General Biology PDF - Semester 1 Finals

GENERAL BIOLOGY SEMESTER 1 II FINALS Lesson 7.1 Energy Flow and Recycling ENERGY Photosynthesis in plants and other autotrophs demonstrates the first law of...

GENERAL BIOLOGY SEMESTER 1 II FINALS Lesson 7.1 Energy Flow and Recycling ENERGY Photosynthesis in plants and other autotrophs demonstrates the first law of Energy is defined as the ability to do work or bring thermodynamics—energy is not created by about a change, allowing organisms to carry out different life processes, including growth, development, the plants, but rather, they obtain it from metabolism, and reproduction. sunlight and convert it into a form that can be stored in chemical bonds of biomolecules. Forms of Energy Kinetic energy is the energy due to the motion of an object. Potential energy is the stored energy of an object whose capacity to accomplish work is not being utilized at the moment. Food has chemical energy because it is composed of organic molecules such as carbohydrates, proteins, and fat, which can be broken down to liberate energy. When a person walks, he or she converts chemical energy into The second law of thermodynamic applies to living mechanical energy. systems. Thermal energy is a type of kinetic energy associated with the random movement of atoms or molecules. The thermal It states that energy cannot be changed from energy that is transferred from one object to another is one form to another without a loss of usable called heat. energy. When cells oxidize food molecules to drive chemical reactions, heat is also released Law of thermodynamics into the surroundings. The first law of thermodynamics is the Cells and Entropy law of conservation of energy. The term entropy is used to indicate the This states that energy cannot be created nor relative amount of disorganization, and the destroyed; rather, energy can be changed universe moves in the direction of greater from one form to another. This means that entropy. However, life forms on earth have the total amount of energy in the universe is the capacity to maintain or increase constant. complexity through the continuous supply of solar energy. The second law of thermodynamics can be shown in the breakdown of glucose and the JCRS | 1  movement of ions across the cell membrane. Structure of ATP These processes naturally tend to proceed into a state of greater entropy. ATP is a nucleotide composed of the nitrogen- containing base adenine, the 5-carbon sugar ribose, and three phosphate groups. The hydrolysis of ATP is exergonic. The cell couples this reaction to an endergonic reaction by transferring a phosphate group from ATP to another molecule. This phosphate transfer is called phosphorylation. Mechanisms of ATP Synthesis Substrate-level phosphorylation is the process of producing ATP by combining ADP and a phosphate group from a phosphorylated molecule instead of an Adenosine triphosphate inorganic phosphate. Oxidative phosphorylation is the common energy currency of cells— when cells require energy to drive their is an ATP synthesizing mechanism that chemical reactions, these cells use ATP. The utilizes the energy derived from the transfer more active an organism is, the greater is its of electrons in an electron transport system demand for ATP molecules. to combine ADP and inorganic phosphate. Photophosphorylation is driven by the proton motive force generated during the flow of electrons in the light reaction stage. stage. The protons flow The ATP-ADP cycle in which ATP carries energy between exergonic and endergonic reactions. The energy released from ATP is used to drive biochemical functions. 2  through the ATP synthase enzyme complex, which triggers ATP synthesis. LESSON 7.2 ADP-ATP CYCLE Structure of ATP and ADP Exergonic reactions Exergonic reactions are energy-releasing processes where the reactants have greater energy than the products. The breakdown of ATP molecules into ADP and inorganic phosphate is an exergonic reaction. The adenosine triphosphate molecule releases energy upon the hydrolysis of its terminal phosphate group. This exergonic process is coupled with an endergonic reaction. Functions of ATP The triphosphate tail is the portion of ATP that provides energy for cellular work. Each of these phosphate groups is negatively Endergonic reactions charged, which makes them repel each other. ATP energizes other molecules in cells by Endergonic reactions are energy-releasing transferring phosphate groups to those processes where the reactantshave less molecules. This transfer of phosphate groups energy than the products. Photosynthesis and helps cells perform mechanical, transport, other forms of biosynthesis are examples of and chemical functions. endergonic reactions. Mechanism of ADP-ATP Cycle 3  The ADP-ATP cycle is an alternation between Chlorophyll a endergonic and exergonic reactions which are essential for continuous cellular maintenance. is the primary pigment during photosynthesis. It is also the universal pigment in all photosynthetic organisms. It participates directly in light reactions and is the most common green photosynthetic pigment in plants, algae, some protists, and cyanobacteria. This pigment absorbs mainly blue, violet, and red light, thus it appears green to us. Accessory Pigments Chlorophyll b an accessory pigment, absorbs mainly blue and orange light but reflects olive green. Although chlorophyll b does not participate LESSON 8.1 Photosynthesis and the Role of Pigments directly in light reactions, it conveys absorbed Photosynthetic Pigments energy to chlorophyll a to work in the light reactions. Photosynthesis is the process in which plants The green leaves of many plants change color harness solar energy and use it to synthesize during autumn because they stop high-energy organic compounds in the form synthesizing pigments in preparation for a of sugars. period of dormancy. The chlorophyll breaks Pigments are organic molecules that down faster than the other pigments, so the selectively absorb light of specific leaves turn red, orange, yellow, or violet as wavelengths and are built into the thylakoid their chlorophyll content declines, and other membranes of the chloroplasts. accessory pigments become visible. Photosynthetic pigments can be classified into primary and accessory pigments based Chlorophyll c on their contribution to light energy the accessory pigment of brown algae, harvesting during photosynthesis. diatoms, and dinoflagellates. Chlorophyll d is found only in red algae. Carotenoids Variegation in the leaves of some plants reduces their are accessory pigments consisting of various capacity for photosynthetic activity. However, in the shades of yellow and orange. wild, this results in an advantage that they become less These pigments absorb mainly violet, blue, likely eaten by herbivores. and green light. Principal Pigment 4  This pigment is important in photoprotection. Electron Flow in Light-Dependent Reactions These pigments also convey light energy harvest from other bands of the visible light A photosystem consists of a number of light- harvesting complexes (LHC) surrounding a from the sun. reaction-center complex. An LHC contains Phycobilins various pigment molecules bound to proteins. Photosynthesis begins in the pigment are also accessory pigments in red algae and molecules of photosystem II, which absorb cyanobacteria that either give red or blue light energy and transfer it to a chlorophyll a coloration. They are especially important for reaction center. This center then excites two deep-sea red algae as they can utilize the blue electrons. light that can penetrate deeper waters. As electrons move in the electron transport chain, their energy is used to pump protons (H+) across the membrane into the thylakoid space. The thylakoid space will then have a high concentration of H+ and a lower concentration in the stroma; thus, an H+ gradient is established. The H+ will diffuse through a protein in the thylakoid membrane called ATP synthase. The diffusion of H+ will rotate the ATP synthase to produce ATP. The second electron transport chain passes Aside from the primary and accessory classification of photosynthetic pigments, they can also be classified into the electrons from photosystem I to a chlorophyll, carotenoids, and phycobilins. molecule of NADP, forming the reduced NADPH. This NADPH is the electron carrier Lesson 8.2 Light-Dependent Reactions that will reduce CO2 in the next phase, while ATP will provide the energy. Noncyclic pathway is the linear mechanism of electron transport The photosynthetic pathway in autotrophs can be from photosystem II to photosystem I, summarized by having carbon dioxide and water on the including the electron transport chains. This reactants side, and with light energy input, sugar (in the is the standard mechanism of light-dependent form of glucose) and oxygen molecules are produced. reactions. Ultimately, it produces NADPH and ATP molecules. Light-Dependent Reactions Cyclic Pathway only occur when solar energy is available. This process happens on the thylakoid involves only the photosystem I and the membrane of chloroplasts which converts electron transport proteins. The electron solar energy into chemical energy. chain in this pathway uses the electron’s energy to move H+ into the thylakoid compartment. The resulting H+ gradient 5  drives ATP formation, just as it does in the The most important input to the Calvin cycle noncyclic pathway. is the carbon dioxide that comes from the atmosphere via the stomata of leaves. Cyclic photophosphorylation Fixation is important to create ATP while maintaining NADPH in the right proportion. The process of incorporating carbon atoms from an inorganic source into an organic molecule. During carbon fixation, the enzyme RuBisCo catalyzes the reaction between ribulose bisphosphate (RuBP) and CO2 to produce 3- phosphoglycerate (3-PGA). Reduction During the reduction phasetwo chemical reactions use energy from ATP and Lesson 8.3 Light-Independent Reactions (Calvin Cycle) electrons donated from NADPH to reduce molecules of 3-PGA into glyceraldehyde 3- phosphate (G3P). This stage is called the reduction reaction phase because it involves the gain of electrons from the NADPH. The two-step process of reduction of 3-PGA to G3P involves the use of ATP and NADPH molecules The chloroplast is the site for both light-dependent and generated from light-dependent reactions. After the light-independent reactions. Light reactions take place reduction process, one phosphate group and electrons in the thylakoids that are stacked into grana. The are transferred to the PGA, thus, also forming ADP and following phase, the light-independent reactions, or NADP+. These will be reused in the thylakoid collectively the Calvin cycle, takes place in the fluid- membrane light reactions. filled space or stroma of this organelle. Calvin Cycle Regeneration ultimately produce glucose in the fluid-filled In this phase, for every three carbon dioxide stroma of chloroplasts. molecules fixed, one G3P molecule leaves the energy from photons is not directly required cycle as a product. This molecule contributes for the chemical reactions to proceed. Instead, to the formation of the carbohydrate they run on the ATP and NADPH molecules molecule, which is commonly known as generated from light-dependent reactions. glucose. 6  During the regeneration stage, a series of is a catabolic pathway that uses glucose chemical reactions utilize energy from ATP to molecules to produce energy in the form of rearrange the atoms in the remaining five ATP (adenosine triphosphate). G3P molecules (total of 15 carbon atoms) into Glycolysis, Krebs cycle, electron transport three molecules of RuBP (likewise, a total of chain, and chemiosmosis are the four stages 15 carbon atoms). of cellular respiration. Kinds of Cellular Respiration Aerobic respiration is the process of producing energy involving oxygen. Anaerobic respiration is the process of producing energy without the presence of oxygen. During the Calvin cycle, an input of three carbon dioxide molecules will produce six G3P molecules. One of these Aerobic Respiration G3Ps will be used for the synthesis of glucose. The other In the first part of aerobic respiration which five molecules will be used to regenerate RuBP with an is glycolysis, oxygen is not used. However, in input of three ATPs. the latter part of the process, oxygen is Products of Calvin Cycle already used as an electron acceptor which results in the formation of water molecules. Overall, to produce one molecule of glucose, a Krebs cycle and electron transport chain total of 18 ATP and 12 NADPH molecules are happen in the mitochondria of the cell. needed while still replenishing the Calvin cycle with RuBP. Reactants and Products of Cellular Respiration In cellular respiration, the reactants are the glucose and oxygen molecules while water, carbon dioxide, and ATP molecules are the products. Lesson 9.2 Aerobic Respiration: Glycolysis Glycolysis This stage involves the breakdown of the six- carbon sugar glucose (C6H12O6) and the production of pyruvate and ATP molecules. Lesson 9.1 Cellular Respiration and the Role of the Mitochondrion Glycolysis happens in the cell cytoplasm. During this stage, the oxidation of glucose Cellular respiration results in the release of electrons. Thereafter, these electrons are picked up by 7  NAD+(nicotinamide adeninedinucleotide), which is then reduced to NADH. To memorize the correct order of enzymes used during glycolysis, you may use the mnemonics below: HE PUT THE PHONE AND TRIED TO GET THE PLASTIC PLATE TO EAT PIE. H- hexokinase P- phosphoglucoisomerase PHO- phosphofructokinase A- aldolase The net products of glycolysis are 2 ATP, 2 NADH, and TRI- triosephosphate isomerase two pyruvate molecules. G- glyceraldehyde-3-phosphate dehydrogenase Pyruvate undergoes oxidation and becomes P- phosphoglycerate kinase acetyl-CoA, which enters the Krebs cycle. P- phosphoglycerate mutase Lesson 9.3 Aerobic Respiration: Krebs Cycle E- enolase Transition Reaction P- pyruvate kinase Pyruvate, a three-carbon molecule, cannot immediately enter the Krebs cycle. It must first undergo oxidation to become another molecule that can enter the pathway. After glycolysis, pyruvate molecules enter the mitochondrion, given that the condition is aerobic. Upon entering, pyruvate is converted into acetyl-CoA. Mechanism of the Krebs Cycle Krebs cycle is the process of oxidizing and further breaking down two pyruvate molecules to produce energy. In the transition reaction before the Krebs cycle, acetyl-CoA is formed from pyruvate through oxidation. CO2 and NADH are also produced in this stage. The series of redox reactions during the Krebs cycle produces NADH, FADH2,CO2, and 8  GTP. The CO2 is released into the environment. NADH and FADH2 are used to produce more ATP in the electron transport chain. GTP is used to drive chemical reactions similar to how cells use ATP. Lesson 9.4 Aerobic Respiration: Chemiosmosis and Electron Transport Chain Electron Transport Chain A series of four multiprotein complexes embeddedin the inner membrane of the mitochondrion where NADH and FADH2 are oxidized to release electrons. There are four proteins embedded in the inner membrane of a mitochondrion that forms this transport complex. These protein complexes receive the electrons from NADH and FADH2. Consequently, hydrogen ions (H+) from the matrix (the central or innermost region) are pumped (through active transport) into the intermembrane space. These hydrogen ions play an essential role in Products of the Krebs Cycle the phosphorylation of ADP to produce ATP through the process of chemiosmosis. Both the electron transport chain and chemiosmosis constitute the oxidative phosphorylation. Complex I The first protein complex that receives electrons from NADH is the complex I. Complex I has two molecular components that undergo reduction and oxidation or redox reactions once they receive and release electrons Complex II and Ubiquinone the transition reaction yields two molecules of CO2 and Complex II accepts electrons from the two molecules of NADH. In the Krebs cycle, there are a oxidation of FADH2 to FAD. total of six NADH molecules, four carbon dioxide, and Ubiquinone (Q) is a mobile hydrophobic two FADH2 molecules produced. molecule that receives electrons from Fe-S found in both complexes I and II. 9  do not go through oxidation, Krebs cycle, and ETC. Complex III The electrons from the Fe-S proteins in Complexes I and II, which are carried by the To regenerate NAD+ in the absence of oxygen, mobile carrier QH2 , are transferred to pyruvate molecules must undergo lactic acid Complex III. or alcoholic fermentation. Lactate is produced in lactic acid Complex IV fermentation while ethanol is produced in is the last place where electrons are alcoholic fermentation. transferred before they reduce oxygen to Lactic acid fermentation form a water molecule. Chemiosmosis Is the process involving the conversion of pyruvate molecules to lactate through an involves the downhill transport of hydrogen enzyme called lactate dehydrogenase. ions from the intermembrane space to the matrix. This movement provides energy to Alcoholic fermentation ATP synthase to phosphorylate ADP into ATP. involves the conversion of pyruvate molecules into ethanol through the help of pyruvate decarboxylase and alcohol ATP Yield dehydrogenase. 1 hydrogen = 1 ATP The products of anaerobic respiration are 2 ATP, 2 NADH, and 2 pyruvate molecules. When pyruvate 1 NADH = 2.5 ATP molecules undergo fermentation the products are either 1 FADH2 = 1.5 ATP ethanol or lactate. Lesson 10.1 Comparing Photosynthesis and Cellular Lesson 9.5 Anaerobic Respiration Respiration Anaerobic fermentation Major Stages is the process by which a glucose molecule is Cellular respiration involves four stages— broken down to produce energy in the glycolysis, Krebs cycle, electron transport chain, absence of oxygen. and chemiosmosis. Fermentation 1. Glycolysis involves the breakdown of glucose molecules. In this stage, ATP and NADH are produced. Is another anaerobic pathway used by most Afterward, three-carbon pyruvate molecules are organisms when deprived of oxygen. produced, which are oxidized into acetyl CoA before Fermentation also starts with glycolysis entering the Krebs cycle. which results in the formation of ATP, NADH, and pyruvate. However, pyruvate molecules 10 2. The Krebs cycle involves the reaction of acetyl CoA yields 3-PGA, which will be reduced by ATP and NADPH with oxaloacetate, which results in the formation of to form G3P. G3P molecules are used to produce glucose citrate. This molecule undergoes further oxidation, and regenerate RuBP. which results in the production of CO2, NADH, and FADH2. The electron carriers then enter the electron Summary of the differences between cellular transport chain. respiration and photosynthesis 3. The electron transport chain involves the oxidation of NADH and FADH2. The electrons from these oxidations cause the pumping of hydrogen ions from the matrix to the intermembrane space. 4. Chemiosmosis involves the passive return of H+into the matrix via the ATP synthase. This movement powers ATP synthase to combine an inorganic phosphate molecule with an ADP molecule to produce ATP molecules. Photosynthesis, just like the cellular respiration, has different stages, namely the light-dependent reaction and the light-independent reaction or the Similarities between Cellular Respiration and Calvin cycle. Photosynthesis 1. The light-dependent reaction involves the initial Photosynthesis and cellular respiration both involve absorption of radiant energy from the sun by the reduction-oxidation reactions and the ATP synthesis chlorophyll. that results from the flow of electrons through the protein complexes and ADP phosphorylation. a. This absorption excites the electrons of PSII, which allows them to move to the reaction center and to the electron transport complexes. b. The transport of electrons causes H+ to be pumped from the stroma to the thylakoid lumen. c. The downhill movement of H+ drives ATP synthesis via ATP synthase. d. The plastocyanin transfers the low-energy electrons to PSI, where they will be re-excited through solar energy absorption to move them to the reaction center. e. From the reaction center, electrons move to the ferredoxin and to NADP reductase, which reduces NADP to NADPH. 2. The Calvin cycle utilizes the ATP and NADPH from the previous reaction. This begins when CO2 reacts with RuBP with the help of RuBisCO. This process eventually 11