Course number and title: Principles of Biology II

Submission date: 3/5/08

Submitted by: Steve Roof

Chapter Topics and Expected Outcomes by Date:

14/21 Jan, Chp 02: The Chemical Basis of Life I

  • Atoms
  • Structure
  • Nomenclature
  • Bonding
  • Isotopes
  • Properties of Water
  • Outcomes
  • Understand subatomic structure, including how electron density affects an atom's ability to interact with another atom.
  • Quantify atomic mass using units such as Daltons and moles.
  • Compare and contrast interactions known as covalent, polar covalent, ionic, and hydrogen bonding.
  • Describe the properties of water that make it an ideal solvent for biological reactions.
  • Understand the concept of pH and how pH might be buffered to maintain a stable environment inside a living cell

21/28 Jan, Chp 03: The Chemical Basis of Life II

  • Organic Chemistry
  • Carbon and Organic Molecules
  • Proteins
  • Saccharides
  • Nucleic Acids
  • Lipids
  • Functional groups
  • Outcomes
  • Explain the properties of carbon that make it the focal point of organic compounds.
  • Compare and contrast different types of isomeric compounds.
  • Appreciate the variety and chemical characteristics of common functional groups of organic compounds.
  • Describe each biological macromolecule, and how monomers of each class are brought together to form the macromolecules.
  • Give examples of several different proteins and the general types of functions they carry out in a cell.

04 Feb, Chp 04: General Features of Cells

  • Microscopy
  • Cell Structure
  • Size of things
  • Prokaryotic, Plant, Animal
  • Cell organelles
  • Outcomes
  • Describe various microscopic techniques, emphasizing differences in resolution and contrast.
  • Compare and contrast basic cell structure between prokaryotes and eukaryotes (plants & animals).
  • Highlight important structural characteristics and cellular functions of cytoskeletal elements.
  • Trace the fates of A) a ribosomal protein, and B) a secreted protein.
  • Define the term semiautonomous, and outline the general functions of organelles that fall into this category.
  • Describe the factors that relate to cell size
  • Calculate the surface to volume ratio
  • Describe the cellular cytoskeleton

11Feb, Chp 06: Systems Biology of Cell Organization

  • Principles of Cell Organization
  • Endomembrane System
  • Rough endoplasmic reticulum
  • Smooth endoplasmic reticulum
  • Semiautonomous organelles
  • Chloroplasts
  • Mitochondria
  • Outcomes
  • Explain why cells cannot be created from reagents in a laboratory.
  • Describe the four interacting systems of eukaryotic cells.
  • Trace the possible fates of a protein or lipid molecule from its origin to either the nuclear envelope or plasma membrane.
  • Differentiate between targeting signals found in proteins with various cellular localizations.
  • Explain the endosymbiotic theory and how it resulted in semiautonomous organelles.

18/25 Feb, Chp 05: Membrane Structure and Transport

  • Membrane Structure
  • Phospholipid by layer
  • Fluid Mosaic Model
  • Transmembrane proteins
  • Transport
  • Passive
  • Active
  • Facilitated
  • Outcomes
  • Explain the basic principles of the fluid mosaic model of biomembranes.
  • Outline the properties of the lipid bilayers and associated proteins that compose biomembranes.
  • Describe the factors that influence membrane fluidity.
  • Compare and contrast the various methods of movement of ions and molecules across a semi-permeable biomembrane.
  • Give examples of endocytosis and exocytosis in living cells.

25 Feb – 03 Mar, Chp 07: Enzymes, Metabolism, and Cellular Respiration

  • Chemical Reactions
  • Energy
  • Enzymes
  • Overview of Metabolism
  • Catabolic reactions
  • Anabolic reactions
  • Aerobic
  • Anaerobic
  • Cellular Respiration
  • Glycolysis
  • Citric Acid Cycle
  • Outcomes
  • Define the terms enthalpy, entropy, and free energy, and describe how these concepts affect the fate of chemical reactions.
  • Explain the various ways in which enzymes increase the rate of biological reactions.
  • Describe the involvement of ATP in a wide variety of cellular processes.
  • Explain why functions/reactions in the cells are regulated.
  • Compare and contrast the various secondary metabolites described in the chapter.
  • Describe how energy is stored and utilized (ie, kinetic energy and potential energy).
  • Describe how enzymes can catalyze reaction and the activation energy needed.
  • Diagram the activation energy of an equation.
  • Describe how temperature affects the rate of the reaction.
  • Explain enzyme recycling and compare and contrast induced fit model and lock and key model.
  • Describe and give examples of enzyme inhibition and competition, positive and negative feedback, and allosteric regulators.

03/17 Mar, Chp 08: Photosynthesis

  • Overview of Photosynthesis
  • Photo part
  • Synthesis part
  • Variations in Photosynthesis
  • Photorespiration
  • C3 plants
  • C4 plants
  • CAM plants

Outcomes

  • Label and describe the function of photosynthetic plant structures (ie, leaf, chloroplasts, stomata).
  • Describe and balance the general equation for photosynthesis.
  • Describe the inputs and outputs of the Calvin Cycle and light reactions in photosynthesis.
  • Describe the physics of light and how it relates to photosynthesis (ie, wavelength).
  • Interpret an absorbance spectrum and relate it to photosynthesis.
  • Compare, contrast, and give the roles of chlorophyll and accessory pigments in plants.
  • Contrast cyclical and non-cyclical electron flow in light reactions.
  • Compare and contrast C3, C4, and CAM photosynthetic pathways and discuss why these are important evolutionarily.

24 Mar, Chp 11: Nucleic Acid Structure and DNA Replication

  • Identification of Genetic Material
  • Nucleic Acid Structure
  • Nucleotides
  • Polynucleotides
  • Double Helix
  • DNA Replication
  • Enzymes
  • Direction
  • Outcomes
  • Describe the experiments that demonstrated that DNA is the genetic material.
  • Outline Gene Theory.
  • Discuss why DNA is the Genetic Material of cells. Outline the History of research to find what material controlled heredity.
  • Know the structure of DNA (prokaryotic and eukaryotic).
  • Discuss DNA replication.
  • Outline DNA proof reading and repair.

31 Mar – 07 Apr, Chp 12: Gene Expression at the Molecular Level

  • Gene Theory
  • DNA to Proteins
  • Transcription
  • mRNA
  • Translation
  • tRNA
  • Amino Acids
  • Ribosomes
  • Outcomes
  • Discuss Gene Theory and its steps (transcription and translation).
  • Given a DNA sequence predict the polypeptide sequence.
  • Compare the structure and function of DNA and RNA.
  • Understand the importance of mutation in gene theory.
  • Define the importance of reverse transcriptase.
  • List the sequence of events during transcription of a gene.
  • Compare and contrast start and stop signals for transcription and translation, and note relevant differences between bacteria and eukaryotes.
  • Trace the fate of a eukaryotic mRNA molecule from initial transcription through its translation.
  • Outline the structure of a ribosome, describing the functional regions and how they contribute to the process of translation.

07/14 Apr, Chp 13: Gene Regulation

  • Gene Regulation
  • In Bacteria
  • In Eukaryotes
  • Regulation of RNA processing
  • Outcomes
  • Identify several different reasons why a cell would regulate its gene expression.
  • Account for the elements of positive and negative control in expression of the lac operon in E. coli.
  • Outline the features involved in efficient expression of eukaryotic structural genes.
  • Describe how transcription factors can be activated by signaling molecules, and the ways in which they can interact with DNA.
  • Explain how gene expression can be regulated beyond the level of transcription.

14/21 Apr, Chp 14: Mutation, DNA Repair, and Cancer

  • DNA Mutations
  • Silent
  • Missense
  • Nonsense
  • Frameshift
  • Repair
  • Cancer

Outcomes

  • Define mutation and describe why cells have so many systems devoted to avoiding or correcting mutations.
  • Predict the phenotypic outcomes of the various types of point mutations if left uncorrected.
  • Identify various methods cells utilize to repair mutations in their genomes.
  • Outline the path of a cancer from initial occurrence through benign growth, malignancy, and finally the death of the individual.
  • Compare and contrast oncogenes and tumor-supressor genes.

28 Apr, Chp 20: Gene Technology

  • Gene Cloning
  • Society
  • Genomics and Proteomics
  • Human genome project
  • Biotechnology
  • Transgenic organisms
  • Outcomes
  • Outline the steps in gene cloning, including predicted outcomes from successful versus unsuccessful steps.
  • Compare and contrast the construction of genomic and cDNA libraries.
  • Describe the steps involved in in vitro DNA synthesis techniques illustrated in the chapter (PCR, dideoxy sequencing).
  • List several examples of how molecular genetics has influenced biotechnology.
  • Explain how DNA profiling is used in identification and relationship testing.