Amino Acids and Proteins (copy)

Amino Acids

Amino Acid Overview and Types

Overview

Proteins are linear heteropolymers of alpha-amino acids

Amino acids share many features, differing only at the R substituent (group)

  • the alpha carbon is chiral when the R group is anything other than hydrogen (so anything other than glycine)

  • all chiral amino acids are optically active

Because of tetrahedral arrangement of bonding orbitals around the alpha-carbon, the four different groups can occupy two unique spatial arrangements and thus have 2 possible stereoisomers: L and D

  • L and D versions of an amino acids are enantiomers

    • nonsuperimposable mirror images

  • only L-amino acids are found in proteins

Amino acids are classified based on their R groups (charge, H-bonding ability, and if they’re acid/basic)

  • Two main categories: Hydrophobic and Hydrophilic

    • Hydrophobic amino acids are non-polar (includes AA’s with alkyl/aliphatic and with aromatic R groups)

    • Hydrophilic amino acids are polar, includes neutral, acidic, and basic R-groups

Hydrophobic, nonpolar, aliphatic/alkyl R groups:

  • Non-polar side chains consist mostly of hydrocarbons

  • any functional groups are uncharged at biological pH

  1. Glycine, Gly, G (-H)

    • only achiral amino acid, has a slightly sweet taste

  2. Alanine, Ala, A (-CH3)

    • canonical example of a simple. small, nonpolar amino acid

  3. Proline, Pro, P (R-group is a ring, bonds with amino group twice)

    • can break up secondary structures due to the kink proline can cause

    • can be found within the turns of beta-pleated sheets

  4. Valine, Val, V (-CH(CH3)2)

    • it substitution for glutamic acid in hemoglobin causes sickle-cell disease

    • contains isopropyl group

  5. Leucine, Leu, L (-CH2CH(CH3)2)

    • essential amino acid (animals and humans cannot synthesize it ourselves so it must be obtained from diet)

  6. Isoleucine, Ile, I (-CH(CH3)CH2CH3)

    • essential amino acid

  7. Methionine, Met, M (-CH2CH2SCH3)

    • C-S bond makes molecule nonpolar, involved in DNA methylation and angiogenesis

    • essential amino acid found especially in eggs

Hydrophobic, non-polar, aromatic R groups

  • Aromatic R-groups can absorb UV light

    • the higher the concentration of protein in a substance, the more UV light is absorbed

  1. Phenylalanine, Phe, F (-CH2-benzene)

    • present in artificial sweetener aspartame

  2. Tryptophan, Trp, W (two rings)

    • precursor of serotonin and melatonin

Hydrophilic, polar, neutral R groups

  • side chains are hydrophilic, thus on surface of proteins and are subjected to chemical modifications

    • can be oxidized or reduced, affecting conformation of protein

  1. Serine, Ser, S (-CH2OH)

    • target for phosphorylation and other processes involved in post-translational modifications and signaling (due to OH group)

  2. Threonine, Thr, T (-CH(OH)CH3)

    • target for phosphorylation due to OH groups

    • essential amino acid

  3. Cysteine, Cys, C (-CH2SH)

    • can form covalent disulfide bridges (important in tertiary structures)

  4. Asparagine, Asn, N (-CH2(CO)NH2)

    • reacts to reducing sugars (glucose and fructose) in baked and fried foods to form acrylamide, a potentially carcinogenic compound

  5. Glutamine, Gln, Q (-CH2CH2(CO)NH2)

    • most common as a free-amino acid in human blood and is involved in a wide range of metabolic reactions

  6. Tyrosine, Tyr, Y (CH2-benzene-OH)

    • can undergo post translational modifications and phosphorylation

    • aromatic

Hydrophilic, polar, basic R groups

  1. Lysine, Lys, K (-(CH2)4NH3+)

    • the primary amine at the end of the chain is fairly reactive and is the target for many covalent modifications (methylation and acetylations)

  2. Arginine, Arg, R (-NHC(NH2+)NH2)

    • plays a role in regulating blood pressure and other biomolecule synthesis

    • guanidino group can be protonated and can be resonance-stabilized (makes arginine the most basic of all amino acids)

  3. Histidine, His, H (CH2-aromatic with N and NH2)

    • is deprotonated at physiological pH

    • can serve as a buffer in pHs slightly more acidic than physiological

Hydrophilic, polar, acidic R groups

  1. Aspartic Acid, Asp, D (-CH2COOH)

    • deprotonated form is called aspartate

    • a component of artificer sweetener aspartame

  2. Glutamic Acid, Glu, E (-CH2CH2COOH)

    • deprotonated form is called glutamate

    • important as a structural amino acid in proteins and important in neurotransmitters

Acid/Bases and Titrations

Acid-Base Chemistry

Titrations

Amino Acid Reactions

Strecker synthesis

Gabriel synthesis

Peptide bond formation