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2.3 The Carbon Cycle
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PHOTOSYNTHESIS LIGHT DEPENDENT REACTION 1. Photosystem II (PSII) – Light Absorption & Water Splitting • Light energy (photons) excites electrons in chlorophyll molecules. • These high-energy electrons leave PSII and are passed into the electron transport chain (ETC). • Meanwhile, water molecules are split (photolysis) into: o O₂ (released as a by-product into the atmosphere) o H⁺ ions (protons, which build up inside the thylakoid) o Electrons (e⁻), which replace the ones lost by PSII. 2. Electron Transport Chain (ETC) • Excited electrons move through protein carriers embedded in the thylakoid membrane. • As they move, their energy pumps H⁺ ions into the thylakoid space, creating a proton gradient (high H⁺ inside, low outside). 3. ATP Production (ATP Synthase) • The buildup of H⁺ ions acts like a “waterfall” of potential energy. • These protons flow back across the membrane through ATP synthase, a protein complex that acts like a turbine. • This flow drives the conversion of ADP + Pi → ATP, which provides energy for the Calvin cycle. 4. Photosystem I (PSI) • Electrons arriving from the ETC enter PSI. • Sunlight excites them again, boosting them to a higher energy level. 5. NADPH Production • The energized electrons are transferred to NADP⁺. • Along with a proton (H⁺), this forms NADPH, another energy carrier. • NADPH is then delivered to the Calvin cycle to help build glucose. End Products of Light-Dependent Reactions: • ATP (energy source for Calvin cycle) • NADPH (reducing power for glucose synthesis) • O₂ (released into the atmosphere as waste) Light-Independent Reactions (Calvin Cycle) • These reactions do not directly require sunlight. • They occur in the stroma of the chloroplast (the fluid-filled space surrounding the thylakoids). • The inputs are ATP and NADPH (from light-dependent reactions) and CO₂ (from the atmosphere). • The outputs are glucose (C₆H₁₂O₆) and other carbohydrates. Think of the Calvin cycle as a factory that uses the energy and “raw materials” made in Stage I (ATP & NADPH) to build sugars. The 3 Main Steps of the Calvin Cycle 1. Carbon Fixation • CO₂ from the atmosphere enters the chloroplast and diffuses into the stroma. • Each CO₂ molecule attaches to a 5-carbon sugar called RuBP (ribulose-1,5-bisphosphate). • This reaction is catalyzed by the enzyme RuBisCO (Ribulose-1,5-bisphosphate carboxylase/oxygenase — the most abundant enzyme on Earth!). • The result is a short-lived 6-carbon compound, which immediately splits into two 3-carbon molecules called 3-PGA (3-phosphoglycerate). Summary: CO₂ + RuBP → 2 × 3-PGA 2. Reduction Phase • The 3-PGA molecules are “energized” and converted into G3P (glyceraldehyde-3-phosphate), a more energy-rich 3-carbon sugar. • This transformation requires: o ATP (provides energy) o NADPH (provides high-energy electrons and hydrogen atoms). • Some of the G3P molecules will eventually be combined to form glucose and other sugars. Summary: 3-PGA + ATP + NADPH → G3P 3. Regeneration of RuBP • Not all G3P molecules leave the cycle. Most of them are used to regenerate RuBP so the cycle can continue. • This regeneration also requires ATP. • For every 3 turns of the cycle, 5 G3P molecules are recycled to regenerate 3 molecules of RuBP. Summary: G3P + ATP → RuBP The Full Cycle Balance • To make one G3P molecule that can exit the cycle (and later form glucose), the cycle must run 3 times, fixing 3 molecules of CO₂. • To make one glucose molecule (C₆H₁₂O₆), the cycle must run 6 times (since glucose needs 6 carbon atoms). Inputs (for 1 glucose): • 6 CO₂ • 18 ATP • 12 NADPH Outputs: • 1 glucose (C₆H₁₂O₆) • 18 ADP + 18 Pi • 12 NADP⁺ Day vs Night Clarification • The Calvin Cycle is called light-independent, but that doesn’t mean it only happens at night. • It usually happens during the day because it depends on ATP and NADPH, which are only produced in light-dependent reactions (when sunlight is available). Simplified Analogy • Carbon fixation = The factory brings in CO₂ as raw material. • Reduction = Workers use energy (ATP & NADPH) to shape the raw material into useful products (G3P). • Regeneration = Some products are recycled to keep the factory running (RuBP is re-formed). • Output = After enough cycles, the factory produces glucose, the “food” of the plant.
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.
Make a test, with answers best on the following: Conduct an investigation to provide evidence that living things are made of cells; either one cell or many different numbers and types of cells. Supporting Content LS1.A: Structure and Function • All living things are made up of cells, which is the smallest unit that can be said to be alive. An organism may consist of one single cell (unicellular) or many different numbers and types of cells (multicellular). (MS-LS-1.1) Further Explanation: Emphasis is on developing evidence that living things are made of cells, distinguishing between living and non-living things, and understanding that living things may be made of one cell or many and varied cells. In multicellular organisms, the body is a system of multiple interacting subsystems. These subsystems are groups of cells that work together to form tissues and organs that are specialized for particular body functions. (MS-LS-1.3) Further Explanation: Emphasis is on the conceptual understanding that cells form tissues and tissues form organs specialized for particular body functions. Examples could include the interaction of subsystems within a system and the normal functioning of those systems. Organisms reproduce, either sexually or asexually, and transfer their genetic information to their offspring. (MS-LS-1.4) • Living things share certain characteristics. (These include response to environment, reproduction, energy use, growth and development, life cycles, made of cells, etc.) (MS-LS1.4) Further Explanation: Examples should include both biotic and abiotic items, and should be defended using accepted characteristics of life. Plants, algae (including phytoplankton), and many microorganisms use the energy from light to make sugars (food) from carbon dioxide from the atmosphere and water through the process of photosynthesis, which also releases oxygen. These sugars can be used immediately or stored for growth or later use. (MS-LS-1.5) Further Explanation: Emphasis is on tracing movement of matter and flow of energy. Supporting Content LS1.C: Organization for Matter and Energy Flow in Organisms • Within individual organisms, food moves through a series of chemical reactions (cellular respiration) in which it is broken down and rearranged to form new molecules, to support growth, or to release energy. (MS-LS-1.6) Further Explanation: Emphasis is on describing that molecules are broken apart and put back together and that in this process, energy is released and on understanding that the elements in the products are the same as the elements in the reactants. Organisms, and populations of organisms, are dependent on their environmental interactions both with other living things and with nonliving factors. (MS-LS-2.1) • In any ecosystem, organisms and populations with similar requirements for food, water, oxygen, or other resources may compete with each other for limited resources, access to which consequently constrains their growth and reproduction. (MS-LS-2.1) • Growth of organisms and population increases are limited by access to resources. (MS-LS-2.1) Further Explanation: Emphasis is on cause and effect relationships between resources and growth of individual organisms and the numbers of organisms in ecosystems during periods of abundant and scarce resources. Similarly, predatory interactions may reduce the number of organisms or eliminate whole populations of organisms. Mutually beneficial interactions, in contrast, may become so interdependent that each organism requires the other for survival. Although the species involved in these competitive, predatory, and mutually beneficial interactions vary across ecosystems, the patterns of interactions of organisms with their environments, both living and nonliving, are shared. (MS-LS-2.2) Further Explanation: Emphasis is on predicting consistent patterns of interactions in different ecosystems in terms of the relationships among and between organisms and abiotic components of ecosystems. Examples of types of interactions could include competitive, predatory, and mutually beneficial. Food webs are models that demonstrate how matter and energy is transferred between producers, consumers, and decomposers as the three groups interact within an ecosystem. Transfers of matter into and out of the physical environment occur at every level. Decomposers recycle nutrients from dead plant or animal matter back to the soil in terrestrial environments or to the water in aquatic environments. The atoms that make up the organisms in an ecosystem are cycled repeatedly between the living and nonliving parts of the ecosystem. (MS-LS-2.3) Further Explanation: Emphasis is on describing the conservation of matter and flow of energy into and out of various ecosystems, and on defining the boundaries of the system. Ecosystems are dynamic in nature; their characteristics can vary over time. Disruptions to any physical or biological component of an ecosystem can lead to shifts in all its populations. (MSLS-2.5) Further Explanation: Emphasis is on recognizing patterns in data and making warranted inferences about changes in populations, and on evaluating empirical evidence supporting arguments about changes to ecosystems. Biodiversity describes the variety of species found in Earth’s terrestrial and oceanic ecosystems. The completeness or integrity of an ecosystem’s biodiversity is often used as a measure of its health. (MS-LS-2.6) Supporting Content LS4.D: Biodiversity • Changes in biodiversity can influence humans’ resources, such as food, energy, and medicines, as well as ecosystem services that humans rely on—for example, water purification and recycling. (MS-LS-2.6) Supporting Content ETS1.B: Developing Possible Solutions • There are systematic processes for evaluating solutions with respect to how well they meet the criteria and constraints of a problem. (MS-LS-2.6) Further Explanation: Examples of ecosystem services could include water purification, nutrient recycling, and prevention of soil erosion. Examples of design solution constraints could include scientific, economic, and social considerations. Genes are located in the chromosomes of cells, with each chromosome pair containing two variants of each of many distinct genes. Each distinct gene chiefly controls the production of specific proteins, which in turn affects the traits of the individual. Structural changes to genes (mutations) can result in changes to proteins, which can affect the structures and functions of the organism and thereby change traits. (MS-LS-3.1) Supporting Content LS3.B: Variation of Traits • In addition to variations that arise from sexual reproduction, genetic information can be altered because of mutations. Though rare, mutations may result in significant changes to the structure and function of proteins. Changes can be beneficial, harmful, or neutral to the organism. (MS-LS-3.1) Further Explanation: Emphasis is on conceptual understanding that changes in genetic material may result in making different proteins. Organisms reproduce, either sexually or asexually, and transfer their genetic information to their offspring. (MS-LS-3.2) Supporting Content LS3.A: Inheritance of Traits • Variations of inherited traits between parent and offspring arise from genetic differences that result from the subset of chromosomes (and therefore genes) inherited. (MS-LS-3.2) Supporting Content LS3.B: Variation of Traits • In sexually reproducing organisms, each parent contributes half of the genes acquired (at random) by the offspring. Individuals have two of each chromosome and hence two alleles of each gene, one acquired from each parent. These versions may be identical or may differ from each other. (MS-LS-3.2) Further Explanation: Emphasis is on using models such as simple Punnett squares and pedigrees, diagrams, and simulations to describe the cause and effect relationship of gene transmission from parent(s) to offspring and resulting genetic variation. The collection of fossils and their placement in chronological order is known as the fossil record and documents the change of many life forms throughout the history of the Earth. Anatomical similarities and differences between various organisms living today and between living and once living organisms in the fossil record enable the classification of living things. (MS-LS-4.1, MS-LS-4.2) Further Explanation: Emphasis is on finding patterns of changes in the level of complexity of anatomical structures in organisms and the chronological order of fossil appearance in the rock layers. The collection of fossils and their placement in chronological order is known as the fossil record and documents the change of many life forms throughout the history of the Earth. Anatomical similarities and differences between various organisms living today and between living and once living organisms in the fossil record enable the classification of living things. (MS-LS-4.1, MS-LS-4.2) Further Explanation: Emphasis is on explanations of the relationships among organisms in terms of similarity or differences of the gross appearance of anatomical structures. Scientific genus and species level names indicate a degree of relationship. (MS-LS-4.3) Further Explanation: Emphasis is on inferring general patterns of relatedness among structures of different organisms by comparing diagrams, pictures, specimens, or fossils. Natural selection leads to the predominance of certain traits in a population, and the suppression of others. (MS-LS-4.4) Further Explanation: Emphasis is on using concepts of natural selection, including overproduction of offspring, passage of time, variation in a population, selection of favorable traits, and heritability of traits. In artificial selection, humans have the capacity to influence certain characteristics of organisms by selective breeding. One can choose desired parental traits determined by genes, which are then passed to offspring. (MS-LS-4.5) Further Explanation: Emphasis is on identifying and communicating information from reliable sources about the influence of humans on genetic outcomes in artificial selection (such as genetic modification, animal husbandry, gene therapy), and on the influence these technologies have on society as well as the technologies leading to these scientific discoveries. Adaptation by natural selection acting over generations is one important process by which species change over time in response to changes in environmental conditions. Traits that support successful survival and reproduction in the new environment become more common; those that do not become less common. Thus, the distribution of traits in a population changes. (MS-LS-4.6) Further Explanation: Emphasis is on using mathematical models, probability statements, and proportional reasoning to support explanations of trends in changes to populations over time. Examples could include Peppered Moth population changes before and after the industrial revolution.
What is a Plant Cell? Plant cells are eukaryotic cells that vary in several fundamental factors from other eukaryotic organisms. Both plant and animal cells contain a nucleus along with similar organelles. One of the distinctive aspects of a plant cell is the presence of a cell wall outside the cell membrane. Plant Cell Structure Just like different organs within the body, plant cell structure includes various components known as cell organelles that perform different functions to sustain itself. These organelles include: Cell Wall It is a rigid layer which is composed of polysaccharides cellulose, pectin and hemicellulose. It is located outside the cell membrane. It also comprises glycoproteins and polymers such as lignin, cutin, or suberin. The primary function of the cell wall is to protect and provide structural support to the cell. The plant cell wall is also involved in protecting the cell against mechanical stress and providing form and structure to the cell. It also filters the molecules passing in and out of it. The formation of the cell wall is guided by microtubules. It consists of three layers, namely, primary, secondary and the middle lamella. The primary cell wall is formed by cellulose laid down by enzymes. Cell membrane It is the semi-permeable membrane that is present within the cell wall. It is composed of a thin layer of protein and fat. The cell membrane plays an important role in regulating the entry and exit of specific substances within the cell. For instance, cell membrane keeps toxins from entering inside, while nutrients and essential minerals are transported across. Nucleus The nucleus is a membrane-bound structure that is present only in eukaryotic cells. The vital function of a nucleus is to store DNA or hereditary information required for cell division, metabolism and growth. 1. Nucleolus: It manufactures cells’ protein-producing structures and ribosomes. 2. Nucleopore: Nuclear membrane is perforated with holes called nucleopore that allow proteins and nucleic acids to pass through. Plastids They are membrane-bound organelles that have their own DNA. They are necessary to store starch and to carry out the process of photosynthesis. It is also used in the synthesis of many molecules, which form the building blocks of the cell. Some of the vital types of plastids and their functions are stated below: Leucoplasts They are found in the non-photosynthetic tissue of plants. They are used for the storage of protein, lipid and starch. Chromoplasts They are heterogeneous, colored plastid which is responsible for pigment synthesis and for storage in photosynthetic eukaryotic organisms. Chromoplasts have red-, orange- and yellow-colored pigments which provide color to all ripe fruits and flowers. Central Vacuole It occupies around 30% of the cell’s volume in a mature plant cell. Tonoplast is a membrane that surrounds the central vacuole. The vital function of the central vacuole apart from storage is to sustain turgor pressure against the cell wall. The central vacuole consists of cell sap. It is a mixture of salts, enzymes and other substances. Golgi Apparatus They are found in all eukaryotic cells, which are involved in distributing synthesized macromolecules to various parts of the cell. Ribosomes They are the smallest membrane-bound organelles which comprise RNA and protein. They are the sites for protein synthesis, hence, also referred to as the protein factories of the cell. Mitochondria They are the double-membraned organelles found in the cytoplasm of all eukaryotic cells. They provide energy by breaking down carbohydrate and sugar molecules, hence they are also referred to as the “Powerhouse of the cell.” Lysosome Lysosomes are called suicidal bags as they hold digestive enzymes in an enclosed membrane. They perform the function of cellular waste disposal by digesting worn-out organelles, food particles and foreign bodies in the cell. In plants, the role of lysosomes is undertaken by the vacuoles. Chloroplasts It is an elongated organelle enclosed by phospholipid membrane. The chloroplast is shaped like a disc and the stroma is the fluid within the chloroplast that comprises a circular DNA. Each chloroplast contains a green colored pigment called chlorophyll required for the process of photosynthesis. The chlorophyll absorbs light energy from the sun and uses it to transform carbon dioxide and water into glucose. Structure of Chloroplast Chloroplasts are found in all higher plants. It is oval or biconvex, found within the mesophyll of the plant cell. The size of the chloroplast usually varies between 4-6 µm in diameter and 1-3 µm in thickness. They are double-membrane organelle with the presence of outer, inner and intermembrane space. There are two distinct regions present inside a chloroplast known as the grana and stroma. • Grana are made up of stacks of disc-shaped structures known as thylakoids or lamellae. The granum of the chloroplast consists of chlorophyll pigments and are the functional units of chloroplasts. • Stroma is the homogenous matrix which contains grana and is similar to the cytoplasm in cells in which all the organelles are embedded. Stroma also contains various enzymes, DNA, ribosomes, and other substances. Stroma lamellae function by connecting the stacks of thylakoid sacs or grana. The chloroplast structure consists of the following parts: Membrane Envelope It comprises inner and outer lipid bilayer membranes. The inner membrane separates the stroma from the intermembrane space. Intermembrane Space The space between inner and outer membranes. Thylakoid System (Lamellae) The system is suspended in the stroma. It is a collection of membranous sacs called thylakoids or lamellae. The green colored pigments called chlorophyll are found in the thylakoid membranes. It is the sight for the process of light-dependent reactions of the photosynthesis process. The thylakoids are arranged in stacks known as grana and each granum contains around 10-20 thylakoids. Stroma It is a colorless, alkaline, aqueous, protein-rich fluid present within the inner membrane of the chloroplast present surrounding the grana. Grana Stack of lamellae in plastids is known as grana. These are the sites of conversion of light energy into chemical energy. Chlorophyll It is a green photosynthetic pigment that helps in the process of photosynthesis. Functions of Chloroplast Following are the important chloroplast functions: • The most important function of the chloroplast is to synthesize food by the process of photosynthesis. • Absorbs light energy and converts it into chemical energy. • Chloroplast has a structure called chlorophyll which functions by trapping the solar energy and is used for the synthesis of food in all green plants. • Produces NADPH and molecular oxygen (O 2 ) by photolysis of water. • Produces ATP – Adenosine triphosphate by the process of photosynthesis. • The carbon dioxide (CO2) obtained from the air is used to generate carbon and sugar during the Calvin Cycle or dark reaction of photosynthesis. Mitochondria “Mitochondria are membrane-bound organelles present in the cytoplasm of all eukaryotic cells, that produce adenosine triphosphate (ATP), the main energy molecule used by the cell.” What are Mitochondria? Popularly known as the “Powerhouse of the cell,” mitochondria (singular: mitochondrion) are a double membrane-bound organelle found in most eukaryotic organisms. They are found inside the cytoplasm and essentially function as the cell’s “digestive system.” They play a major role in breaking down nutrients and generating energy-rich molecules for the cell. Many of the biochemical reactions involved in cellular respiration take place within the mitochondria. The term ‘mitochondrion’ is derived from the Greek words “mitos” and “chondrion” which means “thread” and “granules-like”, respectively. It was first described by a German pathologist named Richard Altmann in the year 1890. Structure of Mitochondria • The mitochondrion is a double-membraned, rod-shaped structure found in both plant and animal cell. • Its size ranges from 0.5 to 1.0 micrometers in diameter. • The structure comprises an outer membrane, an inner membrane, and a gel-like material called the matrix. • The outer membrane and the inner membrane are made of proteins and phospholipid layers separated by the intermembrane space. • The outer membrane covers the surface of the mitochondrion and has a large number of special proteins known as porins. Cristae The inner membrane of mitochondria is rather complex in structure. It has many folds that form a layered structure called cristae, and this helps in increasing the surface area inside the organelle. The cristae and the proteins of the inner membrane aid in the production of ATP molecules. The inner mitochondrial membrane is strictly permeable only to oxygen and ATP molecules. A number of chemical reactions take place within the inner membrane of mitochondria. Mitochondrial Matrix The mitochondrial matrix is a viscous fluid that contains a mixture of enzymes and proteins. It also comprises ribosomes, inorganic ions, mitochondrial DNA, nucleotide cofactors, and organic molecules. The enzymes present in the matrix play an important role in the synthesis of ATP molecules. Functions of Mitochondria The most important function of mitochondria is to produce energy through the process of oxidative phosphorylation. It is also involved in the following process: 1. Regulates the metabolic activity of the cell 2. Promotes the growth of new cells and cell multiplication 3. Helps in detoxifying ammonia in the liver cells 4. Plays an important role in apoptosis or programmed cell death 5. Responsible for building certain parts of the blood and various hormones like testosterone and estrogen 6. Helps in maintaining an adequate concentration of calcium ions within the compartments of the cell 7. It is also involved in various cellular activities like cellular differentiation, cell signaling, cell senescence, controlling the cell cycle and in cell growth. Disorders Associated with Mitochondria Any irregularity in the way mitochondria function can directly affect human health, but often, it is difficult to identify because symptoms differ from person to person. Disorders of the mitochondria can be quite severe; in some cases, they can even cause an organ to fail.
5th Grade Science Quiz: Movement of Matter in Ecosystems 1. Which organisms are responsible for breaking down dead plants and animals into simple nutrients? a) Producers b) Consumers c) Decomposers d) Predators 2. What is the process by which plants use sunlight to make food? a) Respiration b) Decomposition c) Photosynthesis d) Erosion 3. How do animals contribute to the movement of matter in an ecosystem? a) They produce oxygen b) They break down dead organisms c) They release nutrients through waste d) They absorb carbon dioxide 4. What is the primary source of energy for most ecosystems? a) Soil b) Water c) Sunlight d) Air 5. How does matter move through the environment? a) It flows in a straight line b) It cycles through various organisms and the environment c) It remains stationary d) It only moves between plants and animals Answer Key (Always review AI generated answers for accuracy - Math is more likely to be inaccurate.) 1. c) Decomposers 2. c) Photosynthesis 3. c) They release nutrients through waste 4. c) Sunlight 5. b) It cycles through various organisms and the environment
Q1. Tick the properties of water. a. Water is transparent and colourless. b. Water has no smell or taste. c. One litre of water has a mass of one kilogram. d. Water supports life. e. Water has no weight. Q2. List the properties of air. --------------------------------------------------------------------- --------------------------------------------------------------------- ---------------------------------------------------------------------- ----------------------------------------------------------------------- Q3. "Which gases are the most abundant in air?" The most common gas ----------------------------------------- The second most common gas ----------------------------- 8 | Page AZ-Y5-Science- Second Mid-Term Revision2024/2025 Q4. Look at the pie chart of the components of the air and identify P, Q and R. Nitrogen 71% Oxygen 21% Other gases 1% P ------------------------------- Q ------------------------------- R -------------------------------- Q5. Identify the gas for each of these descriptions. Use the name of each gas twice. Oxygen-nitrogen-carbon dioxide. a. The gas we need to breathe. --------------------------------- b. The most common gas in the air. ---------------------------- c. The gas that gives drinks their fizz. ---------------------------- d. The gas that supports burning. -------------------------------- e. A gas used to make fertilizer. ---------------------------------- f. A gas used in fire extinguishers. ------------------------------- 9 | Page AZ-Y5-Science- Second Mid-Term Revision2024/2025 Q6. Draw and label the stages of the water cycle. Use arrows to show how water moves through the cycle." 10 | Page AZ-Y5-Science- Second Mid-Term Revision2024/2025 Q7. The diagram shows how gases in the upper atmosphere trap heat. a. What does the diagram refer to? _____________________________________________________________ b. Give two reasons why the amount of greenhouse gases in the atmosphere is increasing. _____________________________________________________________ _____________________________________________________________ c. If more heat is trapped, how will the earth's temperature change? 1. It will rise. 2. It will fall. d. "Which of the following is a greenhouse gas?" 1. Argon 2. Nitrogen 3. Carbon dioxide 11 | Page AZ-Y5-Science- Second Mid-Term Revision2024/2025 Q8. Write (T) for True or (F) for False. 1. Global warming leads to rising sea levels and more droughts. ( ) 2. Water exists in only one state: liquid. ( ) 3. It is not safe to drink untreated water from lakes and rivers. ( ) 4. Air pollution does not affect the environment. ( ) 5. Nitrogen is the most common gas in the atmosphere. ( ) Q9. Fill in the blanks: a. Air is a mixture of gases, and the most abundant gas in the air is __________. b. The water cycle includes four stages: __________, __________, __________, and __________. c. __________ is a gas used in the production of fertilizers. d. __________ is a harmful gas that contributes to global warming by trapping heat in the atmosphere. Q10. Answer the following questions: 1. What are the four main stages of the water cycle? -------------------------------------------------------------------------------- 2. Name one way to help reduce air pollution. ----------------------------------------------------------------------------------- 12 | Page AZ-Y5-Science- Second Mid-Term Revision2024/2025 3. State one use of oxygen gas. ------------------------------------------------------------------------------------ 4. What is one consequence of global warming? -------------------------------------------------
Organic Nomenclature. What are aliphatic compounds or aliphatic hydrocarbons? An aliphatic compound or aliphatic hydrocarbon is an organic compound containing hydrogen and carbon atoms that are usually linked together in chains that are straight. The term Aliphatic has been derived from the Greek word “Aleiphar” which translates to “fat”. It is used to describe hydrocarbons that are obtained by the chemical degradation of oils or fats. What are aliphatic compounds or aliphatic hydrocarbons? The simplest organic compounds are those composed of only two elements: carbon and hydrogen. These compounds are called hydrocarbons. Hydrocarbons are separated into two types: aliphatic hydrocarbons and aromatic hydrocarbons. Aliphatic hydrocarbons are hydrocarbons based on chains of C atoms. There are three types of aliphatic hydrocarbons: Alkanes are aliphatic hydrocarbons with only single covalent bonds. Alkenes are hydrocarbons that contain at least one C–C double bond, and alkynes are hydrocarbons that contain a C–C triple bond. Occasionally, we find an aliphatic hydrocarbon with a ring of C atoms; these hydrocarbons are called cycloalkanes (or cycloalkenes or cycloalkynes). The simplest alkanes have their C atoms bonded in a straight chain; these are called normal alkanes. They are named according to the number of C atoms in the chain. The smallest alkane is methane: molecule is three dimensional, with the H atoms in the positions of the four corners of a tetrahedron. The diagrams representing alkanes are called structural formulas because they show the structure of the molecule. As molecules get larger, structural formulas become more and more complex. One way around this is to use a condensed structural formula, which lists the formula of each C atom in the backbone of the Molecule. The condensed formulas show hydrogen atoms right next to the carbon atoms to which they are attached, as illustrated for butane: The ultimate condensed formula is a line-angle formula (or line drawing) , in which carbon atoms are implied at the corners and ends of lines, and each carbon atom is understood to be attached to enough hydrogen atoms to give each carbon atom four bonds. For example, we can represent pentane (CH3CH2CH2CH2CH3) and isopentane [(CH3)2CHCH2CH3] as follows: Unsaturated Hydocarbons: Alkenes and Alkynes Alkenes Organic compounds that contain one or more double or triple bonds between carbon atoms are described as unsaturated. Unsaturated hydrocarbons have less than the maximum number of H atoms possible. Unsaturated hydrocarbon molecules that contain one or more double bonds are called alkenes. Carbon atoms linked by a double bond are bound together by two bonds, one σ bond and one π bond. Double and triple bonds give rise to a different geometry around the carbon atom that participates in them, leading to important differences in molecular shape and properties. The differing geometries are responsible for the different properties of unsaturated versus saturated fats. Naming Alkenes and Alkynes Alkenes and alkynes are named in a similar fashion. The biggest difference is that when identifying the longest carbon chain, it must contain the C–C double or triple bond. Furthermore, when numbering the main chain, the double or triple bond gets the lowest possible number. This means that there may be longer or higher-numbered substituents than may be allowed if the molecule were an alkane. For example, this molecule is 2,4-dimethyl-3-heptene (note the number and the hyphens that indicate the position of the double bond). Unsaturated Hydocarbons: Alkenes and Alkynes Unsaturated Hydocarbons: Alkenes and Alkynes Alkynes Hydrocarbon molecules with one or more triple bonds are called alkynes; they make up another series of unsaturated hydrocarbons. Two carbon atoms joined by a triple bond are bound together by one σ bond and two π bonds. The sp-hybridized carbons involved in the triple bond have bond angles of 180°, giving these types of bonds a linear, rod-like shape. The simplest member of the alkyne series is ethyne, C2H2, commonly called acetylene. The Lewis structure for ethyne, a linear molecule, is: Properties of Unsaturated Hydocarbons: Alkenes and Alkynes Ethylene (the common industrial name for ethene) is a basic raw material in the production of polyethylene and other important compounds. Over 135 million tons of ethylene were produced worldwide in 2010 for use in the polymer, petrochemical, and plastic industries. Ethylene is produced industrially in a process called cracking, in which the long hydrocarbon chains in a petroleum mixture are broken into smaller molecules. Halogens can also react with alkenes and alkynes, but the reaction is different. In these cases, the halogen reacts with the C–C double or triple bond and inserts itself onto each C atom involved in the multiple bonds. This reaction is called an addition reaction. One example is Properties of Unsaturated Hydocarbons: Alkenes and Alkynes Hydrogen can also be added across a multiple bond; this reaction is called a hydrogenation reaction. In this case, however, the reaction conditions may not be mild; high pressures of H2 gas may be necessary. A platinum or palladium catalyst is usually employed to get the reaction to proceed at a reasonable pace: CH2=CH2+H2→metalcatalystCH3CH3 CH2=CH2+H2→metalcatalystCH3CH3.
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.