Thermodynamic & enzymes-exam2
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| bioenergetics | energy transformation in living organisms
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| thermodynamics | study of energy of reactions
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| life depends on _________ flow of energy | controlled
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| what is the first law of thermodynamics? | conservation of energy: total amount of energy in the universe (system+surroundings) is constant
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| according to 1st law of thermodynamics, energy can be __________ and ____________ but it can be neither ____________ or ____________ | transferred, transformed, created, destroyed
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| potential energy is energy due to ________ or ______________ | position, chemical composition
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| kinetic energy is due to ___________ | movement
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| what is the second law of thermodynamics? | law of entropy: every energy transfer or transformation in the universe increase the entropy of the universe
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| define entropy | measure of disorder or randomness, often seen as heat, which is random thermal energy
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| free energy (deltaG) is portion of a system's energy that can ___________________ | perform work
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| free energy | deltaG=deltaH-TdeltaS
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| what are the symbols for enthalpy and entropy,? | enthalpy deltaH entropy deltaS
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| when do spontaneous reactions happen? | when there is a net loss of free energy, in other words, negative deltaG
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| in any spontaneous process, the free energy of the system increases | FALSE: the free energy decreases
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| what is the difference between endergonic and exergonic reactions | endergonic reactions require energy input (positive deltaG), exergonic reactions release energy (negative deltaG)
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| oxidation of glucose is ____________ and the reverse reaction is __________ | exergonic, endergonic
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| what is Keq | ratio of production concentrations to reactant concentration at equilibrium.
Keq= [products]eq/[reactants]eq
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| at equilibrium there is ___________________ in the concentrations of reactants or products | no net change
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| extent to which reactants are converted to products (NET change) depends on what? | initial deltaG or reaction
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| How does the sign of deltaG affect the extent of reactants converting into products? | the more negative deltaG is, the farther the net reactions goes toward products
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| TRUE OR FALSE: deltaG reveals information about the rate of reaction | FALSE. it only tells if the reaction will occur
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| Define Catalyst | something that speeds up a reaction but is unchanged when the reaction is over. It only speeds up energetically favorable reactions (-deltaG), it cannot change the sign of deltaG
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| how does a catalyst speed up a reaction? | by lowering Ea or activation energy, it does NOT add energy to reactions.
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| how does a catalyst affect equilibrium point? | it does not. it only allows reaction to reach equilibrium point faster.
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| What are the 2 types of biological catalysts? | Enzymes and Ribozymes
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| what are enzymes? | proteins that act as biological catalysts, most prevalent
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| what are Ribozymes? | RNA molecules that act as biological catalysts. Believed to be primitive possibly 1st type of biological catalysts.
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| what reactions do ribozymes catalyze? | reactions involving RNA in cells, also catalyze peptide bond formation in ribosomes
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| _____________ catalyze peptide bond formation in ribosomes | ribozymes
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| what is the difference between enzymes and ribozymes? | enzymes are protein based, ribozymes are nucleic acid based
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| what is activation energy? | energy barrier that must be overcome before a reaction can occur, even in spontaneous reactions
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| what is transition state? | halfway point of the reaction. It is the peak of Ea Curve.
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| Ea is anything that hinders the course of the reaction, what can that be? | 1. energy needed to bring S to transition state. 2. physical separation (distance) of reactants 3. unfavorable chemical conditions, pH, ionic strength 4. other factors that hinder progress of reaction
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| for uncatalyzed reactions, where does Ea come from ? | random thermal energy
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| heat can overcome activation energy, what are the risk factors of high temperatures? | high temperature denature cellular structures by destroying the hydrogen bonds that hold them in their shape
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| denaturation destroys _______________ at temperature of about ____to ______ C | hydrogen bonds, 40, 45
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| what do catalysts do? | lower activation energy of reactions, in turn allowing favorable reactions to proceed without large inputs of heat.
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| catalysts decrease ___________ input in reactions therefore decreasing chances of ___________ | heat, denaturation
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| what are the three basic properties of catalysts? | 1. increase reaction rate by lowering Ea required 2. form transient reversible complexes with substrate molecules 3. can change the rate at which equilibrium is reached, NOT position of the equilibrium
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| TRUE OR FALSE: enzymes do not bind substrate at all | FALSE. Enzymes bind substrate molecules briefly
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| how do coupled reactions work? | coupled reactions use an exergonic reaction to provide energy for an endergonic reaction.
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| coupled reactions provide energy for a/an____________ reaction by using a/an ___________ reaction | endergonic, exergonic
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| can reactions with positive deltaG ever happen? if so, how? | Yes, through a coupled reaction which uses a reaction with negative deltaG to provide energy for a reaction with positive deltaG
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| what is a feature of enzymes that makes them reusable ? | they return to initial state after releasing reaction products
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| what happens after the enzyme binds to the substrate? | The enzyme returns to its initial shape after releasing reaction products
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| turnover number is ____________ | reactions per sec
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| what is the average turnover number? range? | average ~ 1000 reactions/sec. Range is 0.5-40,000,000 reactions/sec
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| enzymes are reusable, how does that contribute to their efficiency? | Enzymes can effectively catalyze many repeated reactions over and over since they can return to their initial shape.
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| substrates bind to enzymes at a/an __________ which is a ________ like structure | active site, pocket
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| enzymes are _________ with regards to activity | specific
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| what does it mean when we say enzymes are specific? | each enzyme catalyzes one type of reaction for a single type substrate
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| enzymes may have _____________ specificity for closely related substrates | broader
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| how do enzymes recognize substrates? | based on their molecular shape, chemical properties (charge, polarity, etc.)
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| amylase breaks alpha 1-4 bonds between glucose monomers in ________, but not beta 1-4 bonds between glucose monomers in __________ due to amylase's recognition of ___________________ | amylose, cellulose, chemical properties
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| active site contains ________________ which determine which substrates will bind to enzyme | polar charged amino acids
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| How are enzymes named? give examples | 1. based on substrate (protease, ribonuclease, amylase) 2. function (trypsin, catalase)
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| under Enzyme Commission (EC), enzymes are divided into _______ major classes based on ______________________ | six, general function
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| TRUE OR FALSE: thousands of enzymes have been identified with little to no diversity | FALSE. enzymes have enormous diversity
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| What effect does high substrate concentrations have on enzymes? | High [S] saturates the enzymes
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| what effect does the addition of more substrate have on the reaction rate when the enzyme is working at maximal velocity Vmax? | it DOES NOT increase the reaction rate
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| what effect does the addition of more substrate, when little substrate is present, have on the initial reaction rate? | it increases the reaction rate (V)
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| reaction rate is _____________per__________ | amount of product, time
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| what does saturation mean for an enzyme? | it means that all enzyme molecules available are working as quick as possible, to increase reaction rate, add more enzyme molecules. The rate of reaction is constant, or it levels off.
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| What is Km? DON'T GET THIS WRONG!!!!! | substrate concentration at 1/2 maximal velocity (Vmax). The units are those of concentration; M, mM, microM).
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| Is Km read off X-axis or Y-axis? | X-axis since it is referring to concentration
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| What does Km reflect? how? | The affinity of an enzyme for a substrate. Low Km, high affinity; high Km, low affinity (takes longer to reach 1/2 vmax)
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| what are cofactors? | non protein substances that contribute to activity
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| how many types of them are there? what are they? | There are 2 types of cofactors: 1. inorganic: metal ions (e.g. Mg2+, Fe 3+/4+) 2. organic: prosthetic (heme), coenzyme (NAD+/NADH)
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| How are the two types of organic cofactors bound to protein? | prosthetic group: a molecule bound (covalent/non-covalent) to protein. coenzyme: a molecule not tightly bound to protein; only binds during catalysis.
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| how is the function of the 2 organic cofactors different? | A prosthetic group is required for activity e.g. heme in hemoglobin, a coenzyme carries substrates to or products from enzyme, it only binds to protein during catalysis. e.g NAD+/NADH, Coenzyme A
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| Many coenzymes are ______________ or derived from _____________ | vitamins, vitamins
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| What is the active site? where is it located? | site on enzymes that binds substrate(s) and catalyzes reaction. Usually located in cleft or crevice on the surface of an enzyme.
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| active sites have distinct __________ and __________ properties due to the _____________________ that form them | shapes, chemical, amino acids
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| what is the function of carboxypeptidase? | breaks off carboxy terminal in amino acid chain
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| what do the amino acids in the active site do? | Bind to substrate, and push or pull them into shape needed for reaction. i.e. get substrate into transition state.
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| What is the function of phospholipase? | hydrolyzes fatty acid from phospholipids
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| what are some functions of phospholipase isoforms? | 1. intracellular membrane turnover 2. digestion of lipids 3. venom toxin (breakdown cell membrane)
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| anything that affects protein ______________ may affect function | structure
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| what can affect protein structure/function? | 1. Temperature 2. pH
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| activity may be diffusion limited until T above which protein _________ | denatures
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| what is Q10? | RATE AT (T+10)/Rate at T
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| why is there an optimal curve for temp? | T Max May vary for enzyme from poikilothermic organisms from very hot to cold environments
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| why can pH affect enzyme activity? | it affects charge on basic, acidic amino acids
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| What is isoelectric point pI? | PH where net charge on protein is 0. +aa=-aa
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| how are enzymes regulated? | 1. change amount of enzyme- transcription/translation, proteolysis 2. inhibitors 3. allostery 4. feedback inhibition 5. covalent modification
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| what are two ways to change amount of enzymes? | 1. change transcription/translation, regulation of gene expression 2. change rate of proteolysis; ex: ubiquitination- proteasome (shredder for enzymes)
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| when is changing rate of proteolysis useful? what is proteolysis | proteolysis is breakdown of enzymes. It is useful for example when making "anti freezing" agents in animals that tend to be outside in the cold
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| for what reason do inhibitors bind to enzymes? | to decrease activity of enzymes
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| what are the two types of inhibitors? | competitive and non-competitive
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| what is the difference between competitive and noncompetitive inhibitors? | 1. competitive inhibitors bind at the active site non-competitive bind somewhere other than the active site 2. non-competitive inhibitors decrease ability to catalyze reaction, competitive prevents S binding
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| what is allostery? | mechanism to change shape of enzyme to alter its ability to bind substrate
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| Shape of enzyme is controlled by __________ | allosteric regulators
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| what are R vs T states for enzymes? mention Km | R= relaxed state, binds S easily; high affinity. Low Km. T= tense state, low affinity for S. High Km
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| allosteric _________ make T state enzymes. allosteric _________ make R state enzymes | inhibitors, activators
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| what enzymes are subject to allosteric inhibition? what is the result? | enzymes active in the un-complexed form, which has high affinity for S. Stabilizes enzyme in the low affinity form resulting in no activity
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| what enzymes are subject to allosteric activation? what is the result? | enzymes inactive in the un-complexed form, which has low S affinity. Stabilizes enzyme in the high affinity form, resulting in enzyme activity.
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| allosteric regulators bind where? | bind to a domain different from the catalytic domain( active site)
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| what do allosteric regulators affect? | enzyme's affinity for substrate or Km
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| In feedback inhibition, what acts as inhibitor? For what? | products of metabolic pathways act as inhibitors for enzymes active earlier in the pathway
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| Feedback inhibition is often __________ but it may be __________ | allosteric, competitive
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| what affect does the attachment of functional groups have on the enzyme? | attachment may induce a conformational change that changes enzyme activity
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| what is the most common covalent modification? | phosphorylation/dephosphorlyation
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| protein kinase _________ phosphate to ____________ phosphatase _______________ phosphate | adds, protein, removes
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| what is the benefit of covalent modification? | enables rapid on/off switch for enyzmes
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| where is covalent modification often used? | signal cascades in cells
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| Serine, threonine, tyrosine all have _________ in side chain which enables them to be phosphorylated | OH
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