Enzymology
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Enzymology. Lecture 2 by Rumeza Hanif. How enzymes work?. Uncatalyzed reactions tend to be slow. Neutral pH, mild temperature, aqueous environment inside cell are needed for biological molecules

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Enzymology

Enzymology

Lecture 2 by RumezaHanif


How enzymes work
How enzymes work?

  • Uncatalyzed reactions tend to be slow.

  • Neutral pH, mild temperature, aqueous environment inside cell are needed for biological molecules

  • Digestion of food, sending of nerve signals or contraction of muscles do not occur at a useful rate without catalysis.

  • The active site of enzyme encloses a substrate.


Enzymes affect reaction rates not equilibria
Enzymes affect reaction rates, not equilibria

E+S ↔ ES ↔ EP ↔ E+P

ES: Transient complex of enzyme with substrate

EP: Transient complex of enzyme with product


Energy in the biological system
Energy in the biological system

Energy in the biological system is described as free energy, G

G: The energy associated with a chemical reaction that can be used to do work. 

The free energy of a system is the change in its enthalpy (H) minus the product of the temperature (Kelvin) and the entropy (S) of the system

G= H-TS


  • Enthalpy (H) describes the energy it takes for a substance to change from one phase to another (i.e. solid to liquid.). It reflects the number and kinds of bonds.

  • Entropy (S) deals with the randomness ordisorder of particles and substances (i.e. more disorder of the particles as a solid substance is heated to a liquid.) In short, enthalpy looks at the energy needed whereas entropy looks at the organization of the particles themselves.


Free energy change g
Free energy change ΔG

  • Enthalpy change ΔH reflecting the kinds and numbers of chemical bonds and noncovalent interactions broken and formed.

  • Entropy change ΔS describing the change in the system’s randomness

    Equation??


Free energy g
Free Energy G

  • Standard Free Energy (ΔGO): free energy changes for reactions under 298 K temperature, partial pressure of each gas 1 atm or 101.3 kPa, concentration of each solute 1 M

  • Biological standard free-energy change (ΔG’o): standard free energy at pH 7 and other normal biological conditions


G is positive for endergonic reaction while it is negative for exergonic reaction
ΔG is positive for endergonic reaction while it is negative for exergonic reaction.

Amino Acids Proteins (Endergonic)

ATP ADP +P (Exergonic)


Reaction Coordinate 1: ATP ADP+P (the exergonic breakdown of ATP has a large negative free energy)Reaction Coordinate 2: Glucose + P Glucose 6 Phosphate (The formation of Glucose 6 phosphate yields a product of higher energy than the 2 reactants, for this endergonic reaction ΔG is positive)


Reaction coordinate diagram
Reaction coordinate diagram

  • Ground state: The starting point for either the forward or the reverse reaction.

ΔG’o


Keq and g o are measures of a reaction s tendency to proceed spontaneously
Keq and ΔGo are measures of a reaction’s tendency to proceed spontaneously

  • The tendency of a chemical reaction to go to completion can be expressed as an equilibrium constant.

  • aA + bB ---- cC+ dD

  • Keq = [C]ceq [D]deq

    [A]aeq [B]beq

    The relationship between Keq and ΔG’o can be described by thy expression

    ΔG’o= -RT In Keq

    R= Gas constant 8.315 J/mol.K

    T= Absolute temperature 298 K (25 C)


Rate of reaction
Rate of reaction

  • The rate of any reaction is determined by the conc. of the reactant(s) and by a rate constant (k)

  • V = k [S]

  • k reflects the probability of reaction under a given set of conditions (pH, temperature)


Further reading
Further reading

Chapter 6, Lehninger Principles of Biochemistry, David L. Nelson and Michael M. Cox. 5thEd (How enzymes work)

Chapter 1, Lehninger Principles of Biochemistry, David L. Nelson and Michael M. Cox. 5thEd, pg 22-25


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