Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

Enzymes & Metabolism > 5-6: ENZYME MECHANISMS > Flashcards

5-6: ENZYME MECHANISMS Flashcards

1
Q

bronsted acid and bases

A

BA: species that donates H+; HA is acid; A- is conj. base

BB: species that accepts H+; B is base; BH+ is conj. acid

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

why do acids and bases catalyse reactions?

A
  • if the acid/base can interact w/ the molecule during the TS they can help neutralise charges that develop during bond breakage because they can deliver or abstract protons
  • this results in reducing gibbs free energy of activation
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

general acid catalysis

A

process whose rate of reaction is dependent on the concentration of all acids present in the reaction, not just the concentration of protons

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

general base catalysis

A

process whose rate is dependent on concentration of all bases present in reaction, not just concentration of hydroxide

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

specific acid catalysis

A

reaction just dependent on concentration of protons not any added acid

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

specific base

A

reaction dependent on concentration of hydroxide ions, not any added base

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

general acid-base catalysis

e.g. keto-enol tautomerisation

A

UNCATALYSED: in the transition state, the molecule separates charge through breakage of C-H bond; this is disfavored because opposite charges are building up; this makes overall uncatalysed reaction slow
GENERAL ACID CAT: add HA which reduces energy of TS by delivering a proton to the O as its accumulating charge; this enhances rate of reaction
GENERAL BASE CAT: add B which starts to pull of proton which reduces energy level of TS as it reduces degree of charge separation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

ph dependancy of acid-base catalysed reactions

A
  • enzyme shows activity dependent on the concentration of acid in the enzyme
  • can determine pka value: pH at which there is 50% activity
  • reversible inhibition: can increase pH to deprotonate and switch off the enzyme and then reacidify the assay to protonate the enzyme and activity comes back
  • pH optimum: need acid and base in right protonation state for enzyme to be active (B and HA)
  • pH profile of enzyme activity is bell shaped
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

effect of environment on pka values

A
  • enzymes control the pKa value of active site by manipulating the microenvironment
  • hydrophobic region; uncharged species favoured; pKa I
  • negative charge nearby; positive charge stabilised; pKa I
  • positive charge nearby; negative charge stabilised; pKa D because Ka I due to formation of conj. base will be enhanced because of stabilising effect of charge-charge interactions (e.g. glutamic acid and lysine in active site of enzyme)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

covalent catalysis definition

A
  • enzymes provide lower energy pathway by forming covalently bound enzyme intermediates that form from reaction of substrate with an amino-acid side chain or a co-enzyme
  • Asp, glu, his, cys, tyr, lys, ser, thr are potential nucleophiles; only reactive when deprotonated as they need LP of e
  • often E activate their Nu by providing a base close by that will pull off proton and free LP of e
  • in this mechanism, have E and in active site a Nu (ie. a side chain) to perform Nu attack on substrate to form a covalent bond and help catalysis
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

where is covalent catalysis used

A
  • in group transfer reactions

- to make the substrate more reactive

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

what are group transfer reactions

A
  • bisubstrate reactions where substrate A and substrate B come together in the active site and react
  • during course of reaction, groups are transferred
  • could be reactive group ie. amino group NH2 or acyl group R-C=O
  • sometimes unreactive group ie. phosphoryl PO3,2- (ATP is a carrier of this)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

group transfer reaction via ternary complex

A
  • binding substrates A and B into the active site to form ternary complex (E+A+B)
  • group is transferred there; product forms and is then released
  • could occur in ordered process or random binding and release
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

group transfer reaction via ping-pong mechanism

A
  • relies on covalent catalysis
  • ordered process
    1. binding of A in E with Nu and forms EA complex
  • nucleophilic reaction; group is transferred to side chain or co-enzyme
  • forms product P and modified enzyme F which now has group
  • product released; only have F
    2. second substrate comes into active site
  • forms FB complex
  • group is transferred to B to form Q
  • have EQ complex and then Q is released to reform E and can start catalysis again
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

making substrate more reactive in covalent catalysis

A
  • have E with Nu
  • nucleophilic attack on S
  • forms covalent bond and activated form of S, S*
  • can now form P which is still covalently attached to E through amino acid side chain
  • bond breaks between Nu and P to release P and regenerate E
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

activating carbonyl compound

A
  • improve ketone reactivity by converting to schiff base (are analogous)
  • ketone + primary amine
  • addition elimination reaction where water is removed
  • more reactive because its a more polarised system
  • LP of e still available on N and can be protonated by general acid to generate protonated imine which is even more reactive
  • can draw resonance structure, +ve charge on C and neutral N or vice-versa; pi cloud is shifted towards nitrogen to make v. electrophilic C
17
Q

acetoacetate decarboxylase enzyme

A
  • produces acetone and carbon dioxide
  • catalyses bond breakage reaction

UNCAT:

  • usually formation of carbanion is disfavored because of high energy but now have carbonyl group which acts as e sink
  • electronegativity of O in carbonyl group affords some stability to the system because it likes accumulating some negative charge; this aids in breakage of C-C bond (move e into O)
  • end up with enolate anion which helps stabilise the formation of the carbanion through resonance stabilisiation
  • problem: still have -ve charge in the system

CAT:

  • lys (only aa with primary amine functionality) reacts w/carbonyl group to generate protonated schiff base (enamine) which is neutral and thus more stable so TS energy is lower as less charge is accumulating
  • better e sink
18
Q

how to detect formation of schiff base in an enzyme

A
  • chemical trapping of enzyme intermediates
  • treat with NaBH4 (sodium borohydride); a source of H-, a v. strong nucleophile and will react with protonated schiff base
  • N receives e and becomes neutral
  • unreactive so cannot go through catalytic cycle
  • stuck as modified form of lys side chain
  • then digest E and identify which lys residue has been modified and thus gain details of residue involved in covalent catalysis
19
Q

electrostatic catalysis definition

A

-prescence of charges and oriented dipoles within the active site can stabilise the transition state through solvation/electrostatic interaction (+ve with -ve)

20
Q

what affects electrostatic interaction

A
  • the greater the charge, the greater the energy of interaction
  • the further apart the charges, the lower the energy of interaction
  • polar molecules w/permanent dipole (e.g. water- high value of er), reduces the electrostatic interaction
  • coulombic interactions are more effective in non-polar environments
  • enzymes can fine-tune microenvironment to improve charge stabilisation because of the differences in dielectric constant of residues
21
Q

types of metal ion catalysis

A
  • two classes of metal ion requriing enzymes distinguishable by strength of binding:
    1. metalloenzymes contain tightly bound ions (eg. Fe2+, Mn2+) through dative/coordinate bonds; always present
    2. metal-activated enzymes loosely bind ions from the solution (e.g. Na+, K+); come in with S and help in catalysis then go out with S
22
Q

what are metal ions involved in

A

1) electrostatic stabilisation and charge screening; highly effective due to high charge that is pH independent e.g. Mg2+-ATP
2) redox reactions: lots of transition metals can be ox and red so are involved in transferring e in the cell (e transport pathways to oxidise NADH and convert proton motive force to generate ATP)
3) can act as lewis acids so can accept LP of e and can bind e donor in a dative/coordinate covalent bond; this determines the orientation of S so it reacts in most favourable geometry
4) promote nucleophilic catalysis by activating bound water molecules (e.g. Zn2+ ion in carbonic anhydrase); helps activate relatively inert molecules due to its charge

23
Q

Mg2+-ATP complex in metal ion catalysis

A
  • ATP usually at physiological pH carries 3-4 negative charges which can be big hindrance
  • ATP always used as a substrate in Mg-complex
  • Mg2+ associates w/ATP and goes into active site; it offsets some of the -ve charge of ATP to allow nucleophilic attack on it
24
Q

redox roles in metal ion catalysis

A
  • e.g Fe2S2 iron clusters

- dative bond to cysteine residues (2 e from cys are donated to Fe)

25
Q

metal ion catalysis reedox eg. Complex I (NADH: ubiquinone oxidoreductase)

A

-NADH is being oxidised; ubiquinone is being reduced
-enzyme found in mitochondrial membrane
-has large hydrophilic arm that sticks out
-UQ is v. hydrophobic; exists in membrane; comes into active site and is reduced to UQH2 (ubiquinol)
-UQ + 2e + 2H+ = UQH2
-NADH is e carrier/donor which goes into site in hydrophilic arm
-about 8 FeS clusters so e can hop through
-during this process, protons are pumped across the membrane
-

26
Q

metal ion catalysis redox e.g. Photosystem II

A
  • oxidises water to produce O2 + 4H+ + 4e with help of light
  • 4e used to fix CO2 for growth
  • the cluster is made of Mn4CaO5
  • multiple metal ion centres to accept e
27
Q

metal ion catalysis activating water e.g. carbonic anhydrase

A
  • OH- is v.good nucleophile but too little of it
  • to increase OH-, bind water to metal ion
  • CO2 + H2O = HCO3- + H+ involves Nu attack on CO2
  • in carbonic anhydrase enzyme, there is Zn2+ permanently bound into active site because it is ligated by 3 residues; has one empty position which is occupied by a water molecule and forms coordinate bond
  • Zn2+ and OH- there is a charge-charge interaction so there is now stabilisation and pKa could be as low as 7 so at physiological pH now have high accumulation of OH-
  • water pKa of 15-16 so mainly protonated form, v.little OH-
28
Q

catalysis through orientation and proximity effects definition

A
  • increase rate of reaction by taking 2 reactants out of solution and placing them next to each other in the active site of an enzyme thus raising the local concentration of each reactant
  • A and B need to be in right orientation so they can form bonds w/each other
29
Q

entropy changes in bimolecular reactions

A
  • uncatalysed: ^S large -ve value = highly unfavourable because are forcing order
  • catalysed: ^S smaller -ve or +ve = more disordered = more favourable due to binding in active site (split up reaction in 2 steps)
30
Q

preferential binding of transition state enzyme catalysis

A
  • E complementary to TS not S to maximise interaction and reduce gibbs free energy of interaction
  • much better than E-S complementarity
31
Q

how do enzymes catalyse reactions

A
  • uncatalysed reactions are slow because many molecules come together in TS (loss of entropy) and unstable +ve and -ve charges develop in the TS
  • enzymes function to provide strategically placed acids, bases, metal ions and dipoles to stabilise charges
  • provide alternative lower energy reaction pathways through covalent catalysis
  • reduce effect of entropy by incorporating catalytic groups as part of the enzyme

Enzymes & Metabolism (17 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions