Enzymes are commonly named by adding a suffix "-ase" to the root name of the substrate molecule it is acting upon. For example, Lipase catalyzes the hydrolysis of a lipid triglyceride. Sucrase catalyzes the hydrolysis of sucrose into glucose and fructose
A few enzymes discovered before this naming system was devised are known by common names e.g. pepsin, trypsin, and chymotrypsin which catalyse the hydrolysis of proteins
Enzymes are also given a standard reference number (European Commission Number) to help characterise the 1500 or so enzymes
ENZYMES These catalyse a transfer of a phosphate group onto a molecule such as a carbohydrate or protein Kinases To hydrolyse ATP. Many proteins have an ATPase activity which is essential for their function ATPases To hydrolyse phosphodiester bonds Nucleases To hydrolyse peptide bonds to breakdown proteins -> amino acids Proteases FUNCTION NAME
A common model for enzyme action is the lock and key hypothesis
However, this model is a little misleading in that it tends to give the impression that enzymes are rigid structures, whereas in fact, they are quite flexible and can alter their conformation in response to the binding of other molecules
The currently accepted model for enzyme action is the INDUCED FIT MODEL , in which conformational changes to the protein occur on binding of a substrate
Inhibition can either be reversible or non-reversible depending on how the inhibitor binds to the enzyme
Some inhibitors bind irreversibly with the enzyme molecules, inhibiting the catalytic activities permanently. The enzymatic reactions will stop sooner or later and are not affected by an increase in substrate concentration. These are irreversible inhibitors .
Examples are heavy metal ions including silver , mercury and lead ions.
In multi-subunit enzymes, the structure is more complex, and the enzyme often exists in 2 different conformational states:
ACTIVE and INACTIVE
These can be stabilised by binding the modulator
Positive modulators stabilise the active form of the enzyme
Negative modulators stabilise the inactive form
In addition to these modulators changing the activity of allosteric enzymes, sometimes the binding of the substrate itself to one active site enhances binding at the other active sites. This is known as COOPERATIVITY
Covalent modification of enzymes is another strategy used widely in metabolic regulation
One of the most common modifications is the addition of a PHOSPHATE group, which can alter the shape of a protein by attracting positively charged R-groups [phosphates carry 2 negative charges on the 2 single-bonded O atoms]
PROTEIN KINASES add phosphate groups and PHOSPHATASES remove them, thus the effect can be REVERSED
Some proteins are activated by phosphorylation , others are inactivated
An example of phosphorylation activating an enzyme is the skeletal muscle enzyme GLYCOGEN PHOSPHORYLASE
This enzyme releases glucose molecules from glycogen when heavy demands are placed on muscle tissue
This process is highly regulated. Traffic of sugar into and out of storage in glycogen is used to control the level of glucose in the blood, so glycogen phosphorylase must be activated when sugar is needed and quickly deactivated when glucose is plentiful
Glycogen phosphorylase is present as an inactive non-phosphorylated form which is converted to the active phosphorylated form by the addition of a phosphate group to a serine residue in the protein by the enzyme PHOSPHORYLASE KINASE
When the demand for glucose drops, PHOSPHORYLASE PHOSPHATASE removes the phosphate group and inactivates the enzyme
However … glycogen phosphorylase is also regulated by an allosteric effect !
Metabolism is organised as a series of metabolic pathways, and control of these pathways is an important feature of cell biochemistry
One way in which control can be exercised is END-PRODUCT INHIBITION
End-product inhibition is energetically efficient as it avoids the excessive (and wasteful) production of the intermediates of a pathway
This is a form of NEGATIVE FEEDBACK
For example, in the production of the amino acid isoleucine in bacteria, the initial substrate is threonine which is converted by five intermediate steps to isoleucine. As isoleucine begins to accumulate, it binds to an allosteric site of the first enzyme in the pathway thereby slowing down its own production. In this way, the cell does not produce any more isoleucine than is necessary.