Biomolecule synthesis

1
Biomolecule synthesis

• Haixu Tang
• School of Informatics

2
Each cell can be viewed as a tiny chemical
factory
3
Cell Metabolism Is Organized by Enzymes
substrate
product
4
Catabolic and anabolic pathways
5
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.

6
Spontaneous process
7
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).

8
(No Transcript)
9
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)

10
(No Transcript)
11
Photosynthesis
12
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.
13
Oxidation and Reduction

• Oxidation removal of electrons
• Reduction the addition of electrons

14
(No Transcript)
15
(No Transcript)
16
Enzymes Lower the Barriers That Block Chemical
Reactions
17
How enzymes work?
18
How Enzymes Find Their Substrates diffusion model

• Enzymes sit still (move more slowly than
  substrates) in cells.
• Substrates random walks

19
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).
20
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.

21
reversible reaction
22
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.

23
Compensation of concentration difference between
substrates and products
DG0 standard free-energy change
24
Chemical equilibrium
25
Enzymes donot change the equilibrium point for
reactions
26
Activated carrier molecules (co-enzymes)
27
The Formation of an Activated Carrier
28
Adenosine triphosphate (ATP) energy carrier
29
(No Transcript)
30
energetically unfavorable reaction
31
(No Transcript)
32
NAD (nicotinamide adenine dinucleotide) electron
carrier
33
(No Transcript)
34
ACTIVATED CARRIER
ACTIVATED CARRIER GROUP CARRIED IN HIGH-ENERGY LINKAGE
ATP phosphate
NADH, NADPH, FADH2 electrons and hydrogens
Acetyl CoA acetyl group
Carboxylated biotin carboxyl group
S-Adenosylmethionine methyl group
Uridine diphosphate glucose glucose
35
(No Transcript)
36
Food Molecules ? energy (ATP)

• Digestion
• Glycolysis
• Citric acid cycle

37
(No Transcript)
38
(No Transcript)
39
(No Transcript)
40
(No Transcript)
41
Electron-transport chain
42
Metabolism is regulated

• Substrate concentrations
• Enzymes
• Multi-cellular organisms

43
(No Transcript)
44
(No Transcript)