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MCB 150 Lecture Notes

Lecture 2: Technology Intro; Domains of Life

  • Linnaean system of classification (1700s):
    • Based on physical characteristics (e.g., food source, movement).
    • Genus:species scheme.
    • Initially, only two kingdoms: animals and plants.
    • Later, this was insufficient to explain fungi, microbes, etc.
  • Advancements in technology allowed examination of cell contents, leading to the distinction between:
    • Eukaryotes: Cells with a "kernel" (nucleus).
    • Prokaryotes: Cells without a nucleus.
  • Typical Prokaryotic Cell:
    • Nucleoid: Contains a single chromosome, not membrane-bound.
    • Cytoplasmic membrane: Functions as both cytoplasmic and internal membranes.
    • Cell wall: Usually present.
  • Typical Eukaryotic Cell:
    • Contains organelles such as lysosomes, Golgi apparatus, endoplasmic reticulum, and mitochondria.
    • Nucleus present.
    • Animal vs. Plant Cells: Animal cells lack cell walls and chloroplasts.
    • Organelles: Distinct compartments within the cell (representative, not exhaustive).
  • Up until ~1977:
    • Organisms classified into two "superkingdoms":
      • Prokaryotes: Lacking nuclear membrane and membrane-bound organelles.
      • Eukaryotes: Possessing nuclear membrane and membrane-bound organelles.
    • Limitations: Physical characteristics are useful for crude classifications but are insufficient for understanding evolutionary relationships.
  • Carl Woese's Discovery (1977):
    • Compared small subunit ribosomal RNA (rRNA) sequences across species.
    • rRNA is essential for protein synthesis.
    • Conclusion: "Prokaryotes" are two distinct groups: Bacteria and Archaea.
      • (EU)BACTERIA: True bacteria (e.g., E. coli), found ubiquitously.
      • ARCHAEA: "Ancient" prokaryotes, often in extreme environments resembling early Earth (extreme heat, pressure, acids, salts, gases).
    • Basis: Archaeal rRNA sequences are more closely related to eukaryotic rRNA than bacterial rRNA.
  • Revised Tree of Life:
    • Three Domains: Bacteria, Archaea, Eukarya.
    • Archaea's Molecular Processes: More similar to humans than E. coli, despite physical resemblance to bacteria (both are prokaryotes).
  • Comparison of Domains:
    • Nuclear Membrane:
      • Bacteria: No
      • Archaea: No
      • Eukarya: Yes
    • Membrane-Bound Organelles:
      • Bacteria: No
      • Archaea: No
      • Eukarya: Yes
    • Typical Size (microns):
      • Bacteria: 1-10
      • Archaea: 1-10
      • Eukarya: 10-100
    • Typical Number of Chromosomes:
      • Bacteria: 1
      • Archaea: 1
      • Eukarya: >1
    • Shape of Chromosomes:
      • Bacteria: Mostly circular
      • Archaea: Mostly circular
      • Eukarya: Mostly linear (in the nucleus)
    • Examples:
      • Bacteria: E. coli, H. influenzae
      • Archaea: Methanogens, Thermophiles
      • Eukarya: Yeast, Plants, Animals
  • Cellular Basis of Life:
    • No two species are structurally or biochemically identical, but all are made of cells.
    • Life requires a structural compartment (cell) separate from the external environment.
    • This allows molecules to perform unique functions in a constant internal environment.
  • Cell Theory:
    • Cells are the fundamental units of life.
    • All organisms are composed of one or more cells.
    • All cells come from preexisting cells.
  • Cell Size:
    • Cells are small due to the surface area-to-volume ratio.
    • As size increases, the surface area-to-volume ratio decreases.
  • Resolution:
    • Ability to identify the separation of two close objects.
    • Light microscopes: Resolving power is ~0.2 microns (µm; 10^{-6} m).
    • Electron microscopy: Resolution of ~0.5 nm (10^{-9} m).
    • Denser material affects electrons more, appearing darker in electron microscopy.

Lecture 3: Overview of Cell Structure; Begin Carbohydrates

  • Cell Walls:
    • Plants and most prokaryotes have rigid cell walls for shape and protection.
  • Plasma Membrane:
    • Every cell is surrounded by a plasma membrane.
    • Functions:
      • Maintains a constant internal environment.
      • Acts as a selectively permeable barrier.
      • Interface for receiving information from adjacent cells and extracellular signals.
      • Contains molecules responsible for binding and adhering to adjacent cells.
  • Prokaryotic vs. Eukaryotic Cells:
    • Prokaryotic cells are less compartmentalized.
    • Eukaryotic cells (animal cells) are highly compartmentalized with organelles.
      • Examples of eukaryotic cell structures/organelles:
        • Plasma Membrane: 15 nm
        • Nucleus
        • Mitochondria
        • Rough Endoplasmic Reticulum
        • Smooth Endoplasmic Reticulum
        • Golgi Apparatus
        • Ribosomes/Polysomes
  • Major Biological Polymers (Macromolecules):
    • Proteins
    • Nucleic Acids
    • Carbohydrates (Polysaccharides) [sugars]
    • Lipids [fats]
  • Chemical Composition of a Bacterial Cell:
    • Water: 70%
    • Inorganic ions: 1%
    • Monosaccharides and precursors: 1%
    • Amino acids and precursors: 0.4%
    • Nucleotides and precursors: 0.4%
    • Fatty acids and precursors: 1%
    • Other small molecules: 0.2%
    • Macromolecules (proteins, nucleic acids, polysaccharides, and lipids): 26%
  • Monomers and Polymers:
    • Proteins are composed of Amino Acids.
    • Nucleic Acids are composed of Nucleotides.
    • Polysaccharides are composed of Monosaccharides.
    • (Membrane) Lipids are composed of Fatty Acids (and usually Glycerol).
  • Condensation (Dehydration Synthesis):
    • Monomer in, water out
  • Hydrolysis:
    • Water in, monomer out
  • Polysaccharides (Carbohydrates):
    • Made from condensation reactions bringing together monosaccharides.
    • Uses: energy sources, structural roles (insect exoskeletons & cell walls), cell identification & recognition.
    • "Carbohydrate": Can refer to complex sugars (polysaccharides) or simple sugars (monosaccharides).
    • General formula: Cn(H2O)_n with a backbone of H–C–OH
  • Standard Ring Structure of a Monosaccharide (Glucose):
    • Within the ring, if not specified, the atom is Carbon (C).
    • Atoms other than Carbon within the ring must be specified.
    • Above or below the ring, Carbons need to be specified.
    • Above or below the ring, any atom not specified is assumed to be Hydrogen (H).
  • Monosaccharides:
    • Typically found with 3, 5, or 6 carbons.
    • Example: Glucose (C6H{12}O_6)

Lecture 4: Continue Carbohydrates

  • Monosaccharides:
    • Typically found with 3, 5, or 6 carbons.
    • Example: Glucose (C6H{12}O_6)
  • Circularization of Glucose:
    • α-glucose vs. β-glucose
  • Isomers
    • Some monosaccharides have identical formulas but different structures.
    • Hexoses: 6-carbon sugars (C6H{12}O_6): Glucose, Galactose, Fructose.
    • Aldose (Aldehyde Sugar)
    • Ketose (Ketone Sugar)
  • Related Monosaccharides
    • Other monosaccharides have similar (but not identical) formulas, similar structures, and related functions: Deoxyribose, Ribose.
  • Pentoses: 5-carbon sugars (C5H{10}O_5): Ribose, Ribulose.
    • Aldose (Aldehyde Sugar)
    • Ketose (Ketone Sugar)
  • Disaccharides:
    • Two monosaccharides can be brought together to form a disaccharide via a covalent bond called a glycosidic linkage.
      • example: α-1,4 glycosidic linkage.
      • Cellobiose (not shown) is a disaccharide of beta glucose and another glucose connected via a β-1,4 glycosidic linkage.
  • Disaccharides with different Monosaccharides:
    • Lactose (milk sugar) is a disaccharide of glucose and galactose.
    • Sucrose (table sugar) is a disaccharide of glucose and fructose.
  • Disaccharide Formula:
    • The chemical formula for a disaccharide of hexose sugars is C{12}H{22}O_{11}.
    • Differs from the general formula of Cn(H2O)_n because of the removal of water during the formation of the glycosidic bond.
  • Terminology:
    • One monomer: monosaccharide.
    • Two monomers: disaccharide.
    • Several monomers: oligosaccharide (oligo = several).
    • Hundreds or thousands of monomers: polysaccharide (poly = many).
  • Carbohydrate Modification:
    • Linkage of oligosaccharides to other macromolecules.
    • When covalently linked to membrane proteins or lipids, carbohydrates act as identification and recognition molecules (chemical markers), as in blood typing.
  • Addition of Chemical Groups
    • Examples: Fructose-1,6-bisphosphate, Glucosamine, Galactosamine
  • Polysaccharides as Energy Sources or Structural Compounds:
    • Cellulose
    • Starches
    • Glycogen
  • Cellulose:
    • Most abundant carbon-containing (organic) compound on Earth.
    • Found in plant cell walls.
    • Linear, unbranched polymer of glucose.
      • monomers covalently linked by β-1,4 glycosidic linkages
      • linear polymers held together by hydrogen bonding with neighboring strands.
  • Starches:
    • Found chiefly in seeds, fruits, tubers, roots and stems of plants; energy storage
    • Helical, unbranched or loosely branched polymers of glucose.
      • monomers within chains covalently linked by α-1,4 glycosidic linkages
      • chains branch by connecting with other chains by α-1,6 glycosidic linkages
  • Glycogen:
    • Found in muscle and liver cells of animals; energy storage
    • Helical, highly branched polymers of glucose.
      • monomers within chains covalently linked by α-1,4 glycosidic linkages
      • chains branch by connecting with other chains by α-1,6 glycosidic linkages

Lecture 5: Lipids and Biomembranes Part 1

  • Lipids:
    • Defined by physical properties, not chemical structure.
    • Vary widely in structure.
    • Functions: energy storage, biomembrane composition, chemical signaling.
    • Types: triglycerides, phospholipids & glycolipids, steroids.
  • Monomers of Lipids:
    • Glycerol and Fatty Acids
  • Triglycerides:
    • 3 Fatty Acids + Glycerol = Triglyceride
  • Phospholipids:
    • 2 Fatty Acids + Glycerol + Phosphate = Phospholipid
  • Major Membrane Phospholipids:
    • Variety in polar head groups.
  • Fatty Acid Tails in Phospholipids:
    • Vary in length and degree of saturation.
  • Phospholipids are Amphipathic
  • Phospholipids in water:
    • Spontaneously form micelles or bilayers.
  • Bilayers:
    • Exposed edges fold into liposomes.
  • Lipid Properties:
    • Studied through artificial bilayers.
  • Bilayer interface:
    • Exclusion of water.
    • Hydrophilic regions interact with water, hydrophobic regions avoid water.
  • Glycolipids:
    • Some membrane lipids are Glycolipids
  • Steroids:
    • Can be used as circulating hormones or as membrane components.
  • Cholesterol:
    • Animal cells have cholesterol in their biomembranes.
    • Plants & fungi: different steroids; bacteria: none.
  • Biomembranes are Asymmetrical
  • Biomembranes and Associated Proteins:
    • Transmembrane
    • Membrane-associated
    • Lipid-linked
    • Peripheral
  • Protein Functions:
    • Enzymes
    • Signaling molecule Receptor
    • Signal transduction
    • Glycoprotein
    • Transport
    • Enzymatic activity
    • Cell-cell recognition
    • Intercellular joining
    • Attachment to the cytoskeleton and extracellular matrix (ECM)
  • Membrane Permeability:
    • Membrane is selective.
    • Biomembranes are Selectively Permeable

Lecture 6: Lipids and Biomembranes Part 2; Nucleic Acids

  • Membrane Permeability:
    • Selectively Permeable
  • Biological membranes are fluid:
  • Lipids Movement within the Membrane:
  • Membrane Fluidity:
    • Temperature dependent.
    • Influenced by lipid composition of the membrane
  • Cell Regulation of Membrane Fluidity:
    • Number of unsaturated fatty acids.
      • High level is + (more fluid)
      • Low level is - (less fluid)
    • Tail length of fatty acids.
      • Short chains is + (more fluid)
      • Long chains is - (less fluid)
    • Number of cholesterol molecules (at low temperatures).
      • High level is + (more fluid)
      • Low level is - (less fluid)
  • Nucleic Acids:
    • Two types: Deoxyribonucleic Acid (DNA) and Ribonucleic Acid (RNA).
    • Serve an information storage role in a cell.
    • Monomers: Nucleotides (Base, Sugar, Phosphate).
  • Numbering, Labeling, and Naming Conventions:
    • Base + Sugar = Nucleoside
    • Nucleoside + 1 Phosphate = nucleoside monophosphate
    • Nucleoside + 2 Phosphates = nucleoside diphosphate
    • Nucleoside + 3 Phosphates = nucleoside triphosphate
  • Differences Between DNA and RNA Nucleotides:
    • Nitrogenous bases:
      • RNA: Uracil, Cytosine, Adenine, Guanine.
      • DNA: Thymine, Cytosine, Adenine, Guanine.
    • Pyrimidines: Uracil, Cytosine, Thymine
    • Purines: Adenine, Guanine
  • Nucleotide Nomenclature:
    • Adenine (A), Guanine (G), Cytosine (C), Uracil (U), Thymine (T).
    • All nts in DNA chain have the same 5-carbon sugar and a phosphate group.
    • All nts in RNA chain have the same 5-carbon sugar and a phosphate group.
    • For nucleotides of each of these nucleic acids, all that differs is the base, so the designation of the nucleotide is the abbreviation of the base.
  • Differences Between DNA and RNA Nucleotides (Continued):
    • 5-carbon sugar: Ribose or Deoxyribose.
  • DNA Properties:
    • Deoxyribose sugar (H at 2' carbon).
    • Pyrimidine bases: Cytosine (C) and Thymine (T).
    • Purine bases: Adenine (A) and Guanine (G).
    • DNA monomers are called deoxyribonucleotides (or deoxyribonucleoside triphosphates, or dNTPs).
    • Usually double-stranded.
  • RNA Properties:
    • Ribose sugar (OH at 2' carbon).
    • Pyrimidine bases: Cytosine (C) and Uracil (U).
    • Purine bases: Adenine (A) and Guanine (G).
    • RNA monomers are called ribonucleotides (or ribonucleoside triphosphates, or NTPs).
    • Usually single-stranded.
  • Polymerization of Nucleic Acid