1.4 Macromolecules

Overview of Biological Macromolecules

• Building Blocks of Life: There are four primary types of macromolecules: proteins, carbohydrates, lipids, and nucleic acids.

• Scientific Objectives: The study of these molecules focuses on understanding their specific structures and functions.

• Macromolecules in Microbiology:

  • These building blocks are universal across all forms of life.

  • Slight variations in these molecules can determine whether a microbe is virulent (pathogenic) or non-pathogenic.

  • Understanding these structural differences is critical for the diagnosis and treatment of human diseases, allowing for the exploitation of unique microbial traits.

Cellular Composition and Chemical Distribution

• Total Cellular Makeup: A cell is comprised of approximately $70\,\%$ water and $30\,\%$ chemicals.

• Macromolecule Breakdown by Total Cell Mass:

  • Proteins: Account for $15\,\%$ of the total cell mass.

  • Nucleic Acids (DNA and RNA): Account for $7\,\%$ of the total cell mass.

  • Lipids (Phospholipids): Account for $2\,\%$ of the total cell mass.

  • Polysaccharides (Carbohydrates): Account for $2\,\%$ of the total cell mass.

• Prefix Definition: The prefix "macro" signifies that these are large molecules formed from smaller units.

Structural Hierarchy: Monomers and Polymers

• Monomers: These are the building blocks of cells, representing the smallest single units that cannot be further simplified without breaking the molecule apart into non-utilizable components.

  • Sugars: The monomers for polysaccharides and carbohydrates.

  • Fatty Acids: The monomers for lipids and fats.

  • Amino Acids: The monomers for proteins (also referred to as polypeptides or peptides).

  • Nucleotides: The monomers for nucleic acids.

• Polymers: These are larger molecules formed when monomers are covalently linked together.

• Significance of Chemical Structure: The structure of a molecule is inseparable from its cellular function. It dictates:

  • Location within the cell.

  • Interactions with other molecules.

  • Overall cellular behavior.

• Nutrient Cycling: Cells use enzymes to break down large polymers (nutrients) into monomers through a process like digestion. These monomers are then absorbed and used by the cell to synthesize new macromolecules for growth and survival.

• Macromolecular Complexes: Multiple types of macromolecules can assemble into larger complexes.

  • Example: Ribosomes: These are "factories" that assemble globular proteins and RNA into a complex that translates messenger RNA ($mRNA$) into proteins.

Proteins: Functional Diversity and Structure

• Mass Contribution: Proteins constitute more than $50\,\%$ of the dry mass of a cell (the mass remaining after water is removed).

• Functional Array: Proteins are responsible for daily cellular upkeep, behavior, and major life events, including cell division, replication, and managed cellular death (apoptosis).

• Specific Functions of Proteins:

  • Movement: Includes locomotion within the environment (e.g., cilia or flagella), internal movement of substances (e.g., membrane pumps), and cellular contraction (e.g., muscle cells).

  • Catalysts: Enzymes are proteins that speed up chemical reactions without being consumed.

  • Structural Support: Providing shape and form to cells and anchoring cells within tissues.

  • Storage: Sequestering amino acids or other chemical units for future use.

  • Transport: Moving substances across a multicellular organism or acting as a molecular highway within a single cell.

  • Cellular Communication: Acting as signaling molecules (like chemical "text messages") that influence the behavior of receiving cells nearby or at a distance.

  • Immunological Defense: Antibodies are specialized proteins that bind to and restrain pathogens in higher organisms.

Amino Acid Composition and Classification

• Definition: A protein is a polypeptide polymer made from amino acid monomers.

• General Structure: An organic monomer containing a carboxyl group ($COOH$) and an amino group ($NH_2$).

• The 20 Amino Acids: While hundreds of amino acids exist, only $20$ are encoded by the genetic code for use in protein synthesis.

• The R Group (Side Chain):

  • The side chain varies between amino acids and provides each its specific chemical characteristics.

  • Hydrophobic: Side chains made primarily of carbon and hydrogen (nonpolar); these exclude water and are often found in membrane-bound proteins.

  • Hydrophilic: Side chains containing oxygen (polar); these are suitable for aqueous environments like the cytoplasm.

  • Charged: Can be positively charged (basic) or negatively charged (acidic).

• Essential Amino Acids: There are $9$ essential amino acids that humans cannot synthesize and must obtain via diet.

Nucleic Acids: Storage and Information Flow

• Function: Storing genetic information and directing protein production.

• Metaphor: The Cookbook: DNA acts as a recipe book where each recipe corresponds to a gene (a subunit that encodes one specific protein).

• DNA Scale: A single human cell contains approximately $2$ to $3\,\text{meters}$ of DNA. Summed across all cells in the human body, this length is equivalent to nearly $70$ round trips from the Earth to the Sun and back.

• Storage and Packaging:

  • Eukaryotes: DNA is protected within the nucleus.

  • Prokaryotes: DNA is often found in circular structures called plasmids.

  • Histones: Proteins around which DNA coils to allow for condensation into the nucleus.

• DNA Structure:

  • Double Helix: A ladder-like structure formed by two strands.

  • Nucleotides: Adenine ($A$), Thymine ($T$), Guanine ($G$), and Cytosine ($C$).

  • Backbone: Formed by a pentose sugar and a phosphate group (sugar-phosphate backbone).

  • Complementary Base Pairing: Bases match via hydrogen bonds.

    • $A$ pairs with $T$ ($2$ hydrogen bonds).

    • $G$ pairs with $C$ ($3$ hydrogen bonds).

• Purines vs. Pyrimidines:

  • Purines: Adenine and Guanine.

  • Pyrimidines: Cytosine, Thymine, and Uracil (specific to RNA).

The Central Dogma and RNA Comparisons

• The Central Dogma of Biology: Information flows from DNA to RNA to Protein.

  • Transcription: DNA is transcribed into RNA.

  • Translation: RNA is translated into a protein sequence.

• Replication: DNA acts as its own template to be synthesized or replicated.

• Key Differences between DNA and RNA:

  • Sugar: DNA uses deoxyribose; RNA uses ribose.

  • Nitrogenous Bases: RNA uses Uracil ($U$) instead of Thymine ($T$).

  • Strand Structure: DNA is a double-stranded helix; RNA is typically single-stranded and can fold within itself.

  • Replication: DNA is self-replicating; RNA is not.

  • Location: DNA is sequestered in the nucleus, mitochondria, and chloroplasts. RNA is found in the nucleus (origin), the cytoplasm, and associated with ribosomes.

Lipids: Hydrocarbons and Nonpolar Molecules

• Hydrophobic Nature: Lipids are "water-fearing" and do not mix with water (e.g., oil droplets in vinegar).

• Non-Polymeric: Unlike other macromolecules, lipids do not form traditional polymers because monomers do not link to one another in long chains.

• Hydrocarbons: Composed of a carbon backbone linked exclusively to hydrogens, making them highly nonpolar.

• Types of Lipids:

  • Steroids: Used as structural components in membranes or as signaling hormones (e.g., estrogen and testosterone).

  • Triglycerides: Used for long-term energy storage, found in fat tissue. Structurally composed of one glycerol and three fatty acid tails.

  • Phospholipids: The building blocks of plasma membranes and organelle membranes.

• Phospholipid Anatomy:

  • Phosphate Head: Hydrophilic (water-loving).

  • Two Fatty Acid Tails: Hydrophobic (water-fearing).

• The Lipid Bilayer: Formed when hydrophobic tails cluster together to exclude water, creating the basis of the cellular membrane, while the hydrophilic heads face the aqueous environment.