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Biophysics
Table of Contents
Unit 3 Overview: Biochemistry: Macromolecules & Cell Components
3.1 Structure and function of nucleic acids, proteins, lipids, and carbohydrates
3.2 Cellular organization and compartmentalization
3.3 Biomolecular interactions and recognition

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3.1 Structure and function of nucleic acids, proteins, lipids, and carbohydrates

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Macromolecules are the building blocks of life. Nucleic acids, proteins, lipids, and carbohydrates each play unique roles in cellular function. Their chemical structures determine their properties and interactions within cells.

Understanding these molecules is key to grasping how cells work. From DNA's information storage to proteins' diverse functions, lipids' membrane-forming abilities, and carbohydrates' energy provision, macromolecules are essential for life's processes.

Chemical Structures of Macromolecules

Nucleic Acids: DNA and RNA

  • Nucleic acids (DNA and RNA) are polymers composed of nucleotide monomers
  • Each nucleotide consists of three components:
    1. A phosphate group
    2. A five-carbon sugar (deoxyribose in DNA, ribose in RNA)
    3. A nitrogenous base (adenine, guanine, cytosine, thymine in DNA, and uracil in RNA)
  • The nitrogenous bases form complementary base pairs (A with T/U, G with C) through hydrogen bonding
  • The sugar-phosphate backbone forms the structural framework of the nucleic acid polymer

Proteins: Amino Acid Polymers

  • Proteins are polymers of amino acids linked by peptide bonds
  • The sequence of amino acids in a protein determines its primary structure
  • The primary structure further folds into secondary structures (alpha helices and beta sheets) stabilized by hydrogen bonding
  • Tertiary structure arises from interactions between secondary structures, such as hydrophobic interactions, ionic bonds, and disulfide bridges
  • Some proteins form quaternary structures, which are assemblies of multiple polypeptide chains

Lipids: Hydrophobic Molecules

  • Lipids are a diverse group of hydrophobic molecules, including fatty acids, triglycerides, phospholipids, and steroids
  • Fatty acids are long hydrocarbon chains with a carboxyl group at one end
  • Triglycerides consist of three fatty acids attached to a glycerol backbone through ester linkages
  • Phospholipids have a hydrophilic head (phosphate group and polar molecule) and two hydrophobic fatty acid tails
  • Steroids have a four-ring structure with various functional groups attached (cholesterol)

Carbohydrates: Sugars and Polysaccharides

  • Carbohydrates are composed of carbon, hydrogen, and oxygen atoms, typically in a 1:2:1 ratio
  • Monosaccharides are the simplest carbohydrates (glucose, fructose, galactose)
  • Disaccharides are formed by linking two monosaccharides through a glycosidic bond (sucrose, lactose, maltose)
  • Oligosaccharides are short chains of monosaccharides (3-10 units)
  • Polysaccharides are long chains of monosaccharides (starch, cellulose, glycogen)

Macromolecule Properties and Functions

Chemical Properties and Biological Functions

  • The complementary base pairing of nucleic acids (A with T/U, G with C) enables:
    1. Storage and transmission of genetic information
    2. Synthesis of RNA from DNA templates
  • The amphipathic nature of phospholipids allows them to form bilayers, which:
    1. Are the foundation of cell membranes
    2. Enable compartmentalization within cells
  • The hydrophobic nature of lipids makes them excellent energy storage molecules as they can be densely packed without interacting with water (triglycerides in adipose tissue)
  • The diverse functional groups of amino acids allow proteins to fold into specific three-dimensional structures, enabling them to carry out a wide range of functions:
    1. Catalysis (enzymes)
    2. Transport (hemoglobin)
    3. Signaling (insulin)
    4. Structural support (collagen)
  • The hydroxyl groups of carbohydrates make them hydrophilic, allowing them to serve as:
    1. Energy sources (glucose)
    2. Structural components (cellulose in plant cell walls)
    3. Molecular recognition molecules (glycoproteins)

Synthesis and Degradation of Macromolecules

  • Nucleic acids and proteins are synthesized through template-directed processes:
    1. DNA replication
    2. Transcription of DNA into RNA
    3. Translation of mRNA into proteins
  • Lipids and carbohydrates are synthesized through enzyme-catalyzed reactions:
    1. Fatty acid synthesis and triglyceride formation
    2. Glycogen synthesis from glucose monomers
  • Macromolecules are degraded by specific enzymes:
    1. Nucleases degrade nucleic acids
    2. Proteases break down proteins
    3. Lipases hydrolyze lipids
    4. Amylases and other glycoside hydrolases degrade carbohydrates

Macromolecular Interactions in Cells

Protein Interactions

  • Protein-protein interactions are essential for many cellular processes:
    1. Signal transduction (receptor-ligand interactions)
    2. Enzyme regulation (allosteric interactions)
    3. Formation of multi-protein complexes (ribosomes, cytoskeleton)
  • Protein-nucleic acid interactions regulate gene expression and protein synthesis:
    1. Transcription factors binding to DNA
    2. Ribosomes interacting with mRNA during translation
  • Protein-lipid interactions are important for cell signaling, transport, and metabolism:
    1. Membrane-bound receptors (G protein-coupled receptors)
    2. Enzymes involved in lipid metabolism (lipases)

Carbohydrate Interactions

  • Carbohydrate-protein interactions play roles in cell-cell recognition, adhesion, and immune responses:
    1. Glycoproteins on cell surfaces (blood group antigens)
    2. Lectins binding to specific carbohydrate moieties (selectins in leukocyte adhesion)
  • Carbohydrate-lipid interactions are involved in the formation of glycolipids, which are important components of cell membranes (gangliosides in nerve cells)

Structural and Functional Differences of Macromolecules

Polymeric vs. Non-Polymeric Structures

  • Nucleic acids and proteins are linear polymers with a specific sequence of monomers
    • DNA and RNA are composed of nucleotides
    • Proteins are composed of amino acids
  • Lipids and carbohydrates are not necessarily polymeric and do not have a specific sequence
    • Lipids can be single molecules (steroids) or consist of a few components (triglycerides)
    • Carbohydrates can be monomers (monosaccharides), dimers (disaccharides), or polymers (polysaccharides) without a specific sequence

Functional Diversity

  • Nucleic acids store and transmit genetic information
    • DNA stores genetic information in its sequence of bases
    • RNA acts as a messenger (mRNA) and plays structural and catalytic roles (rRNA, tRNA)
  • Proteins carry out a wide range of cellular functions
    • Enzymes catalyze biochemical reactions
    • Transport proteins move molecules across membranes
    • Signaling proteins (hormones, receptors) facilitate cell communication
    • Structural proteins provide support and shape to cells and tissues
  • Lipids form membranes and serve as energy storage
    • Phospholipids are the main components of cell membranes
    • Triglycerides are stored in adipose tissue as an energy reserve
  • Carbohydrates provide energy and structural support
    • Glucose is the primary energy source for most cells
    • Cellulose is a structural component in plant cell walls
    • Glycogen is a storage polysaccharide in animals

Amphipathic vs. Hydrophilic Properties

  • Proteins and some lipids (phospholipids) are amphipathic, having both hydrophobic and hydrophilic regions
    • Amphipathic properties allow proteins to fold into specific structures and interact with other molecules
    • Phospholipids form bilayers due to their amphipathic nature, with hydrophobic tails facing inward and hydrophilic heads facing outward
  • Nucleic acids and most carbohydrates are hydrophilic
    • The sugar-phosphate backbone of nucleic acids is hydrophilic, while the bases are hydrophobic
    • Most carbohydrates are hydrophilic due to the presence of numerous hydroxyl groups