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Lecture 7

BIOL 201 Lecture Notes - Lecture 7: Accessible Surface Area, Genetic Linkage, Miscibility

Course Code
BIOL 201
Robin Young

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Hydropathy Plots to determine Hydrophobicity (Link to BIOL 200)
- Hydropathy Plots predict transmembrane domains
- Hydropathy refers to the R-group polarity (how hydrophobic or
hydrophilic) for each amino acid
- The R-group polarity helps us see their potential for interactions and
thereby functionality
Hydrophobic effect
- the observed tendency of nonpolar substances to aggregate in
aqueous solution and exclude water molecules
- NOT due to water and lipid molecules are repulsing each other
Is it attraction or repulsion?
- In a molecular mixture or lipid and water molecules, the two
components will separate into two phases over time
- There is an attractive force between them (IDID interactions)
- The overall energy of IDIDs does not change during phase separation
- Energy of dipole-dipole interactions and H-bonds is maximized
- Attraction due to increase in motional freedom
The 20 common amino acids Assessing Hydropathy
Different ways of assessing hydropathy:
- Partition methods (amino acid derivatives, peptides)
- Chromatographic methods (peptides)
- Location method (accessible surface area: proteins)
Note: There are at least 25 different scales to determine protein hydropathy
Different methods can yield slightly different values of hydropathy
The Partition Method Comparing amount of AA analogues in two immiscible
- AA analogues are synthesized in the lab, such that the N and
C termini do not ionize (mimic the peptide linkage group)
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