Altering The Three-Dimensional Structure Of An Enzyme Might, Biology Lab L100: Week 4: How Enzymes Function

The ability to do work which means to move matter against opposing forces such as gravity and friction

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ATP, an electrical/ion gradient, concentration gradient, NADH, Chemical BondsWater being held behind a damStored energyDue to structure or location

It has a change in free energy that is greater than 0. That means it has a delta G that is positive and therefore the reaction is endergonic.

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It lowers the Vmax and has no affect on the Km.Fits into the Allosteric site to change the shape of the enzymeCan cause a conformation change which will affect the enzyme”s ability to bind to a substrate

Increase the rate of the reaction by reducing the activation energy.They don”t change the direction of the reactionsThey do not change the amount of free energy availableIt lowers the energy barrier needed for reactants to achieve the transition state or lowers the energy of activation of a reactionTypical biological catalyst Have a high affinity or high degree of specificity for a substrateCan be recycled over and over

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This enzyme”s optimal function is at about 37 degrees C, the enzymatic activity of the enzymes slows down around 40 C

1. substrates bind to enzyme; 2. enzyme and substrate reach transtition state; 3. substrates are converted to products; 4. products are released

Every chemical reaction must increase the total entropy of the universe. Every chemical reaction represents a transfer of energy, which increases entropyEnergy must be spent to retain order – this spending of energy usually releases heat, which increases the entropy elsewhere

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Only raises the KmTries to bind to the active siteSlows down the Vmax when it binds to the allosteric site

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∆G is negative/less than zeroSpontaneous reaction (doesn”t mean it will occur rapidly) Favor making products (going from left to right)Releases free energy

∆G is positive/greater than zeroNot spontaneousAbsorbs free energy Favors making reactantsWhen you go from reaction to products, you have to add energy by coupling it with an exergonic reaction to make the overall ∆G negative

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Universal energy moleculeMonomer of nucleic acidsAdenine, Ribose, and 3 phosphate groups connected to each other in a sequenceEnergy intermediateIs exergonic Gets coupled with endergonic reactions (phosphorylation) — Gives net negative free energy changeSource of energy for 20% of proteinsUndergoes 10,000 cycles of hydrolysis and re-synthesis every dayLikely underestimated because there may be other types of ATP-binding sitesA noncompetitive inhibitor for enzymes The “energy currency” and how that we get work done

Direct transfer of a phosphate group from ATP to a substrate (an example being glucose)It energizes the molecule

Does not imply anything about its speedExergonicDoes not require inout of energyDoes require an enzyme

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Initial input of energy to start a reactionAllows molecules to get close enough to cause bond rearrangement

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Bonds are stretched/strained

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Velocity of reaction near maximum rate

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Substrate concentration at which VMax is at half of max rateShows how good your enzyme is

Enzyme “helper” Organic moleculeVitaminsCarry electrons Tightly bounded to the active site or bounded loosely

Enzyme “helper” Inorganic molecule Carry electrons Tightly bounded to the active site or bounded loosely

Functions in muscle formation (collagen)Deficiency causes scurvy (loss of teeth, pale skin, and sunken eyes)

When structure is lost due to heatOnce a certain temperature is reached, bonds maintaining the 2o, 3o, and 4o structure of the protein collapse and the protein loses function

1. pH – Measure of H+ (0-7 is acidic and 8-14 is basic)2. Temperature (typically when temperature increases, rate of reaction will increase, but not always) (as temperature increases, the enzyme”s active site may become unstable and function poorly)3. Coenzymes/Cofactors

Breaks down reactantsUsed for recycling macromoleculesUsed to obtain energy for endergonic reactions Metabolic pathway is complexLots of intermediates (ATP & NADH)Lots of energy transfer stepsSpontaneous, but does not happen without correct enzyme

Promote synthesis (builds up, not breaks down)Endergonic reactionsMust be coupled to an exergonic reaction

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Releases Is exergonicThe bonds are broken When the terminal phosphate bond is broken, a molecule of inorganic phosphate (Pi) is formed which forms adenosine diphosphate, ADP + (Pi) which generates free energy

Chemicals that interfere with enzyme function Are used to slow down/or stop an enzyme Usually reversible in cells (when hydrogen or ionically bonded)

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NAD is a type of nucleic acidWhen NAD is reduced, NADH is formedIt”s really easy to move electrons back and forth between NAD and NADH Often coupled with reactions to give or remove energy

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Feedback Inhibition- Product of pathway inhibits early steps to prevent over accumulation of product

A. Substrate bindingB. Transition State (induced-fit and Ea is lowered)C. Substrate converted to productD. Product is released

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