Cataliza Enzime Si Proteine

Cambridge Books Online
http://ebooks.cambridge.org/
Chemistry of Fossil Fuels and Biofuels
Harold Schobert
Book DOI: http://dx.doi.org/10.1017/CBO9780511844188
Online ISBN: 9780511844188
Hardback ISBN: 9780521114004
Chapter
2 - Catalysis, enzymes, and proteins pp. 10-18
Chapter DOI: http://dx.doi.org/10.1017/CBO9780511844188.003
Cambridge University Press

2 Catalysis, enzymes, and proteins
2.1 Catalysis
The topic of catalysis recurs throughout fuel chemistry. A catalyst increases the rate
of a chemical reaction without itself being permanently altered by the reaction, or
appearing among the products. The key word is rate. Catalysts affect reaction
kinetics. A catalyst affects reaction rate by providing a different mechanism for
the reaction, usually one that has a markedly lower activation energy than that of
the non-catalyzed reaction. Catalysts do not change reaction thermodynamics; they
do not alter the position of equilibrium [A], but they can help reach equilibrium
much more quickly. And, they cannot cause a thermodynamically unfavorable
reaction to occur.
Catalysts can be classified as homogeneous, in the same phase as the reactants and
products, and heterogeneous, in a separate phase. Homogeneous catalysts mix intim-
ately with the reactants. This good mixing often leads to enormous rate enhancements,
in some cases by more than eight orders of magnitude. But, because they are in the
same phase as the reactants and products, industrial use would require a separation
operation for catalyst recovery downstream of the reaction, unless one were willing to
throw away the catalyst (possibly allowing it to contaminate the products) as it passes
through the reactor. For many catalytic processes, the catalyst costs much more than
the reactants do, so loss of the catalyst would result in a significant economic penalty.
Usually, heterogeneous catalysts have no major separation problems, thanks to their
being in a separate phase from reactants and products. However, because of their being
in a separate phase, mass-transfer limitations can hold up access of the reactants to the
catalyst, or hold up departure of products. Heterogeneous catalysis can also be affected
by various problems at the catalyst surface (discussed in Chapter 13). Large-scale
industrial processing almost always favors use of heterogeneous catalysts, to avoid
possibly difficult downstream separation issues. Nevertheless, steady progress is being
made in finding ways to overcome separation problems with homogeneous catalysts,
including, as examples, membrane separation, selective crystallization, and use of
supercritical solvents.
While, by definition, a catalyst remains unchanged at the end of a reaction, it can,
and often does, change during a reaction. Mechanisms of many catalytic reactions often
involve many steps, which collectively comprise the catalytic cycle. The catalyst might
undergo change during one or more of the elementary reaction steps of the mechanism,
but at the end, when its action is complete, the catalyst must emerge in its original form,
ready for another catalytic cycle.
Downloaded from Cambridge Books Online by IP 81.180.218.244 on Fri Mar 18 08:06:23 GMT 2016.
http://dx.doi.org/10.1017/CBO9780511844188.003
Cambridge Books Online © Cambridge University Press, 2016
2.2 Proteins 11
Most homogeneous catalytic reactions occur in the liquid phase. Some reactions
can be catalyzed in the gas phase by homogeneous catalysts (which, because they
are homogeneous, must be gases themselves). Probably the most important example
of homogeneous catalysis in the gas phase is the chlorine-catalyzed decomposition
of ozone, the reaction responsible for the so-called ozone hole in the atmosphere [B].
Various parameters can be used to describe quantitatively the quality or “goodness”
of a catalyst. Turnover number, and the related turnover frequency, compare the
efficiency of different catalysts. Turnover number indicates the number of molecules
of reactant that one molecule of catalyst can convert into product. The term “turnover”
comes from the notion that the catalytic conversion is “turning over” reactant mol-
ecules into product molecules. Turnover frequency is the turnover number expressed
per unit time. Selectivity expresses the fraction of the desired product, usually in weight
percent or mole percent, among all products of the reaction. Ideally, selectivity should
be as close to 1, or 100%, as possible. Catalyst activity can be broadly defined in terms
of rate of consumption of the reactant(s) or rate of formation of products. (These terms
have slightly different meanings in the field of heterogeneous catalysis, and are revisited
in Chapter 13.) Ideal catalysts are those with high selectivity and high activity.
2.2 Proteins
Biochemical reactions in living organisms rely on homogeneous catalysts called

enzymes. Enzymes provide superb activity and selectivity. Because most enzymes are
proteins [C], we consider composition and structure of proteins first, leading into a
discussion of enzymes and their catalytic behavior.
The building blocks of proteins are amino acids. These compounds contain both an
amine and a carboxylic acid functional group. All naturally occurring amino acids of
biochemical significance are 2-aminocarboxylic acids. Derivatives of carboxylic acids
have sometimes been named using Greek letters to identify the positions on the carbon
chain starting from the atom attached to the carboxylic group, with a- indicating the
carbon attached to the carboxylic acid, b- the next carbon in the chain, and so on.
Hence 2-aminocarboxylic acids can be, and usually are, referred to as a-amino acids.
Twenty naturally occurring a-amino acids are known, which differ in the nature of
the organic substituent, generically called R, attached to the a-carbon atom [D].
Alanine (2.1), leucine (2.2), and cysteine (2.3), provide examples.
O
C OH
H2N CH
O
O
CH2 OH
H2N C C
CH OH H3C CH
CH
H2N
CH3 CH3 CH2 SH
2.1 Alanine 2.2 Leucine 2.3 Cysteine
Amines can react with carboxylic acids to form amides, e.g. the reaction of methylamine
with acetic acid:
O
CH3
H3C NH2 + HO C H3C + H2O

N CH3
O H
Because amino acids contain both functional groups, one molecule of an amino acid
can react with another to form an amide, e.g.
O
O OH
O C OH O C
H 2N C + H2N CH H2 N C CH CH3 + H 2O
CH OH CH N CH
CH CH3 H
CH3 CH3 CH3

H 3C
The two amino acids need not be identical, as shown in this example. With amino
acids, the amide functional group is called a peptide linkage. The dipeptide produced
in the reaction shown above still contains an amine and a carboxylic acid, thus
can react with another amino acid molecule to produce tripeptides, and then tetra-,
penta-. . . and up to very large, high molecular weight polypeptides. Polypeptides
having molecular weights over 10 000 are called proteins. Fibroin (2.4), a constituent
of natural silk, has perhaps the simplest protein structure.
CH3
O HN CH
O C O
HN CH2 O
O HN CH2
C O C O
HN CH O ]x
[ CH3
2.4 Fibroin
Fibroin is a co-polymer of alanine and glycine, the two simplest amino acids.
Proteins have numerous vital roles in living organisms. Certainly their role as enzyme
catalysts is one of the most important.
Protein structure is considered at three levels. The number and kind of the individual
amino acids in the protein, and the way that they are linked together, determines
2.3 Enzymes 13
the primary structure. Even small proteins are likely to contain more than 50 peptide
linkages. The secondary structure of proteins arises from a very specific pattern of
folding of the chain of amino acids into a helix or a pleated sheet. Secondary structure
indicates how various segments of the protein molecule become oriented. Formation
of secondary structure comes from an attempt to maximize the number of possible
intramolecular hydrogen bonds between C¼O and H–N groups. With large proteins,
several secondary-structure helices might be joined together into a tertiary structure
that could arise from intramolecular electrostatic interactions, further hydrogen
bonding, or even formation of covalent bonds such as the disulfide linkage, – S–S –.
The tertiary structure describes how the whole protein molecule acquires its three-
dimensional shape. Folding the protein into its tertiary structure occurs so as to involve
the greatest possible loss of energy. Of all possible tertiary structures of a protein, the
one that actually forms is the one having the lowest DG of formation. Disruption of
the secondary or tertiary structure of the proteins, such as by heating or a change in pH,
destroys their physiological functioning, a process known as denaturation. Cooking egg
whites provides a familiar example of denaturation; the antiseptic action of “alcohol”
(i.e. isopropanol) on the skin comes from its ability to denature the proteins in bacteria.
Proteins are further classified, based on structure, as either fibrous or globular.
Fibrous proteins have long, thread-like structures that often lie adjacent to each other
to form fibers. Strong intermolecular forces facilitate this structural arrangement.
Fibrous proteins are usually insoluble in water. They make the structural materials
in organisms, including muscle, skin, and tendons. In contrast, globular proteins have
roughly spherical structures that result from strong intramolecular forces, but have
weak intermolecular forces. Globular proteins dissolve in water and in many aqueous
solutions. Enzymes that are proteins are invariably globular proteins.
2.3 Enzymes
The excellent catalytic properties of enzymes derive from their molecular configur-
ation, which provides a site at which, usually, only a single kind of molecule can
enter and react. Enzymes are so specific that they catalyze reactions not just of one
particular set of chemical bonds, but a set of bonds in a specific stereochemical configur-
ation. Emil Fischer [E] (Figure 2.1) was probably the first scientist to use the analogy of a
reactant fitting very specifically into the catalytic site on an enzyme in the way that a key fits
into a lock.
In addition to great selectivity, many enzymes also demonstrate phenomenal activity, in
exceptional cases enhancing reaction rates by 17 orders of magnitude. Of all the substances
known to catalyze reactions, whether homogeneous or heterogeneous, enzymes are the
most effective. Turnover frequencies can be of the order of 103 s 1, exceptional in
comparison with many heterogeneous catalysts, for which values might be in the range
102–104 hr 1. The very great enhancement of reaction rates by enzymes means that they
can have a noticeable effect even at very low concentrations, e.g. 10 3 10 4 mole percent.
The compound on which the enzyme acts as a catalyst is known as the substrate.
The nomenclature of enzymes involves adding the suffix –ase to a word that indicates
the function of the enzyme, or its substrate. As an example, the enzyme lactate
dehydrogenase catalyzes the dehydrogenation (i.e. oxidation) of the lactate ion.
Table 2.1 Classes of enzyme catalyst.
Type of enzyme catalyst Reaction being catalyzed

Hydrolase hydrolysis
Isomerase isomerization
Ligase linking two smaller molecules together
Lysase removing a small segment of a larger molecule
Oxidoreductase oxidation or reduction
Transferase transfer of a structural group from one molecule to another
Figure 2.1 Emil Fischer made enormous contributions to our understanding of protein
chemistry and of sugar chemistry in the late nineteenth and early twentieth centuries.
Enzymes fall broadly into six classes, summarized in Table 2.1. Almost every known
type of organic reaction has an enzyme-catalyzed counterpart.
During the reaction, the enzyme interacts with the substrate molecule(s), binding
them to a specific location, the active site, in the enzyme molecule. Enzymatic reactions
occur in three steps: formation of a complex between the substrate and the enzyme;
converting the enzyme-substrate complex into an enzyme-intermediate complex, in
which the configuration of the substrate molecule has changed; and finally formation
of an enzyme–product complex, from which the product dissociates.
Interaction of enzyme with substrate could occur via hydrogen bonding, ionic
attraction, or reversible covalent bonding. Whatever the interaction that occurs
between the active site and the substrate, it is very specific for the substrate. Further,
if the reaction is catalyzed by acid or by base, the active site must be capable of
supplying the needed acidic or basic reactant. The secondary or tertiary structure
of the enzyme strongly controls the orientation of the reactant molecules, such that
they are stereochemically oriented for rapid reaction, and lead to a product having the
biochemically correct stereochemistry. That is, the active site in the enzyme molecule
has to be a perfect stereochemical fit for the substrate – the lock has to be able to accept
the key. The sketch in Figure 2.2 shows this. The complex formed between the enzyme
and its substrate provides the optimum molecular orientation for reaction. Usually
the product detaches immediately from the enzyme, making the enzyme available for
2.3 Enzymes 15
Figure 2.2 The way in which one specific key fits into a lock provides a model for the very
specific structural relationships between an enzyme and its substrate.
another reaction. A product tightly bound to the enzyme active site would effectively
block that site from participating in further reactions, shutting down the catalytic
activity of the enzyme. The turnover frequency is often 103 s 1 per reactive site in the
enzyme; the best enzymes might reach 105 s 1.
Just as a lock will only accept the correct key, enzymes are usually extremely specific
in their action, such that any one particular biochemical reaction has its own corres-
ponding particular enzyme catalyst. In some cases enzyme catalysis is so specific that
only one compound will react with the enzyme. For example, urease catalyzes hydroly-
sis of urea, H2NCONH2, extremely well, yet has no effect for hydrolysis of methylurea,
CH3NHCONH2. However, many enzymes can catalyze the reactions of substrates
other than the desired one, provided that the changes in structure relative to the normal
substrate occur in regions of the substrate molecule that do not affect the key-in-lock fit
of substrate to active site. The catalytic activity of the enzyme might be reduced some-
what, but the reaction still proceeds. Situations occur in which a substrate binds strongly,
often irreversibly, to the active site but does not undergo whatever reaction the enzyme
catalyzes. Substrates of this kind make the enzyme unable to perform its normal catalytic
function. Such substances are catalyst poisons; the analogous problem in heterogeneous
catalysis is discussed in Chapter 13 [F].
Rates of enzymatic reactions can be expressed in several ways. The maximum
velocity, VMAX, represents the theoretical maximum rate when substrate concentration
is high enough such that the active site in the enzyme would be constantly occupied by
substrate. Maximum velocity is a specific property of a given enzyme, a function only of
the amount of enzyme present in the system. The Michaelis constant [G], KM, is the
substrate concentration at which the measured rate of reaction is half the maximum
velocity. Enzymatic reactions involving a single substrate follow Michaelis–Menten [H]
kinetics, given by
n ¼ VMAX S=ðKM þ SÞ
where n is the rate of reaction and S the concentration of the substrate. When n is
plotted as a function of S, in the initial stages of reaction the rate increases rapidly
as substrate concentration is increased, but, at some point, the rate becomes nearly
constant and essentially independent of substrate concentration. Figure 2.3 illustrates
Michaelis–Menten kinetics for a hypothetical enzymatic reaction. This behavior
reflects, first, a situation in which there is more available enzyme than substrate, so
that as substrate concentration increases, more and more of the enzyme can participate
in catalysis; but, second, at some point all of the enzyme is engaged in the reaction and
further increases in substrate concentration can have no effect.
0.12
0.1
reaction velocity
0.08
0.06
0.04
0.02
0
0 0.005 0.01 0.015 0.02 0.025 0.03 0.035
substrate molarity
Figure 2.3 A Michaelis–Menten plot provides a simple model for the kinetics of an enzymatic
reaction, relating reaction rate to substrate concentration. This curve is for a hypothetical
reaction but is typical of the shape of this relationship.
Since the majority of enzymes are proteins, it is worth considering why some, but
by no means all, protein molecules can act as catalysts (i.e. enzymes). In other words,
why aren’t all proteins enzymes? The answer lies in molecular structure, especially in
the secondary and tertiary structure that sets up the appropriate spatial conformation
of C¼O, NH, or other groups that, collectively, provide a site capable of accom-
modating and binding a specific substrate molecule. The side chains on the individual
amino acids may also be configured to create stronger intermolecular interactions with
the desired substrate molecules. Stronger interactions between the substrate and the side
chains of the amino acids in the enzyme could enhance bond-breaking reactions in the
substrate. For some, not all, proteins, the secondary and tertiary structure is geometric-
ally such that it forms the “lock” into which a specific biochemical “key” just fits. In the
many proteins that do not serve as enzymes, the secondary and tertiary structure may not
provide an appropriately configured binding site, or possibly cannot provide the acid or
base needed to complete a reaction.
Because enzyme activity depends on secondary or tertiary structure, denaturation
of an enzyme destroys its catalytic activity. In most cases, denaturation cannot be
reversed. Exact conditions triggering denaturation are specific to each enzyme, but
typically denaturation occurs about 10–15 C above the temperature normally found in
the cell. The temperature at which denaturation occurs can be reduced if major changes
in pH happen at the same time.
In some enzymatic reactions, the enzyme must be activated by the addition, or
presence, of a second substance, the cofactor. Some cofactors are inorganic ions, such
as Feþ2 or Znþ2 [I]. Other cofactors are organic molecules, called coenzymes. During the
catalytic process, the cofactor also attaches to the enzyme, and may experience either
oxidation or reduction. For us, the most important of the coenzymes are the vitamins.
Interest in using enzymes in industrial processes is increasing. Reactions using enzymes
are not limited to occurring in living organisms. Many enzymes have been isolated from
organisms and are commercially available. They can be used to catalyze reactions in
aqueous solution or sometimes in organic solvents. Enzymatic catalysis of reactions
represents an important component of the emerging field of green chemistry, which
Notes 17
includes among its goals using renewable raw materials, minimizing extra reagents or
solvents, and designing processes with very low energy requirements. Green chemistry in
turn is an important component of the broader field of sustainable development, which is
intended to meet our present needs – certainly including energy, chemicals, and materials –
without compromising society’s ability to meet the needs of future generations.
Notes
[A] Wilhelm Ostwald (1853–1932, Nobel Prize 1909), who almost single-handedly
developed the field of physical chemistry, showed that this is a direct consequence
of the First Law of thermodynamics. Consider a gas reaction that proceeds with a
change in the number of moles of gas, and hence with a change in volume. Suppose
that the reacting gases are confined within a cylinder fitted with a piston, and suppose
further that the catalyst was in a small container in the cylinder, such that it could
be alternately exposed to the reacting gases or shielded from them. If the catalyst
could alter the equilibrium composition of the mixture, the piston would move up or
down with the shift in equilibrium, creating a perpetual-motion machine.
[B] The ozone “hole” is not, of course, a hole in the atmosphere, but the term
describes a region of considerably diminished ozone concentration in the southern
hemisphere, particularly over the Antarctic. Ozone in the stratosphere helps
absorb incoming ultraviolet radiation from the sun. Exposure to high levels of
ultraviolet radiation has been implicated as a cause of health problems such as
skin cancer and cataracts. Chlorine atoms from the breakdown of chlorofluoro-
carbon gases, released as aerosol propellants, or from refrigeration and air condi-
tioning units, act as homogeneous catalysts to facilitate ozone decomposition. The
1995 Nobel Prize in chemistry was awarded to Paul Crutzen of the Netherlands
and the American scientists Mario Molina and Sherwood Rowland for their work
in understanding the formation and decomposition of ozone. This award came
exactly one week after a prominent member of the United States Congress
denounced the concept of the ozone hole as “pseudoscience.”
[C] While the great majority of enzymes are proteins, this is not true of all enzymes.
A particularly important exception is the ribosomes, cell components that assem-
ble proteins from amino acids.
[D] In solution, the simple amino acids exist in a dipolar structure formed by transfer
of a proton from the carboxyl group to the amino group, e.g. RCH(NH3)þCOO–.
This type of structure is known as a zwitterion. However, for convenience we use
the formula RCH(NH2)COOH, which seems to be a long-standing convention in
many organic chemistry textbooks.
[E] Emil Fischer (1852–1919, Nobel Prize 1902) is probably best known for enormous
contributions to understanding the structure and chemistry of sugars. He was also
among the first to determine that proteins form from the reaction of amino acids.
While the lock-and-key model remains an excellent way of thinking about enzym-
atic catalysis, it is not always correct. Daniel Koshland (1920–2007) showed in 1960
that some enzymes first accept the substrate molecule and then structurally
rearrange to fit the substrate, the induced-fit model.
[F] Many catalyst poisons harm both homogeneous and heterogeneous catalysts,
because the basic effect is the same for either type of catalyst: the poison binds
strongly to the active sites on the catalyst, blocking them from interacting with the
desired reactant molecules. In fact, many catalyst poisons also poison us, examples
being carbon monoxide and hydrogen sulfide. The underlying catalytic chemistry
is exactly the same. These substances poison us because they destroy the activity of
the enzymes on which our bodily functions depend.
[G] Named in honor of Leonor Michaelis (1875–1949), a German biochemist whose
career in the German scientific system was destroyed when, as a young man, he
published work questioning the validity of a pregnancy test devised by a scientist very
senior in the establishment. Michaelis first moved to Japan, and then to America,
where he worked at Johns Hopkins University and at The Rockefeller Institute.
[H] Maud Menten (1879–1960) was a Canadian biochemist who worked with Michaelis
in Berlin. Also an excellent artist and musician, her contributions to science
in addition to her work on enzyme kinetics included studies of hemoglobin and
the regulation of blood sugar content. She also participated in several expeditions to
the Arctic.
[I] Many inorganic species serve as enzyme cofactors; other examples include copper
and manganese. Inorganic ions that serve as cofactors are sometimes called
essential minerals. Their presence in the diet is critical for good health, specifically
because of their role as cofactors.
Recommended reading
Faber, Kurt. Biotransformations in Organic Chemistry. Springer: Berlin, 2004; Chapter 1. The
first chapter of this book provides a good overview of enzyme catalysis.
Gates, Bruce C. Catalytic Chemistry. Wiley: New York, 1992; Chapter 3. A well-written book
covering many of the fundamentals of catalysis and catalysts. Chapter 3 deals with enzymes.
Grunwald, Peter. Biocatalysis. Imperial College Press: London, 2009. A very detailed treat-
ment of enzymes and the mechanisms of enzyme-catalyzed reactions. Definitely a very useful
book for those wanting to learn more about enzyme chemistry.
McMurry, John. Organic Chemistry. Brooks/Cole: Pacific Grove, CA, 2000; Chapter 26. The
discussion of proteins and enzymes in this chapter is intended to focus on the roles of enzyme
catalysis in biosynthesis and in fermentation; i.e. to provide a background for the material
in the next several chapters. Necessarily, an enormous amount of other information on
enzymes and proteins was left out. A good place to start to explore further is in the relevant
chapters in modern introductory texts on organic chemistry. Many good ones are available;
this text by McMurry is a fine example.
Palmer, Trevor and Bonner, Philip. Enzymes. Horwood Publishing: Chichester, UK, 2007.
A comprehensive look at enzymes, including much useful information on their behavior and
uses in both biochemistry and biotechnology.
Rothenberg, Geri. Catalysis: Concepts and Green Applications. Wiley-VCH: Weinheim,
Germany, 2008. An excellent introduction to catalysis, particularly as it applies to green
chemistry and sustainable development. Chapters 3 and 5 are particularly relevant here.

Cataliza Enzime Si Proteine

Uploaded by

Document Information

Original Title

Copyright

Available Formats

Share this document

Share or Embed Document

Sharing Options

Did you find this document useful?

Is this content inappropriate?

Copyright:

Available Formats

Cataliza Enzime Si Proteine

Uploaded by

Copyright:

Available Formats

Cambridge Books Online

Chemistry of Fossil Fuels and Biofuels

Book DOI: http://dx.doi.org/10.1017/CBO9780511844188

Online ISBN: 9780511844188

Hardback ISBN: 9780521114004

2 - Catalysis, enzymes, and proteins pp. 10-18

Chapter DOI: http://dx.doi.org/10.1017/CBO9780511844188.003

Cambridge University Press

Biochemical reactions in living organisms rely on homogeneous catalysts called

H3C NH2 + HO C H3C + H2O

CH3 CH3 CH3

Table 2.1 Classes of enzyme catalyst.

Type of enzyme catalyst Reaction being catalyzed

You might also like