Biomolecules formulas

Ratio of deprotonated (A-) to protonated (HA) form of one ionisable group, with pKa = -log10 Ka. At pH = pKa the two forms are equal, and a group buffers best within about 1 pH unit of its pKa.

pK1 is the alpha-COOH and pK2 the alpha-NH3+. For any amino acid, pI is the average of the two pKa values that lie on either side of the neutral (net charge zero) form.

Right-handed alpha helix: 3.6 residues per turn, 0.15 nm rise per residue, i to i+4 hydrogen bonds.

n is the number of chiral carbons in the open-chain form (valid when there are no meso forms). Aldohexoses have n = 4, giving 16 (8 D and 8 L); ketohexoses have n = 3, giving 8. Cyclisation adds one more chiral centre, the anomeric carbon.

Idealised B-form: 0.34 nm rise per base pair, 10 bp per turn, so pitch 3.4 nm; diameter about 2 nm; right-handed. B-DNA in solution has about 10.5 bp per turn; use 10 unless a question states otherwise.

Same form as Michaelis-Menten kinetics: flux saturates at Jmax, and Kt is the solute concentration giving half-maximal flux. Simple diffusion has no such limit; its flux rises linearly with the concentration difference.

R = 8.314 J mol${}^{-1}$ K${}^{-1}$, T in kelvin, F = 96,485 C mol${}^{-1}$, z the signed charge of the solute, and $\Delta \psi ={\psi }_2-{\psi }_1$ in volts; $\Delta G$ is in J mol${}^{-1}$. For an uncharged solute z = 0 and only the concentration term remains. A negative value means the movement is spontaneous (passive); a positive value means it needs an energy input.

i is the number of particles each formula unit gives in solution (1 for glucose, about 2 for NaCl), C the molar concentration, R the gas constant (0.0821 L atm mol${}^{-1}$ K${}^{-1}$ gives $\pi$ in atm) and T in kelvin; iC is the osmolarity. Valid for ideal dilute solutions. Water moves by osmosis from lower to higher osmolarity, often through aquaporins; a cell swells in a hypotonic medium and shrinks in a hypertonic one (tonicity also depends on whether the solute can cross the membrane).

One permeant ion at equilibrium; z is its signed charge (+1 for K+ and Na+, -1 for Cl-, +2 for Ca2+). 2.303RT/F = 61.5 mV at 37 degrees C (about 59 mV at 25 degrees C).

Steady-state potential (no net current) with several monovalent permeant ions, assuming a constant electric field across the membrane. P is each ion's permeability; only ratios matter. The Cl- terms are inverted because it is an anion. The result lies between the ions' Nernst potentials, closest to that of the most permeable ion; with only one permeant ion it reduces to the Nernst equation.