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Cell Bio-Koster

Thermodynamic & enzymes-exam2

QuestionAnswer
bioenergetics energy transformation in living organisms
thermodynamics study of energy of reactions
life depends on _________ flow of energy controlled
what is the first law of thermodynamics? conservation of energy: total amount of energy in the universe (system+surroundings) is constant
according to 1st law of thermodynamics, energy can be __________ and ____________ but it can be neither ____________ or ____________ transferred, transformed, created, destroyed
potential energy is energy due to ________ or ______________ position, chemical composition
kinetic energy is due to ___________ movement
what is the second law of thermodynamics? law of entropy: every energy transfer or transformation in the universe increase the entropy of the universe
define entropy measure of disorder or randomness, often seen as heat, which is random thermal energy
free energy (deltaG) is portion of a system's energy that can ___________________ perform work
free energy deltaG=deltaH-TdeltaS
what are the symbols for enthalpy and entropy,? enthalpy deltaH entropy deltaS
when do spontaneous reactions happen? when there is a net loss of free energy, in other words, negative deltaG
in any spontaneous process, the free energy of the system increases FALSE: the free energy decreases
what is the difference between endergonic and exergonic reactions endergonic reactions require energy input (positive deltaG), exergonic reactions release energy (negative deltaG)
oxidation of glucose is ____________ and the reverse reaction is __________ exergonic, endergonic
what is Keq ratio of production concentrations to reactant concentration at equilibrium. Keq= [products]eq/[reactants]eq
at equilibrium there is ___________________ in the concentrations of reactants or products no net change
extent to which reactants are converted to products (NET change) depends on what? initial deltaG or reaction
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
TRUE OR FALSE: deltaG reveals information about the rate of reaction FALSE. it only tells if the reaction will occur
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
how does a catalyst speed up a reaction? by lowering Ea or activation energy, it does NOT add energy to reactions.
how does a catalyst affect equilibrium point? it does not. it only allows reaction to reach equilibrium point faster.
What are the 2 types of biological catalysts? Enzymes and Ribozymes
what are enzymes? proteins that act as biological catalysts, most prevalent
what are Ribozymes? RNA molecules that act as biological catalysts. Believed to be primitive possibly 1st type of biological catalysts.
what reactions do ribozymes catalyze? reactions involving RNA in cells, also catalyze peptide bond formation in ribosomes
_____________ catalyze peptide bond formation in ribosomes ribozymes
what is the difference between enzymes and ribozymes? enzymes are protein based, ribozymes are nucleic acid based
what is activation energy? energy barrier that must be overcome before a reaction can occur, even in spontaneous reactions
what is transition state? halfway point of the reaction. It is the peak of Ea Curve.
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
for uncatalyzed reactions, where does Ea come from ? random thermal energy
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
denaturation destroys _______________ at temperature of about ____to ______ C hydrogen bonds, 40, 45
what do catalysts do? lower activation energy of reactions, in turn allowing favorable reactions to proceed without large inputs of heat.
catalysts decrease ___________ input in reactions therefore decreasing chances of ___________ heat, denaturation
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
TRUE OR FALSE: enzymes do not bind substrate at all FALSE. Enzymes bind substrate molecules briefly
how do coupled reactions work? coupled reactions use an exergonic reaction to provide energy for an endergonic reaction.
coupled reactions provide energy for a/an____________ reaction by using a/an ___________ reaction endergonic, exergonic
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
what is a feature of enzymes that makes them reusable ? they return to initial state after releasing reaction products
what happens after the enzyme binds to the substrate? The enzyme returns to its initial shape after releasing reaction products
turnover number is ____________ reactions per sec
what is the average turnover number? range? average ~ 1000 reactions/sec. Range is 0.5-40,000,000 reactions/sec
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.
substrates bind to enzymes at a/an __________ which is a ________ like structure active site, pocket
enzymes are _________ with regards to activity specific
what does it mean when we say enzymes are specific? each enzyme catalyzes one type of reaction for a single type substrate
enzymes may have _____________ specificity for closely related substrates broader
how do enzymes recognize substrates? based on their molecular shape, chemical properties (charge, polarity, etc.)
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
active site contains ________________ which determine which substrates will bind to enzyme polar charged amino acids
How are enzymes named? give examples 1. based on substrate (protease, ribonuclease, amylase) 2. function (trypsin, catalase)
under Enzyme Commission (EC), enzymes are divided into _______ major classes based on ______________________ six, general function
TRUE OR FALSE: thousands of enzymes have been identified with little to no diversity FALSE. enzymes have enormous diversity
What effect does high substrate concentrations have on enzymes? High [S] saturates the enzymes
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
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)
reaction rate is _____________per__________ amount of product, time
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.
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).
Is Km read off X-axis or Y-axis? X-axis since it is referring to concentration
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)
what are cofactors? non protein substances that contribute to activity
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)
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.
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
Many coenzymes are ______________ or derived from _____________ vitamins, vitamins
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.
active sites have distinct __________ and __________ properties due to the _____________________ that form them shapes, chemical, amino acids
what is the function of carboxypeptidase? breaks off carboxy terminal in amino acid chain
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.
What is the function of phospholipase? hydrolyzes fatty acid from phospholipids
what are some functions of phospholipase isoforms? 1. intracellular membrane turnover 2. digestion of lipids 3. venom toxin (breakdown cell membrane)
anything that affects protein ______________ may affect function structure
what can affect protein structure/function? 1. Temperature 2. pH
activity may be diffusion limited until T above which protein _________ denatures
what is Q10? RATE AT (T+10)/Rate at T
why is there an optimal curve for temp? T Max May vary for enzyme from poikilothermic organisms from very hot to cold environments
why can pH affect enzyme activity? it affects charge on basic, acidic amino acids
What is isoelectric point pI? PH where net charge on protein is 0. +aa=-aa
how are enzymes regulated? 1. change amount of enzyme- transcription/translation, proteolysis 2. inhibitors 3. allostery 4. feedback inhibition 5. covalent modification
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)
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
for what reason do inhibitors bind to enzymes? to decrease activity of enzymes
what are the two types of inhibitors? competitive and non-competitive
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
what is allostery? mechanism to change shape of enzyme to alter its ability to bind substrate
Shape of enzyme is controlled by __________ allosteric regulators
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
allosteric _________ make T state enzymes. allosteric _________ make R state enzymes inhibitors, activators
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
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.
allosteric regulators bind where? bind to a domain different from the catalytic domain( active site)
what do allosteric regulators affect? enzyme's affinity for substrate or Km
In feedback inhibition, what acts as inhibitor? For what? products of metabolic pathways act as inhibitors for enzymes active earlier in the pathway
Feedback inhibition is often __________ but it may be __________ allosteric, competitive
what affect does the attachment of functional groups have on the enzyme? attachment may induce a conformational change that changes enzyme activity
what is the most common covalent modification? phosphorylation/dephosphorlyation
protein kinase _________ phosphate to ____________ phosphatase _______________ phosphate adds, protein, removes
what is the benefit of covalent modification? enables rapid on/off switch for enyzmes
where is covalent modification often used? signal cascades in cells
Serine, threonine, tyrosine all have _________ in side chain which enables them to be phosphorylated OH
Created by: rusulali97