What is the name of the Oracle's bodyguard in The Matrix?

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LESSON 4. Cellular Respiration • Define cellular respiration • Identify the stages of clan respiration You have just learned how the energy from the sun is captured, processed, and stored in the form of glucose. Cellular respiration, another important life process, is the means by which cells release the stored energy in glucose to make adenosine triphosphate (ATP). The primary goal of this life process is to convert stored energy into usable form, such as ATP, for the cells to carry out their functions. Cellular respiration involves several chemical reactions. The reactions can be summed up in the following equation: C6 H12 O6 + 602 ----- 6 CO₂ +6H₂O + ATP Glucose oxygen carbon dioxide water energy Aerobic respiration reactions, or cellular respiration that takes place in the presence of oxygen, can be grouped into three stages glycolysis, Krebs cycle, and electron transport chain (ETC). Stage 1: Glycolysis Glycolysis is the process that breaks down one molecule of 6-C glucose into 3-C pyruvates or pyruvic acids. It also releases four molecules of ATP. This process occurs in the cytoplasm of the cell. The following is the step-by-step process of glycolysis. Take note that several enzymes are involved in this process. 1. The first step of glycolysis requires energy. It can only proceed when the two ATP molecules donate energy to the glucose by transferring a phosphate group with the help of an enzyme, producing glucose 6-phosphate 2. Then, a specific enzyme promotes the rearrangement of the atoms, producing the fructose 6-phosphate. 3. The action of the enzyme in step 2 promotes the transfer of a phosphate group from another ATP molecule, forming fructose 1,6-bisphosphate. 4. The resulting fructose 1,6-bisphosphate molecules, with the help of another enzyme, splits into two molecules, each with three carbon backbones. These two sugars are dihydroxyacetone phosphate and glyceraldehyde 3-phosphate. 5. Another important enzyme then rapidly interconverts the molecules of dihydro-xyacetone phosphate and glyceraldehyde 3-phosphate. This produces two molecules of glyceraldehyde 3-phosphate or 3-phosphoglyceraldehyde (PGAL) 6. The succeeding step involves another enzyme-mediated action. The hydrogen (H) from PGAL is transferred to the oxidizing agent, nicotinamide adenine dinucleotide (NAD), which forms NADH. A phosphate (P) is also added from the cytosol of the cell to oxidize the two molecules of PGAL, forming two 1.3-bisphosphoglycerate. 7. A phosphate (P) from 1,3-biphosphoglycerate is transferred to ADP to form ATP. This happens for each of the two 1,3-bisphosphoglycerate. resulting to a yield of two ATP and two 3-phosphoglycerate molecules. 8. A phosphate is transferred from 3-phosphoglycerate molecules from the third carbon to the second carbon, forming 2-phosphoglycerate molecules A hydrogen atom and a hydroxyl ((OH) group is released, which then combines to form water (H2O). The removal of H2O from 2-phosphoglycerate results in the formation of 2- phosphoglycerate molecules. 9. A hydrogen atom and a hydroxyl ((OH) group is released, which then combines to form water (H2O). The removal of H2O from 2-phosphoglycerate results in the formation of two phosphoenolpyruvic acid (PEP) 10. Phosphate (P) from PEP is transferred to ADP (and forms ATP) and the final product, pyruvic acid. This reaction yields two molecules of pyruvic acid and two ATP molecules In summary, a single glucose molecule that undergoes the process of glycolysis produces two molecules of pyruvic acid, four molecules of ATP, two molecules of NADEL and two molecules of H.O. However, only two molecules of ATP are counted as net products since two molecules of ATP are spent throughout the process. Stage II: Krebs Cycle The Krebs cycle, named after its proponent Sir Hans Adolf Krebs, is a cyclical series of enzyme-controlled reactions. This stage of cellular respiration occurs in the matrix of the mitochondria. It is sometimes. called the citric acid cycle (CAC) since it produces citric acid. Citric acid contains three carboxyl (COOH) groups; hence, it is also called the tricarboxylic acid cycle (TCA). This requires the pyruvic acids produced during glycolysis. The main function of this cycle is to produce high-energy-yielding molecules, namely, NADH and flavin adenine dinucleotide (FADH) that will later on be used in the electron transport chain reaction. Figure 6-7. Summary of glycolysis and corresponding products in each reaction presented (See Appendix F on page 285 for an enlarged and complete version of the image.) An initial process is needed for the Krebs cycle to begin. As a pyruvate molecule from glycolysis enters the mitochondrion, it undergoes an important preliminary ate to form acetyl-CoA reaction. Coenzyme-A (COA) combines with pyruvate help of an enzymatic complex. This conversion also produces CO, and NADH. The Krebs cycle is summarized as follows. Take note that several enzymes are involved in this process. 1. The Krebs cycle technically begins when the acetyl-CoA combines with oxaloacetic acid (OAA), a 4-C molecule, to produce citric acid, a 6-C molecule. 2. With the aid of an enzyme, the citric acid now goes through a series of reactions that releases energy. Water molecule is removed from the citric acid and is returned in a different location. The-OH group is repositioned, forming the molecule isocitrate. 3. Isocitrate is then oxidized, forming the a-ketoglutarate, a 5-C molecule. The byproducts of this reaction are NADH and CO, 4 The a-ketoglutarate loses its CO, and a coenzyme-A is added in its place. The decarboxylation occurs with the help of NAD, which then becomes NADH. The resulting molecule is called succinyl-CoA. 5. Succinyl-CoA is converted into succinate. Also in this reaction, a molecule of guanosine triphosphate (GTP) is synthesized. The GTP molecule has similar structure and energy properties to that of ATP and is used by cells the same way. The free phosphate group attacks the succinyl-CoA molecule, which detaches the COA. Then, phosphate is attached to GDP to come up with GTP, similar to the process that occur in ATP synthesis (from ADP to ATP). 6. Two hydrogens are removed from succinate, A molecule of flavin adenine dinucleotide (FAD), a coenzyme similar to NAD, is reduced to FADH, as it takes the hydrogens from the succinate. This reaction produces the fumarate. 7. Fumarate is then converted into malate as the addition of a water molecule is catalyzed. The final reaction is the regeneration of oxaloacetate. The resulting byproduct of this regeneration is NADH Recall that two pyruvate molecules were produced during glycolysis, causing the Krebs cycle to turn twice. Each tuts produces three molecules of NADH, single ATH one FADIH, and the by-product CO, which is exhaled. Stage III: Electron Transport Chain The electron transport chain (ETC) is a series of photon pumps on the inner membrane of the mitochondrion. Electron transport is the last stage of the cellular respiration. In this stage, the energy from NADH and FADH, from the Krebs cycle is transferred to ADP to produce ATP. This process is generally known as oxidative phosphorylation. This energy coupling mechanism in the cell was revealed by the work of Peter stored energy in the form of proton (1) gradient to phosphorylate (add phosphate) ADP and produce ATP. The pumping of hydrogen sons across the inner membrane creates higher concentration ions in the inner membrane than on the outside of the membrane. This chemiosmotic gradient causes the ions to flow back across the membrane where the concentration of ions is lower. ATP synthase lined in the matrix serve as a channel protein, helping the ions to move across the membrane. The chemiosmotic gradient powers the phosphorylation of ADP to ATP, which also occurs in the ATP synthase. After passing through the ETC, the oxygen, being the final hydrogen acceptor, combines with two electrons and two protons, forming a water molecule. Water is a by-product of cellular respiration and is excreted. MINI TEST 6-3 1. Which energy-releasing pathway yields the most ATF in each glucose molecule? 2. Briefly describe the two stages of aerobic respiration that follow glycolysis: (a) Krebs cycle (b) Electron transport chain Anaerobic Respiration Most cells carry out arrobic respiration when oxygen is present. Aerobic respiration is an efficient process that yields a lot of ATP. However, many organisms thrive in mud, marshes, animal gut, canned goods, sewage treatment pond, and deep oceans where oxygen is scarce. Organisms that can live without oxygen are called anaerobes. Cellular respiration that proceeds without the presence of oxygen is called anaerobic respiration. In the event that the oxygen supply becomes low, aerobic cells also perform fermentation and lactic acid fermentation anaerobic pathways. There are two common anaerobic pathways in these cells, alcoholic fermentation and lactic acid fermentation. In alcoholic fermentation, ethyl alcohol and carbon dioxide are produced by some cells using the pyruvate from glycolysis. Each pyruvate molecule is rearranged into acetaldehyde and carbon dioxide, which is eventually released. NADII gives up electrons to acetaldehyde to form ethanol Fermentation is widely used in the industry. Yeast, a fungus used in making bread. can undergo anaerobic respiration. Bakers aux sugar, flour, water, and yeast to form the bread dough. The dough rises due to the carbon dioxide and alcohol released by the yeast cells trapped in air bubbles. Beer and wine manufacturers, we yeast to ferment the sugars in wheat and grape juice, forming alcoholic beverages such as beer and wine. In some cells, glycolysis produces two pyruvates, two NADH molecules, and two ATP molecules. Pyruvate itself becomes the final acceptor of the electrons from the NADH that produces the final product: lactate. Oftentimes, this product is called lactic acid. Human skeletal muscles can carry out fermentation when the blood cannot supply the cells with adequate oxygen during strenuous activities. When lactic acid builds up in the muscles, fatigue, burning sensation, and cramps result. Lactic acid will continue to build up until there is adequate supply of oxygen. Lactic acid is then converted back into pyruvate in the liver. Muscles also restore normal functions. Have you ever wondered why milk or cream turns sour after some time? Bacterial cells that undergo fermentation are responsible in producing lactate that turns the milk sour. These bacteria are used in manufacturing yogurt and sour milk products. Fermentation pathways do not breakdown and utilize the glucose completely. ATP is no longer produced beyond the process of glycolysis. Thus, energy produced is just enough for some single-celled organisms, or the energy can only be used by multicellular organisms for a short period.

CELLULAR RESPIRATION CELLULAR RESPIRATION What is it? Cellular respiration is the process by which cells break down glucose (a simple sugar) and other organic molecules to release energy in the form of ATP (adenosine triphosphate), which powers cell activities. Overall equation: C6H12O6 + 6O2 ⟶ 6CO2 + 6H2O + ATP (energy) Stages of Cellular Respiration 1. Glycolysis (in the cytoplasm) • Where it happens: Cytoplasm (outside mitochondria) • What happens: o One molecule of glucose (6 carbons) is split into two molecules of pyruvate (3 carbons each). o 2 ATP are used to start the process. o 4 ATP are produced (net gain = 2 ATP). o 2 NADH (electron carriers) are also produced. Summary of glycolysis products per glucose: • 2 ATP (net gain) • 2 NADH • 2 Pyruvate 2. Krebs Cycle (Citric Acid Cycle) (in the mitochondrial matrix) • Where it happens: Mitochondrial matrix • What happens: o Each pyruvate (3C) is converted to acetyl-CoA (2C) before entering the cycle. o Acetyl-CoA combines with oxaloacetate (4C) to form citric acid (6C). o Through a series of enzyme-controlled reactions, citric acid is broken down, releasing CO₂, ATP, NADH, and FADH₂. Summary of Krebs Cycle products (per 2 pyruvates): • 2 ATP • 6 NADH • 2 FADH₂ • 4 CO₂ (exhaled as waste) 3. Electron Transport Chain (ETC) & Oxidative Phosphorylation (in the inner mitochondrial membrane) • Where it happens: Inner mitochondrial membrane (cristae) • What happens: o NADH and FADH₂ donate high-energy electrons to proteins in the ETC. o As electrons move through the chain, protons (H⁺) are pumped across the membrane, creating a proton gradient. o This gradient powers ATP synthase, which makes lots of ATP (like a turbine powered by flowing water). o Oxygen acts as the final electron acceptor, combining with electrons and hydrogen to form water (H₂O). Summary of ETC products: • About 34 ATP • H₂O Total Energy Yield from One Glucose (Aerobic Respiration) • Glycolysis → 2 ATP • Krebs Cycle → 2 ATP • ETC → ~34 ATP Total: ~38 ATP (usually 36 in eukaryotes due to energy costs) Anaerobic Respiration (When Oxygen is Absent) If oxygen is not available, cells switch to fermentation: • Alcoholic Fermentation (yeast & some bacteria): pyruvate → ethanol + CO₂ • Lactic Acid Fermentation (muscles & some bacteria): pyruvate → lactic acid These processes only make 2 ATP per glucose, much less efficient than aerobic respiration. Key Takeaway: Cellular respiration is like the cell’s power plant: glycolysis breaks glucose into smaller pieces, the Krebs cycle extracts more high-energy electrons, and the ETC uses those electrons to generate the bulk of ATP. Oxygen is essential for the final step, which is why we need to breathe to stay alive.

Plant cells have three kinds of structures that are not found in animal cells and that are extremely important to plant survival: plastids, central vacuoles, and cell walls. PLANT CELLS Most of the organelles and other parts of the cell just described are common to all eukaryotic cells. However, plant cells have three additional kinds of structures that are extremely important to plant function: cell walls, large central vacuoles, and plastids. To understand why plant cells have structures not found in ani- mal cells, consider how a plant’s lifestyle differs from an animal’s. Plants make their own carbon-containing molecules directly from carbon taken in from the environment. Plant cells take carbon diox- ide gas from the air, and in a process called photosynthesis, they convert carbon dioxide and water into sugars. The organelles and structures in plant cells are shown in Figure 4-21. SECTION 4 OBJECTIVES ● List three structures that are present in plant cells but not in animal cells. ● Compare the plasma membrane, the primary cell wall, and the secondary cell wall. ● Explain the role of the central vacuole. ● Describe the roles of plastids in the life of a plant. ● Identify features that distinguish prokaryotes, eukaryotes, plant cells, and animal cells. VOCABULARY cell wall central vacuole plastid chloroplast thylakoid chlorophyll Chloroplast Golgi apparatus Mitochondrion Cell membrane Nucleolus Nucleus Cytoskeleton Rough endoplasmic reticulum Pore Smooth endoplasmic reticulum Central vacuole Ribosome Cell wall In addition to containing almost all of the types of organelles that animal cells contain, plant cells contain three unique features. Those features are the cell wall, the central vacuole, and plastids, such as chloroplasts. FIGURE 4-21 Copyright © by Holt, Rinehart and Winston. All rights reserved. 88 CHAPTER 4 CELL WALL The cell wall is a rigid layer that lies outside the cell’s plasma membrane. Plant cell walls contain a carbohydrate called cellulose. Cellulose is embedded in a matrix of proteins and other carbohy- drates that form a stiff box around each cell. Pores in the cell wall allow water, ions, and some molecules to enter and exit the cell. Primary and Secondary Cell Walls The main component of the cell wall, cellulose, is made directly on the surface of the plasma membrane by enzymes that travel along the membrane. These enzymes are guided by microtubules inside the plasma membrane. Growth of the primary cell wall occurs in one direction, based on the orientation of the microtubules. Other components of the cell wall are made in the ER. These materials move in vesicles to the Golgi and then to the cell surface. Some plants also produce a secondary cell wall. When the cell stops growing, it secretes the secondary cell wall between the plasma membrane and the primary cell wall. The secondary cell wall is very strong but can no longer expand. The wood in desks and tabletops is made of billions of secondary cell walls. The cells inside the walls have died and disintegrated. CENTRAL VACUOLE Plant cells may contain a reservoir that stores large amounts of water. The central vacuole is a large, fluid-filled organelle that stores not only water but also enzymes, metabolic wastes, and other materials. The central vacuole, shown in Figure 4-22, forms as other smaller vacuoles fuse together. Central vacuoles can make up 90 percent of the plant cell’s volume and can push all of the other organelles into a thin layer against the plasma membrane. When water is plentiful, it fills a plant’s vacuoles. The cells expand and the plant stands upright. In a dry period, the vacuoles lose water, the cells shrink, and the plant wilts. Other Vacuoles Some vacuoles store toxic materials. The vacuoles of acacia trees, for example, store poisons that provide a defense against plant-eating ani- mals. Tobacco plant cells store the toxin nicotine in a storage vacuole. Other vacuoles store plant pigments, such as the colorful pigments found in rose petals. The central vacuole occupies up to 90 percent of the volume of some plant cells. The central vacuole stores water and helps keep plant tissue firm. FIGURE 4-22 Central vacuole Nucleus Chloroplast Copyright © by Holt, Rinehart and Winston. All rights reserved. CELL STRUCTURE AND FUNCTION 89 PLASTIDS Plastids are another unique feature of plant cells. Plastids are organelles that, like mitochondria, are surrounded by a double mem- brane and contain their own DNA. There are several types of plastids, including chloroplasts, chromoplasts, and leucoplasts. Chloroplasts Chloroplasts use light energy to make carbohydrates from carbon dioxide and water. As Figure 4-23 shows, each chloroplast contains a system of flattened, membranous sacs called thylakoids. Thylakoids contain the green pigment chlorophyll, the main mole- cule that absorbs light and captures light energy for the cell. Chloroplasts can be found not only in plant cells but also in a wide variety of eukaryotic algae, such as seaweed. Chloroplast DNA is very similar to the DNA of certain photosyn- thetic bacteria. Plant cell chloroplasts can arise only by the divi- sion of preexisting chloroplasts. These facts may suggest that chloroplasts are descendants of ancient prokaryotic cells. Like mitochondria, chloroplasts are also thought to be the descendants of ancient prokaryotic cells that were incorporated into plant cells through a process called endosymbiosis. Chromoplasts Chromoplasts are plastids that contain colorful pigments and that may or may not take part in photosynthesis. Carrot root cells, for example, contain chromoplasts filled with the orange pigment carotene. Chromoplasts in flower petal cells contain red, purple, yellow, or white pigments. Other Plastids Several other types of plastids share the general features of chloro- plasts but differ in content. For example, amyloplasts store starch. Chloroplasts, chromoplasts, and amyloplasts arise from a common precursor, called a proplastid. Thylakoid Inner membrane Outer membrane chloroplast from the Greek chloros, meaning “pale green,” and plastos, meaning “formed” Word Roots and Origins A chloroplast captures energy from sunlight and uses that energy to convert carbon dioxide and water into sugar and other carbohydrates. FIGURE 4-23 Copyright © by Holt, Rinehart and Winston. All rights reserved. 90 CHAPTER 4 COMPARING CELLS All cells share common features, such as a cell membrane, cyto- plasm, ribosomes, and genetic material. But there is a high level of diversity among cells, as shown in Figure 4-24. There are signifi- cant differences between prokaryotes and eukaryotes. In addition, plant cells have features that are not found in animal cells. Prokaryotes Versus Eukaryotes Prokaryotes differ from eukaryotes in that prokaryotes lack a nucleus and membrane-bound organelles. Prokaryotes have a region, called a nucleoid, in which their genetic material is concen- trated. However, prokaryotes lack an internal membrane system. Plant Cells Versus Animal Cells Three unique features distinguish plant cells from animal cells. One is the production of a cell wall by plant cells. Plant cells contain a large central vacuole. Third, plant cells contain a variety of plastids, which are not found in animal cells. Cell walls, central vacuoles, and plastids are unique features that are important to plant function. 1. Identify three unique features of plant cells. 2. List the differences between the plasma mem- brane, the primary cell wall, and the secondary cell wall. 3. Identify three functions of plastids. 4. Name three things that may be stored in vacuoles. 5. Describe the features that distinguish prokary- otes from eukaryotes and plant cells from animal cells. CRITICAL THINKING

Lide 1: Introduction to Bioreactor A bioreactor is a vessel used for growing microorganisms, plant or animal cells Provides controlled conditions for biological reactions Maintains optimum pH, temperature, oxygen, and nutrients Widely used in fermentation, enzyme, vaccine, and antibiotic production Ensures sterile and aseptic environment Scale ranges from laboratory to industrial production Slide 2: Basic Design Requirements of a Bioreactor Must be constructed with non-toxic, corrosion-resistant materials Should allow effective mixing and mass transfer Provision for sterilization (in situ sterilization) Must maintain uniform temperature and pH Easy sampling without contamination Should support scalability and automation Slide 3: Materials Used in Bioreactor Construction Stainless steel (SS-316) for industrial bioreactors Glass for laboratory-scale bioreactors Plastic (polycarbonate) for disposable bioreactors Materials must withstand heat and pressure Should be smooth to prevent microbial attachment Resistant to chemicals and cleaning agents Slide 4: Main Parts of a Bioreactor Vessel: holds the culture medium and microorganisms Agitator (impeller): provides mixing Sparger: supplies sterile air Baffles: prevent vortex formation Sensors: monitor pH, temperature, dissolved oxygen Ports: used for inoculation, sampling, and feeding Slide 5: Agitation System Ensures uniform mixing of nutrients and cells Improves oxygen transfer rate Common impellers: Rushton turbine, marine propeller Speed controlled by motor Prevents settling of cells Affects shear stress on cells Slide 6: Aeration System Supplies oxygen for aerobic fermentation Air introduced through sparger Types of spargers: ring, nozzle, sintered Maintains dissolved oxygen concentration Air is filtered for sterility Essential for high cell density cultures Slide 7: Temperature and pH Control Temperature controlled by heating/cooling jackets pH maintained using acid or alkali addition Sensors continuously monitor parameters Automated control systems used Ensures optimal microbial growth Prevents enzyme denaturation Slide 8: Foam Control System Foam formed due to protein and agitation Excess foam reduces oxygen transfer Mechanical foam breakers used Chemical antifoam agents added Foam sensor detects foam formation Maintains efficient fermentation Slide 9: Types of Bioreactors – Based on Mode of Operation Batch bioreactor Fed-batch bioreactor Continuous bioreactor Choice depends on product type Widely used in industrial fermentation Controls productivity and yield Slide 10: Batch Bioreactor All nutrients added at the beginning No addition or removal during process Simple and easy to operate Low risk of contamination Used for antibiotics and enzymes Limited control over nutrient depletion Slide 11: Fed-Batch Bioreactor Nutrients added during fermentation Prevents substrate inhibition High product yield Widely used in industrial fermentation Allows better control of growth rate Used in insulin and enzyme production Slide 12: Continuous Bioreactor Fresh medium continuously added Culture removed at same rate Maintains steady-state conditions High productivity Risk of contamination is high Used in wastewater treatment and SCP production Slide 13: Types of Bioreactors – Based on Design Stirred tank bioreactor Airlift bioreactor Bubble column bioreactor Packed bed bioreactor Fluidized bed bioreactor Photobioreactor Slide 14: Stirred Tank Bioreactor (STR) Most commonly used bioreactor Mechanical agitation using impellers Suitable for aerobic fermentation Excellent mixing and oxygen transfer Used for bacteria and fungi Easy scale-up Slide 15: Airlift Bioreactor Mixing achieved by air circulation No mechanical agitator Low shear stress Energy efficient Suitable for shear-sensitive cells Used in wastewater treatment Slide 16: Bubble Column Bioreactor Air bubbles provide mixing Simple design and low cost No moving parts Limited mixing efficiency Used for microbial fermentation Suitable for large-scale operations Slide 17: Packed Bed Bioreactor Contains immobilized cells or enzymes Substrate flows through packed matrix High cell density Used in continuous processes Limited oxygen transfer Used in enzyme and wastewater treatment Slide 18: Fluidized Bed Bioreactor Immobilized particles kept in suspension Better mass transfer than packed bed Reduced clogging Suitable for continuous operation Used in biotransformations Higher operational complexity Slide 19: Photobioreactor Designed for photosynthetic organisms Provides light source Used for algae and cyanobacteria Controls light, CO₂, and temperature Used in biofuel and pigment production Can be tubular or flat-plate design Slide 20: Applications of Bioreactors Production of antibiotics and vaccines Enzyme and organic acid production Single cell protein production Wastewater treatment Biofertilizer and biopesticide production Biopharmaceutical manufacturing

20 tricks to finally master the Matrix visualization in Power BI!

20 tricks to finally master the Matrix visualization in Power BI!!

Zones in epiphyseal cartilage (regions of cellular activity) Zone 1: Zone of Resting cartilage Zone 2: Zone of proliferating cartilage Chondrocytes aligned as aggregates in lacunae Zone 3:Zone of hypertrophic cartilage Cells enlarge; matrix compressed into bands Zone 4: zone of calcified cartilage Cells calcify the matrix (hydroxyapatite crystals formed); undergo apoptosis Zone 5: Zone of ossification Vessels invade region; osteoblasts deposit osteoid on calcified spicules of cartilage forming woven bone; remodeled as lamellar bone

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