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 o Atoms

Structure
 Nomenclature
 Bonding

Isotopes
 Properties of Water o 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 o Organic Chemistry
 Carbon and Organic Molecules

Proteins

Saccharides

Nucleic Acids

Lipids

Functional groups o 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 o Microscopy o Cell Structure
 Size of things

Prokaryotic, Plant, Animal
 Cell organelles o 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 o Principles of Cell Organization o Endomembrane System

Rough endoplasmic reticulum
 Smooth endoplasmic reticulum o Semiautonomous organelles
 Chloroplasts
 Mitochondria o 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 o Membrane Structure

Phospholipid by layer
 Fluid Mosaic Model
 Transmembrane proteins o Transport
 Passive
 Active

Facilitated o 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 o Chemical Reactions
 Energy
 Enzymes o Overview of Metabolism
 Catabolic reactions
 Anabolic reactions
 Aerobic

Anaerobic o Cellular Respiration
 Glycolysis

Citric Acid Cycle o 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 o Overview of Photosynthesis
 Photo part
 Synthesis part o Variations in Photosynthesis

Photorespiration
 C
3
plants
 Outcomes
 C
4
plants

CAM plants o Label and describe the function of photosynthetic plant structures
(ie, leaf, chloroplasts, stomata). o Describe and balance the general equation for photosynthesis. o Describe the inputs and outputs of the Calvin Cycle and light reactions in photosynthesis. o Describe the physics of light and how it relates to photosynthesis
(ie, wavelength). o Interpret an absorbance spectrum and relate it to photosynthesis. o Compare, contrast, and give the roles of chlorophyll and accessory pigments in plants. o Contrast cyclical and non-cyclical electron flow in light reactions.

o 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 o Identification of Genetic Material o Nucleic Acid Structure
 Nucleotides

Polynucleotides
 Double Helix o DNA Replication

Enzymes
 Direction o 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 o Gene Theory
 DNA to Proteins

Transcription o mRNA

Translation o tRNA
 Amino Acids
 Ribosomes o 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 o Gene Regulation
 In Bacteria
 In Eukaryotes o Regulation of RNA processing o 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 o DNA Mutations
 Silent

Missense
 Nonsense
 Frameshift o Repair o Cancer
 Outcomes o Define mutation and describe why cells have so many systems devoted to avoiding or correcting mutations. o Predict the phenotypic outcomes of the various types of point mutations if left uncorrected. o Identify various methods cells utilize to repair mutations in their genomes. o Outline the path of a cancer from initial occurrence through benign growth, malignancy, and finally the death of the individual. o Compare and contrast oncogenes and tumor-supressor genes.

 28 Apr, Chp 20: Gene Technology o Gene Cloning
 Society o Genomics and Proteomics
 Human genome project o Biotechnology

Transgenic organisms o 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.