Chapter 3: Amino Acids & Peptides

What are the four substituents bonded to the alpha-carbon of an amino acid?

1. Carboxyl group (-COOH), 2. Amino group (-NH2), 3. Hydrogen atom, 4. R group (side chain)

Which amino acid has a second hydrogen atom instead of an R group?

Glycine

What are the two mirror-image forms of amino acids called?

L-isomer and D-isomer (enantiomers)

Which isomer of amino acids is found in proteins?

L-isomers only

At neutral pH, what form do free amino acids exist in?

Dipolar ion (zwitterion) - NH3+ and COO-

What charge does the amino group have at neutral pH?

Positive (+1) - NH3+

What charge does the carboxyl group have at neutral pH?

Negative (-1) - COO-

What are the 5 main classes of amino acids?

1. Nonpolar aliphatic, 2. Aromatic, 3. Polar uncharged, 4. Positively charged, 5. Negatively charged

Which amino acids are in the nonpolar, aliphatic group?

Glycine (G), Alanine (A), Proline (P), Valine (V), Leucine (L), Isoleucine (I), Methionine (M)

Which amino acids are aromatic?

Phenylalanine (F), Tyrosine (Y), Tryptophan (W)

At what wavelength do aromatic amino acids absorb UV light?

270-280 nm

Which amino acids are polar, uncharged?

Serine (S), Threonine (T), Cysteine (C), Asparagine (N), Glutamine (Q)

Which amino acid can form disulfide bonds?

Cysteine (C) - via its -SH (sulfhydryl) group

Which amino acids are positively charged at physiological pH?

Lysine (K), Arginine (R), Histidine (H)

Which amino acid can be protonated OR deprotonated at physiological pH?

Histidine (H) - pKa ~6.0; useful in enzyme active sites

Which amino acids are negatively charged at physiological pH?

Aspartate (D), Glutamate (E)

What is the one-letter code for Tryptophan?

W

What is the three-letter code for Glutamine?

Gln

What is the one-letter code for Lysine?

K

What is the three-letter code for Phenylalanine?

Phe

What is the pKa of the terminal alpha-carboxyl group?

~3.1

What is the pKa of Aspartate/Glutamate side chains?

~4.1

What is the pKa of Histidine side chain?

~6.0

What is the pKa of the terminal alpha-amino group?

~8.0

What is the pKa of Cysteine side chain?

~8.3

What is the pKa of Tyrosine side chain?

~10.9

What is the pKa of Lysine side chain?

~10.8

What is the pKa of Arginine side chain?

~12.5

If pH < pKa, which form dominates?

Protonated form

If pH > pKa, which form dominates?

Deprotonated form

At pH = pKa, what is the ratio of protonated to deprotonated?

50:50

What is the isoelectric point (pI)?

The pH at which the net charge of a molecule is zero

How do you calculate pI for an amino acid WITHOUT an ionizable side chain?

pI = (pK1 + pK2) / 2

How do you calculate pI for an amino acid WITH an ionizable side chain?

Average the two pKa values flanking the isoelectric species (net charge = 0)

For glycine, pK1 = 2.34 and pK2 = 9.60. What is the pI?

pI = (2.34 + 9.60) / 2 = 5.97

At pH > pI, what is the net charge of an amino acid?

Negative

At pH < pI, what is the net charge of an amino acid?

Positive

At pH = pI, what is the net charge?

Zero

Where is buffering capacity greatest?

Near the pKa

What type of reaction forms a peptide bond?

Dehydration (condensation) reaction - loss of H2O

What are the four key features of a peptide bond?

1. Planar, 2. Has resonance (partial double-bond character), 3. Uncharged, 4. Capable of hydrogen bonds

Which six atoms lie in the peptide bond plane?

C-alpha, C, O, N, H, C-alpha

Why can't rotation occur around the peptide bond?

Resonance gives it partial double-bond character

Which configuration of peptide bonds is most common?

Trans configuration (minimizes steric clashes)

What is the N-terminus?

The free amino end of a polypeptide

What is the C-terminus?

The free carboxyl end of a polypeptide

How many amino acids and peptide bonds are in a dipeptide?

2 amino acids, 1 peptide bond

How many amino acids and peptide bonds are in a tripeptide?

3 amino acids, 2 peptide bonds

What is the molecular weight cutoff between a polypeptide and a protein?

10 kDa

What is the average molecular weight of an amino acid residue in a protein?

110 g/mol (128 - 18 = 110)

How do you estimate the number of amino acid residues in a protein?

MW / 110

What is a conjugated protein?

A protein containing permanently associated chemical components other than amino acids

What is the non-amino acid part of a conjugated protein called?

Prosthetic group

What do lipoproteins contain?

Lipids

What do glycoproteins contain?

Sugars (carbohydrates)

What do metalloproteins contain?

Specific metals

What do hemoproteins contain?

Heme (iron porphyrin)

What is primary structure?

Covalent bonds linking amino acid residues in a polypeptide chain (the sequence)

What is secondary structure?

Recurring structural patterns (alpha-helix, beta-sheet, beta-turn)

What is tertiary structure?

3D folding of a polypeptide

What is quaternary structure?

2+ polypeptide subunits assembled together