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

Gene expression can be regulated at several steps. Describe one example for each of the following: 1) regulation of transcription 2) regulation of RNA processing 3) regulation of RNA stability in the nucleus 4) regulation of the initiation of translation 5) regulation of the elongation of translation 6) post-transcriptional modification 7,8) What are the three main ways in which a transcription factor increases the rate of transcription of a target gene? 9) What are proteoglycans? Are they found in the mitochondria, nucleus, cytoplasm, all three, or somewhere else? 10) What is the cause of Gaucher disease? 11) What is the function of filopodia? 12) What are the inclusion bodies in I-cell disease? 13) Where in a cell do tyrosine kinase receptors get synthesized? 14) What has to happen to mitochondrial proteins after they get transported into the mitochondria? What proteins do the job? 15) What part of the cytoskeleton helps macrophages crawl out of your bloodstream and crawl into tissues that are infected? 16) What part of the cytoskeleton helps macrophages change shape to engulf bacteria that are infecting you?

17) There are three STOP codons in the Genetic Code. How many tRNAs are there that bind to STOP codons? 18) What microtubule motor helps move secretory vesicles toward the cell membrane? 19) What happens in the E site of ribosomes? 20) Where does phosphatidylserine get synthesized? 21) What happens if phosphatidylserine is on the outside of a cell? 22) What is meant by, “The ribosome is a ribozyme”? 23) What is the function of snRNPs? 24) Mature, unfertilized eggs of many species have mRNAs for several genes but the proteins haven’t been made yet. What is preventing their synthesis? 25) What is the first amino acid to be added during synthesis of almost all eukaryotic proteins? 26) Describe one way in which nutrition regulates growth by affecting ribosome translation. 27) How does a cell know secreted proteins should be synthesized by the rough ER? 28) How does a cell know transcription factors should be imported into the nucleus? 29) How do most proteins get tagged and targeted for degradation? 30) What are two things that could happen if there are a lot of unfolded proteins in the rough ER? 31) What is the function of the proteasome?

32) Which RNA polymerase (I, II, or III) transcribes genes that code for proteins? 33) Where does the heterochromatin tend to be located within the nucleus? 34) Why is the proximal promoter sometimes called the basal promoter? 35) What is the function of clathrin? 36) What are two ways that transcription is similar in prokaryotes and eukaryotes? 37) Why is the response element for the estrogen receptor sometimes drawn as two arrows pointing in opposite directions? 38) If you had an antibody that could bind specifically to the estrogen receptor, what method would you use to identify all the genes to which the estrogen receptor binds? 39) Is the zinc finger of estrogen receptors part of the DNA binding domain, the ligand-binding domain, or the transcription-activating domain? 40) How does the estrogen receptor repress transcription? 41) During DNA methylation, which of the four nucleotides gets modified? How does that affect gene expression? 42) How do Polycomb proteins affect gene expression? Secondly, do they increase or decrease gene expression? 43) What are prions? 44) What are proteins called that can help move phospholipids across a membrane in either direction?

45) What is the function of desmosomes for the cytoskeleton and tissues? 46) Describe how Heat Shock Transcription Factor gets activated. 47) Where within the nucleus are ribosomal RNAs transcribed? 48) What is the main way the estrogen receptor undergoes post-translational regulation? 49) Glycosylation is not a post-translational modification that occurs for the estrogen receptor. Explain why not. 50) What is the function of the mannose-6 phosphate receptor?