Describe how amino acids are categorized by their chemical properties AP Bio

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• Would you recommend memorizing all 20 amino acids, their structures and their classifications for the MCAT?

  

  • You should be able to classify all the amino acids by polarity, charge, aliphatic vs aromatic, and probably learn the structures and functional groups of the special amino acids (for example: two cysteines close in space may form disulfide bridges under oxidizing conditions, prolines tend to introduce kinks in polypeptides and are often found at the beginning of alpha helices).

• Why are non-polar molecules hydrophobic? I mean, they do not have any partial charge in their structure, thus neither attraction nor repulsion will occur.
  Then why is it hydrophobic?

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    Well you're right that non-polar things will not have any attraction or repulsion with water. It's not that water doesn't like oil, it's that water doesn't like oil as much as it likes other water (or other polar molecules that act like water).
    Each water molecule will try to lower its energy state by maximizing its number of hydrogen bonds with other polar molecules. This is seen at the macroscopic level as oil getting pushed away so that water can maximize the amount of polar-polar bonds.

• I was taught that tryptophan is a polar molecule due to NH bond next to the aromatic making it slightly polar. Your video seems to say otherwise. So is tryptophan polar or non polar?

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    You're right, it would be slightly polar. However, since it is not strongly polar, tryptophan is still generally classified as having a nonpolar R group.

• At

  5:51

  , she says that she remembers that the amino acids are basic because they have N atoms. So why aren't Proline and Tryptophan also polar/basic?

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    The three amino acids are Lysine, Arginine, and Histidine, and how I remember these three is using the abbreviation for the strong base LAH (lithium aluminum hydride). They are basic because their side chain is basic and are positively charged at pH values below their pKa’s. Only the guanidine group (HNC(NH2)2) in Arg (pKa = 12.5) and amine group in Lys (pKa = 10.5) will accept a proton and exist with an overall charge of +1 at physiological pH. The imidazole group (ring structure with two N’s) in His (pKa = 6.0) would exist predominantly in neutral form.

    Proline is not polar and basic because the N is not from the side chain. Proline originates from glutamic acid, the carboxy reduced to an aldehyde, amino group attacking to form the Schiff base, and further reduction. Basically, the N is from the original alpha-amino group. Proline qualifies as nonpolar and cyclic. As for tryptophan, it has an indole substituent on the beta-carbon. The N in the indole group (2 ring structure with one N) has no free lone pair to act as a base because it is already participating in the resonance. Tryptophan qualifies as nonpolar and aromatic.

• At

  4:36

  she says she remembers polar amino acids by the presence of an oxygen or a sulfur atom in their side chains, but at

  2:26

  , she says methionine is a nonpolar amino acid, even though there is a sulfur atom in its side chain. How are we supposed to recognize the difference between those? Is there another way to identify which are polar and which are nonpolar?

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    Methionine contains a sulfur atom in its side chain, but it is surrounded by three carbon atoms. Cysteine, however, is only bonded to one carbon atom and one hydrogen atom. In methionine, then, there is certainly polarity in the molecule, but overall, the three carbons (and their hydrogen atoms) are more significant. When a molecule of some substance mixes with water, it disrupts the hydrogen bonding between water molecules. For very polar molecules, this isn't a problem, because they can interact strongly with water. For only weakly polar molecules, the energy "payoff" of bonding with water isn't enough to compensate for the disruption in water hydrogen bonding. You can see this effect with alcohols of different sizes; small alcohols like methanol and ethanol are miscible with water because they are strongly polar (-OH group attached to only one or two carbon atoms). Larger alcohols (propanol or hexanol) are not miscible with water because even though they are technically polar, they have such large hydrocarbon chains that they can't interact favorably with water, despite the hydroxyl group.

• 4:38

  I'm confused. In the books I'm reading, Basic Medical Biochemistry by Lieberman et al, and Lippincott's Biochemistry, Tyrosine is classified under aromatic amino acids, making it nonpolar like Tryptophan and Phenylalanine. They also say that Tyr and Try are more polar than Phe, but they still are relatively nonpolar. Can anyone help me understand?

  • Tyrosine's phenol group can indeed hydrogen bond with water, but it can also energetically-favorably pi stack with surrounding aromatic amino acids (similar to DNA nitrogenous base stacking), typically within a protein's hydrophobic core. In fact, tyrosine pi stacking is commonly observed in known protein structures, and possibly more often than exposed tyrosines hydrogen bonding with water at the protein surface.

• Do amino acids in a low pH solution always have a positive charge?

  • The word "always" is very difficult in biological science. But in most cases of extremely low pH (1-2) then yes all of the amino acids would carry a positive charge.

• What are aliphatic amino acids?

• Oil is an example of Hydrophobic, isnt it?

  • Yes, oil is a non-polar molecule and so it will not mix with water, which is a polar molecule. This makes oil hydrophobic ("water fearing") and is why oil floats on top of water.

• At

  4:38

  , Tyrosine is included as a Polar aa (also the side box says that it can be included as an aromatic acid. My question then is, is Tyrosine considered both non polar and polar amino acid then? My Kaplan textbook only shows tyrosine as an aromatic.

  • If you get a question on the MCAT about Tyrosine being polar or non-polar, say that it's non-polar.

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