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Chapter 4: Problem 1

Properties of the Peptide Bond In x-ray studies of crystalline peptides, Linus Pauling and Robert Corey found that the \(\mathrm{C}-\mathrm{N}\) bond in the peptide link is intermediate in length (1.32 Å) between a typical \(\mathrm{C}-\mathrm{N}\) single bond \(\left(1.49 \AA^{\circ}\right)\) and \(\mathrm{a} \mathrm{C}=\mathrm{N}\) double bond \((1.27\) A). They also found that the peptide bond is planar (all four atoms attached to the C-N group are located in the same plane) and that the two \(a\)-carbon atoms attached to the \(\mathrm{C}-\mathrm{N}\) are always trans to each other (on opposite sides of the peptide bond). a. What does the length of the \(\mathrm{C}-\mathrm{N}\) bond in the peptide linkage indicate about its strength and its bond order (i.e., whether it is single, double, or triple)? b. What do Pauling and Corey's observations tell us about the ease of rotation about the \(\mathrm{C}-\mathrm{N}\) peptide bond?

Short Answer

Expert verified
The bond length indicates a bond order of about 1.5, suggesting partial double-bond character. Pauling and Corey's observations suggest that rotation around the C-N peptide bond is restricted due to resonance, contributing to its planarity.

Step by step solution

01

Analyze the Bond Length

The given data provides the bond lengths for typical C-N single and C=N double bonds, which are 1.49 Å and 1.27 Å, respectively. The peptide bond length is intermediate at 1.32 Å.
02

Determine Bond Order

Since the peptide bond length of 1.32 Å is between that of a single C-N bond (1.49 Å) and a double C=N bond (1.27 Å), it indicates that the peptide bond is likely between a single and double bond, suggesting a partial double bond character. This implies a bond order closer to 1.5.
03

Analyze Bond Strength

The partial double bond character suggests that the peptide bond is stronger than a single bond but weaker than a double bond. The bond order of 1.5 typically corresponds to increased bond strength compared to a single bond.
04

Interpret Planarity and Configuration

The planarity of the peptide bond, as observed by Pauling and Corey, indicates that there is restricted rotation due to resonance contributing to the planar form. This restriction implies the bond has a relatively higher rigidity compared to typical single bonds.
05

Determine Rotation Ease

The trans configuration of the attached α-carbon atoms and the planarity imply that the C-N bond has restricted rotation. This is typical of bonds with partial double-bond character because the pi-bonding which contributes to the planarity resists rotation, locking the configuration.

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Key Concepts

These are the key concepts you need to understand to accurately answer the question.

Bond Length
The bond length of a peptide bond is a pivotal concept in understanding its properties and nature. In this context, the peptide bond, which is a connection between the carbon (C) and nitrogen (N) atoms, has a measured bond length of 1.32 Å. This length is not simply a numerical value; it tells us much about the bond's characteristics.
The length falls between a standard C-N single bond ( 1.49 Å) and a C=N double bond ( 1.27 Å). This intermediate bond length indicates that the peptide bond is not entirely a single bond nor a complete double bond.
  • The bond length of 1.32 Å suggests that it has partial double bond character.
  • This nuance of having features of both single and double bonds informs its specific properties like bond strength and rigidity.
By understanding bond lengths, we can infer about the stability and behavior of these molecular structures in biological processes.
Planarity
The planarity of the peptide bond is one of its defining features. This planarity means that all atoms connected to the C-N bond are in the same geometric plane. Linus Pauling and Robert Corey's studies revealed this planar nature, emphasizing its importance in understanding peptide bonds.
This planarity is critical for the structure of proteins:
  • It implies that there is a rigid, flat arrangement of atoms, which contributes to the stability of protein structures.
  • Such an arrangement is enforced by resonance, where electrons are delocalized over the bond, supporting its planar structure.
This resonance stabilizes the peptide bond and makes it less prone to changes in shape, critical for protein functionality.
Rotation Restriction
Rotation restriction is a key characteristic of the peptide bond, which arises due to its partial double bond nature. Normally, single bonds allow free rotation, but peptide bonds resist this due to their unique structural properties.
The restriction is largely due to:
  • Resonance, which bestows a partial double bond character on the C-N bond, thus restricting rotation.
  • The pi-bonding nature which helps to lock the connective structure in place.
Because of this resistance to twisting, the configuration remains largely unchanged, maintaining the stability and rigidity essential for the precise function of biomolecules such as proteins in biological processes.
Bond Order
The bond order of a bond is an important concept that indicates the number of chemical bonds between a pair of atoms. For peptide bonds, the bond order is found to be intermediate, nearly 1.5.
Bond order is calculated by understanding the bond's characteristics between a single bond (order of 1) and a double bond (order of 2):
  • A bond order of 1.5 in peptide bonds suggests partial double bond character.
  • This partial character contributes to its strength, making it stronger than a typical single bond but weaker than a double bond.
The bond order not only speaks of its stability but also affects properties such as electronic distribution and structural behavior in biological systems.
Pauling and Corey
Linus Pauling and Robert Corey were pioneers in examining the nature of peptide bonds through x-ray crystallography. Their research laid the foundation for understanding key aspects of peptide bonds:
Their findings include:
  • The intermediate bond length of the C-N bond, described as being between single and double bonds.
  • The planarity of the peptide bond, crucial in maintaining the structural integrity of proteins.
  • The trans configuration of the alpha-carbon atoms, which inform the spatial arrangement of peptides.
These insights were revolutionary at the time, providing a clearer structural blueprint for scientists to explore and comprehend protein structures and functions.

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Most popular questions from this chapter

Margaret Oakley Dayhoff originated the idea of protein superfamilies after noticing that proteins with diverse amino acid sequences can have similar tertiary structures. Why can protein structure be more highly conserved than individual amino acid sequences?

Mirror-Image Proteins As noted in \(\underline{\text { Chapter } 3}\), "The amino acid residues in protein molecules are almost all L stereoisomers." It is not clear whether this selectivity is necessary for proper protein function or is an accident of evolution. To explore this question, Milton and colleagues (1992) published a study of an enzyme made entirely of \(\mathrm{D}\) stereoisomers. The enzyme they chose was HIV protease, a proteolytic enzyme made by HIV that converts inactive viral preproteins to their active forms. Previously, Wlodawer and coworkers (1989) had reported the complete chemical synthesis of HIV protease from L-amino acids (the L-enzyme), using the process shown in Eigure 3-30. Normal HIV protease contains two Cys residues, at positions 67 and \(95 .\) Because chemical synthesis of proteins containing Cys is technically difficult, Wlodawer and colleagues substituted the synthetic amino acid L- \(a\)-amino- \(n\)-butyric acid (Aba) for the two Cys residues in the protein. In the authors' words, this was done to "reduce synthetic difficulties associated with Cys deprotection and ease product handling." a. The structure of Aba is shown below. Why was this a suitable substitution for a Cys residue? Under what circumstances would it not be suitable?

Under the proper environmental conditions, the salt-loving archaeon Halobacterium halobium synthesizes a membrane protein \(\left(M_{\mathrm{r}} 26,000\right)\), known as bacteriorhodopsin, which is purple because it contains retinal (see Fig, 10-20). Molecules of this protein aggregate into "purple patches" in the cell membrane. Bacteriorhodopsin acts as a light- activated proton pump that provides energy for cell functions. X-ray analysis of this protein reveals that it consists of seven parallel \(a\)-helical segments, each of which traverses the bacterial cell membrane (thickness \(45 \AA\) ). Calculate the minimum number of amino acid residues necessary for one segment of \(a\) helix to traverse the membrane completely. Estimate the fraction of the bacteriorhodopsin protein that is involved in membrane-spanning helices. (Use an average amino acid residue weight of 110 .)

Which structural biology method (CD, x-ray crystallography, NMR, or cryo-EM) is best suited to each task? a. Obtaining an ultra-high resolution \((<1.5 \AA)\) structure of a drug bound to its protein target b. Obtaining a low-to-medium resolution (5-10 \AA) reconstruction of the \(11 \mathrm{MDa}(11,000,000 \mathrm{Da})\) bacterial flagellar motor c. Identifying the protonation state and \(\mathrm{p} K_{\mathrm{a}}\). of a His side chain in an enzyme active site d. Determining whether a protein is intrinsically disordered or contains secondary structure elements

Some natural proteins are rich in disulfide bonds, and their mechanical properties, such as tensile strength, viscosity, and hardness, correlate with the degree of disulfide bonding. a. Glutenin, a wheat protein rich in disulfide bonds, imparts the cohesive and elastic character of dough made from wheat flour. Similarly, the hard, tough nature of tortoise shell results from the extensive disulfide bonding in its \(a\) keratin. What is the molecular basis for the correlation between disulfide-bond content and mechanical properties of the protein? b. Most globular proteins denature and lose their activity when they are briefly heated to \(65^{\circ} \mathrm{C}\). However, the denaturation of globular proteins that contain multiple disulfide bonds often requires longer heat exposure at higher temperatures. One such protein is bovine pancreatic trypsin inhibitor (BPTI), which has 58 amino acid residues in a single peptide chain and contains three disulfide bonds. After a solution of denatured BPTI is cooled, the protein regains its activity. What is the molecular basis for this property of BPTI?
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