University of Prince Edward Island

1
H Biochemistr y
6 7
C N O
8
Barr y Linkletter
15 16
P S

Enzyme Catalysis
Chemistry in Action
A catalyst is a molecule that participates in a reaction but is not consumed or
is regenerated during that reaction. A catalyst will provide a faster route to
product.
Enzymes are complex protein molecules that catalyze specific reactions. They
usually are very specific in the reactants that they associate with and so the
reaction is only accelerated for the specific substrates for the given enzyme.
Only the reactions that are catalyzed by enzymes matter in biochemistry – the
others will be too slow. Thus the genetic code controls our living chemistry by
coding for the enzymes that accelerate the chemical reactions of biology.

* This presentation is intended to supplement the assigned textbook reading. No lecture presentation can replace the essential textbook readings. In this presentation I may sometimes
highlight information that is not contained in the textbook. It is my intention to excite curiosity and inspire research questions. In the end though, only the textbook readings and assigned
questions need be considered as you prepare for the exams.
The One-Pager
Outline
∆G*(uncat)
This presentation will introduce the idea of enzyme catalysis. We will
define catalysis and show the parallel between chemical catalysis and
enzyme catalysis (which is just a more complication version of chem-
ical catalysis). We will explore the chemical strategies that are em-
ployed in enzymes and consider the “lock and key” and “induced fit”
models for substrate binding and catalysis.

Learning Goals
After experiencing this presentation, completing the related textbook

Energy
reading and exercises, reviewing the relevant organic chemistry topics
and discussing the ideas with your peers you will...
∆G*(cat)
• Be able to define catalysis
• Understand the difference between equilibrium constant and
rate constant (destination and speed). S ∆G˚
• Have reviewed reaction kinetics and transition state theory and E•S
how catalysts can reduce the energy difference between the initial P
E•P
and transition states for a reaction.
Reaction Coordinate
• Can you describe the reaction kinetics of acid catalysis (pick
your favourite reaction)? Compare the reaction coordinate be-
tween the uncatalyzed and catalyzed mechanisms. Compare the
rate laws.
[ S ]t
v = Vmax
K M + [ S ]t
 N o m a tt
er how
o f 10 0 % lo n g m y
e b o tt le
o o s lo w s m e ll th e th a n o l s it s , I n e v
ti o n is s o sweet s e
cent of r
Catalysis T h is r e a c o b s e r v e it .
we neve
r e th e r .

In 1794, a British housewife named Elizabeth Fulhame was perform- k

ing experiments in oxidation and reduction and noted that water 2 EtOH Et 2O + H 2O
greatly accelerated the reactions. This is the first report of catalysis in 2
v = k [ EtOH ] Th is ra te co ns ta
the literature. Fulhame was no dilettante. Her work was discussed by nt mu st
be ex tr em ely sm
the great scientists of England and America. all

Forty years later, in 1833, Eilhard Mitscherlich investigated the syn- P o o r nu c le

o
p o o r le av in p hi le an d
thesis of diethyl ether from ethanol in sulphuric acid. He observed that g gr o up –
a us ef ul c no t
the acid was not being consumed in the reaction. In 1836, Berzelius o m b in at io n.
coined the term “catalyst” to describe this behaviour. But acid gives a diffe rent
poss ible reac tion that is
much , much , much fast er.

kobs
H 3C OH HO CH3 H3C O CH3 + H2O
H
A c id is us
ed
a m o r e r ea to m ak e +H Ka –H
c ti ve
in te r m ed ia
te ...
Poor nucleop hile
and good leaving k H
group. Hmmm, H3C OH2 HO CH3 H3C O CH3 + H2O
somethi ng might
e
just happen here.. ...a nd th en w
ge t th e ac id
ba ck .

EtOH + H + EtOH 2+
Ka
k
EtOH 2+ + EtOH Et 2OH + H 2O + H +
Th is ra te co ns ta
nt is lar ge k
en ou gh th at th e 2 Often the collection of
oc cu rs qu ick ly
re ac tio n v= H + [ EtOH ] constants is combined
Ka to make a single rate
constant, k obs .

Elizabeth Fulhame’s Eilhard Mitscherlich Jöns Jacob Berzelius Note: The above rate law assumes that k ⎡ +⎤
essay 1794-1863 1779-1848 the extent of protonatio n is small. If
kobs = H
we added a catalytic amount of acid
Ka ⎣ ⎦
then this is a reasonabl e assumptio n.
 H2O G f = 237.1 kJ mole

A Brief Review of Catalysis H3C OH HO CH3 H 3C O

H
CH3 H 3C O CH3 G f = 122.9 kJ mole

G f = 174.1 kJ mole We can

OH ca G f = 11.8 kJ mole
Consider the condensation of ethanol to make c h a n g e in lc u la te th e
diethyl ether. The reaction equilibrium favours the f o r th e free ene
r e a c ti o n rgy
gy d a ta ta b from
products when water concentration is small. But Ac tiv at ion en er le s .
you can boil ethanol all day and never see any fo r un ca ta lyz ed
ether...unless you use an acid catalyst. Boil ethanol re ac tio n.
s
in sulphuric acid and you will rapidly form ether. r e p r e se nt al δ−
T .S . st at e ne ut r HO
from
a c ha ng e ng
to a st r o e .

Relative Energy
Enzyme catalysis is often observed to work the m o le c ul e s
H
st r o ng b as H3 C
same way. We never observe the reaction occur a
ac id an d H
without catalysis. It is just too slow otherwise. In HO δ+
biochemistry we almost never observe a reaction c a ta ly st
T he a c id
a sm a lle r
in a pathway that is not catalyzed by an enzyme. CH3
r e su lt s in
e ne r g y .
Just like how ethanol will never turn into ether a c ti v a ti o n
δ+
without a catalyst. T.S . re pr es en ts H2O
ch ang e fr om a
str on g ac id to
H
H3 C
K eq is the a str on g ac id. H
same for HO δ+
Vale rius Cor dus is the firs t to both cases.
reco rd an ethe r
synt hesis from etha nol and oil of Progress of the Reaction
vitri ol (H 2 SO 4 ) CH3
in 1540 . Ram on Llull repo rted purif
ying etha nol in
its abso lute form 300 year s earli
er and may +H HO CH3 –H
have also synt hesiz ed ethe r. Jabir
ibn Hayy an, the H3 C OH H3C OH2 H3C O CH3 H 3C O CH3
fath er of true chem istry , inves
tigat ed the prop - H
ertie s of vitri ol 400 year s befo
re that and may H 2O
also have synt hesiz ed ethe r.
William Morton famously
demonstrated ether as an
anesthetic in 1846. He per-
formed a surgery in the
“ether dome” at Massachu-
setts General Hospital using
ether with great success.

Cr aw fo rd Lo
ng is
cr ed ite d w ith
us
it in his pr iva te ing
pr ac tic e se ve
ra l
Valerius Cordus Ramon Llull Jabir ibn Hayyan Crawford Long William T. G. Morton ye ar s ea rli er
.
1515-1544 1232-1315 721-815 1815-1878 1819-1868
 Catalysis in Action
Phosphate diester hydrolysis, the kind of reaction that cleaves DNA But, in the presence of an enzyme like a nuclease we will observe rapid
strands, is very, very, very slow. It’s so slow that DNA will break down by hydrolysis of the phosphate diester linkages. It is so much faster than any
other slow reactions that are faster than uncatalyzed phosphate hydrolysis. other possible reaction that it is effectively the only reaction observed.
Let us consider a fairly reactive phosphate diester. Hydrolysis is still very
slow. But in the presence of a copper catalyst, the reaction occurs quickly.

gy
Ac tiv at ion en er
fo r un ca ta lyz ed
re ac tio n. Ad dit ion of wa te
r re su lts
in mu ltip le ch ar
ge s. Th is is
Uncatalyzed a hig h en er gy int
er me dia te .
intermediate

O2N NO2 O O O2N

O O O O
Energy

...a nd on wa rd s
P OP O P
O O O OH
Intermediate to wa rd s th e OH2
NO2
with copper pr od uc ts H2 O O2N NO2
HO
Die st er oo o
Th is st ep is so ep s ar e
D ie s t e an d co pp er liv e Su bs eq ue nt st
r slo w; we wo n’t st ep
co mp lex se e ra pid . Th e fir st
lon g en ou gh to e th at de fin ed
fo rm . is th e on
mu ch pr od uc t
th e ra te .
The cata lyst resu lts
Progress of the Reaction in a smal ler activ ation
ener gy.

ga tiv e ...an d neu tra lize s the sec

ut ra liz es th e ne ond neg ativ e
Th e co pp er ne ph at e.. . cha rge tha t mus t for m.
ph os CuII
ch ar ge on th e
II
CuII Cu
CuII O2N
O2N NO2 O2N NO2 O O O O
O O O O O P O P
P P OH2 O OH
O O O O
NO2
To ta l O2 N NO2 To ta l
ch ar ge H2O ch ar ge
is +1 is +1 HO
ge ar ou nd th e
Th e to ta l ch ar e
ph at e do es no t ch an ge . Th
ph os ine s th e ra te of
de te rm
st ep th at w.
mu ch ea sie r no
th is re ac tio n is
 k
Catalysis and Reaction Kinetics S P
The presence of a catalyst results in a new reaction pathway that has a
lower energy of activation and is therefore faster. The reaction mecha- RO
OR RO OR RO OR
nism may remain fundamentally the same but with a lower energy interme- H2O P O H2O P O
δ− H2O P O
diate or transition state. Or the mechanism may follow an entirely different O δ+
O O
path made possible by a reaction involving the catalyst. In the current exam-
ple, the copper stabilizes the intermediate. This lowers the energy of the
related transition state and greatly increases the speed of the reaction. Th is pa th wa y
is to o slo w to
The copper and the diester must first form a complex. We could imagine ma tt er
that there is an equilibrium between the complexed and uncomplexed re-
actant. Only the reactant complexed with copper will proceed to product
in the time frame of our experiment.

Energy
This is the path way
resp onsib le for the
in an d Ch ap ma n
In 191 3 Bo de ns te s obse rved rate of
em at ica l me th od
de ve lop ed ma th et ics of
this reac tion.
zin g th e kin
fo r an aly
p re ac tio ns .
co mp lex mu ltis te

Progress of the Reaction

OR OR RO OR RO OR
RO RO
H 2O P O H2O P O H2O P O H2O P O
O O δ+
O O
CuII CuII CuII
CuII

kcat
S + Cu S-Cu P + Cu
KD

Max Bodenstein David L. Chapman

1871-1942 1869-1958
d ou t
Ch ap ma n st ar te Don’ t laugh . Gigg lesw ick Scho ol Th is co ur se no w
ha s
ien ce te ac he r is a of
as a sc
Sc ho ol pres tigio us boar ding scho ol that jus t on e de gr ee
at Gi gg les wi ck date s back to 1499 . Anth ony Dani se pa ra tio n fr om
St ar
in En gla nd . els
is just one of its fam ous alum ni. Wa rs !

Anthony Daniels
b. 1946
 Interesting Kinetics
A reaction like phosphate diester hydrolysis is a first order reaction. (Wa- catalyzed case. But what sort of reaction kinetics will we observe? Will
ter is one of the reactants but it is also the solvent and it’s concentration we see the concentration of catalyst in the rate law - it’s concentration
does not change - you can’t double the concentration of water in water). is not changing, after all?
The association with the catalyst in biochemistry is usually reversible. In our It seems that there is a limit to catalysis. Catalysts are usually present in
example, there will be an equilibrium population of catalyst-substrate com- small amounts and, once all of the catalyst is in a complex with the reac-
plex. This complex will proceed toward product much faster than the un- tant, we can’t get any faster.
ut as w e
W e le ve l o m ax im um
ac h a
ap p ro
ra te , V ma x
We get the followin g two facts
from
inspect ing the reactio n scheme
for the
catalyz ed reactio n: we can state
for the dissocia tion constan t, K
can state the rate law for the
D
a term
, and we
rate- [ S ]t
determ ining-ste p.
v = k [S ] v = Vmax
KD =
[S ] [Cu ] and v = k [SCu ]
cat If we have a small amount
K D + [ S ]t
[SCu ] of catalys t then any substra te
bound up in the comple x will
not be enough to change the k kcat
initial total concen tration of S P S + Cu S-Cu P + Cu
[ S ] [ S ]t the substra te.

The small amount of catalys t will KD

t
[Cu ] = [Cu ]t [SCu ] c o n s ta n
have a signific ant portion of its

q u ili b r iu m th e c a ta ly s t-
initial concen tration bound in the
th e e
K D is
catalyti c comple x.
of Maxi mum poss ible cata lyzed
o c ia ti o n x
f o r d is s c o m p le rate for this conc . of cata lyst.
te
([Cu ] [SCu ]) [S ] We can now state KD in terms of s u b s tr a

Obser ved Initial rate of Reaction, ν

Obser ved Initial rate of Reaction, ν

the initial total concen trations of
t t
KD = copper catalys t and substra te.
rearra nge that stateme nt to find
Then

[SCu ] concen tration of the catalyti c

the
comple x.

[ S ]t
[SCu ] = [Cu ]t not
K D + [ S ]t has n oes ance
r ate ce o e d d
ed nda n e rat epen
v = kcat [ SCu ] lyz rat zed ear d onc.
Plug this stateme nt into the
e
rate law to get the equatio n
c ata dep onc. um lity). ta l y c
n r i m C a e a l i nr a t e
that describ es the observ ed
U
nea e c ma
x rea
a li strat
kinetics
[ S ]t b i t to sical hav subst
v = kcat [Cu ]t su lim ph y
on
K D + [ S ]t No cept
The maximum rate is when all ( e x
the copper is in a complex with
a molecule of substrat e. When
complex conc. equals the conc.
Vmax = kcat [Cu ]t of copper available we are at
the maximum rate, or Vmax.
[ S ]t
v = Vmax
K D + [ S ]t
Concentration of substrate, [S] Concentration of substrate, [S]
Unca talyz ed rate is ofte n
insig nific ant com pare d to
cata lyzed rate .
 Car Catalysis
In the cylinders of your car, oxygen can oxidize nitrogen to nitric oxide. NO goes on to react with many chemicals found in the atmosphere and
This reaction is endothermic and vastly favours the starting materials but produces products that give rise to the brown colour of smog. The avail-
at high temperatures the equilibrium constant is 10–4, which would al- ability of catalytic converters for automobiles in 1973 changed the look
low for about 50,000 ppm of NO at equilibrium (1000 ˚C, 10:1 compres- of Los Angeles for the better.
sion ratio). Obviously there is lots of other chemistry going on, it is
exploding gasoline after all, and we do not reach those amounts. It is still Of the many reactions possible for NO in your tailpipe, we would like to
safe to say that we will still make significant amounts of NO. see it disproportionate back to N2 and O2 gas. The metal rhodium will
catalyze this reaction.
At room temperature, the equilibrium constant for NO formation is
10–16. At lower temperatures and pressures we would expect very little Palladium can catalyze the oxidation of carbon monoxide to make the
NO at equilibrium. However, the reaction is very slow outside of the less toxic CO2. Careful balance of the supply of oxygen from the NO
hellish conditions of the engine. In milder conditions we won’t proceed reaction and from engine exhaust is required. Sensors in your tailpipe
towards equilibrium fast enough to reduce NO emissions without a cat- monitor O2 concentration and adjust the fuel mixture in your car to keep
alyst.The catalytic converter in your car allows the reactions rapidly pro- your converter working at its best and your emissions as low as possible.
ceed towards equilibrium. Less NO, less smog.
So we ca tal yz e
re ac tio n the re ac -
W e w an t th is tio n we wa nt an d
ma ke it
to ha pp en . mu ch fa ste r tha
catalyst n ot he r
NO N2 + O2 po ss ibil itie s.
N2 + O2 2 NO H f = +90 kJ mole R C is “r ea
c ti ve hy dr
c ar b o ns ” o-
in th e ai r ; We cont rol our chem ical
Emissio n contro ls are 1000˚C 4 im p o r ta nt an hν
K eq = 2 10 p ho to c he m
in gr ed ie nt
in NO + O2 NO2 + O dest iny by using cata lysts .
an integra l part of ic al sm o g.
the exhaus t system hν Your DNA cont rols your
of your car
K eq25˚C = 2 10 16
O2 + O O3 bioc hem ical dest iny by
Pd/Pt /Rh cataly st
hν codi ng for cata lytic
coats a honey comb NO2 + O2 NO + O3 prot eins - the enzy mes .
th e suppo rt.
in v e n te d
Houdry c o n v e r te r in d
c
c a ta ly ti s he ha
th e 19 3 0 ly s t RC + O3 RCO3
19 5 6 . In a c a ta
ed
d e v e lo p eavy
c k in g h NO + RCO3 NO2 + RCO2
for cra .
u m
p e tr o le Z el do vi ic h
st ud ie d
th e r ea c ti
o ns o f N O
ga s in th e
la te 19 30 s.

ke
N it r o g e n th e o n to m a
H e w e nt cos-
d io x id e is o w n c o nt r ib u ti o ns to
v ie t
yummy
br nd th e s o
f m o lo g y a
c o lo u r o .
Eugene Houdry mb . Yakov Borisovich Zeldovich
on a to m ic b o
c iv ili z a ti 1892-1962 1914-1987
 Bu ch ne r w as
a Ge rm an pa tr
to fig ht at ag iot . He vo lun te
e 57 an d die d er ed
of ba tt le w ou
nd s.

Proteins as Catalysts Invertase with bound substrate

EC 3.2.1.26
Th e su bs tr at e
Early work in enzymology was focused on understanding the process is
sh ow n in gr ee n
of fermentation of starches and sugars. Beer and wine are two words
that mean money.
nt in th e
On 1833, Payen demonstrated that an extract of malt would cat- T he r ea c ta
ed r ea c ti o n is
alyze the release of glucose from starch. He had observed the action c at al yz b st r at e.
su
of the enzyme diastase. c al le d th e Marcellin Berthelot
1827-1907
In 1842, Mitscherlich demonstrated that an extract from yeast could Th is en zy me ha
s be en
catalyze the hydrolysis of sucrose. cr ys ta lliz ed an d
its
st ru ct ur e de te
rm ine d
In 1860, Berthelot isolated a protein from a yeast extract that cat- by X- ra y cr ys ta
llo gr ap hy .
alyzed the same reaction. He had isolated the enzyme invertase.
This proved that the chemistry of life was just organic chemistry and 07

19
the “vital force” of life had nothing to do with biochemistry.
The loc atio n wh ere the
In 1877 Kühne coined the word “enzyme” che mis try hap pen s is
cal led the “ac tive site ”
In 1897, Buchner demonstrated that a cell-free yeast extract could
ferment sugar to alcohol. This proved that only enzymes were
needed to perform the reactions of biochemistry. Wh en su cr os e is Eduard Buchner
pla ce d in a
pu rif ied ye as t ex 1860-1917
tr ac t the
op tic al ro ta tio n
ch an ge s
fr om +6 6.3 ˚ to —3
9.3 ˚. Berthel ot would say that the
sugar has been “inverte d”

ve re d CH2OH CH2OH CH2OH CH2OH

Kü hn e als o dis co
sin
th e en zy me tr yp O O O O
H 2O + OH HO OH + HO
Pa ye n wa s als o
th e O OH HO
th e fir st to ide HO CH2OH HO CH2OH
nt ify
ce llu los e.
OH OH a c t io n OH OH
T h is r e s lo w
Sugar c Sucrose is v e r y Glucose Fructose
an be a t a
verted
w
ls o in - w it h o u .
a n d h e a it h a c id c a t a ly
20
a t a ly st 20 20
t . S h a ll s [ ]D = +66.3 c [ ]D = +52.7 [ ]D = −92.0
some s w e m a k is
Wilhelm Kühne Anselme Payen trawbe e
r r y ja m
? 20
1837-1900 1795-1871 [ ]D = −39.3
“A Brief History of Enyme Kinetics”, Keith J. Laidler; excerpt from “New Beer in an Old Bottle: Eduard Buchner and the Growth of Biochemical Knowledge”, pp. 127–133,
ed. A. Cornish-Bowden, Universitat de València, Valencia, Spain, 1997. Available for free at http://bip.cnrs-mrs.fr/bip10/buchner.htm
“Beginnings of microbiology and biochemistry: the contribution of yeast research”, James A. Barnett, Microbiology, 2003, 149, 557–567. https://doi.org/10.1099/mic.0.26089-0
Structure of invertase data obtained from the Protein Data Bank. http://doi.org/10.2210/pdb1w2t/pdb
 Tr yp sin wa s O
ide nti fie d by H2O +
Enzymes Are Specific Catalysts Ku hne in 187 6 N
H

Whereas a strong acid can transfer a proton to just about anything with
a lone pair of electrons, we observe that protein catalyzed reactions are
very specific. Different enzymes can catalyze the same kind of reaction
but act only on a single, specific substrate. O

In 1892 Adrian John Brown (1852-1919) postulated that enzymes per- O H3N
form catalysis by forming a complex with the reactants. This led Fischer Tr ypsin Chymotr ypsin
to propose the “Lock and Key” hypothesis as a way top explain the
observed reaction kinetics and mysterious specificity of enzymes. H2N NH2
NH3 OH
In the first decade of the 20th century, von Euler and Harden both HN
showed that sugar fermentation was a multistep process. We now know NH
that this process is catalyzed by a set of enzymes that comprise the gly- O O O O O O
colysis pathway. H H H H H
N N N N N
N N N N N
H H H H H
O CH3 O O O O
HO CH3 H3C OH NH
Th es e th re e pr H3C
ot ea se s ca ta lyz N
th e sa me re ac e
Only the right key will turn tio n bu t ea ch
ac ts on ly on a
the lock . Is this a good mode l sp ec ifi c se t of
id e n t if y
a ll Hydrolysis of amides in
am ino ac ids in
for enzy me spec ificit y? a pr ot ein . Is it C a n y o u a m in o water wants to happen
th at on ly th e co e
rr ec t “k ey ” o f t h e s id u e s ? but is verrrry slow. An
tu rn s th e “lo ck es
”? a c id s r enzyme can speed it up.

H.M . Ve rn on su
sp ec te d th e ex
a se co nd en zy me ist en ce of
in tr yp sin ex tr ac
190 1. No rt hr up an ts in
Elas tase was firs t se co nd en zy me
d Ku nit z ide nt ifi
ed th is
obse rved by Eijk man as ch ym ot ry ps
in in 193 4.
in 1904 . Elastase
The “lock and key” mod el
was a good star t, but it 19 2 9
1902 didn’ t expla in ever ythin g. We 19 4 6
shall explo re this idea mor e
later .

Eijkm an was awa rded

the 1929 Nob el priz e
for med icine for his
disc over y of vitam ins.
Emil Fischer Christiaan Eijkman John H. Northrop Moses Kunitz H.M. Vernon
1852-1919 1858-1930 1891-1987 1887-1978 1870-1951
Nor thru p’s Nob el in
chem istry was for his
wor k in enzy molo gy.
 Some Definitions
Catalyst: A molecule that accelerates a chemical reaction and is not consumed or is regenerated
during the reaction. The concentration of a catalyst will not change over the course of the reaction.
Enzyme: A substance produced by a living organism (almost always a protein) that acts as a catalyst
to accelerate a specific biochemical reaction.
Coenzyme: A small molecule required for enzyme function. It’s concentration does not change
significantly in a living cell. It is being regenerated during the reaction or in subsequent reaction in
the pathway that is being investigated. yo u
ac ta nt th at
Pi ck on e re d ca ll th at th e
Prosthetic Group: A coenzyme that is so strongly bound to the enzyme that is is not separated an
ca re ab ou t y ot he rs
en an
during enzyme purification. They are often covalently attached to the protein. su bs tr at e. Th st ra te .
-s ub
ar e th e co
Substrate: The reactant for the enzyme-catalyzed reaction being investigated. The substrate is con-
verted to product and it’s concentration changes as the reaction proceeds. If yo u co ns
id er an en zy
ca ta ly ze th e me
Co-substrate: Other reactants that are used in the reaction that we need to make sure are there tr an sf or m at to
a su bs tr at e, io n of
but that we don’t otherwise care about. Co-substrates are usually added in higher concentrations th en ev er yt
el se in vo lv ed hi ng
to maintain pseudo-first order reaction conditions for the substrate that we do care about. th at is no t
is a co fa ct pr
or . Th ey m us ot ei n
pr es en t fo r t al l be
Cofactor: Everything other than the substrate and enzyme in an enzyme reaction: co-substrates, th e en zy m e
ac tiv e. to be
coenzymes, co-everything else.

M ag ne si um
AT P is alw ay s io n is
be ing m ain ta ine O re qu ir ed fo O O
co ns ta nt co nc d at a fa irl y r ac tiv ity .
en tr at ion in a It is a co fa
a su bs tr at e in liv ing ce ll. It is O P O OH ct or . O P O O P O
m an y en zy m e O O
it ca n als o be re ac tio ns bu t O HO O HO O
ca lle d a co en + ATP + Mg+2 + ADP + Mg+2
re ac tio ns . zy m e in th os e OH OH
Phosphofructokinase 1
OH OH
fructose-6-phosphate fructose-1,6-bisphosphate

1 929
sph ory late d sug ars
Har den iden tifie d that pho
inte rme diat es in fer men tati on in 1908 .
are
fina lly iden tifie d fru cto se-1 ,6-b is-
In 1932 he
pho sph ate .

Triv ia que stio n: How man

von Euler perf orme d deta iled kinet y Nob el
ic stud ies on laur eat es had chil dre n who
the early step s of ferm enta tion. also
His work led won the Nob el?
Hans von Euler-Chelpin Arthur Hardin to the unde rsta nding of coen zyme
s.
1873-1964 1864-1940
w as
Hi s so n, Ul f,
19 70 No be l
aw ar de d th e
ed ic in e
pr iz e fo r m
 Avery was from Halifax, Nova Scotia. he was
nominate d 38 times for the Nobel prize. 17 of
those nominatio ns came before his famous 1944
The Three Steps To The Dogma experime nt.

In 1944 Oswald Avery demonstrated that DNA was the carrier of genetic information.
Had he lived long enough he would likely have shared in the 1958 Nobel prize for 1958
medicine along with George Beadle and Edward Tatum. This prize recognized the
discovery of DNA as the carrier of heredity.
The 1959 Nobel prize in medicine recognized the discovery of the role of RNA. Severo
Ochoa and Arthur Kornberg shared the prize for their pioneering work in the early
1950s.
Oswald Avery George Beadle Edward Tatum
Khorana and Nirenberg shared the 1968 Nobel prize for medicine for their work in 1877-1955 1903-1989 1909-1975
determining the genetic code and its role in protein synthesis. Holley shared in the prize
for determining the structure of transfer RNA.The three stages of the dogma of biology
are now complete. 1 9 59
All the chemical processes of life are mediated by proteins acting as catalysts and gate-
ways. The function of these proteins arises from the arrangement of chemical groups in
the folded structures. These groups can provide for catalysis of biological reactions.
In 1970 Francis Crick stated the famous “Central Dogma”. I would like to add a fourth
step to the dogma of biology. DNA codes for RNA, which codes for proteins that code
for the chemistry of life. M. Grunberg-Manago Severo Ochoa Arthur Kornberg
1921-2013 1905-1993 1918-2007
In 1954, Marianne Grunberg-Manago was
1 9 68 the postdoctoral researcher that made the
discovery that NTP was the building block
of RNA and isolated an enzyme that syn-
thesized RNA from NTPs. Manago went on
to an illustrious career and was president
of the IUBMB and the French Academy of
Sciences

Robert Holley Gobind Khorana Marshall Nirenberg Heinrich Matthaei Nirenberg and Matthaei used Manago’s enzyme to
1922-1993 1922-2001 1927-2010 b. 1929 synthesize the RNA triplets for their research. Man-
ago was the sole supplier of this essential ingredient. Maxine Singer
Matthaei was left out of Maxine Singer was a bench chemist that performed b. 1931
the 1968 Nobel. The will the RNA synthesis for Nirenberg.
stipulates a maximum of
1962 lyp he ny lala nin e
three laureates for an co de d fo r po
award. re po rt ed th at po ly- U RN A n be tw ee n th e gr ou ps of
Nir en be rg a fr an tic ra ce
be ga
de co de all 64
196 1. Th en e fir st to
pr ot ein in an d Kh or an a to be
th
er s at th e NIH
, Oc ho a re se ar ch
Le t us no t fo Nir en be rg et s.
l
Se ve ra l pr inc ipa th Nir en be rg an d wi n on e
rg et tha t Wa tso RN A tr ipl
po ss ibl e to wo rk wi e fir st to
Cr ick pr es en te n an d ow n pr oje ct s te am we re th
in 195 3 an d sta
d the str uc tur
e of DN A st op pe d th eir en eb er g an d th e NIH th e fir st fo r a
rt ed of the de te am . Nir No be l wa s
ra ce fo r the ca de -lo ng fo r th e e ge ne tic co de .
His
r th e Na tio na l
e co mp let mo me nt fo
ge ne tic co de . re po rt th ch er an d a glo rio
us
nt re se ar St at es .
go ve rn me th e Un ite d
James Watson Francis Crick alt h sy st em in
Ins tit ut es of He
b. 1928 1916-2004
 s y n th e s is
e c ts th e r o c e s s
R N A d ir a p
in s in f
o f p r o te b y a c o m p le x o
d
c a ta ly z e .. Carbon ic anhydra se
p r o te in s Z in c
RNA and is an example of an
Protein s direct the enzyme that exploits
chemica l pathwa ys metal ion catalys is.
of the cell.

DNA direc ts the

synt hesis of RNA
in a proc ess cata lyzed
by a prot ein com plex.

DNA RNA Protein Chemistr y

In s o lu b le
The Fourth Level OH2
–H
gas
Zn
car- N N
Catalytic proteins associate specifically with a small number of molecules.This pref- S o lu b le N O
C
erence is informed by the exact structure of the binding site. At or near this binding bonate N
O

site is the chemical machinery that can provide catalysis for a chemical transforma- HO
OH
tion. So we will ultimately observe a very high relative reaction rate for a specific O
O Zn
chemical change in a specific molecule. This control of which reactions are ob- N N
N
served in biological systems is enabled by the production of a given enzyme.
N
Life is the net result of a collection of chemistry enabled by protein catalysts. HO
We have seen how the functional groups in enzymes give rise to catalysis through H2O O
bringing reactants together, solvating and stabilizing the transition state, assisting in O

proton transfer, providing interactions with metal ions and sometimes enabling an N N
Zn

alternate chemical route to the product. N Ac id is pa rt of the

N eq uili br ium . Th is is
Now that we have had a brief overview of some strategies for achieving catalysis a ma jor fa ct or in
in proteins, we have the vocabulary to explore the chemical behaviour of enzymes re gu lat ing blo od pH .
in living chemistry. ibriu m for the hydr ation of CO 2 is
The equil
anhy dras e
esse ntial for meta bolis m. Carb onic
extr emel y
enab les this chem istry to happ en
quick ly.
This Is Only The Very Beginning...
This presentation was never intended to provide all the information that to highlight some important topics, provide stories and context to pique
you are required to digest for this course of study. By definition, university your interest in biochemistry and to inform you of current research chal-
requires that you read books, think about what you have read, and ask lenges to which you might someday make a contribution. As you read your
questions. Otherwise stay at home, watch TV and save your money. textbook and consider this presentation, strive to master the following es-
Always consider the relatively brief presentation in class to be a mere sential skills of biochemistry.
apéritif for your studies. I cannot read the textbook to you but I do hope
Europe has many great examples of
apéritifs but it’s a big world out there.
Let us sample some pre-dinn er drinks
Topics Highlighted in this Brief Presentation from the ancient land of China.

What is a catalyst? How does a catalyst accelerate a reaction? Will a catalyst change the
equilibrium constant of a reaction?
Can you write the rate law for a first order reaction? Can you interpret the rate law for
the reaction in the presence of a catalyst? (assume equilibrium association with the cat-
alyst followed by the rate determining step).
How does the rate of reaction correspond to reactant or catalyst concentration in a
catalyzed reaction?
How is catalysis exploited in living things to allow the genetic code to ultimately direct
the chemistry of life?
Can you explain what an enzyme is? A cofactor? A cosubstrate? A coenzyme? A
prosthetic group?

d is t ill e d
iji u liq u o r , it is a in . T h e
is a b a hum gr
Moutai f s o r g s a llo w s a lo t
a mash o e s
fr o m n p r o c come
is t ill a t io m a lt t o
s in g le d la v o u r o f t h e iji u is c a lle d
f ba
of the though r ic h
. Even en has
t h r o u g h v o d k a ”, it o f t
e
“C h in e s .
s
f la v o u r

Mo uta i is a re ver ed
liqu or in
Ch ina . It has be en pr
odu ce d in
Gu izh ou pr ov inc e sin
Richard Nixon Zhou Enlai ce the 160 0s .
1913-1994 1898-1976
to Pr es ide nt
It wa s se rv ed
xo n du rin g his
Ri ch ar d Ni
Ch ina in 197 2.
fa mo us tr ip to
References and Notes
I have used many images to decorate this presentation. Some of them are in the public domain and some are not. I claim fair use for educational
purposes. This presentation contains mistakes, typographical errors, crimes of grammar and worse. All mistakes are intentional – to see if you are paying
attention. Please report any errors that you find in the class forum.

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References and Notes
I have used many images to decorate this presentation. Some of them are in the public domain and some are not. I claim fair use for educational
purposes. This presentation contains mistakes, typographical errors, crimes of grammar and worse. All mistakes are intentional – to see if you are paying
attention. Please report any errors that you find in the class forum.

Image of Wilhelm Kühne accessed on November 15, 2015 at

http://temasdeinteresporakashavalentine.blogspot.ca/2014_06_25_archive.html
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Image of invertase created with UCSF Chiumera. Data from the RCSB PDB database,
http://dx.doi.org/10.2210/pdb1w2t/pdb

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Images of proteases from “Trypsin”, David Goodsell, Molecule of the Month, 2003,
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References and Notes
I have used many images to decorate this presentation. Some of them are in the public domain and some are not. I claim fair use for educational
purposes. This presentation contains mistakes, typographical errors, crimes of grammar and worse. All mistakes are intentional – to see if you are paying
attention. Please report any errors that you find in the class forum.

Images of Robert Holley and Gobind Khorana accessed on November 15, 2015 at
http://www.nobelprize.org/nobel_prizes/medicine/laureates/1968/
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Image of DNA, RNA, dna polymerase and ribosome adapted from images in
http://www.rcsb.org/pdb/education_discussion/educational_resources/mol-mach-2014-poster.pdf,
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