Comprehensive Biology 181 Study Notes: Fundamentals of Life, Cell Theory, and Biological Chemistry

Fundamentals of Biology and Characteristics of Life

• Biology Definition: Biology is defined as the scientific study of life and living organisms.

• Defining Characteristics of Living Organisms:

  • Ability to move or exhibit internal/external motion.

  • Composed of one or more functional structural units called cells.

  • Capacity to reproduce and pass genetic traits to offspring.

  • Reliance on external environment and outside resources for sustaining life.

  • Requirement to acquire, process, and utilize energy.

  • Maintenance of homeostasis (regulating internal stability despite external changes).

  • Capacity for adaptation and evolutionary change at the population level over generations.

  • Ability to sense and respond to environmental stimuli.

  • Inevitability of mortality and biological death.

  • Ability to intake, transform, and process matter.

  • Intra- and intercellular communication capabilities.

  • Storage, expression, and processing of genetic and cellular information.

• The Cell as the Basic Unit of Life:

  • Definition: A cell is the smallest, membrane-bound unit capable of performing chemical reactions required to grow, function, and reproduce.

  • Serves as the fundamental building block of all living matter.

• Five Core Characteristics of Life:

  1. Cells:

  • All living organisms are constructed from cells.

  • Organisms are categorized as either unicellular (composed of a single cell) or multicellular (composed of multiple specialized cells).

  1. Replication:

  • New cells arise exclusively from pre-existing cells through cell division.

  • Mitosis: Cellular division mechanism producing identical somatic daughter cells.

  • Meiosis: Cellular division mechanism producing haploid gametic cells for sexual reproduction.

  1. Information:

  • Living systems process and store hereditary information within deoxyribonucleic acid (DNA).

  • Genes: Specific functional segments of DNA that contain instructions to code for specific proteins.

  • Chromosomes: Large structures formed from a full strand/pair of DNA containing hundreds to thousands of individual genes.

  1. Energy:

  • Life continuously acquires, transforms, and processes energy.

  • Ingested or synthesized organic matter ("food") is processed metabolically to synthesize adenosine triphosphate (ATP), the universal cellular energy molecule.

  1. Evolution:

  • Populations of organisms undergo genetic change and evolutionary adaptation over time through natural selection and differential survival.

Foundational Biological Theories and the Central Dogma

• Cell Theory:

  • Formulates that all living organisms are composed of cells.

  • Asserts that all new cells arise strictly from pre-existing cells via cellular division.

  • Historically disproved the theory of spontaneous generation.

• Chromosomal Theory of Inheritance:

  • Establishes that genetic material is localized within chromosomes, which are transmitted from parent to offspring during reproduction.

• The Central Dogma of Molecular Biology:

  • Describes the directional pathway of genetic information flow universal to all living organisms:

  • $\text{DNA (genetic information storage)} \rightarrow \text{mRNA (functional working copy of DNA)} \rightarrow \text{Protein (functional machinery executing cellular jobs)}$

Classification and Domains of Life

• Taxonomic Organization and Ancestry:

  • Biological classification organizes life based on evolutionary relationships stemming from the Last Universal Common Ancestor (LUCA), which originated approximately $3.8\text{ billion years ago}$.

• The Three Domains of Life:

  1. Bacteria: Composed entirely of prokaryotic single-celled organisms.

  2. Archaea: Composed of prokaryotic single-celled organisms biochemically distinct from Bacteria.

  3. Eukarya: Composed of eukaryotic organisms possessing membrane-bound nuclei, divided into four primary kingdoms:

  • Kingdom Protista (Protists)

  • Kingdom Fungi (Fungi)

  • Kingdom Plantae (Plants)

  • Kingdom Animalia (Animals)

• Prokaryotic Cells:

  • Taxonomic Scope: Domains Bacteria and Archaea.

  • Structure: Small and structurally simple.

  • Cellularity: Unicellular organisms exclusively.

  • Compartmentalization: Lacks major membrane-bound organelles or a true enclosed nucleus.

  • Four Essential Features Common to All Cells:

  1. Cell / Plasma Membrane: Phospholipid outer boundary separating internal contents from the external environment.

  2. Cytoplasm / Cytosol: Aqueous internal fluid medium sustaining chemical reactions.

  3. DNA: Chromosomal genetic material encoding life instructions.

  4. Ribosomes: Macromolecular structures translating mRNA into functional proteins.

• Eukaryotic Cells:

  • Taxonomic Scope: Domain Eukarya.

  • Structure: Large and complex internal structure.

  • Cellularity: Includes unicellular and multicellular organisms.

  • Compartmentalization: Features prominent membrane-bound organelles, including a membrane-bound nucleus.

Cellular Structures, Organelles, and Functions

• Comprehensive Organelle Breakdown:

  • Plasma / Cell Membrane:

  • Cell Type: All cells (Prokaryotes and Eukaryotes).

  • Number of Membranes: $1$ lipid bilayer membrane.

  • Function: Regulates transport of materials entering and exiting the cell.

  • DNA:

  • Cell Type: All cells.

  • Number of Membranes: $0$ membranes.

  • Function: Serves as the primary genetic repository for hereditary information.

  • Ribosomes:

  • Cell Type: All cells.

  • Number of Membranes: $0$ membranes.

  • Function: Catalyzes protein synthesis by translating mRNA sequences.

  • Cytoplasm / Cytosol:

  • Cell Type: All cells.

  • Number of Membranes: $0$ membranes.

  • Function: Internal fluid environment suspending cellular components and facilitating diffusion.

  • Nucleoid Region:

  • Cell Type: Prokaryotes only.

  • Number of Membranes: $0$ membranes.

  • Function: Unenclosed cytological area containing the circular prokaryotic chromosome.

  • Fimbriae:

  • Cell Type: Prokaryotes.

  • Number of Membranes: $0$ membranes.

  • Function: Filamentous surface appendages aiding in bacterial attachment to substrate surfaces.

  • Flagella:

  • Cell Type: Prokaryotes (and select Eukaryotes).

  • Number of Membranes: $0$ membranes in prokaryotes.

  • Function: Provides cellular propulsion and motility.

  • Nucleus / Nuclear Envelope:

  • Cell Type: Eukaryotes.

  • Number of Membranes: $2$ membranes (double-membrane envelope with nuclear pores).

  • Function: Encloses eukaryotic genetic material and regulates transcription and genomic expression.

  • Nucleolus Region:

  • Cell Type: Eukaryotes.

  • Number of Membranes: $0$ membranes.

  • Function: Sub-nuclear dense region dedicated to ribosomal RNA (rRNA) synthesis and ribosome assembly.

  • Rough Endoplasmic Reticulum (Rough ER):

  • Cell Type: Eukaryotes.

  • Number of Membranes: $1$ membrane system.

  • Function: Studded with surface ribosomes; responsible for protein synthesis, folding, and processing.

  • Smooth Endoplasmic Reticulum (Smooth ER):

  • Cell Type: Eukaryotes.

  • Number of Membranes: $1$ membrane system.

  • Function: Lacks ribosomes; synthesizes lipids and processes metabolic byproducts.

  • Golgi Apparatus:

  • Cell Type: Eukaryotes.

  • Number of Membranes: $1$ membrane system.

  • Function: Modifies, sorts, and packages carbohydrates, lipids, and proteins for cellular transport or secretion.

  • Lysosome:

  • Cell Type: Eukaryotes (specifically animal cells).

  • Number of Membranes: $1$ membrane.

  • Function: Contains acidic hydrolytic enzymes for intracellular digestion, waste degradation, and organelle recycling.

  • Peroxisome:

  • Cell Type: Eukaryotes.

  • Number of Membranes: $1$ membrane.

  • Function: Conducts oxidative reactions to detoxify harmful metabolic toxins and hydrogen peroxide.

  • Large Central Vacuole:

  • Cell Type: Eukaryotes (plant cells).

  • Number of Membranes: $1$ membrane (tonoplast).

  • Function: Stores water, nutrients, and pigments; maintains cell turgor pressure.

  • Mitochondria:

  • Cell Type: Eukaryotes.

  • Number of Membranes: $2$ membranes (outer membrane and highly folded inner cristae membrane).

  • Function: Site of cellular respiration; generates cellular energy in the form of ATP.

  • Chloroplast:

  • Cell Type: Eukaryotes (plant cells and photosynthetic protists).

  • Number of Membranes: $2\text{ to }3$ membranes (outer, inner, and internal thylakoid system).

  • Function: Executes photosynthesis to convert light energy into chemical energy (sugars).

  • Cytoskeleton:

  • Cell Type: Eukaryotes.

  • Number of Membranes: $0$ membranes.

  • Function: Internal fibrous protein network providing mechanical support, shape retention, and intracellular transport tracks.

  • Cell Wall:

  • Cell Type: Most Prokaryotes and select Eukaryotes (plants, fungi).

  • Location: Outer exterior layer surrounding the plasma membrane.

  • Function: Structural protection, prevention of osmotic lysis, and rigidity.

Cellular Efficiency and Compartmentalization

• Prokaryotic vs. Eukaryotic Internal Organization:

  • Prokaryotic cells lack internal organelle compartmentalization; all metabolic pathways occur unseparated within the shared cytoplasm.

  • Eukaryotic cells utilize membrane-bound organelles to isolate biological reactions into specialized environments.

• Advantages of Organelle Compartmentalization:

  • Protection of sensitive cellular molecules from premature chemical enzymatic degradation.

  • Physical separation of incompatible or conflicting biochemical pathways.

  • Concentration of substrates, enzymes, and cofactors within specific regions to accelerate reaction rates.

  • Significant increase in overall cellular metabolic efficiency.

• Semiautonomous Organelles:

  • Mitochondria and Chloroplasts are classified as semiautonomous organelles.

  • Contain their own independent circular DNA genome, specialized ribosomes, and divide independently within the cell.

• Surface Area to Volume Ratio ($SA:V$):

  • Physical Limit on Cell Size: Cells remain small to maximize their surface area to volume ratio ($SA:V$).

  • Volumetric Growth Scaling: As a cell increases in size, its volume increases at a cubic rate, growing significantly faster than its surface area, which grows at a squared rate.

  • Functional Efficiency: Small cells maintain a large surface area relative to volume, enabling adequate molecular exchange of nutrients, oxygen, and metabolic waste across the plasma membrane.

Basic Atomic Structure and Chemical Principles

• The Atom:

  • Defined as the smallest identifiable unit of matter that retains the fundamental chemical properties of an element.

  • Most of an atom's overall volume consists of vast empty space.

• Primary Elements of Biological Systems:

  • Four primary elements constitute approximately $96\%$ of all biological matter in living organisms:

  1. Hydrogen ($H$)

  2. Carbon ($C$)

  3. Oxygen ($O$)

  4. Nitrogen ($N$)

  • Biological macromolecules inside cells frequently contain thousands to millions of these covalently bonded atoms.

  • During early Earth history, $H$, $C$, $N$, and $O$ existed within simple chemical compounds, such as Water ($H_2O$) and Carbon Dioxide ($CO_2$).

• Core Structure-Function Axiom:

  • Structure dictates function across all atomic, chemical, and biological scales.

• Subatomic Particles:

  • Proton ($p^+$):

  • Electric Charge: Positive charge ($+1$).

  • Mass: $1\,amu$ or $1\,Da$.

  • Location: Situated in the central atomic nucleus.

  • Identity Role: Defines the element (atomic number). The number of protons never changes for a given element.

  • Neutron ($n^0$):

  • Electric Charge: Neutral / zero charge ($0$).

  • Mass: $1\,amu$ or $1\,Da$.

  • Location: Situated in the central atomic nucleus.

  • Identity Role: Varies in number to create isotopes, changing atomic mass without altering chemical element identity.

  • Electron ($e^-$):

  • Electric Charge: Negative charge ($-1$).

  • Mass: Approximately $0\,amu$ (negligible mass).

  • Location: Orbits the central nucleus within electron shells.

  • Identity Role: Dictates chemical reactivity, valence, and bond formation.

• Atomic Measurement and Terminology:

  • Element: A pure chemical substance consisting entirely of a single species of atom.

  • Atomic Number: The total number of protons contained within the nucleus of an atom.

  • Mass Number: The total sum of protons and neutrons present within an atom's nucleus.

  • Dalton ($Da$) / Atomic Mass Unit ($amu$):

  • Standard unit of mass used by biologists to quantify subatomic particles and molecules.

  • The mass of one proton and one neutron are each rounded to $1\,Da$ (or $1\,amu$).

  • Atomic Weight: The weighted average mass of an element calculated across all naturally occurring isotopes.

  • Isotopes: Variants of a single element containing identical proton counts (atomic number) but differing neutron counts (mass number).

  • Stable Isotopes: Non-decaying atomic nuclei.

  • Radioactive / Unstable Isotopes: Nuclei that spontaneously decay over time emitting radiation (e.g., Carbon-14, $^{14}C$, containing $6$ protons and $8$ neutrons).

Chemical Bonds and Electronegativity

• Valence Shells and Atomic Stability:

  • Valence Shell: The outermost electron shell of an atom.

  • Valence Electrons: Electrons residing in the valence shell that participate in chemical bonding.

  • Octet / Stability Rule: Atoms achieve chemical stability when their valence shell is completely filled:

  • $1^{\text{st}}$ Shell: Holds a maximum of $2$ electrons ($2\,e^-$).

  • $2^{\text{nd}}$ Shell: Holds a maximum of $8$ electrons ($8\,e^-$ distributed across $4$ orbitals).

  • $3^{\text{rd}}$ Shell: Holds a maximum of $8$ electrons ($8\,e^-$ distributed across $4$ orbitals).

• Pathways to Achieve Full Valence Shells:

  1. Gaining Electrons: Results in an overall negative charge, forming an Anion.

  2. Losing Electrons: Results in an overall positive charge, forming a Cation.

  3. Chemical Bonding: Sharing or transferring electrons with adjacent atoms to build stable chemical compounds.

• Classification of Chemical Bonds:

  • Ionic Bonds:

  • Formation Mechanism: Complete transfer of one or more valence electrons from one atom to another (no electron sharing occurs).

  • Interaction: Strong electrostatic attraction between oppositely charged ions ("opposites attract").

  • Example: Formation of table salt ($NaCl$), where Sodium ($Na$) transfers an electron to Chlorine ($Cl$), producing attracted $Na^+$ and $Cl^-$ ions ($Na^+ + Cl^- \rightarrow NaCl$).

  • Covalent Bonds:

  • Formation Mechanism: Sharing of valence electron pairs between two atoms. Represented as a solid chemical line ($A-B$).

  • Nonpolar Covalent Bonds:

    • Valence electrons are shared equally between the two bonded nuclei.

    • Occurs between atoms possessing identical or near-identical electronegativities.

    • Results in zero partial electrical charges.

    • Examples: Molecular Hydrogen ($H-H$ or $H_2$), Molecular Oxygen ($O=O$ or $O_2$), Carbon-Carbon bonds ($C-C$), Carbon-Hydrogen bonds ($C-H$), and symmetric Carbon Dioxide ($O=C=O$ or $CO_2$).

  • Polar Covalent Bonds:

    • Valence electrons are shared unequally between the two bonded nuclei.

    • Occurs when bonded atoms feature significantly different electronegativities.

    • Shared electrons spend more time closer to the atom with higher electronegativity, generating partial negative ($\delta^-$) and partial positive ($\delta^+$) charges.

    • Example: Water ($H_2O$), where Oxygen is significantly more electronegative than Hydrogen, creating a partial negative charge ($\delta^-$) on Oxygen and partial positive charges ($\delta^+$) on Hydrogen atoms.

• Electronegativity (EN):

  • Definition: The inherent quantitative pull or ability of an atom to attract shared electrons toward itself in a chemical bond.

  • Electronegativity Trends in Biological Atoms:

  • High Electronegativity: Oxygen ($O$) and Nitrogen ($N$).

  • Low Electronegativity: Carbon ($C$) and Hydrogen ($H$).

  • Bond Polarity Rules:

  • Bonded atoms with similar EN values create nonpolar covalent bonds.

  • Bonded atoms with substantially different EN values create polar covalent bonds.

Properties of Water and Solutions

• Hydrogen Bonds (H-Bonds):

  • Definition: A weak non-covalent attraction between a partial positive charge ($\delta^+$) on a hydrogen atom in one polar bond and a partial negative charge ($\delta^-$) on an electronegative atom ($O$ or $N$) in another molecule or region.

  • Water H-Bonding Capacity:

  • Each polar water molecule ($H_2O$) can simultaneously form up to $4$ hydrogen bonds with neighboring polar molecules or ions.

• Biological Significance of Water:

  • Accounts for approximately $75\%$ of total internal cell volume.

  • The single most abundant molecule present in biological organisms.

  • Organisms can survive weeks without food, but only $3\text{ to }4\text{ days}$ without liquid water.

• Solution Chemistry Terms:

  • Solvent: Any liquid medium capable of dissolving solids, liquids, or gases. Water is the central biological solvent.

  • Solute: Any biological substance dissolved in a solvent medium.

  • Hydrophilic ("Water-Loving"):

  • Characteristics: Polar or fully charged ionic molecules.

  • Behavior: Interacts favorably with water's dipole charges and readily dissolves in aqueous solutions.

  • Hydrophobic ("Water-Fearing"):

  • Characteristics: Nonpolar, uncharged molecules.

  • Behavior: Repels water and fails to dissolve in aqueous solutions.

  • Amphipathic:

  • Characteristics: Molecules containing both distinct hydrophilic (polar/charged) regions and hydrophobic (nonpolar) regions.

  • Example: Phospholipids (possess a polar hydrophilic head and nonpolar hydrophobic fatty acid tails).

Carbon Chemistry and Reaction Mechanisms

• Chemical Properties of Carbon:

  • Atomic Number: $6$ (contains $4$ valence electrons).

  • Valence Bonding: Forms up to $4$ covalent bonds simultaneously.

  • Structural Versatility: Can construct diverse molecular geometries including linear chains, branched trees, and closed ring structures.

  • Primary Biological Bonding Partners: Oxygen ($O$), Nitrogen ($N$), Hydrogen ($H$), and adjacent Carbon ($C$) atoms.

  • Energy Storage: Chemical bonds store chemical potential energy; molecules with a higher density of chemical bonds contain greater total potential energy.

• Macromolecular Architecture:

  • Macromolecules: Enormous organic molecules manufactured by living cells.

  • Monomers: Small, repeating individual molecular subunits ($1\text{ monomer unit}$).

  • Polymers: Large chain molecules constructed by covalently linking many monomers together.

• Reaction Mechanisms for Macromolecules:

  • Dehydration Synthesis (Condensation Reaction):

  • Mechanism: Biochemical process that forms a covalent bond between two adjacent monomers.

  • Water Dynamics: Removes a water molecule ($H_2O$) as a reaction product ($-H_2O$).

  • Catalysis: Executed and driven inside cells by specialized enzymes.

  • Hydrolysis:

  • Mechanism: Biochemical process that cleaves covalent bonds holding polymers together into individual monomers.

  • Water Dynamics: Consumes and adds a water molecule ($H_2O$) to break the bond ($+H_2O$).

Macromolecules: Structure, Function, and Classification

• 1. Proteins:

  • Monomer: Amino acid.

  • Polymer: Polypeptide chain (which folds into a functional protein structure).

  • Core Amino Acid Molecular Structure:

  • Consists of a central alpha-carbon ($C$) covalently attached to four groups:

    1. A Hydrogen atom ($-H$).

    2. An Amino functional group ($-NH_2$).

    3. A Carboxyl functional group ($-COOH$).

    4. A distinct side chain or $R$ group.

  • The $R$ group is the variable component that makes each of the $20$ distinct standard amino acids unique in chemical behavior.

  • Functional Diversity:

  • Catalysis of biochemical reactions (enzymes).

  • Immune defense systems (antibodies).

  • Cellular and tissue structural support.

  • Cellular movement and mechanical motion.

  • Transmembrane transport of cellular cargo.

• 2. Nucleic Acids:

  • Monomer: Nucleotide.

  • Polymer: Nucleic acid (DNA and RNA).

  • Biological Function: Encodes, stores, copies, and relays hereditary genetic information throughout the cell.

  • Strict Energy Rule: Nucleic acids are dedicated exclusively to genetic information and are NEVER consumed by the cell as an energy source.

• 3. Carbohydrates:

  • Chemical Composition: Organic compounds composed strictly of Carbon ($C$), Hydrogen ($H$), and Oxygen ($O$) atoms.

  • Monomer: Monosaccharide ("one sugar").

  • Examples: Glucose ($C_6H_{12}O_6$), Fructose, Galactose.

  • Polymer: Polysaccharide ("many sugars").

  • Primary Examples (all polymers constructed exclusively from repeating glucose monomers):

    • Starch: Primary carbohydrate energy storage polymer in plants.

    • Glycogen: Primary carbohydrate energy storage polymer in animals (stored in liver and skeletal muscle).

    • Cellulose: Structural polysaccharide comprising plant cell walls; indigestible by humans and functions as dietary fiber.

  • Biological Function: Immediate biological energy source, short-term energy storage, and cell wall structure.

• 4. Lipids:

  • General Properties:

  • Broad non-polymer category of nonpolar, hydrophobic molecules.

  • Smaller overall structures compared to massive polymers like polysaccharides.

  • Subunits: Fatty acid chains and glycerol.

  • Small Polymer / Assembly: Triglyceride (composed of $1$ glycerol molecule covalently bound to $3$ fatty acid chains).

  • Biological Functions: High-density long-term energy storage, thermal insulation, structural membrane barrier components.

  • Fatty Acid Types:

  • Saturated Fatty Acids:

    • Hydrocarbon chain is fully saturated with Hydrogen atoms (contains zero $C=C$ double bonds).

    • Linear molecular structure allowing chains to pack densely together.

    • Physical State: Solid at room temperature.

    • Source: Predominantly animal fats; considered dietary "bad" fats.

  • Unsaturated Fatty Acids:

    • Hydrocarbon chain contains one or more carbon-carbon double bonds ($C=C$).

    • Double bonds produce structural kinks in the chain, forcing molecules further apart.

    • Physical State: Liquid at room temperature.

    • Source: Predominantly plant oils; considered dietary "good" fats.

  • Specific Lipid Examples:

  • Waxes: Highly hydrophobic protective waterproofing seals.

  • Steroids / Hormones: Lipids formed from four fused carbon rings acting as endocrine chemical signaling messengers (e.g., cholesterol, estrogen, testosterone).

  • Phospholipids: Amphipathic structural lipids composing all cell membranes, possessing a polar hydrophilic head group and two nonpolar hydrophobic fatty acid tails.