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PORTFOLIO ACTIVITY
UNDERSTANDING ENERGY PRODUCTION IN PLANTS AND ANIMALS
Learning outcomes Understand the process of energy production in plants and animals Understand how energy from food is broken down to ATP Explain and understand the glycolysis Explain and understand Krebs cycle Explain and understand the electron transfer chain Explain and understand oxidative phosphorylation what is energy and why is it important in biological systems? Energy Is a property of all matter and it is defined as the capacity to do work it is neither created nor destroyed however, it can be transduced (converted) from one form to another. Energy is stored and utilized in a specific molecule called Adenosine triphosphate or ATP which is the primary energy currency in cells. ATP stores energy in phosphate ester bonds, releasing energy when the phosphodiester bonds are broken: ATP is converted to ADP and a phosphate group. ATP is produced by the oxidative reactions in the cytoplasm and mitochondrion of the cell, where carbohydrates, proteins, and fats undergo a series of metabolic reactions collectively called cellular respiration. This energy is used to facilitate all the cellular activities in living organisms such as chemical reactions, growth, muscle contractions etc… cells are capable of chemical transduction: chemical energy stored in biomolecules such as ATP is converted into mechanical energy when organelles move from one place to another in a cell, electrical energy when ions flow across a membrane or thermal energy when heat is released during muscle contraction. How do plants produce and store energy? Photosynthesis is the process by which phototrophs (plants) trap sunlight energy in their leaves or stems by the chlorophyll pigment to convert carbon dioxide and water into glucose (chemical energy) which is later used to fuel cellular activities.
- Light- Dependent Reaction of photosynthesis - This occurs in the thylakoid membranes of the chloroplast. These reactions harnesses sunlight energy converting it into chemical energy in the form of ATP and NADPH. - These process begins when photons strike chlorophyll molecules, exciting electrons to a higher energy state. - This excitation propels the electrons through a series of events known as the electron transport chain - As electrons transverse this chain they release energy which is used to pump proteins into the thylakoid lumen creating a proton gradient. - This gradient is a form of potential energy like water held behind a dam. - The enzyme ATP synthase, embedded in the thylakoid membrane exploits this gradient to synthesize ATP from ADP and inorganic phosphate. This process is known as phosphorylation. - Simultaneously the electrons that are have travelled through the ETC are transferred through the NADP+ reducing it to NADPH and oxygen is released as byproducts of these two reactions
2. Calvin cycle/ light independent reaction - This takes place in the stroma of the chloroplasts, it doesn’t require light but it uses the ATP and NADPH produced in the light reaction as the energy source to carry out this process. i. Carbon fixation: this initial step is catalyzed by the enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase, commonly known as RuBisCO where carbon dioxide is attached to a five carbon sugar, ribose Bisphosphate (RuPB), producing an unstable six- carbon intermediate. This intermediate quickly splits into two molecules of 3-phospoglycerate(3PGA). ii. Reduction phase: ATP phosphorylates the 3PGA molecules by adding a phosphate group to form 1,3-bisphosphoglycerate (1,3-BPG) - NADPH then reduces this 1,3-bisphosphoglycerate (1,3-BPG) to form glyceraldehyde- 3 - phosphate (GP3), a three carbon sugar. iii. GP3 utilization: some of this exits the cycle to contribute to the synthesis of glucose and other carbohydrates. The remaining G3P molecules are used to regenerate RuBP, ensuring the cycle can continue. ATP is used in this step to help rearrange G3P back into RuBP. 3. Glycolysis - is a foundational metabolic pathway that sets the stage for energy extraction from glucose, it occurs in the cytoplasm of cells independently of oxygen. I. Initiation phosphorylation: ATP is used to phosphorylate glucose to form glucose - 6 - phosphate, which is rearranged into fructose, followed by usage of a second ATP molecule to produce fructose-1,6-bisphosphate. II. Cleavage of Fructose :1,6-Bisphosphate: The six-carbon molecule is split into two three- carbon molecules, glyceraldehyde- 3 - phosphate (G3P) and dihydroxyacetone phosphate. The latter can be converted into G3P. III. Energy harvesting: each G3P undergoes oxidation where their electrons are lost or transferred to NAD+ to form NADH. IV. Formation of pyruvate: theses intermediate of two three-carbons molecules are converted into pyruvate accompanied by the production of ATP via substrate-level phosphorylation (a direct transfer of a phosphate group to ADP) 4. Krebs Cycle or citric Acid cycle – occurs in the mitochondria where the pyruvate molecules derived from glycolysis are further oxidized. I. Formation of citrate: integration of Acetyl-CoA derived from pyruvate into a four carbon compound called oxaloacetate to form a citrate (six carbon) II. Conversion to Isocitrate – Citrate undergoes rearrangement forming isocitrate, another six carbon molecule III. Oxidation and release of carbon dioxide : isocitrate is oxidized and one molecule of carbon dioxide is released. NAD+ is reduced to NADH capturing high energy electrons. The resulting compound is further oxidized to release a second molecule of carbon dioxide. Another NAD+ is converted to NADH.A molecule of CoA is attached, forming succinyl-CoA IV. Production of ATP: conversion of succinyl-CoA succinate and one molecule of ATP is produced by substrate phosphorylation V. FADH₂ Formation - Succinate is oxidized to fumarate, and FAD (another electron carrier) is reduced to FADH₂ VI. Regeneration of Oxaloacetate : fumarate is converted to malate which is then oxidized to regenerate oxaloacetate also reducing NAD+ to NADH.
Step 2: In the second step of glycolysis, an isomerase converts glucose- 6 - phosphate into its isomer, fructose- 6 - phosphate. This enzyme facilitates the rearrangement of the molecule, a crucial change that prepares the sugar for its eventual division into two three-carbon molecules later in the pathway (OpenStax, LibreTextsBiology, n.d.). Step 3: In the third step of glycolysis, the enzyme phosphofructokinase catalyzes the phosphorylation of fructose- 6 - phosphate, by use of a second ATP molecule to produce fructose-1,6-bisphosphate. This step is regulated by phosphofructokinase, a rate-limiting enzyme. It becomes more active when ADP levels are high and less active when ATP levels are sufficient, slowing the pathway through end product inhibition to prevent excess ATP production (OpenStax, LibreTextsBiology, n.d.). Step 4. In the fourth step of glycolysis, the enzyme aldolase cleaves fructose-1,6-bisphosphate, which has been destabilized by the addition of high-energy phosphates. This reaction produces two three-carbon isomers: dihydroxyacetone-phosphate (DHAP) and glyceraldehyde- 3 - phosphate (G3P) (OpenStax, LibreTextsBiology, n.d.). Step 5. In the fifth step of glycolysis, an isomerase converts dihydroxyacetone-phosphate (DHAP) into its isomer, glyceraldehyde- 3 - phosphate (G3P). This allows the pathway to proceed with two identical G3P molecules. At this stage, the cell has made a net investment of energy from two ATP molecules to break down one glucose molecule (OpenStax, LibreTextsBiology, n.d.). Figure 1 shows the first phase of glycolysis
Second Half of Glycolysis (Energy-Releasing Steps)
Step 6. In the sixth step of glycolysis, the enzyme glyceraldehyde- 3 - phosphate dehydrogenase oxidizes glyceraldehyde- 3 - phosphate, extracting high-energy electrons that are transferred to NAD+, forming NADH. The sugar molecule is then phosphorylated with the addition of a second phosphate group, producing 1,3-bisphosphoglycerate. Importantly, this phosphorylation does not require an additional ATP molecule (OpenStax, LibreTextsBiology, n.d.). A key limiting factor for this step is the availability of NAD+, the oxidized form of the electron carrier. NADH must be continuously oxidized back into NAD+ to allow the reaction to continue. In the presence of oxygen, this occurs indirectly through the electron transport chain, with the high-energy electrons from NADH being used to produce ATP. However, in the absence of oxygen, fermentation provides an alternate pathway to regenerate NAD+ by oxidizing NADH (OpenStax, LibreTextsBiology, n.d.). Step 7. In the seventh step of glycolysis, the enzyme phosphoglycerate kinase catalyzes the transferring of a high-energy phosphate group from 1,3-bisphosphoglycerate to ADP, that results in the formation of one
ATP molecule. This is an example of substrate-level phosphorylation. During this reaction, the carbonyl group on 1,3-bisphosphoglycerate is oxidized to a carboxyl group, producing 3-phosphoglycerate. Step 8: In the eighth step, the remaining phosphate group in 3 - phosphoglycerate moves from the third carbon to the second carbon, producing 2-phosphoglycerate (an isomer of 3-phosphoglycerate). The enzyme catalyzing this step is a mutase (isomerase). Step 9. In the ninth step of glycolysis, enolase catalyzes a dehydration reaction, where 2- phosphoglycerate loses a water molecule forming a double bond, increasing the potential energy of the remaining phosphate bond and producing phosphoenolpyruvate (PEP) Step 10. The final step of glycolysis, catalyzed by pyruvate kinase, involves phosphoenolpyruvate (PEP) donation of a high-energy phosphate group to ADP, resulting in the formation of ATP through substrate- level phosphorylation. This reaction produces pyruvic acid (or pyruvate in its salt form). Notably, many enzymes, including pyruvate kinase, are named for their reverse reactions, as these were often observed under non-physiological conditions in laboratory settings (OpenStax, LibreTextsBiology, n.d.). Figure 2 shows the 2nd phase of glycolysis Oxidation of pyruvate and the citric acid cycle The pyruvate molecules produced at the end of glycolysis are transported into mitochondria, which are the sites of cellular respiration. There, pyruvate will be transformed into an acetyl group that will be picked up and activated by a carrier compound called coenzyme A (CoA) resulting in a compound called acetyl CoA before entering the citric acid cycle (OpenStax, Biolibretexts, n.d.) Step 1: A carboxyl group is removed from pyruvate, releasing carbon dioxide. The remaining two-carbon hydroxyethyl group becomes bound to the enzyme pyruvate dehydrogenase. This step occurs twice for every glucose molecule metabolized, removing two of the six carbons (OpenStax, LibreTextsBiology, n.d.). Step 2: The hydroxyethyl group is oxidized to form an acetyl group. Electrons released during this process are picked up by NAD+, producing NADH, which will later contribute to ATP generation (OpenStax, LibreTextsBiology, n.d.).
Step 3. In step three, isocitrate is oxidized, producing a five-carbon molecule, α-ketoglutarate, together with a molecule of CO2 and two electrons, which reduce NAD+ to NADH. This step is also regulated by negative feedback from ATP and NADH, and a positive effect of ADP (OpenStax, n.d.). Step 4. Steps three and four of the citric acid cycle involve oxidation and decarboxylation reactions. In both steps, electrons are released and transferred to NAD+, reducing it to NADH, while carboxyl groups are removed to form CO₂ molecules. Step three produces α-ketoglutarate, while step four generates a succinyl group, which binds to Coenzyme A (CoA) to form succinyl CoA. The enzyme catalyzing step four is regulated by feedback inhibition from ATP, succinyl CoA, and NADH (OpenStax, n.d.). Step 5. In step five of the citric acid cycle, a phosphate group replaces coenzyme A, forming a high- energy bond. This energy drives substrate-level phosphorylation, converting succinyl CoA into succinate and producing either guanine triphosphate (GTP) or ATP. The specific product depends on the tissue's enzyme isoform: in energy-demanding tissues like heart and skeletal muscle, ATP is formed; in anabolic tissues like the liver, GTP is produced. Although GTP is equivalent in energy to ATP, its use is more specialized, such as in protein synthesis (OpenStax, n.d.). Step 6. In step six of the citric acid cycle, succinate is converted into fumarate through a dehydration process. During this reaction, two hydrogen atoms are transferred to FAD, forming FADH₂. While the energy of these electrons is insufficient to reduce NAD+, it is adequate to reduce FAD. Unlike NADH, FADH₂ remains attached to the enzyme and transfers its electrons directly to the electron transport chain. This step is facilitated by the enzyme's localization within the inner mitochondrial membrane (OpenStax, n.d.). Step 7. In step seven of the citric acid cycle, water is added to fumarate, converting it into malate. The final step then oxidizes malate, regenerating oxaloacetate and completing the cycle. This oxidation also results in the production of another molecule of NADH, which will later contribute to ATP generation in the electron transport chain (OpenStax, n.d.). Electron transport chain Over view of the ETC The electron transport chain is the last and final step of the aerobic reparation and it is the only part of glucose metabolism that uses atmospheric oxygen it occurs in the inner mitochondrial membrane. Electron transport chain is a series of redox reactions resembling a relay race where electrons are rapidly passed from one component to the next to the end point of the chain where the electrons reduce molecular oxygen producing water. There are four complexes composed of proteins (I, II, III, IV) and the aggregation of these four combined with associate mobile electron carriers is labelled as the “Electron Transport Chain (OpenStax, BioLibreTexts, n.d.).”
Figure 4 shows electron transports embedded in the inner mitochondrial membrane that transports electrons from the NADH and FADH to molecular oxygen. the protons are pumped from the mitochondrial matrix to the intermembrane space and oxygen is reduced to form water COMPLEX I To start two electrons are carried from NADH to the complex 1, it composed of Flavin mononucleotide (FMN) derived from vitamin B2 (riboflavin) and an iron-sulfur (Fe-S)-containing protein, both of which serves as essential cofactors. The enzyme NADH dehydrogenase is large protein with 45 amino chains (a non-peptide molecule bound to a protein) that’s facilitates electron transfer within the complex. This transfer of electrons powers the pumping of four hydrogen ions (H⁺) from the mitochondrial matrix into the intermembrane space. Through this process the hydrogen gradient is established and maintained between the two compartments separated by the inner mitochondrial membrane (OpenStax, BioLibreTexts, n.d.). COMPLEX II Complex II receives electrons from FADH₂, bypassing Complex I entirely. These electrons are transferred to ubiquinone (Q), a lipid-soluble molecule that moves freely through the hydrophobic core of the mitochondrial membrane. Once ubiquinone is reduced to QH₂, it carries electrons to the next complex in the chain. Ubiquinone (Q) accepts electrons from NADH via Complex I and from FADH₂ via Complex II, which includes the enzyme succinate dehydrogenase. This enzyme forms a small complex with FADH₂ to directly deliver electrons to the electron transport chain, skipping Complex I. Because these electrons bypass the proton pump in Complex I, fewer ATP molecules are generated from FADH₂- derived electrons. The overall ATP yield depends on the number of protons pumped across the inner mitochondrial membrane (OpenStax, BioLibreTexts, n.d.). COMPLEX III
Complex III, also referred to as cytochrome oxidoreductase, consists of cytochrome b, an iron-
sulfur (Fe-S) protein, the Rieske center (2Fe-2S center), and cytochrome c proteins. The key
component, cytochrome, contains a prosthetic heme group, which is structurally similar to
hemoglobin's heme but carries electrons rather than oxygen. Within the heme group, the iron ion
alternates between its reduced (Fe²⁺) and oxidized (Fe³⁺) states during electron transfer. Each
heme molecule has unique properties influenced by its binding proteins, giving distinct features
to different complexes. Complex III serves a dual function: it facilitates proton (H⁺) pumping
across the mitochondrial membrane, contributing to the proton gradient essential for ATP
synthesis, and it transfers electrons to cytochrome c. While ubiquinone (Q) transports pairs of
REFERENCE
OpenStax. (n.d.). Biolibretexts. Retrieved from biolibretexts.org: https://bio.libretexts.org/Workbench/South_Texas_College_-Biology_for_Non- Majors/06%3A_Cellular_Respiration/6.04%3A_Oxidation_of_Pyruvate_and_the_Citric_Acid_Cyc le OpenStax. (n.d.). BioLibreTexts. Retrieved from biolibretexts.org: https://bio.libretexts.org/Workbench/South_Texas_College-Biology_for_Non- Majors/06%3A_Cellular_Respiration/6.05%3A_Oxidative_Phosphorylation OpenStax. (n.d.). LibreTextsBiology. Retrieved from biolibretexts.org: https://bio.libretexts.org/Workbench/South_Texas_College-_Biology_for_Non- Majors/06%3A_Cellular_Respiration/6.03%3A_Glycolysis
