General Biology 1 Module for Remedial Class PDF 2024-2025

ANTIPOLO CITY NATIONAL SCIENCE AND TECHNOLOGY HIGH SCHOOL General Biology 1 MODULE FOR REMEDIAL CLASS S.Y. 2024-2025 Coupled Reaction Processes After going through this module, you are expected to: 1. Explain coupled reaction processes and describe th...

ANTIPOLO CITY NATIONAL SCIENCE AND TECHNOLOGY HIGH SCHOOL General Biology 1 MODULE FOR REMEDIAL CLASS S.Y. 2024-2025 Coupled Reaction Processes After going through this module, you are expected to: 1. Explain coupled reaction processes and describe the role of ATP in energy coupling and transfer. 2. Describe ATP’s role as the cellular energy currency 3. Infer that ATP is important in maintaining cellular functions of an organism. COUPLED REACTION PROCESSES Introduction A cell can be thought of as a small, bustling town. Carrier proteins move substances into and out of the cell, motor proteins carry cargoes along microtubule tracks, and metabolic enzymes busily break down and build up macromolecules. Even if they would not be energetically favorable (energy-releasing, or exergonic) in isolation, these processes will continue merrily along if there is energy available to power them (much as business will continue to be done in a town as long as there is money flowing in). However, if the energy runs out, the reactions will grind to a halt, and the cell will begin to die. ATP structure and hydrolysis Adenosine triphosphate, or ATP, is a small, relatively simple molecule. It can be thought of as the main energy currency of cells, much as money is the main economic currency of human societies. The energy released by hydrolysis (breakdown) of ATP is used to power many energy-requiring cellular reactions. Why are the phosphoanhydride bonds considered high-energy? All this really means is that an appreciable amount of energy is released when one of these bonds is broken in a hydrolysis (water-mediated breakdown) reaction. ATP is hydrolyzed to ADP in the following reaction: 1 | REMEDIAL CLASS FOR 2ND QUARTER 24-25  Note: Pi just stands for an inorganic phosphate group. Like most chemical reactions, the hydrolysis of ATP to ADP is reversible. The reverse reaction, which regenerates ATP from ADP and Pi requires energy. Regeneration of ATP is important because cells tend to use up (hydrolyze) ATP molecules very quickly and rely on replacement ATP being constantly produced. You can think of ATP and ADP as being sort of like the charged and uncharged forms of a rechargeable battery (as shown above). ATP, the charged battery, has energy that can be used to power cellular reactions. Once the energy has been used up, the uncharged battery (ADP) must be recharged before it can again be used as a power source. The ATP regeneration reaction is just the reverse of the hydrolysis reaction: Reaction coupling How is the energy released by ATP hydrolysis used to power other reactions in a cell? In most cases, cells use a strategy called reaction coupling, in which an energetically favorable reaction (like ATP hydrolysis) is directly linked with an energetically unfavorable (endergonic) reaction. The linking often happens through a shared intermediate, meaning that a product of one reaction is “picked up” and used as a reactant in the second reaction. 2 | REMEDIAL CLASS FOR 2ND QUARTER 24-25  Chemical events of Cellular Respiration The module is about the chemical events of chemical respiration. After going through this module, you are expected to: 1. Identify the events in cellular respiration; 2. Explain the overview of the different stages of cellular respiration; and 3. appreciate the importance of cellular respiration. CHEMICAL EVENTS OF CELLULAR RESPIRATION: Cellular respiration is a metabolic pathway that breaks down glucose and produces ATP. The stages of cellular respiration include glycolysis, pyruvate oxidation, the citric acid or Krebs cycle, and oxidative phosphorylation. Glycolysis is a series of reactions that extract energy from glucose by splitting it into two three-carbon molecules called pyruvates. Glycolysis is an ancient metabolic pathway, meaning that it evolved long ago, and it is found in the great majority of organisms alive today. In organisms that perform cellular respiration, glycolysis is the first stage of this process. However, glycolysis doesn’t require oxygen, and many anaerobic organisms—organisms that do not use oxygen—also have this pathway. In glycolysis, glucose—a six-carbon sugar—undergoes a series of chemical transformations. In the end, it gets converted into two molecules of pyruvate, a three carbon organic molecule. In these reactions, ATP is made and NAD+ is converted to NADH. This takes place in the cytosol of a cell, and it can be broken down into two main phases: the energy-requiring phase and the energy- releasing phase. The energy-requiring phase, the starting molecule of glucose gets rearranged, and two phosphate groups are attached to it. The phosphate groups make the modified sugar— now called fructose-1,6-bisphosphate—unstable, allowing it to split in half and form two phosphate-bearing three-carbon sugars. Because the phosphates used in these steps come from ATP, two ATP molecules get used. The energy- releasing phase, each three-carbon sugar is converted into another three-carbon molecule, pyruvate, through a series of reactions. In these reactions, two ATP molecules and one NADH molecule are made. Because this phase takes place twice, one for each of the two three-carbon sugars, it makes four ATP and two NADH overall. In pyruvate oxidation, each pyruvate from glycolysis goes into the mitochondrial matrix—the innermost compartment of mitochondria. There, it’s converted into a two-carbon molecule bound to Coenzyme A, known as acetyl CoA. Carbon dioxide is released and NADH is generated. In eukaryotes, this step takes place in the matrix, the innermost compartment of mitochondria. In prokaryotes, it happens in the cytoplasm. Overall, pyruvate oxidation converts pyruvate—a threecarbon molecule—into acetyl CoA- a two-carbon molecule attached to Coenzyme Aproducing an NADH and releasing one carbon dioxide molecule in the process. Acetyl CoA acts as fuel for the citric acid cycle in the next stage of cellular respiration. 3 | REMEDIAL CLASS FOR 2ND QUARTER 24-25  The citric acid cycle is the final common pathway for the oxidation of fuel molecules—amino acids, fatty acids, and carbohydrates. Most fuel molecules enter the cycle as acetyl coenzyme A. The citric acid cycle is the central metabolic hub of the cell. It is the gateway to the aerobic metabolism of any molecule that can be transformed into an acetyl group or dicarboxylic acid. The cycle is also an important source of precursors, not only for the storage forms of fuels, but also for the building blocks of many other molecules such as amino acids, nucleotide bases, cholesterol, and porphyrin. What is the function of the citric acid cycle in transforming fuel molecules into ATP? Recall that fuel molecules are carbon compounds that are capable of being oxidized—of losing electrons. The citric acid cycle includes a series of oxidation-reduction reactions that result in the oxidation of an acetyl group to two molecules of carbon dioxide. The citric acid cycle, in conjunction with oxidative phosphorylation, provides the vast majority of energy used by aerobic cells—in human beings, greater than 95%. It is highly efficient because a limited number of molecules can generate large amounts of NADH and FADH2. The four-carbon molecule, oxaloacetate, that initiates the first step in the citric acid cycle is regenerated at the end of one passage through the cycle. The oxaloacetate acts catalytically: it participates in the oxidation of the acetyl group but is itself regenerated. Thus, one molecule of oxaloacetate is capable of participating in the oxidation of many acetyl molecules. In oxidative phosphorylation, the NADH and FADH2 made in other steps deposit their electrons in the electron transport chain, turning back into their "empty" form (NAD+ and FAD). As electrons move down the chain, energy is released and used to pump protons out of the matrix, forming a gradient. Protons flow back into the matrix through an enzyme called ATP synthase, making ATP. At the end of the electron transport chain, oxygen accepts electrons and takes up protons to form water. The flow of electrons from NADH or FADH2 to O2 through protein complexes located in the mitochondrial inner membrane leads to the pumping of protons out of the mitochondrial matrix. The resulting uneven distribution of protons generates a pH gradient and a transmembrane electrical potential that creates a proton-motive force. ATP is synthesized when protons flow back to the mitochondrial matrix through an enzyme complex. Thus, the oxidation of fuels and the phosphorylation of ADP are coupled by a proton gradient across the inner mitochondrial membrane. 4 | REMEDIAL CLASS FOR 2ND QUARTER 24-25  GLYCOLYSIS AND KREBS CYCLE It is a cytoplasmic process that breaks down the glucose into two compounds of three carbon and generates energy. Glycolysis is an ancient metabolic pathway, which means it evolved a long time ago and is present in the vast majority of species that are alive today. It is the first stage of this process in organisms which perform cellular respiration. Glycolysis does not require oxygen, however, and many anaerobic organisms- organism that do not use oxygen- have this pathway as well. Glucose is captured by phosphorylation, using the hexokinase enzyme. This reaction uses adenosine triphosphate (ATP) and the product, glucose-6-phosphate , inhibits hexokinase. Glycolysis occurs in 10 steps of which five are in the preparatory phase and 5 are in the pay-off phase. The rate limiting enzyme is phosphofructokinase. High-energy compounds, such as 1,3-bisphosphoglycerate and phosphoenolpyruvate, produce ATP by substrate-level phosphorylation. Pyruvate in aerobic settings is the final result of glycolysis and lactate in anaerobic conditions. For more energy generation, pyruvate joins the Krebs cycle. Energy-requiring phase Step 1. Hexokinase. Conversion of D-glucose into glucose-6-phospate. The glucose ring is phosphorylated by adding a phosphate group to a molecule derived from ATP. As a result, 1 molecule of ATP has been consumed. Hexikinase is an enzyme that catalyzes the phosphorylation of many six-membered glucose-ring structures. Step 2. Phosphoglucose isomerase. The conversion of glucose-6-phosphate to fructose-6-phosphate occurs with the help of the enzyme phosphoglucose isomerase (PI). The reaction involves the rearrangement of the carbon-oxygen bond to transform the six-membered ring into a five- membered ring. Step 3. Phosphofructokinase. Fructose-6-phosphate is converted to fructose 1,6-biphosphate (FBP), a second molecule of ATP provides the phosphate group that is added on the F6P molecule. Step 4. Aldolase. Fructose1,6-biphosphate splits into two sugars that are isomers of each other with the help of aldolase enzyme. One molecule is called glyceraldehyde-3-phosphate (GAP) and the other one is called dihydroxyacetone phosphate (DHAP). Step 5. Triosephosphate isomerase. Among the two molecules, only GAP will continue to the glycolytic pathway. As a result, the DHAP molecules produced are further acted on by the enzyme triosephosphate isomerase (TIM), which reorganizes the DHAP into GAP so it can continue to glycolysis. Energy-releasing phase Step 6. Glyceraldehyde-3-phosphate dehydrogenase. Two main events happen: 1) glyceraldehyde- 3-phosphate is oxidized by the coenzyme nicorinamide adenine dinucleotide (NAD); 2) the molecule is phosphorylated by the addition of a free phosphate group. The enzyme that catalyzes this reaction is glyceraldehyde-3- phosphate dehydrogenase (GAPDH). 5 | REMEDIAL CLASS FOR 2ND QUARTER 24-25  Step 7. Phosphoglycerate kinase. The 1,3 bisphoglycerate is converted to 3- phosphoglycerate by the enzyme phosphoglycerate kinase (PGK) as it involves the loss of phosphate group. The phosphate is transferred to a molecule of ADP that yields our first molecule of ATP. Step 8. Phosphoglycerate mutase. Involves a simple rearrangement of the position of the phosphate group on the 3 phosphoglycerate molecule, making it 2 phosphoglycerate. The molecule responsible for catalyzing this reaction is called phosphoglycerate mutase (PGM). Step 9. Enolase. Conversion of 2 phosphoglycerate to phosphoenolpyruvate (PEP) by the enzyme enolase. It works by removing a water group or dehydrating the 2 phosphoglycerate. Step 10. Pyruvate kinase. The conversion of phosphoenolpyruvate into pyruvate with the help of the enzyme pyruvate kinase. The reaction involves the transfer of phosphate group attached to the 2΄ carbon of the PEP is transferred to a molecule of ADP. CITRIC ACID CYCLE/TRICARBOXYLIC ACID CYCLE/KREBS CYCLE The cycle of citric acid refers to the first molecule produced during the process of reactions- citrate or citric acid in its protonated form. Nevertheless, after its discovered Hans Krebs, you can also hear this sequence of reactions called the tricarbocylic acid (TCA) cycle, for the three carboxyl groups on their two intermediate, or the Krebs cycle. Reaction 1. Formation of citrate. The condensation of acetyl CoA with oxaloacetate to form citrate, catalyze by citrate synthase. Once oxaloacetate is joined with acetyl CoA, a water molecule attacks the acetyl leading to the release of coenzyme A form the complex. Reaction 2. Formation of isocitrate. The citrate is rearranged to form an isomeric form isocitrate by an enzyme acontinase. A water molecule is removed from the citric acid and then put back on in another location. 6 | REMEDIAL CLASS FOR 2ND QUARTER 24-25  Reaction 3. Oxidation of isocitrate to α-ketoglutarate. Isocitrate dehydrogenase catalyzes oxidative decarboxylation of isocitrate to form α- ketoglutarate. In this reaction, generation of NADH from NAD is seen. Reaction 4. Oxidation of α-ketoglutarate to succinyl-CoA. Alphaketoglutarate is oxidized, carbon dioxide is removed and coenzyme A is added to form the 4-carbon compound succinyl-CoA. During this oxidation, NAD+ is reduced to NADH + H+ by the enzyme alpha-ketoglutarate dehydrogenase. Reaction 5. Conversion of succinyl-CoA to succinate. CoA is removed from succinyl-CoA to produce succinate. The energy release is used to make guanosine triphosphate (GTP) from guanosine diphosphate (GDP) and Pi by substrate-level phosphorylation. Reaction 6. Oxidation of succinate to fumarate. During the oxidation of succinate to fumarate, FAD is reduced to FADH2. The enzyme succinate dehydrogenase catalyzes the removal of two hydrogens from succinate. Reaction 7. Hydration of fumarate to malate. Reversible hydration of fumarate to L-malate is catalyzed by fumarase (fumarate hydratase). Reaction 8. Oxidation of malate to oxaloacetate. Malate is oxidized to produce oxaloacetate, the starting compound of the citric acid cycle by malate dehydrogenase. Electron Transport System and Chemiosmosis At the end of this module, you should be able to: 1. identify the organelle/s involved in electron transport system and chemiosmosis; 2. describe electron transport system and chemiosmosis in terms of the starting materials and end products of aerobic respiration; and 3. cite the importance of these two cellular respirations to human body. 7 | REMEDIAL CLASS FOR 2ND QUARTER 24-25 OXIDATIVE PHOSPHORYLATION Every single organism in this planet knows the importance of oxygen in our body. We need to take in oxygen so that our body could do its processes and if we stopped breathing, or just tried holding our breath for too long, our body will respond like we will feel dizzy or will eventually die. One of the body processes is that, our cells need oxygen in oxidative phosphorylation, which is the final step in cellular respiration. As mentioned, oxidative phosphorylation is composed of electron transport chain and chemiosmosis. Oxygen is found at the end of electron transport chain where it accepts electrons and protons to form water. What if there’s no oxygen available because the person is holding his breath? The electron transport chain will stop, and chemiosmosis will not proceed. Thus, ATP won’t be produced. If there is no ATP or enough ATP, cells won’t be that functional like it does and eventually, will die. You know what will happen after that. ELECTRON TRANSPORT CHAIN What is included in the electron transport chain? It is called as such because of the connecting multiprotein complexes and electron carriers. In figure 3, we can see that there are 4 large multiprotein complexes (from I to IV) and 2 small electron carriers (ubiquinone and cytochrome c). What happens in the electron transport chain? From the name itself, it implies that electron is being transported through a chain. And we know that there are multi protein complexes in the said chain. So, from one complex to the other, the electron is transferred. Let us go to the details of it. Remember that the by-products of Krebs cycle are 2 ATP, 6 NADH and 2 FADH2 and from these, the NADH and FADH2 will be used in the electron transport chain. At the start of the electron transport chain, NADH will approach COMPLEX I and through oxidation it will become NAD+ leaving the proton (H+) in the mitochondrial matrix and the electron (e-) in the complex I. Complex I being charged can now pump the protons from mitochondrial matrix into intermembrane space (see figure 3). Thus, intermembrane space will now have more protons than the mitochondrial matrix. After a while, the electron from complex I will go to Coenzyme Q or CoQ (ubiquinone) and will stay there until the next trigger happens. 8 | REMEDIAL CLASS FOR 2ND QUARTER 24-25 Next step is, FADH2 (still from Krebs cycle) will approach COMPLEX II. And same with NADH, FADH2 will be oxidized resulting to FAD+. The proton will be left in the mitochondrial matrix and the electron is donated in complex II. Unlike complex I, complex II can’t pump protons thus the electron it carries will then be passed to CoQ. After CoQ receives the electron from complex II, it will pass the electrons it carries to COMPLEX III. Complex III being charged can now pump protons from mitochondrial matrix into intermembrane space. At this moment, the intermembrane space has an accumulation of protons from the pumping of complex I and complex III making it more positively charged than the mitochondrial matrix. The next step is, complex III will pass the electron to Cytochrome C and from CytC, the electron will be passed to Complex IV. When complex IV receives the electron, it will now have enough energy to pump the protons from mitochondrial matrix into intermembrane space where proton gradient continues to form. The last part of the electron transport chain is the passing of electron from complex IV to oxygen (that is sitting in the mitochondrial matrix). Once the oxygen receives the electron, it will split into two oxygen ions and protons will be added creating two water molecules. This is where the electron transport chain ends. CHEMIOSMOSIS Still under oxidative phosphorylation, chemiosmosis happens after the electron transport chain. This is where the greatest number of ATP is produced. Chemiosmosis as defined by Reece, 2011 is an energy- coupling mechanism that uses energy stored in the form of H+ gradient across a membrane to drive cellular work. Remember that in the process of electron transport, the intermembrane space has a massive proton gradient and the mitochondrial matrix has fewer protons. The proton gradient created during the ETC is then used in chemiosmosis. At this point, chemiosmosis will start. The last complex needed here is the ATP synthase (see figure 4). The ATP synthase will use the movement of protons from intermembrane space to mitochondrial matrix to generate massive amounts of ATP. ADP or adenosine diphosphate, just lying around the ATP synthase, is waiting to become ATP (adenosine triphosphate) which is a higher energy molecule that is most needed by our body. To make this happen, we need an energy source. 9 | REMEDIAL CLASS FOR 2ND QUARTER 24-25 This is where ATP synthase will make use of the proton gradient from intermembrane space. Since there is imbalance in the proton number, the protons want to move from intermembrane space (higher concentration) into mitochondrial matrix (lower concentration) to achieve equilibrium. ATP synthase will be their way to move, and this will become the energy source of the ATP synthase to convert ADP to ATP (inorganic phosphate is also part of this process and they are also found lying around the ATP synthase). Since there is a large number of protons passing through, a large number of ATP is also produced. In summary, chemiosmosis will yield about 26 or 28 ATP (Reece, 2011). Looking back at the previous cellular respiration processes, glycolysis yields 2 ATP and the citric acid cycle yields 2 ATP. Thus, the total ATP produced from the entire cellular respiration (from a molecule of glucose) is about 30 – 32 (Reece, 2011) 10 | REMEDIAL CLASS FOR 2ND QUARTER 24-25  IMPORTANCE OF THE PRODUCTION OF ATP What if mitochondria failed to produce ATP or enough ATP? There is what we called mitochondrial disease that are genetic disorders of metabolism (LumenLearning, n.d.). Symptoms of these diseases includes, muscle weakness, stroke-like episodes, and lack of coordination. Adenosine triphosphate, also known as ATP is the “energy currency” of the cells, “energy of life” and “molecular unit of currency”. In short, ATP is the “energy” that the cells need in order to function. Without ATP, cells can’t do its job. We know that every living organism is made up of millions of cells and if these cells do not perform its function because of lack of energy, the cell will eventually die. If the cells die, the organism will also die. Prepared by: CORAZON ADRALES-CALDERON Subject Teacher 11 | REMEDIAL CLASS FOR 2ND QUARTER 24-25