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