Lecture 11: Enzymes II- Catalysis Flashcards

1
Q

What do enzymes do?

A
  1. Lower activation rate

2. Stabilize the transition state

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2
Q

What DON’T enzymes do?

A
  1. Change the Delta G (Enthalpy/Free energy) of the reaction

2. Irreversibly change shape

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3
Q

Catalyst

A

Increases rate (speed) of a reaction, but does not undergo any permanent chemical change as a result

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4
Q

How do we speed up reaction/ overcome ACTIVATION BARRIER?

A
  1. Increased the energy of all molecules by increasing the temp (however proteins can be denatured)
  2. Lower the energy barrier by DECREASING the energy of the transition state**
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5
Q

Induced Fit Model

A

When substrate binds, the enzyme changes shape so that the substrate is forced into the transition state

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6
Q

How is catalysis achieved?

A
  1. Substrate orientation
  2. Straining substrate bonds
  3. Creating a favorable microenvironment
  4. Covalent and/or non-covalent interactions between enzyme and substrate
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7
Q

Catalysis Strategy #1- Covalent Catalysis

A

Enzyme covalently binds to the transition state (electrons transfer)

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8
Q

Catalysis Strategy #2- Acid-Base Catalysis

A

Partial proton transfer to the substrate

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9
Q

Catalysis Strategy #3- Approximation

A

For e/p’s to be exchanged, they must be in proper spatial orientation and close contact (proximity) for the reactant molecules must occur
–> If molecules held together in proper orientation, they are likely to interact = CALLED ENTROPY REDUCTION

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10
Q

If entropy (S) increases then

A

G (energy) increases always!

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11
Q

Catalysis Strategy #4- Electrostatic Catalysis

A

Stabilization of unfavorable changes on the transition state by polarizable side chains in the enzyme and/or metal ions

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12
Q

**Active site for Serine Proteases/Chymotrypsin

A

Catalytic triad and oxyanion hole

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13
Q

**Active site for Carbonic Anyhdrases

A

3 His + Zn++ - OH

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14
Q

**Specificity for Serine Proteases/Chymotrypsin

A

Hydrophobic specificity pocket

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15
Q

**Specificity for Carbonic Anhydrases

A

(Size of entryway)

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16
Q

Why do we need proteases?

A

Recycling
Regulation (remove from circulation)
Defense (chew it up)

17
Q

At the active site of Chymotrypsin (called catalytic triad)

A

Serine= nucleophile
Histidine=a base (proton acceptor)
Aspartic Acid= an acid (proton donor)

18
Q

Papain (human cysteine proteases)

A

Calpains and caspases
(Require Ca2+ as cofactor, apoptosis, split active site residues over a heterodimer)
-Found in Euks, Eubacteria, but not Archea

19
Q

HIV Protease

A

Aspartyl protease;

  • Cleave precursor proteins
  • Homodimer with 1 active site Asp per subunit
20
Q

Example of HIV protease

A

Renin;

Secreted by kidneys, helps increase BP and retain water/salt

21
Q

Cysteine proteases

A

Papain and caspases

22
Q

Aspartyl proteases

A

HIV protease and renin

23
Q

Metalloproteases

A

Thermolysin, MMP’s, ADH

24
Q

Thermolysin

A
  • Active site is His-His-Glu with Zn and another Glu holds H2o
  • Secreted from Gram bacteria
25
MMP's
- Active site is His-His-Glu | - Degrade the extracellular matrix
26
ADH
-Active site is His-Cys-Cys-H20 -In the liver, ADH uses NAD+ to convert alcohols to acetylaldehyde Note: NAD+ resides in the active site of ADH
27
Oxyanion hole
Stabilizes the tetrahedral intermediate (transition state) - Serine - Glycine * *Note: interactions with amides in backbone, not side chains!
28
Specificity (S1) pocket
Determines placement of cut
29
Physiological relevance of why we use Carbonic Anhydrases (CA)?
- pH regulation (more CO2, more acidic) | - Enzyme pathway regulation
30
Med and industrial application of CA?
Artificial lungs; CO2 scrubbers to decrease greenhouse gas emissions --> Plants use CA for carbonic fixation
31
Active site of CA?
Contains a Zn++ ion (Coordinated to 3 Histidines and a water) --> similar to metalloproteases
32
What type of evolution are CA?
CONVERGENT evolution- due to similar active site, however everything else is different (Humans produce more than 15 splice variations)
33
In CA what facilitates the transition state?
H2O; - Deprotonated - Catalytic strategy of Approximation (oriented properly)
34
Entry channel of CA's determine
Size of substrate
35
Reaction Mechanism for CA
1. Water binds to Zn++, lowering its pKa. @ phys pH, water loses a proton (deprotonated) 2. Catalytic strategy of approximation* as substrate enters an activation site 3. Nucleophilic addition (adds functional group to CO2) 4. Release of product and regeneration of enzyme (histidine proton shuttle)