Humboldt State University ® Department of Chemistry

Richard A. Paselk

Chem 438 - Introductory Biochemistry - Spring 2013

Lecture Notes:

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To give some perspective, lets look at the relative sizes of these objects. [overhead-sizes of molecules, one million times magnification]

All of these molecules together go to make up cells.

Ted Video(dynamics at the molecular scale)

So what have we learned?

Organic Reactions in Metabolism

Organic Reaction Mechanisms: A slight variation on the view of your text authors allows us to categorize all common biological reactions into four groups:

1. Group-transfer reactions (transfer of an electrophile [acyl {RCOX}, phosphoryl {OPO₃X^2-}, and glycosyl groups] between nucleophiles [alcohols, amines, thiols, etc.])
   1. Nucleophilic substitution
2. Redox Reactions
3. Eliminations {eliminate H₂O, NH₃, ROH or RNH₂}, Isomerizations, Rearrangements
   1. Eliminations
   2. Isomerization & rearrangement
4. C-C bond formation or breakage (condensation and cleavage reactions).

Thermodynamics in Metabolism

Remember, the cool thing about thermo is that it is pathway independent - we can tell how much energy is available in an M&M by burning it in pure oxygen in a stainless steel container and tell you how far you can run on that M&M!

The tragedy of thermo, the other side of the coin, is that it tells nothing about the details - thermo gives us no idea about how the energy is used, or what steps are involved in its loss.

Review a bit:

q = the quantity of heat exchanged by the system:

• if the system gains heat, q = positive, and we say the process is endothermic.

• if the system loses heat, q = negative, and we say the process is exothermic.

Notice in each case endo- and exo- are in respect to the system, not the surroundings. For example, a fire is exothermic, because heat comes out of the fire - the fuel loses heat, even though you (part of the surroundings) may gain some of it.

Keep in mind that heat always flows naturally from hotter to cooler systems. Energy must be used up to move heat in the opposite direction, as in a refrigerator.

w (in chemistry) = the work done by or on the system:

• w = positive when work is done on the system (e.g. as gas is compressed)
• w = negative when the system does work on its surroundings (e.g. a gas moves a piston by expansion - notice that an ideal gas expanding in space does no work!)

Note that if no heat is transferred to or from a system (it is isolated in a "thermos"), then all energy must appear as work. On the other hand, if no work is done, then all energy must appear as heat (this is utilized in calorimetry which is discussed below).

For chemists and biologists the thermodynamic term generally of most interest is the Free Energy for a reaction, that is the energy available to do work.

• The free energy is defined as: G = G_products- G_reactants = H - T S.
• When the free energy is negative we say the reaction is spontaneous, which simply means the reactants are favored in the reaction equation as written.
• Note when a reaction is at equilibrium then the G is zero.

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© R. A. Paselk 2010; Last modified 28 January 2013