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Protein Structure Class: 1. Primary

Protein Structure Class: 1. Primary

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primary protein structure
  • The polypeptide sequence of amino acids that comprises the basic structure of a protein.
  • Proteins are linear polymers that vary widely in length, and comprise amino acids joined by peptide bonds.
    • Intertextual variation exits regarding the exact length of a polypeptide that qualifies as a protein.
  • Every protein has its own unique and specific amino acid sequence, which is called its primary structure.
  • Primary protein structure is generated during translation, where peptide bonds link amino acids to each other.
  • During translation, translational machinery translates a three-letter sequence of bases to a single amino acid.
  • Peptide bonds are covalent bonds between the alpha-carboxyl group of one amino acid and the alpha-amino group of another amino acid; these are the bonds that hold proteins together.
  • Polypeptide sequences have direction and are always read from the N-terminal to the C-terminal, such that the free amino terminal always represents the beginning of a polypeptide chain, and the free carboxyl terminal always represents the end of a polypeptide chain.
The Amino Acid Sequence
We use a short polypeptide sequence as an illustration: we show a chain of amino acids (represented as circles) connected with lines. We label the N-terminal at the left and C-terminal at the right.
  • The protein's amino acid sequence tells us for 4 key things:
1. Every amino acid sequence determines a distinct 3-dimensional protein structure; they provide the link between DNA and the 3D structure of a protein, which carries out its biological function. 2. The amino acid sequence of a protein directly relates to its mechanism of action, so when we know the amino acid sequence of a protein, we can hypothesize its function. 3. Changes in amino acid sequence (even of a single amino acid) can disrupt normal protein function and result in disease. For instance, cystic fibrosis, neurofibromatosis, Tay-Sachs disease and sickle cell anemia are caused by a single amino acid changes in a key protein. 4. Protein sequence gives insight into its evolutionary history as proteins with a common ancestor have similar sequences.
peptide bond characteristics
We show a peptide bond between two amino acids in 3D with one R-group coming towards you and one R-group facing away from you. We label the central carbons of the amino acid residues as C-alpha.
  • The peptide bonds linking amino acids are planar, meaning that both alpha carbons and the atoms of the peptide bond lie in the same plane.
resonance
This is the term that we apply to the fact that the double bond within the peptide bond can shift between carbon-oxygen to carbon-nitrogen. We can see from our peptide bond drawing one of the resonance structures of the peptide bond. Below the peptide drawing, we redraw this resonance structure and also draw the second resonance structure to show that peptide bonds have double-bond character.
  • Resonance constrains the peptide bond, so that it CANNOT rotate, which gives the polypeptide sequences a backbone with little room for conformational change.
two possible configurations for the peptide bond
  • trans – in which the oxygen and hydrogen atoms face two different directions,
  • cis – in which the oxygen and hydrogen atoms face the same directions.
We draw two peptide bonds: one in cis configuration and one in trans configuration. To each of these drawings, we add the R-groups as follows: for the trans bond, we draw one R-group coming towards you and one going away from you and for the cis bond, we draw both R-groups coming towards you.
  • Almost all peptide bonds are in trans configuration.
We draw large circles around the R-groups of the cis to help us visualize why peptide bonds favor this configuration.
  • R-groups represent large groups of atoms (like in the side chains of tryptophan and histidine) that can interact with or interfere with each other if they get too close.
  • If they face the same direction (the cis configuration), the R-groups can interact, which is unfavorable because it puts strain on the molecule. For this reason, almost all peptide bonds are in trans configuration.
  • An exception is proline.
    • Because of proline's unusual ring-form amino group, both its cis and trans forms have steric clashes, making them both rather unfavorable, and thus almost equally likely to exist.
single bonds between the alpha carbons (and either the amino or carboxyl group)
  • Because these are single bonds, significant rotation can occur around them: two bonds of each amino acid residue can rotate freely and this allows proteins to fold in a variety of ways.
  • They allow for different dihedral angles at those bonds
    • Dihedral angles are at the bonds between the central carbon atom and the amino or carboxylic acid functional groups.
    • Dihedral angles specify the torsional rotation about the C-alpha bonds.
  • The phi angle is the angle of rotation about the carbon-nitrogen bond between the alpha carbon and the amino group.
We draw a curved arrow around this bond to show that it can rotate at an angle phi.
  • The psi angle as the angle of rotation about the carbon-carbon bond between the alpha carbon and the carboxyl group.
We draw a curved arrow around this bond to show that it can rotate at an angle psi.
  • Steric strain or steric collision between amino acid side chains eliminates many combinations of phi and psi. -Ramachandran, a physicist who studied protein structure, created a two-dimensional diagram call the Ramachandran plot to visualize favorable combinations of phi and psi.

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