Naming and characteristics of enzymes – Enzymes (Senior 4 Biology) | Ganzaa

Enzymes

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Senior 4 · Biology

Enzymes

4 lessons

Lesson 1 of 4

Naming and characteristics of enzymes

25 min

A mountain of foam in ten seconds

Hydrogen peroxide, $\mathrm{H_2O_2}$ , breaks down into water and oxygen on its own, but so slowly that a bottle of it keeps for months. Stir in some yeast and, within seconds, foam full of oxygen pours out of the container (see the photo below). The yeast cells contain an enzyme, catalase, which speeds up the same reaction enormously:

2\,\mathrm{H_2O_2} \xrightarrow{\text{catalase}} 2\,\mathrm{H_2O} + \mathrm{O_2}

Your liver cells hold catalase too, because hydrogen peroxide is a poisonous by-product of metabolism. In S2 you met enzymes as biological catalysts. This lesson adds how biologists name and classify them, and the full list of their characteristics.

Definition

Enzyme: a biological catalyst, usually a globular protein, that speeds up a specific chemical reaction in a living organism without being used up.

Catalyst: a substance that increases the rate of a reaction and is unchanged at the end of it.

Substrate: the molecule an enzyme acts on. Product: the molecule formed. Active site: the small region of the enzyme where the substrate binds and reacts.

Intracellular enzyme: one that works inside the cell that made it, such as catalase. Extracellular enzyme: one secreted to work outside the cell, such as salivary amylase or the digestive enzymes that fungi release onto their food.

Turnover number: the number of substrate molecules one enzyme molecule converts to product per second when working at its maximum rate.

How enzymes are named

Rule	Examples
Name of the substrate + -ase	Maltase (hydrolyses maltose), lactase (lactose), sucrase (sucrose), lipase (lipids), protease (proteins), urease (urea)
Type of reaction + -ase	Dehydrogenase (removes hydrogen), oxidase (adds oxygen), decarboxylase (removes $\mathrm{CO_2}$ ), isomerase (rearranges a molecule), polymerase (builds a polymer)
Substrate and reaction	Lactate dehydrogenase, DNA polymerase, pyruvate decarboxylase
Old or trivial names, kept by tradition	Pepsin and trypsin (proteases), ptyalin (salivary amylase), rennin (clots milk protein)

Because ordinary names can be vague, the International Union of Biochemistry and Molecular Biology gives every enzyme an EC number (EC for Enzyme Commission) of four parts. The first number shows the class of reaction. There were six classes until August 2018, when a seventh, the translocases, was added.

Class	Type of reaction catalysed	Example
EC 1 Oxidoreductases	Oxidation and reduction: transfer of hydrogen, electrons or oxygen	Dehydrogenases of respiration; catalase
EC 2 Transferases	Transfer of a group (such as phosphate or amino) from one molecule to another	Hexokinase (moves a phosphate from ATP to glucose)
EC 3 Hydrolases	Hydrolysis: splitting with water	Amylase, lipase, pepsin, maltase
EC 4 Lyases	Removal or addition of a group without hydrolysis, often forming a double bond	Pyruvate decarboxylase (removes $\mathrm{CO_2}$ )
EC 5 Isomerases	Rearranging atoms within one molecule	Glucose-6-phosphate isomerase (in glycolysis)
EC 6 Ligases	Joining two molecules, using energy from ATP	DNA ligase
EC 7 Translocases	Moving ions or molecules across membranes	The sodium–potassium pump

Worked example 1: name and classify

For each reaction, suggest a name for the enzyme and its EC class. (a) Sucrose + water → glucose + fructose. (b) Lactate → pyruvate + 2 H (taken by a coenzyme). (c) Two pieces of DNA are joined, using ATP.

(a) Water splits the substrate sucrose: sucrase, a hydrolase (EC 3).
(b) Hydrogen is removed from lactate: lactate dehydrogenase, an oxidoreductase (EC 1).
(c) Two molecules are joined using ATP: DNA ligase, a ligase (EC 6).

Characteristics of enzymes

Most are globular proteins. Their tertiary structure gives each a precisely shaped active site. (A few catalysts made of RNA, called ribozymes, also exist.)
They are specific. Each enzyme acts on one substrate, or a small group of similar ones, because only that substrate fits and binds in its active site.
They are not used up, so a tiny amount can convert a huge amount of substrate. Turnover numbers range from a few per second to millions per second for catalase.
They speed up reactions without changing the end point. Many reactions are reversible, and an enzyme speeds up both directions; carbonic anhydrase, for example, catalyses $\mathrm{CO_2} + \mathrm{H_2O} \rightleftharpoons \mathrm{H_2CO_3}$ in either direction.
They lower the activation energy of the reaction (lesson 2).
They are sensitive to temperature and pH: each works best at an optimum, and is denatured by high temperature or extreme pH (lesson 3).
Some need cofactors, non-protein helpers such as metal ions or vitamin-derived coenzymes (lesson 2).
They can be inhibited by other molecules, which is how cells control them and how many poisons and medicines work (lesson 3).

Investigating catalase activity

The rate of an enzyme reaction is measured either as the amount of product formed, or of substrate used, per unit time. For catalase, the product oxygen is easy to collect (Figure 1). Cut equal discs of raw potato, place them in a flask, add a fixed volume of hydrogen peroxide solution, close the flask at once and record the volume of oxygen every minute. Repeat with discs that have been boiled, as a control.

Figure 1. Collecting the oxygen released by catalase over water. A gas syringe can be used instead of the measuring cylinder.

Worked example 2: rates from results

Results (illustrative):

Time / min	0	1	2	3	4	5
Oxygen, raw potato / $\mathrm{cm^3}$	0	12	21	27	31	33
Oxygen, boiled potato / $\mathrm{cm^3}$	0	0	0	0	0	0

(a) Calculate the rate in the first minute and in the fifth minute. (b) Calculate the mean rate over 5 minutes. (c) Explain the results.

(a) First minute: $\frac{12 - 0}{1} = 12\,\mathrm{cm^3\,min^{-1}}$ . Fifth minute: $\frac{33 - 31}{1} = 2\,\mathrm{cm^3\,min^{-1}}$ .
(b) $\frac{33}{5} = 6.6\,\mathrm{cm^3\,min^{-1}}$ .
(c) The rate falls because the substrate, hydrogen peroxide, is being used up, so substrate molecules meet active sites less often. Boiled potato releases no oxygen: heat denatured the catalase. The control shows that the oxygen comes from the enzyme, not from the potato or the peroxide alone. The initial rate (12) is the fairest measure of enzyme activity, because the substrate concentration is still known.

Worked example 3: how fast is fast?

Suppose one catalase molecule converts $5 \times 10^{6}$ molecules of hydrogen peroxide per second (catalase converts millions per second), while a typical enzyme has a turnover number of about 10 per second. (a) How many $\mathrm{H_2O_2}$ molecules does one catalase molecule convert in a minute, and how many moles is that? (b) How many times faster is catalase than the typical enzyme? (Avogadro constant $= 6.02 \times 10^{23}\,\mathrm{mol^{-1}}$ .)

(a) $5 \times 10^{6} \times 60 = 3 \times 10^{8}$ molecules. Moles $= \frac{3 \times 10^{8}}{6.02 \times 10^{23}} = 5.0 \times 10^{-16}\,\mathrm{mol}$ .
(b) $\frac{5 \times 10^{6}}{10} = 5 \times 10^{5}$ : half a million times faster.
Even a fast enzyme handles a tiny number of moles per molecule, but a cell holds many enzyme molecules and they are never used up, so small amounts are enough.

FuseSchool: "Enzymes". Watch for the properties of enzymes and why each enzyme has an optimum temperature and pH.

Warning

Common mistakes and safety

Writing that enzymes are "living". They are molecules; they still work after being extracted from dead cells, as long as they are not denatured.
Saying an enzyme "is used up" as the reaction slows. The substrate is used up; the enzyme is unchanged.
Thinking every name ending in -ase is a hydrolase. Dehydrogenases, ligases and isomerases all end in -ase too.
Safety: hydrogen peroxide irritates skin and eyes and is corrosive when concentrated. Use dilute solution, wear eye protection and wash off any splashes.

Tip

Memory hook for the seven classes: "Old Tigers Hunt Lazy Impala Like Thieves": Oxidoreductases, Transferases, Hydrolases, Lyases, Isomerases, Ligases, Translocases (EC 1 to 7).

✦

Practice: naming and characteristics

Distinguish between an intracellular and an extracellular enzyme, with one example of each.
Suggest names for the enzymes that (a) hydrolyse urea, (b) remove hydrogen from succinate, (c) build RNA from nucleotides.
To which EC class does each belong: (a) lipase, (b) DNA ligase, (c) an enzyme that converts glucose-6-phosphate into fructose-6-phosphate?
In a catalase experiment, 18 $\mathrm{cm^3}$ of oxygen was collected in the first 2 minutes. Calculate the mean rate.
Explain why the rate of oxygen release in a catalase experiment falls with time even though the enzyme is not used up.
Explain why a boiled-potato control is needed in the catalase experiment.
A pupil says: "Enzymes make reactions happen that could never happen without them." Evaluate this statement.

Show answersHide answers

An intracellular enzyme works inside the cell that made it (catalase, DNA polymerase); an extracellular enzyme is secreted and works outside the cell (salivary amylase, pepsin, fungal digestive enzymes).
(a) Urease. (b) Succinate dehydrogenase. (c) RNA polymerase.
(a) Hydrolase (EC 3). (b) Ligase (EC 6). (c) Isomerase (EC 5).
$\frac{18}{2} = 9\,\mathrm{cm^3\,min^{-1}}$ .
Hydrogen peroxide (the substrate) is used up, so its concentration falls and substrate molecules collide with active sites less often; fewer enzyme–substrate complexes form per second.
It shows that the oxygen comes from the action of the enzyme, not from the potato tissue or from hydrogen peroxide breaking down by itself; boiling denatures the enzyme but leaves everything else the same.
Not correct. Enzymes only speed up reactions that are already possible: hydrogen peroxide breaks down without catalase, just very slowly. By lowering the activation energy, enzymes make such reactions fast enough to be useful at body temperature.

Quick check

Match each enzyme to its EC class.

Tap one on the left, then its partner on the right.

Key points

Enzymes are biological catalysts, mostly globular proteins, named after their substrate or reaction with -ase; EC numbers sort them into seven classes (oxidoreductases to translocases).
They are specific, unchanged by the reaction, effective in small amounts, speed up both directions of reversible reactions, lower activation energy, are sensitive to temperature and pH, may need cofactors and can be inhibited.
Rate = amount of product formed (or substrate used) per unit time; the initial rate is the fairest measure.

Sources and credits

2.3.6: Enzymes, from Biology 2e by OpenStax (Mary Ann Clark, Matthew Douglas, Jung Choi), via LibreTexts Biology, licensed under CC BY 4.0. Used for the nature and characteristics of enzymes. Adapted by Ganzaa.
"Enzyme Commission number" and "Catalase", Wikipedia contributors, licensed under CC BY-SA 4.0. Used for the EC classes (including the translocase class added in 2018) and catalase's turnover. Adapted by Ganzaa.
Figure 1, the tables, worked examples (the results and the turnover of $5 \times 10^6$ per second are illustrative), practice and quick check: written by Ganzaa.
Photos: Jhon Matthew O. Leron, CC BY-SA 4.0; Rohit Sharma, CC BY 4.0; both via Wikimedia Commons.
Video: "Enzymes | Cells | Biology | FuseSchool", FuseSchool - Global Education, embedded from YouTube.
This lesson adapts CC BY-SA material and is shared under CC BY-SA 4.0.

1A mountain of foam in ten seconds

2How enzymes are named

3Characteristics of enzymes

4Investigating catalase activity

A mountain of foam in ten seconds

How enzymes are named

Characteristics of enzymes

Investigating catalase activity