‫انواع ممسير هاي كاتاليزآنزيم ها‬:‫عنوان تحقيق‬
(contributed by Henry Jakubowski)
Exquisite mechanisms have evolved that control the flux of metabolites through metabolic
pathways to insure that the output of the pathways meets biological demand and that energy
in the form of ATP is not wasted by having opposing pathways run concomitantly in the
same cell.
Enzymes can be regulated by changing the activity of a preexisting enzyme or changing the
amount of an enzyme.
A. Changing the activity of a pre-existing enzyme: The quickest way to modulate the
activity of an enzyme is to alter the activity of an enzyme that already exists in the cell. The
list below, illustrated in the following figure, gives common ways to regulate enzyme activity
a. Substrate availability: Substrates (reactants) bind to enzymes with a characteristic
affinity (characterized by a dissociation constant) and a kinetic parameter called Km
(units of molarity). If the actual concentration of a substrate in a cell is much less
than the Km, the activity of the enzyme is very low. If the substrate concentration is
much greater than Km, the enzyme active site is saturated with substrate and the
enzyme is maximally active.
b. Product inhibition: A product of an enzyme-catalyzed reaction often resembles a
starting reactant, so it should be clear that the product should also bind to the activity
site, albeit probably with lower affinity. Under conditions in which the product of a
reaction is present in high concentration, it would be energetically advantageous to
the cell if no more product was synthesized. Product inhibition is hence commonly
observed. Likewise it be energetically advantageous to a cell if the end product of an
entire pathway could likewise bind to the initial enzyme in the pathways and inhibit it,
allowing the whole pathway to be inhibited. This type of feedback inhibition is
commonly oberved
c. Allosteric regulation: As many pathways are interconnected, it would be optimal if
the molecules of one pathway affected the activity of enzymes in another
interconnected pathway, even if the molecules in the first pathway are structurally
dissimilar to reactants or products in a second pathway. Molecules that bind to sites
on target enzymes other than the active site (allosteric sites) can regulate the activity
of the target enzyme. These molecules can be structurally dissimilar to those that
bind at the active site. They do so my conformational changes which can either
activate or inhibit the target enzyme's activity.
d. pH and enzyme conformation: Changes in pH which can accompany metabolic
process such as respiration (aerobic glycolysis for example) can alter the
conformation of an enzyme and hence enzyme activity. The initial changes are
covalent (change in protonation state of the protein) which can lead to an alteration in
the delicate balance of forces that affect protein structure.
e. pH and active site protonation state: Changes in pH can affect the protonation state of
key amino acid side chains in the active site of proteins without affecting the local or
global conformation of the protein. Catalysis may be affected if the mechanism of
catalysis involves an active site nucleophile (for example), that must be deprotonated
for activity.
f. Covalent modification: Many if not most proteins are subjected to post-translational
modifications which can affect enzyme activity through local or global shape changes,
by promoting or inhibiting binding interaction of substrates and allosteric regulators,
and even by changing the location of the protein within the cell. Proteins may be
phosphorylated, acetylated, methylated, sulfated, glycosylated, amidated,
hydroxylated, prenylated, myristolated, often in a reversible fashion. Some of these
modifications are reversible. Regulation by phosphorylation through the action of
kinases, and dephosphorylation by phosphates is extremely common. Control of
phosphorylation state is mediated through signal transduction process starting at the
cell membrane, leading to the activation or inhibition of protein kinases and
phosphatases within the cell.
Figure: Regulation of the Activity of Pre-existing Enzymes
Extracellular regulated kinase 2 (ERK2), also known as mitogen activate protein
kinase 2 (MAPK2) is a protein the plays a vital role in cell signaling across the cell
membrane. Phosphoryation of ERK2 on Threonine 183 (Thr153) and Tyrosine 185
(Tyr185) leads to a structural change in the protein and the regulation of its
activity.
Jmol: Erk2 -Structural Comparison of phosphorylated and dephosphorylated enzyme
B. Changing the amount of an enzyme: Another and less immediate but longer duration
method to modulate the activity of an enzyme is to alter the activity of an enzyme that
already exists in the cell. The list below, illustrated in the following figure, shows way in
which enzyme concentration is regulated.
a. Alternation in transcription of enzyme's gene: Extracellular signal (hormones,
neurotransmitters, etc) can lead to signal transductions responses and ultimate
activation or inhibition of the transcription of the gene for a protein enzyme. These
changes result from recruitment of transcription factors (proteins) to DNA sequences
that regulate transcription of the enzyme gene.
b. Degradation of messenger RNA for the enzyme: The levels of messenger RNA for a
protein will directly determin the amount of that protein synthesized. Small inhibitor
RNAs, derived from microRNA molecules transcribed from cellular DNA, can bind
to specific sequences in the mRNA of a target enzyme. The resulting double-stranded
RNA complex recruits an enzyme (Dicer) that cleaves the complex with the effect of
decreasing translation of the protein enzyme from its mRNA.
c. Co/Post translational changes: Once a protein enzymes is translated from its mRNA,
it can undergo a changes to affect enzyme levels. Some proteins are synthesized in a
"pre"form which must be cleaved in a targeted and limited fashion by proteases to
active the protein enzyme. Some proteins are not fully folded and must bind to other
factors in the cell to adopted a catalytically active form. Finally, fully active protein
can be fully proteolyzed by the proteasome, a complex within cells, or in lysosomes,
which are organelles within cells containing proteolytic enzymes.
Next we will consider which enzymes in pathways make the best target for regulation.
Navigation:
Cell Metabolism
A cell's daily operations are accomplished through the biochemical reactions that take place
within the cell. Reactions are turned on and off or sped up and slowed down according to the
cell's immediate needs and overall functions. At any given time, the numerous pathways
involved in building up and breaking down cellular components must be monitored and
balanced in a coordinated fashion. To achieve this goal, cells organize reactions into various
enzyme-powered pathways.
What Do Enzymes Do?
Enzymes are protein catalysts that speed biochemical reactions by facilitating the molecular
rearrangements that support cell function. Recall that chemical reactions convert substrates
into products, often by attaching chemical groups to or breaking off chemical groups from
the substrates. For example, in the final step of glycolysis, an enzyme called pyruvate kinase
transfers a phosphate group from one substrate (phosphoenolpyruvate) to another substrate
(ADP), thereby generating pyruvate and ATP as products (Figure 1).
/scitable
uninitedaudio
Figure 1: Glycolysis
Energy is used to convert glucose to a 6 carbon form. Thereafter, energy is generated to
create two molecules of pyruvate.
© 2010 Nature Education All rights reserved.
Figure Detail
Enzymes are flexible proteins that change shape when they bind with substrate molecules. In
fact, this binding and shape changing ability is how enzymes manage to increase reaction
rates. In many cases, enzymes function by bringing two substrates into close proximity and
orienting them for easier electron transfer. Shape or conformational changes can also act as
an on/off switch. For example, when inhibitor molecules bind to a site on an enzyme distinct
from the substrate site, they can make the enzyme assume an inactive conformation, thereby
preventing it from catalyzing a reaction. Conversely, the binding of activator molecules can
make an enzyme assume an active conformation, essentially turning it on (Figure 2).
/scitable
uninitedaudio
Figure 2: Activation and inactivation of of enzyme reaction
Enzymes are proteins that can change shape and therefore become active or inactive. An
activator molecule (green pentagon) can bind to an enzyme (light green puzzle shape) and
change its overall shape. Note the transformation of the triangular point on the green enzyme
into a rounded shape. This transformation enables the enzyme to better bind with its substrate
(light pink puzzle piece). In contrast, an inhibitor molecule (pink circle) can prevent the
interaction of an enzyme with its substrate and render it inactive.
© 2010 Nature Education All rights reserved.
Figure Detail
What Are Metabolic Pathways?
Many of the molecular transformations that occur within cells require multiple steps to
accomplish. Recall, for instance, that cells split one glucose molecule into two pyruvate
molecules by way of a ten-step process called glycolysis. This coordinated series of chemical
reactions is an example of a metabolic pathway in which the product of one reaction becomes
the substrate for the next reaction. Consequently, the intermediate products of a metabolic
pathway may be short-lived (Figure 3).
/scitable
uninitedaudio
Figure 3: Reaction pathway
Enzymes can be involved at every step in a reaction pathway. At each step, the molecule is
transformed into another form, due to the presence of a specific enzyme. Such a reaciton
pathway can create a new molecule (biosynthesis), or it can break down a molecule
(degradation).
© 2010 Nature Education All rights reserved.
Sometimes, the enzymes involved in a particular metabolic pathway are physically
connected, allowing the products of one reaction to be efficiently channeled to the next
enzyme in the pathway. For example, pyruvate dehydrogenase is a complex of three different
enzymes that catalyze the path from pyruvate (the end product of glycolysis) to acetyl CoA
(the first substrate in the citric acid cycle). Within this complex, intermediate products are
passed directly from one enzyme to the next.
How Do Cells Keep Chemical Reactions in Balance?
Cells are expert recyclers. They disassemble large molecules into simpler building blocks and
then use those building blocks to create the new components they require. The breaking down
of complex organic molecules occurs via catabolic pathways and usually involves the
release of energy. Through catabolic pathways, polymers such as proteins, nucleic acids, and
polysaccharides are reduced to their constituent parts: amino acids, nucleotides, and sugars,
respectively. In contrast, the synthesis of new macromolecules occurs via anabolic pathways
that require energy input (Figure 4).
Cells must balance their catabolic and anabolic pathways in order to control their levels of
critical metabolites — those molecules created by enzymatic activity — and ensure that
sufficient energy is available. For example, if supplies of glucose start to wane, as might
happen in the case of starvation, cells will synthesize glucose from other materials or start
sending fatty acids into the citric acid cycle to generate ATP. Conversely, in times of plenty,
excess glucose is converted into storage forms, such as glycogen, starches, and fats.
/scitable
uninitedaudio
Figure 4: Catabolic and anabolic pathways in cell metabolism
Catabolic pathways involve the breakdown of nutrient molecules (Food: A, B, C) into usable
forms (building blocks). In this process, energy is either stored in energy molecules for later
use, or released as heat. Anabolic pathways then build new molecules out of the products of
catabolism, and these pathways typically use energy. The new molecules built via anabolic
pathways (macromolecules) are useful for building cell structures and maintaining the cell.
© 2010 Nature Education All rights reserved.
How Do Cells Manage All Their Chemical Reactions?
/scitable
uninitedaudio
Figure 5: Feedback inhibition
When there is enough product at the end of a reaction pathway (red macromolecule), it can
inhibit its own synthesis by interacting with enzymes in the synthesis pathway (red arrow).
© 2010 Nature Education All rights reserved.
Figure Detail
Not only do cells need to balance catabolic and anabolic pathways, but they must also
monitor the needs and surpluses of all their different metabolic pathways. In order to bolster a
particular pathway, cells can increase the amount of a necessary (rate-limiting) enzyme or use
activators to convert that enzyme into an active conformation. Conversely, to slow down or
halt a pathway, cells can decrease the amount of an enzyme or use inhibitors to make the
enzyme inactive.
Such up- and down-regulation of metabolic pathways is often a response to changes in
concentrations of key metabolites in the cell. For example, a cell may take stock of its levels
of intermediate metabolites and tune the glycolytic pathway and the synthesis of glucose
accordingly. In some instances, the products of a metabolic pathway actually serve as
inhibitors of their own synthesis, in a process known as feedback inhibition (Figure 5). For
example, the first intermediate in glycolysis, glucose-6-phosphate, inhibits the very enzyme
that produces it, hexokinase.
Conclusion
The management of biochemical reactions with enzymes is an important part of cellular
maintenance. Enzymatic activity allows a cell to respond to changing environmental demands
and regulate its metabolic pathways, both of which are essential to cell survival.
Several enzymes can work together in a specific order, creating metabolic pathways. In a
metabolic pathway, one enzyme takes the product of another enzyme as a substrate. After the
catalytic reaction, the product is then passed on to another enzyme. Sometimes more than one
enzyme can catalyze the same reaction in parallel; this can allow more complex regulation:
with, for example, a low constant activity provided by one enzyme but an inducible high
activity from a second enzyme.
Enzymes determine what steps occur in these pathways. Without enzymes, metabolism
would neither progress through the same steps nor be fast enough to serve the needs of the
cell. Indeed, a metabolic pathway such as glycolysis could not exist independently of
enzymes. Glucose, for example, can react directly with ATP to become phosphorylated at one
or more of its carbons. In the absence of enzymes, this occurs so slowly as to be insignificant.
However, if hexokinase is added, these slow reactions continue to take place except that
phosphorylation at carbon 6 occurs so rapidly that, if the mixture is tested a short time later,
glucose-6-phosphate is found to be the only significant product. As a consequence, the
network of metabolic pathways within each cell depends on the set of functional enzymes
that are present.
http://en.wikipedia.org/wiki/File:Glycolysis.svg:‫منابع‬
http://www.nature.com/scitable/topicpage/cell-metabolism-14026182