L8- Introduction to the structure/function relationship Flashcards
What is the function of a binding site
For ligand binding, binding sites induce distal conformational changes
For enzymes binding sites bring substrates near the catalytic residues or bring substrates close to each other
What are the major features of a binding site
TWO features confer high specificity and affinity for its ligand
1. complementary shape
2. extensive interactions are formed between the ligand and the residues of the binding pocket
True or false: The shape and electrostatic interactions determine the specificity and affinity of substrate for a protein
True
How do enzymes increase the rate of reaction?
Enzymes catalyse by providing an alternate pathway with a lower activation energy
This is achieved through binding
interactions between the substrate/intermediates and active
site residues
How does binding pocket structure affect enzyme catalysis?
The binding pocket brings substrates into the correct geometrical and orientational positioning to increase reaction rate
What are the four ways enzymes utilise one or several amino acid residues, or co-factors, in specific conformations to catalyse their chemical reactions?
Through co-factor catalysis, approximation, covalent catalysis, acid-base catalysis
These mechanisms use active-site interactions to stabilise the transition state intermediate
Approximation
Bringing together of reactants in the correct orientational and geometrical form
- achieved through extensive interactions with the binding pocket
- the decrease in entropy is compensated by favoured substrate-enzyme interactions
- Binding in the correct orientation and geometry increases the effective concentration
Acid-Base catalysis
Side chains are used to deprotonate and then reprotonate substrates
the enzymes adjust pKa to allow for favourable interactions to occur at physiological pH, this creates a high energy transition state that is established by an oxyanion hole
covalent catalysis
cleavage of a peptide bond by nucleophilic attack creates a tetrahedral intermediate
held by protein folding the cleaved peptide bond forms an oxyanion hole that stabilises the negative charge build-up in the transition state
Give an example of a catalytic mechanism and how the transition state is stabilised.
Co-factor catalysis
FAD catalyses transfer of hydride to the
N5 of FAD
Substrate is positioned for orbital overlap by FAD
Transition state is stabilised to optimise
orbital overlap, promoting transfer ->
increase reaction rate
Describe the energy landscape concept of protein folding.
The likelihood of the protein being in a
particular conformation depends on the protein environment
A protein will continue changes confirmation from a state of high free energy to a state of low energy
“Events” that change the protein
environment regulates the activity of a
protein by changing its confirmation
Know that the native conformations in various activation states are energetically stable conformational sub-states.
What are the two main initiators of conformational change?
Interactions with other molecules i.e. Binding of a substrate/ligand or protein:protein interaction
Phosphorylation of amino acid side chains – particularly tyrosine, serine, threonine (hydroxyl groups)
Describe an example of a protein conformational change and its effect on protein function.
Describe how DNA mutations can affect protein structure and function
Primary structure determines tertiary structure (mostly) and determines function
DNA mutations may lead to changes in protein primary structure affecting the
interactions that can be formed between residues
Give an example of how protein mutation can cause disease
P53 gene mutation
