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$$$CH_4$$).

  • Ionic Bonding: Attraction between positive and negative ions.

    • Cations: Positively charged ions (e.g., $Na 0rightleftharpoons Na^+ + e^-$$$Na 0rightleftharpoons Na^+ + e^-$$.

    • Anions: Negatively charged ions (e.g., $Cl + e^- 0rightarrow Cl^−$$$Cl + e^- 0rightarrow Cl^−$$).

    • Ionic compound: $Na^+Cl^−$$$Na^+Cl^−$$.

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$$$H_2O$$ -> 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 <-> denatured state (3-dimensional conformation change).

• Functional <-> non-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.