OCR Preliminary Exam 3 Review PDF

PRELIMINARY Exam 3 Review Instructions and Concepts: All information covered during lecture/lab (both written in the slides, in the additional notes, and verbally), and in the assigned readings and homeworks may be included on this exam. Concepts list may be updated next days prior to the exam....

PRELIMINARY Exam 3 Review Instructions and Concepts: All information covered during lecture/lab (both written in the slides, in the additional notes, and verbally), and in the assigned readings and homeworks may be included on this exam. Concepts list may be updated next days prior to the exam. Make sure to be familiar with all the vocabulary as used in lecture and throughout the book (bolded/italicized terminology in textbooks). It may also be helpful to become familiar with the Learning Objectives, the Assess yourself and the Smart-grid questions within the reading assignments, as well as the reading topics (Connect), including the post-lab practice questions, and the Connect homework questions. Focus on the concepts allowing you to solve these questions, not the answers to each specific individual question as the questions are not directly re- used, but at least 7 and 15 questions on the exam will be directly based on the relevant concept questions for the chapters covered. The exam may only be taken during the scheduled open period at the start of our scheduled class period on campus in the room assigned. The exam is not scheduled to take the entire class period and we will continue with lecture/lab material after the open period has ended. You must be on time as exams will be collected at the end of the scheduled exam period. I encourage you to arrive early to find the correct room so you can begin reviewing the instructions and start the exam by no later than 5 minutes after our class start time to ensure you get your full time limit. Late arrivals cannot be awarded more time to complete the exam so arrive in a timely fashion. Exam timing and format are designed to mimic standardized tests. There will be approximately 45-55 questions depending on the exact mix of types, and there may be a mix of the following: multiple choice, select all that apply multiple choice, fill-ins, matching, and short answers. Try to budget your time wisely to ensure you have time to complete all the questions within your time limit. Professor Note: There will always be at least one question from each concept on the review, but for all the concepts on the review to be included in the test that means there will generally be only 1-4 questions for each review topic and/or textbook section. Make sure you are spreading your study efforts out and not focusing too heavily on only 1 or 2. ~~~~~~~~~~~~~~~~~~~~~~~~~~ LAB RELATED – Lab Related (Textbook Ch 3.2) - Be familiar with the purpose, background reading and information, procedures, and interpreting results for each of the exercises we covered in this unit. Review the textbook sections that refer to microscopy & staining, including the vocabulary & purposes, as well as reviewing the background information for each of the following experiments. Reminders for Microscopy: Focus on the definitions and specific types we used/mentioned in class, know the different types and examples from the book (light microscope vs. phase contrast vs. electron, etc). Know how to perform the exercises below using microscopes to view results (remember you view individual cells on microscope slides, what terms do you use to describe cellular shapes?), the purpose of each exercise, and how to interpret the results. Lab Exercises: 1 and 8 review, 11 and 13 NEW: (background information, procedures and interpreting results. These exercise numbers are based on our assigned manual, adjust if you are using an older or alternative manual). a) Know the part names, functions, and use of microscopes. I. Review the terminology for microscopy (resolution, magnification, contrast, etc.) and what needs to be done to maximize each (staining for contrast,  adjusting wavelength of light, adding oil, changing to electron microscope for resolution, changing lens for magnification, etc.) II. Recall how to prepare specimen for viewing: wet mount and smear a. Know what you can see for a wet mount (motility) vs. a smear (better for staining) III. What does heat fixing do? How is it accomplished? What happens to your cells if you heat-fix too long or too short? IV. What will happen if your smear is too thick? What objectives are used to view bacterial smears and what total magnification are they viewed at? b) Dyes (stains): Know the definitions for the different kinds and how they work (negative vs. direct) and the procedure and what the general steps/effects are for the staining procedures a. What is the goal of each individual staining technique? What dyes are used in each technique? b. What are example dyes that we covered (in class, in practice, and in the reading)? c. What are the properties of each stains (aka what are direct stains vs. negative stains?) d. What are the examples of results (different cellular shapes and arrangements) you see after staining and what is each called in scientific classification? Is there different terms for these shapes in bacteria vs. eukaryotes? (examples coccus vs. yeast) e. MAIN FOCUS: What are the differences in the procedures? (simple vs. differential procedures) Which did you practice in lab AND the simulations? (at least one question will be asked about each procedure) i. What are the steps and dye(s) used in a simple stain procedure: Do the color(s) mean anything with a simple stain procedure? ii. What steps and dye(s) used for Gram-stain procedure? Do the color(s) means anything in this procedure? iii. What steps and dye(s) used for endospore (Schaeffer-Fulton) stain procedure? Do the color(s) means anything in this procedure? iv. What are the properties of all of these stains (aka what are direct stains vs. negative stains?) 1. Notice that certain dyes (safranin) are used in multiple techniques, because of this the color it gives cells (pink/red) can mean different things depending on what procedure you following (simple vs. gram staining vs. Schaeffer-Fulton (endospore) staining v. Know the common errors that can happen (excessive de-colorization during Gram stain would lead to what? Failure to decolorize? What is gram-variability? Failure to completely cool endospore stain will cause what? Relevant Chapter 3 Concept Check questions: What is the importance of contrast? How is contrast adjusted? Describe the difference between simple and differential stain.  What is the purpose of the Gram stain? How will the results appear if an error is made at each step of the gram-stain? What is the purpose of the endospore stain? How will the results appear if an error is made at each step of the endospore stain? Chapter 13: Host Microbe Relationship: a) Recall the definitions and give examples of the terms (host, vector, parasitism, mutualism, commensalism, pathogen, microbiota, disease, infection, colonization, resident, source, reservoir etc.) and be familiar with notable scientists and examples throughout the chapter and lecture and the Concept Check questions. b) How do we acquire microbiota and what are common areas in the body where such can be found? o Know examples of genera (and species mentioned in class) which colonize each body system when healthy, and how the different body regions vary in environmental conditions. What part did the Human Microbiome Project play in determining this? c) Pathogenicity (we termed this virulence). Connect with terms like colonization, virulence genes, Infectious Dose (ID) etc. o Know that influence disease outcome – microbial and host factors that affect if a microbe will cause disease d) Know the 5 steps to establishing an infection, what happens at each, and factors that contribute (know the figure very well) o Portals of entry / exit o Adherence Methods o Ways microbes overcome host defenses e) Remember the enzymes and toxins expressed and their role in pathogenicity and disease progression o Know examples mentioned in class, what is and endotoxin, and exotoxin. What is a toxoid, which does it work on? f) Kinds of diseases and examples of infection patterns – examples include focal, local, systemic, chronic, latent, etc. g) What are the stages of clinical infection? o What are the modes of transmission and how do you prevent the transmission of infectious diseases h) What is Etiology? How do Koch’s Postulates relate? Relevant Chapter 13 Concept Check question: A condition in which pathogenic microorganisms penetrate host defenses, enter the tissues, and multiply is a(n) Blank. The Human Blank Project collects genetic sequences of microbes from many body sites.  True/False: The lungs are sterile sites. True/False: Your gut biota can determine your mood and mental health. List and describe three factors that weaken host defenses and increase susceptibility to infection. True/False: Babies born by cesarean section are colonized by the same biota as babies born vaginally. True/False: If a virus causing a respiratory disease is ingested, it will not cause disease. The minimum number of microbes required to cause a disease is the Blank. Bacterial Blank are toxic to the host in minute amounts. A(n) Blank is objective evidence of disease. During the period of Blank, a pathogen exhibits its greatest virulence. Chapter 14: Epidemiology : Focus heavily on the sections related to topics covered during lecture a) Epidemiology: define and recall terms – give examples of case study o Know the historical figures mentioned in class o What are the patterns of infectious diseases in populations? o Define various kinds of epidemics, what do the terms surveillance, index case, prevalence, incidence, morbidity, mortality, etc. mean. b) Publications and Healthcare Organizations examples o What are notifiable diseases? Why are some notifiable and others not? o What are healthcare associated infections? o What is herd immunity? c) What is Bioterrorism? Agroterrorism? Consider how these scientists/doctors relate to the topics in this section (refer back to the Unit 1 lecture powerpoint and chapter readings if need be): Dr. Oliver Holmes, Dr. Ignatz Semmelweis, Dr. Joseph Lister, Rober Koch, John Snow, etc. Are there any other scientists of note involved in asepsis/antisepsis or etiology/epidemiology Relevant Chapter 14 Concept Check question: The science that studies health events among populations of people is blank. What five questions are epidemiologists trained to think about? True/False: Florence Nightingale hypothesized that the water coming from a specific pump harbored the cholera bacterium. The number of new cases of disease over a certain time period is the blank. The blank rate is the number of persons afflicted with infectious disease.  A(n) blank disease is seen at a steady frequency over a long period of time in a particular location. A(n) blank is an epidemic occurring over multiple continents. True/False: The rates of occurrence, mortality, morbidity and transmission of infections are associated with disease surveillance. Describe healthcare-associated infections. blank diseases are caused by newly identified microbes. Chapter 8 and 18.5-6: Genetic Engineering and Tools Utilizing Techniques a. What are the purposes of bioengineering? What are examples of how it is used in modern times? Review the 3 types of Horizontal Gene Transfer (transformation, transduction, conjugation) and the details of each, especially how they can be used for genetic engineering. b. Understand the tools and techniques used in genetic engineering. Recall restriction enzymes, cloning vectors (what are the ideal characteristics, examples like plasmids, etc.) and other terms used. c. Familiarize yourself with the methods and products of genetic engineering and recombinant DNA technology. Familiarize yourself with the methods and outcomes of gene amplification, genetic fusion, protoplast fusion, hybridomas, Transgenic/GMOs, synthetic biology, etc d. What are the techniques and methods of recombinant DNA technology? Procedures for hybridization tests, PCR, gel electrophoresis, etc. What is DNA profiling? How is it accomplished (steps) How is DNA sequencing accomplished? What are the tools and steps? What are hybridization tests? What are the steps and purpose of Southern Blot? FISH? e. Understand the processes of gene therapy. What types of gene therapy exist? What are the drawbacks and advantages? What are other ways that genetic engineering or tools created from its techniques are used in medicine? f. Familiarize yourself with the methods of genome analysis, including maps, profiles, and screening. Know the basics of transcriptomics and proteomics and the methods mentioned in class and the book. What is a DNA microarray, how is it made and used? What are chips? How are genetic engineering tools used in diagnosis and genotypic identification techniques? Be familiar with the “Assess yourself” questions, the homework questions, the end of chapter practice questions from the online book. Relevant Chapter 8 Concept Check questions: Describe two scenarios in which genetic information can be manipulated in order to accomplish goals to benefit human beings. DNA can be cut into smaller pieces by using enzymes called blank. cDNA is produced using the enzyme blank. True/False: PCR uses specialized DNA polymerase adapted to high temperatures.  Microbial DNA and RNA can be rapidly amplified using the blank blank blank. Fluorescently labeled probes are used in blank techniques. The F I S H method of analysis of blank from patient or environmental samples can identify an organism without culturing it. List and describe two cloning vectors and two cloning hosts. Describe the steps involved in whole-genome shotgun sequencing. Blank genomes provide a complete understanding of cell function, disease development, and other issues. DNA profiling depends on blank enzymes. A(n) blank allows scientists to view gene expression in any given cell. List and describe three products produced through recombinant DNA technology. Recombinant organisms produced through the introduction of foreign genes are known as blank. Blank therapy describes gene therapy introduced to an egg, sperm, or embryo. True/False: Naked DNA is often used in gene therapy. True/False: C R I S P R-Cas9 system naturally occurs in bacteria. True/False: Using current technologies, diagnosis of septicemia takes at least 18–24 hr. MALDI-TOF uses blank blank to analyze protein fingerprints from pure culture isolates. Chapter 9: Growth and Nutrition a) Know how nutrients and water enter a cell. Practice the appropriate terminology and be able to connect these concepts to the media from the lab where appropriate. a. Differences between active and passive transport, different kinds of each b. Know the differences and similarities between osmosis and diffusion, what happens to cells under osmotic pressure? Know what happens under isotonic, hypotonic, and hypertonic conditions (and what each term means about the environment compared to the cells) c. Transport proteins: differences between channels and porins vs. permeases and pumps b) Where do organisms obtain their energy, carbon, electrons, and other nutrients? a. KNOW the appropriate terminology for each type! b. Understand how the elements cycle in the environment and what forms most microbes obtain them as c) What factors affect bacterial growth? Know special terms that describe microbes adapted to those conditions. a. Physical factors i. Temperature types (5 terms + stenothermal and eurythermal) ii. Oxygen usage (terms, enzymes used to deal with ROS) iii. 3 other physical factors microbes encounter in the environment iv. Biofilms, 5 terms for microbial associations  b. Chemical factors i. Nutrients, toxins, water, etc. d) Understand bacterial growth and the relevant terms. What is cell division? How do you define growth in bacteria. a. How does binary fission happen (steps) in bacteria and how is it different from budding? From mitosis? e) What are the phases of bacterial growth? a. What methods did we discuss in class for measuring bacterial growth? What are the drawbacks/advantages to each b. Know how to calculate bacterial growth rate, generation time, number of generations, etc. You may bring a scientific calculator to the exam, but you may not use your phone calculator. Practice questions are located in the Student Outline. f) How do microorganisms cope with diminished nutritional supply or any other harsh environmental conditions? (recall endospores) a. What method could you use to prevent cells from dying/entering death phase? Or forming endospores? Be familiar with the “Assess yourself” questions, the homework questions, the end of chapter practice questions from the online book. Relevant Chapter 9 Concept Check questions: Compare and contrast macronutrients and micronutrients. A(n) blank requires organic molecules for carbon and energy. True/False: Water requires a specialized membrane protein in order to enter or exit a cell. A(n) blank environment has a higher concentration of solutes outside the cell than inside the cell. Pathogenic microbes have an optimum growth temperature in the blank range. A(n) blank anaerobe can grow in the presence of oxygen but does not require it. Obligate blank inhabit the Dead Sea. In a(n) blank relationship, one member benefits and the other is harmed in some way. True/False: The average generation time of most bacteria under optimum conditions is 24–48 hr. Place the four steps of the growth curve in the proper order: a. Log phase b. Death phase c. Lag phase d. Stationary phase  e. A(n) blank can differentiate between live and dead cells. Additional Supplemental Study Materials Relevant Learning Outcome c) H.Cowan and McGraw Hill (also recommended are the “Assess Yourself” questions at the end of each textbook section, the associated homeworks, and the end of Chapter Resources, including the SmartGrid questions). Chapter 3: Chapter 13 Chapter 14 (limited) Chapter 8 + 18: Chapter 9: