• The science of Biology, Basic chemistry. (Raven and Johnson)*
• Molecules. Chapters 2, and 3
• The Molecular Composition of Cells
• Cells
• Membranes
• Osmosis and diffusion
• Energy, metabolism, and cellular energetics
• Meiosis
• Genetics
• The Five Kingdoms of Life

• The Science of Biology, Chapter 1, page 2.
  DEFINITIONS AND TERMINOLOGY:

  Deductive reasoning

  indirect method of analysis of a specific question or problem using established, general principles such as geometry, physics, chemistry, etc. [e.g. measurement (estimation) of the earth's circumference by indirect means through application of geometric prinicples.

  Inductive reasoning

  direct method of analysis of a specific problem or question by careful examination of specific cases which lead to the discorvery of general principles.

  Model

  a formulation of working rules, general principles, and practical concepts consistent with observable phenomena. A model may or may not be testable but does attempt to explain how something works or what is observed (e.g. macroevolution, microevolution, scientific creationism, classical and molecular genetics, etc.).

  Hypothesis

  a testable, suggested explanation that accounts for the available data, observations, and known facts concerning a particular area of science (e.g. 'there is no light in the room because the light switch is turned off'; can be tested, proven correct, or proven incorrect).

  HYPOTHESIS TESTING:

  Experimentation

  method of testing a given hypothesis by evaluation of a specific situation and an alternative hypothesis(ses) as well.

  Alternative hypothesis

  e.g. and alternative hypothesis to the dark room problem posed above would be 'the light is burned out' or 'I am going blind'.

  Elimination of alternative hypotheses

  provision of support for one hypothesis while eliminating alternative hypotheses through experimentation and testing; involves designing and conducting experiments which test each hypothesis.

  The scientific method

  involves the rejection of hypotheses that are not consistent with experimental results or observations. Hypotheses consistent with available data are conditionally accepted.

  Theory

  a hypothesis which is supported by experimental testing and observations, and is not rejected according to the criteria established for the elimination of alternative hypotheses.

  
  FORMATION OF THEORIES
  A theory is, therefore, a hypothesis that is supported by a significant amount of scientific, experimental evidence. A theory can still be rejected in the future. Some theories are so stongly supported that they will not likely be rejected and eventually become 'law' in some cases.
• Basic chemistry
  1. Review Chapter 2 (pp. 20 - 40) with emphasis on the following sections and terms:
     • Atoms
     • Molecules
     • Chemical Bonds
     • covalent bond
     • ionic bond
     • oxidation and reduction
     • Atoms in Living Organisms
     • Properties of water significant to life
     • hydrogen bond
     • cohesion
     • adhesion
     • hydrophobic vs. hydrophilic
  2. Answer the review questions (1, 2, 5, 8, 9, and 10) at the end of Chapter 2, page 40.

• Molecules and the chemical building blocks of life Read Chpter 3 with emphasis on the following sections and terms:
  • macromolecules
  • functional groups
  • hydorxyl group
  • polymer

The Molecular Composition of Cells. From The Biology of Plants (1986) Raven, Evert, and Eichhorn.

• Elemental components.
  • Macronutrients - C, H, O, P, S make up roughly 97 to 99% of total fresh weight of most organisms.
  • Micronutrients - K, Na, Ca (relatively high concentrations in most organisms, especially plants), Zn, Co, and Cu (very low concentration; considered trace elements).
• Organic compounds; four general groups of biologically important macromolecules.
  • Carbohydrates - sugars, starches, glycogen, cellulose, chitin, peptidoglycan; general formula (CH2O)n. To general types:
    • Monomers - subunits such as simple sugars (e.g. glucose) which are polymerized to make more complex polymeric carbohydrates; the subunits are also called monosacharides.
    • Polymers - covalent linkage of monomers to form a polymeric chain of subunits; the polymers are also called polysaccharides. Types of polysaccharides include:
      • Disaccharides - composed of two monosaccharides joined covalently [e.g. sucrose (table sugar) which is composed of glucose and fructose (a herteropolymer of two different monosaccharides)]
      • Oligosaccharides - short chains composed of three to twenty monomers, usually the same monomer (homopolymer) such as glucose polymerized to form starch, glycogen, or cellulose precursors.
      • Macromolecular polysaccharides - composed of more than 20 monomers. Examples include:
        • Starch - glucose polymerized to form an energy storage form of glucose; glucose itself is used directly either as an energy source for 1) catabolism - breakdown to yield energy in the form of ATP or 2) anabolism - synthesis of complex organic molecules from simple starting materials and requiring the use of energy in the form of ATP.

          Starch is composed of glucose monomers in the form of an alpha-glucose ring (see page 48, Fig. 3-5). These alpha-glucose rings are attached in the starch unbranched backbone by covalent alpha 1-4 linkages. Such a backbone is called amylose (alpha 1-4 linkages only, see page 47). A complete starch polymer is also composed of amylopectin [contains alpha 1-4 (backbone) and alpha 1-6 (branches) linkages. Amylopectin and starch are essentially the same.

          Amylose contains 1000 or more glucose units in an unbranched chain. Amylopectin has a molecular weight (MW) of 1 to 6 million Daltons (D); therefore, amylopectin is at least 5 times the MW of amylose.

          Branching occurs about every 20 to 25 glucose units; relatively low amount of branching. Common in plants.

        • Glycogen - same general structure as starch, except more highly branched (every 6 to 12 glucose residues). Common glucose storage form in animals, fungi, and bacteria; MW up to 100 million D.

          What do you think is the significance of these two different forms of glucose storage with regard to branching?

        • Cellulose - (see page 48) structural polymer of glucose used to make rigid, supportive and protective structures in plants such a the cell wall (major component of the plant cell wall and in some cases the entire plant cell itself).

          Cellulose is composed of beta-glucose rings linked in a beta 1-4 manner. Usually forms a single, linear chain which can interact which can interact with other cellulose chains by either 1) non-covalent bonds such as hydrogen bonds (weak interactions), 2) covalent bonds (strong interactions) involving organic compounds such as lignin, 3) ligand-type interactions involving inorganic ions such as Calcium, or 4) combinations of any or all of the above.

        • Chitin - polymer of N-acetylglucoseamine; found in fungal cell walls, arthropod exoskeletons, etc.; structural form; forms chains which can be covalently, ligand crosslinked, or H-bonded like cellulose. Usually ligand crosslinked via Ca for strong crosslinking.
  • Lipids - fats, waxes, fatty acids, glycerides, phospholipids; generally hydrophobic and contain long hydrocarbon chains (large numbers of C and H atoms covalently linked in linear manner). Examples include:
    • Fats - storage form of lipids, found in lipid bodies (p. 49). Can be an energy storage or eventually used for structural purposes (e.g. cell membranes).

      Liquid fats are oils and most-readily used as an energy source for embryos developing as seedlings and in seeds and fruits. Cells synthesize fats from sugars. A fat consist of three fatty acids covalently linked to glycerol. Fatty acid - long-chain hydrocarbon with carboxylic acid end group; saturated and unsaturated (p. 50); also called a Triglyceride.

    • Cutin, suberin, and waxes - (p. 50) solid lipids which are insoluble in water and even some other lipids. Found on the epidermis of plants and serve as protective, water-impermeable barriers within the cuticle of the epidermis; found on outside of the epidermal cell wall to the exterior portion of the plant, especially found on leaves and stems.
    • Phospholipids - diglyceride containing a phosphate group (phosphotidic acid) and usually a charged organic group such as choline (phosphotidyl choline); have hydrophilic and hydrophobic portions (moieties) - called amphipathic

      The amphipathic nature of phospholipids allow them to function well as cell membranes.
  • Proteins - polymers of amino acids (nitrogen-containing, small, organic acids. Some general types of proteins include: structural proteins - extra- and intracellular proteins used for protection and support; functional proteins - enzymes which catalyze metabolic reactions and regulatory proteins which control gene expression and or activity of certain proteins and metabolic processes.
  • Nucleic acids - polymers of nucleotides (complex molecules mad up of a phosphate group, 5-carbon sugar - ribose or deoxyribose, and a nitrogenous base abbreviated A, T, G, C, or U). Examples include: DNA which is the genetic hereditary material in nearly all organisms; some viruses have RNA as the genetic material; and RNA which is serves as an informational intermediate between the DNA and protein level.

Answer the following review questions at the end of Chapter 3 of your textbook, page 61: 1, 4, 5, 8, 10, and 11.

Cells

Read Chapter 5 and answer the review questions as discussed during our last Sunday night meeting.

Read Chapter 6 focusing on:

• The lipid foundation of membranes
  1. Phospholipids
  2. Bilayers
  3. Glycoproteins
• Passage of molecules into and out of cells
  1. diffusion
  2. osmosis
  3. facilitated diffusion
  4. active transport

1, 2, 5, 6, 7, 9, 11, and 12.

Energy, metabolism, and cellular energetics

Read chapters 7 and 8, and answer the review questions at the end of the chapter.

Chapter 11:

Chapter 12:

Chapter 28:

1. Kingdom Monera - the bacteria; prokaryotic cells that lack a nuclear membrane, plastids, mitochondria, and other membrane-bound organelles; unicellular but sometimes aggregate into filaments or other superficially "multicellular" bodies called colonies; obtain nutrients primarily by absorption, but some species are photosynthetic or chemosynthetic; reproduction is primarily asexual by binary fission or budding, but portions of DNA molecules may also be exchanged between cells under certain circumstances; some species are motile by flagella, others are non-motile. There are approx. 2500 identified and classified species of bacteria; most have cell walls of a complex polysaccharide called peptidoglycan; the mycoplasmas lack cell walls.

2. Kingdom Protista - eukaryotic (have membrane-bound nucleus and organelles) unicellular and multicellular organisms; modes of nutrition include ingestion (animal-like organisms called protozoa), photosynthesis (uni- and multicellular algae), and absorption (also many protozoa and some unicellular algae); reproduce asexually by binary fission in unicellular species, specialized DNA-transfer mechanisms in some unicellular species, and sexually via fusion of gametes; many unicellular species are motile by flagella or other means, some species are non-motile; many algae species have cell walls of cellulose or other complex polysaccharides.

3. Kingdom Fungi - eukaryotic multicellular and unicellular species (the unicellular species are often referred to as the yeasts; nuclei occur in a nearly continuous cellular mass of structures called mycelia composed of hyphae (filaments) in the vegetative portion (non-reproductive) and spore bearing reproductive structures called sporangia; nutritionally, they are heterotrophic by absorption; reproduction by asexual and sexual means - asexually by binary fission and budding in yeasts, or vegetative growth in multicellular species, sexually by formation of spores which are haploid, unicellular individuals which divide to form a haploid, multicellular phase which produces gametes for sexual reproduction, the multicellular stage may be maintained by mitotic cell division with meiosis occurring just before spore formation, or meiosis may occur shortly after zygote formation followed by mitotic cell division to maintain a haploid, multicellular individual; have cell walls of the polysaccharide chitin.

4. Kingdom Plantae - eukaryotic multicellular photosynthetic autotrophs (some parasitic heterotrophs exist) with extensive tissue differentiation; have alternation of distinct reproductive and vegetative phases; cell walls of cellulose; reproduction asexually by vegetative propagation of various tissues ranging from leaf, root, and stem portions, and sexually by formation of gametes during the reproductive phase. Contain the photosynthetic pigment chlorophyll in organelles called chloroplasts.

5. Kingdom Animalia - eukaryotic multicellular heterotrophs with extensive tissue differentiation; lack cell walls; reproduction both asexually by budding, fragmentation and regeneration in simple invertebrates, and parthenogenesis (development of a new individual from an unfertilized egg) in invertebrates and some vertebrates (e.g. frogs), and sexually by formation of gametes. Divided into two main, non-taxonomic groups: the invertebrates and vertebrates.

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