Amino Acids

structures and features

Glycine

• non polar, aliphatic, hydrophobic

• R-group: -H

• the only amino acid with 2 protons

• the only amino acid that is not chiral

Alanine

• non polar, aliphatic, hydrophobic

• R-group: -CH₃

• pretty hydrophobic

Valine

• non polar, aliphatic, hydrophobic

• R-group: -CH(CH₃)₂

• looks like a “V”

• multiple saturated hydrocarbons

  • can become bulky

• would put as far away from water when it comes to structure

Leucine

• non polar, aliphatic, hydrophobic

• R-group: -CH₂CH(CH₃)₂

• compared to valine, similar but has extra CH2

• high hydrophobicity

• larger

Isoleucine

• non polar, aliphatic, hydrophobic

• R-group: CH(CH₃)₂CH₂

• isomer of leucine so same number of C and H

• methyl sticking out to side affects packing

• has a second chiral carbon (C that is attached to 4 different groups)

  • second choral carbon is the CH attached to the alpha carbon

Proline

• non polar, aliphatic, hydrophobic

• R-group: a cyclic 𝛂-imino acid (-CH₂-CH₂-CH₂-NH)

• only amino acid that makes contact with either functional group

• severely constraining rotation and bonding

• the H₂C and H₂N⁺ makes a covalent bond

Methionine

• non polar, aliphatic, hydrophobic

• R-group: -CH₂-CH₂-S-CH₃

• one of two amino acids with sulfur

  • cannot form disulfide bonds

• doesn't do much because S isn’t at the end

Phenylalanine

• non polar, aromatic (lots of delocalization of electrons)

• R-group: -CH₂-C₆H₅ (benzene ring)

• benzene ring

  • very rigid

  • can’t bend cause of partial double bonds

  • absorbs less light compared to other aromatics

Tyrosine

• polar, aromatic

• R-group -CH₂-C₆H₄OH

• so CH₂ with benzene ring and hydroxyl

• not as hydrophobic compared to phenylalanine

• rigid side chain (due to benzene)

• very weak weak acid

• the H in OH can ionize off at high pH

• absorbs light better than F

Tryptophan

• non polar, aromatic

• R-group: -CH₂-C₈H₆N (indole ring)

• 2 rings

• absorbs light really well

• can fluorescence

• big, heavy

• can affect what proteins can do

• the N in the ring DOESN”T gain or lose proton

Serine

• polar, uncharged, hydrophilic

  • can hydrogen bond, more on outer surface of protein

• R-group: CH₂OH

• the H at the end, it can lose but because of high pKa (alcohol pKa = 13.6), not likely

• not too important but that H at the end can be replaced with a phosphate (helps to signal)

Threonine

• polar, uncharged, hydrophilic

• R-group: -CH(OH)-CH₃

• not as polar as serine because of methyl

• proton in OH wouldn’t come off because of high alcohol pKa (13.6)

• has a second chiral carbon

Cysteine

• polar, uncharged, hydrophilic

• R-group: -CH₂-SH

  • has a thiol/sulfhydryl group

• other amino acid with sulfur in it

• the H in the thiol group can come off

• 2 nearby Cys can form a disulfide bond in an oxidizing environment

  • sulfur must lose BOTH proton and electron

  • covalent bond will be formed between S and S, meaning strong

  • help stabilize protein structure

Asparagine

• polar, uncharged, hydrophilic

• R-group: -CH₂-C(O)-NH₂ (amide side-chain)

• polar, hydrogen bonding potential

Glutamine

• polar, uncharged, hydrophilic

• R-group: -CH₂-CH₂-C(O)-NH₂ (amide side-chain)

• extra CH₂ between alpha carbon and amide

Aspartate

• acidic, negative at pH 7

• aspartic acid (protonated); aspartate (deprotonated)

• R-group: -CH₂-C(O)-O^-

• can be deprotonated in biological pH

  • at pH 7, lose side chain

• carboxyl pKa = 3.9 (acid)

Glutamate

• acidic, negative at pH 7

• glutamic acid (protonated); glutamate (deprotonated)

• R-group: -CH_2-CH₂-C(O)-O^-

• side chain will be deprotonated

• similar to glutamine except for O^- at end

• carboxyl pKa = 4.2

Lysine

• basic, positive at pH 7

• R-group: -CH₂-CH₂-CH₂-CH₂-NH₃⁺

• will be protonated under biological conditions

• epsilon-amino pKa = 10.5

  • very weak acid (also tyrosine)

Arginine

• basic, positive at pH 7

• R-group: -CH₂-CH₂-CH₂-NH-C(NH₂)₂⁺ (guanidine, pKa = 12.5)

• look for the two N at the end for help identifying

• long

• some hydrophobicity character

• ex. Glu + Arg can have electrostatic interaction

Histidine

• basic, positive at pH 7/polar

• R-group: -CH2-C3H3N2 (imidazole, pKa = 6.0)

  • pKa is close to physiological pH (90% will be in form at pH 7, while 10% will be in protonated form

  • can buffer/has buffering capacity

• fairly rigid ring

• 2 nitrogens

Leucine

Isoleucine

Proline

Methionine

Phenylalanine

Tyrosine

Tryptophan

Serine

Threonine

Cysteine

Asparagine

Glutamine

Aspartate

Glutamate

Lysine

Arginine

Histidine

Glycine

Gly, G

Alanine

Ala, A

Valine

Val, V

Leucine

Leu, L

Isoleucine

Ile, I

Proline

Pro, P

Methionine

Met, M

Phenylalanine

Phe, F

Tyrosine

Tyr, Y

Tryptophan

Trp, W

Serine

Ser, S

Threonine

Thr, T

Cysteine

Cys, C

Asparagine

Asn, N

Glutamine

Gln, Q

Aspartate

Asp, D

Glutamate

Glu, E

Lysine

Lys, K

Arginine

Arg, R

Histidine

His, H