BIOCHEM2027 Specialised Subject · 4.4
2027 · High School Specialised Subject · Biochemistry

6.1 Overview of Enzymes

Enzymes: proteins, catalytic RNA and EC classification

Enzyme definition and catalytic cycle, active site and stereospecificity, ribozymes, cofactors and holoenzymes, and the IUBMB EC 1 to 7 classes.

5 SECTIONS20 FIGURESEnglish edition
01

Most enzymes are proteins

  • An enzyme speeds a specific reaction and is not consumed net in the process
  • Most are built from one or more polypeptide chains, and the sequence-derived three-dimensional structure is the basis of catalysis
  • The catalytic cycle can involve structural change or transient covalent intermediates, so the enzyme is not literally identical at every instant
  • Basic cycle E + S to ES to EP to E + P; not every enzyme has two separable ES and EP states
  • The active site is the three-dimensional region of binding and catalysis, using hydrogen bonds, electrostatics, van der Waals forces and the hydrophobic effect
  • Lock-and-key and induced fit are teaching descriptions; real structural change is more varied
표 6.1-1Basic terms of an enzyme reaction
Figure 6.1-1The chemical nature of enzymes: most catalysts are proteins, but folded RNA can also catalyse.
Figure 6.1-2Reaction path with and without an enzyme: the barrier falls while the free-energy difference between start and end is unchanged.
Figure 6.1-3Simplified enzyme cycle repeating substrate recognition, catalysis and product release.
Figure 6.1-4Concept diagram of active-site interactions; favourability must include surrounding water and charge.
Figure 6.1-9Teaching model comparing substrate complementarity with induced fit; induced fit alone does not explain every enzyme.
02

The protein nature of enzymes and its exceptions

  • Primary structure fixes which residues take part in binding and catalysis and where they sit
  • Secondary, tertiary and quaternary structure gather distant residues into the active site and create substrate selectivity
  • Heat, pH or denaturants that destroy structure lower activity, but a change in activity does not always mean global unfolding
  • Ribozymes are catalytically active RNAs, with self-splicing RNA and the ribosomal peptidyl transferase centre as key examples
  • Peptide bond formation in the ribosome depends on rRNA at the catalytic centre, so all enzymes are proteins is false and most are proteins is correct
  • Apoenzyme plus essential cofactor gives the holoenzyme; a coenzyme is an organic cofactor and a prosthetic group is tightly bound
  • Catalytic rate depends on temperature, pH, ionic strength, substrate supply, cofactors and inhibitors, and there is no universal optimum
표 6.1-2Cofactors, apoenzyme and holoenzyme
Figure 6.1-5Concept diagram of catalytic RNA folding to promote a reaction; not all RNA is an enzyme.
Figure 6.1-8Hierarchy from amino acid sequence to higher structure; quaternary structure applies to multi-subunit enzymes.
Figure 6.1-6Model of holoenzyme formation from apoenzyme plus cofactor; not every enzyme needs a cofactor.
Figure 6.1-7Representative metal ions and coenzymes with their actions; each participates in different reactions.
03

Enzymes are classified by the reaction they catalyse

  • The IUBMB enzyme commission classifies by the chemical reaction actually catalysed
  • An EC number has four positions: class, subclass, sub-subclass and serial number
  • EC 7 translocases were added in 2018, so there are now seven classes rather than six
  • Common names usually end in -ase, but a name never fully describes the mechanism
  • Procedure: compare reactants and products, identify the group moved, check whether water takes part in hydrolysis, test for energy-coupled bond formation, then check for membrane transport
표 6.1-3The seven IUBMB enzyme classes
Figure 6.1-10The seven current IUBMB enzyme classes, including EC 7 translocases alongside the traditional six.
Figure 6.1-11How to read the four numbers of EC 2.7.1.1; each position denotes a different classification level.
Figure 6.1-20Flow chart for assigning an EC class from the reaction; exact assignment follows the official reaction definition.
04

The seven classes and representative reactions

  • EC 1 oxidoreductases: lactate dehydrogenase moves reducing power from lactate to NAD+
  • EC 2 transferases: hexokinase transfers the terminal phosphate of ATP to glucose; using ATP is not itself the criterion
  • EC 3 hydrolases: alpha-amylase consumes water to cleave glycosidic bonds, and not every cleavage is hydrolysis
  • EC 4 lyases: fumarase adds or removes water across a double bond, so water alone does not make an enzyme EC 3
  • EC 5 isomerases: triose phosphate isomerase interconverts GAP and DHAP, same composition and different arrangement
  • EC 6 ligases: glutamine synthetase forms a C-N bond coupled to ATP, where energy coupling rather than simple joining is the point
  • EC 7 translocases: Na+/K+-ATPase uses one ATP to export three Na+ and import two K+
Figure 6.1-12Simplified redox reaction catalysed by lactate dehydrogenase; direction depends on cellular conditions.
Figure 6.1-13Concept equation for the phosphate transfer catalysed by hexokinase.
Figure 6.1-14Overview of the alpha-amylase reaction; cleavage depends on the actual polysaccharide structure.
Figure 6.1-15Water addition and removal by fumarase; EC 3 and EC 4 are not separated by the mere presence of water.
Figure 6.1-16Concept equation for the interconversion of GAP and DHAP.
Figure 6.1-17Glutamine synthesis forming a new C-N bond coupled to ATP use.
Figure 6.1-18Energy-coupled transport by Na+/K+-ATPase; sidedness and stoichiometry follow the usual working model.
05

How enzyme activity is established in practice

  • Presence of the protein, shown immunologically, and catalytic activity are different kinds of evidence
  • Equal protein amounts can give different activity through denaturation, inhibition, cofactor loss or pH change
  • Registering a new enzyme needs direct experimental evidence for the reaction, not sequence similarity alone
  • Catalase 2 H2O2 to 2 H2O + O2 requires no-enzyme and heat-treated controls at matched volume and concentration
  • Foam height alone cannot give an oxygen volume, and observations also reflect temperature, mixing and surface effects
  • An enzyme raises the rate but does not change ΔG°′ or the equilibrium constant
Figure 6.1-19Simulated oxygen release at different enzyme amounts; the values are teaching data, not measurements.
2027 High School Specialised Subject · Biochemistry · Sangil Park (Asan High School) · Reference material is printed as an appendix.
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