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Amino Acid labelling
Shaista_4645
#1 Posted : Saturday, May 08, 2021 2:40:09 AM
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Can you please go over which amino acids are hydrophilic and hydrophobic ex) tyrosine has an OH and also a breeze so is it amphipathic?
Youssef_6546
#2 Posted : Saturday, May 08, 2021 8:38:54 AM
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Hi Shaista,

I took a bunch of biochemistry courses for my undergrad, so I might be able to help. For the most part, we rely on the "R-group" or side chain of the amino acid to determine if they are hydrophobic vs hydrophilic.

Non-polar (hydrophobic) amino acids:

- Glycine: "R-group" or side chain is a hydrogen and has no charge
- Alanine: has a methyl (-CH3) as a side chain, which has no charge
- Valine: side chain is a branched hydrocarbon chain with no charge
- Leucine: same as valine
- Isoleucine: same as valine
- Methionine: despite its side chain having a sulfur atom, the sulfur is found between two carbons which gives the side chain a zero net dipole (base on what I understand)
- Tryptophan: yes, the side chain does have a nitrogen which could participate in H-bonds, but there is also a benzene ring and most of the side chain is made of hydrocarbons, which largely contributes to the amino acids hydrophobicity.
- Phenylalanine: benzene ring is hydrophobic
- Proline: cyclic carbon chain is hydrophobic

Polar (hydrophilic) uncharged

- Serine: side chain has a hydroxyl (-OH) which allows it to make H-bonds, thus hydrophilic
- Threonine: same as serine
- Cystine: side chain is a sulfhydryl (-SH)
- Tyrosine: same as serine, the hydroxyl makes it polar
- Glutamine: has an amide, whose "-NH2" contributes to polarity
- Asparagine: same as glutamine

Polar positively charged (basic)

- Lysine: side chain ends with a "-NH3+", which is obviously pos charged and contribute to polarity
- Arginine: same as lysine, side chain ends with a pos charged nitrogen (but now there are two more nitrogens)
- Histidine: side chain (called imidazole) is cyclic and has two nitrogens that could participate in H-bonding, as well one nitrogen is pos charged (contributing to polarity).

Polar negatively charged (acidic)

- Glutamate: side chain has a carboxyl group, which has a deprotonated "-OH" that contributes polarity
- Aspartate: same as glutamate

These are how I learned my amino acids. I hope they help! If anyone could correct my logic, that would be much appreciated. Thank you! :)
INSTR_Sydney_132
#3 Posted : Thursday, May 20, 2021 5:04:56 PM
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Hi Shaista,

In agreement with Youssef - you can classify each amino acid based on their characteristic side chain. The properties of these side chains are essential for the function of proteins, so it is a high yield MCAT topic!

You can break them down into 4 groups... polar, non-polar, acidic (polar negative charge) and basic (polar positive charge).

Non-Polar: These side chains are considered nonpolar due to their aliphatic nature; they are primarily composed of carbons and hydrogens. These amino acids include glycine, alanine, valine, leucine, isoleucine, methionine, phenylalanine, tryptophan and proline. Note that due to their nonpolar nature, these amino acids will not be attracted to water surrounding the protein, and as such they will often located in the core of proteins to aggregate away from unfavourable interactions with water.

Polar: The polar amino acids are serine, threonine, cysteine, tyrosine, asparagine and glutamine. The polar AAs will often be positioned on the outside of the protein to interact with water.

Acidic: There are two acidic amino acids: aspartate and glutamate. These residues are proton donors. They will often lose a proton in solution becoming negatively charged.

Basic: There are three basic amino acids: lysine, arginine, and histidine. These residues are proton acceptors. Each of these basic amino acids has a nitrogen that can accept a hydrogen to become positively charged.
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