October 7, 1997 Dr. Jakubowski

For exam one, you should be able to:

  1. Understand the difference between elements, atoms, subatomic particles, and molecules.
  2. Understand how the periodic table organizes our understanding of the chemical properties of elements and how the table is a succinct expression of . periodic law.
  3. Understand the chemical basis for the organization of the periodic table.
  4. Describe the octet rule and the basis for chemical reactivity of the elements.
  5. Draw Lewis structures for the elements and both ionic and covalent compounds, including molecular ions.
  6. Determine the formal change on an atom in a molecule or molecular ion,
  7. Explain the following concepts: ionic bonds, polar and nonpolar covalent bonds, electronegativity.
  8. Identify and explain the different types of intermolecular forces (IMF) including ion..ion, H bond, and London forces, and explain how the strenght of IMF affects boiling and melting points.
  9. Understand and explain the significance of IMF in biological interactions
  10. Explain the role of receptors in membranes of cells.
  11. Draw "cartoon" structures for simple lipids and use them to explain the solubility properties of lipids in water.
  12. Explain how detergent micelles and bilayers form through IMF.
  13. Explain and be able to draw a representation of chromosomes, single and double stranded DNA, and a gene.
  14. Explain the intermolecular forces which hold ds-DNA together
  15. Explain how a limited number of monomeric units (4 for DNA and RNA, and 20 for proteins) can combine to form polymers of almost infinite variety and complexity.
  16. Describe and identify the constituents of the backbone chain and bases on DNA, and how to identify the different ends of the polymer.
  17. Describe and identify the constituents of the main chain (backbone) and side chains of a protein, and how to identify the different ends of the polymer
  18. Be able to identify the H-bond donors and acceptors in any molecule, including proteins and nucleic acids.
  19. Identify the intramolecular forces which cause a protein chain to fold to a unique 3D shape.
  20. Identify the intramolecular H-bonds among H-bond donors and acceptors in the main chain and how H-bonds among these groups lead to alpha helices and beta strands/sheets.
  21. Explain the central dogma of biology and:
    • explain the difference between replication, transcription, and translation
    • name the enzymes used in replication and transcription
    • explain how gene expression is regulated
    • explain the nature and role of transcription factors
    • explain how different cell types differ from each other
    • explain the difference between cell division and cell differentiation
    • explain the structure of a typical gene, including regulatory sequences and introns/exons
  22. Given the template and coding strands of DNA, and the genetic code, determine the mRNA sequence and the protein sequence which would derive from the DNA sequence.
  23. Given a mutation in the DNA, and knowing whether the mutation would alter a surface or buried amino acid in the protein, speculate as to the effect of the mutation on protein structure/function.
  24. Explain how drugs, hormones, and neurotransmitters might interact with their target molecules (such as proteins and DNA) within cells.
  25. With regard to the immune system. explain:
    • the common motiff used by immune cells to respond to foreign substances.;
    • the functions of B, plasma, Thelper, Tcytotoxic, and natural killer cells;
    • the role and sources of antibodies, antigens, Tcell receptors, and interleukins
    • the role of MHC proteins;
    • d. the concept of immune surveillance;
    • how the immune system discriminates self from nonself;
    • the role of genetic recombination in the generation of antibody diversity;
  26. With regards to bacteria and viruses, explain:
    • the differences between a bacteria and virus;
    • in general how antibiotics work;
    • how antibiotic resistant strains of bacteria arise
    • why, theoretically, it is easier to develop antibiotics than antiviral drugs
  27. With respect to drug discovery and development, explain:
    • how potential drugs can be found in nature;
    • how new drugs can be found in the lab;
    • the process of rational drug design;
    • the processes required for new drugs to "arrive" in the marketplace;
    • how diseases are chosen for drug development by pharmaceutical companies.
    • the difference between drugs marketed by pharmaceutical companies and substances found in "herbal" remedies
    • how drugs work
  28. Understand and articulate, from our discussions in class, the experiments in lab, and from the Exchange conference, the nature and use of the scientific method. This certainly will be the subject of a significant essay question on the exam. Be prepared to explain how you might use this method to address the efficacy of traditional and alternative medical therapies.

Read the article on Cell Suicide on Reserve.

The following questions are based on the article: Cell Suicide in Health and Disease, by R. Duke, D. Ojcius, and J. Young, which appeared in the December 1996 issue of Scientific American. Two copies of this article have been placed on reserve at each library. This article represents the kind of article that you should hopefully be able to read and understand after the first part of this course. It is one of the best written articles I have read from Scientific American in many years. The topic, Cell Suicide, is one of the exciting areas of modern biological/biochemical/medical research, as you will undoubtedly discern after reading the article. Most scientist investigating cellular phenomena have spent almost all their effort in studying how a cell lives and replicates, and paid little attention to how and why cells die. Most scientists probably never even thought of asking the latter question

I have derived five questions from the article. One will appear on the first exam. You may NOT use any notes or articles during the exam. In preparation for the exam, I would suggest that you answer these questions as you read the article. Your answers should include cartoon diagrams to help explain your ideas.

  1. Differentiate between programmed cell death (apoptosis) and necrosis.
  2. Describe why cells have programmed into their genetic information the molecular machinery to commit suicide. List several cell type that routinely undergo apoptosis and explain why it is biological advantageous for these cells to do so.
  3. The proteins Bcl, p53, ICE-like proteases, Fas, and Fas-ligand are involved in apoptosis and its regulation. Explain their roles.
  4. Below are listed a type of cell and an associated disease. What kinds of defects might you expect in the genes for the proteins involved in apoptosis (listed in Question 3) in the cells listed below, and how would the defect help cause the associated disease?
    • cancer cell - cancer
    • T helper cells - AIDS
    • virally infected cells (excluding immune cells) - viral infection
    • T cells which recognize self antigens - autoimmune disease
  5. Give an explanation why melanocytes (cells which produce the skin pigment melanin) which become cancerous are so aggressive and metastatic.