of prokaryotic cells. It plays a central role in cellular respiration and photosynthesis,
facilitating the synthesis of ATP. ATP synthase is a remarkable molecular machine that exemplifies the
efficiency of cellular energy conversion. Its ability to couple proton flow with ATP synthesis provides cells
with a highly efficient mechanism for energy storage and utilization.

Autotrophy: A biological process by which organisms produce their own organic molecules, such as
carbohydrates, from inorganic sources like carbon dioxide and water.

Beta–oxidation: It is a catabolic process that takes place in the mitochondria of eukaryotic cells and the
cytoplasm of prokaryotic cells. This process is involved in the breakdown of fatty acids, specifically long-
chain fatty acids, to generate acetyl-CoA, which can enter the citric acid cycle (also known as the Krebs cycle)
for energy production through oxidative phosphorylation. Beta-oxidation is a crucial pathway for utilizing
stored fats as an energy source.

Blade: The broad, flat part of the leaf where most photosynthesis occurs, capturing sunlight for energy
conversion.

Bundle sheath cells: They are specialized cells arranged in tightly packed layers surrounding the vascular
bundles (veins) in the leaves of certain plants, particularly those employing the C4 photosynthetic pathway.
These cells play a crucial role in the C4 photosynthesis process by spatially separating the initial carbon
fixation and the Calvin cycle. In C4 plants, such as maize (corn) and sugarcane, the initial fixation of carbon
dioxide occurs in mesophyll cells, where phosphoenolpyruvate carboxylase (PEP carboxylase) catalyzes the
formation of a four-carbon compound, oxaloacetate, from phosphoenolpyruvate (PEP) and carbon dioxide. The
oxaloacetate is then converted to other four-carbon compounds (malate or aspartate) and transported to the
bundle sheath cells.

C3 Photosynthesis: The process in which plants fix carbon dioxide into a three-carbon compound during the
Calvin cycle. The first stable product formed during the Calvin cycle is 3-phosphoglycerate (3-PGA). This
three-carbon compound is produced when carbon dioxide (CO2) is fixed and incorporated into a five-carbon
sugar molecule, ribulose-1,5-bisphosphate (RuBP), with the help of the enzyme ribulose-1,5-bisphosphate
carboxylase/oxygenase (RuBisCO). The immediate product of this reaction is an unstable six-carbon
compound that immediately splits into two molecules of 3-PGA. The majority of plants, including most crops
and trees, employ C3 photosynthesis.

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C4 Photosynthesis: A photosynthetic pathway in which plants initially fix carbon dioxide into a four-carbon
compound before entering the Calvin cycle. In C4 photosynthesis, the first stable product is not 3-
phosphoglycerate (3-PGA), as in C3 photosynthesis, but rather a four-carbon compound known as
oxaloacetate. The initial step in C4 photosynthesis involves the fixation of carbon dioxide into
phosphoenolpyruvate (PEP) to form oxaloacetate, a reaction catalyzed by the enzyme PEP carboxylase. This
enzyme has a higher affinity for CO2 than does the enzyme RuBisCO (ribulose-1,5-bisphosphate
carboxylase/oxygenase), which is responsible for the initial fixation in C 3 photosynthesis. In C4
photosynthesis, there is a spatial separation of initial carbon fixation and the Calvin cycle, which occurs in two
types of photosynthetic cells: mesophyll cells and bundle-sheath cells. This separation is a distinctive feature of
C4 plants and contributes to their efficiency in concentrating carbon dioxide and reducing photorespiration,
particularly in hot and dry environments. This pathway is an adaptation to hot and arid conditions, and plants
using C4 photosynthesis include certain grasses and some crops like maize.

Calvin cycle: It is the second stage of photosynthesis, occurring in the stroma of chloroplasts, where carbon
dioxide is fixed and converted into glucose through a series of enzymatic reactions. It is a light-independent
process that relies on the ATP and NADPH produced during the light-dependent reactions to drive the
synthesis of organic molecules, supporting the growth and energy needs of plants. The key steps in the Calvin
Cycle are Carbon fixation, Reduction, Regeneration of RuBP and Synthesis of Carbohydrates.

CAM Photosynthesis (Crassulacean Acid Metabolism): A photosynthetic adaptation in which plants open
their stomata at night to take in carbon dioxide and fix it into organic acids. During the day, these acids release
carbon dioxide for use in the Calvin cycle. In CAM (Crassulacean Acid Metabolism) photosynthesis, the first
stable product is a four-carbon organic acid, typically malate or oxaloacetate. Unlike C3 and C4 photosynthesis,
CAM plants exhibit a temporal separation of carbon fixation. CAM photosynthesis is common in succulent
plants, such as cacti and some orchids, and is an adaptation to conserve water in arid environments.

Carbon cycle: It is a natural process that describes the movement of carbon through the Earth's atmosphere,
oceans, soil, and living organisms. It involves various interconnected processes such as photosynthesis,
respiration, decomposition, and combustion.

Carbon fixation: It is the process by which atmospheric carbon dioxide is "fixed" or incorporated into organic
molecules, particularly sugars, through the Calvin cycle. This crucial step occurs during the light-independent
reactions, specifically in the Calvin cycle, which takes place in the stroma of chloroplasts. The enzyme
RuBisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase) catalyzes the initial step of carbon fixation. It

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combines carbon dioxide (CO2) from the atmosphere with ribulose-1,5-bisphosphate (RuBP), a five-carbon
sugar with two phosphate groups.

Carotenes: They are a type of carotenoid pigment that consists of hydrocarbons, meaning they contain only
carbon and hydrogen atoms. Beta-carotene, alpha-carotene, and lycopene are examples of carotenes. Carotenes
are important pigments involved in photosynthesis. They absorb light in the blue and green regions of the
spectrum, complementing the absorption spectrum of chlorophyll. Carotenes contribute to the orange, red, and
yellow colors in various fruits and vegetables.

Carotenoids: They are a class of pigments that are widespread in nature, found in plants, algae, and some
bacteria. These pigments contribute to the vibrant colors of various fruits and vegetables and play essential
roles in photosynthesis and photoprotection. Carotenoids assist chlorophyll in capturing light energy during
photosynthesis by absorbing light in different regions of the spectrum (especially in the blue and green
wavelengths), thus broadening the range of light that can be used for energy conversion.

Catabolism: The set of metabolic pathways that involve the break down complex molecules into simpler ones,
releasing energy in the process. This energy is often used for various cellular activities. Catabolic processes are
crucial for extracting energy from nutrients, such as the breakdown of glucose during cellular respiration.

Chemical Energy: It is the potential energy stored in the bonds between atoms and molecules within chemical
compounds. It is released or absorbed during chemical reactions. In the context of photosynthesis, the chemical
energy stored in the form of glucose and other organic compounds is the result of converting light energy into
chemical energy through a series of biochemical reactions.

Chemiosmosis: It is a process that occurs in biological systems, specifically in the context of cellular
respiration and photosynthesis, where the movement of ions across a membrane is coupled to the synthesis of
ATP. It involves the generation of a proton gradient across a membrane and the subsequent flow of protons
back across the membrane through ATP synthase, leading to ATP production. In both cellular respiration and
photosynthesis, chemiosmosis couples the flow of protons across a membrane with the synthesis of ATP,
demonstrating a fundamental principle of energy conversion in living organisms.

Chlorophyll: It is a green pigment found in the chloroplasts of plant cells. Chlorophyll absorbs light in the red
and blue regions of the electromagnetic spectrum and reflects or transmits light in the green region, giving
plants their characteristic green color.

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Chlorophyll-a: It is the primary photosynthetic pigment in chloroplasts, responsible for capturing light energy
during the light-dependent reactions of photosynthesis. It absorbs light most effectively in the red and blue
regions of the electromagnetic spectrum and plays a central role in the conversion of light energy into chemical
energy, leading to the synthesis of ATP and NADPH.

Chlorophyll-b: It is an accessory photosynthetic pigment that works in conjunction with chlorophyll-a. It

absorbs light in slightly different wavelengths compared to chlorophyll-a. By capturing light energy in regions
where chlorophyll-a is less efficient, chlorophyll-b enhances the overall light absorption capacity of
photosynthetic organisms. It transfers absorbed energy to chlorophyll-a during photosynthesis.

Chloroplast: A specialized organelle found in plant cells and some algae, responsible for conducting
photosynthesis. Chloroplasts contain chlorophyll, enzymes, and other pigments that capture sunlight and
convert it into chemical energy to synthesize organic compounds.

Citrate: It is a key intermediate in the citric acid cycle, also known as the Krebs cycle or tricarboxylic acid
(TCA) cycle. Citrate is a tricarboxylic acid, meaning it contains three carboxyl groups. Its chemical structure
includes three carboxyl groups attached to a six-carbon tricarboxylic acid backbone. Citrate is formed in the
citric acid cycle when acetyl-CoA combines with oxaloacetate. The condensation reaction is catalyzed by the
enzyme citrate synthase.

Citric acid cycle: The citric acid cycle, also known as the Krebs cycle or tricarboxylic acid (TCA) cycle, is a
central component of cellular respiration. It takes place in the mitochondrial matrix of eukaryotic cells and the
cytoplasm of prokaryotic cells. The cycle is named after Sir Hans Krebs, who elucidated its key components in
the 1930s and 1940s.

CoA (coenzyme A): It is a coenzyme that functions as a carrier of acyl groups (acyl-CoA), which are essential
intermediates in various biochemical pathways. It is a small, water-soluble molecule composed of three main
components: Adenosine diphosphate (ADP), Pantothenic acid (vitamin B5) and 3'-phosphoadenosine
diphosphate (3'-phospho-ADP).

Compensation point: In photorespiration, it refers to the point at which the rates of carbon dioxide (CO2)
uptake and release through photorespiration are balanced. At this point, the net exchange of CO2 by the plant
becomes zero. The compensation point is influenced by various factors such as temperature, oxygen
concentration, and the efficiency of the photosynthetic and photorespiratory pathways. The compensation point
is particularly important in understanding the relationship between photosynthesis and photorespiration.

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Complex I: It is a crucial component of the electron transport chain (ETC) in mitochondria. Complex I is the
first and largest protein complex in the electron transport chain. It accepts electrons from NADH, a product of
glycolysis and the citric acid cycle. Complex I functions as a NADH dehydrogenase, catalyzing the transfer of
electrons from NADH to ubiquinone (coenzyme Q), a lipid-soluble carrier in the inner mitochondrial
membrane. As electrons move through Complex I, protons (H+ ions) are pumped across the inner
mitochondrial membrane from the matrix to the intermembrane space. This creates a proton gradient,
establishing the proton motive force.

Complex II: It is a critical component of the electron transport chain (ETC) in mitochondria. Complex II is
embedded in the inner mitochondrial membrane. It consists of four protein subunits, including flavoprotein and
iron-sulfur protein subunits, which are involved in the electron transfer reactions. Unlike Complex I in the
electron transport chain, Complex II does not pump protons across the inner mitochondrial membrane. As a
result, it does not directly contribute to the establishment of the proton motive force.

Complex III: Complex III, also known as cytochrome bc1 complex, is a crucial component of the electron
transport chain (ETC) in mitochondria. This protein complex is involved in the transfer of electrons from
ubiquinol to cytochrome c, facilitating the flow of electrons through the ETC. As electrons move through
Complex III, protons are pumped across the inner mitochondrial membrane from the mitochondrial matrix to
the intermembrane space. This contributes to the establishment of the proton motive force.

Complex IV: Complex IV, also known as cytochrome c oxidase, is a crucial component of the electron
transport chain (ETC) in mitochondria. This protein complex plays a central role in the final step of electron
transfer, facilitating the reduction of molecular oxygen to water. As electrons move through Complex IV,
protons are pumped across the inner mitochondrial membrane from the mitochondrial matrix to the
intermembrane space. This contributes to the establishment of the proton motive force.

Coupled reactions: The coordinated interaction of multiple chemical reactions, where the energy released in
one reaction (exergonic) is used to drive another reaction (endergonic). This coupling allows the overall
process to be energetically favorable and contributes to the efficiency of cellular processes. Cellular respiration
involves a series of coupled reactions to efficiently harvest energy from organic molecules and convert it into a
form (adenosine triphosphate, ATP) that cells can use for various functions. The coupling of reactions is
essential for maintaining energy flow and sustaining cellular activities.

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Creatine phosphate (Phosphocreatine): It is a compound that plays a crucial role in the energy metabolism
of cells, particularly in tissues with high and fluctuating energy demands, such as muscle cells. By
participating in coupled reactions, creatine phosphate helps maintain the cellular pool of ATP, ensuring a
readily available source of energy for various cellular processes It is a phosphorylated creatine molecule,
meaning it contains a phosphate group.

Cuticle: A waxy, protective layer on the leaf surface that minimizes water loss and protects against pathogens.

Cyclic Photophosphorylation: It is a type of light-dependent reaction in photosynthesis where electrons, after

being excited by light, follow a cyclic pathway in the thylakoid membrane. Electrons are returned to the
reaction center of the photosystem, and ATP is produced through chemiosmosis. In cyclic
photophosphorylation, the excited electrons from the reaction center of photosystem I are transferred to an
electron transport chain, creating a proton gradient across the thylakoid membrane. The flow of protons back
through ATP synthase generates ATP. Importantly, the electrons are cycled back to photosystem I, completing
a circular pathway.

Cytochrome b6f: It is a complex of proteins found in the thylakoid membrane of chloroplasts in plants. This
complex plays a crucial role in the light-dependent reactions of photosynthesis, facilitating the transfer of
electrons between Photosystem II (PSII) and Photosystem I (PSI). Cytochrome b6f is part of the electron
transport chain that helps generate the proton gradient necessary for ATP synthesis.

Cytochrome c: It is a small protein located in the intermembrane space of mitochondria. It transfers electrons
between Complex III and Complex IV.

Cytoplasm: It is the gel-like substance that fills the cell and surrounds the cellular organelles in eukaryotic
cells. It plays a crucial role in various cellular processes, including glycolysis.

Cytosol: The cytosol, also known as the cytoplasmic matrix, is the semi-fluid component of the cytoplasm that
surrounds organelles in eukaryotic cells. It plays a crucial role in cellular respiration, particularly in the
glycolysis pathway. Glycolysis, the first stage of cellular respiration, occurs in the cytosol.

Deamination: It is a biochemical process in amino acid metabolism that involves the removal of an amino
group (-NH2) from an amino acid. This process results in the formation of ammonia (NH3) and a keto acid.
Deamination is a key step in the catabolism of amino acids, allowing the body to utilize the carbon skeletons of
amino acids for energy production or other metabolic pathways.

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Dihydroxyacetone phosphate (DHAP): It is a three-carbon compound that serves as an intermediate in
several metabolic pathways, most notably in glycolysis. DHAP is formed during the second half of the
aldolase-catalyzed cleavage of fructose-1,6-bisphosphate in glycolysis. This cleavage results in two three-
carbon molecules: dihydroxyacetone phosphate (DHAP) and glyceraldehyde-3-phosphate (G3P).

Electron transport chain (ETC): It is a series of protein complexes and electron carriers embedded in the
inner mitochondrial membrane (in eukaryotes) or the thylakoid membrane (in chloroplasts). In prokaryotes, it
is located in the cell membrane rather. It plays a crucial role in cellular respiration and photosynthesis,
facilitating the movement of electrons and contributing to the production of energy-rich molecules. In cellular
respiration, the electron transport chain is part of the oxidative phosphorylation process that occurs in the inner
mitochondrial membrane. In photosynthesis, the electron transport chain is involved in the light-dependent
reactions that take place in the thylakoid membrane of chloroplasts.

Endergonic Reaction: It is a chemical reaction that absorbs energy from its surroundings. The products of
endergonic reactions have higher potential energy than the reactants, and these reactions are often associated
with anabolic processes, such as the synthesis of complex molecules like proteins or the formation of glucose
during photosynthesis.

Energy transformation: The process by which energy changes from one form to another. This conversion can
occur between various types of energy, such as potential to kinetic, electrical to thermal, or chemical to
mechanical.

Energy: The capacity or ability to do work.

Ethanol: It is the primary end product of alcohol fermentation, a metabolic process in which microorganisms,
especially yeast like Saccharomyces cerevisiae, convert sugars into alcohol and carbon dioxide in the absence
of oxygen. The production of ethanol is a key feature of various fermentation processes, including those used
in the production of alcoholic beverages and biofuels.

Exergonic Reaction: It is a chemical reaction that releases energy to its surroundings. Exergonic reactions
release energy to the surroundings, with the reactants having higher potential energy than the products. These
reactions are spontaneous, releasing energy that can be harnessed for cellular work, and are often associated
with catabolic processes, such as the breakdown of molecules during cellular respiration.

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FADH2 (Reduced Flavin Adenine Dinucleotide): It is a reduced form of FAD. It carries electrons and
functions as an electron donor in the electron transport chain. FADH₂ is a coenzyme that functions as an
electron carrier during the citric acid cycle of cellular respiration. Its role in accepting and transferring high-
energy electrons is crucial for the generation of ATP, providing an additional pathway for electron flow in the
respiratory chain.

Fermentation: It is a metabolic process that involves the conversion of sugars into other organic compounds,
often in the absence of oxygen. It is a common pathway used by microorganisms to produce energy when
oxygen is limited or unavailable. Fermentation can occur in various contexts, including the production of food
and beverages, industrial processes, and the metabolism of certain cells in the absence of oxygen.

Ferredoxin: It is an iron-sulfur protein that accepts electrons from Photosystem I and transfers them to
NADP+ reductase, facilitating the reduction of NADP+ to NADPH.

Fructose-1,6-bisphosphate: It is a key intermediate in the glycolytic pathway, playing a crucial role in the
breakdown of glucose to produce energy. Fructose-1,6-bisphosphate is formed in the third step of glycolysis.
In the preceding steps, glucose is phosphorylated to glucose-6-phosphate and then isomerized to fructose-6-
phosphate. Fructose-6-phosphate is then phosphorylated again at the 1-position by the enzyme
phosphofructokinase-1 (PFK-1), using ATP to form fructose-1,6-bisphosphate.

Fructose-6-phosphate: It is an important intermediate in cellular metabolism, particularly in glycolysis, where

it plays a crucial role in the conversion of glucose to pyruvate. Fructose-6-phosphate is formed in the second
step of glycolysis. In the first step, glucose is phosphorylated to glucose-6-phosphate, and then, in the second
step, an isomerization reaction occurs to convert glucose-6-phosphate into fructose-6-phosphate.

Fucoxanthin: It is a brown pigment found in the chloroplasts of brown algae (Phaeophyta) and diatoms. It is a
type of xanthophyll, which is a class of carotenoids that contain oxygen in their molecular structure. The
distinctive brown or olive-green color of these algae is largely attributed to the presence of fucoxanthin.

Fumarate: It is an intermediate in the Krebs cycle. Fumarate is formed in the citric acid cycle during the
dehydrogenation reaction of succinate. The enzyme succinate dehydrogenase, embedded in the inner
mitochondrial membrane, catalyzes the conversion of succinate to fumarate. Fumarate is hydrated to malate in
a reaction catalyzed by the enzyme fumarase or fumarate hydratase.

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Gibbs free energy change: The Gibbs free energy change (ΔG) is a thermodynamic parameter that describes
the amount of free energy available to do work in a system. It is widely used to predict the spontaneity of a
chemical reaction and provides insight into the thermodynamic favorability or unfavorability of a process.

Glucose: It is a primary respiratory substrate for many organisms, serving as a key source of energy through
the process of cellular respiration. Glucose is a highly energy-rich molecule. Through the process of cellular
respiration, organisms can extract a significant amount of energy stored in the chemical bonds of glucose. This
energy is then used to synthesize ATP.

Glucose-6-phosphate: It is an important intermediate in various metabolic pathways, and its presence marks
the commitment of glucose to specific cellular processes. Glucose-6-phosphate is formed in the first step of
glycolysis. This reaction involves the phosphorylation of glucose, catalyzed by the enzyme hexokinase (or
glucokinase in the liver). The reaction uses one molecule of ATP, resulting in the conversion of glucose to
glucose-6-phosphate.

Glyceraldehyde-3-phosphate (G3P): It is a crucial three-carbon molecule in the Calvin cycle. G3P is

produced during the reduction phase of the Calvin cycle, where carbon dioxide is fixed and converted into
organic compounds. Specifically, G3P is formed when 3-phosphoglycerate (3-PGA), a three-carbon molecule
generated in the initial stages of the Calvin cycle, is phosphorylated and reduced with the help of ATP
(adenosine triphosphate) and NADPH (nicotinamide adenine dinucleotide phosphate). G3P serves as a key
precursor for the synthesis of glucose and other carbohydrates, playing a central role in storing and
transporting energy produced during photosynthesis. Additionally, some of the G3P molecules are used to
regenerate the initial acceptor molecule, ribulose-1,5-bisphosphate (RuBP), ensuring the continuity of the
Calvin cycle.

Glyceraldehyde-3-phosphate dehydrogenase (GAPDH): It is an enzyme that plays a key role in both

glycolysis and the Calvin cycle. In glycolysis, GAPDH catalyzes the conversion of G3P to 1,3-
bisphosphoglycerate. In the Calvin cycle, it catalyzes the conversion of glyceraldehyde-3-phosphate (G3P) to
1,3-bisphosphoglycerate (BPG), which is then used to regenerate ribulose-1,5-bisphosphate (RuBP), the
starting molecule of the Calvin cycle.

Glycerol: Glycerol plays a crucial role as it is one of the products obtained during the breakdown of
triglycerides. Triglycerides are the primary storage form of fats in adipose tissue, and their hydrolysis during
lipolysis results in the release of glycerol and fatty acids. In the liver, glycerol can be converted into

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glyceraldehyde-3-phosphate through a series of enzymatic reactions. This glyceraldehyde-3-phosphate can
then enter gluconeogenesis, a pathway that leads to the synthesis of glucose.

Glycolysis: It is the metabolic pathway that breaks down glucose into two molecules of pyruvate, producing a
small amount of adenosine triphosphate (ATP) and reducing equivalents in the form of nicotinamide adenine
dinucleotide (NADH). Glycolysis is a central process in cellular respiration, occurring in the cytoplasm of the
cell, and it can operate in both aerobic and anaerobic conditions.

Granum: A stack of flattened thylakoid sacs arranged like pancakes within chloroplasts. Multiple granal
stacks collectively enhance the efficiency of light absorption and energy conversion during photosynthesis.

Guanosine triphosphate (GTP): It is a nucleotide and a close relative of adenosine triphosphate (ATP) that
serves as energy carriers in cellular processes. GTP consists of three phosphate groups, a ribose sugar, and a
guanine base. GTP is produced in the Krebs cycle through a substrate-level phosphorylation reaction. In one of
the steps of the Krebs cycle, succinyl-CoA is converted to succinate. This reaction is catalyzed by the enzyme
succinyl-CoA synthetase. During this conversion, a high-energy phosphate group is transferred to guanosine
diphosphate (GDP), forming guanosine triphosphate (GTP). GTP is involved in various cellular processes,
acting as an energy source for specific reactions. It plays a crucial role in protein synthesis during translation,
where it serves as an energy donor for the formation of peptide bonds between amino acids.

Heterotrophy: A mode of nutrition in which organisms obtain organic compounds and energy by consuming
pre-formed organic substances derived from other living organisms.

Inner mitochondrial membrane: It is a phospholipid bilayer that separates the mitochondrial matrix from the
intermembrane space. It is highly convoluted, forming cristae, which increase the surface area of the
membrane and provide a large surface area for oxidative phosphorylation, the process by which mitochondria
generate ATP.

Interganal Lamellae: The regions that connect and link the individual thylakoid stacks (grana) within
chloroplasts. These lamellae provide structural support and facilitate communication between thylakoids in
different granal stacks.

Intermembrane space: It is the region located between the inner and outer mitochondrial membranes in
mitochondria. During the process of oxidative phosphorylation, protons (H⁺ ions) are pumped across the inner
mitochondrial membrane from the matrix into the intermembrane space.

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Iron-Sulfur Proteins: They are non-heme iron-containing proteins that participate in electron transfer. They
are found in various complexes of the electron transport chain.

Isocitrate: It is an intermediate in the citric acid cycle, also known as the Krebs cycle or tricarboxylic acid
(TCA) cycle. Isocitrate is formed in the citric acid cycle through the isomerization of citrate. The enzyme
aconitase catalyzes this isomerization reaction, converting citrate into isocitrate.

Lactate: Lactate, also known as lactic acid in its ionized form, is an organic compound produced during lactic
acid fermentation. Lactate is a key intermediate in various metabolic processes, particularly in anaerobic
glycolysis and certain types of fermentation. Lactate is formed when pyruvate, a product of glycolysis, is
reduced during lactic acid fermentation. This process is catalyzed by the enzyme lactate dehydrogenase.

Lactic Acid Fermentation: It is a metabolic process in which sugars are converted into lactic acid by certain
microorganisms, particularly bacteria and some fungi. This anaerobic pathway is commonly employed in the
food industry for the production of fermented foods and beverages. Lactic acid fermentation is also relevant in
cellular metabolism, occurring in muscle cells during periods of intense physical activity when oxygen
availability is limited.

Leaf base: The part of a leaf where it attaches to the stem or a branch. It is the lowermost portion of the leaf,
often characterized by its point of attachment and the transition from the blade to the petiole.

Leaf epidermis: The outermost layer of cells covering the surface of a leaf. It serves as a protective barrier,
playing a crucial role in regulating water loss, preventing pathogens from entering, and providing some
defense against herbivores. The leaf epidermis typically consists of two main types of cells: upper epidermis
and lower epidermis.

Leaf: The primary organ of photosynthesis and transpiration in plants.

Light energy: It is a form of electromagnetic radiation that is visible to the human eye. It is part of the broader
electromagnetic spectrum and consists of photons. In the context of photosynthesis, light energy is absorbed by
photosynthetic pigments, such as chlorophyll, to initiate the process of converting light energy into chemical
energy.

Light-Dependent Reactions: They are the initial stage of photosynthesis that take place in the thylakoid
membranes of chloroplasts. These reactions involve the absorption of light by chlorophyll and other pigments
to generate chemical energy in the form of ATP and NADPH. During light-dependent reactions, light energy is

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used to split water molecules, releasing oxygen as a byproduct. The energy from this process is used to
generate ATP through photophosphorylation and reduce NADP+ to NADPH. The ATP and NADPH produced
in the light-dependent reactions are subsequently utilized in the Calvin cycle (light-independent reactions) to
convert carbon dioxide into carbohydrates.

Light-independent reactions: It is also known as the Calvin cycle or Calvin-Benson cycle. It is the second
stage of photosynthesis. Unlike the light-dependent reactions that occur in the thylakoid membrane and require
light energy, the light-independent reactions take place in the stroma of chloroplasts and do not directly rely on
light. It is responsible for converting carbon dioxide (CO2) into organic molecules, particularly glucose.

Lipolysis: It is the biological process through which triglycerides, stored in fat cells (adipocytes), are broken
down into glycerol and fatty acids. This process is a crucial aspect of energy metabolism and plays a
significant role in providing a source of energy during times of fasting or increased energy demand. Lipolysis
primarily occurs in adipose tissue and is regulated by various hormones.

Lower Epidermis: The lower layer of cells on the underside of the leaf. It contains tiny openings called
stomata, which regulate gas exchange (such as the uptake of carbon dioxide for photosynthesis and the release
of oxygen).

Malate: It is an intermediate in the Krebs cycle. Malate is formed in the citric acid cycle during the hydration
reaction of fumarate. The enzyme fumarase (or fumarate hydratase) catalyzes the conversion of fumarate to
malate. In photosynthesis, it is a four-carbon organic acid that plays a significant role in carbon fixation,
particularly in certain photosynthetic pathways, including C4 and CAM (Crassulacean Acid Metabolism)
photosynthesis. In these pathways, malate is involved in the transport of carbon dioxide (CO2) between
different cellular compartments and serves as an intermediate in the overall carbon fixation process.

Malic enzyme: It is an enzyme that plays a role in cellular metabolism, particularly in the conversion of malate
to pyruvate. There are two main types of malic enzyme: NAD-dependent malic enzyme (NAD-ME) and
NADP-dependent malic enzyme (NADP-ME). Both types are involved in different physiological processes
and are found in various organisms, including plants, animals, and microorganisms.

Mesophyll: The internal tissue within the leaves of plants, where most photosynthesis takes place. It is located
between the upper and lower epidermis and consists of two main types of cells: palisade and spongy
mesophyll.

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Metabolism: It is the sum total of all the chemical processes that occur within a living organism to maintain
life. Metabolism is typically divided into two main categories: anabolism and catabolism.

Midrib: The central, prominent vein running along the center of a leaf. It extends from the base of the leaf to
the tip and provides structural support for the leaf. The midrib is a part of the leaf's vascular system, containing
vascular tissues such as xylem and phloem.

Mitochondria: Double-membraned organelles found in the cells of eukaryotic organisms. Often referred to as
the "powerhouses of the cell," mitochondria are crucial for generating energy in the form of adenosine
triphosphate (ATP). Mitochondria have an outer membrane and an inner membrane, which encloses the
mitochondrial matrix. The inner membrane is extensively folded into structures called cristae, increasing the
surface area for various metabolic reactions. The mitochondrial matrix is the innermost compartment and
contains enzymes involved in the citric acid cycle (Krebs cycle) and fatty acid oxidation.

Mitochondrial matrix: It is the central compartment within mitochondria, the double-membraned organelles
found in eukaryotic cells. It plays a crucial role in various metabolic processes, including the citric acid cycle
(Krebs cycle) and the conversion of pyruvate to acetyl-CoA. The matrix contains a semi-fluid substance with a
composition similar to the cytoplasm of the cell. It contains water, ions, enzymes, mitochondrial DNA
(mtDNA), and ribosomes.

NADH (Reduced Nicotinamide Adenine Dinucleotide): It is a reduced form of NAD+ that carries high-
energy electrons. It is a key electron donor in the early stages of the electron transport chain. It is a coenzyme
that plays a fundamental role in cellular respiration, which is the process by which cells generate energy in the
form of adenosine triphosphate (ATP). NADH functions as an electron carrier, shuttling high-energy electrons
from one set of reactions to another within the cell.

NADP (Nicotinamide Adenine Dinucleotide Phosphate): It is a coenzyme derived from NAD (Nicotinamide
Adenine Dinucleotide) by the addition of an extra phosphate group. It exists in two forms: NADP+ (oxidized
form) and NADPH (reduced form). NADP acts as an electron carrier in anabolic reactions, particularly those
involved in biosynthesis, such as fatty acid and nucleotide synthesis. It is a crucial player in the light-
dependent reactions of photosynthesis, where it participates in the reduction of carbon dioxide to form
carbohydrates.

NADP+ reductase: It is also known as ferredoxin-NADP+ reductase (FNR). It is an enzyme that plays a crucial
role in the light-dependent reactions of photosynthesis. This enzyme is involved in the reduction of NADP +

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(Nicotinamide Adenine Dinucleotide Phosphate) to NADPH, which is a key molecule in the synthesis of
organic compounds during photosynthesis.

NADPH (Reduced Nicotinamide Adenine Dinucleotide Phosphate): It is the reduced form of NADP,
meaning it has gained electrons and a hydrogen ion. It is the active, energy-rich form of the coenzyme.
NADPH serves as a reducing agent in various cellular processes. It provides the necessary reducing power
(electrons and hydrogen ions) for anabolic reactions, helping in the synthesis of macromolecules like lipids and
nucleic acids. In photosynthesis, NADPH is produced during the light-dependent reactions and utilized in the
Calvin cycle to reduce carbon dioxide and form carbohydrates.

Non-Cyclic Photophosphorylation: It is a type of light-dependent reaction where electrons flow in a linear

pathway, ultimately reducing NADP+ to NADPH. Both ATP and NADPH are produced during this process. In
non-cyclic photophosphorylation, light energy is absorbed by both photosystem I and photosystem II.
Electrons are excited in photosystem II, and water molecules are split, releasing electrons, protons, and
oxygen. The electrons follow a linear pathway, moving from photosystem II to photosystem I, generating ATP
and reducing NADP+ to NADPH. Oxygen released in this process is a byproduct of water splitting.

Oxaloacetate: It is a four-carbon compound that plays a role in certain phases of photosynthesis, particularly
in the C4 photosynthetic pathway. In C4 plants, such as maize (corn) and sugarcane, oxaloacetate is involved in
the initial steps of carbon fixation and is an intermediate in the conversion of atmospheric carbon dioxide
(CO2) into organic compounds.

Oxidative phosphorylation: It is a fundamental process that takes place in the mitochondria of eukaryotic
cells, where energy is extracted from nutrients to produce adenosine triphosphate (ATP), the primary energy
currency of the cell. This process involves a series of redox reactions and the flow of electrons through protein
complexes in the inner mitochondrial membrane.

Oxygen: It serves as the final electron acceptor in the electron transport chain (ETC) during cellular
respiration. This process occurs in the inner mitochondrial membrane (in eukaryotes) or the plasma membrane
(in prokaryotes). The transfer of electrons through the ETC ultimately leads to the reduction of molecular
oxygen (O2) to water (H2O).

P680: It stands for the reaction center chlorophyll molecule that absorbs light at a wavelength of around 680
nanometers. P680 is associated with Photosystem II (PSII), the first photosystem in the light-dependent

17
reactions of photosynthesis. It plays a crucial role in the primary photochemical reaction of PSII, where it
absorbs light energy and undergoes photoexcitation, leading to the release of high-energy electrons.

P700: It stands for the reaction center chlorophyll molecule that absorbs light at a longer wavelength, around
700 nanometers. P700 is associated with Photosystem I (PSI), the second photosystem in the light-dependent
reactions. It plays a key role in the photochemical reactions of PSI, where it absorbs light energy and
participates in the generation of reducing power needed for the reduction of NADP+ to NADPH.

Palisade Mesophyll: The layer of cells in the leaf responsible for most photosynthesis, located beneath the
upper epidermis.

Petiole: The stalk that connects the leaf blade to the stem, providing support and facilitating nutrient transport.

Phosphoanhydride bonds: They are high-energy bonds that link the phosphate groups in certain molecules,
particularly in compounds like adenosine triphosphate (ATP) and guanosine triphosphate (GTP). These bonds
store and release energy during cellular processes, making them crucial for various biochemical reactions. In
the context of ATP, which is often referred to as the "energy currency" of cells, the phosphoanhydride bonds
connect the three phosphate groups. The hydrolysis of these bonds releases energy that can be used for cellular
activities.

Phosphoenolpyruvate (PEP): It is a versatile molecule involved in both glycolysis and certain phases of
photosynthesis. In glycolysis, PEP is an intermediate in the second half of glycolysis and is formed from 2-
phosphoglycerate during the conversion of phosphoenolpyruvate to pyruvate. The reaction is catalyzed by the
enzyme enolase. PEP is a high-energy compound, and its subsequent conversion to pyruvate generates ATP
during the final steps of glycolysis. In certain photosynthetic pathways, such as C4 and CAM photosynthesis,
PEP is involved in the initial steps of carbon fixation. Here, PEP carboxylase catalyzes the carboxylation of
PEP to form oxaloacetate, which is subsequently converted to other four-carbon compounds. This occurs in
mesophyll cells of C4 plants during the day and in CAM plants during the night.

Phosphoenolpyruvate carboxylase (PEP carboxylase): It is a key enzyme involved in certain metabolic

pathways, particularly in photosynthesis. It catalyzes the carboxylation of phosphoenolpyruvate (PEP), a three-
carbon compound, to form oxaloacetate, a four-carbon compound. This enzyme plays a significant role in the
initial fixation of carbon dioxide (CO2) in certain photosynthetic pathways, including C4 and CAM
(Crassulacean Acid Metabolism) photosynthesis.

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Phosphoglycolate: It is a two-carbon compound that is a byproduct of the oxygenation reaction catalyzed by
the enzyme RuBisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase) during the process of
photorespiration in plants.

Photolysis: It is a process in which light energy is used to break down or split a chemical compound. In the
context of photosynthesis, the term "photolysis" commonly refers to the light-driven splitting of water
molecules (H2O) during the light-dependent reactions in chloroplasts. This process takes place in the thylakoid
membrane and is a crucial step in the generation of chemical energy. It not only provides electrons to replace
those lost during the absorption of light by chlorophyll but also releases molecular oxygen as a byproduct,
which is essential for sustaining aerobic life on Earth.

Photophosphorylation: It is a process that occurs during the light-dependent reactions of photosynthesis,

where light energy is used to generate ATP (adenosine triphosphate) from ADP (adenosine diphosphate) and
inorganic phosphate (Pi). There are two main types of photophosphorylation: cyclic and non-cyclic.

Photorespiration: It is a process in which oxygen competes with carbon dioxide at the active site of the
enzyme RuBisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase). It leads to the formation of 3-
phosphoglycerate and 2-phosphoglycolate. The 2-phosphoglycolate undergoes a series of reactions in the
peroxisomes and mitochondria, leading to the formation of glycolate. Glycolate is then transported to the
chloroplast. In the chloroplast, glycolate is converted to glyoxylate, and subsequently to glycerate. This
conversion involves the release of one molecule of carbon dioxide and consumes ATP. Glycerate re-enters the
Calvin cycle, contributing to 3-phosphoglycerate production. Overall, photorespiration consumes oxygen,
releases carbon dioxide, and diminishes the efficiency of photosynthesis. C4 and CAM plants have evolved
strategies to minimize photorespiration, enhancing their photosynthetic efficiency in challenging environments.

Photosynthesis: The process by which green plants, algae, and some bacteria convert light energy into
chemical energy stored in the form of glucose or other organic molecules.

Photosynthetic pigments: They are molecules that play a crucial role in the process of photosynthesis. These
pigments absorb light in specific wavelengths and are responsible for capturing and transferring light energy to
drive the photosynthetic reactions. The absorption of light by these pigments initiates a series of biochemical
reactions that ultimately lead to the synthesis of organic compounds.

Photosystem I (PSI): It is the second photosystem in the light-dependent reactions of photosynthesis,

positioned downstream of Photosystem II. PSI absorbs light energy, primarily in the P700 range (wavelength

19
around 700 nanometers). Photons of light energize electrons in PSI, and these energized electrons are passed
through a second electron transport chain. PSI provides the energy needed to reduce NADP+ (Nicotinamide
Adenine Dinucleotide Phosphate) to NADPH. Electrons from PSI, along with protons, combine with NADP +
to produce NADPH. PSI can also participate in cyclic electron flow, where electrons are recycled back to PSI
without reducing NADP+.

Photosystem II (PSII): It is the first photosystem in the light-dependent reactions of photosynthesis. It is

responsible for absorbing light energy and initiating the process of photosynthesis. PSII absorbs photons of
light, primarily in the P680 range (wavelength around 680 nanometers). Photons of light energize electrons in
PSII, which are then transferred to an electron transport chain. PSII also facilitates the splitting of water
molecules into oxygen, protons (H⁺), and electrons. Oxygen is released as a byproduct. Electrons from water
move through the electron transport chain, creating a proton gradient across the thylakoid membrane.

Photosystem: It is a complex of proteins, pigments, and other molecules found in the thylakoid membrane of
chloroplasts and in the membranes of certain photosynthetic bacteria. Photosystems play a central role in the
process of photosynthesis, where they capture and convert light energy into chemical energy, ultimately
leading to the synthesis of organic compounds. There are two main photosystems in the thylakoid membrane:
Photosystem II (PSII) and Photosystem I (PSI). These photosystems work together in a series of light-
dependent reactions, contributing to the conversion of light energy into chemical energy, which is then used in
the synthesis of carbohydrates during the light-independent reactions (Calvin cycle) of photosynthesis.

Phycobilins: They are water-soluble mostly red, orange, and blue pigments found in cyanobacteria and some
eukaryotic algae. Phycobilins are responsible for the blue-green color of many of these organisms.

Plastocyanin: It is a copper-containing protein that transfers electrons from cytochrome b6f to Photosystem I.

Plastoquinone: It is a mobile electron carrier in the thylakoid membrane during the light-dependent reactions
of photosynthesis. It transfers electrons from Photosystem II to the cytochrome b6f complex.

Primary pigments: They are the main pigments directly involved in the light-absorption and light-dependent
reactions of photosynthesis. Chlorophyll-a is the primary pigment in the chloroplasts of plants. It plays a
central role in capturing light energy and initiating the process of photosynthesis.

Propionyl–CoA: It is an intermediate in metabolism that plays a role in the breakdown of certain fatty acids
and amino acids. It is a three-carbon compound with a coenzyme A (CoA) group attached to it. Propionyl-CoA

20
is particularly important in the catabolism of odd-chain fatty acids and certain amino acids with an odd number
of carbon atoms.

Proton gradient: It is a difference in proton (H⁺ ion) concentration across a biological membrane, creating an
electrochemical potential. This gradient is a form of stored energy that arises when protons are actively
transported across the membrane, typically against their concentration gradient. Proton gradients are essential
in various cellular processes, and one of their primary roles is to provide the energy needed for ATP synthesis.

Proton pump: A mechanism that actively transports protons (hydrogen ions, H⁺) across a membrane against a
concentration gradient. This process involves the movement of protons from an area of lower concentration to
an area of higher concentration, consuming energy in the form of ATP (adenosine triphosphate) or utilizing
other sources of energy.

Pyruvate oxidation: It is a crucial step in cellular respiration that links glycolysis with the citric acid cycle
(also known as the Krebs cycle). It occurs in the mitochondrial matrix, and its primary purpose is to further
break down the three-carbon pyruvate molecules produced during glycolysis into acetyl-CoA. Acetyl-CoA
then enters the citric acid cycle to generate more reduced cofactors and contribute to the overall production of
adenosine triphosphate (ATP) through oxidative phosphorylation.

Pyruvate: It is the end product of glycolysis, the initial stage of cellular respiration that takes place in the
cytoplasm of cells. In glycolysis, one molecule of glucose (a six-carbon sugar) is broken down into two
molecules of pyruvate (each containing three carbons). Pyruvate acts as a central player in the transition
between glycolysis and aerobic respiration.

Reaction Center: It is a specialized chlorophyll molecule within the photosystem that plays a central role in
converting light energy into chemical energy. When a photon of light is absorbed by the antenna complex, the
energy is transferred to the reaction center chlorophyll. The reaction center chlorophyll undergoes a
photochemical reaction, resulting in the release of high-energy electrons. These electrons are then used in
subsequent electron transport processes to generate a proton gradient and produce chemical energy in the form
of ATP and NADPH.

Reduction phase of the Calvin cycle: It is a series of biochemical reactions that occur within the stroma of
chloroplasts during the light-independent reactions of photosynthesis. The reduction phase follows the carbon
fixation phase, during which atmospheric carbon dioxide is incorporated into an organic molecule (3-
phosphoglycerate, 3-PGA) with the help of the enzyme RuBisCO. In the reduction phase, each molecule of 3-

21
phosphoglycerate (3-PGA) is phosphorylated and reduced. ATP (adenosine triphosphate) donates a phosphate
group to each molecule of 3-PGA. NADPH (nicotinamide adenine dinucleotide phosphate), which carries
high-energy electrons, donates electrons to the phosphorylated 3-PGA, resulting in the conversion of 3-PGA
into glyceraldehyde-3-phosphate (G3P).

Respiration: It is a process that generates ATP by breaking down organic molecules. The primary purpose of
cellular respiration is to produce energy in the form of ATP, which is utilized by cells for various functions.
The overall process involves the oxidation of organic molecules, such as glucose, and the transfer of electrons
through a series of biochemical pathways. There are two main types of cellular respiration: Aerobic respiration
and Anaerobic respiration.

RuBisCO (Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase): It is an enzyme that plays a central role in

the Calvin cycle. It is responsible for catalyzing the first major step in carbon fixation by facilitating the
incorporation of carbon dioxide (CO2) into an organic molecule during photosynthesis. RuBisCO is an enzyme
with dual functionality. It can carboxylate ribulose-1,5-bisphosphate (RuBP), leading to the formation of 3-
phosphoglycerate (3-PGA) in the presence of CO2. However, RuBisCO can also react with oxygen (O2),
initiating a process called photorespiration, which can be considered a wasteful side reaction under certain
conditions.

RuBP (Ribulose-1,5-Bisphosphate): It is a five-carbon sugar molecule with two phosphate groups attached. It
is the initial acceptor of carbon dioxide in the Calvin cycle, serving as the substrate for the action of RuBisCO.
RuBP is crucial in the Calvin cycle as it combines with carbon dioxide in the presence of RuBisCO, resulting
in the formation of an unstable six-carbon compound that immediately breaks down into two molecules of 3-
phosphoglycerate (3-PGA). The regeneration of RuBP is also an essential step in the continuation of the Calvin
cycle.

Spongy Mesophyll: The tissue beneath the palisade mesophyll that aids in gas exchange and contains air
spaces.

Standard enthalpy change: The standard enthalpy change (ΔHO) is a thermodynamic quantity that represents
the heat absorbed or released during a chemical reaction under standard conditions. Standard conditions
typically refer to a pressure of 1 atmosphere (atm) and a temperature of 25 degrees Celsius. The standard
enthalpy change is a key parameter in understanding the thermodynamics of chemical reactions and is often
used to calculate the heat of reaction.

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Stomata: Small pores on the leaf surface that allow gas exchange, enabling the uptake of carbon dioxide for
photosynthesis and the release of oxygen.

Stroma: The gel-like matrix or fluid-filled space that surrounds the thylakoid membranes inside a chloroplast.
The stroma plays a crucial role in the second stage of photosynthesis, known as the light-independent reactions
or the Calvin cycle.

Succinate: It is an intermediate in the citric acid cycle. Succinate is formed in the citric acid cycle during the
conversion of succinyl-CoA to succinate. The enzyme succinyl-CoA synthetase catalyzes this reaction, leading
to the release of CoA and the generation of ATP through substrate-level phosphorylation. It contributes to the
generation of reducing equivalents (FADH2) and serving as a substrate for the subsequent reactions in the
cycle.

Succinyl-CoA: It is an intermediate in the citric acid cycle. Succinyl-CoA is formed in the citric acid cycle
during the conversion of α-ketoglutarate to succinate. The enzyme α-ketoglutarate dehydrogenase complex
catalyzes this reaction, leading to the release of carbon dioxide and the formation of succinyl-CoA. Succinyl-
CoA is a crucial intermediate in the citric acid cycle, contributing to the generation of reducing equivalents
(NADH and FADH2) and ATP precursors. The conversion of succinyl-CoA to succinate is a key reaction for
the production of ATP in the citric acid cycle. It represents one of the steps where ATP is directly generated
through substrate-level phosphorylation.

Thylakoid Lumen: The interior space or compartment enclosed by the thylakoid membrane, where protons
(H⁺ ions) accumulate during the light-dependent reactions of photosynthesis.

Thylakoid Membranes: The phospholipid bilayer within thylakoids that houses the photosynthetic pigments
and protein complexes involved in capturing and converting light energy during photosynthesis.

Thylakoids: Flattened, membranous sacs inside chloroplasts that contain the pigments and molecular
machinery necessary for the light-dependent reactions of photosynthesis.

Transition reaction: The transition reaction, also known as the link reaction or pyruvate decarboxylation, is a
critical step in aerobic cellular respiration. It connects the glycolysis pathway, which occurs in the cytoplasm,
with the citric acid cycle (Krebs cycle), which takes place in the mitochondrial matrix. The primary goal of the
transition reaction is to convert the three-carbon pyruvate molecules produced during glycolysis into acetyl-
CoA, a two-carbon compound that can enter the citric acid cycle.

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Ubiquinone (Coenzyme Q): It is a mobile electron carrier that moves within the inner mitochondrial
membrane. It accepts electrons from both NADH and FADH2 and transfers them to Complex III.

Upper Epidermis: The upper layer of cells on the top surface of the leaf. It is often transparent and lacks
chloroplasts, allowing light to pass through to the underlying photosynthetic cells.

Veins: Vascular bundles within the leaf that transport water, nutrients, and sugars. Veins include xylem (for
water transport) and phloem (for nutrient transport).

Wavelength: It refers to the characteristic distance between successive peaks or troughs of electromagnetic
waves, particularly those within the visible light spectrum. Different pigments have distinct absorption spectra,
meaning they absorb light most efficiently at specific wavelengths. Shorter wavelengths correspond to higher
energy, while longer wavelengths correspond to lower energy.

Xanthophylls: They are a type of carotenoid pigment that contains oxygen in their chemical structure. The
name "xanthophyll" is derived from Greek words meaning "yellow leaves." Xanthophylls play a crucial role in
photosynthesis by absorbing light energy in different regions of the spectrum, particularly in the blue and green
wavelengths. They also contribute to the yellow and brown colors in leaves.

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