DISCLAIMER: REVIEW / STUDY GUIDE Bioethics (BME80G) midterm, Fall 2010 Science part only (no ethics, sorry) Made by Andrew Uzilov This review has not been seen or approved by the professors (Jake or Mark). This is just one TA s opinion of what material seems fair to have on the exam. I have not seen the exam, so this is just a guess based on prior experience. I give no guarantee that this covers everything that will be on the exams. That said, if you know most of the material in this guide, you should be in great shape for the test! HOW TO USE: Know the definition of each term used in this review sheet! Also be able to say, briefly, why it is important. The material is roughly organized by chronological order of lectures in which it was presented. Each category usually corresponds to a lecture a PDF. Sometimes two lectures are consolidated into one category. INTRO LECTURE Evidence for Mark s pet peeves: multitasking smoking Factors that affected life expectancy during the 20 th century: 1917 influenza pandemic World Wars Major advancements in technology during the 20 th century: penicillin insulin to treat diabetes heart-lung machines kidney dialysis smallpox eradication through vaccination 1
INTRO TO MOLECULAR BIO Molecular biology overview The Central Dogma of molecular biology: DNA replicates to DNA DNA transcribed to RNA RNA translated to protein The 5 universal features of life on Earth. DNA What are the building blocks of DNA? How does it replicate? Where in the cell is it stored? What is the relationship between DNA and chromosomes? Different cell types: red/white blood cells, neurons, rod cells in retina Other terms to know: zygote, plasma membrane, replisome, RNA (specifically, mrna), cytosol, polymerase (both DNA and RNA), splicing, ribosome Diabetes and gene cloning Only need to know Type 1 diabetes: In Type 1 diabetes patients, what is the body failing to do? What is insulin? Where is it made? What does it do? Know Mark s ethical argument for cloning insulin into yeast or bacteria. The 8 (maybe 9?) steps for cloning an insulin gene into yeast or bacteria: 1. Find human DNA that codes for insulin protein. a. What are some ways in which this can be done? 2. Isolate mrna. a. Why mrna? Why not just use genomic DNA directly? 3. Copy insulin mrna into cdna using reverse transcriptase (RT). a. Why do we need cdna? Why not use mrna? b. What is a primer? What do they allow us to do? 4. Use the polymerase chain reaction (PCR) to make lots of copies of insulin cdna. a. What is PCR? What does it do? How (in general terms) does it work? 5. Insert insulin cdna into an expression vector (plasmid). a. What s on the plasmid that wasn t on the cdna? Hints: What s on the plasmid that allows the expression of the cdna? What s on the plasmid that allows selection in Step 7? 6. Insert (transform) plasmid into a yeast or bacterium cell. 2
7. Select for successfully transformed cells by growing on an antibiotic (for example, ampicillin). a. Why is this step done? Why not just grow all the cells? 8. Grow many cells to make proinsulin protein. 9. Modify proinsulin to insulin and purify. (This step isn t really part of cloning, just part of commercial insulin production.) GENETICS AND GENOMICS Terms: allele What is cancer? How does it arise? What mutations, and how many of them, lead to cancer? (This is a trick question.) Huntington s Disease (aka chorea, disorder) autosomal dominant CAG repeats in Huntingtin protein. What are they? What does the repeat count tell us? If you have it, what is the likelihood your parent will have it? If your parent has it, what is the likelihood you will have it? Cystic fibrosis autosomal recessive If both of your parents are carriers, what is the likelihood you will have it? What if only one parent is a carrier? What if one parent is a carrier and one has the disease? Understand this chart and every term in it! What do you do with resulting blastocyst? Implant in mother s uterus Destroy to culture pluripotent stem cells How is the zygote made in vitro? Donor sperm fertilizes a donor egg in vitro fertilization (IFV) Embryonic stem cells Nucleus from somatic cell inserted into donor egg (also called SCNT) Reproductive cloning Therapeutic cloning 3
DAVID HAUSSLER LECTURE What is cancer genomics? What is the point of this area of study? (Specifically, think about: Why do genomics on cancerous tissue? What does that tell us when compared with normal tissue?) o Look for what mutations lead to different cancer types and in what order they occur. o Finding different cancer sub-types that would look the same by histology. o Ultimate goal is custom diagnosis and treatment based on DNA of your cancer tissue. What is a pathway? Why is the pathway context so important? o Drug is like a temporary mutation idea. What is the Personal Genome Project? Terms: apoptosis, single nucleotide polymorphisms (SNPs) RICHARD (ED) GREEN LECTURE Terms: purifying versus positive selection, phylogeny, coalescence, mitochondrial versus nuclear DNA, admixture Why is mitochondrial DNA particularly useful for phylogeny? Always inherited from the mother Doesn t undergo recombination o Related question: why does recombination make using nuclear DNA for phylogeny more difficult? Other take-home points: There is some evidence of (very small) admixture between human and Neandertal during the out-of-africa migration. Result is no Neandertal DNA in Africans, but some in French, Chinese, Papua New Guinea. RUNX2 gene variant in Neandertal causes Cleidocranial dysplasia disorder in humans. Why is this important? CLINICAL TRIALS The most important thing is to know and understand the steps that it takes to bring a drug (or medical treatment) to market: Identify drug molecule Cell culture studies Animal studies Clinical trials on humans (know the difference between these!) o Phase 1 o Phase 2 o Phase 3 4
Examples of clinical trials: At which stage did IRESSA (Gefitinib) drug fail? Despite its failure, was there any success with the drug? Beta carotene trial how well did it work for lung cancer? Was the trial completed? Gleevec for Chronic Myelogenous Leukemia (CML) did it work? HIV / AIDS What are the non-hiv theories about what causes AIDS? How can each of these theories be ruled out? (Hint: most of these were ruled out when AIDS discovered in hemophiliacs, newborns.) o Early theories: Autoimmune reaction to foreign sperm antigens Amyl nitrite (inhalant) Cytomegalovirus (CMV) infection 1/3 of human population has it o Duesberg theories: Amyl nitrite (inhalant) AZT anti-hiv drugs Factor VIII used for hemophilia treatment HIV drugs and their targets o AZT (targets reverse transcriptase) o Protease inhibitors (target protease) Why is it so hard to design drugs and vaccines against HIV? Which HIV enzyme is to blame? What is HAART? What is Koch s Postulate? Why has it not been satisfied for HIV? DNA FORENSICS and CRIMINAL JUSTICE Know the reasons why false convictions and confessions tend to occur, for example Fritz & Williamson case Frank Sterling case and the Reid technique/method Know the key concepts used in DNA forensics What do the DNA forensics tests specifically tell us? Chain of custody: What is it? Why is it important? How the tests are done: o Short tandem repeats (STRs) whose length is the fingerprints o PCR to selectively amplify the STR-containing regions o Resulting DNA is separated on a gel be able to read these gels! o Why are they so accurate? 5
What is monoamine oxidase A (MAO-A)? What is the Warrior Gene? (Hint: They re not necessarily the same thing.) What is the Warrior Gene linked to and in which circumstances? STEM CELLS (CAMILLA FORSBERG LECTURE, also see Mark s intro lecture) What defines a stem cell? Self-renewal Differentiation What is the third criterion that makes a stem cell an embryonic stem cell? Types of stem cells: totipotent stem cells pluripotent stem cells o embryonic stem cells (ESC) o induced pluripotent stem cells (ips) adult stem cells For each of the above types, know their: Source Lineage potential in vivo self-renewal ability in vitro self-renewal ability function Stages of fetus development: Fertilization to form zygote First cleavage, other cell divisions Blastocyst formation o What is it and why is it important for embryonic stem cells? o How big is it? (about 100 cells) o When does it form? Is that before or after implantation? o What is it made of? (placental cells and inner cell mass) Implantation, resulting in pregnancy Therapeutic uses: Why do stem cells have so much potential for therapy? What are the pros/cons of using: o ESCs for therapy? o Adult stem cells for therapy? o ips cells for therapy? Understand the point of bone marrow (hematopoetic stem cell (HSC)) transplants and the main steps/challenges: Collecting enough HSCs 6
Getting the cells into the bone marrow of the recipient o Recipient BM already occupied; can t get more cells in o How to put the donor cells specifically into the bone marrow? Can ips presently replace ESCs for: research therapy and why (or why not)? Other terms: oocyte, factor, in vitro versus in vivo OTHER RANDOM STUFF What s the difference between whole genome sequencing and genetic testing? Whe a company like 23andMe or Navigenics analyze your genome, which one are they actually doing? USEFUL RESOURCES You will not be tested on material from these specifically, but it will really help you understand lecture material on a much deeper level. So, try to explore even a fraction of these: Watch the HHMI videos mentioned in Mark s lectures. You don t have to absorb the technical details the most important this is that you understand the general meaning of each process. The Personal Genome Project study guide at http://www.pgpstudy.org/ 7