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The Story of Catalysis
•Why Catalysis?•What is a Catalyst?•A Petrochemical Application•How Catalysts Work
Why Catalysis?
Need to make chemicals faster
Most Reactions are too slow to be useful...
What is a Catalyst?
Catalysts speed up a chemical reaction without being used up...
Catalyst + Reactants
Catalyst-Reactants
Catalyst + Products
The Nature of Enzyme Catalysis
●● Enzyme provides a catalytic surfaceEnzyme provides a catalytic surface
●● This surface stabilizes transition stateThis surface stabilizes transition state
●● Transformed transition state to productTransformed transition state to product
B
BA Catalytic surface
A
Juang RH (2004) BCbasics
Stickase
Substrate
If enzyme just binds substrate then there will be no further reaction
Transition state Product
Enzyme not only recognizes substrate, but also induces the formation of transition state
Adapted from Nelson & Cox (2000) Lehninger Principles of Biochemistry (3e) p.252
X
Examples of Reactions w/o Catalysis
Oxygen in theair mixes with iron to formrust
HydrogenPeroxideforms a chemicalreaction withyour body
1 week to several months
Plants & animals decompose to oil & coal
Millions of years
Seconds
Ways to Make Ways to Make Chemicals FasterChemicals Faster
Add other Chemicals Catalysts!!!!
Disadvantage--Too hot!
Disadvantage--Separate chemicals Disadvantage--Costly
Pressure
Disadvantage--Cause Explosions
Temperature
Enzyme Stabilizes Transition State
S
P
ES
EST
EP
ST
Reaction direction
Energy change
Energy required (no
catalysis)
Energy decreases (under
catalysis)
What’s the difference?T = Transition state
Adapted from Alberts et al (2002) Molecular Biology of the Cell (4e) p.166
Active Site Is a Deep Buried Pocket
Why energy required to reach transition stateis lower in the active site?
It is a magic pocket
(1) Stabilizes transition(2) Expels water(3) Reactive groups(4) Coenzyme helps
(2)
(3)(4)
(1)CoE
+
-
Juang RH (2004) BCbasics
Enzyme Active Site Is Deeper than Ab Binding
Instead, active site on enzymealso recognizes substrate, butactually complementally fits the transition state and stabilized it.
Ag binding site on Ab binds to Agcomplementally, no further reactionoccurs.
Adapted from Nelson & Cox (2000) Lehninger Principles of Biochemistry (3e) p.252
X
Active Site Avoids the Influence of Water
Preventing the influence of water sustains the formation of stable ionic bonds
Adapted from Alberts et al (2002) Molecular Biology of the Cell (4e) p.115
-+
Reaction RatesReaction Rates
0
1
2
3
4
5
6
7
8
9
0 2 4 6 8 10 12 14
Time
En
erg
y
Without Catalyst
With Catalyst
Cyclar...An Example of A Catalytic
Process
2 ( C - C - C ) + Catalyst + Catalyst
Propane Benzene
• Propane is unreactive• Benzene is in higher demand than propane
How Does Cyclar Work?
Surface Area!!
Catalysts are not solid Catalysts are porous
What Does Surface Area Do?
Increases the amount of available reaction sites
2 propanes
Reactive Sites
Benzene Benzene product
Do Catalysts Live Forever?
NO!!!Catalysts can last from 2 hours to 2 years
They can die from:--poisons which contaminate the catalyst--large molecules which cover the catalyst --over heating, over pressurizing--crumbling/crushed
Conclusions
Catalysts are reusable Catalysts help increase reaction rates
Catalysts work using surface area
Who Uses Catalyst?Who Uses Catalyst?
Oil Industries
Your body (Enzymes)
Chemical/Pharmaceutical Companies
Catalytic Converters in your car
Examples of Reactions w/Catalysts
C - C - C +
Propane + Catalyst = Benzene + Catalyst
= +
+ =ProteinsFatsSimple Sugars
+
Food + Enzymes = Small Molecules + Enzymes
Examples of Catalysis
Basic substances like ashes catalyze the burning of sugar
A non-reactive substance like water turns reactive when mixed with catalyst
What Makes a Catalyst Work?
Surface Area!!!!
Steel Wool has a large surface area, so it oxidizes easily
Enzyme Inhibition (Mechanism)
I
I
S
S
S I
I
I II
S
Competitive Non-competitive Uncompetitive
EE
Different siteCompete for
active siteInhibitor
Substrate
Ca
rtoo
n G
uid
eEq
uatio
n an
d De
scrip
tion
[II] binds to free [E] only,and competes with [S];increasing [S] overcomesInhibition by [II].
[II] binds to free [E] or [ES] complex; Increasing [S] cannot overcome [II] inhibition.
[II] binds to [ES] complex only, increasing [S] favorsthe inhibition by [II].
E + S → ES → E + P + II↓EII
←
↑
E + S → ES → E + P + + II II↓ ↓EII + S →EIIS
←
↑ ↑
E + S → ES → E + P + II ↓ EIIS
←
↑
EI
S X
Juang RH (2004) BCbasics
Km
Enzyme Inhibition (Plots)
I II Competitive Non-competitive Uncompetitive
Dir
ect
Plo
tsD
ou
ble
Rec
ipro
cal
Vmax Vmax
Km Km’ [S], mM
vo
[S], mM
vo
II II
Km [S], mM
Vmax
II
Km’
Vmax’Vmax’
Vmax unchangedKm increased
Vmax decreasedKm unchanged
Both Vmax & Km decreased
II
1/[S]1/Km
1/vo
1/ Vmax
II
Two parallellines
II
Intersect at X axis
1/vo
1/ Vmax
1/[S]1/Km 1/[S]1/Km
1/ Vmax
1/vo
Intersect at Y axis
= Km’
Juang RH (2004) BCbasics
Competitive Inhibition
Succinate Glutarate Malonate Oxalate
Succinate Dehydrogenase
Substrate Competitive InhibitorProduct
Adapted from Kleinsmith & Kish (1995) Principles of Cell and Molecular Biology (2e) p.49
C-OO-
C-H C-H C-OO-
C-OO-
H-C-H H-C-H C-OO-
C-OO-
H-C-H H-C-H H-C-H C-OO-
C-OO-
C-OO-
C-OO-
H-C-H C-OO-
Sulfa Drug Is Competitive Inhibitor
-COOHH2N-
-SONH2H2N-
PrecursorFolicacid
Tetrahydro-folic acid
SulfanilamideSulfa drug (anti-inflammation)
Para-aminobenzoic acid (PABA)
Bacteria needs PABA for the biosynthesis of folic acid
Sulfa drugs has similar structure with PABA, andinhibit bacteria growth.
Adapted from Bohinski (1987) Modern Concepts in Biochemistry (5e) p.197
Domagk (1939)
Enzyme Inhibitors Are Extensively Used
●● Sulfa drug (anti-inflammation)
Pseudo substrate Pseudo substrate competitive inhibitor
●● Protease inhibitorPlaques in brain contains protein inhibitor
● HIV protease is critical to life cycle of HIV
HIV proteaseHIV protease (homodimer):(homodimer):
↑inhibitor is used to treat AIDS Symmetry
Notsymmetry
→ Human aspartyl protease:(monodimer)
domain 1
Asp Asp
domain 2
subunit 2
Asp
subunit 1
Asp
Juang RH (2004) BCbasics
Alzheimer's disease
HIV protease vs Aspartyl protease
Asymmetric monomer
↓ HIV protease HIV protease (homodimer)
HIV Protease inhibitor is used in treating AIDS
Symmetricdimer
Asp
subunit 2
↑Aspartyl protease (monomer)
subunit 1
Asp
domain 1 domain 2
Asp Asp
Juang RH (2004) BCbasics
O ON–C–C–N–C–C N–C–C–N–C–C R H R’
Chymotrypsin Has A Site for Specificity
O -
CSer
Active SiteActive Site
SpecificitySite
SpecificitySite Catalytic Site
Juang RH (2004) BCbasics
Specificity of Ser-Protease Family
COO-
CAsp
COO-
CAsp
Active Site
Trypsin Chymotrypsin Elastasecut at Lys, Arg cut at Trp, Phe, Tyr cut at Ala, Gly
Non-polarpocket
De
ep
and
neg
ativ
ely
cha
rged
poc
ket
Shallow andnon-polar
O O–C–N–C–C–N– C C C C NH3+
O O–C–N–C–C–N– C
O O–C–N–C–C–N–
CH3
Jua
ng
RH
(2
00
4)
BC
ba
sics
Stereo Specificity
BC
DBC
DBC
D
These two triangles are not identical
A
The tetrahedral structure of carbon orbital has rigid steric strain which makes the basic building unit of protein conformation
Juang RH (2004) BCbasics
sp3
Enzyme surface
Control Points of Gene Regulation
Prokaryotics
DNA
ribosomemRNA
proteins
Post-translationalcontrol Eukaryotics
proteins
cap5’ 3’
tail
mature mRNA
DNA
5’3’process
mRNA
Juang RH (2004) BCbasics
Translation
Activity
Proteolysis
Transcription
RNA ProcessingRNA Transport
RNA Degradation
xRegulatory
subunit
o
Regulation of Enzyme Activity
o xS I
x oS
Sx
S
oS
AA
Po R xR
+
III
or
inhibitor
proteolysis
phosphorylation
cAMP orcalmodulin
or
regulatoreffector
P
(-)
(+)
Inhibitor Proteolysis
Phosophorylation
Signal transduction
Feedback regulation
Jua
ng
RH
(2
00
4)
BC
ba
sics
Cascade Amplification of Signals
Cascade
nS nP1 Enzyme
Juang RH (2004) BCbasics
How
to S
epara
te T
hese
Ob
jects
1 2 3
9 10 11 12
6
4 85
7
4
5
8
wood stone cotton wood wood cotton stone wood stone cotton stone cotton
cotton
wood
stone
ShapeSizeDensity
Shape
Density
Size
Sieving different sizes Different sedimentationDifferent rolling speed
4 6 7 85
1 3 4 6 7 8 9 10 11 122 5
Juang RH (2004) BCbasics
Basic Principles of Protein Purification
Ammonium sulfate fractionation
Cell OrganelleHomogenization
MacromoleculeNucleic
acid Carbohydrate (Lipid)
Size Charge Polarity Affinity
Small molecule Cell DebrisProtein
Amino acid, Sugar,
Nucleotides, etc
Gel filtration,SDS-PAGE,Ultrafiltration
Ion exchange,Chromatofocusing,
Disc-PAGE,Isoelectric focusing
Reverse phasechromatography,
HIC,Salting-out
Affinitychromatography,Hydroxyapatite
Juang RH (2004) BCbasics