2 BIO 326R Chemistry 1 and 2

2 BIO 326R Chemistry 1 and 2 - BIO 326R Chemistry I &...

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    BIO 326R Chemistry I & II
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    Some Terms Hydrophobic – Water hating Hydrophilic – Water loving Charged – has a permanent charge of + or - Polar – has a slight positive or negative charge
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    Hydrophobic or Hydrophilic?  Hexane Water Add C14 labeled molecules MIX Allow phase separation Withdraw sample from each phase and measure C14 content Amino acids have had their relative hydrophobicity assigned by using a method like this. Note that all amino acids in their free form are charged (they have amino and carboxyl groups) and therefore will mostly partition to the aqueous (water) phase. They will differ in how much, though.
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    Cellular Chemistry – Chemical  Bonds Covalent Ionic Hydrogen bonding Van der Waals interactions
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    Covalent bonds Shared electron pairs Can be “stiff” or allow rotation Strong bonds, typically tolerant to heat Examples Peptide bonds Phosphodiester bonds in DNA, RNA C-C bonds
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    Single, Double, Triple bonded  Carbon H – C – C – H H H H H C = C H H H H H – C C – H Ethane: The two carbons and their associated hydrogens can rotate relative to each other. Ethene or ethylene: the two carbons do not rotate relative to each other. The hydrogens will always be a relatively constant distance from each other. Ethyne or acetylene: no rotation
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    Cellular Chemistry – Electrostatic or  ionic bonds Formed by interaction of a charge pair (oppositely charged ions) Examples “salt bridges” in proteins e.g. Aspartate (-) and Lysine (+) Cell surface interactions – Phospholipid (-) and divalent cations (++) such as Calcium, Magnesium.
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    Cellular Chemistry – Hydrogen bonds Shared Hydrogen atom Hydrogen attached to strongly electronegative atom (Oxygen, Nitrogen). This means the hydrogen will have a partial positive charge and be attracted to a molecule with a negative charge. Sensitive to heat (not strong) Examples Nucleic Acid hybridization Water Proteins
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    Cellular Chemistry –  Van der Waals interactions Not really a bond Also called hydrophobic interactions Temporary dipoles cause molecules to stick together Very weak, usually need multiple interactions to have noticeable effects Favored with long and thin molecules or flat/planar molecules (large surface area contact) Examples Lipids in cell membrane Internal (hydrophobic) amino acids in proteins Stacking of bases in double stranded nucleic acids
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    Van der Waals interactions - Hydrogen H2 H2 H2 H2 δ - δ - δ + H2 δ - δ + δ + Temporary dipole in one molecule (electrons are always moving) Induced dipole in second molecule { Attraction between partial pos and neg H2
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    Chemical bonds and interactions in  proteins Proteins are highly complex molecules which adopt a specific three dimensional shape.
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2 BIO 326R Chemistry 1 and 2 - BIO 326R Chemistry I &...

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