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Chapter 1–8: Introduction to Cellular Biology and Macromolecules

Course Overview and Instructor

  • Dr. Tanya Levansky, subject matter expert for the class.
  • Broad background in field science and education; currently assistant professor of marine biology and sustainable aquaculture at Unity.
  • Excited to start; biology intersects many disciplines.
  • This class provides fundamentals of cellular biology using a scaffolding approach: start with simple scale, then gain complexity as we understand cellular life.
  • Week structure (overview):
    • Week 1: baseline elements and molecules that compose life.
    • Week 2: membranes and their function in separating cells from the external environment and internal membrane structures.
    • Week 3: detailed cellular functioning focusing on energy acquisition and transformation via metabolic pathways.
    • Week 4: cellular information, DNA as information storage and transmission across generations.
    • Week 5: synthesis and application of first four weeks to real-world biology settings.
  • Emphasis on approach: building foundational knowledge before complexity.

Week-by-Week Plan (Structure and Focus)

  • Week 1: baseline elements and molecules that compose life.
  • Week 2: membrane function and internal membrane structures.
  • Week 3: cellular energy and metabolism.
  • Week 4: DNA, information storage, and inheritance.
  • Week 5: synthesis of topics and real-world applications in biology.
  • Scaffolding approach: start simple and increase complexity as internal cellular processes are understood.

Week 1 Learning Objectives and Core Idea

  • Learning objectives may feel overwhelming due to vocabulary; read them carefully in Canvas as you work through materials.
  • Core connection: biology is chemistry.
  • Chemistry is practical and applied, though it can feel intimidating.
  • Whale as a running analogy: everything in the image is chemicals; the whale’s body is made of molecules, and its environment is chemicals (sea water and dissolved materials).
  • The whale exchanges chemicals with the atmosphere when surfacing to breathe; its feeding of krill involves breaking down chemicals to fuel various bodily functions.
  • All of life’s processes are chemistry.

The Whale Analogy: Chemistry of Life

  • The whale’s body and its environment are comprised of chemicals and chemical processes govern temperature, acidity, gas exchange, and metabolism.
  • Understanding life begins with studying functional molecules present in all living organisms.
  • A molecule is a group of atoms bonded together in a functional unit.
  • Elements most common in life: ext{C}, ext{H}, ext{N}, ext{O}, ext{P}, ext{S}
  • On a planetary abundance graph, these elements appear at high abundance, reflecting life’s origin using available chemical resources.
  • Carbon forms the backbone of many large biological molecules due to its ability to form multiple stable bonds, including bonds with itself, enabling diverse molecular structures.

From Atoms to Macromolecules

  • Major elements that build life provide the backdrop for macromolecules.
  • Macromolecules: large molecules used in biological processes.
  • Monomer: a smaller, stable molecule that serves as a functional unit.
  • Example of a monomer reference: the presenter holds a marker, which could be considered its own functional unit.
  • Polymerization: the process of linking monomers to form larger polymers with new functions.
  • Four major classes of macromolecules (based on structure and function):
    • Carbohydrates
    • Lipids
    • Nucleic acids
    • Proteins
  • These macromolecules are often linked to everyday foods and nutrition, illustrating their roles in replenishing body molecules.

Carbohydrates

  • Function: sugars used for energy and structure.
  • Monomers: monosaccharides (simple sugars).
  • Ring structures: carbohydrate monomers often shown in ring form with carbon atoms at ring junctions.
  • Polysaccharides form when monosaccharides link together; longer chains store energy or provide structural support.
  • Examples mentioned: glucose as a monosaccharide; starch as a complex polymer of glucose.

Lipids

  • Functions: energy storage, cushioning (insulation), and other roles in membranes.
  • Visualization: often depicted as squiggly carbon/hydrogen chains with a terminal carboxyl group indicating a fatty acid.
  • Structural peculiarity: lipids do not follow a strict monomer-to-polymer pattern; fats are typically formed by linking multiple fatty acids to a glycerol head.
  • Example: triglycerides (three fatty acids linked to glycerol).
  • Phospholipids: highlighted as important for membranes and will be studied in more depth next week due to their unique membrane roles.

Nucleic Acids

  • DNA: genetic code; long strands with a sugar-phosphate backbone.
  • Nucleotides: monomers of nucleic acids; components include a nitrogen base, a five-carbon sugar (pentose), and a phosphate group.
  • Structure concept: one strand pairs with a second strand via nitrogen bases to form the double helix in DNA.
  • Primary functions: information storage and information transfer.
  • ATP is also a nucleic acid; energy currency in cells (noted as a nucleic acid in this overview).
  • Week 4 focus will delve deeper into DNA/RNA roles in information storage and transmission.

Proteins

  • Proteins are diverse in size and shape and perform many cellular roles.
  • Functions include: enzymes (catalysis), structural support, transport, cellular communication, immune defense, and more.
  • Proteins essentially drive many cellular processes – they "run the cellular show."
  • Protein diversity arises from sequence and folding properties, enabling numerous functions across biology.

Protein Structure and Folding (Hierarchy)

  • Primary structure: a linear sequence of amino acids.
  • Amino acid structure: central carbon, carboxyl group, amine group, and an R group (side chain).
  • There are 20 standard amino acids; examples include lysine, cysteine.
  • The R group defines the chemical properties and behavior of each amino acid.
  • Secondary structure: formed by hydrogen bonds between backbone atoms, leading to alpha helices and beta-pleated sheets.
  • Tertiary structure: three-dimensional folding driven by interactions among R groups (hydrogen bonds, ionic interactions, hydrophobic effects, disulfide bonds, etc.).
  • Quaternary structure: assembly of multiple polypeptide chains into a functional protein.
  • Proteins are chemically complex and sensitive to environmental changes; misfolding or unfolding can occur due to changes in internal chemistry.
  • Protein folding and stability are linked to disease states when misfolding occurs.

Chemistry, Biochemistry, and Cross-Disciplinary Relevance

  • Our shared evolutionary ancestry means biochemistry is connected across all life.
  • Plants and fungi produce compounds that can be used medicinally and are often compatible with human cells.
  • The week will explore these natural compounds as potential medicines, highlighting practical and ethical implications of using natural products in therapy.

Real-World Relevance, Ethics, and Practical Implications

  • Biology-as-chemistry perspective informs understanding of health, disease, and environmental interactions.
  • Ethical considerations include the sourcing and sustainability of natural medicines, access to therapies, and safety in biomedical applications.
  • Practical implications include discovering how chemistry underpins medical and biotechnological advances.

Week 1 Takeaways and Encouragement

  • Biology is chemistry: foundational idea to frame all topics.
  • The whale example illustrates how life is embedded in a chemical world: molecules, interactions, energy transfer, and environmental chemistry all matter.
  • Expect to connect molecular details to cellular functions in each week’s topics.
  • Reach out to the instructor with questions; the course emphasizes active engagement and clarifying concepts.

References to the Transcript's Key Phrases (Summary Verbatim Cues)

  • Scaffold approach: start simple, progressively add complexity.
  • Week progression: membranes (week 2), metabolism (week 3), DNA and inheritance (week 4), synthesis and real-world application (week 5).
  • Core idea: biology is chemistry; life’s processes are chemical interactions within organisms and their environments.
  • Four major macromolecule classes: carbohydrates, lipids, nucleic acids, proteins.
  • Protein structure hierarchy: primary (amino acids), secondary (alpha helices and beta sheets), tertiary (3D folding via R-group interactions), quaternary (multi-chain assemblies).
  • 20 amino acids: 20
  • Key elements in life: ext{C}, ext{H}, ext{N}, ext{O}, ext{P}, ext{S}
  • Notable examples: glucose (monomer for carbohydrates), starch (polysaccharide), DNA and ATP (nucleic acids), triglycerides (lipids), glycerol with fatty acids (lipids), marker example as a functional monomer reference.
  • Importance of environment: temperature, acidity, and gas exchange affect chemistry and life processes.