Term
reaction coordinate graph (draw, label Ea, transition state, ∆G) |
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Definition
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Term
| First law of thermodynamics |
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Definition
| law of conservation of energy – energy cannot be created or destroyed, can only be changed from one form to another. When the energy of a system decreases, the energy of the universe increases (and vice versa). |
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Term
| Second law of thermodynamics |
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Definition
| things naturally move toward disorder. The chaos of the universe will increase when left alone (entropy, symbol=S) |
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Term
Gibbs free energy
(∆G=∆H - T∆S) |
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Definition
equation - S=entropy, T=temperature in Kelvin, H=enthalpy
Negative ∆G is spontaneous – if negative, reaction will progress toward the product side. This is an exergonic reaction – energy leaving the system. Endergonic – requires energy to progress (takes energy into the system)
∆G depends on concentration of products and reactants. |
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Term
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Definition
equation - E=change in bond energy of products and reactants, P is pressure, V is volume.
Enthalpy is negative for spontaneous reactions – exothermic, releasing energy as opposed to requiring it to make the reaction progress. |
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Term
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Definition
| point at which the system is balanced, concentrations are no longer changing rate to product side=rate to reactant side. |
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Term
| what does thermo tell you about reaction rate? |
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Definition
| o Spontaneous reactions occur when ∆G<0, says nothing about rate. Thermodynamics tells you whether a reaction will occur, not anything about the rate. ∆G doesn’t look at pathways that you can take to get there, only looks at the energy states of the products and the reactants |
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Term
| reaction kinetics - define activation energy |
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Definition
| all reactions go through a higher energy intermittent phase between reactants and products. Some of these require more energy to produce=higher activation energy which is basically the amount of energy you need to put into the system to reach the hump, downhill from there and will go to completion |
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Term
| reaction kinetics - define transient state |
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Definition
| o Transient state – exists in between reactant and product for a very short time, temporary higher energy state |
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Term
| reaction kinetics - define catalyst |
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Definition
| lowers the activation energy without changing ∆G by stabilizing the transient state. Catalysts are not consumed in a reaction, they can be used again and again. They take a spontaneous reaction (must be spontaneous!) and speed it up |
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Term
| what is the energy source in the cell? |
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Definition
take a spontaneous reaction (must be spontaneous!) and speed it up.
o ATP is the energy source for the cell. Removal of one phosphate group is very favorable, this energy can be used to drive unfavorable reactions such as conformational changes in proteins. Can also couple favorable ATP cleavage with unfavorable reaction to make overall reaction favorable (-∆G) |
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Term
| define enzyme and active site |
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Definition
Most enzymes are proteins that act as catalysts that must undergo 3D folding to achieve proper confirmation.
active site - this is part of the catalyst where the action happens. Active sites are highly specific. |
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Term
| define substrate and recognition pocket |
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Definition
substrate - reactant in a catalyzed reaction
recognition pocket - near active site, attracts certain residues on polypeptide chains (helps recruit proper substrates to the active site) |
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Term
| define allosteric regulation |
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Definition
modification of active site activity through interactions of molecules with other specific sites on enzyme
Allosteric literally means “other space” – in this, looking at regulation sites far away from the active site, leads to a conformational change in the protein that increases/decrease its catalytic activity. |
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Term
| explain feedback inhibition (negative feedback) |
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Definition
| pathway where product of one reaction becomes substrate for the next. The end product of the pathway binds to the first unique enzyme (allosteric site) in the pathway, shutting it down. This occurs when there is an excess of the final product in the system. |
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Term
| define enzyme cooperativity and describe the curve [subtrate] vs RXN rate |
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Definition
– most enzymes have subunits. Addition of subunits causes confirmation change (allosteric) that makes the binding site for the substrate more attractive. Must have more than one active site.
Curve for these guys is an S – flat part=not very attractive, steep=added subunit and very attractive, flat part 3 is Vmax |
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Term
| define Km for enzyme kinematics |
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Definition
| – Michaelis constant, do 1/2 Vmax on y axis, draw across to graph line, concentration=Km |
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Term
| explain competitive inhibitors and describe graph [substrate] vs RXN rate |
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Definition
compete for active sites with the substrate, depressing formation of product, can be overcome by adding more substrate.
Vmax not affected, just takes more substrate to reach saturation point. Graph is more like a line than a hill |
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Term
| define non-competitive inhibitor |
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Definition
| bind to allosteric site, not active site. This form does diminish Vmax, cannot be overcome with more substrate |
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Term
| define autotroph and heterotroph |
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Definition
autotroph - make own food
heterotroph - obtain food from other living things |
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Term
| where do organisms store energy? |
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Definition
| in reduced molecules such as carbs and fats |
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Term
| what are the 3 meanings of oxidize? |
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Definition
| 1) to remove an oxygen (or decrease number of bonds to an oxygen), 2) add a hydrogen, 3) add electrons |
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Term
| what are the three meanings of reduction? |
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Definition
| 1) to attach an oxygen (or increase number of bonds to an oxygen), 2) remove a hydrogen, 3) add electrons |
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Term
| define catabolism and anabolism |
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Definition
catabolism - breaking down molecules (think “catastrophe breaks things down”)
anabolism - making molecules and building them up (think “add a”) |
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Term
| what are the 4 steps in cellular respiration? |
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Definition
| glycolysis, pyruvate dehydrogenase complex (PDC), Krebs cycle, electron transport/oxidative phosphorolation |
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Term
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Definition
glucose splitting – split into two identical molecules (pyruvic acid molecules), produces small amount of NADH and ATP, occurs in cytoplasm
extraction of energy from carbs |
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Term
| describe glycolysis under aerobic vs anaerobic conditions. |
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Definition
aerobic conditions - oxygen present - pyruvate produced in glycolysis enters PDC and krebs cycle to be oxidized completely to CO2, NADH and FADH2 are reoxidized in electron transport where O2 is the final acceptor
anaerobic conditions - absence of oxygen - electron transport cannot function and limited supply of NAD+ converted to NADH. fermentation allows for regeneration of NAD+ in anaerobic conditions, uses pyruvate for the acceptor of the high energy electrons |
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Term
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Definition
Krebs cycle – acetyl group added to oxaloacetate to form citric acid, small amount of ATP, lots of NADH and FADH2 produced. PDC and Krebs need oxygen in cell, but neither actually uses oxygen
• Takes 2 carbon acetyl unit from PDC, combines with oxalacetate and releases 2 CO2 molecules , generates NADH and FADH2
• Take home, at the end we get lots of NADH, FADH2, GTP – used in electron transport chain |
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Term
| describe the electron transport chain, including all players, where it occurs, etc. |
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Definition
occurs in mitochondria. goal of process - reoxidize all the electron carriers (pull of the H’s), store energy in form of ATP
Process – start of process – 2 electrons passed from NADH into NADH dehydrogenase complex, NADH-->NAD+, electrons passed to ubiq (Q) which is a carrier, passes it to second complex – cytochrome C reductase – electrons passed to cytochrome C carrier, electrons then moved over to cyctochrome C oxidase which attaches the electrons to an oxygen molecule, giving rise to the final product, H2O
Coupled with each protein that handles the electrons is the pumping of protons across the membrane into the intermembrane space. This gradient is utilized by ATP synthase to run reaction ADP + Pi -->ATP |
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Term
| differences in electron transport between prokaryotes and eukaryotes? |
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Definition
| prokaryotes have no membrane bound organelles, do this process on their cell membranes instead of the mitochondrial membrane. For eukaryotes, cytosolic NADH has to be moved into the mitochondria matrix at an energy expenditure |
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Term
| describe the mitochondria and its structures. where is H+ pumped during electron transport? |
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Definition
where electron transport occurs. Two membranes (inner and outer), outer one has pores. Inner membrane is impermeable and is densely folded in cristae (projections into the matrix – inner most portion of the mitochondria). Have intermembrane space.
electrons are pumped from matrix into intermembrane space between the two membranes. |
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