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Biological Functions of Proteins• Facilitate biochemical reactions• Structural support• Storage and Transport• Immune protection• Generate movement• Transmission of nerve impulses• Control growth and differentiation
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Key Properties of Proteins
• Linear polymers of amino acids• Contains a wide range of functional groups• Forms complex assemblies of more than
one polypeptide chain• Versatile structure – some are rigid while
others are flexible
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Globular and Fibrous Proteins• Globular protein• Usually water soluble,
compact, roughly spherical
• Hydrophobic interior, hydrophilic surface
• Globular proteins include enzymes,carrier and regulatory proteins
• Fibrous protein• 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
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General Structure of Proteins• Twenty common a-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
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Zwitterions • 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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Amino acid side chains
• Nine non-polar aa• Six polar uncharged aa• Five charged aa• Three basic aa• Two acidic aa• Two aa with sulfur groups• Four ring-forming aa• Three have aromatic rings 9
Hydropathy• Relative hydrophobicity of the
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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Polymer of amino acid• 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)
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Dihedral angle of proteins
• The phi angle is the angle around the -N-Cα- bond• The psi angle is the angle around the -Cα-C- bond• The omega angle is the angle around the -C1-N- bond (i.e.
the peptide bond)
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Primary structure
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>2CQG:A|PDBID|CHAIN|SEQUENCEGSSGSSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRHMIDGRWCDCKLPNSKQSQDSGPSSG
Supersecondary structure: Motifs• Secondary
structures often group together to form a specific geometric arrangements known as motifs
• Since motifs contain more than one secondary structural element, these are referred to as super secondary structures 27
Domains• stable, independently folding, compact
structural units within a protein, formed by segments of the polypeptide chain, with relative independent structure and function distinguishable from other regions and stabilized through the same kind of linkages than the tertiary level
• Often each domain has a separate function to perform for the protein, such as:• Bind a small ligand• Spanning the plasma membrane
(transmembrane proteins)• Contain the catalytic site (enzymes)• DNA-binding (in transcription factors)• Providing a surface to bind specifically to
another protein• In some (but not all) cases, each domain in a
protein is encoded by a separate exon in the gene encoding that protein.
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Tertiary Structure
• Forces holding the tertiary (and higher order) structure together• Salt bridge• Covalent bond
(disulfide bridges)• Hydrophobic
interaction• Hydrogen bonding 29