Enzyme Structure and Function

What are Enzymes

Enzymes are proteins (or in some cases RNA) which catalyze reactions but are not themselves used up during the reaction. The reactants are known as substrates. There are many biological functions which require enzymes ranging from DNA replication to digestion of ingested food. The most common method of naming enzymes is with the suffix ASE (eg: lactase).

Enzyme Classification

There are six major ways to classify enzymes and they are based on the reaction types the enzymes are associated with.

  1. Oxidoreductase: Catalyzes the transfer of electrons in oxidation-reduction reactions.
  2. Transferase: Catalyzes the transfer of groups between molecules.
  3. Hydrolase: Catalyzes the transfer of groups to water (can be seen as a form of transferase but more specifically catalyzes hydrolysis reactions).
  4. Lyase: The addition or removal of functional groups by breaking or adding double bonds, respectively.
  5. Isomerase: Catalyzes reactions with allow the conversion of isomeric forms of a molecule.
  6. Ligase: Coupled with the cleavage of ATP, allows for the ligation of two substrates.

Enzymes and Activation Energy

A primary way enzymes function is by stabilizing the transition state of a reaction. Additionally, the activation energy (the energy required to initiate the reaction) is reduced in the presence of enzymes. The following figure demonstrates the phenomenon of reducing activation energy.

Activation Energy Enzymes
[[en:User:|]] at the English language Wikipedia [GFDL (http://www.gnu.org/copyleft/fdl.html) or CC-BY-SA-3.0 (http://creativecommons.org/licenses/by-sa/3.0/)], via Wikimedia Commons

Enzyme-Substrate Specificity

The part of the enzyme that is involved with the catalysis is called the active site. There are two models which account for the specificity of enzymes and substrates.

Active Site Model (Lock & Key Hypothesis)

The enzyme acts like a “lock” and the substrate a “key”. The active site does not change and only the correct substrate, or “key” can activate the enzyme.

Lock and Key Hypothesis
By Hottuna080 (Paint) [GFDL (http://www.gnu.org/copyleft/fdl.html) or CC BY-SA 3.0 (http://creativecommons.org/licenses/by-sa/3.0)], via Wikimedia Commons

Induced Fit Model

This is the most widely accepted model. It suggests that upon binding of the substrate, the enzyme’s active site undergoes a conformational change to better accommodate the substrate.

Induced Fit Model
By Created by TimVickers, vectorized by Fvasconcellos (Provided by TimVickers) [Public domain], via Wikimedia Commons

Mechanisms of Enzyme Catalysis

Enzymes can be assisted in their job of catalyzing reactions by means of various other molecules. Vitamins generally function as organic co-factors and co-enzymes.

  • Vitamins A,D,E,K are fat soluble
  • Vitamins B and C are water soluble

Co-Enzyme

Co-Enzymes are organic carrier molecules which allow the catalysis reaction to occur more efficiently. They carry parts from one molecule to another to assist the enzyme in its job.

Co-Factor

Co-Factors directly participate in the catalysis reactions by helping the enzyme directly with the reaction. For example, Mg ions stabilize the negative charge on DNA to allow DNA polymerase to work.

Environmental Conditions & Enzymes

Enzymes require optimal environmental conditions to allow them to function optimally. These factors can include temperature and pH. If enzymes are added to sub-optimal environments, normal function is generally disrupted.

 

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  • Activation Energy Enzymes
  • Lock and Key Hypothesis
  • Induced Fit Model
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