Biology Lecture Notes Review: Emergent Properties to Prokaryotes vs Eukaryotes

Emergent Properties and Levels of Biological Organization

• Emergent property: a property that appears only through interaction with others; not evident in the isolated components.

  • Example: Consciousness arises from interactions among neurons in the brain; neither a single neuron nor a small subset alone shows consciousness.
  • Emphasizes that higher levels of organization display novel properties not predictable from lower levels.

• Levels of biological organization (from small to large):

  • Molecules -> Organelles -> Cells -> Tissues -> Organs -> Organisms -> Population -> Community -> Ecosystem
  • Each level adds complexity and new interactions; properties emerge at each higher level.

• Basic idea: Unity of生命 and diversity across life forms

  • All life shares a common ancestor (unity).
  • Differences arise through diversification driven by natural selection (diversity).
  • This leads to similar core features (e.g., molecular building blocks) but different adaptations and structures across organisms.

• Foundational element groups to know for biology (Chapter 2 context)

  • Major elements: Carbon (C), Nitrogen (N), Oxygen (O), Hydrogen (H)
  • Essential/minor elements: Calcium (Ca), Phosphorus (P), Potassium (K), Sulfur (S)
  • These elements underpin biomolecules and energy processes in living systems.

Elements and Atomic Relationships in Biology

• Common biological elements form the basis of macromolecules (carbohydrates, lipids, proteins, nucleic acids).

• Electronegativity and bond types determine molecular polarity and interactions:

  • Nonpolar covalent bonds: electrons shared roughly equally; small or no dipole moment; typically between like atoms (e.g., O=O in O2, C–C).
  • Polar covalent bonds: unequal sharing due to differences in electronegativity; create partial charges and dipoles (e.g., O–H in water).
  • Ionic bonds: transfer of electrons leading to charged ions; attraction between positive and negative ions; often formed in salts (e.g., NaCl).
  • Hydrogen bonds: weak attractions between partial positive H atoms and electronegative atoms (e.g., O or N); crucial for water properties and the structure of biomolecules.

• Water and life: water’s properties arise from its polarity and hydrogen bonding, influencing chemistry in biology.

Water: Properties and Biological Significance (Chapter 3)

• Oxygen’s higher electronegativity compared to hydrogen creates polar O–H bonds in H2O, resulting in a polar molecule with partial negative charge on oxygen and partial positive charges on hydrogens.

• Intermolecular forces (IMFs) in water enable:

  • Hydrogen bonds between water molecules: relatively weak individually but collectively strong.
  • High cohesion (water–water attraction) and adhesion (water–other surfaces).
  • Water as a universal solvent due to its polarity, enabling dissolution of many solutes.
  • Temperature stability and heat capacity: hydrogen bonds absorb heat, buffering temperature changes.
  • Ice expansion: frozen water forms a crystalline structure that expands, making ice less dense than liquid water.

• Water in biological systems:

  • Adhesion and cohesion support capillary action and transport in organisms.
  • Universal solvent facilitates chemical reactions and transport of nutrients.
  • Heat capacity and buffering stabilize internal environments (homeostasis).
  • Hydrogen bonds contribute to the structure of biomolecules (e.g., DNA base pairing, protein folding).

Biomolecule Basics: Energy, Synthesis, and Hydrolysis

• ATP and energy currency (Chapter on metabolism basics):

  • ATP (Adenosine Triphosphate) stores energy; cells extract energy by converting ATP to ADP and inorganic phosphate (P_i).
  • General equation: \text{ATP} + \mathrm{H2O} \rightarrow \mathrm{ADP} + \mathrm{Pi} + \text{energy}.
  • In cellular conditions, hydrolysis of ATP provides usable energy for biochemical work (muscle contraction, active transport, biosynthesis).

• Dehydration synthesis (condensation) and hydrolysis (hydration):

  • Dehydration synthesis: monomers join to form polymers with the release of a water molecule.
  • General peptide-bond (amide) formation between amino acids:
    \text{R-COOH} + \text{R'}-\text{NH}2 \rightarrow \text{R-CO-NH-R'} + \mathrm{H2O}.
  • Result: peptide bond formation producing a polypeptide chain.
  • Hydrolysis: water is used to break a bond, splitting polymers into monomers.
  • General peptide bond hydrolysis:
    \text{R-CO-NH-R'} + \mathrm{H2O} \rightarrow \text{R-COOH} + \text{R'-NH}2.

• Key takeaway: macromolecules are built by dehydration synthesis and broken down by hydrolysis; these processes underlie metabolism and nutrient cycling.

Carbohydrates

• Monomers and polymers:

  • Monosaccharides: simplest carbohydrates (e.g., glucose) – building blocks for larger carbohydrates.
  • Disaccharides: two monosaccharides linked by a glycosidic bond.
  • Polysaccharides: many monosaccharides linked by glycosidic bonds; major energy storage and structural molecules.

• Nomenclature and properties:

  • Monosaccharides typically contain 3–7 carbon atoms (e.g., glucose C6H12O6).
  • Glycosidic linkages connect monosaccharides (often α- or β- linkages; α-glucose in starch/glycogen; β-linkages in cellulose).
  • Major storage carbohydrates include starch (plants) and glycogen (animals).

• Biological roles:

  • Primary energy source for cells (glucose).
  • Building blocks for other biomolecules (e.g., kin to amino acids or lipids).
  • Structural roles in some organisms (e.g., cellulose in plant cell walls).

Lipids

• General features:

  • Hydrophobic and nonpolar; do not form true polymers.
  • Hydrophobic tails and hydrophilic heads in phospholipids contribute to membrane structure.

• Major lipid categories:

  • Triglycerides: glycerol backbone with three fatty acid chains; primary energy storage molecules.
  • Saturated fats: no double bonds; typically solid at room temperature; can contribute to health risks when consumed in excess.
  • Unsaturated fats: one or more double bonds (kinks) in fatty acids; typically liquid at room temperature.
  • Cholesterol (steroid lipid): precursor to steroid hormones and component of cell membranes; influences membrane fluidity.
  • Phospholipids: phospholipid bilayer that forms the structural basis of cell membranes; amphipathic (hydrophilic head, hydrophobic tails).

• Functional implications:

  • Energy storage with high energy density.
  • Membranes regulate what enters and exits cells and organelles.
  • Hormones and signaling molecules often derive from lipids.

Proteins

• Building blocks and structure:

  • Monomer: amino acids.
  • Polymer: polypeptide (proteins after folding).
  • Each amino acid has a central carbon with an amino group, a carboxyl group, a hydrogen, and a side chain (R-group).
  • Amino acids can be acidic, basic, polar, or nonpolar, influencing protein folding and function.

• Peptide bonds and polymerization:

  • Peptide bonds form by dehydration synthesis between the carboxyl group of one amino acid and the amino group of the next.
  • Energy release accompanies peptide bond formation; hydrolysis can break peptide bonds.

• Protein properties and classifications:

  • Hydrophobic vs hydrophilic tendencies influence folding and localization.
  • Ionic, polar, and nonpolar side chains contribute to tertiary structure and function.

• Types of proteins (functions):

  • Enzymes: catalyze chemical reactions.
  • Storage proteins: store amino acids and other nutrients.
  • Transport proteins: carry substances within organisms (e.g., hemoglobin).
  • Hormones: signaling molecules that regulate physiology.
  • Motor proteins: movement (e.g., myosin).
  • Receptors: receive signals and initiate cellular responses.
  • Structural proteins: support and shape cells and tissues.

• Protein structure levels:

  • Primary structure: sequence of amino acids held by peptide bonds.
  • Secondary structure: local folding patterns stabilized by hydrogen bonds (e.g.,
  • alpha helix,
  • beta-pleated sheet).
  • Tertiary structure: overall 3D structure determined by R-group interactions (hydrophobic effects, hydrogen bonds, ionic bonds, disulfide bridges, van der Waals).
  • Quaternary structure: arrangement of multiple polypeptides into a functional unit (e.g., hemoglobin has four subunits).

• Structural stability factors:

  • Hydrogen bonds stabilize secondary structures.
  • Disulfide bonds (covalent) stabilize tertiary/quaternary structures.
  • Ionic interactions and van der Waals forces contribute to folding and stability.

Nucleic Acids

• Monomer and polymer overview:

  • Monomer: nucleotide (nitrogenous base + five-carbon sugar + phosphate group).
  • Polymer: nucleic acids (DNA, RNA) formed by polynucleotide chains.
  • Backbone: sugar-phosphate backbone linked by phosphodiester bonds.

• Backbone and bonding:

  • Phosphodiester bonds connect nucleotides through the phosphate of one nucleotide and the sugar of the next.
  • Bases project inward to form the genetic code via hydrogen bonding between complementary bases.

• Bases and types:

  • Purines: Adenine (A) and Guanine (G).
  • Pyrimidines: Cytosine (C) and Thymine (T) in DNA; Cytosine (C) and Uracil (U) in RNA.

• Primary functions:

  • DNA: stores hereditary information; templates for replication and transcription.
  • RNA: transmits information from DNA to synthesize proteins; various RNA types (mRNA, tRNA, rRNA) participate in translation and gene expression.

• Connections to the central dogma (contextual idea):

  • DNA replication and transcription produce RNA, which is translated into proteins.

Chapter 6: Cells — Prokaryotes vs Eukaryotes

• Prokaryotes (Mokaryote in transcript):

  • No nucleus; DNA is not enclosed in a membrane-bound nucleus.
  • Lacks membrane-bound organelles; generally simpler and smaller.
  • Includes Bacteria and Archaea.

• Eukaryotes (Eukaryote):

  • Have a nucleus where DNA is stored within a membrane-bound compartment.
  • Contain membrane-bound organelles (mitochondria, ER, Golgi, lysosomes, etc.).
  • More complex organization and larger cell size.

• Shared features and differences: highlighting how cellular organization underpins tissue and organ systems in multicellular organisms.

Chapter 2, 3, 5, 6: Connections and Takeaways

• Unity in biology:

  • All life uses a common set of biomolecules (carbohydrates, lipids, proteins, nucleic acids).
  • Core metabolic pathways (e.g., ATP production, glycolysis) demonstrate shared ancestry.

• Diversity through natural selection:

  • Variation in gene sequences and regulation leads to diverse phenotypes best adapted to environments.
  • This drives adaptation across ecosystems (e.g., forests, oceans, humans).

• Practical implications and applications:

  • Understanding bond types and water properties informs fields from biochemistry to pharmacology.
  • Knowledge of proteins and enzymes underpins medicine, agriculture, and biotechnology.
  • Nucleic acids are central to genetics, forensic science, and biotechnology (genetic engineering and sequencing).

• Ethical and philosophical reflections (general):

  • As we manipulate biological systems, consider implications for health, privacy, biodiversity, and equity.
  • The unity of life emphasizes responsibility to protect ecosystems and public well-being.

ext{Key equations and concepts recap:}

• Dehydration synthesis (peptide bond formation):
  \text{R-COOH} + \text{R'}-\text{NH}2 \rightarrow \text{R-CO-NH-R'} + \mathrm{H2O}.

• Hydrolysis (peptide bond cleavage):
  \text{R-CO-NH-R'} + \mathrm{H2O} \rightarrow \text{R-COOH} + \text{R'-NH}2.

• ATP hydrolysis (energy release):
  \text{ATP} + \mathrm{H2O} \rightarrow \text{ADP} + \text{Pi} + \text{energy}.

• Glycosidic bonds (carbohydrates linkage) concept: two monosaccharides join via an oxygen bridge, forming a disaccharide or longer polysaccharide chain; examples include starch and glycogen as α-linkages (storage), cellulose as β-linkages (structure).

• Phosphodiester bonds (nucleic acids backbone):
  \text{Sugar-Phosphate-O-}\text{P-}\text{O-}\text{Sugar}
  (simplified representation of backbone linkage)

• Hydrogen bonds in biomolecules (conceptual):

  • Water: H–O–H with partial charges enabling H-bonds between water molecules, contributing to cohesion/adhesion and solvent properties.
  • Secondary structures in proteins: hydrogen bonding between backbone amide and carbonyl groups stabilizes α-helices and β-pleated sheets.

• Notation reminders:

  • Distinguish polar vs nonpolar regions by electronegativity differences and molecular polarity.
  • Remember that small-scale interactions (hydrogen bonds, ionic interactions) drive large-scale structures (folding, membranes, DNA base pairing).

• Quick mental map of topics for the exam:

  • Emergent properties and levels of organization
  • Basic elements in biology (CHNOPS and trace elements)
  • Bond types, water properties, and IMF concepts
  • Macromolecules: carbohydrates, lipids, proteins, nucleic acids
  • Protein structure hierarchy (primary to quaternary) and functions
  • Nucleic acids structure and backbone chemistry
  • Prokaryotic vs eukaryotic cell organization and examples