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Lecture 6

BIOL 200 Lecture Notes - Lecture 6: Chemical Bond, Peptide, Pharmacology

Biology (Sci)
Course Code
BIOL 200
Mathieu Roy

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S1 is a polypeptide, P1 and P2 are products. The first chemical step (3) includes the formation of a
covalent acyl-enzyme intermediate. The second step (4) is the deacylation step. It is important to
note that the group H+ , initially found on the enzyme, but not in water, appears in the product
before the step of hydrolysis, therefore it may be considered as an additional group of the
enzymatic reaction.Thus, the reaction (3) shows that the enzyme acts as a powerful reactant of
the reaction. According to the proposed concept, the H transport from the enzyme promotes the
first reactant conversion, breakdown of the first initial chemical bond (between groups P1 and
P2). The step of hydrolysis leads to a breakdown of the second chemical bond and regeneration
of the enzyme.The proposed chemical mechanism does not depend on the concentration of the
substrates or products in the medium. However, a shift in their concentration mainly causes free
energy changes in the first and final steps of the reactions (1) and (2) due to the changes in the
free energy content of every molecule, whether S or P, in water solution. This approach is in
accordance with the following mechanism of muscle contraction. The final step of ATP
hydrolysis in skeletal muscle is the product release caused by the association of myosin heads
with actin. The closing of the actin-binding cleft during the association reaction is structurally
coupled with the opening of the nucleotide-binding pocket on the myosin active site.
Notably, the final steps of ATP hydrolysis include the fast release of phosphate and the slow
release of ADP. The release of a phosphate anion from bound ADP anion into water solution
may be considered as an exergonic reaction because the phosphate anion has low molecular
mass.Thus, we arrive at the conclusion that the primary release of the inorganic phosphate
H2PO4- leads to transformation of a significant part of the free energy of ATP hydrolysis into the
kinetic energy of the solvated phosphate, producing active streaming. This assumption of a local
mechano-chemical transduction is in accord with Tirosh’s mechanism of muscle contraction,
where the muscle force derives from an integrated action of active streaming created by ATP
An enzyme inhibitor is a molecule which binds to enzymes and decreases their activity. Since
blocking an enzyme's activity can kill a pathogen or correct a metabolic imbalance, many drugs
are enzyme inhibitors. They are also used as herbicides andpesticides. Not all molecules that
bind to enzymes are inhibitors;enzyme activators bind to enzymes and increase their enzymatic
activity, while enzyme substrates bind and are converted to products in the normal catalytic cycle
of the enzyme.
The binding of an inhibitor can stop a substrate from entering the enzyme's active site and/or
hinder the enzyme from catalyzing its reaction. Inhibitor binding is either reversible or
irreversible. Irreversible inhibitors usually react with the enzyme and change it chemically (e.g.
via covalent bond formation). These inhibitors modify key amino acid residues needed for
enzymatic activity. In contrast, reversible inhibitors bind non-covalently and different types of
inhibition are produced depending on whether these inhibitors bind to the enzyme, the enzyme-
substrate complex, or both.Many drug molecules are enzyme inhibitors, so their discovery and
improvement is an active area of research inbiochemistry and pharmacology. A medicinal
enzyme inhibitor is often judged by its specificity (its lack of binding to other proteins) and its
potency (its dissociation constant, which indicates the concentration needed to inhibit the
enzyme). A high specificity and potency ensure that a drug will have few side effects and thus
low toxicity.Enzyme inhibitors also occur naturally and are involved in the regulation of
metabolism. For example, enzymes in ametabolic pathway can be inhibited by downstream
products. This type of negative feedback slows the production line when products begin to build
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