Amino Acid Groups and Bonds

Nonpolar, Aliphatic R groups

• Glycine, Gly, G

• Alanine, Ala, A

• Proline, Pro, P

• Valine, Val, V

• Leucine, Leu, L

• Isoleucine, Ile, I

• Methionine, Met, M

Aromatic R groups

• phenylalanine, Phe, F

• Tyrosine, Tyr, Y

• Tryptophan, Trp, W

Polar, Uncharged R groups

• Serine, Ser, S

• Threonine, Thr, T

• Cysteine, Cys, C

• Asparagine, Asn, N

• Glutamine, Gln, Q

Positively Charged R groups

• Lysine, Lys, K

• Histidine, His, H

• Arginine, Arg, R

Negatively Charged R groups

• Aspartate, Asp, D

• Glutamate, Glu, E

Hydrogen Bonds

• when 2 closely spaced EN atoms share a proton

  • EN atom: partial negative

  • proton: partial positive

• N,O,F

Hydrophobic interactions

• stabilize bimolecular structure

• has the hydrophilic heads and the hydrophobic tails

2 reasons why non-polar groups avoid interaction with water

1. can’t H bond to water, so when in water, they reduce the number of H bonds water can make (UNFAVORABLE CHANGE IN ENTHALPY)

2. water molecules on their surface become highly ordered (UNFAVORABLE CHANGE IN ENTROPY)

4 Types of non-covalent interactions

1. H bonds

   1. b/w neutral groups

   2. peptide bonds

2. Ionic Interactions

   1. attraction

   2. repulsion

3. Hydrophobic Interactions

4. Van der Waals: 2 atoms close in proximity

Structure of an Amino Acid

• Amino Group

• Carboxyl Group

• H

• R group

Residue

• single building block (monomer) in a polymer

Glycine

• Gly, G

• nonpolar, aliphatic

Alanine

• Ala, A

• Nonpolar, aliphatic

Proline

• Pro, P

• Nonpolar, aliphatic

Valine

• Val, V

• nonpolar, aliphatic

Leucine

• Leu, L

• nonpolar, aliphatic

Isoleucine

• Ile, I

• nonpolar, aliphatic

Methionine

• Met, M

• nonpolar, aliphatic

Phenylalanine

• Phe, F

• Aromatic

Tyrosine

• Tyr, Y

• Aromatic

Tryptophan

• Trp, W

• Aromatic

Serine

• Ser, S

• Polar, uncharged

Threonine

• Thr, T

• Polar, uncharged

Cysteine

• Cys, C

• Polar, uncharged

• can form disulfide bonds

  • covalent bonds between 2 cysteine residues

• Polar, uncharged

Asparagine

• Asn, N

• Polar, uncharged

Glutamine

• Gln, G

• Polar, uncharged

Aspartate

• Asp, D

• Neg charge

Glutamate

• Glu, E

• Neg charge

Lysine

• Lys, K

• Pos charge

Histidine

• His, H

• Pos charge

Arginine

• Arg, R

• Pos Charge