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
• 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.
Spontaneous process
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 )
• 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)
Photosynthesis
Respiration
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: removal of electrons
• Reduction: the addition of electrons
Enzymes Lower the Barriers That
Block Chemical Reactions
How enzymes work?
How Enzymes Find Their
Substrates: diffusion model
• Enzymes: sit still (move more slowly than
substrates) in cells.
• Substrates: random walks
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
• Free energy
change DG
measures the
amount of disorder
created in the
universe (cell +
environment) when
a reaction takes
place.
reversible reaction
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
 B 
DG  DG  RT ln  
 A 
0
DG0: standard free-energy change
Chemical equilibrium
DG  0
B  e DG / RT
A
0
Enzymes donot change the
equilibrium point for reactions
Activated carrier molecules (coenzymes)
The Formation of an Activated
Carrier
Adenosine triphosphate (ATP):
energy carrier
energetically unfavorable reaction
NAD (nicotinamide adenine
dinucleotide): electron carrier
ACTIVATED CARRIER
ACTIVATED CARRIER
GROUP CARRIED IN
HIGH-ENERGY LINKAGE
ATP
phosphate
NADH, NADPH, FADH2
Acetyl CoA
Carboxylated biotin
S-Adenosylmethionine
electrons and hydrogens
acetyl group
carboxyl group
methyl group
Uridine diphosphate
glucose
glucose
Food Molecules  energy (ATP)
• Digestion
• Glycolysis
• Citric acid cycle
Electron-transport chain
Metabolism is regulated
• Substrate concentrations
• Enzymes
• Multi-cellular organisms