Kinetics of enzymes

What is the reaction formula

E + S → Kf/Kr ← ES → Kcat → E + P

Explain the kinetic reaction formula graph (time vs concentration)

S starts at high concentration and goes to 0 because it gets used up

P starts low then goes high because your creating it

E starts high then goes low then slowly back up high because it binds then releases substrate

ES starts low then goes high then slowly goes back low because it forms then falls as subsrate becomes depleated

Explain the velocity vs substrate concentration graph

Velocity speeds up as more concentration is added until it plateaus, at the beginning there is lots of free enzyme avaliable, then at intermediate concentration more enzyme is occupied but adding more substrate still increases velocity slowly, at the highest point most enzyme sites occipied, adding more substrate doesnt do anything

Explain the kenetic parameters

Vmax = maximum reaction velocity

Km = substrate concentration at 1/2Vmax

Kd = equilibrium dissociation constant for binding (Kd = Kr/Kf)

Kcat = turnover rate

Kcat/Km = catalytic efficiency

What is the linear graph formula

1/V = Km/(Vmax[S]) + 1/Vmax

X - int is -1/Km

Y-Int is 1/Vmax

Slope is Km/Vmax

What is competitive inhibition

Inhibitor competes with substrate for the active site, prevents substrate fromo binding

What happens to the reaction when there is competitive inhibition

Substrate cannot bind, but increasing substrate concentration can overcome inhibition. Instead of an ES being created an EI is create with Ki being rate of binding.

Vmax remains unchanged, so 1/2Vmax remains unchanged

Km increases because you need more substrate to reach Vmax, so x-intercept moves towards 0

Slope increases

What is noncompetitive inhibition

Inhibitor binds at site different from active site, substrate can still bind to the active site, inhibitor reduces catalytic activity

What happens to the reaction when there is noncompetitive inhibition

Inhibitor can bind to E or ES, to create either EI or ESI, more substrate does not solve this.

Vmax decreases so y intercept increases

Km remains unchanged so x intercept is unchanged

slope increases

What is uncompetitive inhibition

Inhibitor binds only to ES complex, to create ESI complex, prevents or reduces product formation

What happens to the reaction with uncompetitive inhibition

Vmax decreases so y intercept increases

Km decreases so x intercept becomes more negative

Lines and slope is parallel

What are irreversible inhibitors and example

Inhibitors where if you remove it the damage is not restored. A covalent bond is often formed with enzyme, can modify residues that are important for enzyme function. Some are mechanism based (suicide) inhibitors.

Penicillin is an example, the enzyme and penecillin form a covalent bond so penicillin goes from a closed ring to an open ring and a ester bond is formed between the two so the OH can no longer act as a catalyst

Receptors and Ligand binding

Ligands bind to specific sites on receptors, binding can change receptor conformation and activity. Ligand binding allows for an intracellular signalling protein to bind. When the messanger binds to the receptor the receptor changes shape which can allow a protein to bind, or another option is it creates an active site when the shape changes which allows a reaction to be catalyzed intracellularly

Overall the shape change can cause messages to be sent, proteins to bind, or reactions to be catalyzed

What are agonists and example

They activate receptors when bound to them, many bind at the same site as a natural messanger

Asthma drugs are adrenaline agonists, adrenaline receptors in lungs stimulate bronchial opening when activated, The drug shares similar structural features as the adrenaline, so it can react with receptors in a way that mimics aspects of the natural messanger

What are allosteric agonists and example

Agonists that bind to Sites differently from the original messagers site.

Benzodiazepines are allosteric modulators. GABA is the natural messanger and still binds and activates the receptor, but benzodiazepines bind at a different site and enhance the effect of GABA

What are Antagonists and example

They bind to the receptors but do not activate them, they reduce or prevent activation. Many bind at the same site as natural messanger, but can also bind at different sites.

Cimetidine is a receptor antagonist. Histamine is the natural messanger which activates the receptor and promotes stomach acid secretion. Cimetidine binds to the receptor but does not activate it so reducses stomach acid.

Allosteric antagonists

These are antagonists that bind to a different site than the normal messanger, so it reduces the receptorrs response to the messanger but do not directionly compete for the same binding site. May block the binding site (umbrella affect)

What are partial agonists and example

They bind and activate the receptor but produce a smaller maximum response than a full agonist, have a lower efficacy, and can reduct the effect of a full agonist when both are present.

Buprenorphine is a partial agonist of opioid receptor, it binds strongly to the receptor and activatets it but with lower efficacy than full agonists, can reduce the effects of full opiod agonists and is used in the treatment of opioid use disorder.

Inverse agonists

Some receptors have background activity which is activity even in the absence of a messanger, the inverse agonists reduce this background activity. It produces the opposite effect of an agonist

Summary of all receptor ligands

Agonist - Increases activity to a full 100% capacity

Partial agonist - Increases an effect of small capacity

Antagonist - Causes zero affect

Inverse agonist - Lowers the effect if there is any already