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Enzymes

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Enzymes

Enzymes are biological catalysts in biochemical reactions.

Let us break down this definition. Biological means that they occur naturally in living things. Catalysts accelerate the rate of chemical reactions and are not consumed or 'used up' but remain unchanged. Therefore, enzymes can be reused to speed up many more reactions.

Biochemical reactions are any reactions that involve the formation of products. In these reactions, one molecule transforms into another. They take place inside the cells.

Almost all enzymes are proteins, more specifically globular proteins. From our article on proteins, you might remember that globular proteins are functional proteins. They act as enzymes, carriers, hormones, receptors, and more. They perform metabolic functions.

Ribozymes (ribonucleic acid enzymes), discovered in the 1980s, are RNA molecules with enzymatic capabilities. They are examples of nucleic acids (RNA) functioning as enzymes.

One example of an enzyme is the human salivary enzyme, alpha-amylase. Figure 1 shows the structure of alpha-amylase. Knowing that enzymes are proteins, spot the 3-D structure with regions coiled in α-helix and β-sheets. Brush up on your knowledge of four different protein structures in our article Protein Structure.

Figure 1

Where do enzymes get their names?

You may have noticed that all enzyme names end in -ase. Enzymes get their names from the substrate or the chemical reaction they catalyse. Have a look at the table below. Reactions involving various substrates such as lactose and starch, and chemical reactions such as oxidation/reduction reactions, are catalysed by enzymes.

Table 1. Examples of enzymes, their substrates and functions.

SUBSTRATE

ENZYME

FUNCTION

lactoselactaseLactases catalyse the hydrolysis of lactose into glucose and galactose.
maltosemaltaseMaltases catalyse the hydrolysis of maltose into glucose molecules.
starch (amylose)amylaseAmylases catalyse the hydrolysis of starch into maltose.
proteinproteaseProteases catalyse the hydrolysis of proteins into amino acids.
lipidslipaseLipases catalyse the hydrolysis of lipids to fatty acids and glycerol.

REDOX REACTION

ENZYME

FUNCTION

Oxidation of glucose.glucose oxidaseGlucose oxidase catalyses the oxidation of glucose to hydrogen peroxide.
Production of deoxyribonucleotides or DNA nucleotides (reduction reaction).

ribonucleotide reductase (RNR)

RNR catalyses the formation of deoxyribonucleotides from ribonucleotides.

Glucose oxidase (sometimes written in the shorter form GOx or GOD) exhibits antibacterial activities. We find it in honey, serving as a natural preservative (i.e., it kills microbes). Female honey bees produce glucose oxidase and do not reproduce (unlike queen bees, they are called worker bees).

The structure of enzymes

Like all globular proteins, enzymes are spherical in structure, with polypeptide chains folded to form the shape. The amino acid sequence (the primary structure) is twisted and folded to form a tertiary (three-dimensional) structure.

Because they are globular proteins, enzymes are highly functional. A particular area of the enzyme that is functional is called an active site. It is a slight depression on the surface of the enzyme. The active site has a small number of amino acids that can form temporary bonds with other molecules. Typically, there is only one active site on each enzyme. The molecule that can bind to the active site is called a substrate. An enzyme-substrate complex forms when the substrate temporarily binds to the active site.

How does an enzyme-substrate complex form?

Let us take a step-by-step look at how an enzyme-substrate complex forms:

  1. A substrate binds to the active site and forms an enzyme-substrate complex. The substrate's interaction with the active site needs a specific orientation and speed. The substrate collides with the enzyme, i.e. it psychically comes into contact to bind.

  2. The substrate converts into products. This reaction is catalysed by the enzyme, forming an enzyme-product complex.

  3. The products detach from the enzyme. The enzyme is free and can be used again.

Later, you will learn that there can be one or more substrates in this process, and therefore, one or more products. For now, you must understand the difference between enzymes, substrates, and products. Have a look at the image below. Notice the formation of both enzyme-substrate and enzyme-product complexes.

Figure 2

Enzymes' 3-D structure is determined by their primary structure or the sequence of amino acids. Specific genes determine this sequence. In protein synthesis, these genes require enzymes made of proteins to make proteins (some of which are enzymes!) How could have genes started making proteins thousands of years ago if they needed proteins to do so? Scientists only partially understand this fascinating 'chicken-or-the-egg' mystery in biology. Which do you think came first: the gene or the enzyme?

The induced-fit model of enzyme action

The induced-fit model of enzyme action is a modified version of an earlier lock-and-key model. The lock-and-key model assumed that both the enzyme and the substrate were rigid structures, with the substrate fitting precisely into the active site, just as a key fits into a lock. The observation of enzyme activity in reactions supported this theory and led to the conclusion that enzymes are specific to the reaction they catalyse. Have another look at figure 2. Can you see the rigid, geometric shapes that the active site and substrate supposedly had?

The scientists later found that the substrates bind to the enzymes at sites other than the active site! Consequently, they concluded that the active site is not fixed, and the shape of the enzyme changes when the substrate binds to it.

As a result, the induced-fit model was introduced. This model states that the active site forms only when the substrate binds to the enzyme. When the substrate binds, the shape of the active site adapts to the substrate. Consequently, the active site does not have an identical, rigid shape but complementary to the substrate. These changes in the shape of the active site are called conformational changes. They maximise the enzyme's ability to act as a catalyst for a particular chemical reaction. Compare Figures 2 and 3. Can you spot the difference between the active sites and the general shapes of enzymes and substrates?

Figure 3

Often, you will see cofactors bound to an enzyme. Cofactors are not proteins, but other organic molecules that help enzymes catalyse biochemical reactions. Cofactors cannot function independently but must bind to an enzyme as helper molecules. Cofactors can be inorganic ions like magnesium or small compounds called coenzymes. If you are studying processes such as photosynthesis and respiration, you may come across coenzymes, which naturally make you think of enzymes. However, remember that coenzymes are not the same as enzymes, but cofactors that help enzymes do their jobs. One of the most important coenzymes is NADPH, essential for ATP synthesis.

The function of enzymes

As catalysts, enzymes speed up the rate of reactions in living things, sometimes by millions of times. But how do they actually do this? They do this by lowering the activation energy.

Activation energy is the energy needed to initiate a reaction.

Why do enzymes lower the activation energy and not raise it? Surely they would need more energy to make a reaction go faster? There is an energy barrier that the reaction has to 'overcome' to start. By lowering the activation energy, the enzyme allows the reactions to 'get over' the barrier faster. Imagine riding a bicycle and reaching a steep hill that you need to climb. If the hill was less steep, you could climb it easier and faster.

Enzymes allow reactions to occur at lower than average temperatures. Typically, chemical reactions occur at high temperatures. Considering that the human body temperature is about 37 °C, the energy needs to be lower to match that temperature.

In Figure 4, you can see the difference between the blue curve and the red curve. The blue curve represents a reaction occurring with the help of an enzyme (it is catalysed or accelerated by an enzyme) and therefore has lower activation energy. On the other hand, the red curve occurs without an enzyme and therefore has higher activation energy. The blue reaction is thus much faster than the red one.

Figure 4

Factors affecting enzyme activity

Enzymes are sensitive to certain conditions in the body. Can enzymes, these powerful little machines, ever be altered? Do substrates bind to altered enzymes? Several factors affect enzyme activity, including temperature, pH, enzyme and substrate concentrations, and competitive and non-competitive inhibitors. They can cause the denaturation of enzymes.

Denaturation is the process in which external factors such as temperature or changes in acidity alter the molecular structure. Denaturation of proteins (and, therefore, enzymes) involves modifications of the complex 3-D protein structure to such an extent that they no longer function properly or even stop functioning altogether.

FIgure 5

Temperature changes affect the kinetic energy required to carry out reactions, especially the collision of enzymes and substrates. Too low a temperature results in insufficient energy, while too high results in denaturation of the enzyme. Changes in pH affect the amino acids in the active site. These changes break the bonds between the amino acids, causing the active site to change shape, i.e. the enzyme denatures.

Enzyme and substrate concentration affect the number of collisions between enzymes and substrates. Competitive inhibitors bind to the active site and not to the substrates. In contrast, non-competitive inhibitors bind elsewhere on the enzyme, causing the active site to change shape and become non-functional (again, denaturation).

When these conditions are optimal, the collision between enzymes and substrates is most significant. You can learn more about these factors in our article Factors Affecting Enzyme Activity.

There are thousands of enzymes involved in different pathways, where they perform different roles. Next, we will discuss some of the functions of enzymes.

The function of enzymes in catabolism

Enzymes accelerate catabolic reactions, collectively known as catabolism. In catabolic reactions, complex molecules (macromolecules) such as proteins break down into smaller molecules like amino acids, releasing energy.

In these reactions, one substrate binds to the active site, where the enzyme breaks down chemical bonds and creates two products that separate from the enzyme.

The process of food digestion in the digestive tract is one of the major catabolic reactions catalysed by enzymes. Cells cannot absorb complex molecules, so molecules need to break down. Essential enzymes here are:

Another example of a catabolic reaction is cellular respiration. Cellular respiration involves enzymes such as ATP synthase, which is used in oxidative phosphorylation to produce ATP (adenosine triphosphate).

The function of enzymes in anabolism or biosynthesis

Anabolic reactions are the opposite of catabolic reactions. Together they are referred to as anabolism. A synonym for anabolism is biosynthesis. In biosynthesis, macromolecules like carbohydrates build up from their constituents, which are simple molecules such as glucose, using the energy of ATP.

In these reactions, not one but two or more substrates bind to the enzyme's active site. The chemical bond is formed between them, resulting in a single product.

  • Protein synthesis with the enzyme RNA polymerase as the central enzyme in the process of transcription.
  • DNA synthesis with the enzymes DNA helicase breaking bonds and separating the DNA strands, and DNA polymerase joining the nucleotides together to form the "lost" second strand.

Photosynthesis is another anabolic reaction, with RUBISCO (ribulose bisphosphate carboxylase) as the central enzyme.

Macromolecules, formed in anabolic reactions catalysed by enzymes, build tissues and organs, for example, bone and muscle mass. You could say that enzymes are our bodybuilders!

Enzymes in other roles

Let's take a look at enzymes in other roles.

Cell signalling or cell communication

Chemical and physical signals are transmitted through cells and eventually trigger a cellular response. Enzymes protein kinases are essential because they can enter the nucleus and affect transcription once they receive a signal.

Muscle contraction

The enzyme ATPase hydrolyses ATP to generate energy for two proteins central to muscle contraction: myosin and actin.

Replication of viruses and spread of diseases

Both use the enzyme reverse transcriptase. After a virus inhibits host cells, reverse transcriptase makes DNA from the virus' RNA.

Gene cloning

Again, the enzyme reverse transcriptase is the main enzyme.

Enzymes - Key takeaways

  • Enzymes are biological catalysts; they accelerate the rate of chemical reactions and can be reused.
  • The active site is a slight depression on the surface of the enzyme that is highly functional. Molecules that bind to the active site are called substrates. An enzyme-substrate complex forms when a substrate temporarily binds to the active site. An enzyme-product complex follows it.
  • The induced-fit model states that the active site forms only when the substrate binds to the enzyme. The model suggests that the active site has a form complementary to the substrate.
  • Enzymes lower the activation energy required to initiate a reaction.
  • Enzymes catalyse catabolic reactions such as food digestion (enzymes amylases, proteases, and lipases) and cellular respiration (enzyme ATP synthase).
  • However, enzymes also catalyse anabolic reactions, such as protein synthesis with the enzyme RNA polymerase and photosynthesis with RUBISCO.

Frequently Asked Questions about Enzymes

Enzymes are biological catalysts in biochemical reactions. They accelerate the rate of chemical reactions by lowering the activation energy.

All enzymes are proteins. However, ribozymes (ribonucleic acid enzymes) exist, which are RNA molecules with enzymatic abilities.

Carbohydrases, lipases, and proteases.

Enzymes catalyse (accelerate) chemical reactions by lowering the activation energy necessary for the reaction to start.

Final Enzymes Quiz

Question

What are enzymes?

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Answer

Enzymes are biological catalysts in biochemical reactions. They accelerate the rate of chemical reactions by lowering the activation energy.

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Question

What does it mean when we say enzymes are catalysts?

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Answer

Enzymes as catalysts are not consumed or 'used up' in reactions but remain unchanged. As a result, they can be reused to speed up many more reactions.

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Question

What kind of proteins are enzymes?

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Answer

Globular proteins

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Question

Enzymes get their names from the substrate or the chemical reaction they catalyse. Which substrate corresponds to the enzyme amylase?

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Answer

Protein

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Question

Which enzyme is essential in the hydrolysis of lactose?

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Answer

Lactase

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Question

What is the active site? 

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Answer

The active site is a specific region of the enzyme that is highly functional. The active site has a small number of amino acids that can form temporary bonds with other molecules. Usually, there is only one active site on each enzyme.

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Question

What kind of complex do the enzyme and the substrate form?

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Answer

An enzyme-substrate complex.

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Question

What are the molecules that detach from the enzymes’ active site called?

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Answer

Products.

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Question

The induced-fit model of enzyme action is a modified version of which other model?

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Answer

The lock-and-key model.

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Question

Which model proposes that both active site and substrate have rigid, geometrical shapes?

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Answer

 The lock-and-key model

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Question

Define the induced-fit model of enzyme action.

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Answer

The induced-fit model states that the active site forms only when the substrate binds to the enzyme. The model suggests that the active site has a shape complementary to the substrate.

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Question

What does it mean when we say that the active site has a shape complementary to the substrate?

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Answer

It means that the active site is not the same shape as the substrate. When the substrate binds, the form of the active site adapts to the substrate. This indicates that the active site does not have an identical, rigid shape but is complementary to the substrate.

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Question

Coeznymes are enzymes. TRUE or FALSE?


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Answer

False. Coenzymes are cofactors, non-protein, organic molecules that help enzymes catalyse biochemical reactions. Cofactors cannot function independently, so they need to bind to an enzyme as helper molecules.

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Question

Why is it important that enzymes lower the activation energy?

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Answer

There is an energy barrier that the reaction has to 'overcome' to start. By lowering the activation energy, the enzyme allows the reactions to 'get over' the barrier faster. 

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Question

What is the role of enzymes in catabolic reactions?

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Answer

Enzymes catalyse catabolic reactions, which involve breaking complex molecules (macromolecules) into smaller ones, releasing energy.

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Question

List two examples of catabolic reactions and at least two enzymes essential in those reactions.

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Answer

  1. Food digestion, with proteases, lipases, amylases, etc.
  2. Cellular respiration, with ATP synthase.

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Question

Enzymes accelerate anabolic reactions as well as catabolic reactions. How many products do such reactions produce?

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Answer

One product. Two or more substrates bind to the enzyme's active site during anabolic reactions. The chemical bond forms between them, resulting in a single product.

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Question

Anabolic reactions are, collectively, called anabolism. A synonym for anabolism is biosynthesis. List at least two examples of biosynthesis in living organisms, along with enzymes that catalyse them.

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Answer

  1. Protein synthesis with the enzyme RNA polymerase.
  2. DNA synthesis with DNA helicase.
  3. Photosynthesis with RUBISCO.

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Question

Enzymes have various roles. Two of them, namely replication of viruses and gene cloning, have a common enzyme. What is the name of this enzyme?


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Answer

Reverse transcriptase.

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Question

How is enzyme activity important in muscle contraction?

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Answer

During muscle contraction, enzyme ATPase hydrolyses ATP to generate energy for two central proteins: myosin and actin.

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