Mechanisms Flashcards
How do biological catalyts differ from ordinary chemical catalysts
higher reaction rates
milder reaction conditions
greater reaction specificity
capacity for regulation
Overview of a structure and function of a biological catalyst
most are proteins, although ribozymes exist
may require a co-factor ( such as inorganic ions, organic or metalloorganic molecules (coenzymes)
can be extremely specific for a substrate, and may even be stereospecific
Cofactors
Any factor required for enzyme activity or protein function.
Cofactor = inorganic ions
Coenzyme = vitamins, or a protein, can be further divided into cosubstrates and prosthetic groups
prosthetic group
a tightly or covalently associated cofactor
Apoenzyme
protien part of enzyme
Holoenzyme
complete catalytic entity, including both the apoenzyme and the non-protien constituents
Substrate specificity
active site is geometrically and electonically complemntary to the substrate
permissive enzymes and theri substrates
example = chemotrypsin, a protease that can clease hydrophobic peptides that he N-terminus, however it may also clease esters
How do enzymes work tho
provide an envrionment within whihc a given reaction is energetically more favourable
Reactive site: pocket called “active site”
- where substrate is bound
- form enzymes-substrate complex
- plays a role in catalytic process
What do enzymes affect about a given reaction
They affect the reaction rate, NOT the position of the equilibrium
Collision therory of reaction rates
1 The particles must collide in order to react
2 Not all collisions result in a reaction, and the reactants must collide in the correct orientation.
- The reactants must possess a minimum energy, the activation energy to initiate the chemical reaction
Energy diagrams
Only colliding particles that are properly orientated can deliver kinetic energy into potential energy as least as large as delta G double dagger to be able to climb over the “hill” and produce products
Distribution of energies for ideal gases
note: only a small fraction of molecules have sufficient energy to react (overcome delta G double dagger)
also, at higher temperatures, more molecules possess the kinetic energy to overcome delta G double dagger, and the reaction rate increases
Effect of temperature on reaction rate
at approximately RT, a 10C increase in temperature increases a typical reaction rate by about 2-3 times
Rate =K[A]^n
where, k is temperature depended: K is only a constant if T= constant
Which order of reaction are most enzymes
first order
What is the purpose of the arrhenius equation
relates temperature to reaction rate and activation energy,
higher K = faster rate
HIgher delta G double dagger the lower the rate, and the higher the temp the faster the rate
What is the effect does delta G have on rate
delta G has no effect on rate
What is reaction rate linked to
delta G double dagger
Note: enzymes cannot force an unfavorable reaction to go in the forward direction, ie// enzymes do not affect the position of equilibrium
What determines the position of equilibrium
delta G Prime at stp,
thus the equilibrium constant is related to delta G prime STP for the overall reaction and not to the activation energy barrier delta G double dagger
How do enzymes solve the problem of the fact that particles need to collide in order to react
particles must collide in order to react, thus enzymes need to increase the frequency of the collisions
increasing the temperature, and concentration is not realistic for biological systems, however you can increase the local concentration in the enzyme active site.
How do enzymes solve the problem of the fact that reactants must collide i the correct orientation
enzymes can help to orient the reactants properly in the active site
How do enzymes solve the problem of the reactants needing to posses a minimum energy to overcome delta G double dagger
enzymes need to increase the number of reactants with the energy to overcome the delta G double dagger
the could increase the kinetic energy of the reactants (increase in temperature), but this is not realistic for biological sytems.
They can however lower the energy barrier for delta G double dagger
Catalytic stratagies commnly used by enzymes
procimity and orientation effects
preferential binding of the transition state complex
- binding energy
- induced fit
acid/base catalysis
covalent catalysis
metal ion catalysis
electrostatic catalysis
Prosimity effects
intramolecular reactions greatly increase the rate