Humboldt State University ® Department of Chemistry

Richard A. Paselk

Chem 438 - Introductory Biochemistry - Spring 2011

Lecture Notes:

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Lecture illustrations from Moran text in [Brackets]

Note the titration behavior of amino acids, and be able to draw the structure for an amino acid at each point in the curve. [Table 3.2; Fig. 3.6, 3.7]

Peptides and Protein Primary Structure

Peptide bond formation:

Note that a peptide bond is simply an amide bond between the alpha carboxyl and amino groups of amino acids. If we write the reacting groups in their unionized (acid and amine) forms, then we can see the reaction takes place with the loss of the elements of water, via an attack of the lone-pair electrons of the amine on the carbonyl carbon of the carboxyl group [Fig 3.9]:

Now that we have looked at peptide bond formation, we next want to look at the structure of this bond and the sequence of amino acid residues (primary structures) of proteins. (Note that "residue" refers to the remainder of a molecule after it is incorporated into a polymer.)

• The peptide bond is formed with the elimination of water, giving a planar bond between the carboxyl carbon and the amino nitrogen. [Figure 4.5, 4.6] This is due to the partial double bond character on the amide/peptide bond as seen in the shorter bond length (0.133 nm vs. 0.146 nm). This bond is nearly always trans in proteins due to steric interactions of the amide hydrogen and oxygen, except for proline. [Figure 4.7]
• Linear peptides will have free amino- and carboxy- terminal groups. Thus they will exhibit titration curves similar to a free amino acid, but with the pK_a values shifted closer to simple acid and amine values (there will be no charge stabilization).
• By convention the amino terminal residue is written on the left progressing to the carboxyl terminal residue on the right: ⁺H₃N-aa-aa-aa-aa-CO₂^-.
• Can determine the composition of a peptide by acid hydrolysis and amino acid analysis.
• Can sequence proteins by specific enzyme and chemical hydrolysis to give peptides which can then be run through sequenators (up to about 100 aa's).
• Amino acid sequences have been used to help determine relatedness of organisms.

3-D Structure of Proteins

Overview: Proteins are commonly large (MW > 6,000), globular molecules serving many functions.

Proteins are complex systems - difficult to understand at a fundamental structural level. Thus we search for patterns using normal perceptual tools: regularity, clustering, cleavage/separation/emptiness.

We are then able to discern alpha helices, beta sheets, beta turns, and "random" regions. 3₁₀ helical regions show up with computer searches. [Figure 4.15]None of these is necessarily more or less random than others, they are simply easier or more difficult for us to perceive as ordered. They exist through our rationalization. Often structural elements also appear to serve a functional role, thou this is through our dissection of the molecular machine.

Look at theoretical possibilities resulting from the available bond angles around the peptide bond system

• Most peptide bonds are trans because of reduced steric hindrance. [Figure 4.7] Most exceptions are with proline which has nearly equal hindrance in both cis and trans.
• Any rotation in the peptide chain will therefore take place around the two bonds of the alpha carbon, referred to as the phi () and psi () bonds [Figure 4.8]. There are a restricted number of angles which these bonds can achieve [Figure 4.8]. Of course the range of angles will be further reduced due to side chains.
• If we assume hard spherical atoms with van der Waals radii, we can determine the accessible phi () and psi () angles. This procedure was followed by Ramachandran to produce the Ramachandran plot, an example is seen in your text. [Figure 4.9a]
  • There are only a few regions of possible angles available to the alpha carbon bonds as shown on this plot.
  • Note that the common secondary structures, the alpha helix, the beta strand, and the collagen triple helix all occur in these regions.
  • Of course real atoms are somewhat compressible and real bonds can bend a little, so we might wonder how this plot stacks up to reality. A study of the distribution of conformation angles of a thousand amino acid residues in eight proteins as determined by x-ray diffraction showed that most of the values do indeed fall in the predicted regions. Most of the residues outside of these regions are glycines, with the least restriction. [Figure 4.9b]

Let's go back and look at overall shape and interpret it. Look for substructures that recur in various molecules. Perhaps we see a globule is made of subglobules. Look closer and we see alpha helices and beta structures. Finally we can discern aa residues.

In order to understand and categorize their organization, protein structure has been divided into four hierarchical levels and a couple of sublevels [Figure 4.1]:

• Primary structure (1°) : the linear order or sequence of peptide bonded amino acid residues, beginning at the N-terminus. (Characteristic bond type: covalent.)
• Secondary structure (2°): the steric relations of residues nearby in the primary structure which give rise to local regularities of conformation. These structures are maintained by hydrogen bonds between peptide bond carbonyl oxygens and amide hydrogens. The major secondary structural elements are the alpha helix and the beta strand. (Characteristic bond type: hydrogen.)
• Tertiary structure (3°): the steric relations of residues distant in the primary sequence; the overall folding pattern of a single covalently linked molecule. (Characteristic bond type: hydrophobic; others: hydrogen, ion-pair, van der Waals, disulfide.)

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Last modified 8 February 2013