Structure & Reactivity in Chemistry
MP4. Regulation of Metabolic Pathways A: How is enzyme
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
- 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.
- 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
- 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.
- 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.
- 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.
- 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
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.
- 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.
- 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.
- 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
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