Sept 13 Protein Function and Regulation Flashcards
(40 cards)
what activity is the basis of the many diverse functions of proteins?
binding
proteins bind to one another, macromolecules, small molecules and ions
what is the molecule to which a protein binds?
the ligand
what happens in some cases when the protein binds to its ligand?
ligand binding can change the conformation of the protein
ligand induced conformational change is integral to the mechanism of action of many proteins
what are the two most important properties in ligand binding?
specificity and affinity
what is specificity?
the ability of a protein to bind to only one particular ligand, even in the presence of a big excess of irrelevant molecules
what is affinity?
the tightness/strength of binding, expressed as a dissociation constant Kd
stronger interaction –> lower Kd
what does protein binding specificity arise from?
arises from numerous interactions which are individually weak but collectively strong
binding is an interaction between complementary molecular surfaces
how do antibodies bind to their antigens and what allows them to do so?
antibodies bind to their antigens with high specificity and high affinity
antibodies two identical heavy chains and two identical light chains linked by disulfide bonds
antigen binding surface or CDR (complementarity determining region) involves multiple protein loops from both the heavy and light chains
what are enzymes and what is their ligand called?
extremely diverse class of catalylitcally active proteins whose ligands are the substrates of the reactions they catalyse
where does substrate binding and reaction catalysis occur?
occurs at the enzymes active’s site
the active site includes the substrate binding site (complementary to the specific substrate)
and the catalytic site which carries out the chemical reaction once the substrate is bound
what is Vmax?
the maximal rate of catalysis given saturating amounts of substrate
depends on the amount of enzyme and how fast it can work
turnover number–> number of enzymatic cycles per second at top speedw
what is Km?
the substrate concentration that supports a rate of catalysis equal to one half of the V max
depends on, and is a measure of the affinity of enzyme:substrate binding
how do the values of Vmax and Km differ when you the concentration of enzymes changes?
the Vmax is higher, proportional to how many more enzymes were added
however the Km stays the same, because in general, binding affinity is independent of concentrations, but depends only on the chemical properties of the enzyme and the substrate?
what does the fact that enzymes exhibit pH optima reflect?
- evidence of active site acid base chemistry
- sensitivity of the overall protein to charge distribution
what happens to enzymes in a common pathway? (what is metabolic coupling)
there are three ways
1. the enzymes can become associated together into a quaternary structure which is much more efficient
each enzyme is coded for by a different gene
2. the enzymes can bind to a common “scaffold” protein
3. by evolution, enzymes can combine into a single polypeptide, coded for by a single gene
a multifunctional enzyme which has different domains(!!!)
what is allosteric effect?
binding of a ligand at one site of a protein can lead to the conformational change that affect the binding of another ligand at a different site
can be used to control protein activity, turn it “on” or “off”
in what other ways can protein conformation and activity be modified?
through phosphorylation and dephosphorylation
phosphorylation of amino acid side chains is a rapidly reversible covalent modification of protein structure –> post translational modification
what needs to happen for high affinity and highly specific interactions to take place?
the shape and chemical properties of the binding site must be complementary to those of the molecule
what is the induced fit model?
substrate binding site is not rigid, but flexible
and that substrate binding induces the enzyme to change shape and consequently bind more strongly to the transition state
what is the enzyme substrate complex?
the bound substrate to the enzyme
the ES complex is in equilibrium with the unbound enzyme and substrate and is an intermediate step, followed by the conversion of the substrate to the product
how do enzymes catalyse the process of a reaction?
they divide the it into multiple, discrete chemical reactions, in which the product of one reaction is the substrate for another
different ES complexes are generated before the final product
what is a cofactor/prosthetic group?
helpergroup, non polypeptide small molecule or ion that is bound in the active site and plays an essential role in the reaction mechanism
also called coenzymes
some (not all) are chemically modified during the reaction and therefore need to be replaced or regenerated
what are enzyme inhibitors?
bind to active sites and disrupt catalytic reactions
what are competitive inhibitors?
bind directly on an enzyme’s binding site and this compete directly with the normal substrate
