Humboldt State University ® Department of Chemistry

Richard A. Paselk

Chem 431	Biochemistry	Fall 2001
Lecture Notes:: 5 September	© R. Paselk 2001
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Thermodynamics in Biology

Thermo is the study of energy, so very important to our understanding of living systems. For thermo purposes organisms are open systems at approximate steady state -they gain energy as fast as they lose it.

We will be looking at thermo again as we progress, for now let's just review some major aspects.

• Energy is conserved. This is the so-called First Law of Thermodynamics = The Law of Conservation of Energy. Mathematically:

DU = U_final - U_initial = q - w

• In biology and chemistry convenient to define a new quantity, the heat at constant pressure = Enthalpy = H. Enthalpy is also usually close to the energy, since there is usually little change in volume in biological reaction.
• The Entropy of the Universe increases. This is the Second Law of Thermodynamics.
  • Entropy is a measure of disorder, given the symbol S.

Free Energy

The energy definition most commonly employed in chemistry and biology is the Free Energy, DG. This is the energy actually available to do work, that is the energy left after the inevitable loss of entropy. Thus the free energy gives one the maximum possible useful energy from a process, so efficiency is usually expressed as a percentage of free energy, not total energy

DG = DH - TDS <0

• Chemical Equilibria and Free Energy

Chapter 2: Water

Water is a very unusual, even incredible substance whose amazing properties are often unappreciated because of its ubiquitousness. Water's special properties include extremely high mp and bp (0 °C & 100 °C K, compare to methane, -183 °C & -161 °C, with a MW of 16 vs. water's 18); a high heat capacity (18 cal/°C mol vs. 8 cal/°C mol for methane); it has a high viscosity; its solid form is less dense than the liquid form at the same temperature (ice floats on water - very rare), it has a large surface tension, and it has a high dielectric constant (78.5 vs. 1.9 for hexane).

The high mp, bp, and heat capacity of water all predict relatively strong bonding between water molecules, so let's first review the types of bonding which occur between atoms and molecules. The most stable bonds are of course covalent bonds (with bond energies of 50 [S-S] to 80 [C-C] to 110 [O-H] kcal/mol), occurring when we have significant overlap of atomic orbitals.

 

Water of course is a covalent structure: H-O-H. But what gives it its special properties is the polarity of its O-H bonds and the resultant dipole moments of the bonds and the molecule itself.

The water molecule itself is bent, with an angle of 104.5° between the hydrogens (compare to 109.5° for sp³ tetrahedron) as seen in Figure 2.1 on pg. 23 of your text. [overhead 3.1, NP]

Because of the very strong dipole moments of these bonds and the very small size of the hydrogen substituents on water, a slight degree of orbital overlap occurs between adjacent water oxygens and hydrogens to give partial covalent bonds known a H-bonds (effectively, can only form with O, N, & F).

Note that the partial covalent character means that they are directional! Figure 2.2 (p 24) shows a representation of H-bonds.

• Compare the bond length of water H bonds (0.18 nm) to the covalent bond-length between O and H of 0.096 nm - notice that the bond distance is nearly twice the true covalent bond distance, but significantly less than the van der Waals radius of 0.26 nm. [overhead 3.3, NP]

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Last modified 5 September 2001