Increases the rate of reaction by decreasing the energy barrier
Why are enzymes a special type of catalyst?
- They can increase the rate by 106 to 1012 greater than non-catalyst reactions, and 103 increase greater than non-enzymatic catalysts.
- Can occur in mild conditions (pH 7, >100C°, 1atm)
- Can be regulated by biologcial molecules
Unit (when measuring ezymic activity)
Amount of substrate converted to product in a given time (ex: 1µmol/min)
Number of units per a mg of protein
Temperature optimum: definition and average for humans
The temperature at which ezymes perform the best. Typically 37C° for humans
pH optimum for pepsin
pH of 2
pH optimum of Trypsin
pH of 8
Catalyze reduction-oxidation reactions
Catalyses the transfer of a group (glycosyl, methyl, phosporyl)
Catalyzes hydrolytic cleavage of bonds
(C-C, C-O, C-N, and others)
Catayzes atom elimination to leave double bonds
(C-C, C-O, C-N, and others)
Catalyses geometric/structural changes in a molecule
Catalyzes the joining of 2 molecules.
Coupled to hydrolysis of ATP
Specific region on the enzyme where the catalysis occurs. Substrates bind to the active site (plus any required elements) in a specific manor. Enzyme structure determines active site structure, so changes in structure may (or may not) affects the active site.
Catalysis by proximity
Molecules must come within bond forming distance. Active sites create a high local concentration of the target molcule by binding it. Substrates are bound in a specific orientation conducive to the reaction.
Ionizable functional groups of amino acids may act as an acid or base in the catalysis
Catalysis by strain
If catalyzing reaction is to break bonds, the substrates may be bound in such a way that the bonds are destabilized.
The enzyme and substrate covalently bond. The modified enzyme becomes the subtrate for a different reaction.
Keq of the modified enzyme > Keq of the inital substrate to the product
Tightly/stably incorporated into the proteins (sometimes by covalent bonds). Metal ions are the most common.
Most common metal prostetic groups
Co, Cu, Mg, Mn, Zn
Bind transiently to the substrate or enzyme, but are required for activity
Enzymes that contain a metal prostetic group
Accept a group from one reaction, and supplies groups in other reactions
Ex: CoA transfers acyl groups, Folates transfer 1 carbon groups
Physically different enzymes that catalyze the same reaction. May have different properties like substrate affinities or activity regulation. May be expressed differently by different tissues.
Vmax is maximum reaction velocity
Km is the substrate concentration when v= 1/2 Vmax
When [S] = Km, v=1/2 Vmax
Significance of the slope, y and x intercept of the Kineweaver-Burk plot
Y-intercept — 1/Vmax
X-Intercept — -1/Km
Inhibitor competes with the substrate for the active site of the enzyme. Inhibitor is usually structurally similar to the substrate and only binds to the free enzyme.
What value do competetive inhibitors increase?
Km is increased due to the decrease in available enzymes
Vmax is unaffected because inhibitors can be overcome by the substrates
Bind to either the E or ES in a place other than the active site. Heavy metals act via this inhibition.
What values do noncompetitive inhibitors affect?
Vmax is affects because the inhibitor cannot be displaced by substrates
Km is unaffected
Only binds to the ES
What values do uncompetitive inhibitiors affect?
Km and Vmax are both affects, creating a parallel line in the Lineweaver-Burk plot
When are the top and bottom equations used to calculate Ki?
Vappmax is used to calculated the Ki of noncompetitive and uncompetitive enzymes
Kappm is used to calculate the Ki of uncompetitive enzymes
The binding of one molecule facilitiates the binding of subsequent molecules to the enzyme.
If enzyme has positive cooperativity, will respond quickly to a low amount of S. Binding of S promotes an active conformation
What is the Hill equation used for?
To describe the kinetics of allosteric enzymes
Binding of S to allosteric enzyme increases the affinity of other catalytic sites for S
Regulatory molecule distinct from the substrate that bonds to a site other than the catalytic sites. Can be positive or negative
Effectors that affect the catalytic rate, thus influencing Vmax
Effectors that affect the bonding of the substrate, thus influencing K0.5. Can be positive or negative.
Conflicting metabolic pathways are restricted to specific organelles to keep everything physically separate
Hormones produce second messengers which are allosteric effectors of various enzymes.
Ex: hormones stimulate cAMP production and increase cytosolic [Ca2+] that interacts with calmodulin
Enzymes are affected by phophorylation via a protein kinase (can be specific or general)
Some enzymes are synthesized in an inactive form that must be activated via a proteolytic cleavage. (Digestion and coagulation)
Name the 3 positive regulators of glycogen phophorylase given in class
- AMP (allosteric effector)
- Ca2+-calmodulin (Allosteric regulation)