Amino Acids, Peptides, Protein Primary Structure

Chapter 3

Amino Acids

• Basic structural units of proteins• All have 3 common functional grps:

– -NH2, -COOH, -H

• Individual aa’s each have diff R grp• These 4 grps att’d to a C

– Is this a chiral C?• At neutral pH, exist as dipole

(zwitterion)– Amino grp as NH3+– Carboxyl grp as COO-

• Chiral C, so have D,L stereo-isomers– L form

aa’s polymer-ize prot’s

• Side chains vary in size, shape, charge, reactivity, H-bond capacity

• Five groups of aa’s, based on R grp similarities

• Some notes:– Glycine – only optically inactive aa– Cysteine – highly reactive sulfhydryl grp– Histidin – R grp may be proton donor or

acceptor at physio pH

• 1) Nonpolar w/ aliphatic R grps– Glycine (Gly, G)– Alanine (Ala, A) – Proline (Pro, P)– Valine (Val, V)– Leucine (Leu, L)– Isoleucine (Ile, I)– Methionine (Met, M)

• 2) Aromatic R grps– Phenylalanin

e (Phe, F)– Tyrosine (Tyr,

Y)– Tryptophan

(Trp, W)

– Hydrophobic

• 3) Polar w/ uncharged R grps– Serine (Ser, S)– Threonine (Thr, T)– Cysteine (Cys, C)– Asparagine (Asn, N)– Glutamine (Gln, Q)

• 4) Polar w/ + charged R grps at physio pH– Lysine (Lys, K)– Histidine (His, H)– Arginine (Arg, R)

• 5) Polar w/ - charged R grps at physio pH– Aspartate (Asp, D)– Glutamate (Glu, E)

Cysteine/Cystine

• Reactive SH grp of cys oxidizes disulfide bond

• Forms cystine– Hydrophobic

mol– Impt to protein

3D structure

Amino Acid Titration Curves

• Aa’s – weak acids– Construct titration curves for each– REMEMBER: Add OH-, measuring

change in pH as titrate w/ OH-. Plot OH- added on x axis vs. pH on y axis

• Have 2 abstractable H’s, both on grps att’d to C (bottom p. 81)– One on carboxyl grp– One on amino grp

• 2 inflection pts– Shape of each inflection sim to

inflection seen w/ monoprotic acid (Chpt 2)

– Each aa has 2 pKa’s• At midpoint of titration ([OH-]=1

eq), cmpd fully dipolar– No net electrical charge– “Isoelectric point”– Isoelectric pH = pI

• Each aa has characteristic pI– At any pH<pI, aa has net + charge– At any pH>pI, aa has net - charge

• pKa1 <<<< pKa2– First H+ released from aa is much

more easily given up than second H+

• 2 pKa’s = 2 regions of buffering capacity

• Aa’s w/ ionizable R grps (lys, arg, his) have 3rd pKa

Peptide Bonds

• Links two aa’s Dipeptide

– Condensation rxn; H2O removed

– Endothermic rxn– Stable under physio cond’s; broken w/ boiling

in strong acid/base

carboxyl of aa1 joined to amino of aa2• In living systems, peptide bond form’n

assisted by ribosomes in translation process

• Oligopeptide = several aa’s joined by peptide bonds

• Polypeptide = many aa’s = small protein– Protein commonly MW > 10,000

• Aa residue of peptide w/ free amino grp called amino terminus

• Aa residue of peptide w/ free carboxyl grp = carboxy terminus

• At neutral pH, peptides have 1 free NH3+ and 1 free COO-

• BUT R grps on each aa may be ionized – Each peptide has

characteristic pI

• Peptide ionization = sum of all R grp charges of aa’s which make up the peptide