Amino Acids and the Primary Stucture of Proteins

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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)
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Globular proteins

• Usually water soluble, compact, roughly spherical
• Hydrophobic interior, hydrophilic surface
• Globular proteins include enzymes,carrier and
  regulatory proteins

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Fibrous proteins

• Provide mechanical support
• Often assembled into large cables or threads
• a-Keratins major components of hair and nails
• Collagen major component of tendons, skin,
  bones and teeth

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3.1 General Structure of Amino Acids

• Twenty common a-amino acids have carboxyl and
  amino groups bonded to the a-carbon atom
• A hydrogen atom and a side chain (R) are also
  attached to the a-carbon atom

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Zwitterionic form of amino acids

• Under normal cellular conditions amino acids are
  zwitterions (dipolar ions)
• Amino group -NH3
• Carboxyl group -COO-

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Stereochemistry of amino acids

• 19 of the 20 common amino acids have a chiral
  a-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)

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Four aliphatic amino acid structures
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Proline has a nitrogen in the aliphatic ring
system

• Proline (Pro, P) - has a three carbon side chain
  bonded to the a-amino nitrogen
• The heterocyclic pyrrolidine ring restricts the
  geometry of polypeptides

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Aromatic amino acid structures
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Methionine and cysteine
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Fig 3.4 Formation of cystine
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D. Side Chains with Alcohol Groups

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

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Structures of histidine, lysine and arginine
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Structures of aspartate, glutamate, asparagine
and glutamine
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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

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Table 3.1
Free-energy change for transfer (kjmol-1)
Aminoacid

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

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Fig 3.5 Compounds derived from common amino
acids
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Fig 3.6 Titration curve for alanine

• Titration curves are used to determine pKa values
• pK1 2.4
• pK2 9.9
• pIAla isoelectric point

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Fig 3.7 Ionization of Histidine
(a) Titration curve of histidine pK1 1.8pK2
6.0pK3 9.3
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Fig 3.7 (b) Deprotonation of imidazolium ring
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Table 3.2
pKa values of amino acid ionizable groups
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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 a-carboxyl of one
  amino acid with the a-amino of another amino acid
  (loss of H2O molecule)
• Primary structure - linear sequence of amino
  acids in a polypeptide or protein

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Fig 3.9 Peptide bond between two amino acids
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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 a-carboxyl and a-amino groups of the
  free amino acids

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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

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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

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Fig 3.13 Acid-catalyzed hydrolysis of a peptide
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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
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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

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Fig. 4.7 Trans and cis conformations of a
peptide group

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

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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 a-helices and b-sheets
• Tertiary structure - describes the shape of the
  fully folded polypeptide chain
• Quaternary structure - arrangement of two or more
  polypeptide chains into multisubunit molecule

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Fig. 4.10 The a-helix
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Fig. 4.11 Stereo view of right-handed a helix

• All side chains project outward from helix axis

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Fig. 4.13 Horse liver alcohol dehydrogenase

• Amphipathic a helix (blue ribbon)
• Hydrophobic residues (blue) directed inward,
  hydrophilic (red) outward

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Fig 4.15 b-Sheets (a) parallel, (b) antiparallel
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Fig. 4.19Common motifs
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Fig. 4.23 Common domain folds
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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)

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Fig 4.25 Quaternary structure of multidomain
proteins
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Fig. 4.42 Hemoglobin tetramer
(a) Human oxyhemoglobin (b) Tetramer schematic