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Ch.6 Enzymes - Coggle Diagram
Ch.6 Enzymes
enzyme kinetics 酵素動力學
rate is affected by :
substrate
effectors
enzyme
temperature
Derivation of Enzyme Kinetics Equations
Identify constraints and assumptions
:star: Carry out algebra
Start with a model mechanism
Simplest Model Mechanism: E + S :left_right_arrow: ES :arrow_right: E + P
effect of substrate concentration
雙倒數作圖
Enzyme Efficiency Is Limited by Specificity: Kcat /Km
Diffusion from the active site limits the maximum value for specificity.
Can gain efficiency by having high velocity or affinity for substrate
— catalase vs. acetylcholinesterase
Kinetic mechanism
:check: sequential mechanism
:check: ping-pong mechanism
catalyst 催化劑
reaction conditions : pH ≒ 7 , 37℃
enzymatic catalysis
enzymes affect
:red_cross: equilibrium (Keq)
:check: ↓ △G≠ :arrow_right: reaction rates (K) ↑
enzymes decrease △G≠
How to lower △G≠
Uncatalvzed (entropically unfavorable)
bimolecular reactions :
Two free reactants :arrow_right: single restricted transition state conversion
unimolecular reactions :
Flexible reactant :arrow_right: rigid transition state conversion
Catalyzed (entropically neutral)
The entropy cost is paid during binding.
Rigid reactant complex :arrow_right: transition state conversion is entropically neutral.
:star: Enzymes bind transition states best.
Enzyme active sites are complimentary to the transition state of the reaction.
Enzymes bind transition states better than substrates.
Stronger/additional interactions with the transition state as compared with the ground state lower the activation barrier.
catalytic mechanisms
metal ion catalysis : use redox cofactors 氧化還原反應
covalent catalysis : change reaction paths 鍵結形成
:star: chymotrypsin
serine protease 絲胺酸蛋白水解酶
:one: substrate binding
:two: nucleophilic attack
:three: substrate cleavage
:four: water comes in
:five: water attacks
1 more item...
中文版本：
:one: 首先Ser 195會被移除一個質子，使它變成一個更強的親核試劑
:two: 活化的Ser 195會去攻擊胜肽鍵，形成一個暫時的四面體中間產物
:three: 一個質子的貢獻到新形成的氨基促進胜肽末端氨基的釋放藉由His 57，產生一個乙醯化的Ser 195中間產物
:four: His 57和Asp 102共同活化一個水分子，活化後的水分子會攻擊乙醯化的Ser 195，形成一個第二的四面體中間產物
:five: 最後整個系統貢獻一個質子給Ser 195，促進四面體中間產物的分解，並釋放出一個帶有COOH的胜肽
:six: 結論：Ser 195有和受質形成共價鍵結，所以稱為共價催化
acid-base catalysis : give and take protons 氫鍵有無
:star: cleavage of peptidoglycan by lysozyme
peptidoglycan
a polysaccharide found in many bacterial cell walls
lysozyme
antibacterial enzyme
:red_flag: C-1 carbon is located between Glu 35 and Asp 52 residues
Glu 35 :butterfly: general acid : protonate the leaving group in the transition state
Glu 35 :butterfly: general base : deprotonate water in the second SN2 step
Asp 52 :bee: nucleophile : attack the anomeric carbon異頭碳 in the first SN2 step
Water hydrolyzes the covalent glycosyl-enzyme intermediate
Cleavage of the cell wall leads to the lysis of bacteria
Enzyme Activity Can Be Regulated
regulation can be :
covalent modification
irreversible
noncovalent modification (allosteric異位)
*positive modulator
*negative modulator 似「抑制劑」
reversible
enzyme inhibition
inhibitors
reversible
often used as drugs to slow down a specific enzyme
can bind to :
free enzyme :checkered_flag: prevent the binding of the substrate
enzyme-substrate complex :checkered_flag: prevent the reaction
often structural analogs of substrates or products
competitive inhibition 競爭型抑制
non-competitive inhibition 無競爭型抑制
uncompetitive inhibition 非競爭型抑制
mixed inhibition
irreversible (inactivators)
One inhibitor molecule can permanently shut off one enzyme molecule.
They are often powerful toxins but also may be used as drugs.
