Summary 05032021

Enzymes

They can be classified as:

1. Oxidoreductase

2. Transferase

3. Hydrolase

4. Lyase

5. Isomerase

6. Ligase

These catalyze redox reactions.

These catalyze the transference of groups like methyl, glucoside, and phosphoryl.

These catalyze the hydrolysis of bonds between C, O and N, as well as other covalent bonds.

These catalyze the breaking of bonds between C, O and N by eliminating atoms and generating double bonds.

These catalyze changes in the geometry or structure of a molecule.

These catalyze the union of two molecules in company of the hydrolysis of ATP.

They are really specific.

They increase the speed of the reaction up to 10^6 times.

These have:

Prosthetic groups

Cofactors

These join the structure of the protein by covalent or non-covalent bonds.

These make the union and orientation of substrates easier, as well as the conformation of covalent bonds with the intermediaries of the reaction. They can act as Lewis' acids or bases.

They weakly bond temporarily to enzymes or substrates establishing dissociative complexes.

They must be present in the environment to promote the formation of complexes and for the catalysis to happen.

They are usually metal ions.

Metal activated enzymes.

A lot of them are derivates of B vitamins.

Coenzymes

These are reusable, they transport substates from one point to the other within the cell.

They increase the contact between the substrate and the enzyme. They also increase the affinity and specificity.

They conform:

Enzyme and substrate complexes.

These have more thermal stability than the enzyme on its own.

They have active sites.

It recognizes the substrate.

It helps to obtain the right alignment.

It also protects the substrate from water, it offers an optimal environment for the rection.

Catalysis mechanisms

By proximity

Acid-base

Tension

Covalent

The molecules must be in the range of distance to be able to bind.

It will be easier to bind when the concentration of the substrate is higher.

The functional groups contribute to the catalysis by acting as acids or bases.

Specific

General

Only protons or hydroxyl ions participate.

All of the acids and bases that are present react.

To break the covalent bonds, the enzyme binds to the substrate in a conformation that weakens the bond to break it by physical distortion and electronic polarization.

It imitates the intermediate state of the transition.

A covalent bond is established between the enzyme and its substrate. The modified enzyme is turned into a reactive.

At the end of the reaction the enzyme goes back to its original unmodified state.

It is common among group transfer reactions.

Models

Induced fit

Lock and key

Fischer

Daniel Koshland

Enzyme-substrate interaction has a high specificity and the active site is rigid.

When the substrate binds, it induces a conformational change in the enzyme, in return this binding energy is used to facilitate the transformation.

They can also be:

Homologous

Isozymes

Proteins that have a common ancestor but recognize different substrates.

Different versions of an enzyme, each of them catalyzes the same reaction.

References

Baynes, W. & Dominiczak, M. (2014). Medical Biochemistry (4th ed.). Elsevier.

Gomez, L. (2021). Biochemistry I 2017983: Catálisis enzimática I y II, class notes week 3 [Class notes]. Universidad Nacional de Colombia.

Rodwell, V., Bender, D., Botham, K., Kennelly, P. & Weil, P. (2018). Harper Illustrated Biochemistry (31st ed.). McGraw Hill Education.

Biochemistry I

Paola Pimiento

Nearly all of them are proteins.

They do not alter the equilibrium of the reaction.

They decrease the activation energy required for the reaction.

Their regulation allows the metabolism to adapt to different situations.

There are some ribonucleic acids called ribozymes.

They can be affected by some factors:

Temperature

PH

They have an optimal temperature at which they function the best.

They function better at a certain PH according to their amino acids.

They have catalytic activity:

Their activity can be measured by:

Katal

Amount of enzyme that catalyzes the reaction of 1 mole of substrate to 1 mole of product in a second.

International unit (IU)

Amount of enzyme that catalyzes the reaction of 1 micromole of substrate to product in a minute.

Preferred unit.

Their specificity is measured in IU/mg of protein.

It depends on the size, structure, charges, polarity, and hydrophobicity of the binding site.

Enzymes bound to a coenzyme with covalent or non-covalent bonds are referred to as holoenzyme.

A holoenzyme without a coenzyme is called apoenzyme.

They can also be inhibited by:

Competitive inhibition

By substances that are similar in structure to the substrate.

Noncompetitive inhibition

They increase the Km but do not change the maximal velocity.

These bind to the active site.

It binds to the enzyme-substrate complex, not to the enzyme's active site.

They change the maximal velocity but not the Km.

They are regulated:

Metabolic pathways are regulated by rate limiting steps.

Some other ways enzymes can be regulated are:

The expression of the enzymes changes according to the cell's environment and the metabolic requirements.

Enzymes can be activated or inactivated by proteolytic enzymes or covalent modification (like phosphorylation).

Allosteric regulation can occur through the binding of small molecules in a different part of the enzyme (not the active site).

Degradation of enzymes in the lysosome or the cytosol.

This happens with digestive enzymes which are secreted as zymogens of proenzymes. They are activated in the intestinal tract.

Enzyme kinetics

Michaelis-Menten equation

Lineweaver-Burk plot

Eadie–Hofstee plot

Developed in 1913 by Leonor Michaelis and Maud Menten.

It assumes the enzyme binds to the substrate forming the enzyme-substrate complex (ES).

This complex undergoes the reaction in the enzyme surface, the result is the enzyme and the product. This is the rate limiting step.

It has different variables:

Kcat

Number of substrate molecules converted to product

per enzyme molecule per unit time.

It corresponds to the maximal velocity.

Km

Substrate concentration at which half of the maximum velocity is reached.

It is correlated to the enzyme's affinity.

High Km

Requires high concentration of substrate to work efficiently.

Low Km

Operates efficiently in trace levels of substrate.

They are in equilibrium.

It is obtained by using the reciprocal Michaelis-Menten equation.

This equation yields a straight-line equation (y=mx+b)

It has a small experimental error, especially in low concentrations.

It does not compress the data at high substrate concentrations.

Thermodynamics

They indicate whether a reaction can happen or not.

Spontaneous reactions are exothermic.

Kinetics can help study enzyme's mechanism.

Enzymes must be purified for their study.

Thanks to the purification the 3D structure of the enzyme can be studied.

The active site can also be identified.

It is necessary to find the right method of purification for the specific enzyme.

Enzymes can be separated by different methods according to their features:

By charge

By size

Other features.

Isoelectric point and size.

An estimate of the proteins present can be done.

When the weight is known, it can help identify the enzyme.

Mixed inhibition

In this inhibition both Km and the maximal velocity change.