Bio 141 Final Exam 2025

Bio 141 Final Exam 2025 Bonds with higher or lower energy - -- Bonds with higher potential energy = C-H bonds; longer and weaker/non-polar - Bonds with lower potential energy: O-H or O=C bonds; shorter, stronger/polar Exergonic reactions - -- energy is released, products have less free energy than reactants, spontaneous, negative delta G, products are more disordered - Ex: breakdown of polymers into monomers, burning of glucose through respiration - energy is lost as heat/light Endergonic reactions - -- energy is required, products have more free energy than reactants, non-spontaneous, positive delta G, products are less disordered - Ex: polymerization of DNA or proteins, formation of glucose through photosynthesis - Energy is stored in products: more bonds or higher energy bonds Mechanism for how enzymes catalyze reactions - -- Enzymes speed up reactions by lowering Ea - Enzymes CANNOT change free energy of reactants or products, only transition state free energy - The height of Ea (activation energy) determines how easily/quickly the reaction can proceed - Transition state has high free energy level that reaction must pass through - Heat allows systems to reach the high energy state of the transition state - Enzymes lower Ea by making the transition state more energetically favorable Competitive inhibition - -- binding at the active site - prevents substrate binding by physically blocking it - The substrates cannot bind when a regulatory molecules binds to the enzyme's active site before it Allosteric regulation - -- binding not at the enzyme's active site - can activate or deactivate the enzyme by changing its shape Allosteric inhibitors and activators - -- Allosteric activation: the active site becomes available to the substrates when a regulatory molecule binds to a different site on the enzyme - Allosteric deactivation: the active site becomes unavailable to the substrates when a regulatory molecule binds to a different site on the enzyme How does feedback inhibition regulate the amount of product synthesized? - -- In biological pathways, products often regulate the enzymes that makes them to ensure the cell doesn't waste energy making too much product - Feedback inhibition: products feedback into the pipeline to inhibit the process Bio 141 Bio 141 'Free Energy' and the gains/losses of free energy in biological systems - -- Free energy = the energy available in a system to do useful work - Products with more free energy = endergonic - Products with less free energy = exergonic - Products with more disorder/entropy = exergonic - Products with less disorder/entropy = endergonic - Products with more bond energy = more free energy - Products with less bond energy = less free energy Influence of molecule concentrations, temperature, and pH on enzyme function - -- Change of temperature or pH can affect 3-D shape of proteins (enzymes) and hence their function - Rate increases with increased temp as for any reaction, but once it reaches optimal temperature, the rate rapidly fall as after ~40C, and the enzyme loses its proper shape/function(same follows for pH level) - As the temperature and/or concentration of substrate increases, the reaction rate increases - Enzymes will speed up the reaction, but once every enzyme is constantly catalyzing reactions, adding more substrate won't make the reaction happen more quickly, as all enzymes already working at max speed (Saturation) Carbohydrates functioning as energy storage - -- Starch: used for energy storage in plants cells (ex: potatoes) - Unbranched helix (all alpha 1,4 linkages) - Occasional branch point/branches helices at alpha 1,6 linkages - Glycogen: used for energy storage in animal cells (ex: in liver and muscles) - Highly branched helices with many alpha 1,6 linkages Alpha sugar summary - -- Helical structure - Easy to separate - Less stable - No hydrogen bonds between monomers - Used to store and access energy Carbohydrates functioning for structural support - -- Cellulose: used for structural support in cell walls of plants and many algae - Beta 1,4 linkages - Parallel strands joined by hydrogen bonds - Chitin: used for structural support in the cell walls of fungi and the external skeletons of insects and crustaceans - Beta 1,4 linkages - Parallel strands joined by hydrogen bonds Bio 141 Bio 141 - Peptidoglycan: used for structural support in bacterial cell walls - Beta 1,4 linkages - Parallel strands joined by peptide bonds Beta sugar sumary - -- Solidly packed - Hard to separate - More stable - Many hydrogen bonds between monomers - Used for structural support Potential energy in relation to its distance from nucleus - -- Electrons closer to nucleus have lower potential energy - Electrons further away from nucleus will have more potential energy How potential energy of electrons in C-H bonds is captured as the electrons are moved closer to oxygen in the process of oxidative respiration - -- Non-polar bonds (weak, high energy) on the left (C-H) are replaced with polar bonds (strong, low energy) on the right (O=C). - Products are less ordered → enthalpy decreases/entropy increases → spontaneous reaction Glycolysis - -- breakdown of 1 glucose into 2 pyruvate - located in cytosol in eukaryotes and prokaryotes (cytoplasm) Inputs and outputs of glycolysis - -IN - 1 glucose - 2 ATP - 4 ADP - 2 NAD+ OUT - 2 pyruvate 2 ADP 4 ATP (net 2) 2 NADH Pyruvate processing/'link reaction' - --"links" glycolysis to aerobic respiration - production of 2 Acetyl CoA - located in mitochondrial matrix in eukaryotes, cytosol in prokaryotes Inputs and outputs of pyruvate processing - -IN (per glucose) - 2 pyruvate - 2 NAD+ - 2 Coenzyme A Bio 141 Bio 141 OUT - 2 CO2 2 Acetyl CoA 2 NADH Krebs Cycle/Citric Acid Cycle - -- further oxidation of carbons from Acetyl CoA - located in mitochondrial matrix in eukaryotes, cytosol in prokaryotes Inputs and outputs of Krebs Cycle - -IN (per glucose) - 2 acetyl CoA - 2 ADP + 2P - 6 NAD+ - 2 FAD OUT - 2 coenzyme A - 4 CO2 - 2 ATP - 6 NADH Number of carbons throughout cellular respiration - -- From glycolysis to pyruvate processing, one 6-carbon molecule (C6) → two 3-carbon molecules in pyruvate (C3) - From pyruvate processing to citric acid cycle, output is 2 CO2, which leaves as waste, so we are still left with 4 carbons - Result of citric acid cycle is 4 CO2 which accounts for the other 4 carbons, but is then released as waste Feedback inhibition regulating Glycolysis - -- substrate-level phosphorylation: direct production of a molecule of ATP from AP by adding a phosphate group enzymatically - PFK: provides a mechanism to stop or slow glucose breakdown when the cell has plenty of ATP (it's better to save the glucose for when the cell needs more ATP) - two binding sites 1. regulatory store with lower affinity for ATP (allosteric) - Lower affinity → will only bind ATP when there is a high concentration of ATP - ATP binds at high concentrations to inhibit PFK, stopping glycolysis - Has weak affinity for ATP; only binds to ATP when there are very high concentrations in cell 2. active site with high affinity ATP is kinase substrate; high affinity will bind ATP readily Feedback inhibition regulation pyruvate processing - -Pyruvate DeHydrogenase - For high concentrations of substrate molecules (CoA, NAD+, pyruvate), pyruvate processing is sped up - For high concentrations of products (acetyl CoA, NADH), molecules inhibit via phosphorylation (feedback inhibition) Bio 141 Bio 141 Feedback inhibition regulation krebs cycle - -- Step 1: Acetyl CoA is allosterically regulated by ATP - Step 3: completely regulated by NADH Location and form of the energy captured in the catabolism of glucose - -- During glycolysis, the six carbon glucose molecules is split into half (two 3-carbon molecules of pyruvate) - The initial split requires an energy investment of 2 ATP molecules per glucose - The 3-carbon molecules then donate high-energy electrons to NAD+, forming NADH - NADH is a coenzyme which has the ability to transfer electrons - Electrons are transferred from the NADH to several electron carriers that power the proton gradient - Once the electrons go through the ETC, oxygen is the final acceptor - Oxygen combines with two protons and forms water - Catabolic pathways: breakdown of molecules to generate energy (ex: most efficient is the breakdown of glucose) - Glucose → pyruvate (through link-reaction) → Acetyl CoA → citric acid cycle which creates NADH2 (which drives ETC further) to produce high quantities of ATP Redox reactions transfer energy - -- FAD and NAD+ both serve as electron acceptors; they are reduced to FADH2 and NADH - FADH2 and NADH serve as electron donors/carriers → essential for respiration - While being reduced, they also accept 2 (FAD) or 1 (NAD+) hydrogen protons - LEO SAYS GER - lose electrons oxidation, gain electrons reduction Proteins and fats as energy sources used by cells - -- Protein, glucose, and fat enter into the citric acid cycle - Proteins are broken down into amino acids, and amino acids are converted into pyruvic acid which is then converted into acetyl CoA and then channelized into citric acid cycle - The breakdown of fatty acids begin in the cytoplasm, where fatty acids are converted into fatty acetyl CoA molecules - This fatty acetyl CoA is transported to the mitochondrial matrix, where it is broken down and oxidized to Acetyl CoA in a process called fatty acid oxidation or beta oxidation. Lactic acid fermentation - -- Fermentation in humans - during glycolysis, one glucose molecule is converted to two pyruvate molecules, producing two net ATP and two NADH. The two pyruvate are then converted into 2 lactate - No intermediate; pyruvate accepts electrons from NADH - 2 lactate can be reverted back into pyruvate; when oxygen is available again, respiration can be resumed Inputs and outputs of lactic acid fermentaion - -- INPUTS: 2 pyruvate, 2 NADH Bio 141 Bio 141 - OUTPUTS: 2 lactate, 2 NAD+ Fermentation in yeast - -- alcohol fermentation - in contrast with lactate fermentation, ethanol cannot be reverted back into pyruvate; it is excreted as waste (cannot be retained because it is toxic) Inputs and outputs of alcohol fermentation - -- INPUTS: 2 pyruvate, 2 NADH - OUTPUTS: 2 alcohol, 2 CO2, 2 NAD+ How does the absence of oxygen force eukaryotic cells to rely solely on glycolysis for ATP production? - -- in the absence of O2 or another e- acceptor, cells cannot generate energy via pyruvate processing, citric acid cycle, and ETC - Cells could still run glycolysis to generate 2 ATP per glucose if they could recycle NADH to NAD+ - Fermentation allows glycolysis to continue by recycling NADH to NAD+ Energy yield in aerobic vs. anaerobic respiration - -- Aerobic respiration creates up to 38 ATP molecules from a single glucose molecule - Anaerobic respiration is much less energy efficiency and only produces 2 ATP per glucose molecule - Aerobic respiration produces 19 times more ATP compared to anaerobic respiration Role of ethanol and lactic acid formation for enabling glycolysis - -- Fermentation begins with glycolysis which breaks down glucose into two pyruvate molecules and produces two ATP (net) and two NADH - Fermentation allows glucose to be continuously broken down to make ATP due to recycling of NADH to NAD+. - Lactic acid fermentation uses electrons in NADH to generate lactic acid from pyruvate, which allows glycolysis to continue and thus a smaller amount of ATP can be generated by the cell - Fermentation does not make ATP, but it allows glycolysis to continue - Fermentation removes electrons from NADH and recycles NAD+ molecules for glycolysis - If NAD+ was not regenerated (alcohol fermentation), glycolysis would stop in the yeast cell Phosphorylation - -- One phosphate group from ATP is transferred to a substrate (ex: B); because of the really high potential energy in ATP, this is an exergonic reaction - The newly phosphorylated molecule (ex: BP) now has increased potential energy which is used for the reaction to create another molecule (ex: AB) Enzymes capturing energy by coupling reactions - -- To drive endergonic reactions like polymerization, enzymes can couple the endergonic reaction with an exergonic one - Using molecules like glucose to generate molecules like ATP, FADH2, or NADH allows exergonic reactions to push forward endergonic reactions Bio 141 Bio 141 - During oxidative phosphorylation, electrons derived from NADH and FADH2 combine with O2, and the energy released from these oxidation/reduction reactions is used to drive the synthesis of ATP from ADP. - ATP: can be used to do things; couples energy releasing actions → energy consuming actions so cell is driven to build the things it needs to build - NADH and FADH2: can exchange for cash; high energy electron carriers; can exchange for "cash" or ATP - Glucose: large bills easy to trade in for smaller bills - Fats and stored cards: like savings accounts; less accessible but can be tapped into as energetic demands are met Proton gradient formation and energy yield in Prokaryotes - -- Occurs in the cell membrane → cytoplasm - Can be gram-positive (one thick cell wall) or gram-negative → 2 membrane structure - negative charge in gram-positive Proton gradient formation and energy yield in Eukaryotes - -- Occurs in the mitochondrial inner membrane; also ATP synthase - Outer membrane only in gram-negative = 2 membrane structure Why is the ETC located in a membrane? - -- By having the electron transport chain located in a membrane, a proton gradient is able to be built up and used to produce large amount of ATP - The electrons are shuttled between proteins which are used to pump protons (H+) to the space between the inner and the outer membrane Why does a concentration gradient contain potential energy? - -- Oxygen is the final electron acceptor - Holes e- tightly (in H2O) so low potential energy state - Organisms can use wide variety of final electron acceptors, but because of its strong electronegativity, the use of oxygen exceeds ATP production of all others - Proton gradient stores energy similar to how dams store potential energy - When allowing a small channel for water to flow where it passes a turbine, it will push the turbine, which can be used to capture energy in useable form - Cells have their own H+ turbine ATP synthase - Solutes tend to move from high concentration to low concentration, driving diffusion which represents potential energy. How does ATP synthase use the proton motive force to drive oxidative phosphorylation? - -- Couples proton motive force and ATP production - There is lots of potential energy stored in gradient (lots of protons (H+) that don't want to be in one confined space → channel in ATP synthase that these protons can fit through - As they fit through/fall down concentration gradient, potential energy in that gradient is captured to spin a rotor at base of molecule - This spinning catalyzes a reaction to link an ADP + PI to make a molecule of ATP Bio 141 Bio 141 Inputs and outputs of - -- IN (per glucose) - 10 NADH - 2 FADH2 OUTS - NADH ~ 3 ATP (3 X 10) = 30 ATP max - FADH2 ~ 2 ATP (2 X 2) = 4 ATP MAX - 34 possible ATP from oxidative phosphorylation, but in most cases it's 25 How different respiratory poisons (that disrupt cellular respiration) would affect a cell/organism - -- Cyanide is a nasty protein that blocks Component IV (cytochrome oxidase) of the ETC. If you add to cells that are actively carrying out respiration, oxygen will not be consumed, and no ATP will be produced - ETC is blocked, so no more oxygen is used as final electron acceptor, and no H+ gradient is set up to drive ATP synthase - Oligomyscin blocks ATP synthase by blocking its proton channel. If you add oligomycin to cells that are actively carrying out respiration, oxygen will not be consumed, and no ATP will be prod