Quiz 11 Flashcards
protein motions
support catalysis in several ways
enzymes differ from ordinary chemical catalysts in
reaction rate, reaction conditions, reaction specificity and regulation
the unique physical and chemical properties of
the active site limit an enzymes activity to specific substrates and reactions
some enzymes require metal ions or
organic factors
enzymes catalyze thermodynamically favorable reactions, causing them to proceed at extraordinarily
rapid rates
-> therefore enzymes provide cells with the ability to exert kinetic control over thermodynamic potentiality
kinetic
used to describe rates
oxidation-reduction (redox) reactions
any chemical reaction in which the oxidation numbers (oxidation states) of the atoms are changed
transfer of functional groups
the transfer of a functional group (e.g a methyl or phosphate group) from one molecule to another
hydrolysis
a chemical compound decomposes by a reaction with water. the hydrolysis reaction breaks down a variety of polymers, including proteins, carbohydrates, proteins, fats and nucleic acids
lyases
catalyzes the breaking of various chemical bonds by means other than hydrolysis and oxidation, often forming a new double bond
isomerization
structural rearrangement of isomers (same molecular weight, but different structural formula)
ligases
reaction joining of two large molecules by forming a new chemical bond
substrate specificity is determined by
interactions at the active site
exquisite stereospecificity is
observed for some enzymes
cofactors
- metal ions
- coenzymes (organic molecules)
holoenzyme
a catalytically active enzyme with its cofactor complex
apoenzyme
enzyme without the cofactor
coenzymes
must be regenerated for completion of a “catalytic cycle”
zymogens
are inactive precursors of enzymes
- proteolytic cleavage produces the active enzyme
enzyme catalytic power
the ratio of the enzyme catalyzed rate of a reaction to the uncatalyzed rate
enzyme catalytic power
the ratio of the enzyme catalyzed rate of a reaction to the uncatalyzed rate
enzyme specificity
the term used to define the selectivity of enzymes for their substrates
enzyme regulation
ensured the rate of the metabolic reactions is appropriate to cellular requirements
enzyme classification
the nomenclature that provides a systematic way of naming metabolic reactions
enzymes coenzymes and cofactors
nonprotein components essential to enzyme activity
an enzyme provides a lower energy pathway from substrate to product BUT
does not affect the overall energy change for the reaction
the large rate accelerations of enzymes correspond to
large changes in the free energy activation for the reaction which is not a state function
all reactions pass through a
transition state on the reaction pathway
the active sites of enzymes
bind the transition state of the reaction more tightly than they bind to the substrate
- the enzyme stabilizes the transition state and lowers the activation energy of the reaction
the transition state
sits at the apex of the energy profile in the energy diagram
- knows as the free energy activation, the higher it is the slower the reaction
- decreasing the g increases the reaction rate[speed of rxn]
high G+= slow
low g+ = speeds
thermodynamics
the overall free energy change for a reaction delta g, is a state function related to the eq constant, keq
kinetics
the free energy of activation for a reaction delta g plus is related to the rate constant, k, not a state function.
the catalytic role of an enzyme is
to reduce the energy barrier between substrate S and transition state X+
rate acceleration by an enzyme means that
the energy barrier between ES and EX+ must be smaller than the barrier between S and X+
- the enzyme must stabilize the EX+ transition state more than it stabilizes ES
binding cannot be too tight because
the goal is to make the energy barrier between ES and EX+ small
raising the starting energy of ES to a more positive delta g
will increase the catalyzed rate
accomplished by
- loss of entropy due to formation of ES
- destabilization of ES complex by desolation and strain/distortion
the es complex is a more highly ordered
low entropy state for the substrate
desolvation raises the energy of the
es complex
- electrostatic destabilization of a substrate may arise from juxtaposition of like charges in the active state,
destabilizing the ES
transition state analogs make ideal enzyme inhibitors because
tight binding
acid/base catalysis
amino acid side chains that can donate or accept protons can participate in chemical reactions as acid and/or base catalysts
nucleophilic attack
groups can catalyze reactions through the transient formation of covalent bonds with the substrate
metal ion catalysis
the unique electronic properties of a metal ion facilitate the rxn
proximity and orientation
enzymes accelerate reactions by bringing reacting groups together and orienting them for a reaction
transition state stabilization
significantly lowers the activation energy for a reaction
proton transfer
can change a nucleophile into an electrophile
active site histidine
can be deprotenated by another group and then act as a base, accepting a proton from the substrate
active site can
approximate an intramolecular reaction, increasing rate
serine proteases residues
- serine histidine and aspartic acid
a binding pocket
determines the substrate specificity of the various serine proteases
serine proteases catalyze peptide bond hydrolysis via
proximity and orientation effects, acid-base catalysis, covalent catalysis [nucleophilic attack], electrostatic catalysis and transition state stabilization
- they cleave zymogens to produce the active form
a mixture of 4 catalytic mechanisms
proximity and orientation: asp102 functions only to orient his57
acid/base catalysis: his57 acts as a general acid and base
nucleophilic attack: ser195 forms a transient covalent bond with peptide to be cleaved- turns trigonal c to tetrahedral c
transition state stabilization: the tetrahedral oxyanion intermediate is stabilized by the backbone N-H groups and ser 195 the oxyanion hole
mechanisms of serine proteases
1: general base catalysis, nucleophilic attack and formation of the tetrahedral oxyanion intermediate
2. general acid catalysis and breakdown of tetrahedral oxyanion intermediate, leaving the acyl enzyme intermediate on ser 195
3. polypeptide (R’) with new amino terminus is released, and replaced by a second substrate: a water molecule
4. general base catalysis, nucleophilic attack and formation of the tetrahedral oxyanion intermediate
5. general acid catalysis and breakdown of tetrahedral oxyanion intermediate releases the polypeptide with a new C- terminus
ribozymes
segments of RNA that display enzyme activity
