Biomolecules: Nucleic Acids, Proteins, and Carbohydrates - A Comprehensive Review

Comparison of Biomolecules: Nucleic Acids, Proteins, and Carbohydrates

• Bonding Mechanisms:

  • Nucleic Acids: Nucleotides are joined by phosphodiester bonds. A nucleotide attaches to the 3' prime end of another nucleotide's sugar.
  • Proteins: Amino acids are joined by peptide bonds. This occurs between the carboxyl end of one amino acid and the amino end of the next.
  • Carbohydrates: Monosaccharides (the building blocks) are joined together by glycosidic bonds.

• Primary Structure:

  • All: Represent a linear sequence of their respective building blocks.
  • Proteins: Amino acids linked together by peptide bonds.

• Secondary Structure:

  • Proteins: Includes common folding patterns such as alpha helices (\alpha-helices) and beta sheets (\beta-sheets).
  • RNA: Can form stem-loop structures.
  • DNA: Forms a double helix, stabilized by hydrogen bonds between complementary base pairs.
  • Carbohydrates: Do not display any recognized secondary structures.

• Tertiary Structure:

  • Proteins: Involves many chemical interactions that stabilize a complex three-dimensional shape.
  • DNA: Can twist upon itself to form some tertiary structures.
  • RNA: Can fold into complex shapes, stabilized by hydrogen bonds, reminiscent of protein folding.
  • Carbohydrates: Not discussed in this context.

The Diverse World of Proteins

• Diversity and Function: Proteins exhibit immense diversity in both structure and function, playing countless roles in the biological world.

  • Roles: Transport nutrients, catalyze chemical reactions (enzymes), build structural components of living things.

• Building Blocks: Despite their diverse functions, all proteins are made from the same 21 standard building blocks called amino acids.

• Amino Acid Composition and Structure:

  • Composed of carbon, oxygen, nitrogen, and hydrogen atoms. Some contain sulfur atoms.
  • Selenocysteine: The only standard amino acid that contains a selenium atom.
  • Structure: Each amino acid has an amino group, a carboxyl group, and a side chain (also known as the R-group), all attached to a central alpha carbon atom.
  • Side Chain (R-group): This is the only part that varies from amino acid to amino acid and determines the amino acid's unique properties.
    • Hydrophobic Amino Acids: Have carbon-rich side chains that do not interact well with water (e.g., found on the interior of globular proteins or exterior of membrane proteins).
    • Hydrophilic Amino Acids: Interact well with water.
    • Charged Amino Acids: Interact with oppositely charged amino acids or other charged molecules.

Protein Structure Levels

• Primary Structure:

  • Definition: The linear sequence of amino acids, directly encoded by DNA.
  • Bonding: Amino acids are joined by peptide bonds, which form between the amino group of one amino acid and the carboxyl group of another.
  • Dehydration: A water molecule (H_2O) is released each time a peptide bond is formed.
  • Protein Backbone: This linked series of carbon, nitrogen, and oxygen atoms forms the fundamental backbone of the protein chain.

• Secondary Structure:

  • Definition: Localized folding patterns of the polypeptide chain.
  • Alpha Helices (\alpha-Helices):
    • A right-handed coiled structure.
    • Stabilized by hydrogen bonds between the amine (N-H) and carboxyl (C=O) groups of nearby amino acids within the same polypeptide chain.
  • Beta Sheets (\beta-Sheets):
    • Formed when hydrogen bonds stabilize two or more adjacent strands of amino acids, which can be part of the same or different polypeptide chains.

• Tertiary Structure:

  • Definition: The overall three-dimensional shape of a single protein chain, resulting from interactions between the side chains of amino acids.
  • Determinants: This shape is primarily determined by the characteristics of the amino acids making up the chain (e.g., hydrophobic interactions, hydrogen bonds, disulfide bridges, ionic bonds).
  • Globular Proteins: Often form compact, spherical shapes with hydrophobic side chains sheltered on the inside, away from the aqueous environment.
  • Membrane-Bound Proteins: Have hydrophobic amino acids clustered together on their exteriors to interact favorably with the lipids in the cell membrane.
  • Charged Amino Acids: Allow proteins to interact specifically with molecules that possess complementary charges.
  • Functionality: The functions of many proteins fundamentally rely upon their unique three-dimensional shapes. For example, hemoglobin forms a specific pocket to hold heme.

• Quaternary Structure:

  • Definition: The arrangement of two or more separate polypeptide chains (subunits) that come together to form one functional protein complex.
  • Example: Hemoglobin: Composed of four subunits. These subunits cooperate, allowing the complex to more easily pick up oxygen in the lungs and release it efficiently in the body's tissues.

Visual Representations of Proteins

• Different visual representations provide clues about protein structure and function:
  • Space-Filling Diagram: Shows all the atoms that constitute the protein, providing a sense of its overall volume and surface.
  • Ribbon or Cartoon Diagram: Illustrates the organization of the protein backbone and clearly highlights secondary structures like alpha helices and beta sheets.
  • Surface Representation: Displays the areas on the protein that are accessible to water molecules, revealing its overall shape and potential binding sites.

Examples of Protein Functions and Structures

• Size: Most proteins are smaller than the wavelength of light. For instance, a hemoglobin molecule is approximately 6.5 nanometers (nm) in size.
• Hemoglobin:
  • Found in high concentrations in red blood cells.
  • A typical red blood cell contains about 280 million hemoglobin molecules.
  • Its specific three-dimensional shape determines its function of binding and transporting oxygen.
• Antibodies:
  • Possess flexible arms that recognize and bind to pathogens (disease-causing agents).
  • Target bound pathogens for destruction by the immune system, thus protecting the body from disease.
• Insulin:
  • A small, stable protein hormone.
  • Its stability allows it to maintain its shape while traveling through the bloodstream to regulate blood glucose levels.
• Alpha Amylase (\alpha-Amylase):
  • An enzyme found in saliva.
  • Initiates the digestion of starches in the mouth.
• Calcium Pump:
  • Aided by magnesium (Mg^{2+}) ions.
  • Powered by ATP (adenosine triphosphate) hydrolysis.
  • Functions to move calcium ions (Ca^{2+}) back into the sarcoplasmic reticulum after each muscle contraction, facilitating muscle relaxation.
• Ferritin:
  • A spherical protein with channels.
  • Allows iron (Fe) atoms to enter and exit depending on an organism's requirements.
  • Forms a hollow space internally where iron atoms attach to the inner wall.
  • Crucially, ferritin stores iron in a non-toxic form, preventing cellular damage from free iron.
• Collagen:
  • Forms a strong triple helix structure.
  • Used extensively throughout the body for structural support, particularly abundant in skin and tendons.
  • Individual collagen molecules can aggregate to form elongated fibrils, which further assemble into much larger collagen fibers.

Further Resources

• For more information on the functions and three-dimensional structures of proteins and other molecular machines, the RCSB Protein Data Bank is a valuable resource.