Lecture 8 - Bioenergetics & Enzymes Flashcards
def: no net fixation of carbon into organic compounds
chemoheterotrophs
def: a subset of thermodynamics, the quantitative analysis of how the biological world gains and uses energy
bioenergetics
where do chemotrophs get their energy from?
oxidizing metabolic fuels
what are catabolic metabolic pathways?
oxidative reaction sequences that result tin the transfer of electrons away from carbon
how many oxidation states does carbon have?
5
what is the most highly oxidized form of carbon found in living organisms?
carbon dioxide
in carbon hydrogen bonds, how are the electrons shared?
the more electronegative carbon owns the two electrons shared with hydrogen
in carbon oxygen bonds, how are the electrons shared?
electron sharing is unequal in favour of oxygen
T or F: entropy decreases when monomers are ordered into more complex molecules
true
what relates changes in enthalpy and changes in entropy?
Gibbs Free Energy
a reaction can occur spontaneously only if deltaG is ________, thus the process is _______-
negative, exergonic
a reaction cannot occur spontaneously if deltaG is ________, thus the process is _________
positive, endergonic
what is deltaG when the system is at equilibrium?
0
what is the deltaG of the cellular environment?
-11.5 kcal/mol
def: the ratio of product concentration to reactant concentration at equilibrium
equilibrium constant
is homeostasis equivalent to equilibrium?
No!
what is a better term for the steady state in which a cell holds itself?
dynamic steady state
def: the maintenance of dynamic steady state by regulatory mechanisms that compensate for external changes
homeostasis
______ and ________ catalyze virtually all cellular processes and reactions
enzyme and ribozymes
what are the 7 properties of catalysts?
- only small amounts required
- function at physiologically relevant temp and pH
- aren’t irreversible altered during the reaction
- highly specific to their substrate
- they generate a very specific product
- can be regulated to meet the needs of the cell
- they change the RATE, not the THERMODYNAMICS of the reaction
def: state in which reactants are thermodynamically unstable but do not have enough energy to exceed the activation energy barrier
metastable state
def: the minimum amount of energy required by reactants before collisions between them will lead to product formation
activation energy (Ea)
def: the precise point at which weak chemical reactions between substrate and enzyme are at the stage where the reaction has an equal chance of going to product or back to substrate
transition state
T or F: if reactants can be bound on a surface and brought closer together, their interaction will be favoured and the required Ea will be reduced
treu
a _______ enhances the rate of a reaction by providing a binding surface and effectively lowering Ea
catalyst
what are 3 ways enzymes reduce the activation energy?
- maintain precise substrate orientation
- change the substrate reactivity (influence the distribution of electrons)
- exert physical stress (conformational change = destabilizing bonds)
def: characteristic cluster of amino acids on every enzyme, region of the enzyme that binds substrate (and cofactor)
active site
the active site is usually a __________ _______ ___ ________ that accommodates the substrates with high affinity
complimentary groove or pocket
what does the active site contain?
residues that directly participate in the making and breaking of bonds
which amino acids comprise the active site?
Cysteine (C)
Serine (S)
Aspartate (D)
Glutamate (E)
Histidine (H)
Lysine (K)
def: organic, participate in catalysis, but not a substate, derived from vitamins, bind loosely
co-enzymes
def: inorganic, help increase the rate of catalysis, often electron carriers, bind tightly
metals
def: enzyme not bound to its co-factor
apoenzyme
def: enzyme found bound to its co-factor
holoenyzme
what are the 4 other purposes of the rest of the enzyme structure?
- support structure to allow the 3 dimensional creation of active site from primary sequence
- regulatory sites
- sites of interaction with other proteins
- substrate channels
what characterizes enzymes?
their sensitive to temperature and pH
at low temperatures, how does the rate of enzyme activity change with temperature?
it increases with temperature due to increased kinetic activity of enzyme and substrate molecules
beyond a certain point of temperature increase, what happens to enzymes?
they denature and lose enzyme activity
most enzymes are active within a pH range of about ____ units
3-4
pH dependence is usually due to the presence of ________ _____ ____ __ _____ ____ or on the substrate
charged amino acids at the active site
pH changes affect the charge of such residues, and can disrupt ______ and _______ bonds
ionic and hydrogen bonds
what are two other factors that enzymes are sensitive to?
- molecules and ions that act as inhibitors or activators
- ionic strength of the environment which affects hydrogen bonding and ionic interactions needed to maintain tertiary conformation
what kind of bonding does substrate bonding involve?
usually hydrogen, ionic or both
def: the quantitative aspects of enzyme catalysis and the rate of substrate conversion into products
enzyme kinetics
def: discrete locally folded unit of the overall tertiary structure, usually with a specific function
domain
T or F: proteins will similar functions often have completely different domains
false, they often share common domains
proteins will multiple functions usually have a separate ________ for each function
domain
what processes regulate enzyme concentrations in a cell?
synthesis and degradation
how can cells regulate protein activity?
- inhibition
- allosteric regulation
- cleavage
- phosphorylation
- kinase localization
- Ca2+ sequesteration
- receptor internalization
what are enzymes most influenced/inhibited by?
products, alternative substrates, substrate analogues, drugs, toxins, and allosteric effectors
def: regulation of an enzyme by binding an effector molecule at a site other than the enzymes active site
allosteric regualtion
what does binding of a regulatory ligand do?
change of a proteins conformation
T or F: all covalent modification can be reversed
False, some can be reversed
Phosphorylation/Dephosphorylation:
Kinases _______
Phosphatases ________
Kinases phosphorylate
Phosphatases dephosphorylate
