II - Enzymes and Bioenergetics Flashcards
Protein catalysts that increase the velocity of a chemical reaction and are not consumed during the reaction they catalyze
Enzymes
Physically distinct enzymes which catalyze the same reaction
Isozymes
Catalyzes oxidations and reductions (transfers an electron from one molecule to another)
Dehydrogenase/Oxidoreductase
Catalyzes transfer of moieties such as glucosyl,methyl or phosphoryl groups
Transferase
Catalyzes hydrolytic cleavage of C-C, C-O, C-N and other bonds
Hydrolase
Catalyzes hydrolytic cleavage of C-C, C-O, C-N and other bonds by atom elimination, leaving double bonds
Lyase
Catalyzes geometric or structural changes within a molecule
Isomerase
Catalyzes the joining together of two molecules coupled to the hydroolysis of ATP
Ligase
Uses ATP to add high-energy phosphate onto a substrate
Kinase
Adds inorganic phosphate onto a substrate without using ATP
Phosphorylase
Removes a phosphate group from a substrate
Phosphatase
Adds a hydroxyl group (-OH) onto a substrate
Hydroxylase
Transfers CO2 groups with the help of biotin
Carboxylase
Relocates a functional group within a molecule
Mutase
Properties of Enzymes
contain an active site, efficient, specific, require cofactors, compartmentalized, regulated/inhibited
Substrate fits into the preformed active site
Lock & Key Model
Active site is slightly deformable to accomodate the shape of the substrate
Induced Fit Theory
Apoenzyme + Cofactor
Holoenzyme
Distinguished by their tight, stable incorporation into a protein’s structure by covalent or noncovalent forces
Prosthetic Groups
Binds in a transient, dissociable manner either to the enzyme or to a substrate
Cofactor
Serves as a recyclable shuttle (group transfer agent) that transports many substrates from their point of generation to teir point of utilization
Coenzyme
Why are enzymes compartmentalized?
To protect from inhibitors and to promote a favorable environment
Non-proteins required for enzyme function
Cofactors
Organic Cofactors
Coenzymes
Not required for enzyme function but can alter the rate of reaction
Effectors
Enzymes lower _____.
free energy of activation
Enzymes _____ the energy of the reactants and products , and the equilibrium of the reaction.
do not change
Describes how reaction velocity varies with substrate concentration
Michaelis-Menten Equation
Vi = (Vmax[S]) / (Km + [S])
Michaelis-Menten Equation
Enzymes that follow Michaelis-Menten kinetics have a _____ curve.
hyperbolic
Allosteric reactions have a _____ curve.
sigmoid
Tells you how fast the reaction is
Vi
The maximum velocity or the maximal number of substrate molecules converted to products per unit time
Vmax
The substrate concentration where Vi = Vmax/2
Km
High Km =
Low Substrate Affinity
Low Km =
High Substrate Affinity
Above Km - ___-order kinetics, rate ___ [S]
zero-order kinetics, rate not affected by [S]
Below Km - ___-order kinetics, rate ___ [S]
first-order kinetics, rate directly proportional to [S]
Reciprocal of Michaelis-Menten Equation
Lineweaver-Burk Plot
Used to calculate Km and Vmax
Lineweaver-Burk Plot
Determines the mechanism of action of enzyme inhibitors
Lineweaver-Burk Plot
Any substance that can diminish te velocity of an enzyme-catalyzed reaction
Enzyme Inhibitor
Similar to substrate, competes for the binding site and reversibly attaches to the enzyme
Competitive Inhibitor
Competitive Inhibitor: reversed by increased ___, Km - ___, Vmax - ___
reversed by increased [S], Km - increased, Vmax - not changed
Irreversibly binds to the allosteric site of the enzyme and changes the conformation of the binding site
Non-competitive Inhibitor
Non-competitive Inhibitor: reversed by increased ___, Km - ___, Vmax - ___
reversed by increased [E], Km - not changed, Vmax - lowered
Regulation of Enzyme Activity: change in substrate concentration
immediate
Regulation of Enzyme Activity: allosteric binding sites
immediate
Regulation of Enzyme Activity: covalent modification
immediate to minutes
Regulation of Enzyme Activity: induction/repression of enzyme synthesis
hours-days
The substrate itself serves as an effector
Homotropic Effector
The effector is different from the substrate
Heterotropic Effector
Fed State: Phosphorylated or Dephosphorylated?
Dephosphorylated
Fasting State: Phosphorylated or Dephosphorylated?
Phosphorylated
Transfer and utilization of energy in biologic systems
Bioenergetics
Measure of the heat content of the reactants and products
Enthalpy (ΔH)
Enthalpy (ΔH) is measured in ____.
joules (J)
Endothermic
(+) ΔH - needs heat
Exothermic
(-) ΔH - releases heat
Measure of the change in randomness or disorder of the reactants and products
Entropy (ΔS)
Entropy (ΔS) is measured in ____.
joules/Kelvin (J/K)
Change in Free Energy
ΔG = ΔH - TΔS
Standard Free Energy Change: ΔG under _____ conditions, reactants and products are _____ each, T is _____, pressure is _____
standard conditions, 1 mole, 25°C or 298K, 1 atm
The natural tendency for processes is to proceed from a state of ___ energy to a state of ___ energy.
high to low
Net loss of energy (exergonic), spontaneous - ΔG _ 0
ΔG < 0
Net gain of energy (endergonic), not spontaneous - ΔG _ 0
ΔG > 0
Equilibrium, forward reactions = backwards reactions - ΔG _ 0
ΔG = 0
(-) ΔH, (+) ΔS
spontaneous
(+) ΔH, (-) ΔS
not spontaneous
(+) ΔH, (+) ΔS
spontaneous at high T
(-) ΔH, (-) ΔS
spontaneous at low T
All ΔGs of a pathway are additive
Coupling Reactions
“Energy Currency/Cash” of the cell, transfers free energy derived from substances of higher energy potential to those of lower energy potential
ATP - adenosine triphosphate
ΔG of ATP → ADP + Pi
-7300 cal/mol or -7.3 kcal/mol
ATP Production: Phosphoenolpyruvate
creates ATP
ATP Production: Carbamoyl phosphate
creates ATP
ATP Production: 1,3-bisphosphoglycerate to 3-phosphoglycerate
creates ATP
ATP Production: Creatine phosphate
creates ATP
ATP Production: ADP → AMP + Pi
requires ATP
ATP Production: Pyrophosphate
made from ATP
ATP Production: Glucose 1-phosphate
made from ATP
ATP Production: Fructose 6-phosphate
made from ATP
ATP Production: AMP
made from ATP
ATP Production: Glucose 6-phosphate
made from ATP
ATP Production: Glycerol 3-phosphate
made from ATP
The greatest quantitative source of high energy phosphate in aerobic organisms
Oxidative Phosphorylation
Free energy comes from successive oxidation of substances in the respiratory chain within mitochondria
Oxidative Phosphorylation
The final substance to be reduced in oxidative phosphorylation
molecular oxygen
Loss of Electrons
Oxidation
Gain of Electrons
Reduction
Done through coupling reactions where a phosphate group is transferred to ADP from another substance with a higher ΔG°
Substrate Level Phosphorylation
“Bank” of the cell
ETC - Electron Transport Chain
“Cheques” of the cell
NAD+, FAD
Final common pathway by which electrons from different fuels of the body flow to oxygen
ETC - Electron Transport Chain
Electron carrier which produces 3 ATP
NAD+ - Nicotinamide Adenine Dinucleotide
Electron carrier which produces 2 ATP
FAD - Flavin Adenine Dinucleotide
Electron carrier derived from B3 (niacin)
NAD+ - Nicotinamide Adenine Dinucleotide
Electron carrier derived from B2 (riboflavin)
FAD - Flavin Adenine Dinucleotide
NAD+ is derived from _____.
B3 (niacin)
FAD is derived from _____.
B2 (riboflavin)
Mitochondria: freely permeable to most molecules
outer membrane
Mitochondria: impermeable to most molecules, selective
inner membrane
Mitochondria: folds in the inner membrane
cristae
Mitochondria: contains enzymes, mtDNA, mtRNA and mitchondrial enzymes
matrix
“Tellers” of the ETC “Bank”
complexes
Complex I
NADH Dehydrogenase
Complex II
Succinate Dehydrogenase, accepts FADH2, part of the Kreb’s Cycle
Coenzyme Q
Ubiquinone, lipid, only non-protein part of the ETC
Complex III
Cytochrome b/c1 (Fe/heme protein)
Cytochrome c
Fe/heme protein, mobile part of the ETC
Complex IV
Cytochrome a/a3 (Cu/heme protein), where oxygen is reduced
Complex V
ATP Synthase
NADH Dehydrogenase
Complex I
Succinate Dehydrogenase, accepts FADH2, part of the Kreb’s Cycle
Complex II
Ubiquinone, lipid, only non-protein part of the ETC
Coenzyme Q
Cytochrome b/c1 (Fe/heme protein)
Complex III
Fe/heme protein, mobile part of the ETC
Cytochrome c
Cytochrome a/a3 (Cu/heme protein), where oxygen is reduced
Complex IV
ATP Synthase
Complex V
Energy from oxidation of components in the respiratory chain is coupled to the translocation of hydrogen ions (H+/protons)
Mitchell’s Chemiosmotic Theory
H= moves from inside to outside the inner mitochondrial membrane and accumulates in the intermembranous space
Mitchell’s Chemiosmotic Theory
ETC generates an electrical gradient and a pH gradients across the inner mitochondrial membrane
Oxidative Phosphorylation
Oxidative Phosphorylation: intermembranous space is more _____
positive
Oxidative Phosphorylation: intermembranous space has ___ H+ ions
more
Oxidative Phosphorylation: protons are driven ___ the mitochondrial matrix
towards
Part of ATP Synthase that generates ATP from ADP and Pi
F1
Part of ATP Synthase that acts as a channel where protons pass through
F0
Anaerobic glycolysis is not enough for highly aerobic tissues like _____.
heart & nerves
Stops electron flow from substrate to oxygen
ETC Inhibitor
ETC Inhibitors: Barbiturate
Complex I
ETC Inhibitors: Piericidin A
Complex I
ETC Inhibitors: Amytal
Complex I
ETC Inhibitors: Rotenone
Complex I
ETC Inhibitors: Malonate
Complex II
ETC Inhibitors: Carboxin
Complex II
ETC Inhibitors: TTFA
Complex II
ETC Inhibitors: Antimycin A
Complex III
ETC Inhibitors: Dimercaprol
Complex III
ETC Inhibitors: Cyanide
Complex IV
ETC Inhibitors: Carbon monoxide (CO)
Complex IV
ETC Inhibitors: Sodium Azide
Complex IV
ETC Inhibitors: Hydrogen Sulfide
Complex IV
Increase the permeability of the inner mitochondrial membrane so proton gradient is lost (ATP synthesis stops but ETC continues and produces heat)
Uncouplers
Synthetic Uncouplers
2,4-dinitrophenol, aspirin
Uncoupler Protein
thermogenin (brown fat)
Directly inhibits Complex V so the proton gradient continues to rise but there is no escape valve for protons
ATP Synthase Inhibitors
Example of ATP Synthase Inhibitor
Oligomycin
Unstable products that are formed as byproducts of the ETC when molecular oxygen is partially reduced
Reactive Oxygen Species/Free Radicals: superoxide O2-, hydrogen peroxide H2O2, hydroxyl radical •HO
Produced by neutrophils to kill phagocytosed bacteria
Reactive Oxygen Species/Free Radicals
Increased during reperfusion injury due to the sudden burst of ETC activity with the introduction of oxygen
Reactive Oxygen Species/Free Radicals
Denatures and precipitates proteins and other substrates
Reactive Oxygen Species/Free Radicals
ROS Defense: Catalase
2H2O2 → 2H20 + O2
ROS Defense: Peroxidase
H2O2 + AH2→ 2H2O + A
ROS Defense: Superoxide Dismutase
2O2- + 2H+→ 2H2O + O2
2H2O2 → 2H20 + O2
Catalase
H2O2 + AH2→ 2H2O + A
Peroxidase
2O2- + 2H+→ 2H2O + O2
Superoxide Dismutase
Mitochondrial Diseases: Fatal Infantile Mitchondrial Myopathy
All Complexes
Mitochondrial Diseases: MELAS (Mitochondrial Encephalopathy, Lactic Acidosis and Stroke-like episodes)
Complex I
Mitochondrial Diseases: Kearns-Sayre Syndrome
Complex II
Mitochondrial Diseases: Leber’s Hereditary Optic Neuropathy
Complex III
Mitochondrial Diseases: Leigh’s Disease
Complex IV
Mitochondrial Diseases: MERRF (Myoclonic Epilepsy with Ragged-Red Fibers)
Complex IV
