Question

Compare the \(\alpha\)-helix of proteins and the double helix of DNA in these ways. (a) The units that repeat in the backbone of the polymer chain (b) The projection in space of substituents along the backbone (the R groups in the case of amino acids; purine and pyrimidine bases in the case of double- stranded DNA) relative to the axis of the helix

Short answer

Answer: The key differences between the α-helix of proteins and the double helix of DNA are: (1) In the α-helix, the repeating units in the backbone are amino acids connected through peptide bonds, while in the double helix, the repeating units are nucleotides connected through phosphodiester bonds. (2) In the α-helix, the R groups of amino acids project outward and perpendicular to the helix axis, while in the double helix, the purine and pyrimidine bases project into the center of the helix, forming hydrogen bonds with their complementary bases in the opposite strand.

Step-by-step solution

(Step 1: Understanding the structure of the α-helix of proteins)

The α-helix is a common secondary structure found in proteins, formed by the polypeptide chain backbone adopting a helical conformation due to hydrogen bonds between the amino acids in the chain. The repeating units in an α-helix backbone are the amino acids which are connected through peptide bonds. In an α-helix, the R groups of amino acids (substituents) project outward from the helix axis, perpendicular to the axis.

(Step 2: Understanding the structure of the double helix of DNA)

The double helix structure of DNA consists of two complementary strands that are twisted around each other, forming a helical shape. The repeating units in the backbone of DNA are the nucleotides which are connected through phosphodiester bonds. In the double helix, the purine and pyrimidine bases (substituents) project into the center of the helix, forming hydrogen bonds with the complementary base in the opposite strand.

(Step 3: Comparing the repeating units)

In the α-helix of proteins, the repeating units in the backbone are the amino acids connected through peptide bonds, while in the double helix of DNA, the repeating units are the nucleotides connected through phosphodiester bonds.

(Step 4: Comparing the projection of substituents in space relative to the helix axis)

In the α-helix, the R groups of amino acids project outward from the helix axis, perpendicular to the axis. In the double helix of DNA, the purine and pyrimidine bases project into the center of the helix, forming hydrogen bonds with the complementary base in the opposite strand.

Key concepts

Secondary Structure of Proteins

The secondary structure of proteins refers to the local spatial arrangement of the polypeptide backbone atoms without regard for the conformations of the side chains or the relationships of such conformations to the rest of the protein. Within the protein's secondary structure, two main types stand out: the \(\alpha\)-helix and the \(\beta\)-sheet.

An \(\alpha\)-helix is often visualized as a right- or left-hand screw, where the polypeptide backbone forms the core of the helix, and the side chains (R groups) extend outward from the helical axis. This structure is stabilized by hydrogen bonds that form between the oxygen atom of one peptide bond and the hydrogen atom four residues away in the polypeptide chain. The \(\alpha\)-helix is unique in its ability to afford a high degree of structural organization while still allowing flexibility and movement within the protein's overall tertiary structure.

Understanding the \(\alpha\)-helix is fundamental in studying protein folding, as errors in this process can result in a variety of diseases. The robustness of the helical structure aids in the biological functions of proteins, which range from transporting oxygen in the blood to catalyzing biochemical reactions as enzymes.

Nucleotide Structure and Bonding

Nucleotides are the building blocks of DNA and RNA, crucial macromolecules for life. A single nucleotide is comprised of three components: a sugar molecule (deoxyribose in DNA and ribose in RNA), a phosphate group, and a nitrogenous base (adenine, thymine, cytosine, guanine, or uracil in RNA instead of thymine).

The sugar and phosphate groups form the spine of the nucleic acid strands, with the phosphate connecting to the 5'-carbon of one sugar and the 3'-carbon of the next - a connection known as a phosphodiester bond. This formation creates a 'backbone' for the DNA or RNA strand with a directionality denoted as 5' to 3'.

The nucleobases, however, are responsible for the genetic encoding due to their specific hydrogen bonding patterns—adenine pairs with thymine (or uracil in RNA) and cytosine pairs with guanine. This complementary base pairing is essential for DNA replication and RNA transcription, underscoring the importance of nucleotide structure and bonding in the fundamental processes of life.

Peptide Bonds in Proteins

Peptide bonds are covalent chemical bonds that link amino acids together in a polypeptide chain, the backbone of protein structure. When two amino acids are joined, the carboxyl group of one molecule reacts with the amino group of another molecule, releasing a molecule of water (H2O) in a process known as a condensation or dehydration synthesis reaction.

The resulting bond forms between the carbon atom of the carboxyl group in one amino acid and the nitrogen atom of the amino group in the next amino acid. This peptide bond is planar, due to its partial double-bond character, restricting the rotation around it and imposing certain constraints on the folding of the protein's polypeptide chain, influencing its final 3D structure.

Proper formation of peptide bonds is crucial for the synthesis and structure of proteins, and by extension, the correct function of cells and organisms. Errors or alterations in the peptide-bonding process can lead to malfunctions in protein assembly, resulting in diseases or disorders at the biological level.

Hydrogen Bonding in Macromolecules

Hydrogen bonding is a type of weak chemical bond that is highly significant in dictating the structure and properties of macromolecules such as proteins and nucleic acids. It occurs when a hydrogen atom covalently attached to a more electronegative atom like oxygen or nitrogen also interacts with an adjacent electronegative atom.

In proteins, hydrogen bonding is critical in stabilizing secondary structures, such as the \(\alpha\)-helix and \(\beta\)-sheets. In the case of DNA, hydrogen bonds between complementary nucleobases enable the two strands of the double helix to hold together.

The specificity and directionality of hydrogen bonds are key to their role in biological functions. They also play a central role in the dynamic behavior of macromolecules, such as in the recognition of substrates by enzymes, the pairing of DNA strands, and the interaction of DNA with proteins during gene expression. Understanding hydrogen bonding in macromolecules is, therefore, fundamental in biochemistry and molecular biology.