Proteins and amino acids
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Proteins and Amino Acids. Biological Functions of Proteins. Facilitate biochemical reactions Structural support Storage and Transport Immune protection Generate movement Transmission of nerve impulses Control growth and differentiation. Key Properties of Proteins.

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Biological functions of proteins
Biological Functions of Proteins

  • Facilitate biochemical reactions

  • Structural support

  • Storage and Transport

  • Immune protection

  • Generate movement

  • Transmission of nerve impulses

  • Control growth and differentiation


Key properties of proteins
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


Globular and fibrous proteins
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


General structure of proteins
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


Zwitterions
Zwitterions

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

    Amino group = -NH3+

    Carboxyl group = -COO-


Stereochemistry of amino acids
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)


Amino acid side chains
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


Hydropathy
Hydropathy

  • Relative hydrophobicity of the amino acid

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

  • Hydropathyaffects protein folding: hydrophobic side chains tend to be in the interiorhydrophilic residues tend to be on the surface



Isoelectric point
Isoelectric point

  • pH at which the amino acid bears zero net charge



Polymer of amino acid
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)



Trans and cis configuration of peptide bond
Trans and Cis configuration of peptide bond

  • Usually in the trans configuration



Dihedral angle of proteins
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)



Primary structure
Primary structure

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Determining 2 o structure ramanchandran plot
Determining 2o structure: Ramanchandran Plot


Supersecondary structure motifs
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


Domains
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 (transmembraneproteins)

    • 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.


Tertiary structure
Tertiary Structure

  • Forces holding the tertiary (and higher order) structure together

    • Salt bridge

    • Covalent bond (disulfide bridges)

    • Hydrophobic interaction

    • Hydrogen bonding