Module 5: V1 - V4 Flashcards
How do enzymes lower ΔG?
enzyme active sites are complementary to the transition state of the reaction
stronger/additional interactions with the transition state as compared with the ground state lower the activation barrier
What are enzymes?
enzymes are biomolecules (not necessarily proteins) that have a distinctive 3-D structure and employ catalytic mechanisms
What is the structure of enzymes?
the active sites of enzymes are lined with functional groups (usually from amino acids) that bind the substrate(s) and catalyze the chemical transformation to product(s)
Do enzymes affect the equilibrium of a reaction?
no, they only affect the reaction rate
What is enzyme catalysis formally described as?
the stabilization of the transition state through tight binding to the enzyme
What are three common catalytic mechanisms and what are they involved in?
acid-base catalysis: give and take protons
covalent catalysis: change reaction paths
metal ion catalysis: use redox cofactors, pKa shifters
Why are enzymes important?
living organisms must be able to catalyse the conversion of carbon fuel sources into cellular energy (e.g. ATP) in an appropriate timescale
some diseases are caused by excessive / too little enzymatic activity
many drugs target enzymes either by inhibiting or activating the enzyme target
What are cofactors?
small inorganic molecules which are used by enzymes for activity
What are coenzymes?
more complex molecules used by enzymes that transiently carry functional groups during catalysis of a reaction
What are kinases?
enzymes which catalyse the phosphoryl transfer from one molecule (usually ATP) to another e.g. hexokinase
What are phosphorylases?
enzymes which catalyse the covalent addition of inorganic phosphate (Pi) to a molecule; e.g. glycogen phosphorylase
What are phosphatases?
enzymes which catalyse the cleavage of a phosphate to yield the dephosphorylated product and Pi; e.g. glucose-6-phosphatase
What are dehydrogenases?
enzymes which catalyse an oxidation/reduction reaction commonly using NADH/NAD+, NADPH/NADP+ or FADH2/FAD as cofactors; e.g. glyceraldehyde-3-phosphate dehydrogenase
What are mutases?
enzymes which catalyse the shift of a phosphoryl group from one atom to another within the same molecule; e.g. phosphoglycerate mutase
What are isomerases?
enzymes which catalyse the conversion of one isomer to another; e.g. triose phosphate isomerase
What are hydratases?
enzymes which catalyse the addition/removal of water e.g. enolase
What are synthases?
enzymes which catalyse the synthesis of a product e.g. citrate synthase
What does the activation of an enzyme affect?
the rate of the forward and backward reactions
Where are intermediates located on a free energy plot?
found at local minima as they are ‘stable’ states
What are transition states?
transient species (maxima on a free energy plot)
Why are energy barriers to reactions important?
prevent complex molecules from reverting spontaneously to their simpler precursors
What is the binding free energy?
the difference between the activation energies of the uncatalysed and catalysed reactions caused by the enzyme binding the transition state
What are the different ways in which enzymes reduce the activation energy and accelerate rates of reaction?
binding substrates in the correct orientation relative to the active groups
providing catalytically active groups (side chains, acids, bases, metal ions)
polarizing bonds, stabilising charged species
stabilising the transition state
Why does rate decrease with time?
(main reason) S is depleted by conversion to product
the reaction is reversible, so as [P] increases the rate of the reverse reaction increases
the enzyme may be unstable under the reaction conditions
What is the rate of an enzyme catalysed reaction proportional to?
enzyme concentration
What is a Michaelis-Menten plot?
a graph which shows initial velocity (µm/min) vs. substrate concentration (mM)
Does the reverse reaction get faster, or only the forward reaction?
both sides of the reaction get faster
Why is the transition state more stable when an enzyme is involved? How is that helpful?
because enzymes are complementary to the transition state of the reaction and therefore, form stronger/additional interactions with the transition state
