Old EXAM 1 BIO409/509 NAME. Please number your answers and write them on the attached, lined paper.

Transcription

1 Old EXAM 1 BIO409/509 NAME Please number your answers and write them on the attached, lined paper.

2 1) Describe euchromatin and heterochromatin. Which form of chromatin would the insulin gene be found in the pancreas and which form in the brain? 2) What is typically formed when the side chains of cysteine amino acids get oxidized? 3) What is genomic equivalence? 4) Why is hemoglobin protein made in the bone marrow and not in the brain? 5) What is endocrine signaling and what is paracrine signaling and give an example of each. 6) Describe two examples of nuclear receptors. 7) What is a kinase? 8) Describe the JAK/Stat signal transduction pathway. 9) Describe where the Estrogen Receptor protein is located in a target cell and why it is located there. 10) Describe the coregulator transcription factors that bind to the Estrogen Receptor protein to help it repress or activate target gene expression. 11) What activates the CREB protein? What type of protein is CREB? 12) Describe one example of a monomeric G protein. 13) Nuclear receptor proteins like the Estrogen Receptor have three functional domains. What are the functions of the three protein domains? 14) Describe the main way that a G protein-coupled receptor pathway gets turned off after it has been activated?

3 15) Describe one example of the signal transduction steps leading from activation of a tyrosine kinase receptor to activation of a transcription factor. 16) In class, the field of biology was described as being composed of what three legs? 17) What is a bacteriophage? Describe one reason molecular biologists have studied bacteriophage. 18) What are orthologs? Describe an example. 19) Describe the DNA changes you would make in order to cause jellyfish Green Fluorescent Protein (GFP) to be made in the red blood cells of a mouse. 20) If you wanted the transgenic mouse created in the previous question to have all the normal genes plus your new GFP transgene should you design the gene to be inserted into the chromosome by homologous or nonhomologous recombination? Why? 21) Describe the two most important differences between cancer cells and normal cells growing in cell cultures. 22) Draw the tripeptide: Leucine Hydroxyproline - Cysteine 23,24) Next label the following on your drawing: one peptide bond amino terminus carboxy terminus a hydrophobic side chain 25) What is Western blotting used for? Also, briefly describe how is it done. 26) Which of the following signaling molecules can diffuse across the cell membrane? glucocorticoid, nitric oxide (NO), a peptide, and a neurotransmitter

4 27) What does a Ramachandran plot depict? 28) What organisms replicate their DNA by semiconservative replication? 29,30) Label the following with TU if it is part of the transcription unit, or a P if it is part of the promoter or an N if it is part of neither coding region enhancer coregulator intron response element hormone-binding domain 31) If the human genome were magnified so it stretched all the way from Portland, ME, to Los Angeles, CA, about how tall would each nucleotide be? (Don t calculate this, just estimate). 32) If a cell were magnified so it was as big as the Boston metropolitan area, estimate the size of a hemoglobin protein? Estimate the size of a water molecule? 33) Some examples in Chapter 16 Cell Signaling involve ubiquitination. What happens when a protein gets ubiquitinated? 34) What is RNAi? 35) What are the two main reasons RNAi is studied? 36) What is X-ray crystallography used to study? 37) What effect do enzymes have on the activation energy of a chemical reaction? 38) Describe three methods how scientists get purified DNA back into a living cell.

5 39) Describe how one of the following activates a transcription factor: Notch, Wnt, TNF, or TGF-β. 40) Why do scientists create cosmids, bacterial artificial chromosomes, yeast artificial chromosomes, etc.? 41) What is Next-generation (Next-gen) sequencing? 42) Is super resolution microscopy an example of electron microscopy, fluorescence microscopy, or light microscopy? 43) The theory of endosymbiosis refers to what parts of a cell? 44) All the forms of centrifugation described in our textbook have the same purpose. What is that? 45) What is DNA ligase? 46) What does the Fluid Mosaic model describe? 47) Put the following in the correct order: 1) primary transcript 2) translation 3) nuclear export 4) RNA processing 48) Why would deletion of three nucleotides in the coding region of a gene probably be less of a problem than deletion of two nucleotides? 49) What are SH2 domains used for? 50) When does reverse transcription occur?

6 32) Give two examples of how gene expression can be affected by post-translational modification.