Spring 2007

For the second examination, you should be able to:

  1. Draw a reaction mechanism to show and explain how hydroxide and water chemically reacts with aldehydes, ketones, carboxylic acids, and carboxylic acid derivatives (whose structures will be given to you).
  2. Identify hydrolysis reactions.
  3. Given a pair of similar molecular species, predict which would be a better leaving group.
  4. Explain the relationship between reactivity, energy, and stability of a molecule.
  5. Given a protein structure, identify the main chains atoms, the backbone, the amino acid side chains, and amide links that connect the individual monomers. 

  6. Identify hydrogen bond donors (δ+ Hs) and acceptors (lone pairs on δ- Os and Ns) on proteins.

  7. Describe the properties of the main chains and side chain amino acids of a protein given their structure.

  8. Describe substructures within a protein including alpha helices and beta sheets.

  9. Describe how a protein can be chemically cleaved by water to form individual, separated amino acids.

  10. Describe the structure and properties of double stranded DNA including the backbone, double helix, bases, base pairs, and major and minor groves.

  11. Describe the differences in structure between DNA and RNA. 

  12. Describe the flow of information in the Central Dogma of Biology.

  13. Explain the differences between DNA replication, DNA transcription, and RNA translation.

  14. Given a dsDNA structure, and which strand is the template strand, determine the amino acid sequence of the protein derived from transcription of the DNA using the genetic code.

  15. Define a gene.

  16. Predict the probable effect of a mutation in the DNA on the resulting protein's structure AND function for mutations that changed buried, surface, and surface-active site amino acids.

  17. Explain and use images to discuss how gene transcription is regulated.
  18. Describe structures involved in regulation of gene transcription including RNA polymerase, transcription factors, DNA major grove.
  19. Describe cell differentiation at the cell and DNA level.  (i.e.  describe typical changes in cell structure/function)
  20. Describe the process of signal transduction.
  21. Given diagrams, explain steps in signal transduction pathways that activate or inhibit specific cellular activities such as glycogen breakdown, gene transcription, etc.
  22. Describe the roles of kinases, phosphatases, and second messengers in signal transduction pathways.
  23. Describe the role of Na+/K+ ATPase and ungated K+ channels in establishing transmembrane ion gradients and membrane potentials in neurons.
  24. Describe the role of neurotransmitter-gated and voltage-gated (such as sodium and potassium) channels in nerve firing (action potential).
  25. Describe changes in transmembrane potentials and ion concentrations during an action potential.
  26. Describe the effects of stimulatory (ex: Glutamate channels) and inhibitory channels (ex: GABA) in neuron firing.
  27. Describe the effects of antianxiety agents (benzodiazepenes like valium) and ethanol on GABA channels, and the effects of benzodiazapene inhbitors (antagonists) like Ro-15-4513.
  28. Define tolerance, sensitization and dependence.
  29. Describe long term effects on gene transcription that affect addictive behaviors such as tolerance, sensitization, and dependence.