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Amino Acids and the Primary Stucture 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
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)
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
D. Side Chains with Alcohol Groups
• Serine (Ser, S) and Threonine (Thr, T) have uncharged polar side chains
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 interiorhydrophilic 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)
Aminoacid
Fig 3.6 Titration curve for alanine
• Titration curves are used to determine pKa values
• pK1 = 2.4
• pK2 = 9.9
• pIAla = isoelectric point
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
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 artif icial 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. 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. 4.13 Horse l iver alcohol dehydrogenase
• Amphipathic α helix (blue ribbon)
• Hydrophobic residues (blue) directed inward, hydrophilic (red) outward
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)