L10 - Introduction to enzymes Flashcards
What are enzymes? What are they usually like?
- proteins that catalyse the conversion of substrates to products without being chemically changed
- stereospecific (chiral environment)
What do enzymes do to the eq?
nothing
What is important for activity regarding enzymes?
folding into a specific 3D conformation
What are the 2 models of catalysis?
- lock and key
- induced fit
what is induced fit particularly important for?
multi-substrate enzymes
How do most enzymes work?
by lowering the activation energy of the reaction
What type of interactions are there on enzymes?
- hydrophobic
- ionic
- hydrogen bond
- hydrogen bond to charged group
- hydrogen bond to main chain
what are substrates and reacting groups like in chemical catalysis of enzyme reactions?
substrates and reacting groups held together
what are reacting groups orientated like in chemical catalysis of enzyme reactions?
with respect to each other
what happens to the hydrogen bonds in chemical catalysis of enzyme reactions?
typically stretched or bent
(resembles transition state)
what are active sites usually rich in in chemical catalysis of enzyme reactions? and so what?
hydrophobic residues
- can change pKa of charged amino-acid-side-chains and substrate groups
what is excluded from enzyme active sites?
the bulk solvent
- charged groups are not masked
what often participates in the reaction?
ordered water molecules within active sites
what can happen by active site groups?
protons can be donated or accepted
- acid (adds H+)/ base (remove H+) catalysis
what intermediates are there in nucleophilic catalysis?
acyl-enzyme intermediates
What do enzymes often use?
- cofactors (metal ions)
- cosubstrates (nucleotides)
derived from vitamins and minerals
what are enzyme active sites often complementary to?
transition states
- distortion of bond lengths and bond angles
When is the rate higher?
when the degrees of freedom are smaller
how do enzymes substantially mediate catalysis?
by locking substrate into a fixed position in the active site
what is important in enzyme reactions?
- carbonyl chemistry
- control of stereochemistry
what are the number of reactions like?
there’s a large number of them
- but there’s only a small number of types of reactions
what should small molecules have?
the correct bond angles
What is ‘R’?
non-reacting parts of the molecule
when is it necessary to draw enzyme residue side-chains?
when covalent intermediates are formed when explicitly asked for
what are the steps in acyl-substitution reactions?
- activation of active site nucleophile by deprotonation
- acyl substitution using active site nucleophile
- acyl substitution by water to regenerate enzyme
What enzymes are typically used in acyl substitution reactions?
- serine proteases
- cysteine proteases
- penicillinases and other b-lactamases
- lipases
- esterases and thioesterases
what type of leaving groups often require protonation?
poor leaving groups
RO-, RHN-
when does an acyl-substitution reaction often not occur? and why?
for aldehydes and ketones
- as H atoms, alkyl groups and aryl groups cannot leave
