Biochemistry

TLO 1: Define enzymes, proenzymes and cofactors.

Enzymes play an essential role in each living cell of our body—whether they are organs, muscles, bones, nerves etc. Without enzymes our body would not function at all. Try to recall back all the processes that we have discussed so far—carbohydrate metabolism, lipid metabolism and protein metabolism. All of these metabolism (either anabolic or catabolic) uses enzymes to produce products.

Enzymes are biological catalyst produced by living tissues. A catalyst is a substance that help to speed up chemical reactions in our body without itself undergoing any permanent chemical changes. They speed up chemical reactions by lowering the activation energy needed to start the process.

Figure 1 Enzyme work as a catalyst that speeds up chemical reaction by lowering the activation energy (source: https://wou.edu/chemistry/courses/online-chemistry-textbooks/ch450-and-ch451-biochemistry-defining-life-at-the-molecular-level/chapter-7-catalytic-mechanisms-of-enzymes/)

Some enzymes consist of two parts—a protein portion known as the apoenzyme and a non-protein portion known as the cofactors. Cofactor is an additional component that helps to optimize the enzyme’s activity. It may be organic compounds called coenzymes or it may be inorganic ions called activators. There are many vitamins that function as coenzymes. The list of coenzymes and activators are given in the table below.

Table 1 List of coenzymes with its function.

Table 2 List of activators and the enzymes they activating

A number of enzymes found in the blood or digestive tract are present in precursor or inactivated enzyme known as the proenzymes. Precursor proteins or inactive enzyme names have the prefix “pro-” like prothrombin, proelastase etc. or suffix “-ogen” like trypsinogen, chymotrypsinogen, pepsinogen etc.

TLO 2: Describe the general properties of enzymes

Enzymes catalyze specific reactions. They do so with great efficiency and with many built-in controls. There are three important properties of enzymes that includes:

Enzymes are highly specific

Each particular enzyme binds only to specific substrates (the reactant molecules on which the enzyme acts).  There are more than 1,000 known enzymes in our body, each has a characteristic three-dimensional shape with specific surface configuration allowing it to recognize and bind to certain substrates. In certain cases, the part of the enzyme that catalyzes the reactions known as active site is thought to fit the substrate like a key fit in a lock (Lock and Key Model suggested by Emil Fisher). On the other hand, the active sites change its shape to fit adequately around the substrates once the substrates enter the active site. This change is known as the induced fit (Induced-fit model suggested by Daniel E. Koshland).

Figure 2 Diagram showing lock and key model of enzyme action suggested by Fisher (source://saylordotorg.github.io/)

Figure 3 Induced-fit model of enzyme action suggested by Koshland (source: //thebiologynotes.com/)

Enzymes are very efficient

Under optimal conditions, enzymes are able to catalyze reactions that are ranging from 100 million to 10 billion times more rapid than those of similar reactions without enzymes. The number of substrate molecules that a single enzyme can convert into product molecules in one second is generally between 1 and 10,000 and can be as high as 600,000.

Enzymes are subject to a variety of cellular controls

Their rate of synthesis and their concentration at any given time are under the control of a cell’s genes. Substances within the cell may either enhance or inhibit the activity of a given enzyme. Many enzymes have both active and inactive forms in cells. The rate at which the inactive form becomes active or vice versa is determined by the chemical environment inside the cell.

Figure 4 Multiple factors that can enhance or inhibit enzyme activity

TLO 3: List the different classification of enzymes

According to the International Union of Biochemistry (IUB), enzymes are classified into six major classifications as follows:

1.      Oxireductases

2.      Transferases

3.      Hydrolases

4.      Lyases

5.      Isomerases

6.      Ligases

Oxireductases

Group of enzymes that catalyze oxidation-reduction reactions are included in this class which can be illustrated as follows:

Oxidation is the process of electron loss during a reaction by molecule, atom or ion. The opposite process is called as reduction which means the molecule, atom or ion gains electron during a reaction.

Enzymes in this category include:

1. Dehydrogenases
2. Reductases
3. Oxidases
4. Peroxidases

Specific example:

This reaction is the conversion of lactate to pyruvate. Lactate or lactic acid is the result of anaerobic (absence of oxygen) respiration. Once the oxygen supply replenish, lactate will convert back to pyruvate by lactate dehydrogenase enzyme.

Transferases

Group of enzymes that catalyze the transfer of a functional group like amino, carboxyl, methyl or phosphoryl etc. from one molecule to another. The reactions can be illustrated as below:

Some common enzymes grouped under this category includes:

1. Amino transferase or transaminase
2. Kinase
3. Transcarboxylase

Specific example:

Alanine aminotransferase (ALT) also formerly known as glutamate pyruvate transaminase (GPT) is an enzyme catalyzing the conversion process of alanine into pyruvate for cellular energy production. During this conversion process, amino group from alanine transfers to α-ketoglutarate molecules, forming pyruvate and glutamate. The process is illustrated as below: