Amino Acids and the Primary Structure of Proteins

Important biological functions of proteins 1. Enzymes, the biochemical catalysts 2. Storage and transport of biochemical molecules 3. Physical cell support and shape (tubulin, actin,

collagen) 4. Mechanical movement (flagella, mitosis,

muscles) (continued)

Globular proteins

• Usually water soluble, compact, roughly spherical

• Hydrophobic interior, hydrophilic surface

• Globular proteins include enzymes,carrier and regulatory proteins

Fibrous proteins

• Provide mechanical support

• Often assembled into large cables or threads

• α-Keratins: major components of hair and nails

• Collagen: major component of tendons, skin, bones and teeth

3.1 General Structure of Amino Acids

• Twenty common α-amino acids have carboxyl and amino groups bonded to the α-carbon atom

• A hydrogen atom and a side chain (R) are also attached to the α-carbon atom

Zwitterionic form of amino acids

• Under normal cellular conditions amino acids are zwitterions (dipolar ions):

Amino group = -NH3+

Carboxyl group = -COO-

Stereochemistry of amino acids

• 19 of the 20 common amino acids have a chiral α-carbon atom (Gly does not)

• Threonine and isoleucine have 2 chiral carbons each (4 possible stereoisomers each)

• Mirror image pairs of amino acids are designated L (levo) and D (dextro)

• Proteins are assembled from L-amino acids (a few D-amino acids occur in nature)

Four aliphatic amino acid structures

Proline has a nitrogen in the aliphatic ring system

• Proline (Pro, P) - has a three carbon side chain bonded to the α-amino nitrogen

• The heterocyclic pyrrolidine ring restricts the geometry of polypeptides

Aromatic amino acid structures

Methionine and cysteine

Fig 3.4 Formation of cystine

D. Side Chains with Alcohol Groups

• Serine (Ser, S) and Threonine (Thr, T) have uncharged polar side chains

Structures of histidine, lysine and arginine

Structures of aspartate, glutamate, asparagine and glutamine

G. The Hydrophobicity of Amino Acid Side Chains

• Hydropathy: the relative hydrophobicity of each amino acid

• The larger the hydropathy, the greater the tendency of an amino acid to prefer a hydrophobic environment

• Hydropathy affects protein folding: hydrophobic side chains tend to be in the interior hydrophilic residues tend to be on the surface

Table 3.1

• Hydropathy scale for amino acid residues

(Free-energy change for transfer of an amino acid from interior of a lipid bilayer to water)

Free-energy change for transfer (kjmol-1)

Amino acid

Fig 3.5 Compounds derived from common amino acids

Fig 3.6 Titration curve for alanine

• Titration curves are used to determine pKa values

• pK1 = 2.4 • pK2 = 9.9 • pIAla = isoelectric

point

Fig 3.7 Ionization of Histidine

(a) Titration curve of histidine

pK1 = 1.8 pK2 = 6.0 pK3 = 9.3

Fig 3.7 (b) Deprotonation of imidazolium ring

Table 3.2

pKa values of amino acid ionizable groups

3.5 Peptide Bonds Link Amino Acids in Proteins

• Peptide bond - linkage between amino acids is a secondary amide bond

• Formed by condensation of the α-carboxyl of one amino acid with the α-amino of another amino acid (loss of H2O molecule)

• Primary structure - linear sequence of amino acids in a polypeptide or protein

Fig 3.9 Peptide bond between two amino acids

Polypeptide chain nomenclature

• Amino acid “residues” compose peptide chains

• Peptide chains are numbered from the N (amino) terminus to the C (carboxyl) terminus

• Example: (N) Gly-Arg-Phe-Ala-Lys (C) (or GRFAK)

• Formation of peptide bonds eliminates the ionizable α-carboxyl and α-amino groups of the free amino acids

Fig 3.10 Aspartame, an artificial sweetener

• Aspartame is a dipeptide methyl ester (aspartylphenylalanine methyl ester)

• About 200 times sweeter than table sugar

• Used in diet drinks

3.7 Amino Acid Composition of Proteins

• Amino acid analysis - determination of the amino acid composition of a protein

• Peptide bonds are cleaved by acid hydrolysis (6M HCl, 110o, 16-72 hours)

• Amino acids are separated chromatographically and quantitated

• Phenylisothiocyanate (PITC) used to derivatize the amino acids prior to HPLC analysis

Fig 3.13 Acid-catalyzed hydrolysis of a peptide

Fig. 4.5 Resonance structure of the peptide bond

(a) Peptide bond shown as a C-N single bond

(b) Peptide bond shown as a double bond

(c) Actual structure is a hybrid of the two resonance forms. Electrons are delocalized over three atoms: O, C, N

Fig. 4.6 Planar peptide groups in a polypeptide chain

• Rotation around C-N bond is restricted due to the double-bond nature of the resonance hybrid form

• Peptide groups (blue planes) are therefore planar

Fig. 4.7 Trans and cis conformations of a peptide group

• Nearly all peptide groups in proteins are in the trans conformation

4.1 There Are Four Levels of Protein Structure

• Primary structure - amino acid linear sequence

• Secondary structure - regions of regularly repeating conformations of the peptide chain, such as α-helices and β-sheets

• Tertiary structure - describes the shape of the fully folded polypeptide chain

• Quaternary structure - arrangement of two or more polypeptide chains into multisubunit molecule

Fig. 4.10 The α-helix

Fig. 4.11 Stereo view of right-handed α helix

• All side chains project outward from helix axis

Fig. 4.13 Horse liver alcohol dehydrogenase

• Amphipathic α helix (blue ribbon)

• Hydrophobic residues (blue) directed inward, hydrophilic (red) outward

Fig 4.15 β-Sheets (a) parallel, (b) antiparallel

Fig. 4.19 Common motifs

Fig. 4.23 Common domain folds

4.8 Quaternary Structure

• Refers to the organization of subunits in a protein with multiple subunits (an “oligomer”)

• Subunits (may be identical or different) have a defined stoichiometry and arrangement

• Subunits are held together by many weak, noncovalent interactions (hydrophobic, electrostatic)

Fig 4.25 Quaternary structure of multidomain proteins

Fig. 4.42 Hemoglobin tetramer

(a) Human oxyhemoglobin (b) Tetramer schematic