Chemistry of Life Before Wrap Up 2 PDF

After Wrap Up I Before Wrap Up 2 Enzymes Biological Catalysts · · Speed up chemical reactions A mumB C num D M 2...

After Wrap Up I Before Wrap Up 2 Enzymes Biological Catalysts · · Speed up chemical reactions A mumB C num D M 2 Transition Site e A - B ↑ PAGO i C D ~ Progress of the reproducts 7 assist in metabolic pathways · · help make reactions start so that less energy is required · proteins that speed up chemical reactions · enzymes make chemical reactions more likely to happen · don't make reactions happen that wouldn't have happened otherwise · make reactions cheaper to run push reactants up the hill until they reach · an energy state high enough that the bonds begin to break-transition state Transition State : point in which we transition fromneedingtoputenergyintothe on reaction Ea energy of activation = ↳ happens at transition state in bond represents it being ready to break ~ · Reactants energy> than products = Exothermic · Products energy , than reactants Endothermic = Enzymes speed up a reaction by lowering Ea 1 Course of reaction or Progress of the reaction Products ( a get products faster · want to the benefit with minimal effort get · Characteristics of Enzymes · do not create reactions · not altered or use up by reaction (recycled · substrate specific (specific to reaction type) · function is based on 3-dimensional shape mostly proteins ! · ↳ if something is wrong with shape it functionality maybe to point where it can't do its job # of diseases and malfunctions and cellular processes that are related to enzyme malfunction and absence of certain enzymes ↳ Lactose intolerance : lactose sugar that's in milk. Without proper enzyme Dactase) body is reallybadatbreakdown acta · A key function of enzymes is their ability to bind their substrates with high specificity. This is due to the structure of the enzyme's active site * Substrate it's : thing working on ↳ interacts to help the reaction go Enzyme mode of action enzyme structure ensures specificity of function ·. The substrate sucrose , consists of 1 , glucose active sites Where and fructose bonded together (infoldings) work happens. The 2 substrate binds active site of the to the enzyme forming and enzyme-substrate complex , water is added in. The binding of the substrate and enzyme 3 places stress on the glucose-fructose bond, and the bond breaks. Products are released and the enzyme is 4 , free to bind other substrates * enzyme not used up ! It can cycle back and be used again degrade over time - > can Factors influencing level of enzyme activity ~ enzyme is less active temperature (sweet spot) * Core over extremities · · DH · substrate concentration ↳ Concentration then rate i PH · pepsin-optimal activity at acid pH typical cellular enzyme optimal activity at neutral · = PH · Trypsin = optimal activity at basic pH Regulation of enzyme activity cells regulate metabolism by regulating enzymes · · Genes producing enzymes can be turned on or off to regulate enzyme production be made to Changes can existing enzyme · Structure to increase decrease function or · Allosteric effection cofactors and coenzymes · assist With the enzymatic reaction ; may be inorganic ions or nonprotein organic molecules NAD + · FAD · NADP + · Competitive and noncompetitive inhibition · competitive inhibitor blocks where substrate = wants to bind to active site · doesn't block inhibitor binds noncompetitive = , somewhere else-not active sites change active site shape - Feedback Inhibition · end product is on enzyme I · doesn't show intermediates Living Organisms maintain homeostasis · Feedback inhibition prevents the formation of too much product of a metabolic pathway Energy Kinetic energy (movement) · Potential energy llocation) · - a diver has more potential energy on the platform than in the water - diving converts potential energy toKinetic energy Climbing up converts the Kinetic energy of - muscle movement to potential energy · Energy transfers are subject to laws of thermodynamics System · Surroundings · · The quantity of energy in the universe is constant , but the quality is not Solar < chemical > mechanical Gibbs Free Energy (G) energy available to do work · change in free energy (DG) · spontaneous reactions · decrease free energy in a system · negative AG in system - increases entropy in surroundings Exergonic Reaction · Catabolic (decomposition) Products have less free energy than the · reactants net loss of free (-DG) from system energy · · Spontaneous · release free energy (-AG) - ndergonic Reaction · Anabolic (synthesis) products have free than the more energy · reactants · requires energy input (+AG) to system · not spontaneous consumes free energy (+AG) ·  mmmcroducts F · Mo Y ergy released (a) ExeProgress ofthereactionenergy released 1 Products reactants (b) mmmmmmm e Progress of the reaction > 7 endergonic reaction : energy required  Metabolism - all chemical reactions orderly : can't skip ahead · orderly enzyme-mediated reactions and can't go backwards Start point is the Step by step or cyclic pathways · end point · ATP most common energy coupling molecule Catabolic pathways < Anabolic pathways All chemical reactions have a specific ↑ · Energy of Activation (a) · taking things apart to build something new out of those parts · ATP provides energy for cellular work mechanical (to movel · transport (cell membrane) · Chemical (take reactants and make · products) · Adenosine triphosphate (ATP) · RNA nucleotide with unstable phosphate bonds adenine + N - C = O L 90 N Hc - I -0 - pro - p - o - 0 - CH2 N- 2 N= Ch o o- Fi H H Phosphate group OH OH ribose  Oxidated phosphorylation in the Mitochondria · ATP Synthesis involves phosphorylation Endergonic · · Phosphate groups are hydrolyzed to release energy · Exergonic H20 7 ATP + me m Energy for Energy from L cellular work catabolism ADP + Pi Cendergonic , lexergonic energy-consuming energy-releasing processes) processes) ATP is a common energy coupling mechanism glucose 7 A- PvPvP exergonic endergonic -Protein (glucose CATP synthesis) breakdown) exergonic endergonic CATP breakdown) (protein L Synthesis) CO2 +20 +heat A - P-D + p aming acids  Cellular Metabolism cellular respiration S · · fermentation z Catabolic pathways that yield energy by oxidizing organic fuels · Breakdown of organic molecules is exergonic cellular respiration a releasing energy · - Aerobic (requires O2) from bonds · Fermentation Anaerobic - Redox Reactions : Oxidation and Reduction · Transfer of electrons releases energy to Synthesize ATP Oxidation lose electrons, or is oxidized I · - · Reduction- gain electrons or is reduced , positive reducing charge - oxidized- Xe + Y > X + Ye- - reduced Oxidation i Oss eduction S air · During cellular respiration , fuel (such as glucose is oxidized , and O2 is reduced Hydrogen gets extra 7 electrons becomes oxidized ~ Cotti206 + 102 < GCO2 + GHz0 + Energy breakso becomes reduced many as electrons can't just around hang so they · are transferred molecules down organic are broken in a · series of steps (H--Lenergy) electrons from food -- 2H + + 1202 = Hz0 to produce energy released for ATP Synthesis Substrate level phosphorylation - Direct transfer of phosphate Oxidative phosphorylation Electron transport and electrogenic - proton pump (chemiosmosis) The Stages of Cellular Respiration cellularrespiration has four stages · - Glycolysis (breaks down glucose into two moleculesOfPvtecarbonmocetedintomitochondria enzymei - The Citric Acid Cycle (Kreps Cycle) (completes the breakdown of pyruvates - Oxidative phosphorylation (Electron transport chain) (accounts for most of ATP synthesis) Oxidizing and adding phosphates ↳ with or without * Stages 2-4 in the mitochondria < outside mitochondria I Glycolysis in cell Glucose NADH + S P Pyruvate -electron V s Pyruvate NADH S Oxidation > CO2 I Acetyl-CoA Kreb ↳ Keeps V cycle going NADH > CO2 Krebs > - in mana > - electron Shutteof intermediatesta Cycle matrix #ADH2 < deenergized versions NADTFAD O2 H2O e- V nN V M H+ ~ e- Electron e- Chemiosmos is Transport Chain Y ATP Synthase Getting water e-to flow to do work-waterwheel through chain to create some · power pumping of H from + energy to mitochondrial matrix to intermembrane space ↳ thenfall through ATP synthase Synthasize or build ATP - -fall powered by H+ through down gradient they turn enzyme and it reconstructs ATP from ADP-chemiosmosis  C · 8 O : ·S S 8 S · e ↳- S -- & & n =& I B F J 27 T & G ↳ · · · & L - I I & · &: · sG · · 3 · · * 5 S # & & ↓ J · · & · ·S · 3 H" falls through ATP synthase which pushes on the complex complex rotate makes the pinwheel more Ht Spins faster ↳ - = as it rotates it grabs ADP and phosphate to Jam them together NADH drops electrons off in electron transport chain · Etc moves electrons in a series of steps - Each carrier in the chain is more and more electronegative - The energy released is used indirectly to synthesize ATP ATP Synthesis · free energy used to phosphorylate ADP forms ATP What if there is no oxygen ? Glycolysis can produce ATP with or without · 8 2 (in derobic or anaerobic conditions) · Fermentation Fermentation · used by organisms that can't respire - lack of suitable electron acceptor or lack of electron transport chain partial oxidation of glucose - · NADH oxidized back to NAD+ uses organic compound as terminal · electron acceptor - Typical pyruvate or derivative Lactate Fermentation Glucose ADD + Pi B - NADH + NAD HT CH3 CHE Ho- H - - COO- Pyruvate Lactate Alcoholic Fermentation Glucose + ADD + P: NAD n * NADH - + H+ PH3 - C coo- = Pyruvate 0 CO2 a Acetaldehyde I CH3 H Ethyl alcohol  300 · · · , · - ·E ↳ · · & S S s % 8 ! · s  Mitochondrion Cytoplasm - - · ⑤ I ·T -L · & & · Electron Transport Chain ·  Photosynthesis my light m mmr n CO2 + H2@ mone produce Cellular is done to Photosynthesis andSo a cel organicmolecules occurs producing The cellular respiration are necessary for CO2 and 20 which Photosynthesis · Life powered is solar · Photosynthesis - converts solar energy into chemical energy · Autotrophs are the producers of the biosphere · Photoautotrophs · Photosynthetic organisms a) plants b) multicellular alga c) unicellular protist 6) cyanobacteria e) purple sulfur bacteria · Heterotrophs are the consumers of the biosphere Typically depend on photoautotrophs for food - and 02  Plant Leaf Morphology 7) some structure evolved to absorb sunlight · Leaves are area for photosynthesis - half a million chloroplasts per square mm - color of leaf is from Chlorophyll · Chloroplasts found mainly in mesophyll - cells densely packed with chloroplasts - Typical 30-40 per cell · Have high surface area so they act as photosynthetic arrays wide and thin-job is to absorb sunlight · to power photosynthesis · organs-composed of leaves are & +issues (layers of cells) mesophyll middle = · CO2 and O2 enters and exits through Stomata - open/close state controllable by plant · H20 enters through roots reaches leaves through network of veins - veins export sugar to roots and other - non-photosynthetic parts of the plant * both chloroplasts for plants have photosynthesis and mitochondria for cellular respiration · have multiple membranes because chloroplasts - they were once free living organisms (bacterium that already had its own membrane that was engulfed by another organism (eating) ↳ deposited another membrane Endosymbiotic Theory Thylakoid-cookie shaped sacks in stacked structure called granum (lumen empty) = ↳ where photosynthesis is happening · stroma = space around thylakoids · chemical equation for photosynthesis GCO2 + 12H20 + light 1Cotti20b + RO2 + 6H2O chemical of cellular change is reverse · respiration · Endergonic redox process - H2O is oxidized to O2 and CO2 is reduced to glucose * Goal is to make sugar for food or structure * Oxidizing water to oxygen and reducing CO2 with it to Ob < more energy associated  2. stages of photosynthesis reaction · Light - light energy converted to ATP NADH reducing power (sent to Calvin Cycle) - - thylakoid membranes transporte- · Calvin Cycle (light independent reaction) ATP and NADPH from light reaction is used - to fix carbon Goal = CO2 - > Glucose Stroma - H20 CO2 · · ⑧ Light Thylakoid · membrane T · T · I Chloroplast ·re 02 ·  Light is electromagnetic energy or radiation · electromagnetic spectrum - 380 to 750nm visible light spectrum - - travels in rhythmic waves but consists of discrete particles , called photons - fixed quantity of energy · Pigments absorb visible light make ATP through same process as cell respiration · Hydrogen ion gradient ATP Synthase Dropped through · · Spins to produce ATP Stoma/Stomata = CO2 and O2 in and out through openings e- Excitea M #He · * F photon I Photon -Ground (fluorescence) trophyllmolecule state a) Excitation of isolated Chlorophyll molecule  Light absorption light energy causes electrons to get excited · - Move to higher energy shell - Unstable State Fall back to stable ground state - ↳ heat and photon (fluorescence) released · Pigments are organized into photosystems in thylakoid membrane Light harvesting complexes proteins with · = suspended chlorophyll molecules that can absorb the photons of light energy. Energy is handed off until it gets to paired Chlorophyll A molecules. Energizes an electron that jumps up to the primary electron acceptor found in the reaction-center complex. ↳ doesn't let it fall back down Two photosystems (11 - > 1) - Photosystem 1 (P700) - replacement e- from PSI wavelengths of 700nm (far-red) absorbs · Photosystem 11 (P680) replacement from H20 - - - · absorption peaks at 680 nm (also red part) Light drives the Synthesis of NADPH and ATP · key - energyto transformation is flow of electrons through photosystems May be non-cyclic or cyclic electron flow - * Primarily non-cyclic * water is oxidized - provides electrons ) why O2 is produced ↳ · goes to an electron transport chain between photosystems provides energy to regenerate ATP · sticks electrons on NADP + to regenerate NADPH Need Ht Stick on hydrogen then stick.. hydrogen on NADP + * non-cyclic = one direction (linear) · electrons travel down chain to PTOO get energized to primary acceptor but sometimes it hands a few high energy electrons off to an intermediate acceptor that will dump it into chain to get more energy to power the production of a little more ATP ↳ cyclic = cycle backwards * + membrane into thylakoid pump H across membrane to create a gradient so It can be pumped through ATP Synthase The Calvin Cycle · Cyclic and occurs in Stroma Builds molecules organic · - carbon dioxide from air fixed into sugar - consumes ATP and NADPH from light reaction · three phases - Carbon fixation (catalyzed by rubisco) - Reduction - Regeneration of the CO2 acceptor (RuBP) · Consumes three molecules of CO2 to produce one molecule of glyceraldehyde 3-phosphate (63P) used to make glucose and other organic - compounds · Requires ATP and NADPH to power cycle - from light reaction Phase 1 : Carbon fixation CO2 is incorporated into an organic molecule · via rubisco Phase 2 : Reduction and Carbohydrate production · ATP is used as a source of energy , and NADPH donates high-energy electrons Phase 3 : Regeneration of RuBP Two G3P are used to · make glucose andother 10 G34 are needed to Sugars ; the remaining RuBP via several enzymes ATP is regenerate. required for RuBP regeneration ↳ ribulose bisphosphate  Input 6XCO2 biscot ~ 6 xRuBp cccc in so GADPGY C 12 X 1,3 BPG p Cc C i ↓ 12 NADPH 12 NADP + 12 xG3pY12p : I cc C 10 x G3P CCC 2x63P C Breaking Down Photosynthesis Stages 6 CO2 + 12H20 + light Sugar H20 02 4 con source of elections - from stripping Source of carbon H2O of electrons and H fixed into molecules organic * water > O2 light dependent reactions Calvin Cycle light ATP ATP > 3 + sugar ↑ t H20 NADPH NADPH ↑ t t from NADP + 02 CUz