Chapter 8: Enzymes Flashcards
what is an enzyme?
a catalytic molecule (protein or sometimes, RNA)
what is activation energy?
energy needed to get from starting state to transition state of a rxn
what is happening to a rxn when delta G = 0?
rxn is at equiilibrium
what does it mean to have a rxn with a negative delta G?
rxn is spontaneous
what does it mean to have a rxn with a POSITIVE delta G?
rxn NOT spontaneous
what 2 things to enzymes do?
- creates alternative pathways for rxns that have lower net activation energy
- makes rxns occur faster (by decreasing delta G double dagger)
do enzymes change rxn equilibrium?
no. they just change how fast the rxn achieves equilibrium
what is an RNA based enzyme called?
ribozyme
what are ribozymes made of?
RNA or RNA:protein complexes
what are 3 factors (other than enzymes) that can impact the rate of a rxn?
changes in:
temperature
pH
pressure
can a catalyzing enzyme change during a rxn?
yes but it must get changed back to its original state before the rxn ends
How much can an enzyme increase a rxn’s speed?
it can make the rxn 10 million to 10 million, million times faster
when did Dr. Shimko first mention ester linkages without explaining what those were?
chpt 8 part 1, 9 mins in
what does the term ‘ester linkage’ describe?
the bond connecting an ester’s carbonyl carbon to its OR group
in what macromolecule are ester bonds/linkages found?
lipids
are enzymes still impacted by allosteric regulators and enzyme concentration?
Yes
why did Dr Shimko show us carbonic anhydrase?
to show us how the carbonic anhydrase speeds up a bicarbonate rxn from 1 every 5 seconds to 1 million per second
video chpt 8 part 1, 11:32
why did Dr Shimko show us chymotrypsin?
to show us how the chymotrypsin speeds up a rxn to cleave amide bonds (in amino acid chains) by breaking the bonds without the need to boil them in 6M HCl for extended periods
Uncatalyzed- 1 rxn every 20 years
Catalyzed- 90 rxns per second
video chpt 8 part 1, 11:32
do enzymes still have specificity and affinity?
yes
what does it mean to say that an enzyme is permissive?
it’s not selective
is alcohol dehydrogenase still an example of selective enzyme?
yes. it will bind to ethanol, methanol, or isopropanol but prefers ethanol
are digestive enzymes examples of selective or permissive enzymes?
permissive
are transition states inherently stable or unstable?
unstable
what is a ‘nonproductive rxn’?
a rxn that achieves a transition state but reverts to substrates instead of products
are transition state UNfavorable (high energy) or favorable (low energy)?
UNfavorable
what does the delta G double dagger symbol (transition state) mean on the energy diagram?
the change in energy from substrates to the transition state
what does the delta G_rxn mean on a energy diagram?
the NET change in energy from substrates to products
what is the delta G double dagger (transition state) the same as/also called?
activation energy
do large activation energies result is fast rxns or slow?
slow
the bigger the Ea, the slower the rxn
if a forward equilibrium is unfavorable/non spontaneous, what do you know about the REVERSE rxn?
the reverse rxn is spontaneous
what two components comprise gibbs free energy
enthalpy and delta entropy (of the entire system)
can a catalyzed rxn be faster even if it involves multiple steps/transition states?
yes
In a catalyzed rxn with multiple steps, which step is the rate determining step?
The step with the larges hump/activation energy
Do catalytic enzymes form ES complexes in order to speed up rxns?
Yes
what does the ‘S’ on an energy diagram represent?
starting materials or substrate
what does the ‘P’ on an energy diagram represent?
products
How can water/solvation impact activation energy for an enzyme and a ligand?
If there is water between the binding site and the ligand, energy must be used to move it out of the way before the enzyme and the ligand can bond
What are the 5 means by which enzymes induce rxn rate enhancements according to Dr. Shimko?
- proximity, orientation, or entropy reduction
- Transition state stabilization (preferential binding of the transition state
- acid-base catalysis
- covalent catalysis
- metal ion catalysis
what is ‘preferential binding of the transition state’ also called?
transition state stabilization
What is ‘transition state stabilization’ also called?
preferential binding of the transition state
In the context of rate enhancement types, what do proximity, orientation, entropy reduction and preferential binding all involve?
Weak but favorable binding energy between the enzymes and substrate; Shimko calls this behavior ‘passive’
What did Shimko say was common across acid-base catalysis, covalent catalysis, and metal ion catalysis?
they all involve enzymes that actively engage in interactions with specific catalytic groups
Shimko calls this behavior ‘active’
How do enzymes exploit ‘proximity’ in order to execute rxn enhancement work?
they are shaped such that they can physically bring multiple substrates together in physical space to enable them to interact with each other
like when one person gives two people a hug at the same time; everyone ends up touching each other.
How do enzymes exploit ‘orientation’ in order to execute rxn enhancement?
they are shaped such that they can physically bring multiple substrates together in physical space, AND orient them in the necessary orientation/alignment to enable them to interact with each other
How do enzymes exploit ‘entropy reduction’ in order to execute rxn enhancement?
they are able to hold substrates still in the proper orientation/alignment long enough for them to interact in the desired manner
less free motion means less entropy
Why is the reduced entropy phenomenon tolerated by the system?
the reduced entropy is offset by the energetic favorability of the interactions between the substrates being held together.
How do enzymes exploit ‘preferential binding of the transition state’ in order to execute rxn enhancement?
they make the unstable transition state a little less unstable by making relatively favorable interactions with the transition state that it DOES NOT make with the substrate or the products
Why did Dr. Shimko tell us about stickase enzyme?
stickase is a fictional enzyme that demonstrates preferential interactions with the transition states through magnets and trying to break a metal rod into 2 pieces.
what does that transition state describe (conceptually)?
contortions of the molecule(s) that lead to chemical reactions
do enzymes that exploit ‘preferential binding of the transition state’ ever stick to other things (besides the transition state) by mistake?
Yes.
If another molecule looks enough like the desired transitions state, the enzyme will exhibit affinity to it instead of to the substrate or product (just like it does with regular transition states).
what is special about serine protease enzyme (in terms of its ability to execute preferential binding of the transition state)?
It has 2 extra H atoms (in its oxyion hole) between the enzyme and the transition state that are not found between the enzyme and substrates/intermediates, and that give the transition state increased stability
This gives 1 million fold rate enhancement for the enzyme
what is the advantage of using enzymes to change rxn rate (instead of altering temperature, pH, or pressure)?
Using enzymes allow the rxn’s rate to be altered with ‘specificity’.
It’s a more targeted approach than making a change that will impact all enzymes/ligands within the entire immediate environment
what is a transition state analog?
a molecule that resembles a transition state that a preferential enzyme is attracted to
when we make transition state analog (drugs), are they more attractive (to preferential enzymes) than natural transition states or less attractive?
The drugs will be more attractive if they have a smaller Kd value
why did Dr. Shimko show us proline isomerase?
It’s an example of a preferential enzyme that can get cat fished and inhibited by transition state analog (like drugs that we make)
what does proline isomerase do when it isn’t getting cat fished?
It converts L proline to D proline
what it is about the proline transition state that is so attractive to the proline isomerase enzyme?
the planarity of the functional group?
This is the same quality that attracts the proline isomerase to transition state analogs
what are the 2 transition state analogs that are used to cat fish the proline isomerase
Pyrrole-2-carboxylate
delta-1-Pyrroline-2-carboxylate
how does proline isomerase enzyme convert L-Proline to D-Proline?
H is removed from the C attached to the COO- carbon, and then H is replaced in a different stereochemistry.
Dashed H gets replaced by wedged H
What is a keto-enol tautomerism and why did Dr. Shimko show it to us
It’s an equilibrium between an enol and a ketone.
Dr. Shimko showed it to us bc it can be catalyzed by enzymes via acid-base catalysis
what is a tautomer (such as the tautomer described in the acid base catalysis of enol-ketone tautomers)?
structural isomers (constitutional isomers) of chemical compounds that readily interconvert.
How is the keto-enol tautomerism equilibrium impacted by acid-base catalysis?
acid and/or basic amino acids found on an enzyme’s surface can stabilize the otherwise high energy/unfavorable transition state
How does an enzyme with acidic amino acids stabilize the transition state for the keto-enol tautomerism equilibrium?
The entire acidic amino acid gets nucleophilic attacked (kidnapped) by the ketone and the resulting bond between the two stabilizes the transition state.
How does an enzyme with BASIC amino acids stabilize the transition state for the keto-enol tautomerism equilibrium?
The basic amino acid nucleophilic attacks a H on the ketone, creating a carbanion with partial charge that stabilizes the transition state???????
what is an enol (such as the tautomer described in the acid base catalysis of enol-ketone tautomers)?
an alkene with a hydroxyl group on it
Do amino acids (on catalytic enzyme surfaces) serve as acids AND bases in acid base catalysis?
Yes! They have to be able to perform both roles in order to ensure that the catalyzing enzyme is restored to its original state at the end of the rxn
How might an amino acid (on catalytic enzyme surfaces) behave both as an acid AND as a base?
It might start as a base and attack an H2O molecule/become an acid, so the remaining OH becomes a good nucleophile for creating a transition state.
Later, it can have it’s H nucleophilic attacked away (to stabilize the products) and return to a basic state.
Which amino acids make for good acids/bases during acid base catalysis?
The one’s whose R groups have pkas
Why is acid base catalysis most likely to occur when the pH = the amino acid’s pka?
this indicates that both the protonated and deprotonated versions are equally favorable, which you need in order to ensure that the amino acid can act both as an acid and a base/be able to be restored to its original state at the end of the rxn)
What does ‘acid base catalysis’ describe?
when a chemical reaction is sped up by the addition of an acidic or basic catalyst that donates or accepts protons in order to stabilize developing charges in the transition state.
This typically has the effect of activating nucleophile and electrophile groups, or stabilizing leaving groups.
what is a catalytic cycle?
a multistep reaction mechanism that involves a catalyst.
what is hydrolysis?
the chemical breakdown of a compound due to reaction with water.
What does ‘covalent catalysis’ describe?
enzyme amino acids temporarily make covalent bonds with a substrate
what is covalent catalysis also called?
nucleophilic catalysis
electrophilic catalysis
do covalent bonds (between enzyme’s amino acids and substrates) stay bound throughout the entire rxn?
No. They break apart again once/when/as the transition state transforms into the product
what is decarboxylation?
a chemical reaction that removes a carboxyl (COOH) group and releases carbon dioxide.
why did Dr. Shimko show us the decarboxylation of acetoacetate?
to show us how covalent catalysis can speed up a rxn (that is normally high energy, relatively non-spontaneous) by creating an alternative, Schiff base/imine transition state that has lower activation energy
what is an electron sink?
a source of electrons
a group that can pull electrons from a reactive centre and thus stabilize an electron-deficient intermediate or transition state
what does it mean to ‘change the electronics’ of a transition state?
???
what is an imine?
a carbonyl like structure that has a N where the O would normally be
when Dr. Shimko showed us the decarboxylation of acetoacetate (in order to demonstrate covalent catalysis with a Schiff Base/imine), how was the Schiff base created?
Schiff base was created from the carbonyl, through the loss of water
when you make a Schiff Base/imine (in order to speed up a rxn like the decarboxylation of acetoacetate), is the Schiff Base/imine creation reversible?
In other words, can you un-make a Schiff base?
yes. Dr. Shimko says that formation of the Schiff base is reversible.
it is specifically reversible in the aqueous environment; but NOT reversible in the organic environment.
How does covalent catalysis speed up the acetoacetate decarboxylation rxn that Dr. Shimko showed us?
It presents an alternative intermediate (Schiff Base/imine) that has more steps but lower activation energy than the rxn’s original/uncatalyzed intermediate (oxyanion/enolate)
what type of attack most commonly results in the covalent bonds involved in covalent catalysis?
a nucleophilic attack on an electrophile (usually a carbonyl)
what are 2 electrophiles that are commonly involved/attacked in covalent catalysis?
carbonyls and imines
What product do you get after a decarboxylation of acetoacetate?
acetone
what is a cofactor?
A non-chemical components that an enzyme needs in order to become catalytic
does the term ‘metal ion catalysis’ describe one specific thing or is it an umbrella term for a bunch of things?
an umbrella of things that are similar because they all involve metal ions
do catalysts in metal ion catalyst need to be restored to their original state at/by the end of the rxn?
yes! in these way, metal ion catalysts are just like any other catalyst; they cannot be permanently changed or consumed by the rxn
what are 4 major ways metal ions can participate in/contribute to catalysis?
- they can bind to substrates to hold them in the correct orientation (proximity)
- they can bind to/stabilize rxn transition states
- they can serve as electron sinks (sources) for redox steps that catalyze rxns
- they can offset the impact of negative charges on a structure, making it more stable for catalysis
why did Dr. Shimko tell us about how positively charged metal ions can surround negatively charged phosphodiester backbones in DNA and RNA?
b/c this was an example of how metal ions can offset the impact of negative charges on a structure, making it more stable for catalysis
what is electrostatic stabilization?
when one structure can offset the impact of charges on another structure, making it more stable for catalysis
what is so special about the ‘metallic’ bonds that metal ions can make?
they have both covalent and ionic character
what does it mean to say that a metal ion is coordinated?
that the metal is a central atom surrounded by bonds to other things
what does it mean to say that a metal ion is ‘coordinated to’ water molecules?
it means the metal ion is in the center of the structure and is surrounded by bonds to water molecules
how does coordinating a metal ion to water impact catalysis?
when a metal ion coordinates a water molecule, the structure exists in equilibrium where one version contains neutral H2O and the other version contains -OH, which is much more nucleophilic for doing the nucleophilic attacks (on the substrate) that catalyze rxns
why did Dr. Shimko show us the carbonic anhydrase enzyme?
it’s an exp of an enzyme that uses metal ion catalysis
how does carbonic anhydrase use metal ion catalysis to catalyze the conversion of CO2 to HCO3- in the blood buffering system?
a Zn2+ coordinates to 3 Histidines and a water, and the water, being in its nucleophilic state attacks/forces a bond with the CO2 to create HCO3-
The HCO3- is freed from the complex and the catalytic water is restored to normal water when a free H2O molecule comes, replaces the OH is the enzyme, and causes the HCO3- to be released
what is ‘catalytic’ water?
water in it’s activated/nucleophilic state (as you see when water is ‘coordinated’ to metal ion
How does a catalytic water molecule get restored to its original state after carbonic anhydrase uses it for turning CO2 into HCO3-?
the H2O that broke it’s bond to the CO2 replaces it
see pics on Notablity slides
Where (within the carbonic anhydrase) do the metal ion live?
deep down within a binding site pocket
How do the carbonic anhydrase’s metal ion reach the CO2 substrate when they’re all the way deep down inside the enzyme?
a chain of deprotonations propagates across a series of H2O molecules until one of them, in their deprotonated/activated/catalytic state is close enough to a CO2 to nuke attack it.
How does carbonic anhydrase sustain the chain of deprotonations needed in order for the catalytic water at the end of the line to do its nucleophilic attack?
a deprotonated His 64 (bound to one of the Zn’s coordinated His) binds to the H+, causing the His 64 to change conformation to face the bulk sovlent. Once here, the His 64’s pka changes, causing it to release the H+ and return to it’s original conformation
which 2 (or 4) amino acids are ideal for executing acid base catalysis at physiological pH?
His
Cys
Sometimes Ser and Thr (because even their pkas aren’t technically close to physiological pH, they can adopt a pka closer to physiological pH under certain conditions)
why are His and Cys particularly good at doing acid base catalysis?
Their pkas are pretty close to physiological pH
At what pH value will acid base catalyses most likely occur?
at the pH = the pka of the acid/base
If you have multiple acids/bases in your acid base catalysis, at what pH value will acid base catalyses most likely occur?
at the pH = the the average of all the pkas for the acids/bases
does covalent catalysis generally stabilize existing transition states or introduce alternative transition states?
this generally involves the introduction of an alternative rxn pathway/alternative transition state
What does ‘metal ion catalysis’ describe?
When an enzymes’ active site has a metal ion that can coordinate to and activate a water molecule, which then go on to execute a nucleophilic attack on the substrate.
when enzymes (amino acids) have charges that can temporarily attract substrates
