BMS2062 Lecture Notes - Lecture 17: Digestive Enzyme, Duodenum, Chymotrypsin
30 May 2018
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Week 9. Enzymes and Protein Binding and Recognition
FROM STRUCTRE TO FUNCTION – ENZYMES
• Enzymes are proteins that catalyse (accelerate) biochemical reactions
o enzymes accelerate the rate of a reaction by a factor of 1015 to 1017
o allow chemical reactions to occur at normal temperatures
o can act as catalysts again and again (reused/recycled)
• Enzymes act on substrates eg. pepsin, trypsin
o The substrate binds to the active site (usually a small area of the whole protein)
• Enzymes are classified by the reactions they catalyse
• Enzyme reaction steps:
• Enzymes function by lowering the activation energy (binding to the transition state) of a reaction
o Difference between ground state (substrate energy) and peak that corresponds to
transition state
o Net energy stays the same regardless of enzyme*
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• Structural information can explain the reaction and substrate specificity, identify catalytic
residues and explain how mutations can affect function
• Enzyme characteristics:
1. Enzymes work very rapidly
2. Activity is dependent on pH (pH changes the charge, most are at pH 7)
3. Activity is dependent on temperature
4. Enzymes are substrate specific
5. Many enzymes require cofactors or coenzymes
Cofactors: Fe, Cu, Zn – are recycled (another enzymes puts it back together after
use)
Coenzymes: vitamins, niacin, riboflavin
Can remove metals by chelating
6. Enzyme inhibition
Reversibly and irreversibly
Often enzymes in a metabolic pathway are inhibited by the end-products of the
pathway: feedback inhibition / controls level of metabolism
Enzyme inhibitors make good leads for drug design
eg. inhibitors of carbonic anhydrase are used to treat glaucoma
• How do enzymes work?
o Can bring reactants close together (eg. spliceosome, cuts out introns and brings exons
together)
o Enzymes stabilise the transition state of a reaction and lowers the activation energy
required for the reaction
o The bigger the activation energy, the lower the rate constant (slower the reaction)
• Transition state:
o Corresponds to the top of the energy barrier and represents the moment when bonds
are broken and formed
o Is not a stable chemical species and has no lifetime (lifetime is infinitely small)
o Transition state makes better contacts with the enzymes than the substrate of product
does
o Drugs that mimic the reaction transition state show very strong binding to the enzymes
(strongest possible binding)
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o Some atoms are more electron negative than others, that is they more strongly attract
electrons – bonds between different chemical elements are polarised
o Many reactions involve an electron rich atom (a nucleophile – partial negative charge)
reacting with an electron deficient atom (an electrophile – partial positive charge)
o Electron pushing arrows in the mechanism diagrams originate either near electron pair
dots or near bonds that are broken. They point to either electrophilic atoms being
attacked or at the bond being formed as a result of electron movement
• Example: Chymotrypsin
o Is a digestive enzyme produced by pancreas and secreted into the duodenum
o Hydrolyses proteins y leaig peptide ods i.e. it’s a protease/peptidase
o Catalyses peptide hydrolysis
o Specifically catalyses the cleavage peptide bonds on the carboxy terminal side of Phe,
Trp, Tyr residues
o Member of the serine protease family
o Cleavage of peptide bond requires a catalytic triad of aa in its substrate binding pocket
-> Ser, His, Asp are catalytic residues and mutation of any of the three reduces reaction
rate by 1000 fold or more (significant reduction)
o Apolar residues that line the pocket only contribute to substrate binding but no
catalysis. Mutation of any of them may lead to ~10 fold reduction in the enzyme acitivity
find more resources at oneclass.com
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