General Biology I PDF

# General Biology I ## Energy - The ability to do work or bring about a change - Entropy: indicates the relative disorganization of a system, a measure of randomness ## Laws of Thermodynamics - **First Law:** states that energy can't be created nor destroyed; rather, they can be transformed from...

# General Biology I ## Energy - The ability to do work or bring about a change - Entropy: indicates the relative disorganization of a system, a measure of randomness ## Laws of Thermodynamics - **First Law:** states that energy can't be created nor destroyed; rather, they can be transformed from one energy to another - **Second Law:** states that energy cannot be changed from one form to another without a loss of usable energy (turned to heat) - **Third Law:** states that the entropy of a system approaches a constant as the temperature approaches absolute zero ## Types of Couples Reactions - **Exergonic:** the products have less energy than the reactants - **Endergonic:** the products have more energy than the reactants ## Types of Energy in Cells ### ATP (Adenosine Triphosphate) - contains three phosphate groups (left), ribose (center), and adenine (right) - responsible for mechanical, transport, and chemical functions - and gets synthesized for energy production ### ADP (Adenosine Diphosphate) - contains two phosphate groups (left), ribose (center), and adenine (right) - the phosphate groups (triphosphate tail) provide energy when being broken down to ADP ### Mechanisms of ATP Synthesis #### Substrate-level Phosphorylation - combines ADP and a phosphate group from a phosphorylated molecule to form ATP ## Oxidative Phosphorylation - Uses the energy derived from electron transfer to combine ADP and inorganic phosphate into ATP ## Photophosphorylation - Driven by protons generated from moving electrons moving through the ATP synthase enzyme complex, triggering ATP synthesis ## ATP-ADP Cycle - Process wherein ATP is turned to ADP (endergonic) and vice versa (exergonic) to produce energy for the cells to use - Chemical Formula: $C_{10}H_{16}N_5O_{13}P_3 - H_2O = C_{10}H_{15}N_5O_{10}P_2 + PO_4 + 3H^+$ ## Photosynthesis - A system where water and carbon dioxide is converted into food and oxygen. - Chemical Equation: $6CO_2 + 6H_2O \xrightarrow{Light \ Energy, \ Chlorophyll} C_6H_{12}O_6 + 6O_2$ - Is done by photosynthesis pigments, which can be either classified into principal (main doer of photosynthesis) and accessory (supports the process) pigments ## Types of Photosynthesis Pigments - **Chlorophyll a:** Converts solar energy to chemical energy, has a blue-green color - **Parts of the Chlorophyll a** - Outer Membrane - Intermembrane Space - Stroma (aqueous fluid) - Granum (stack of thylakoids) - Thylakoid - Lamella - Lumen - **Chlorophyll b:** Absorbs light energy for chlorophyll a, has a yellow-green color - **Chlorophyll c:** Found mainly in brown algae, has a blue-green color - **Chlorophyll d:** Found mainly in red algae, has a green color - **Carotenoids:** Absorbs and dissipates excess light energy that would have disrupted photosynthesis (photoprotection), color depends on the type - **Carotenes:** Red to orange, split into α-carotene, β-carotene, and lycopene - **Xanthophyll:** Yellow to brown, split into lutein and fucoxanthin - **Phycobilins:** Water-soluble, allowing red (phycoerythrin) and blue (phycocyanin) algae to perform photosynthesis in the deep sea ## Process of Photosynthesis ### Light-Dependent Reaction - Occurs in the thylakoid membrane of the chloroplasts and captures photons from light energy and stores it in ATP and NADPH (nicotinamide adenine dinucleotide phosphate). - Produces oxygen as a byproduct - Overall Chemical Reaction: $12H_2O + 12O_211129N7O17P3+ 18C101115N3010P2 + 18PO_4 \xrightarrow{LightEnergy, Chlorophyll} 6O₂ + 12(H_3)N7O1713 +18C10H16N50131'3 $ ### Photosystem I (P700) - Functions roughly the same as Photosystem II - Passes down the electrons to NADP and forms NAPDH ### Photosystem II (P680) - Place where the process of photosynthesis begins due to light exciting electrons gaining energy. - Electrons coming from H₂O get donated into PS II when it splits up into 2H and 2O (photolysis). - Electrons get ejected from chlorophyll a (green color). - As the electrons moves in the electron transport chain (represented by purple sections), their energy is used to pump H+ through the thylakoid lumen. ## Noncyclic Pathway - Represents the movement of electrons from PS II to PSI ## Cyclic Pathway - Produces ATP at high oxygen levels or the accumulation of NADPH inside the stroma. - NADPH does not form in here because electrons are only accepted by photosystem I and electron transport chain (ETC). - Oxygen does not form here because photosystem I does not depend on photolysis for resupplying itself with electrons. ## Calvin Cycle - Also called the light-independent reaction, it occurs in the stroma and does not require any photons for the chemical reactions to proceed. - It ultimately produces glucose (energy of the cell) from Ribulose 1,5 bisphosphate (RuBP) and CO₂. - This process is split into three steps: carbon fixation, reduction, and regeneration. ### Phase 1: Carbon Fixation - 2 molecules of Ribulose 1,5 bisphosphate (RuBP) and carbon dioxide react with the help of the enzyme RuBisCo (Ribulose-1,5-bisphosphate carboxylase oxygenase) to form 2 molecules of 3-phosphoglycerate (3-PGA). - Chemical Formula: $C_5H_{12}O_{11}P_2 + CO_2 + H_2O \xrightarrow{RuBisCo} 2C_3H_7O_6P $ ### Phase 2: Reduction - 2 molecules of 3-phosphoglycerate (3-PGA) and Adenosine Triphosphate react to form a molecule of 1,3-bisphosphoglycerate (1,3BPG). - 2 molecules of (1,3BPG) and Nicotinamide Adenine Dinucleotide Phosphate (NADPH) will react. - Chemical Formulas: $2C_3H_7O_6P_2 + 2H_7N_7O_{14}P_3 \xrightarrow{ATP, NADPH} 2C_3H_8O_{10}P_2 + 2C_{21}H_{29}N_7O_{14}P_2 + 2PO_4 + 2H^+$ ### Phase 3: Regeneration - 5 molecules of Glyceraldehyde 3-phosphate (G3P) and 3 molecules of Adenosine Triphosphate (ATP) react to form 3 molecules of Ribulose 1,5-bisphosphate (RuBP), 3 molecules of Adenosine Diphosphate (ADP), and 2 molecules of phosphate. - Chemical Formulas: $5C_3H_7O_6P + 3C_{10}H_{16}N_5O_{13}P_2 \xrightarrow{ATP} 3C_5H_{10}O_{11}P_2 + 3C_{10}H_{15}N_5O_{10}P_2 + 2PO_4$ ### Summary of Chemical Reactions: | Region | Chemical Reactions | |---|---| | Thylakoid | $12H_2O + 18C_{10}H_{15}N_3O_{10}P_2 + 18PO_4 + 12C_{21}H_{29}N_7O_{17}P_3 \xrightarrow{WATER, ADP, Phosphate, NADP} 6O_2 + 18C_{10}H_{16}N_5O_{13}P_3 + 12C_{21}H_{30}N_7O_{17}P_3$ | | Stroma | $6CO_2 + 18C_{10}H_{16}N_5O_{13}P_3 + 12C_{21}H_{30}N_7O_{17}P_3 \xrightarrow{Carbon Dioxide, ATP, NADPH} C_{6}H_{12}O_6 + 18C_{10}H_{15}N_3O_{10}P_2 + 12C_{21}H_{29}N_7O_{17}P_3$ | # Cellular Respiration - The process of breaking down glucose to produce energy. - Chemical Equation: $C_6H_{12}O_6 + 6O_2 → 6CO_2 + 6H_2O + energy$ ## Types of Cellular Respiration - **Aerobic Respiration:** Requires oxygen for the process to take place. - **Anaerobic Respiration:** Does not require oxygen for the process to take place. ## Parts of the Mitochondria - **Intermembrane Space:** Holds the protons pumped out of the matrix - **Matrix:** Place where ATP synthesis and Krebs cycle occur - **Cristae:** Folds of the inner membrane increasing the surface area for ATP production. - **Inner Membrane:** Contains the protons involved in ETC and the ATP synthase. ## Process of Aerobic Cellular Respiration 1. **Glycolysis:** Takes place in the cytoplasm and converts glucose to pyruvate with a gain of 2 ATP and 2 NADPH. ### Process (Steps) | Process (Steps) | Chemical Formulas + Diagram (taken from Quipper) | |---|---| | 1: Phosphorylation of glucose to glucose 6-phosphate | $C_6H_{12}O_6 + C_{10}H_{16}N_{5}O_{13}P_3 \xrightarrow{Hexokinase} C_6H_{13}O_9P + C_{10}H_{15}N_5O_{10}P_2$ | | 2: Isomerization of glucose 6-phosphate to fructose 6-phosphate | $C_6H_{13}O_9P \xrightarrow{Phosphoglucose Isomerase} C_6H_{13}O_9P$ | | 3: Phosphorylation of fructose 6-phosphate into fructose 1,6-bisphosphate | $C_6H_{13}O_9P + C_{10}H_{16}N_5O_{13}P_3 \xrightarrow{Phosphofructokinase} C_6H_{14}O_{12}P_2 + C_{10}H_{15}N_5O_{10}P_2$ | | 4: Splitting of fructose 1,6-bisphosphate into the isomers DHAP and G3P | $C_6H_{14}O_{12}P_2 \xrightarrow{Fructose \, 1,6-bisphosphate \, Aldolase} C_3H_7O_6P + C_3H_7O_6P$ || | 5: Triosephosphate isomerase catalyzes the transformation of DHAP to G3P | $C_3H_7O_6P \xrightarrow{Triosephosphate \, Isomerase} C_3H_7O_6P$ | | 6: Oxidation and phosphorylation of G3P molecules | $C_3H_7O_6P + 2C_{21}H_{27}N_7O_{14}P_2 \xrightarrow{Glyceraldehyde \, 3-phosphate \, dehydrogenase} C_3H_8O_{10}P_2 + 2C_{21}H_{25}N_7O_{14}P_3 + 1H^+$ || | 7: Phosphate from 1,3BPG gets picked up by ADP to form ATP wherein one ATP is formed per 3-PGA | $2C_3H_8O_{10}P_2 + 2C_{10}H_{15}N_5O_{10}P_3 \xrightarrow{Phosphoglycerate \, Kinase} 2C_3H_7O_6P + 2C_{10}H_{16}N_5O_{13}P_3 $ | | 8: Phosphoglycerate mutase transforms 3-PGA into 2-PGA | $2C_3H_7O_7P \xrightarrow{Phosphoglycerate \, mutase} 2C_3H_7O_7P$ | | 9: Enolase removes water in 2-PGA, forming PGA | $2C_3H_7O_7P + 2H_2O \xrightarrow{Enolase} 2C_3H_4O_6P$ | | 10: PEP releases phosphate and forms another ATP molecule with pyruvate kinase, forming pyruvate | $2C_3H_4O_6P + 2C_{10}H_{15}N_5O_{10}P_2 \xrightarrow{Pyruvate \, kinase} 2C_3H_4O_3 + 2C_{10}H_{16}N_{5}O_{13}P_3$ | - To summary, the process uses 2 ATP and produces 4 ATP and 2 NADH, giving a total net energy output of 8 ATP. 2. **Transition Reaction:** Converts pyruvate into acetyl coenzyme a, producing CO₂ and NADH on the way. 3. **Krebs Cycle:** Named after Hans Adolf Krebs, a German-British scientist who discovered it in the 1930s, it produces NADH, FADH2, GTP, and CO₂. ### Process (Steps) | Process (Steps) | Chemical Formulas + Diagram (taken from Quipper) | |---|---| | 1: Acetyl CoA reacts with oxaloacetate to form citrate with the catalyst citrate synthase, producing citric acid in the process | $C23H38N7O17P3S+ C2H2O3 + H2O \xrightarrow{Water, Citrate Synthase} C21H36N7O1GPS + C6H8O7$ | | 2: Citrate is isomerized to isocitrate with aconitase as a catalyst | $C6H8O7 \xrightarrow{Isocitrate} C6H8O7 $ | | 3: Isocitrate is oxidized into α-ketoglutarate with the isocitrate dehydrogenase, with α-ketoglutaric acid as a byproduct | $C6H8O7 + C21H27N7O14P2 \xrightarrow{Isocitrate Dehydrogenase, NAD} CO2 + C5H6O5 + C21H28N7O11P2 + H+$ | | 4: α-ketoglutarate is oxidized into succinyl COA with the α-ketoglutarate dehydrogenase complex | $C5H6O5 + C21H27N7O14P2 + C25H40N7O19P2S \xrightarrow{α-Ketoglutarate Dehydrogenase Complex, NAD} CO2 + C4H4O5 + C21H28N7O14P2+ C25H39N7O19P2S + H+$ | | 5: Succinyl CoA, GDP (guanosine diphosphate), and PO, react to form succinate, with succinic acid as a byproduct | $C21H30N7O14P2S + C4H4O5+ C10H16N5O14P3 \xrightarrow{Succinyl \ Coenzyme \ A \ Synthase, GDP, Phosphate} C21H30N7O14P2S + C4H6O4+ C10H15N5O11P2 + PO4$ | | 6: Succinate gets oxidized by succinate dehydrogenase and turns into fumarate, with fumaric acid as a byproduct | $C4H6O4 + C21H25N7O15P2 \xrightarrow{Succinate \, dehydrogenase} C4H4O4 + C21H26N7O15P2$ | | 7: Water combines with fumarate with the help of fumarase to form malate, with malic acid as a byproduct | $C4H4O4 + H2O \xrightarrow{Water, Fumarase} C4H6O5$ | | 8: Malate is oxidized with the help of malate dehydrogenase to form oxaloacetate, with oxaloacetic acid as a byproduct | $C4H6O5 + C21H27N7O14P2 \xrightarrow{Malate \, dehydrogenase, NAD+} C4H4O5 + C21H28N7O14P2 + H+$ | 4. **Electronic Transport Chain (ETC)** - Electrons move through the intermembrane space, generating ATP that can be used in other processes ### Process | Process | Diagrams | |---|---| | **Complex I** <br> - The proteins FMN and Fe-S receive and transfer electrons from the oxidation of NADH, which is then transferred to ubiquinone (labeled as Q), product QH₂ | [Image of Complex I Diagram] | | **Complex II** <br> - Succinate dehydrogenase react with FAD to produce FADH2. Fumarate, and 2 hydrogen ions during the Krebs Cycle (Step 6). Electrons are received from the oxidation of FADH, and is received by the Fe-S centers | [Image of Complex II Diagram] | | **Complex III** <br> - Contains three molecules, being cytoplasm b (Cyt b), Rieske center (2Fe-S center), and cytochrome c1 (Cyt c1) <br>- An electron from QH₂ gets oxidized into Q, which can either go to the Rieske center then Cyt c1 then Cyt c (transferring from complex III to complex IV), or get transferred to Cyt b then a molecule Q inside complex III, reducing Q into its radical ion (Q) <br>- It is also possible for Cyt b to be directly synthesized into Q, which can be turned into QH, after receiving electrons | [Image of Complex III Diagram] | | **Complex IV** <br> - Step 1: electrons travel from Cyt c to the CuA/CuA center, then to Cyt a, and ends up at Cyt a. <br> - Step 2: when another electron arrives from Cyt c, it ends up at Cu instead of Cyt a. <br> - Step 3: Since Cyt a, and Cu are now reduced after receiving electrons, an oxygen (O₂) molecule binds to them, forming a peroxide bridge connecting them together. <br>- Step 4: Two more electrons coming from Cyt c are transferred inside, going with the same process as steps 1 and 2; two molecules of Ht also enter inside complex IV to set up for step 5. <br> - Step 5: Due to the electrons that came inside via Cyt c in step 4, the peroxide bridge in step 3 gets broken, forming a hydroxyl group in Cyt as and Cug leading to Cyt a3-OH and CuB-OH. <br> - Step 6: Two more hydrogen atoms enter complex IV to oxidize Cyt a3-OH and CuB-OH back to their original forms in steps 1 and 2. <br> - Step 7: two water molecules are formed thanks to the previous step, returning the two molecules back to their original form | [Sequence of Complex IV Diagrams] | 5. **Chemiosmosis:** Movement of hydrogen ions across a membrane (similar to how in Photosystem I and II, hydrogen ions move from outside to inside) ### Overall Production: | Process | Electron Carriers | Number | Number of ATP Produced | |---|---|---|---| | Glycolysis | ATP | 2 | 2 ATP | | | NADH | 2 | 6 ATP | | Transition Reaction | NADH | 2 | 6 ATP| | Krebs Cycle | ATP/GTP | 2 | 2 ATP | | | NADH | 6 | 18 ATP | | | FADH2 | 2 | 4 ATP | | ETC and Chemiosmosis | NADH | 10 | 30 ATP | | | FADH2 | 2 | 4 ATP | | **Total ATP Yield** | | | **72 ATP Molecules** | ## Types of Fermentation 1. **Lacto-Fermentation** - Started by the bacteria lactobacillus, converting glucose into lactic acid and carbon dioxide, giving these food a distinct sour flavor. - Includes foods such as sauerkraut, kimchi, and yogurt. - This bacteria are salt and acid tolerant, which helps them survive in hostile environments. - Is present in vegetables, and can be done through a lactobacillus culture, allowing fermentation of many things including water. 2. **Alcohol Fermentation** - Done by yeasts that turn glucose in alcohol, ethanol, and carbon dioxide gases. - Can spontaneously occur in damaged or overripe fruits without any human intervention. 3. **Aceto-Fermentation** - Done by aceto-bacter, responsible for creating vinegar. - Making vinegar is split into two phases, alcohol fermentation (from sugar to alcohol until yeast dies) and aceto-fermentation, converting alcohol + oxygen into acetic acid. - Overall process of making vinegar takes from 6 to 8 weeks. 4. **Mold Fermentation** - Generally associated with food spoilage, but is not necessarily harmful. - Traditionally derived in cultures with food such as cheese, koji, sake, miso, and tempeh. - The type of mold depends on the surrounding environment. 5. **Symbiotic Fermentation** - The cause of fermentation forms a synergistic relationship with the fermented product, where either one type cannot happen than the other, or more than one is happening at the same time.