Enzymes yo Flashcards
Enzyme definition
- protein catalyst (usually) that increases the rate of reactions without being changed in the overall process
- converts substrates into products and direct all metabolic events
- increase rate,do not invent new reactions
Recommended or common name
- usually have “ase” added to the name of the substrate in the reaction
- or describe the action performed
- or retain original trivial name
Systemic name
- Classification: divided into 6 major classes
- name: includes names of all substrates involved plus ase
- number: each enzyme is assigned a unique number
Systemic name classifications
- oxidoreductases(oxidation/reduction)
- transferases(transfer of C,N,P)
- hydrolases(cleavage by addition of water)
- lysase(cleavage of C-C,S,N bonds)
- isomerases(racemization of isomers)
- ligases(forms OSN bonds)
Synthase vs synthetase
synthase: no ATP required
Synthetase: ATP required
Phosphatase vs phosphorylase
Phosphatase: removes a P group
Phosphorylase: generate a P group
Oxidase vs oxygenase
oxidase: uses oxygen as an acceptor without incorporating it into a reaction
oxygenase: oxygen is incorporated
Arrow indication about reaction
Arrow pointing in both directions: it can catalyze either reaction
Arrow pointing in one direction: it can only catalyze in one direction (reverse might be possible, but not with that enzyme)
Enzyme structure: active site
- special pocket that binds to the substrate
- formed by folding of the protein that allows specific side chains to participate in binding
- Binding makes Enzyme-Substrate complex which includes a conformational change
- Enzyme-Product complex dissociates to enzyme and product
Enzyme Structure: allosteric site
- any other part of the enzyme that is not the active site
- binds different regulatory molecules
Enzyme Efficiency
- extremely high (10^14 times faster)
- turnover number is the number of substrate molecules converted to product per enzyme molecule per second(kcat)(hella lot)
Enzyme Specificity
- HIGHLY SPECIFIC
- only one or few substrates
- only one type of reaction
- if there is more than one function, there are multiple binding sites
- enzymes present in the cell determine the type of reaction that can happen
Coenzymes
organic molecules that are required by certain enzymes to carry out catalysis
-NAD+,FAD,NADP+
Cofactors
inorganic substances that are required for or increase rate of catalysis
-ZN2+, Mg2+
Holoenzyme
enzyme+nonprotein component=active
Apoenzyme
enzyme without nonprotein component=inactive
Regulation by inhibitors and activators
-the amount of the end product produced is regulated by its own concentration (feedback)
Post-transitional modifications
-regulation through covalent modulation of the enzyme molecule(phosphorylation)
Enzyme protein production
transcription and translation of enzyme genes
Regulation through specific local
-environment/ pH
Enzyme compartmentalization
-different metabolic pathways occurring in different cellular compartments
Advantages of compartmentalization
- isolates substrates and products from competing reactions
- organizes enzymes into purposeful pathways that can proceed simultaneously
- more precise regulation
Free energy
-gibbs free energy (G)- quantitative measure of the energy transfers between chemical reactions
Energy Barrier
energy difference between the reactant and a high energy intermediate
Free energy activation
the difference in free energy between the reactants and intermediate
Stabilization of transition state
(chemistry on the active state)
- creates bonds in intermediate that are not like the ones in the substrates or products
- increases the concentration of the reactive intermediates that can be converted to products
Chemistry on the active site
- provide chemical groups that participate in reactions with the substrate
- enhance probability of transition state formation
- enzyme is returned to its unaltered state before the release of the product
- decrease the activation energy
Factors that affect reaction velocity
- substrate concentration
- temp
- pH
Substrate concentration affect on reaction velocity
- Rate of velocity-number of substrates converted to product per unit of time
- VMax- the rate of an enzyme catalyzed reaction increases with the substrate until VMax is reached. represents saturation of all available binding sites
- hyperbolic curve
- sigmoidal curve is less common(no michaelis-menten)
Temperature affect on reaction velocity
- reaction velocity increases with temp until peak is reached
- increases the amount of molecules that can overcome energy gap
- After peak, velocity decreases with rising temp
- human optimum is 37 degrees celcius
pH affect on reaction veocity
- Enzyme and substrate usually require certain things protonated/un so change in pH results in decreased velocity
- protein structure requires certain pH so you can denature protein with change
- pH optimum is specific for each enzyme
Components of reaction model
-S,E,ES,P, rate constants
Michaelis Menton
- describes how reaction velocity varies with substrate concentration at a given concentration of enzyme
- assumes concentration of substrate is much greater than enzyme concentration
- assumes ES is in a steady state
- initial velocity is used in analysis
Michaelis Menton Km
- characteristic of an enzyme and its particular substrate and reflects the affinity of the enzyme for that particular substrate
- THE AMOUNT OF SUBSTRATE NEEDED TO HALF MAXIMAL VELOCITY (1/2 VMax)
- Small Km=high affinity
- high Km=low affinity
Relationship of velocity to enzyme concentration
- reaction rate is directly proportional to E a all concentrations of S
- if E is halved, V0 and VMax are halved too
Order of Reaction
- when S is much lower than Km, velocity is proportional to the substrate concentration(first order)
- when S is much greater, velocity is constant and equal to VMax and independent of S. (zero order)
Lineweaver-burk plot purpose
- uses 1/V0 vs 1/S
- results in a straight line which lets us determine Km and Vmax more accurately.
Lineweaver-burk plot understanding
- the intercept on the x axis is equal to -1/kM
- intercept on the y axis is equal to 1/Vmax
- double reciprocal plot
- increase Km or Vmax, they will be closer to zero
- decreasae km or vmax, they will be further from zero.
Inhibitors
- any substance that can diminish the velocity of an enzyme catalyzed reaction
- irreversible and reversible
Irreversible inhibitors
- bind to E through convalent bonds
- only way to recover E activity is to synthesize a new molecule
- suicide inhibitor-enzyme converts inhibitor into a reactive form in its active site(product is inhibitor)
Reversible inhibitors
- bind through non covalent bonds which allows for full recovery of enzyme
competitive: inhibitor competes with substrate for active site
noncompetitive: inhibitor binds to allosteric site
Competitive inhibition
- the effect of the inhibitor can be overcome with large concentrations of S so NO EFFECT ON VMAX
- lowers affinity so KM IS INCREASED
- example:statin drugs
Noncompetitive inhibition
- cannot be overcome by substrate concentration so VMAX IS DECREASED
- does not interfere with substrate binding so NO EFFECT ON KM
- example: allopurinol
Effectors
- can affect KM or Vmax or neither or both
- can be negative or positive (inhibit or increase enzyme activity)
Homotropic effectors
- the substrate itself serves as an effector
- most often positive
- enhances catalytic activity
- cooperativity effect
Heterotropic effectors
- the effector is different than the substrate molecule
- feedback inhibition: an end product of a metabolic pathway inhibits upstream step
- example:phosphofructokinase in glycolysis
Regulation by posttranslational covalent modifications
- most common is phosphorylation/dephosphorylation of hydroxyl group in ser,thr,tyr
- protein kinase-phosphorylate
- protein phosphatase-dephosphorylate
Regulation by control of enzyme production
- alter the rate of synthesis or degradation of the enzyme
- these enzymes are usually only needed under certain conditions and are not in constant use.
timing of enzyme regulation
-gene expression regulation: take from hours-days
-covalent changes: immediate to minutes
allosteric control: immediate
Blood vs plasma vs serum
blood=plasma+blood cells
plasma: fluid part of the blood without the cells
Serum: plasma without coagulating factors. not made in the body
Plasma Enzymes
actively secreted: have certain function in plasma.small group of enzymes. do not play a role in diagnosis
-not actively secreted: function intracellularly not in plasma. released from cell lysis during normal turnover.levels are at a steady state. when there is an increase in these enzymes, it signifies tissue damage.
