Enzymes: Quick Revision

A brief note on Enzymes. Read it before a test. Try each question at the end before you open its answer.

What an enzyme is

• An enzyme is a biological catalyst. It speeds up a reaction and is not used up.
• Almost all enzymes are proteins. A ribozyme is an enzyme made of RNA.
• The substrate fits the active site: $\text{E} + \text{S} \rightleftharpoons \text{ES} \longrightarrow \text{EP} \longrightarrow \text{E} + \text{P}$.
• The activation energy is the energy needed to reach the transition state. An enzyme lowers it.
• An enzyme does not change the energy of the substrate or of the product.

What changes the rate

• Temperature: each enzyme has an optimum. Cold makes it inactive. Heat denatures it.
• pH: each enzyme has an optimum pH.
• Substrate: the rate rises and levels off at Vmax. Km is the substrate concentration at half of Vmax.
• Competitive inhibitor: looks like the substrate and blocks the active site. More substrate reduces its effect. Example: malonate with succinate dehydrogenase.

Classes and cofactors

• Six classes: oxidoreductases, transferases, hydrolases (water), lyases, isomerases, ligases (join, with ATP).
• Apoenzyme (protein) + cofactor = holoenzyme.
• Prosthetic group: tight, as in the haem of catalase. Coenzyme: loose, as in NAD and NADP, which contain niacin. Metal ion: as in the zinc of carboxypeptidase.

A worked example

An enzyme reaches half of its maximum rate when the substrate is at $2$ mmol/L. At that substrate level its rate is $40$ µmol/min. What is the maximum rate?

1. Km: the substrate level that gives half of Vmax is $2$ mmol/L, so the enzyme is at half speed.
2. At the Km: the rate of $40$ µmol/min is half of the maximum.
3. Maximum rate: $40 \times 2 = 80$ µmol/min.

Practice with new numbers

A program to try

The program lists three enzymes with the cofactor each one needs and the kind of cofactor.

Mistakes to avoid

• Saying cold destroys an enzyme. Cold only makes it inactive. Heat denatures it.
• Saying Km is a rate. It is a substrate concentration.
• Saying more substrate cannot beat a competitive inhibitor. It can.
• Mixing up hydrolases and lyases. Hydrolases use water. Lyases do not.

Check yourself

1. Which part of an enzyme is the pocket that fits the substrate?

2. What does the rate do at a very high substrate concentration, and why?

3. Which class of enzyme joins two molecules using ATP?

4. What is a holoenzyme?