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Biomolecule synthesis. Haixu Tang School of Informatics. Each cell can be viewed as a tiny chemical factory . Cell Metabolism Is Organized by Enzymes. substrate. product. Catabolic and anabolic pathways . The 2nd law of thermodynamics.

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biomolecule synthesis

Biomolecule synthesis

Haixu Tang

School of Informatics

the 2nd law of thermodynamics
The 2nd law of thermodynamics
  • In any isolated system (a collection of matter that is completely isolated from the rest of the universe), the degree of disorder can only increase.
  • Entropy: measure of disorder. The greater the disorder, the greater the entropy.
  • The systems will change spontaneously toward arrangements with greater entropy.
how do cells generate order
How do cells generate order?
  • A cell is not an isolated system.
  • A cell takes in energy from its environment
    • Food, photons from the sun, etc.
  • A cell uses the energy to generate order within itself and discharge part of the energy (heat) into the environment.
  • The total entropy (of the cell + the environment) increases, while the entropy of the cell decrease (disorder  order).
this conversion of energy in the cell 1st law of thermodynamics
This conversion of energy in the cell (1st law of thermodynamics )
  • an animal cell: converts chemical bond energy (in the chemical bonds between the atoms of the molecules in food) into heat energy (the random thermal motion of molecules)
  • A plant cell: converts photon energy (in the sun light) into chemical energy (the chemical bonds in the synthesized molecules)

A cell obtains energy from sugars or other organic molecules by allowing their carbon and hydrogen atoms to combine with oxygen to produce CO2 and H2O, respectively.

oxidation and reduction
Oxidation and Reduction
  • Oxidation: removal of electrons
  • Reduction: the addition of electrons
how enzymes find their substrates diffusion model
How Enzymes Find Their Substrates: diffusion model
  • Enzymes: sit still (move more slowly than substrates) in cells.
  • Substrates: random walks
random walk
Random walk

Average distance: proportional to the square root of the time involved.

1 second 1 mm, it takes 4 seconds to travel 2 mm, 100 seconds to travel 10 mm, etc.

Diffusion is an efficient way for small molecules to move the limited distances in the cell (a typical animal cell is 15 mm in diameter).

the free energy change for a reaction
The Free-Energy Change for a Reaction
  • Free energy change DG measures the amount of disorder created in the universe (cell + environment) when a reaction takes place.
d g is not only influenced by energy
DG is not only influenced by energy
  • DG becomes more negative for the transition A  B (and more positive for the transition BA) as the ratio of A to B increases.
compensation of concentration difference between substrates and products
Compensation of concentration difference between substrates and products

DG0: standard free-energy change

food molecules energy atp
Food Molecules  energy (ATP)
  • Digestion
  • Glycolysis
  • Citric acid cycle
metabolism is regulated
Metabolism is regulated
  • Substrate concentrations
  • Enzymes
  • Multi-cellular organisms