From Biolk483


A brief description of the parts of an Eukaryotic cell (continued)


  • approximately same size as mitochondria
  • single lipid bilayer membrane
  • has 40 hydrolytic enzymes
    • hdyro = water, lytic = cut; so it cuts by adding using water
  • if one of the 40 enzymes continually does not get transported to the lysosome then the lysosome begins to swell as it cannot break everything down. These are called lysosomal storage diseases and tay-sachs is an example.
    • Lysosomal storage diseases are almost all 100% fatal, usually by the age of 4.
    • A classic example of knowing exactly what the problem is and the solution, but not how to realize the solution.


  • gets rid of stuff by putting oxygens on it --called oxidizing-- makes the oxidized molecule chemically polar and therefore more soluble
  • includes d-amino acid oxidase for breaking down d-amino acids (because living things use a different conformation of amino acids called L-amino acids and d-amino acids therefore have the potential to break lots of biochemical processes)
    • catastrophe theory and L vs. D amino acids: catastrophe theory would say that life evolved with both L and D amino acids until L gained some sort of an advantage (perhaps easier to make or something of the like) at which point the presence of D nearly drops to zero (hence the catastrophe part).
    • D amino acids are often made by bacteria and they have bad effects on our biochemical processes, hence we have peroxisomes.

Member Vesicles

  • secretory vesicle: gets rid of stuff (from inside the cell to the outside)
  • endosome (aka receptosome): receives stuff into the cell (from outside the cell to the inside)


  • microtubules make up cilia, flagella, etc.
  • microfilaments:
    • actin and myosin, etc.
    • bind to plasma membrane and manipulate it


  • very viscous
  • made up of salts, sugars, etc.
  • 90% water by weight

Sizes in Biochemistry

  • resolving power of the human eye is 0.1 mm (10^-4 meters)
    • this is 100 micrometers (aka microns)
  • liver cells = 200K angstrums = 2 x10^-5 meters = 20 micrometers
    • so liver cell would have to be 5 times larger to be seen by naked eye
  • prokaryotic cell = 2 micrometers so it is 50 times too small to be seen
  • know the units and their scientific notations (i.e. y.y x10^z)
  • there will be number conversion questions on the fist and third exams in multiple choice format.

Semester Class Topics

  1. Water
  2. Amino acids and proteins (this is about 40% of the entire class)
  3. Lipids and membranes
  4. Sugars and carbohydrates
  5. Bioenergetics (Another big portion of the semester)
  6. Some metabolic pathways


  • water is important for searching for life
  • What is so important about water?
  1. It is liquid
  2. Has a low molecular weight so we can have lots of it in small places
  3. it is mobile (a function of being small)
  4. it is abundant (55.5 molar); most things in biochem are millimolar or micromolar.
  5. High melting point (0C)
  6. High heat of fusion: the amount of heat it takes to melt it; means the structure must be tight because it takes lots of energy to make it a liquid.
  7. High boiling point (100C): methane is -164C, so this says that H20 stick together so well that it takes lots of heat to break it apart.
  8. High heat of vaporization: (the energy to move from liquid to gas) so we see that the parameters of life are the temperatures at which ice->water and water->gas
  9. High Surface Tension: cohesive, it sticks together; responsible for hydrophobic effect (which is, in turn, responsible for all of biochemical structure.
  10. Very good solvent for polar and charged solvents
  11. High di-electric constant: responsible for number 5-10
  12. Does not dissovle hydrocarbons

Functions of water

1. Reagent

  • used in polymer building (polymerization) and cutting (hydrolysis)
  • respiration: h20 is the sink (where we get rid of) electrons (e-) from respiration
  • photosynthesis: source of e- for photosynthesis

2. Solvent for life (remember that 55.5 Molar thing....)

3. Insulation: high specific heat

4. Controls pH

5. Hyrdophobic effect: responsible for all biochemical structure

Structure of water

  • Oxygen is electronegative so it is pulling e- from the hydrogens thus making itself have a slightly more negative charge.
  • 4 hydrogen bonds can form between two electronegative atoms
    • C-H bonds cannot hydrogen bond because the C-H bond is not electronegative
    • H-bond is 4.5 kcal/mol, as a comparison, alcohol bonds (which are considered weak in the organic world) are 110 kcal/mol, so H-bond are extremely weak. However, when you consider the shear sum of H-bonds they are very powerful.
  • be sure to see a diagram here of liquid water molecules hydrogen bonding.
  • To give an idea of how well structured water is in terms of continuity of h-bonding this chart is given as measurements of the clusters found at various temperature levels in water:
Temperature (c) # (percent of molecules all clustered together by h-bonding)
0(c) ice 100
0(c) liquid 91
40(c) 38
100 0
  • so we can see that it only took a couple of h-bonds to break to move from a solid to a liquid form of water.
  • also, at 100C there is no structure left and the water molecules are independently steam

Dissolving Stuff in Water

  • NaCl dissolves really well in water --see a diagram.
  • Dissolving hydrocarbons doesn't work so well in water.
    • this is because of the hydrophobic effect
    • as an example: Hexane
      • there are no h-bonds between water and hexane because the C-H bonds on hexane are not electronegative.
      • so if you put hexane in water, it will all clump together in a ball (if no gravity were in affect; a lump on the bottom of the container when gravity is in affect)
      • whenever you see a sphere or (c)lumps like this, you know something is hydrophobic
    • This is all explainable by surface tension.
      • when you put in a hydrocarbon, the water molecules would rather be next to other water molecules so they can h-bond, not next to the hydrocarbon, so there is surface tension as they "try" to get away from the hydrocarbon into the crowd of other water molecules
      • the more h-bonds the more stable, hence the water wants into the crowd
      • this makes things float and small things able to move on surface of water (like insects)
      • putting an hydrocarbon in water makes a new surface and that takes energy, so this is unfavorable.
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