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Metabolism (Enzymes (Cofactor-non protein helpers for catalytic activity…
Metabolism
Enzymes
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Lowers Activation energy- the amount of energy needed to push the reactants to the top of an energy barrier or "uphill" so that the "downhill" part of the reaction can occur... also is often supplied by heat in the form of thermal energy that reactant molecules absorb from surroundings
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Substrate-reactant enzyme acts on. enzyme-substrate complex- when the enzyme is binded to its substrate . Binded by weak hydrogen and ionic bonds
Active site-the restricted region of the enzyme molecule that binds to a substrate...usually a pocket or groove where catalysis occurs
Induced fit-tightening of binding of substrate to enzyme's active site (Only specific substrates will fit in a specific enzyme's active site)
Saturated enzymes mean the rate of the reaction is determined by the speed in which the active site coverts substrate to product
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Cofactor-non protein helpers for catalytic activity (often for chemical processes like electron transfers that cannot be easily carried out by the enzyme's amino acids)
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Inhibitors
Competitive -some reversible inhibitors resemble the normal substrate molecule and compete for admission into the active and block the actual substrates from entering
Non-competitive- (irreversible) do not compete with the substrate at the active site, but instead bind to other parts of the enzyme which changed shape of the active site and becomes less effective at catalyzing the conversion of substrate to product. EXP are toxins and poisons
Feedback inhibitor- the end product of enzyme reaction binds to the enzyme inhibiting its ability to keep making the end product
Regulation
Allostaric regulation- when a protein's function at one site is affected by the binding of a regulatory molecule to a separate site
Activator- the binding of an activator to a regulatory site stabilizes the shape that has functional active sites (affects all the subunits)
Inhibitor -the binding of an inhibitor stabilizes the inactive form of the enzyme. (affects all the subunits)
Sub-units of an allosteric enzyme are so close that a change in shape of one subunit totally changes the shape of the others
ATP binds to catabolic enzymes allosterically lowering their affinity for the substrate and thus lowering their activity (inhibitors as seen below)
Cooperativity- the regulation where one subunits shape change by a substrate binding causes a shape change in all other subunits
Cellular respiration
Terms
Fermentation-partial degradation of of sugars or other organic fuel that occurs without the presence of oxygen
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Redox reactions-The transer of the electrons from one reactant to the other during chemical process which yields energy. Oxidation-the loss of electrons from a substance. Reduction-addition of electrons to another substance
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Electron transport chain-consists of a number of molecules mostly proteins, built into the inner membrane of the mitochondria of eukaryotic cells . Electrons removed from glucose are shuttled by NADH to the "top" higher energy end of the chain. Electron transfer from NADH to oxygen is an EXORGONIC reaction
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Cristae-infolding of the inner membrane of mitochondrion,the inner membrane houses the electron transport chains
Goal is to harvest energy from glucose made by photosynthesis and breaks it down to make ATP from ADP and a phosphate group... it relates to Gibb's free energy bc some energy leaves as heat causing more disorder (entropy) in the universe (-deltaG).
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The catabolic pathways of aerobic and anaerobic respiration, which break down organic molecules and use an electron transport chain for the production of ATP .
STEPS in cell. resp.
1)Glycolosis-it takes 2 ATP to "power" the breakdown (catabolic) of a glucose (containing 6 carbon atoms) into 2 molecules of pyruvate (3 carbon atoms each).. It also yields 4 ATP and 2 NADH)...this is a catabolic AND exorgonic reaction since bonds are broken and energy is released. occurs in cytoplasm increases entropy
2)Pyrovate- enters the mitochondria of eukaryotes and is oxidized (loses its electron/electrons) and loses a carbon atom Catabolic each (expelled as CO2 increases entropy) . The remaining 2 carbon fragment are oxidized (creating one NADH per acetyl CoA) (Anabolic increases enthalpy) Now we have Acetyl CoA which then enters the...
3)Citric acid cycle aka krebs cycle where the breakdown of glucose to carbon dioxide is completed. The 2 Acetyl CoA molecules (2 carbons each) each bind to a 4 carbon molecule called Oxelocetic acid (Anabolic /enthalpy). The now 6 carbon molecule is called citric acid. Each Acetyl CoA triggers one turn of the cycle and during each turn two carbons are lost as CO2 (Catabolic/exergonic/entropy). With each turn 1 ATP, 3 NADH, and1 FADH2 are made. This all occurs in the matrix of mitochondria
4)Electron transport chain-The 2 FADH2 and 10 NADH coenzymes that have been made are now transporting all the electrons to the electron transport chain which is in cristae of mitochondria...h+ are pumped into the intermembrane. At the end of the chain electrons bind to h+ and oxygen and present h2o as a waste product.
FINALLY an enzyme at the very end called ATP SYNTHASE turns ADP into ATP (anabolic and endergonic).H+ powers ATP synthase. Bc 10 NADH were produced in this process (which can phosphorale 3 adp each), and 2 Fadh2 were produced (which can phosphorolate 2 adp each) then ideally 34 ATP were made in Cell. Resp. Endergonic,anabolic and increases enthalpy)
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ATP
Contains a sugar ribose, the nitrogenous nase adenine and 3 phosphate groups bonded to it.
Energy coupling-use of exergonic process to drive endorgomic process (for example the 2 exergomic processes that happen before the endergomic process in photosynthesis)
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The regeneration of ATP
ATP cycle-the shuttling of inorganic phosphate and energy and it couples the cells energy-yielding (exergonic) processesto the energy consuming ones (endergomic).
free energy required to phosphoralate ADP comes from exergonic breakdown reactions (catabolism) in the cell NOT spontaneous
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Catabolic (exergonic) pathways, ESP cell. resp. provide the energy for the endergonic process of making ATP
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Photosynthesis
TERMS
Chloraplast-organelle found in plants and photosynthesis protists that absorb sunlight and uses it to drive the synthesis of organic compounds from carbon dioxide and water
Photosynthesis-captures energy from the sun and converts it to chemical energy that stored in sugar and other organic molecules.
mesophyll-leaf cells specialized for photosynthesis. in c3 and CAM plants. they are located between upper and lower epidermis
Stomata-microscope pore surrounded by guard cells in the epidermis of leaves and stems that allows gas exchange between the enviroment and interior of the plant
Stroma-the dense fluid within the chloraplast surrounding the thylakoid membrane containing ribosomes and DNA.
Thylakoid-a flattened membranous sac inside the chloraplast. Thylakoids often exist in stacks called grana that are interconnected . their machinery convert light into energy
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Steps in Photosynthesis
Step 1) Light from sun goes through photosystem 2 powering the movement of an electron anabolic/ Endergonic/increase enthalpy (created by the breaking of a water molecule) through the electron transport chain. Oxygen (also broken off from those water molecules) is released as a by product and hydrogen atoms are being pumped into the lumen of the thylakoid via the cytochrome complex from the stroma making the inside positely charged .
Step2)- the electrons move up Photosystem 1 where another bit of sunlight recharges them (anabolic/endergonic/increase enthalpy) and they head to the enzyme NADP+ reductionase where NADP+ gains a H+ and 2 e- and become the hydrogen carrier and coenzyme NADPH. That will be used later
Step 3)- Bc of the high concentration of H+ inside the thylakoid they start to diffuse out of the enzymne ATP synthase. The diffusion of the H+ also turns ADP into ATP into the stroma
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Step 4)- that ATP just made in ATP synthase (anabolic)now powers up the Calvin cycle (exorgonic)where the enzyme rubisco breaks down 3 atoms of carbon dioxide (1 carbon each) and 3 molecules of RUBP (5 carbons each) and creates 6 molecules of PGA (3 carbons each).
Step 5)-ATP then donates a phosphate to energize PGA into the molecules in the intermediate step. NADPH is then the energy source for the breakdown and build up of G3P molecules still with 3 carbons each
Step 6)-1of those G3P's ditches the group and the remaining 5 get turned inot RUBP again by ATP and the cycle starts over again. 2 turns of the calvin cycle creates one glucose molecule (2 G3P's) :arrow_left:Anabolic/increases enthalpy
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Laws of thermodynamics
1st law of thermodynamics (aka principle of conservation energy)- Energy cannot be created or destroyed just transferred ... (EXP food energy to kinetic energy)
2nd law of thermodynamics - Even though energy can be transferred, during each transfer some gets lost as "un-workable" energy...aka heat... into the universe. So with each transfer available energy becomes less and less.
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Forms of energy
Potential energy-Energy that matter posseses because of it's location or structure (water behind a dam)
Chemical energy is a form of potential energy available to release is in a chemical reaction ( breakdown of food)
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