module 6 Flashcards
what does life depend on?
-the ability to efficiently and selectively catalyze chemical reactions
-many biomolecules are very stable with rates if uncatalyzed transformations that are too slow to permit life
what is the introduction of enzymes?
-provide a mechanism for acceleration, regulation and coordination of these reactions
-side reactions leading to useless or dangerous molecules must be avoided
-some enzymes are information sensors as well as catalysts
what is the most striking feature about enzymes?
-their catalytic power and specificity (can’t screw up)
what is vitalism?
-originally, biochemical molecules were believed to be inseparable from life
-vitalism is the belief that living things are fundamentally different from non-living things; that they contain some non-physical element and are governed by different principles than inanimate objects
-has famous supporter such as louis pasteur
what did Edward Buchner demonstrate?
-that dead yeast still convert sugars into alcohol, indicating reactions of life were separate from life
-there was a factor in yeast catalyzing the reaction; the term enzyme if from the greek word “in yeast”
-this work won him a nobel prize, ten years before he was killed in WWI
proteins are well suited to form ____________
-a variety of complex three-dimensional structures that enable binding of a variety of substrates
do all enzymes need co-factors or co-enzymes?
-for some enzymes, the protein component alone is fully active
-other do require them for activity
what are co-enzymes, co-factors and prosthetic groups?
-co-factors= inorganic ion (Mg, Fe, etc) (pick up and put down hammer)
-co-enzymes=complex organic molecules (vitamins) (pick up hammer)
-a co-enzyme or co-factor that is tightly associated with the enzyme is called a prosthetic group (the different is the degree of association)(glue hammer to hand)
what is an example of an enzyme with a co-enzyme?
what are catalysts?
-lower the amount of energy required for a reaction to proceed
-sped up attainment of equilibrium but do not change equilibrium
-are unchanged by the reaction; recycled to participate in another reaction
(can’t hammer 1 nail, must hammer for years)
enzymes offer incredible __________ in the rate enhancement they provide
-CATALYTIC POWER
enzymes vs. chemical catalysts
- speed: enzymes are often much faster than chemical catalysts, some approaching catalytic perfection
- conditions: many chemical catalysts that require extremes of temperature, pressure and pII while enzymes function under physiological conditions
- specificity: enzymes have a higher degree of specificity (including stereospecificity) than most chemical catalysts. This includes specificity for what they act upon and what they produce
- regulation: unlike chemical catalysts, many enzymes are responsiveness to the dynamic need of the cell and organism (how much product to produce, respond to changes)
what is the Circe effect?
-enzymes rates of catalysis can approach the physical limit of rates of diffusion of molecules in solution
-some enzymes have rate-determining steps that are roughly as fast as the binding of substrates to the enzymes
-some enzymes are able to catalyze reaction faster than predicted by diffusion-control limits
-this is called the Circe effect, named after a figure in green mythology who was renowned for her ability to draw her enemies to her, then transform them into animals
Enzymes catalyze the interconversion of substrate and product formula?
-substrate (S): the molecule acted upon the enzyme
-product (P): the molecule produced by the enzyme
-active site: the portion of enzyme (E) responsible for binding the substrate to formation of an enzyme-substrate (ES) complex
what are the active sites of enzymes?
BINDING SITE
1. is a 3D cleft formed from different parts of the polypeptide chain
2.represents just a small part of the enzyme
3. are unique microenvironments
4.substrates are bound to enzymes by multiple weak interactions
5. the specificity of substrate binding depends on the precisely defined arrangement of atom in the active site. Enzymes and their active sites can be quite flexible. Substrate binding can caused “induced fit” or “conformation selection”
what is the lock and key vs key in glove of enzyme specificity?
what does change in G depend on?
-G of a reaction depends only on the free energy of the product minus the free energy of the reactants.
-G of a reaction is independent of the steps of the transformation
what does G provide information for?
-no information about the rate of a reaction
-a negative G indicates that a reaction can take place spontaneously but does not signify whether it will proceed at a perceptible rate
what happen when +G, -G or G=0?
-+G= reaction cannot take place spontaneously, an input of free energy is required (endergonic)
–G= reaction is spontaneous, will proceed without input of energy and the reaction releases energy (exergonic)
-G=0: system at equilibrium, there is no net change in the concentrations of the products and reactants
what determines the rate at which equilibrium is reached?
-activation energy, G between S and P (difference of free energy)
what is the relationship between the rate of a reaction and the activation energy?
-is inverse and exponential
what does no influence the equilibrium?
-enzymes do not influence the difference in free energy between S and P and therefore do not influence the equilibrium
enzymes provide ______________________, lowering ____
what increases the rate of reactions? and what do they no affect?
-enzymes provide a lower-energy pathway between the substrate and product, decreasing the activation energy of the transition state and increasing the rate of reaction
-enzymes do not affect the different in free energy between the substrate and product and therefore do not influence the equilibrium of a reaction
what are the mechanisms that lower the activation energy?
-catalytic capabilities of enzymes result from both chemical and binding effects
binding effects
1. substrate binding
2. transition-state stabilization
chemical effects
1. acid/base catalysis
2. covalent catalysis
what provides specificity and increases rates?
-binding of substrate in the active site provides specificity and catalytic power
-catalytic mechanisms limited to the binding properties can still increase reaction rates by over 10,000 fold
what are the binding effects?
-there is conceptual overlap between substrate binding and transition state stabilization
-active has to be complimentary enough to give specificity, but enough to promote change
what are the 5 categories in which substrate binding promotes reactions?
- reducing entropy (decreased freedom of motion of two molecules in solution)
- alignment of reactive functional groups of the enzyme with the substrate
- desolvation of the substrate (removal of water molecules) to expose reactive groups
- distortion of substrates (conformation)
- Induced fit of the enzyme in response to substrate binding
what is a very important sentence?
active cite must be similar enough to substrate to ensure specificity, but different enough to promote change (towards transition state)
what is transition-state (TS) stabilization?
-an increased interaction of the enzyme and substrate occurs
-the essence of catalysis is stabilization the transition state
-the enzyme distorts the substrate, forcing it toward the transition state
what is the active site complementary to?
-the transition-state in shape and chemical character
enzymes may bind their transition states ___________ than their substrates
10^10 to 10^15 times more tightly
what is the graph with no enzyme, complementary to substrate and complementary to transition state?
what are TSAs?
-transition-state analogs are stable compounds that resemble unstable transition states
-they have potential therapeutic applications as competitive inhibitors
-can bind the active site of a target enzyme active site with high affinity, precenting substrate binding
-plug active site (with similar transition state ) with higher affinity
what are competitive inhibitors?
-molecules that bind to the active site of an enzyme, they tend to resemble the substrate molecule
how do viruses have a complex relationship with immune system?
virus needs host to take on certain properties
-food poisoning: virus wants to spread so you poop and puke
-rabies : virus wants to make you bite things
two commonly observed mechanisms of chemical catalysis are:
-acid/base catalysis
-covalent catalysis
what do active sites often contain?
-chemically reactive sidechains
-this includes polar, ionizable side chains (triprotics) such as Asp, Glu, His, Cys, Tyr, Lys, Arg, and Ser
what happens after substrate binding?
-the enzyme can act upon the substrate to promote formation of the product
what is the pKa of a functional group influenced by?
-the chemical microenvironment
-functional groups of AA can have different pKas within the active site which make them more suitable for acid/base catalysis
what is the example of covalent catalysis?
-group is transferred from A-X to B in two steps via the covalent complex of X-Enz
-stage 1: forcing covalent linkage between enzyme and substrate molecules, in order to break into 2 pieces
-stage 2: getting enzyme back to original form
what is sucrose phosphorylase?
-example of covalent catalysis
what are the general properties of enzyme kinetics?
-kinetics is the study of the velocity of reactions
-the velocity of a reaction is quantified as the change in concentration of product over time
-enzyme kinetics measured in units of concentration over time, for example: mmoles/sec or moles/min
what is initial velocity?
-the velocity at the beginning of an enzyme catalyzed reaction, prior to product accumulation
-K1 and k2 represent rapid, non-covalent interactions between enzyme and substrate
-K2 is rate constant of formation product of ES
what is the steady state assumption mathematically?
what is the equation and plot of Michaelis-Menten?
-describe the relationship between substrate concentration and initial velocity
-going to have limit on how fast they con convert to product
-velocity becomes independent of substrate concentration
what is Km?
-the concentration of substrate required for the enzyme to function at half maximal velocity
-for many enzymes, Km provides an accurate approximation of the in vivo substrate concentration
-this means that most enzymes are usually functioning at about half their maximum velocity
what does it mean when S>Km< S<Km< S+Km
-[S]<Km : enzymes are highly sensitive to changes in substrate concentration but have very little activity
-[S]>Km : enzymes have high activity but are insensitive to changes in substrate concentration
-[S]=Km ; enzymes has significant activity and is responsive to changes in substrate concentration
what are lineweaver-burke plots?
-also describe the relationship between S and V (same as menden)
-are a double-reciprocal plot of 1/V vs 1/S
-are more precise method of analysis of kinetic date
-are used to determine Vmax and Km
what is the enzyme turnover number?
-also called kcat
-equals the number of molecules of substrate converted to product per unit time under saturating conditions
-is calculated by Vmax/ [Et]
what are the type of reversible inhibitors?
-reversible enzymes bind to the enzyme by non-covalent interactions
-competitive
-uncompetitive
-noncompetitive
what are competitive inhibitors?
-resemble the substrate and compete with the substrate for binding the active site
-bind only the free enzyme
how do competitive inhibitors affect Km and V max?
-Vmax is the same
-Km is increased (amount of substrate)
what is an uncompetitive inhibitor?
-bind only to the ES complex
what do uncompetitive inhibitors decrease and increase?
-Vmax is decreased by the conversion of ES to ESI which cannot form product
-reduce ES
-as E binds S to replenish ES this apparent increase in affinity of the E for S causes a decrease in Km
what do non-competitive inhibitors increase and decrease?
-V max is decreased with no change in Km
-don’t influence S binding, therefore there is no change in Km
what is the graph of changes in a reversible inhibitors
what is the catalytic triad? (each play a specific role in the catalytic mechanism)
-His: acts to accept and donate a proton at each of the two stages of the reaction mechanism (acid base catalysis)
-Asp: stabilizes the positively-charged His to facilitate serine ionization
-Ser: attacks the carbonyl group of the peptide bond to be cleaved (covalent catalysis)
far in primary, close in teritary
what is the chymotrypsin mechanism?
what is the graph of chymotrypsin mechanism?
what is the graph of a negative feedback inhibition?
what are negative feedback in a branched pathway?
-often occurs by the final product of each brand acting to inhibit the enzyme catalyzing the first unique and committed step of the branch
what is regulation of enzyme activity when two pathways cooperate to form a single product?
-the final product can inhibit the first unique step of each branch
-the molecules preceding the merger can inhibit the first step of their branch as well as activating the first step of the opposing branch
do allosteric enzymes obey Michaelis-Menten kinetics?
-no, instead has sigmoidal curves
what is the threshold effect?
-below a certain substrate concentration, there is a little enzyme activity; after the threshold has been reached, the enzyme activity increases rapidly (on/off)
-similar to hemo and myoglobin
what happens when the ratio PEP/ADP is high?
-PFK1 is inhibited
-when ratio is low, PFK1 is activated and glycolysis produces more ATP from ADP
-thus the concentrations of PEP and ADP act allosterically through PKF1 to regulate the activity of the entire pathway
what is the activation of PFK1 by ADP?
-the activity of PKF1 is responsive to the concentration of the substrate as well as the allosteric inhibitors and activators
-even at constant levels of substrate, the activity of the enzyme can be modulated through changes in levels of the allosteric modulators
what is the most common post-translation modification?
-phosphorylation
-kinase ass phosphoryl groups, phosphatases removes them
what are the enzymes used in glycogen metabolism (example of phosphorylation)?
production and utilization of glycogen is controlled by two enzymes:
-glycogen synthase (anabolic) which catalyzes production of glycogen from glucose
-glycogen phosphorylase (catabolic) which catalyzes the breakdown of glycogen into glucose
-reciprocal regulation: only one will be active at one time
what is the first step of glycogen metabolism?
-in response to hormones that are released when you are hungry (glucagon) or scared (epinephrine) both enzymes are phosphorylated
-phosphorylation activates the catabolic enzyme and inactivates the anabolic enzyme
-this situation favors the breakdown of glycogen into glucose
what is the second step of glycogen metabolism?
-in response to hormones that are released in the fed state (insulin) both enzymes are unphosphorylated
-when unphosphorylated, the anabolic enzyme is active and the catabolic enzyme is inactive
-this situation favors the storage of glucose within glycogen
