General Biology Reviewer PDF

GENERAL BIOLOGY REVIEWER Exergonic Reaction - Catabolic Reaction, spontaneous and or favorable chemical ENERGY TRANSFORMATION reactions wherein the products are at low Adenosine Triphosphate (ATP) - It is the energy...

GENERAL BIOLOGY REVIEWER Exergonic Reaction - Catabolic Reaction, spontaneous and or favorable chemical ENERGY TRANSFORMATION reactions wherein the products are at low Adenosine Triphosphate (ATP) - It is the energy level than the reactants (occur major energy currency of the cell that without the addition of energy) provides the energy for the most energy Energy - ability to do work (Kinetic: consuming activities of the cell. One big energy possessed by being in molecule that is made up of 5 smaller motion, Potential - energy stored molecules bonded together. due to position ATP-ADP CYCLE Composition: 1 Adenine 1 Ribose (Sugar) 3 Phosphate Group Adenosine Diphosphate (ADP) - a molecule that is composed of Adenosine and phosphates just like ATP, the only (Think of ATP as a charged battery and difference is ADP has only 2 phosphates. ADP as a battery that needs to be charged) ATP to ADP: It transfers energy from the breakdown of food molecules to cell function. ADP to ATP: It is changed into ATP when the phosphate group is added (P) from the Composition: breakdown of food 1 Adenine 1 Ribose (Sugar) Process of ATP-ADP Cycle: 3 Phosphate Group 1. When the third phosphate group of ATP is removed by hydrolysis (ATP Two Types of Reaction: + H2O > ADP + Pi), a substantial Endergonic Reaction - also known as amount of free energy is released. Anabolic reaction, nonspontaneous and usually occur in organisms, because they (ADP is adenosine diphosphate and Pi is need to synthesize complex molecules such inorganic phosphate) as fats, amino acids, and sugars (Needs energy input to synthesize. When energy is… Pigment Types Chlorophyll a - found in the chloroplast and is the site for photosynthesis. It converts solar energy to chemical energy. Green in color Structure: 2. When ATP breaks apart and releases its energy, the now ADP uses that energy and gains an extra P and is recharged back to ATP (Practically the same with chlorophyll b except for one functional group) 3. The now recharged ATP assists activities inside the cell (powers up Chlorophyll b - reflects olive green and all activities which needs energy) absorbs blue and orange light. Does not participate directly in light reactions. It is PIGMENTS present only in algae and higher plants, it also breaks down faster than other pigments Structure: Fact: The color reflected by the plants is what we see it as, meaning plants absorb the colors blue and red and reflects green and yellow (Most plants we see are green and/or yellow) Carotenoids - reflects various shades of red, orange, and yellow while absorbing Pigments - organic molecules built in the mainly violet, blue, and green light. It starts thylakoid membranes of plants, selectively to appear when chlorophyll starts to break absorb light on specific wavelengths down (Ex. Autumn leaves, ripe bell peppers) - Some plants reflect varying colors Divided into two: which reduces their photosynthetic - Carotenes: includes alpha-carotene, ability but protects them from beta carotene, and lycopene predators because animals do not - Xanthophyll: includes lutein and see the plant as food due it being a fucoxanthin color that is not green Chlorophyll c - accessory pigment, brown Process of Light Dependent Stage: in color (Brown algae) Chlorophyll d - accessory pigment, red in color (Brown algae) Phycobilins - found in red algae and cyanobacteria. It is water soluble and Light-dependent reactions involve the present in the aqueous cytoplasm or stroma striking of light to P680 (photosystem II of plants primary donor) and P700(photosystem I primary donor), which results in a series of LIGHT REACTIONS OF electron flow that drives the synthesis of PHOTOSYNTHESIS ATP and NADPH. Sun - the primary source of light energy on our planet. Photosystem - consists of a number of light harvesting complexes (LHC) surrounding a Photosynthesis - process that converts reaction-center complex solar energy to chemical energy. Happens only to autotrophs (another name for Photosystem II: plants), specifically, it occurs in the 1. Light striking photosystem II which chloroplasts absorbs light energy and transfers it Overview of Photosynthesis to chlorophyll a reaction center, the center that excites two electrons (gain energy) Light Dependent Reaction - takes place in thylakoid membrane and is the reason how light energy is converted to chemical energy (ATP and reduced NADP). Only occur when solar energy is available 2. The “excited” electrons are ejected from the chlorophyll a reaction center and grabbed by the first protein in the electron transport chain that links the two photosystems. (Pigment molecules capture kinetic energy from photons and store it as potential energy in the chemical bonds of two molecules, ATP and NADPH) 3. The two electrons are replaced by Photosystem I (functions as much as electrons from water molecules that photosystem II does): donate two electrons when it splits 1. The reactive chlorophyll molecule into oxygen gas (O2) and two ejects electrons to an electron protons (H+ ). carrier molecule in the second electron transport chain in the thylakoid membrane. 4. As the electrons continue to move in the electron transport chain, their energy is used to pump protons (H+) 2. The boosted electrons in from the stroma across the photosystem I are then replaced with membrane into the thylakoid lumen electrons passing down from the first or space. electron transport chain from photosystem II. 3. The second electron transport chain passes the electrons to a molecule of NADP+, reducing it to NADPH (This NADPH is the electron carrier that will reduce CO2 in the next phase, while ATP will provide the 5. The H+ will diffuse through a protein energy) in the thylakoid membrane called ATP synthase. The diffusion of H+ will rotate the ATP synthase to produce ATP Noncyclic pathway - linear mechanism of electron transport from photosystem II to photosystem I, including the electron transport chains. This is the standard mechanism of light dependent reactions. Ultimately, it produces NADPH and ATP molecules Cyclic pathway - involves only the - Phase 1 results in the formation of photosystem I and the electron transport an unstable six-carbon molecule, proteins. The electron chain in this pathway which spontaneously splits into two uses the electron’s energy to move H+ into 3-PGA. the thylakoid compartment. The resulting H+ gradient drives ATP formation, just as it does in the noncyclic pathway For easier understanding, please watch this video: 2. Reduction - process involves the gain of Photosynthesis (Light Dependent Stage) electrons from the NADPH (reduced). https://www.youtube.com/watch?v=1D74e1 Steps: BL_Jg - ATP and electrons donated from NADPH reduce molecules of 3-PGA Light Independent Stage (Calvin Cycle): into G3P. The chloroplast is the site for both light-dependent and light-independent reactions. Light reactions take place in the thylakoids while Calvin Cycle takes place in the stroma. Energy from photons are not directly required for the chemical reactions to proceed. It ultimately produces glucose, a sugar, in the fluid-filled stroma of chloroplasts. - After the reduction process, one phosphate group and electrons are Three Phases of Light Independent Stage: transferred to the PGA, thus also 1. Carbon Fixation - process that involves forming ADP and NADP+. These will incorporating carbon atoms from an return to light-dependent reactions inorganic source into an organic molecule. for them to be reenergized. Steps: - The enzyme RuBisCo catalyzes the reaction between the carbon dioxide and the five carbon sugar RuBP 3. Regeneration - process involves Whole Process of Calvin Cycle: regenerating RuBP. Steps: - For every three CO2 molecules fixed, one G3P molecule leaves the cycle as a product which contributes to the formation of glucose. - During the Calvin cycle, an input of CELLULAR RESPIRATION three CO2 molecules will produce Cellular Respiration - process that involves six G3P molecules. One of those the oxidation and reduction of molecules G3P molecules will be used to to produce energy in the form of adenosine create glucose. triphosphate (ATP). Formula of Cellular Respiration: - Since six CO2 molecules are needed in photosynthesis, the products shown above will be doubled. Take note that two G3P molecules (total of six carbons) are needed to make glucose (likewise a total of six carbons. - The remaining ten G3P molecules (total of 30 carbons), from six CO2 molecules that are fixed, will be regenerated to six RuBP (likewise, a total of 30 carbons). Cellular Respiration is divided into two: Aerobic and Anaerobic Flowchart:  During glycolysis, each glucose molecule is broken down into two pyruvate Four Processes of Aerobic Respiration: molecules. The redox reactions also yield 1. Glycolysis ATP molecules in the process. 2. Krebs cycle 3. Electron Transport Chain Overall Glycolysis process: 4. Chemiosmosis Reactants and Products of Cellular Respiration: Ten Steps of Glycolysis: 1. Phosphorylation of glucose to glucose-6-phosphate GLYCOLYSIS Glycolysis - First phase of Aerobic Respiration. It is divided into two: 2. Isomerization of glucose-6-phosphate to - Energy-investment phase: involves fructose-6-phosphate the use of ATP molecules. - Energy-harvesting phase involves the production of ATP and NADH. 3. Phosphorylation of fructose-6-phosphate 7. The phosphate released from 1,3-BPG into fructose-1,6-bisphosphate will be picked up by ADP (adenosine diphosphate) to form ATP. In this process, one ATP molecule is produced for every 3-PGA. 4. The fructose-1,6-bisphosphate splits into two molecules DHAP and G3P, which are 8. Phosphoglyceromutase transfers a considered as isomers. phosphate group from the third carbon of 3-PGA to its second carbon, which results in the 2-phosphoglycerate (2-PGA). 9. 2-PGA becomes phosphoenolpyruvate (PEP), which is accomplished by the 5. Triosephosphate isomerase catalyzed the removal of water from 2-PGA through an transformation of DHAP into G3P. enzyme called enolase. 10. PEP releases its phosphate molecules and are picked up by ADP to form ATP. This process is catalyzed by pyruvate kinase and results in the formation of 6. Oxidation and phosphorylation of G3P pyruvate and ATP molecules. (Pyruvate molecules undergoes oxidation and becomes acetyl- CoA, which enters the Krebs cycle) Total molecular products of Glycolysis: 2. Formation of Isocitrate: the citrate is rearranged to form an isomeric form isocitrate by an enzyme acontinase. A water molecule is removed from the citric acid and then put back in another location. 3. Oxidation of isocitrate to α-ketoglutarate: The net products of glycolysis are 2 ATP, 2 Isocitrate dehydrogenase catalyzes NADH, and two pyruvate molecules. oxidative decarboxylation of isocitrate to form α-ketoglutarate. In this reaction, KREBS CYCLE generation of NADH from NAD is seen. Krebs Cycle - It is also known as citric acid 4. Oxidation of α-ketoglutarate to cycle or tricarboxylic cycle. Sequence of succinyl-CoA: Alpha-ketoglutarate is reaction by which most living cell generate oxidized, carbon dioxide is removed and energy during the process of aerobic coenzyme A is added to form the 4-carbon respiration. Takes place in mitochondria of compound succinyl-CoA. During this cell consuming oxygen, producing CO2 oxidation, NAD+ is reduced to NADH + H+ and converting ADP-ATP. by the enzyme alpha-ketoglutarate dehydrogenase. Hans Adolf Krebs - He is a German-British 5. Conversion of succinyl-CoA to succinate: scientist who discovered the Krebs cycle in CoA is removed from succinyl-CoA to the 1930s. produce succinate. The energy release is used to make guanosine triphosphate Eight steps of the Krebs Cycle: (GTP) from guanosine diphosphate (GDP) and Pi by substrate-level phosphorylation. 6. Oxidation of succinate to fumarate: During the oxidation of succinate to fumarate, FAD is reduced to FADH2. The enzyme succinate dehydrogenase catalyzes the removal of two hydrogens from succinate. 7. Hydration of fumarate to malate: Reversible hydration of fumarate to L- malate is catalyzed by fumarase (fumarate hydratase). 8. Oxidation of malate to oxaloacetate: Malate is oxidized to produce oxaloacetate, the starting compound of the citric acid cycle by malate dehydrogenase. 1. Formation of Citrate: the condensation of acetyl CoA with oxaloacetate to form citrate, catalyze by citrate synthase. Once oxaloacetate is joined with acetyl CoA, a water molecule attacks the acetyl leading to the release of coenzyme A form the complex. Products of Krebs Cycle: 3. Complex 3 The series of redox reactions during the Krebs cycle produces NADH, FADH2, CO2, and 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. ELECTRON TRANSPORT CHAIN AND CHEMIOSMOSIS Electron transport chain - series of four multiprotein complexes embedded in the inner membrane of the mitochondrion where NADH and FADH2 are oxidized to release electrons. ETC Process: 1. Complex 1 2. Complex 2 and Ubiquinone 4. Complex 4 5. Electron Transport Chain and Proton Pumps NADH and FADH2 are oxidized to release electrons into the protein complexes. These electrons pass through protein complexes and cause the pumping of hydrogen ions from the matrix to the intermembrane space. Chemiosmosis - involves the downhill transport of hydrogen ions from the intermembrane space to the matrix. This movement provides energy to ATP synthase to phosphorylate ADP into ATP. Chemiosmosis Process: ATP Synthase - The hydrogen ions return to the matrix through ATP synthase. ATP Yield of of the Electron Transport Chain and Chemiosmosis: Net ATP yield for the whole aerobic respiration process: