BIO 114 Lecture Notes

Scientific Method

  • Dynamic Process
    • Observation: Utilizing senses and consulting existing literature.
    • Hypothesis: Forming an explanation for the observation.
    • Experimental Design: Includes control and experimental variable(s).
    • Results: Statistical analysis and graphing of data.
    • Discussion: Interpretation of results.
    • Conclusion: Determines if the hypothesis is supported or refuted.
    • Refinement: If the hypothesis is incorrect, refine the procedure and re-evaluate.
    • Control vs. Experimental: A control group has everything except the experimental variable.
    • Bias: Recognizing and addressing scientific prejudice.
    • Scientific Fraud: Avoiding data manipulation.

Biological Hierarchy

  • Biosphere, Ecosystems, Communities, Populations, Organism, Organ Systems, Organ, Tissue, Cells, Macromolecules, Molecules (building blocks for macromolecules), Atom (Protons, Neutrons, and Electrons).

Definition of a Living Cell/Organism

  • Ability to independently reproduce without external influence.
    • Viruses: Not considered living, require a host to reproduce.
    • Prions: Abnormal proteins, also not considered living.

Life Functions

  • Eating: Obtaining nutrients.
  • Metabolism: Producing energy.
  • Waste Elimination: Removing toxic substances.
  • Reproduction: Passing genes to the next generation.
  • Growth: Increasing in size or complexity.
  • Environmental Interaction: Responding to the surroundings.
  • Mobility: Ability to move.

Classification of Biological Entities

  • Domain (Eukarya, Bacteria, Archaea), Kingdoms, Classes, Orders, Families, Genus, Species.
  • Humans: Homo sapiens (Homo sapiens neandrathalis).

Organic vs. Inorganic Molecules

  • Organic Molecules: Contain Carbon (C) and Hydrogen (H) with a covalent bond between them.
  • Inorganic Molecules: Examples include NH3, H2O, CO2, HCl, H3PO4, H2SO_4.
    • Essential elements CHONPS, Na, K, Mg, Ca (must be ionic).
    • Covalent Bonding: Sharing of valence electrons (octet rule), Carbon has a valence of 4 (e.g., CH_4).
    • Ionic Bonding: Attraction between positive and negative ions.
      • Cations: Positively charged ions (e.g., Na 0rightleftharpoons Na^+ + e^-.
      • Anions: Negatively charged ions (e.g., Cl + e^- 0rightarrow Cl^−).
      • Ionic compound: Na^+Cl^−.

Non-Bonding Associations

  • Hydrogen Bonding: Occurs between H and an electronegative element (e.g., in water); affects physical properties.
  • Dipole-Dipole Interaction: Molecules with positive and negative ends.
  • Van der Waals: Temporary dipoles (weaker interactions mentioned in Watson and Crick's DNA structure paper).

Functional Groups

  • Examples: -CH3, -OH, O=C-, -NH2, -PO_4H, -COOH.
  • Found in building blocks (monomers) and polymers.
  • Impact chemical reactivity and impart specific qualities to a molecule.

Dehydration and Hydrolysis

  • Dehydration: Removing water to make a bond (anabolic/synthesis of larger molecules).
  • Hydrolysis: Breaking a bond with water (polymer + H_2O -> monomers; catabolic breakdown of larger molecules).

Carbohydrates

  • Monomer: Glucose (monosaccharide).
  • Polysaccharides: Glycogen (in animals), starch (in plants).
  • Function: Energy storage, structure (cellulose), chitin (exoskeleton component of arthropods).

Lipids

  • Materials that do not dissolve in water; includes fatty acids and glycerol.
  • Function: Stored energy, phospholipids (membrane), cholesterol, steroids (hormones).
  • Hydrocarbon Tail (non-polar) -> Hydrophobic.
  • Polar Head (contains O, N, P) -> Hydrophilic.
  • Fatty Acid Example: CH3CH2CH2CH2CH2CH2CH_2-COOH
  • Fatty acid + glycerol -> fat (mono-, di-, tri-glycerides).

Proteins

  • Monomers: 20 amino acids.
  • Polymers:
    • Primary Structure: Specific amino acid sequence (dictated by DNA).
    • Secondary Structure: Alpha helix, beta pleated sheet.
    • Tertiary Structure: 3-D shape/folding into a functional polypeptide.
    • Quaternary Structure: Association of two or more polypeptides (collagen, hemoglobin).
  • Function: Enzyme, support, actin, myosin, antibody.

Nucleic Acids

  • DNA: Double-stranded, deoxyribose sugar, ATCG (contains blueprints to make polypeptides).
  • RNA: Single-stranded, ribose sugar, AUCG; types include mRNA, tRNA (carries an amino acid), rRNA (structural component of the ribosome, made in the nucleolus).

Protein Synthesis

  • Nucleus (site of transcription)
    • DNA -> mRNA (made on DNA template)
  • Cytoplasm (site of translation)
    • mRNA leaves nucleus and attaches to ribosome, and translation begins
    • Amino acids, Released tRNA reenters the cytoplasmic pool of free tRNA, ready to be recharged with a new amino acid
    • Growing polypeptide chain
    • Peptide bond
    • Correct amino acid attached to each species of tRNA by an aminoacyl-tRNA synthetase enzyme
    • As the ribosome moves along the mRNA, a new amino acid is added to the growing protein chain
    • Incoming aminoacyl-tRNA hydrogen bonds via its anticodon to complementary mRNA sequence (codon) on the ribosome
    • tRNA "head" bearing anticodon
    • Large ribosomal subunit
    • Portion of mRNA already translated
    • Direction of ribosome advance
      • Small ribosomal subunit

Saturated vs. Unsaturated Lipids

  • Saturated Lipids: All carbon molecules with single bonds; typically animal in origin.
  • Unsaturated Lipids: Carbons may be bonded with double/triple bonds; typically plant in origin (e.g., olive, sunflower).
  • Oils: Liquid at room temperature, unsaturated.
  • Solids: Higher MW, butter, lard, beeswax.

Denaturation

  • Breakdown of polypeptide/protein structure, leading to loss of function.
  • Causes: Heat, light, salt, acid, base (e.g., egg white).
  • Native state
  • Functional

Cell Structure (Eukaryotes)

  • Eukaryotes: Unicellular (protista) and multicellular organisms; contain compartmentalization with organelles.
    • Golgi Apparatus: Packaging/deployment, vesicle formation (secretory and transitory vesicles).
    • Nucleus: Double membrane, nuclear pores, contains genetic material.
    • Rough Endoplasmic Reticulum (RER): Protein synthesis.
    • Smooth Endoplasmic Reticulum (SER): Lipid synthesis.
    • Ribosomes: Site of protein synthesis (70% protein, 30% with rRNA).
    • Mitochondrion: Double-membraned, produces energy.
    • Lysosomes: Digestive enzymes/housekeepers.
    • Peroxisomes: Break down peroxides.
    • Chloroplasts: Double-membraned (photosynthesis); grana (thylakoid membranes); stroma, lamellae.
    • Cytoskeleton: Filaments (actin (microfilaments), intermediate filaments, microtubules).
    • Centrioles: 9 triplets microtubule arrangement + 0; active during cell division.
    • Flagellum: 9 doublets microtubule + 2 microtubules in the center; for mobility.
    • Cilia: 9 doublets + 2; for mobility (paramecium), stereocilia.
    • Basal Body: 9 + 0 arrangement.
    • Extracellular Matrix: Collagen, elastin, keratin, glycoprotein, glycolipids.
    • Cell Wall: Cellulose (plants).

Bacteria, Archaea

  • All unicellular.
  • Cell Envelope: Capsule, cell wall, plasma membrane, fimbriae, sex pilus.
  • Cytoplasm: Nucleoid body (1, 2 chromosomes), ribosomes, inclusion bodies, plasmid.