Nature of chemical rxn in biology world?
thermodynamic favorable but kinetics controlls (very slow without catalyst)
How to change the rate of reaction?
increase temperature, concentration of reactants, add catalyst
What are enzyme characteristics?
enhance rxn rate
mild condition
reaction speicificty
regulation activity
What are the forces that are used in enzyme/substrate interactions?
Vander Waals interactions
H-bond
hydrophobic interactions
electrostatic interactions
Factor contributes to substrate binding
geometric complimentarity
electronic complimentarity (lock and key)
induced fit
induced fit
the binding of substrate can induce conformational change in enzyme to accomodate both geometric and electronic complementarity
Type of enzyme
Oxidoreductase
Transferase
Hydrolase
Lyases
Isomerases
Ligases
Oxidoreductase
transferase
hydrolase
redox reaction
transfer of funcional groups
hydrolysis reactions
Lyase
Isomerase
Ligase
Group elimination to form double bonds
isomerization rxn
bond formation coupled with ATP hydrolysis
How does enzyme distinguish the substrates?
through enzyme's functional groups in active site
Mild condition of enzyme
enzyme-rxn can occur at normal temp and pressure
Regulation activity of enzyme
allosteric regulation
post-translational modification of enzyme
up and down regulation for concentration of enzyme
What doe enzyme do to the delta G++?
It lower the activation energy by lowering the transition state energy
What are 3 chemical catalytic mechanism of enzymes?
acid-base catalysis
transient covalent catalysis
metal ions catalysis (charge-charge interaction)
What do 3 chemical catalytic mechanisms need?
amino acid side chains
cofactor
Type of cofactos
required for functional group transfer or redox reaction
metal ions and coenzymes (cosubstrate and prosthetic group)
cosubstrate
prosthetic group
transient association with enzyme - leave/enter with substrate
permanent association with active site of enzyme
Common metal ions in cofactors
Ca2+, Mg2+, Fe3+, Cu2+, Zn2+
Apoenzyme
Holoenzyme
enzymes after removing cofactors
enzyme-cofactor complex
vitamin
Where does vitamin exist? Can it be synthesized by our body?
the compounds are used as precursors for coenzyme biosynthesis
No, it exists only in diet
Type of vitamin
which one is used for biosynthesis?
water soluble and water insoluble
water soluble
transition state
Delta G++
the state where bonds are broken and formed (A- - B - -C)
activation energy - energy required for reactants to reach the transition state
The higher delta G++
The lower delta G++
the longer the rxn will take
the shorter the rxn will take
How much delta-G++ have to decrease to increase rxn by 10-fold?
1.36 kcal/mol (5.71 kJ/mol)
Formula for calculate the increase rxn rate by decreasing delta G++?
V = e^(delta-G++ /RT)
What does enzyme have when at the transition state? What is downside of this?
higher affinity to the substrate
for compounds mimics the transition state, it can have very high affinity to bind with enzyme and can be great inhibitors
acid catalysis
the process in which the transfer of proton from acid lower the free energy of reactant's transition state
base catalysis
the process in which the abstraction of proton by a base lower the free energy of reactant's transition state
Covalent catalysis
what is the other name for covalent catalysis
the process in which the covalent bonds form between enzyme and substrate
nucleophilic catalysis
nucleophilic catalysis
the process in which nucleophiles of enzyme attack the electrophile on substrates
