Bi201-- introduction to enzyme kinetics

what are enzymes

biological catalysts

DNA encoded proteins

folded into specific secondary and tertiary structures

may also require transient interaction with another molecule (a cofactor) to catalyze the reaction e.g. NAD+

single or several polypeptide chains

what do enzymes recognise and do

• recognise substrate or reactant— specific ‘substrate specificity’

• catalyze specific reactions-→ accelerate reaction rate

• tightly regulated, allowing pathways and chemical reaction in the cell to be coordinated (e.g. regulation of phosphofructokinase[PFK])

why are enzymes important

• break down food during digestion

• essential for cellular processes— DNA replication, transcription, translation

• defective enzymes can cause malfunctions and diease— immunodeficinecies, food intolerance

• can be targeted by drugs, important for medical applications— aspirin, ibuprofen

• essential in metabolic pathways

• biotech processes— laundry detergent has lipases to break down fat and proteases to breakdown proteins

lock and key theory

• “specificity of an enzyme (lock) for its substrate (key) arises from geometrically complementary shapes”

• active site: site of substrate binding and catalysis of chemical reaction

induced fit model

• some enzymes able to bind moleules that resemble substrate, but do not catalyze a reaction

• more than just lock/key complementarity required for substrate binding and enzyme catalysis to occur

exmaple of induced fit: hexokinase

• catalyses first reaction of glycolysis

• phsophorylates glucose to form glucose-6-phosphate

properties of active site

• properties of amino acid residues lining the active site are essential to bind the substrate and for the reaction

• examples of interaction between substrate and active site

  • complementary charges (electrostatic)

  • hydrogen bonds

  • hydrophobic interactions

• forces/interactions involved similar in nature to those that dictate protein structure

• properties of the active site also essential for catalytic mechanism, which depends on properties of catalytic groups

catalytic groups

• chemical groups of amino acid residues in active site that come into contact with substrate

• promote formation or breaking of chemical bonds in the substrate but also between substrate and catalytic residues of the enzymes

• e.g. lysozyme

  • glycoside hydrolase that digests the bacterial cell wall digestion

  • GLU35 catalytic residue with catalytic carboxyl group that is important to start the reaction

enzymes accelerate chemical reaction

bag of sugar can be stored for years with littel conversion to CO” and H2O (respiration)

without enzymes— 750,000,000 years

with enzymes— 22 milliseconds

chemical reactions and free energy

• free enthalpy or Gibbs free energy or free energy

• kJ/mol

• energy available in a system that cna be made into work

• the lower the free enthalpy of a system, the more stable it is

• abberviation: G

enzymes are biological catalysts

not changed by the reaction

• used temporarily

• re-used

• very little need to help in many reactions

• products and substrates are the same and have the same free energy as those obtained and used in absence of enzyme

• transition state corresponds to an intermediate step in the reaction— it is very unstable