Professional Documents
Culture Documents
BIOCHEMISTRY
AND
MOLECULAR BIOLOGY
Enzymes/Membrane Transport
Copyright 1999, E.C. Niederhoffer. All Rights Reserved.
All trademarks and copyrights are the property of their respective
owners.
This and other study guides are provided to help you focus on the
topics that are important in the biochemistry curriculum. These are
designed to guide your studying and provide information that may
not be readily available in other resources. They are not designed to
replace textbooks, and are not intended to be complete. They are
guides for starting your reading and reviewing the material at a later
date.
B. Textbooks:
tions.
4. Marks, Marks, and Smith, Basic Medical Biochemistry: A
Clinical Approach, (‘96), Williams & Wilkins. Good basic
presentation with clinical relevance.
5. Cohn and Roth, Biochemistry and Disease, (‘96), Williams
& Wilkins. A good bridge between the basic sciences and
clinical medicine.
6. Garrett and Grishham, Biochemistry, 1st ed., (‘95), Saun-
ders College Publishing.
7. Garrett and Grishham, Molecular Aspects of Cell Biology,
1st ed., (‘95), Saunders College Publishing.
C. Journals/Reviews.
You may find worthwhile reading in some of the more popular jour-
nals and review series (see also the searchable SIU-SOM database).
These resources typically contain specific articles involving enzymes
and membrane transport. Suggestions for journals include American
Family Physician, Journal of Biological Chemistry, Nature, Science, and
Scientific American (and SA’s Science and Medicine). Excellent reviews
may be found in the Annual Review of Biochemistry, Cell and Develop-
mental Biology, Genetics, Medicine, and Microbiology.
D. Lecture/Discussions
Sets.
Activators
Coenzymes
Competitive inhibitors
Enzyme concentration
Irreversible inhibitors
Noncompetitive inhibitors
pH
Products
Substrate concentration
Temperature
6. Discuss the criteria that must be met for a valid enzyme assay
and for using an enzyme as a reagent.
10. Use the material covered on the above objectives and previous
objectives to solve new, related problems such as those given in the
Prestest and Post Test.
Pretest:
A Pretest is available for those interested in assessing their current
knowledge base and conceptual understanding. You may hyper-jump
to Study Guide-1.
Sample questions:
a. What can be inferred about this enzyme from the terms alka-
line phosphatase and phosphomonoesterase? answer
b. The anticoagulants EDTA and citrate may not be used in
this assay. Why? answer
c. Must the reaction be done at exactly pH 9.0? Why? answer
glyceraldehyde-3-phosphate + NAD+ →
3-phosphoglycerate + H+ + NADH
These enzymes are used because the appearance of NADH can be
easily measured spectrophotometrically. How much of the two
enzymes must be added? answer
Sample questions:
a. Explain the meaning of the phrase "reactive serine at the cat-
alytic site". answer
b. What is calcium ion called with respect to trypsin? answer
c. What is meant by the phrase "from the amino terminal of
the zymogen"? answer
d. What is the significance of the fact that when trypsinogen "is
dissolved in neutral or slightly alkaline solution conversion
to trypsin occurs"? answer
e. What is the significance of the fact that "the rate of this acti-
vation increases rapidly"? answer
f. The small intestine, into which trypsinogen is released and
in which trypsin acts, is slightly alkaline; but what is the pH
optimum of trypsin? answer
g. What is a zymogen? answer
6. The following statements are taken from the article "The Isola-
tion and Properties of Phenylalanine Hydroxylase from Human
Liver" by S.L.C. Woo, S.S. Gillman, and L.I. Woolf, Biochem.
J., 139, 741-749 (1974), but not in the order in which they orig-
inally appeared. "Phenylketonuria is a genetically determined
disease in which the enzyme phenylalanine 4-hydroxylase (EC
1.14, 16.1) is absent or has very low activity . . . The phenylala-
nine hydroxylase activity of the liver was confined to a single
protein of molecular weight of approximately 108,000 . . . It
seems to consist of two polypeptide chains, each with a molecu-
lar weight of approximately 54,000 . . . By using the double-
reciprocal plots, the apparent Km values for phenylalanine were
3.5 x 10-4 M for the full-term infant and 3.8 x 10-4 M for the
adult preparations, respectively. For the synthetic cofactor,
apparent Km values were 6.8 x 10-5 M and 6.6 x 10-5 M, respec-
tively . . . The activity of the enzyme was assayed, by using vari-
ous concentrations of phenylalanine, in the presence and absence
of 0.5 mM p-chlorophenylalanine . . . Iron-chelating and cop-
per-chelating agents inhibited human phenylalanine hydroxy-
lase. Thiol-binding agents inhibited the enzyme but, as with the
2. a. Oligomeric
b. Quaternary
c. It can be inferred that the active site contains a sulfhydryl
6. a. Decreases
b.
CO2H CO2H
H2 N CH H2 N CH
CH2 CH2
NADPH + H+ NADP+
O2 H2O
OH
phenylalanine tyrosine
STUDY GUIDE-1
I. Where are enzymes Enzymes are present in the cytosol, in all organelles (e.g., the nucleus,
located? mitochondria, ribosomes, etc.), and in membranes. They are found
singly and in multienzyme complexes.
II. What are catalysts Enzymes are proteins (or ribonucleic acids, ribozymes) that are cata-
and how do they work? lysts. As catalysts:
Molecules must have a certain energy level before they can react, i.e.,
before S can be converted into P, they must be activated. The
amount of energy required is called the activation energy. (∆E, Fig-
ure 2; energies exceeding that given by the solid vertical line in Figure
1.) It is seen that the distribution that pertains at the higher temper-
ature has a larger number of molecules with the necessary activation
energy than does the low temperature distribution. Consequently,
there will be a proportionately larger number of molecules undergo-
ing reaction per unit time in the case of the high temperature distri-
bution.
Each of these reactions has its own activation energy, which is much
E+S ES E+P
O
H2N-C-NH2 + H2O → CO2 + 2NH3
Urea
Urease lowers the activation energy for the reaction to less than
10,000 cal.mol-1. Eact for the acid-catalyzed reaction is = 25,000
cal.mol-1. What this means for the reaction can be seen from the fol-
lowing table:
Table 1:
k(first-order rate
Eact, cal.mol-1 half-time
constant)(sec-1)
III. What are zero- Consider the reaction S → P. The reaction rate is the amount of S
order and first-order reacted in a unit of time or the amount of P formed in a unit of time.
reactions? d[S] d[P] n
rate ( v ) = – ----------- = ----------- = k [ S ]
dt dt
n = order of reaction
time S P
zero a zero
t a-x x
dc
– ------ = k 1 [ c ]
dt
1 a
k 1 = --- ln -----------
t a–x
All units except 1/t cancel. Hence, the unit for k1 is 1/t. For exam-
ple, if for a certain reaction with first-order behavior k1 = 0.001 sec-1,
this means that each succeeding second finds 1/1000th of the remain-
ing reactant [S] converted into product (Figure 4).
dc
– ------ = k 0
dt
(c is to the zero power, i.e., [c]i = 1 and the reaction is, therefore,
zero-order)
IV. What factors affect The following factors affect enzyme-catalyzed reactions:
enzyme-catalyzed reac- 1. Concentration of substrate
tions? 2. Concentration of enzyme
3. Concentration of cofactors (activators and coenzymes)
4. Concentration of inhibitors
5. Temperature
6. pH
7. Concentration of allosteric effectors
V. What is the effect of When doing enzyme assays, i.e., determining the amount of enzyme
substrate concentra- activity, enzyme solutions are added to substrate solutions and the
initial rate is measured. Under these conditions, the concentration of
tion? product (P) is zero and the equation becomes.
E+S ES EP E+P
Zero order v = k0
Vmax/2
Km [S]
Figure 6
This effect can be likened to a crew rowing a boat. Two crew mem-
bers can row the boat faster than one, and three faster than two.
However, a point is reached when all crew positions are filled, there
are no more available oars, and no more crew can be put in the boat.
At this point the boat is going at its maximum speed, and no matter
how many additional crew are standing on the shore, watching, the
boat cannot go faster because those not in the boat cannot increase its
speed.
VI. What is the The enzyme concentration ([E]) also enters into the rate equation
importance of Km? but, when it is held constant as above, the numerical value of [E]
merges into the rate constant (k). When [S] is held constant and [E]
What is the basis of is varied, the substrate concentration becomes part of the propor-
enzyme assays? tionality constant and the initial rate is proportional to the enzyme
concentration, i.e.
dc
v = – ------ = k [ E ]
dt
k –1 [E][S]
K m = ------- = -----------------
k1 [ ES ]
Where
k1 k2
E+S ES (EP) E+P
k-1
V max [ S ] V max
v = ---------------------
- = -----------------
Km + [ S ] Km
1 + ------- -
[S]
which is the equation for any surface catalysis. If one solves for Km,
then
V max
K m = [ S ] ------------ –1
v
To find Km, which has the units of concentration, several plots can be
used. The most common is the Lineweaver-Burke plot (Figure 8)
which is based on a reciprocal form of the Michaelis-Menten equa-
tion.
1 Km + [ S ] Km 1 1
- = ------------ × -------- + ------------
--- = ---------------------
v V max [ S ] V max [ S ] V max
It should be noted here that these derivations and equations are for
single substrate reactions and that biochemical reactions often involve
two and three substrates reacting together.
slope = Km/Vmax
1/v
-1/Km
1/Vmax
1/[S]
Figure 8
On the other hand, 4.5 mM approximates the K0.5 for liver glucoki-
nase. It is acting within the region of the v versus [S] curve in which
the rate would change with any change in glucose concentration; a
situation in keeping with the physiological role of the liver in control-
ling blood glucose levels.
However, this says nothing about the total amount of glucose con-
verted to glucose-6-phosphate and thus taken up respectively by the
two tissues. What determines that is the relative Vmax's, the relative
rates of the conversions catalyzed by the two enzymes at 4.5 mM glu-
cose, and the relative concentrations of the two enzymes in their
respective tissues.
VII. What is the effect As will be discussed later, many enzymes require inorganic ions for
of the concentration of activity, coenzymes that are cosubstrates and act as acceptor or donor
molecules, and/or coenzymes that are cocatalysts. The concentration
coenzymes and activa- of these cofactors, if limiting, will affect the rate of the enzyme-cata-
tors? lyzed reaction. Hence in any determination of enzyme activity, the
concentrations of required cofactors must be in amounts that are in
excess of the stoichiometric requirements.
Activators are not required for enzyme activity but can increase
enzyme activity by putting the enzyme molecule in the proper state
to combine with the substrate or remove inhibitors.
VIII. What are com- Studies of the effects of enzyme inhibitors on the kinetics of enzyme-
petitive and noncom- catalyzed reactions are a most important part of biochemistry and
pharmacology.
petitive inhibitors?
What is their effect on As has been discussed above, enzymes are catalysts. Therefore, as the
reaction proceeds, the concentration of products continuously and
enzyme-catalyzed reac- stoichiometrically increases at the expense of the disappearance of the
tions? corresponding substrates, while, ideally, the total concentration of
enzyme (in all its possible forms) remains fixed and invariant. Thus,
a consideration of the rate behavior or kinetics of such reactions fur-
nishes a powerful tool, not only for their determination, but also for a
definition of their properties and possible modes of action. On the
molecular level, we are always dealing with interrelations between
structure and function. Kinetics provides us with the most important
(and with impure preparations, the only means of coming to grips
with enzyme function).
ficity (high affinity for specific compounds) and the catalytic function
of the active protein molecule. The active site (or active center) is fre-
quently spoken of in terms of binding sites that hold the substrate in
a specific conformation and the catalytic site where reaction takes
place. Active site = binding sites + catalytic site.
Enzymes are often much, much larger than their substrates; at least
they are much larger than the part of the substrate with which they
interact. Therefore, only a small portion of the enzyme can be in
contact with the substrate. Sometimes part of the protein molecule is
dispensable, sometimes not. The bulk of the enzyme may be required
to bring the active site in contact with the substrate. It certainly is
required in most cases to put the reactive groups into proper juxtapo-
sition to each other.
Emil Fischer pictured a "lock and key fit" between the enzyme and
the substrate. Koshland and others have suggested that some
enzymes change their shape on combination with their substrate, i.e.,
the substrate induces the enzyme to conform to the binding geometry
("induced fit" hypothesis).
H2 N CO2-
p-aminobenzoate
O
H2 N S-NH2
O
sulfanilamide
E+S ES EP E+P
V max [ S ]
v = --------------------------------------------
[I]
K m 1 + ------ + [ S ]
Ki
[E][I]
where K i = ---------------
[ EI ]
from which it can be seen that, if [S] >> [I], the effect of the inhibitor
can be overcome.
Increasing [I]
1/v
[I] = 0
-1/{Km(1 + [I]/KI)}
1/Vmax
1/[S]
Figure 9
E+S ES EP E+P
E+I EI
ES + I ESI
V max [ S ]
v = -------------------------------------------------
[I]
( K m + [ S ] ) 1 + ------
Ki
[I] = 0
1/[S]
-1/Km Figure 10
Some inhibitors are true competitive inhibitors, but many others are
neither true competitive nor noncompetitive inhibitors. Hence,
other kinds of inhibition (uncompetitive) have been hypothesized
and treated mathematically in attempts to explain the observed Lin-
eweaver-Burke plots.
IX. What is the effect There are at least two classes of inhibitors that form covalent or very
of irreversible inhibi- tight linkages with the enzyme and effectively prevent catalysis.
tion? In many enzymes, sulfhydryl (-SH) groups are required for activity
and the reaction of heavy metal ions (e.g. silver, mercury, lead, etc.)
with sulfhydryl groups on these enzymes render them irreversibly
inactive. The effect of this type of inhibitor on enzyme kinetics is to
decrease the apparent Vmax without affecting the Km. Consequently,
the kinetic plots that occur for this class of irreversible inhibitors are
identical to those observed for noncompetitive reversible inhibitors.
This has led to confusion as to the differences between reversible
noncompetitive and irreversible inhibition. Reversible noncompeti-
tive inhibitors can be distinguished from irreversible inhibitors by
dialyzing the enzyme preparation containing the inhibitor. Full
enzyme activity will be regenerated on dialysis of the enzyme prepara-
tion containing a non-competitive inhibitor but not with an enzyme
preparation containing an irreversible inhibitor.
E+S ES E+P
I I
EI + S EIS
Irreversible inhibition:
E+S ES E+P
EI
CO2- CO2-
NH3+ NH3+
GABA gabaculine
Enzyme
pyridoxal phosphate
CO2- CO2- CO2-
H :B
H
NH3 + NH+ NH2+
2- OH O-
2-
3 OPO 3 OPO
N+ CH3 N+ CH3
H H
X. What is the effect As with other chemical reactions, the rates of enzyme-catalyzed reac-
of temperature? tions are increased by increases in temperature. However, because
enzymes are proteins, thermal denaturation of the protein with
increasing temperature will decrease the effective concentration of the
enzyme. The result on an enzyme-catalyzed reaction is depicted in
Figure 11. The upper limit for most human enzymes is 40 to 50˚C
(normal body temperature 37˚C).
XI. What is the effect Changes in pH will change the ionization of the enzyme that is, of
of pH on enzyme-cata- course, amphoteric; for example,
lyzed reactions?
H+ H+
+ +
E+S ES (EP) E+P
EH+ EHS+
If the substrate possesses ionizable groups, as many do, its ionic state
will change with changes in pH; for example, focusing on the sub-
strate ionization.
H+ H+ H+
+ + +
HE + S- HES- (HEP-) HE + P-
E- + H + SH HESH+ E- + H + PH+
to bind, and the pK of the group is, e.g., 8.0. Furthermore, let us say
that the substrate has to be negatively charged in order for it to be
attracted to the enzyme active site and the pK of the group on the
substrate is, e.g., 4.0.
At low pH the substrate is protonated (SH) and will not want to bind
to the enzyme that also is in its protonated form (EH+). As the pH is
increased we remove the proton from substrate to form S-, which is
the form that will bind to enzyme. Thus, we will see an increase in
enzymatic activity proportional to the fraction of substrate molecules
in the S- form. At pH 6 we should have essentially 100% of the sub-
strate as S- and maximum catalytic activity will be observed. As we
go to pH values higher than 6, we begin to remove the proton from
the group at the enzyme active site. There will be a decrease in activ-
ity proportional to the amount of unprotonated enzyme present
because the unprotonated form will not bind substrate (S-). The
result is the bell-shaped pH profile seen in Figure 12.
XII. What are allos- Allosteric enzymes are enzymes whose kinetic properties cannot
teric enzymes and be accounted for by the Michaelis-Menten model. The activity of
allosteric enzymes is altered by regulatory molecules, and there is a
allosteric effectors? cooperative binding of substrates.
metabolism.
XIII. Why do enzyme The thing you as a physician will be most interested in is the enzyme
assays? concentration. This parameter varies from patient to patient and is
important in diagnosis. In some cases, a low concentration is signifi-
cant (e.g., erythrocyte glucose-6-phosphate dehydrogenase is
decreased in some cases of non-spherocytic hemolytic anemia), and
in some cases a high concentration is important (e.g., serum creatine
phosphokinase is increased following a myocardial infarction).
Now, let us consider how enzymes get into the serum. The concen-
tration of an enzyme in serum is a result of (a) its rate of release from
the tissue and (b) the rate at which it is removed from the circulation.
There is some leakage of enzymes into serum from normal cells.
XIV. How does one Specific activity can be determined in one of two ways. In the "one-
assay an enzyme? point method," the reaction is allowed to proceed for a time and then
the enzyme is denatured by acid, base, or heat. The reaction is then
analyzed by a chemical or physical method to see how far it has gone.
The normal values vary according to the method used. With the
Bodansky method the normal adult serum activity is 1.5 to 4.0
Bodansky units. With the King-Armstrong method, the normal
range is 1.35 to 4.0. These are both arbitrary units. In International
Units (Bessey-Lowry method), the normal range is 20 to 85 mU/ml.
glucose oxidase
peroxidase
XV. How are enzymes There are four ways of naming enzymes. Three give the enzyme a
named? trivial name. The first enzymes discovered were given names that
have no relationship to their activity; these are largely digestive
enzymes (e.g., pepsin, trypsin, chymotrypsin). Another way to name
enzymes is to name the substrate and add the suffix :"ase" (e.g., mal-
tase, fructose-1,6-disphosphatase, fumarase, ribonuclease, urease) or
the reaction alone can be named and the suffix "ase" added (e.g.,
invertase). A third way names the substrate and the reaction cata-
lyzed and adds the suffix "ase" (e.g., malic dehydrogenase, glutamic-
oxaloacetic transaminase, hexokinase). (Kinases are enzymes that
transfer a phosphate group from ATP to a substrate.)
XVII. What are isoen- Some proteins are associations of several polypeptide chains. Each
zymes? individual chain is termed a subunit; thus, a subunit is any polypep-
tide chain in the completed functioning protein that is not covalently
bound via a peptide linkage to other peptide units and can thus be
readily separated from other subunits. A protomer is a subunit in a
protein containing a finite number of identical subunits. Oligomers
are combinations of similar or different subunits to form the totally
functioning protein. Allosteric enzymes have such a structure. Those
enzymes consisting of a single polypeptide chain are termed mono-
meric enzymes. Those enzymes consisting of two or more polypep-
tide chains are termed oligomeric enzymes.
CO2 CO2
C O + NADH + H+ HO C H + NAD+
CH3 CH3
pyruvate lactate
k1 k2
E+S ES E+P
k-1 k-2
k1 k2
E+S ES E+P
k-1
ES
k –1 + k 2
K m = ------------------- and when k2 << k-1
k1
k –1 [E][S]
then K m = ------- = -----------------
k1 [ ES ]
v1 = v-1 + v2
k1 [E] [S] = k-1 [ES] + k2 [ES]
[E]t = total enzyme concentration
[S]t = total substrate concentration
but [S]t >>> [E] by experimental design
therefore [S]t >>> [ES]
and since [S]t = [S] + [ES]
then [S]t = [S] = concentration of free substrate
[E] = [E]t - [ES] = concentration of free enzyme
k –1 + k 2 ( [ E ] t – [ ES ] ) [ S ] [E][S]
------------------- = ----------------------------------------
- = ----------------- = K m
k1 [ ES ] [ ES ]
[ E ]t
-----------
- – 1 [ S ] = K m
[ ES ]
[ E ]t [ S ] – [ S ]
- = Km or
-------------------------------
[ ES ]
[ E ]t [ S ]
[ ES ] = ---------------------
-
Km + [ S ]
k2 [ E ]t [ S ]
Therefore, v = -----------------------
-
Km + [ S ]
Post Test
1. Definitions
a. What is meant by the order of a reaction? answer
b. Define Km, Ks, kcat. answer
c. Km is all too frequently equated with Ks. In fact, in most
reactions there is an appreciable disparity between the values
HCO CH2OH
H C OH C O
OH C H OH C H
H C OH H C OH
H C OH H C OH
CH2OPO3 2- CH2OPO3 2-
glucose-6-phosphate → fructose-6-phosphate
k1 k2 k3
E+S ES EP E+P
k-1 k-2 k-3
2.0 X 10-1 60
2.0 X 10-2 60
2.0 X 10-3 60
2.0 X 10-4 48
1.5 X 10-4 45
1.3 X 10-5 12
k –1 + k 2
K m = -------------------
k1
Ks = dissociation constant of the ES complex for
k1
E+S ES
k-1
k –1
K S = -------
k1
In the case where k2 is much smaller than k-1, Km
approaches k-1/k1 = Ks. Under these conditions, the Km
determined kinetically is equal to the dissociation constant,
Ks.
kcat = the turnover number and is equal to k2 in the
Michaelis Menten mechanism.
The turnover number of an enzyme is equal to the number
of moles of substrate converted to product per minute per
mole of enzyme present when the enzyme is fully complexed
with substrate.
c. A+E EA E+B
If k2 << k-1, Km = Ks
Conditions where Km not equal Ks
If k2 is approximately equal to k-1
If k2>>k-1
d. The steady state approximation assumes that the concentra-
tions of the intermediates in a reaction do not change while
the rate of product formation is being measured. This holds
for the early stages of a reaction, after the ES complex has
formed and before appreciable changes have occurred in
either the substrate or product concentrations.
2. a. True. Vmax = k2[E]t
b. True
c. False. The value of Km is independent of enzyme concentra-
3. a. Stoichiometry
b. kcat
c. Competitive
d. homotropic
e. negative
4.
[S], M v(µmol/min
0.1 0.1 Vmax
0.01 0.09999
0.001 0.09990
0.000001 0.050 Km = 1 x 10-6 M
5. a. glc-6-P fru-6-P
or S P
k1 k2
b. E+S ES E+P
k-1 k-2
6. a. The rate constant for each step is inversely related to the dif-
7. a. Vmax = 60µmol/min
b. v is constant because it has reached Vmax; the enzyme is satu-
rated with substrate.
c. The concentration of free enzyme is negligible because all of
the enzyme is in the ES form.
0.25
0.20 = -------------------------------
Km
1 + --------------------- –5
-
5.0x10
Solve: Km= 1.25 X 10-5 M
c. If the reaction follows simple Michaelis-Menten kinetics,
then the Michaelis-Menton equation should relate v to [S]
over a wide range of [S]. This can be tested by determining
whether the equation yields the same value of Km at several
different values of [S] and v < Vmax. Under the conditions of
this problem, the same value, Km = 1.3 x 10-5 M, is obtained
at [S] = 5.0 x 10-6 M, v = 0.071 µmol/min and at [S] = 5.0 x
37 37
v = ------------------------------ –3
- ≈ 37 µmol/min.
- = ------------------------------
–5
1.0x10 1 + 1.0x10
1 + --------------------- –2
-
1.0x10
[S], Km v, Vmax
0.20 0.17
0.50 0.33
1.0 0.50
2.0 0.67
4.0 0.80
10.0 0.91
c. When you plot these values you will be able to see that the
best range of [S] for studying the dependence of v on [S] is in
the neighborhood of Km or below it, since changes in [S]
below Km cause greater changes in v than do changes in [S]
above Km. Therefore, when using graphic methods to deter-
mine Km and Vmax, several measurements should be made at
[S] well below Km.
Problem Set
1. In the cases of severe liver damage, an enzyme EL is released into
the blood. After severe exercise, an isozyme from muscle, EM, is
found in the blood. EL and EM can be differentiated since they
have different kinetic constants. The Km of the liver enzyme is 3
x 10-4 M; the Km of the muscle enzyme is 7 x 10-5 M.
Data from assays on an unconscious patient's blood are given
below. Ten microliters of blood was used in each assay.
S (M) v (µmol/min/10 µl
3 x 10-2 990
3 x 10-3 909
1 x 10-3 769
7 x 10-4 700
3 x10-4 500
1 x 10-4 250
7 x 10-5 190
3 x 10-5 91
1 x 10-5 32
Your choice for axes are: Energy, [E], Temperature, [S], 1/[S], 1/v, v.
(You may use the same label on more than one graph.) answer
CO2-
H CO2-
C HO C H
+ H2 O
C H H
-O
2C H
CO2-
10. Answer the following with true or false; justify your answer in
each case.
a. The initial rate of an enzyme-catalyzed reaction is indepen-
dent of substrate concentration. answer
b. If enough substrate is added, the normal Vmax of an enzyme-
catalyzed reaction can be attained even in the presence of a
noncompetitive inhibitor. answer
c. The rate of an enzyme-catalyzed reaction in the presence of a
rate-limiting concentration of substrate decreases with time.
answer
d. The sigmoid shape of the v-versus-[S] curve for some regula-
tory enzymes indicates that the affinity of the enzyme for
substrate decreases as [S] is increased. answer
CH2-COOH CH2-COOH
HC COOH H C H
+ NAD+ + H+ + NADH
or NADP+ or NADPH
HO C COOH C-COOH
H O
isocitric acid α-ketoglutaric acid
16. The levels of LDH isozymes in the blood are indicative of certain
disease states: Some of the isozymes present will react with a
particular substrate while others will not. Thus, one can experi-
mentally measure the activity of these particular isozymes while
other isozymes are also present in the sample. In particular, this
assay makes particular use of:
a. the colligative properties of the solution.
b. the substrate specificity of the isozyme of interest.
c. the preincubation phase of the isozyme of interest.
d. the tertiary structure of the isozymes of interest.
e. the total activity of all enzymes species.
answer
17. Let's say the following assay was established to measure E1 levels
in serum.
E1
A B (1)
E2
+
B + NAD NADH + H+ + C (2)
a. List the solution conditions you would have to control to
make this a valid assay. answer
b. List the species to equation 1 and 2 whose concentrations
18. Clinical data for enzymes are often reported in terms of interna-
tional units. What is an enzyme unit of activity and what rela-
tionship does it bear to specific (enzyme) activity? answer
1 Km 1 1
c. --- = ------------ -------- + ------------
v V max [ S ] V max
d. Vmax = k [E0]
V max
e. when Km >> [S], v = ------------ [ S ]
Km
f. [S0] - [Sf ] + [ES]
answer
4.
Upper L: vo vs [S]
Upper R: Vmax vs [E]tot
Lower L: vo vs Temperature
Lower R: vo vs [S] for a Km-type allosteric enzyme showing +ve
homotropy.
b.
1/v
slope = KmI/VmaxI
Km/Vmax
1/VmaxI
-1/KmI = -1/Km
1/Vmax
1/[S]
6. a. Quaternary (oligomeric)
b. pH 6.5
c. Competes with fumarate because of similar structure, there-
fore a competitive inhibitor
d.
+malonate
1/v
slope = KmI/VmaxI
-malonate
-1/KmI
Km/Vmax
-1/Km
1/Vmax = 1/VmaxI
1/[S]
8. a. Greater
b. Yes
c. Yes
9. a. [S] >> Km
Therefore, vo = Vmax
Therefore, the velocity is doubled when [E]tot is doubled
10. a. F
b. F
c. T
d. F (positive Km-type)
11. a. Cofactor
b. Coenzyme
c. Allosteric (positive Km-type)
d. Oligomeric
e. Quaternary
f. +ve heterotropic effector
g. -ve heterotropic effector
h. Equal, coenzyme
i.
1. If NAD+/NADP+ and NADH /NADPH and isocitrate and
a-ketoglutarate all at 1 M concentration are mixed at 1 atm
pressure, since the free energy change under standard condi-
tions for the forward (L R) reaction is negative,
NAD+/NADP+ and isocitrate will be converted into
NADH/NADPH and α-glutaric acid. (Also, at equilibrium,
the ratio of products to reactants (Keq), will be greater than
1, i.e., the equilibrium lies to the right.)
12. c
13. b
14. b
15. b
16. b
Vmax
coenzyme
Km
zero order reaction
saturation velocity
specific activity
active site
substrate specificity
isoenzyme
enzyme assay
8. Elevation of concentrations.
a. Describe the relationships between enzyme and substrate
concentrations which provide the best evaluation of enzyme
activity (see goal 3).
b. Differentiate between enzyme concentration and enzyme
activity.
c. Depending on the spectrophotometric equipment available,
a number of approaches are possible for evaluating reaction
rate from a given assay system. Describe three ways that
reaction rate may clinically be evaluated and give the advan-
tages and disadvantages of each.
CLINICAL PROBLEM:
STUDY GUIDE-2
I Diagnostic Enzyme levels are often altered in disease. There are two basic situa-
tions:
Glucose-6-phosphatase Ordinarily, this enzyme is only expressed in liver and kidney calls. It
deficiency allows glucose-6-phosphate, produced by breakdown of liver or kid-
ney glycogen under conditions where blood glucose is low, to be con-
verted into glucose that can then be released into the bloodstream for
by other tissues, particularly the brain and muscles. If its activity is
too low, a severe hypoglycemia results.
Measurements Units The International Enzyme Unit (I.U.): typically, the amount of
enzyme converting 1 mmole of substrate into produce min-1, usually
at 37 or 25ºC. (However, if the enzyme is of intrinsically low activ-
ity, the units might be, say, nmoles hr-1.)
µmole min-1 µmole-1 = min-1, the units of a first order rate constant.
Thus, if we know the molecular weight of our enzyme, we can inter-
convert kcat and the specific activity,
SpAct ,pureEnzyme × MW
k cat = --------------------------------------------------------------------- ( 1µmole = ------------ mg )
MW
1000 1000
Students are sometimes confused by the fact that when they are intro-
duced to Vmax, they see the equation,
This is because if we multiply the above equation for Vmax by the vol-
ume of the system, we obtain
Vmax
µmoles min-1
or mM min-1
V max V max
E T = ---------------- mg , or E T = ------------µmoles
SpAct k cat
Absorption bands
I0 Aλ
I0 = initial intensity
I = intensity after
passage through sample
λ nm
Aλ = log(I/I0)λ = -log(I0/I)λ
Aλ = ελcl,
∆A λ ε λ ∆c
----------- = -----------
-
∆t ∆t
i.e., the rate of the reaction is effectively given by the rate of change
of the absorbance.
NAD+/NADP+
NADH/NADPH
Aλ
Our sample is usually serum, so that many enzymes and other extra-
neous molecules including enzymes that use NADH/NADPH will be
present during the assay, which may cause oxidation/reduction of the
NADH or NAD+ that we add to the assay medium. Also, our moni-
tored molecule may be unstable, and also contribute to any change in
A340 - this is particularly true of NADH or NADPH. Suppose we
have oxidation of NADH to NAD+,
Rates ~ slopes
A340 preincubation
phase
Time
Synthetic Chromoge- For a lot of enzyme activities we may wish to measure, NAD+/
nic Substrates NADP+ may not be a cosubstrate, but many synthetic (chromogenic)
substrates that either absorb light or give products that absorb light
are now available, e.g., p-nitrophenolphosphate (pNPP). This is used
in the determination of phosphatase activities.
O- phosphatase
O2N P O- + H2 O O2N OH + PO4 3
O
p-nitrophenol
p-nitrophenolphosphate
measure the rate of change in A400 before and after adding our sam-
ple (serum), and substract the background rate. I.e. although we cor-
rect for instability of the artificial substrate by following background
breakdown of the pNPP, we do not strictly actually do a ‘preincuba-
tion’ of the serum in this situation.
True rate = Rate after adding serum - Rate before adding serum
E1
A B
E2
B + NADH + H+ BH2 + NAD+
or
E1
A BH2
E2
BH2 + NAD+ B + NADH + H+
Provided the two sets of assay media are compatible, we can combine
the two assays into a single system, so that as B/BH2 is formed from
A by E1, it is converted into BH2/B by E2 with the concomitant oxi-
dation/reduction of NADH/NAD+, i.e., we can indirectly follow the
E1 activity using the rate of change of A340. We have coupled the
two reactions. We must ensure:
but in addition,
Thus,
(iii) the second enzyme, E2, must be present at sufficiently high levels
that the overall rate will not depend on the second reaction, i.e.,
the second reaction is not limiting.
(2) the serum sample containing the enzyme whose activity we want
to measure (E1).
Note that after we have added A, the reaction at first accelerates over
a period of time called the ‘lag phase’. The part of the progress curve
whose slope we use for the determination of activity is the linear
phase after the lag phase has ended. The lag phase arises because after
we have first added A, although E1 is now saturated with its substrate,
and that reaction is going at its maximum rate, the steady state level
of B, the product of E1 and substrate for E2 has not yet been attained.
This takes a finite period of time to be generated. The second reac-
tion (catalyzed by E2), which is the reduction of B with the concom-
itant oxidation of NADH, will increase in rate until the
concentration of its substrate B has achieved its steady state level.
I II preincubation
III lag
Add serum
A340 Add excess ‘A’ IV Steady-State linear
Depletion
V of NADH
Time
Albumin This transport protein is made by the liver, and serum levels of albu-
min are one of the indications of liver dysfunction. Since gamma
globulin is synthesized by the immune system, while albumin is made
BUN, Blood Urea Used to monitor renal function. It may be elevated in renal disease,
Nitrogen and in states of dehydration.
Creatinine levels Used along with BUN to monitor renal function. Creatinine is
formed by spontaneous (non-enzymatic) breakdown of creatine phos-
phate in the muscles,
NH2+ O H
N
HN
spontaneous C O
+ PO4 3-
-O CH2 C P C
C N N O-
H O- N CH2
O CH3 H3C
and is normally excreted only by the kidney into the urine. Serum
levels of creatinine are raised in renal insufficiency. The rate of for-
mation is proportional to muscle mass, and is normally at a constant
rate, which allows the creatinine level in a urine sample to be used as
a measure of the time over which the urine was produced.
Ceruloplasmin This is a serum protein (an α2-globulin) that has two functions.
Firstly, it carries 90% of the Cu in the blood. Secondly, it acts as a
ferroxidase, oxidizing Fe2+ to Fe3+. This is important in the blood,
because the major Fe carrier, transferrin, can only bind Fe in its ferric
(Fe3+) state. Ceruloplasmin thus acts to link Cu and Fe metabolism.
Its main diagnostic use is as an indicated of Wilson's disease (a genet-
ically determined hepatoreticular degeneration), when there is a fail-
ure of the liver to excrete Cu into the bile, and Cu accumulates in the
organs of the body. Although an abnormality in ceruloplasmin is not
the primary cause of Wilson's disease, its levels are decreased in that
condition.
ALP, Alkaline Phos- Another non-specific phosphatase, but with an alkaline pH optimum
phatase (~10). Also assayed with p-nitrophenylphosphate. It has less specific
locations than acid phosphatase. It is present in high levels in liver,
bone (osteoblasts), and the intestine. The hepatic content of ALP is
increased in cholestasis (obstruction of the bile duct), and can give
increased serum concentrations. It is released into the blood by active
osteoblasts, and can therefore indicate active bone formation. Thus,
it is at high levels in infants of 1-2 years and in the early teens. It is
an important indicator of bone pathology, and is a valuable guide to
the activity of Paget's Disease. It indicates bone remodelling due to
bone resorption. The serum activity is often elevated in bone cancer.
The physiological function of this enzyme is unclear.
The Amylases These are digestive enzymes produced in two tissues, namely the sali-
vary glands and the exocrine pancreas. There are tissue-specific
isozymes, which can be distinguished by the effect of inhibitors, and
by mobility on electrophoresis.
Pancreatic Lipase This is a digestive enzyme of the exocrine pancreas released into the
duodenum that hydrolyses the ester links at the 1 and 3 positions of
triglycerides in the presence of colipase, bile and Ca2+ to give 2-
monoglyceride and the fatty acids from the 1 and 3 positions (see
Module 3, PU6).
O
O H2 C O CR1 2H2O O CH2OH
R2 C O CH O R2 C O CH + R1COOH + R3COOH
H2 C O CR3 CH2OH
triglyceride 2-monoglyceride
LPL, Lipoprotein This enzyme is bound to the lumen of the capillaries, and catalyses
Lipase the breakdown of triglyceride to 2-monoglyceride and R1COOH and
R3COOH, (like pancreatic lipase). (It is discussed in detail in PU 6,
Modules 3 and 4.)
O
OH2 C O CR1 2H2O O CH2OH
R2 C O CH O R2 C O CH + R1COOH + R3COOH
H2 C O CR3 CH2OH
triglyceride 2-monoglyceride
Its levels are low in Type I diabetes (juvenile onset), and lipoprotein
lipase activity may be greatly reduced in Type I hyperlipoproteinemia,
an autosomally recessive inherited disease.
CK, Creatine Kinase/ This enzyme of the muscle sarcoplasm catalyzes the transfer of a
CPK, Creatine Phos- phosphoryl group from creatine phosphate to ADP to regenerate
ATP used up in muscle contraction (creatine phosphate is the imme-
phokinase diate energy reserve in muscle.)
NH2+ O NH2+
H2 H2
-O -O
C C P C C
C N N O- + ADP C N NH2 + ATP
H -
O
O O
creatine phosphate creatine
MM in skeletal muscle
MB 30% of the CK in the heart
BB Brain and Thyroid
LDH, Lactate Dehy- This catalyzes the interconversion of ketopyruvate and L-lactate,
drogenase
O O
O- O-
C C
HO CH + NAD+ C O + NADH + H+
CH3 CH3
lactate ketopyruvate
α-HBD, α-Hydroxy- An important difference between the LDH isozymes is that H4 and
butyrate Dehydroge- H3M show higher activity with α-hydroxybutyrate as the substrate
nase than with the normal substrate, lactate, while the other isozymes do
not.
O O
O- O-
C C
HO CH + NAD+ C O + NADH + H+
CH2 CH2
CH3 CH3
L-α-hydroxybutyrate α-ketobutyrate
α-HBD
The Transaminases These enzymes catalyze the transfer of an α-amino group from an α-
amino acid to an α-keto acid.
NH3+ NH3+
O O
H C CO2- + C CO2- C CO2- + H C CO2-
R1 R2 R1 R2
NH3+
O
C CO2- H C CO2-
NH3+ CH2 CH2
O
H C CO2- + C CO2- +
CH2 CH2
R1 R1
CO2- CO2-
AST, Aspartate Tran- This catalyzes the transfer of the amino group of apartate to α-keto-
saminase/GOT, glutarate,
Glutamate Oxaloace-
NH3+
tate Transaminase O
NH3+ C CO2- H C CO2-
(SGOT = Serum O
GOT) H C CO2- CH2 C CO2- CH2
CH2 + CH2 +
CH2 CH2
CO2- CO2-
CO2- CO2-
ALT, Alanine Transam- This catalyzes the transfer of the amino group of alanine to α-ketogl-
inase/GPT, Glutamate utarate,
Pyruvate Transami-
nase (SGPT = Serum
GPT)
NH3+
O
C CO2- H C CO2-
NH3+ CH2 CH2
O
H C CO2- + C CO2- +
CH2 CH2
CH3 CH3
CO2- CO2-
The levels of CK, AST (GOP), and α-HBD have characteristic time
courses in the serum after a myocardial infarction (MI).
CK
Relative
Enzyme AST
Activity α-HBD
5 10
Time, Days
GGT, γ-Glutamyl This is located in the ER of liver cells (where its function is not clear),
Transferase and in the plasma membrane of renal tubular cells, where it may be
involved in the transport of certain amino acids in the kidney. It is
used as an indicator of some hepatobiliary diseases, when it is released
into the blood.
Sorbitol Dehydroge- Increased serum levels are seen after liver damage.
nase
Other Enzyme Activi- Clearly, if a specific condition is suspected, then other assays may be
ties carried out, e.g., for glucose-6-phosphatase if glucose-6-phosphatase
deficiency is likely, etc, etc. Click on the hypertext link for a listing
of some popular enzyme-based diseases and syndromes.
II. Therapeutic The major use of our knowledge of enzymes is in the treatment of
disease by enzyme inhibitors. There are many examples of this, e.g.,
the use of lovostatin, an inhibitor of cholesterol synthesis in the
treatment of certain hyperlipoproteinemias. Occasionally, an
enzyme may be used directly, e.g., the use of asparaginase to destroy
asparagine,
O O
NH2 O-
C
H2O C
CH CH
H3 N+ CO2- H3 N+ CO2-
L-Asn L-Asp
Post Test
1. All of the following enzymes are markers for liver disease
EXCEPT
a. alanine transaminase (ALT)
b. aspartate transaminase (AST)
c. creatine phosphokinase (CPK)
d. sorbitol dehydrogenase
e. lactate dehydrogenase (LDH)
answer
STUDY GUIDE-3
I. Membrane Trans- Biological membranes are constructed around the phospholipid
port bilayer. This is a 2-dimensional micelle, with the non-polar acyl
chains of the phospholipids forming an oily internal film sandwiched
between two polar hydrophilic surfaces formed by the head groups of
the phospholipids, together with the solvating medium of water and
counterions. The phospholipid bilayer represents a barrier to the free
diffusion of solutes, acting to separate the internal contents of the cell
from the external medium, and to form internal compartments
between different functional parts of the cell. Because of the high
electrical resistance of the hydrocarbon chains in its interior, the
bilayer also acts as a capacitor, separating electrical charges across the
membrane. Operation of three phenomena, the Donnan effect, the
differential permeability of the membrane to ions and the Na+, K+-
pump combine to give the interior of the cell a negative potential rel-
ative to the outside. There is an electrical potential gradient across
the plasma membrane tending to pull positively charged solutes into
the cell, and push negatively charged solutes out.
inorganic ions K+
Ca2+
Na+
Cl-
JM
facilitated
J0 hyperbolic
JM/2
linear simple
KM ∆c
Facilitated (Mediated) Clearly, since the cell needs to admit and expel an enormous number
Passive Diffusion and of different solutes in a highly selective way for many purposes, spe-
cial mechanisms must have evolved to control movement of mole-
Active Transport cules and ions across biological membranes. These all use proteins,
which, since they all act to lower the activation free energy for move-
ment, have the characteristics of enzymes. (Only O2 and CO2 move
across cell membranes without special proteins being involved-there
are even specific channels for water.) A fixed, limited, number of pro-
tein molecules, often located in special regions of the membrane are
involved. These are usually very specific for the solute whose trans-
port they are catalyzing, and must be regulatable to control the flux.
We can divide the transport proteins into two broad classes: facili-
tated passive diffusion and active transport.
Facilitated (Mediated) Here the driving force for the transport process is just the electro-
Passive Diffusion chemical gradient for the solute, which moves spontaneously down
its electrochemical gradient. ∆G is negative, and the process is pas-
sive just as with the simple case, because we do not have to do any-
thing to the system to make the net transport occur. Because there
are only a limited number of transporter protein molecules, the flux
will reach a limiting value as the concentration difference of the sol-
ute across the membrane is increased and all the protein molecules
become occupied in transporting the solute; i.e., we have saturation
kinetics, as shown in Fig. 2. The protein effectively catalyzes the
transport of the solute and we get equations for J0 and ∆c very similar
to the Michaelis -Menten equation for v0 and [S].
∆c
J 0 = J M ---------------------
∆c + K M
and the J0 vs. ∆c curve looks just like the hyperbolic curve for an
ordinary Michaelis-Menten enzyme.
Since the binding sites on the protein molecules which catalyze trans-
port can only accomodate the particular solute or structurally similar
molecules, facilitated (mediated) passive diffusion thus differs from
from simple (passive) diffusion by:
+I -I
1/J0
1/JM
Sub-Types of Facili- Uniport:-A single type of solute moves down its electrochemical gra-
tated Diffusion dient
Uniport
Gap Junctions The GLUT class of Ion Channels
(Allows ions and glucose transporters
small molecules to e.g. in red blood
move from one cell cells, muscle, adi-
to another) pocytes
Ligand Voltage
Gated Gated
Symport and Antiport In symport, two different types of solute are transported in the same
Coupled Cotransport direction across the membrane
Ionophores provide These are organic molecules, often from microorganisms, that medi-
good examples of facil- ate facilitated diffusion of ions across membranes. They sometimes
have antibiotic properties. The driving force for net solute flow is
itated diffusion. again the electrochemical gradient of the solute. There are two classes
of ionophore:
Active Transport Here the electrochemical gradient for the process is unfavorable -in
the absence of the transporter, the ∆G is positive (> 0), and transport
will not occur spontaneously in the direction needed. The electro-
chemical gradient opposes the desired movement. To get movement
Primary (Direct) In this, an energy source is used directly to push the solute against its
Active Transport electrochemical gradient. There are three main forms:
1. Where the free energy of hydrolysis of ATP is coupled to the
transport process. Examples are the P-type ATPases, in which a
phosphorylated intermediate is formed, such as the Na+, K+-
ATPase in the plasma membrane, and the Ca2+, H+-ATPases in
the plasma membrane and SER. The V-type H+ transporting
ATPases of endosomes and lysosomes represent another class,
where a phosphorylated intermediate is not formed.
2. Where the transport of H+ against their concentration gradient
out of the mitochondria is coupled to passage of electrons
through Complexes I, III, and IV of the electron transport chain
in the inner mitochondrial membrane.
3. Where light energy is captured and used to move H+ across
membranes, as in bacteriorhodopsin.
chemical gradients in symport with Na+ moving back down its elec-
trochemical gradient into the intestinal epithelial cell. Another
example is the movement of Ca2+ out of a heart muscle cell against its
electrochemical gradient in antiport with Na+ moving into the cell
down its electrochemical gradient. This is catalyzed by the Na+-Ca2+
exchanger,
(Since digitalis inhibits the Na+, K+ pump, which thus reduces the
Na+ gradient across the sarcolemma of the muscle cell, less Ca2+ are
pumped out, and the concentration of Ca2+ in the muscle cell rises.
This increases the contractile force of the heart muscle cell, and is the
basis for the positive inotropic effect of the cardiac glycosides.)
Post-Test
1. Selective permeability of cell membranes is achieved, in part, by
active transport systems. Active transport differs from passive
transport in that it
a. requires energy but no transport carrier
b. depends primarily on diffusion and osmosis
c. requires a carrier but no energy
d. requires energy, usually in the form of phosphate anhydride
bonds
3. Ionophores include
a. pore-forming antibiotics that act by passive transport
b. carrier antibiotics that act by active transport mechanisms
c. pore-forming and carrier antibiotics that act by active trans-
port and passive transport respectively
d. pore-forming and carrier antibiotics that act by passive trans-
port and active transport, respectively
answer
2. e
3. a
7. e Three potassium ion are NOT translocated per ATP, only two
potassium ions are translocated per ATP.
Practice Exam
The two hour exam for Biochemistry PU02 will be composed of
multiple choice questions. The pretest, post test, and problem sets in
this Problem Unit provide examples of short answer questions to
check your knowledge base while the (25) questions below are actual
questions of the "Board Type" given to a previous MSI class. You
may wish to time your use of this Practice Exam to one hour or less in
order to pace yourself for the exam.
For each of the following multiple choice questions, choose the most
appropriate answer.
answer
E1 E2
A+B P1 P2 (measured product)
1.0 x 10-3 65
5 x 10-4 63
1 x 10-4 51
5 x 10-5 42
3 x 10-5 33
2 x 10-5 27
1 x 10-5 17
5 x 10-6 9.5
1 x 10-6 2.2
5 x 10-7 1.1
The best estimates from this data with respect to this enzyme are:
a. Km = about 5 x 10-5 M, Vmax about 63 µmol/min.
b. active sites are unoccupied on the great majority of enzyme
molecules when the substrate concentration equals 3 x 10-5
M.
c. Km = about 3 x 10-5 M, Vmax about 65 µmol/min.
d. Km = about 2 x 10-5 M, Vmax about 130 µmol/min.
e. the enzyme's active sites are approximately half-saturated at
1 x 10-4 M.
answer
e. to "spark" metabolism.
answer
11. What is one good reason why initial velocities are employed in
enzyme assays?
answer
18. All of the following statements about enzymes are true EXCEPT:
a. enzymes reduce the activation energy needed for a reaction
to occur.
b. pH affects enzyme activity by determining the degree of ion-
ization of catalytic groups.
c. turnover number is a measure of the maximal activity on a
molecular level.
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COMMENTS
I hope that you find this pdf file useful. Comments on how to make
it better would be greatly appreciated. Please notify me in person or
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removed. The online version on the Biochem server can be easily
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