MB 230 Lecture Notes Updated Dr. Kenton Hokanson. Introductory Microbiology. Syllabus and Guided Lecture Notes. MB 230 Winter 2018

Transcription

1 Introductory Microbiology Syllabus and Guided Lecture Notes MB 230 Winter 2018 Lecture: LINC 200 Lab: Nash 304 Instructor: Kenton Hokanson, Ph.D. Copyright 2017 Oregon State University

2 Course Syllabus Instructor: Kenton Hokanson, Ph.D. Office: Nash Hall, room 323 Office Hours: by appointment Lecture: MB (CRN#30351) MWF LINC 200 Lab Sections: MB (CRN#30352) W 10:00am-11:50am Nash 304 MB (CRN#31066) F 12:00pm-1350pm Nash 304 Lab Instructor: Jesse Coutu (coutuj@oregonstate.edu) Course Outcomes: Microbes are an amazingly diverse and important group of organisms! This a four-credit course with no prerequisites will allow you to explore these fascinating, useful, and sometimes harmful organisms. MB 230 meets requirements for OSU Perspectives Biological Sciences Baccalaureate Core (Bacc Core) course credit. This course emphasizes the interrelationships between the microbial world and topics including human health, antibiotics and vaccines, industry, agriculture, genetic engineering, food production and global nutrient cycles. Students will be challenged to critically assess relevant topics at the intersection of microbiology and their daily lives. Scientific theories, including Cell Theory, Germ Theory of Infectious Disease, and Gene Theory of Inheritance are discussed. OSU Perspectives Biological Sciences Learning Outcomes: 1. Recognize and apply concepts and theories of basic physical or biological sciences. 2. Apply scientific methodology and demonstrate the ability to draw conclusions based on observation, analysis and synthesis. 3. Demonstrate connections with other subject areas. Lecture Outcomes: 1. Be able to define, identify and use the technical terms, keywords and concepts characteristic of basic microbiology. 2. Be able to distinguish between different groups of microorganisms and their unique characteristics. 3. Recognize specific pathogenic microorganisms and their relationship to human disease. 4. Evaluate and select appropriate ways by which to control or eliminate microorganisms in specific environments. 5. Explain both direct and indirect microbial impacts on human life, including economic, environmental and health impacts. 6. Apply basic microbiological knowledge to everyday interactions with microorganisms. Laboratory Outcomes: 1. Demonstrate competence in the use of a light microscope to visualize microorganisms. 2. Demonstrate competence in performing basic microbiological techniques, including: a. Preparation of bacterial smears b. Gram staining c. Use of aseptic technique d. Streak plate inoculation e. Bacteriophage plaque assay 3. Evaluate the application of Koch s postulates in demonstrating a microorganism/disease correlation. 4. Record, interpret and evaluate observations made in the laboratory

3 My pledge to you: I am here to help you learn about the microbiology and to assist you in developing the skills that you need to succeed as an informed person who will be armed with a collegiate-level general scientific background in microbiology upon completion of this course. My goal is to develop your technical understanding, as well as your critical thinking and laboratory skills. In the end, you are ultimately responsible for your own learning. I will do my best to facilitate your learning, answer your questions, show you how to improve your own learning, and help you develop the kinds of critical thinking skills that you will need in future jobs, regardless of your chosen major. I am here to foster an inclusive learning environment for everyone enrolled in the course, and I will do everything within my power to achieve that objective! If you succeed, then I succeed we re in this together! However, I can only do this if we have two-way communication. One feature of a large class such as this is that I cannot evaluate everyone s detailed level of understanding easily. Your mission, should you choose to accept it, is to ask me if you have questions or require clarification. I will strive to create an atmosphere in which we can have constructive dialogue through interactions in the classroom, discussions during office hours, discourse on the Canvas discussion board assignments, and through your homework assignments. I will do my best to be clear in my communications of my expectations. Each of you can help by asking questions when you have them. Do not hesitate to ask a second time if my first answer is either not clear or needs additional explanation. This requires you to recognize when my explanations are insufficient and ask for clarification. I will happily try again until I express a concept in a way that is understandable for you. Communication: Outside of class, the two best ways to communicate with me are through Canvas and . General questions about the syllabus, assignments, due dates, terminology or lecture content, or any other aspects of the class that are likely to interest other students should be directed to the General Discussion Board on Canvas. Do you have a question about a lecture concept or something in the reading? Are the assignment instructions confusing? Would you like additional explanation about a particular task? If the answer is yes, please post your course-related questions in the General Discussion Board so the entire class may benefit from our conversation. Additionally, if you feel you can answer another student's question on the general discussion board, please do! I will check the Canvas General Discussion Board daily on weekdays, but perhaps only occasionally on weekend days. Please contact me directly ( , Canvas Inbox message, or you can leave a comment on an assignment directly in Canvas) for specific questions about feedback on your assignments specifically or matters of a personal nature that do not concern the entire class. In general, I prefer to Canvas because I can more easily provide links and attachments via . Correspondence with any of your instructors (lecture or lab) is considered an extension of participation, so please remember that a professional tone and proper grammar and punctuation are required. I will make every effort to respond to s within one business day, but during high-volume periods expect delays up to two or three business days. Please start the subject of all classrelated s with: MB230: [Insert your subject here]. This allows me to easily identify class-related s so that I can attend to them quickly. correspondence with any of your instructors must be conducted through your ONID address or through the Canvas inbox (left-hand menu in Canvas). Use of Canvas: Canvas is the forum we will use for handing in homework and having discussions. I will also post the lecture slides and other material to Canvas after class. In addition, I will send important announcements about class via Canvas. Steps you should take at the beginning of the class include: i

4 Access Canvas at: Login using your ONID username. There are separate Canvas portals for the lecture and your lab section. Make sure you have access to both. Set up your Canvas notifications (instructions: so that you get class announcements as they are posted or at the end of the day. I recommend that you choose either the notify me right away or the send daily summary option for announcements. This ensures that you will get notifications about items related to class in a timely manner. If you have the send weekly summary selected, you may not get an announcement that I send until a week after I have sent it. Subscribe to the General Discussion Board (instructions: ) so that you will get notifications when other students post questions that might interest you. Again, I recommend setting your discussion post notification setting to either notify me right away or send daily summary. Note that you need to set your notification setting for discussion posts just like you did for the announcements in the step above. Expectations for Student Conduct: You are responsible for understanding Oregon State s Expectations for Student Conduct. You can view the full code of conduct at: 15_ pdf and you can view abbreviated information here: As a student at OSU, all of your classes require you to conduct yourself as described in these documents. I have listed a few items below about academic integrity. This is part (only one part) of the Student Conduct Code. All of you are adults. I expect everyone to be honest and forthright and to understand their responsibilities as an OSU student. I do not want to have to take this topic up with any of you, but I will not hesitate to do so if you are acting outside of the code of conduct. Academic Integrity: The following is a condensed version of the Student Conduct Code on Academic Dishonesty. Academic or Scholarly Dishonesty is defined as an act of deception in which a student seeks to claim credit for the work or effort of another person, or uses unauthorized materials or fabricated information in any academic work or research, either through the student's own efforts or the efforts of another. It includes: (A) CHEATING - use or attempted use of unauthorized materials, information or study aids, or an act of deceit by which a Student attempts to misrepresent mastery of academic effort or information. (B) FABRICATION - falsification or invention of any information including but not limited to falsifying research, inventing or exaggerating data, or listing incorrect or fictitious references. (C) ASSISTING - helping another commit an act of academic dishonesty. (D) TAMPERING - altering or interfering with evaluation instruments or documents. (E) PLAGIARISM - representing the words or ideas of another person or presenting someone else's words, ideas, artistry or data as one's own, or using one's own previously submitted work. Plagiarism includes but is not limited to copying another person's work (including unpublished material) without appropriate referencing, presenting someone else's opinions and theories as one's own, or working jointly on a project and then submitting it as one's own. ii

5 Course Materials and Resources Required materials are described in detail below and include: the course packet, one of the two Turning Technologies clickers described below, access to Canvas, and the textbook: Alcamo s Microbes and Society (4 th edition) Course Packet: The course packet can be purchased at the OSU Book Store or printed from Canvas. You must purchase the packet. This packet contains two important things: the lab manual for the laboratory portion of the class. You MUST bring the lab manual to the lab each session, including the first lab session. a skeleton outline of the lecture slides on which you can take notes (called the guided lecture notes). You should bring the guided lecture notes to each lecture. Guided lecture notes are designed to give you a framework on which to take notes. I provide these for the term to facilitate your ability to learn in the classroom and to help you develop active notetaking skills. The guided lecture notes do not contain all the material on the slides, so they are not a substitute for coming to lecture. In addition, based on class feedback or questions on the General Discussion Board in Canvas, I often adjust lectures to clarify material. You will receive the guided lecture notes for the entire term at the beginning of class, but I reserve the right to change the content of lectures as needed to assist in your learning. Turning Technologies ResponseCard NXT or QT: This is also known as a clicker. Clickers can be purchased at the OSU Bookstore. Reading quizzes and other in-class activities will be administered using clickers. After you purchase your clickers, you need to register your clicker. ( See below under Course Policies for additional information. Canvas (my.oregonstate.edu): Use of Canvas is required as described above. Textbook: The required text is Alcamo s Microbes and Society 4 th Edition. Jeffrey C. Pommerville; ISBN Alcamo s text is a somewhat casual text about how microbiology impacts our lives on a daily basis. This book will provide you with the necessary foundation in microbiology. You will be asked to do the reading prior to coming to class. This way, I can then use class time to clarify your questions. Optional book: Prescott s Microbiology 8 th Edition, Willey/Serwood/Woolverton; ISBN Prescott s is used by serious students of microbiology who desire a much deeper understanding of the material beyond the scope of MB 230. Generally, I feel this level of text is only required for those who will be undertaking microbiology as a major discipline, and it is not generally needed for this class. Grading: Midterms pts A % C % Final Exam pts A % C % Reading Quizzes pts B % D % Homework pts B % D % Discussion Boards pts B % D % Laboratory pts C % F % or lower Total pts iii

6 Midterms: The three midterms are worth 44 pts each and will be multiple choice format. The dates for the midterms are listed in the lecture schedule. If you miss an exam for any reason, you will need to take a make-up version of the exam in essay question format within one week of the regularly scheduled exam date. If the make-up exam is not taken within the given timeframe, you will receive a zero for the midterm. Any questions regarding grading of exams must be submitted in writing to the instructor for consideration within one week of the exam being returned to you (see below under Grades ). Final Exam: The final exam is worth 74 points and will be a comprehensive final. Approximately 44 points of the final will cover material from the third unit and the remaining 30 points will review material from the first and second units. The final exam is scheduled for Wednesday, March 21st at 2:00 pm. No accommodations for alternate final exam times or make up exams will be offered. Reading Quizzes: Points for in-lecture reading quizzes are earned using Turning Technologies, a personal response system. This is also used for other in-lecture activities. You are responsible for bringing a functioning device with them to earn participation points. No written responses are allowed. You may accumulate up to 40 points for reading quizzes. Reading quizzes will generally be given at the start of class, and they will cover the text material you were expected to read prior to coming to class that day. You must be present in class to take the reading quizzes. No make-up options for reading quizzes are available. There are 27 non-exam class sessions. You can earn 2 points per day for the reading quizzes, for a total of 40 points (2 points over 20 class sessions). If you take the reading quizzes on 25 days, I will take your highest 20 grades. If you take the reading quizzes on 20 days, I will use those 20 scores. If you take the reading quizzes on 18 days, you will score two zeros for sessions 19 and 20. This provides some built in flexibility regarding both lecture attendance and understanding of the material. Homework: There will be three homework assignments during the course, each worth 10 pts. 30 pts maximum are available for homework. Scores for late work will be reduced by 20% per day of the total homework score for that assignment. Homework instructions and grading rubrics will be available on Canvas. Discussion Boards: There will be four discussion board assignments during the term. Discussion board assignments will take place via Canvas to give you a chance to practice expressing your thoughts in writing. Detailed explanations of the scoring for the discussion boards will be provided in class and will be available on Canvas prior to the first discussion assignment. Scores for late work will be reduced by 20% per day of the total discussion board score. Discussion board instructions and grading rubrics will be available on Canvas. Laboratory: The laboratory portion is worth 100 pts of the total course points. See the lab manual for a detailed breakdown of the lab points. You cannot earn a passing grade in MB 230 if you do not pass the lab portion of the course. In addition, this course has a no-show-drop policy. This means that you will be dropped from this class if you do not attend the first lab session. All lab related questions should be directed to the lab instructors. iv

7 Extra Credit: Extra credit points (2 pts) are available if you complete BOTH a pre-assessment survey AND a postassessment survey. The pre-assessment survey will be available on Canvas during the first two days of the course. The post-assessment survey will be available after the last lecture session and until midnight on the day of our scheduled final. Extra credit points (0.5 pts) are also available when you state that you have read and understood the syllabus, which you can do via Canvas before the second class session. Students with Disabilities: Accommodations are collaborative efforts between students, faculty and Disability Access Services (DAS). Students with accommodations approved through DAS are responsible for contacting the faculty member in charge of the course prior to or during the first week of the term to discuss accommodations. Students who believe they are eligible for accommodations but who have not yet obtained approval through DAS should contact DAS immediately at (541) Diversity Statement: The College of Science strives to create an affirming climate for all students including underrepresented and marginalized individuals and groups. Diversity encompasses differences in age, color, ethnicity, national origin, gender, physical or mental ability, religion, socioeconomic background, veteran status, sexual orientation, and marginalized groups. We believe diversity is the synergy, connection, acceptance, and mutual learning fostered by the interaction of different human characteristics. Religious Holiday Statement: Oregon State University strives to respect all religious practices. If you have religious holidays that are in conflict with any of the requirements of this class, please see me immediately so that we can make alternative arrangements. v

8 Tentative Lecture and Assignment Schedule (Subject to change; announcements will be made in lecture and on Canvas) Week Day Date Lecture Number Topic Alcamo s Textbook Chapters Assignments: due before class (9am) on the day listed 1 M Jan 8 1 Course introduction/basics 1 W Jan 10 2 History of Microbiology 1-2 Pre-course survey; Discussion #1 post due F Jan 12 3 Genes/Information flow M Jan 15 Martin Luther King Day, no class W Jan 17 4 Growth 3-4, 9 Discussion #1 closed F Jan 19 5 Metabolism I 9 3 M Jan 22 6 Metabolism II 9 Homework #1 W Jan 24 Midterm 1 (Lectures 1-6) F Jan 26 7 Taxonomy 2 4 M Jan 29 8 Cell Structure 3-5 W Jan 31 9 Prokaryotic Microbes 5 Discussion #2 post due F Feb 2 10 Pro/Eukaryotic Microbes 5,7 5 M Feb 5 11 Eukaryotic Microbes 7 Discussion #2 closed W Feb 7 12 Fungi 8 F Feb 9 13 Acellular entities 6 Homework #2 6 M Feb 12 Midterm 2 (Lectures 7-13) W Feb Human Microbiota 17 F Feb Innate Immunity 17 7 M Feb Adaptive Immunity 17 W Feb Chemotherapy 11 Discussion # 3 post due F Feb Epidemiology 8 M Feb Pathogens (Viruses) 18 Discussion #3 post due W Feb Pathogens (Bacteria, 19 Homework #3 Eukaryotes) F Mar 2 Midterm 3 (Lectures 14-20) 9 M Mar 5 21 Global Nutrient cycles W Mar 7 22 Pollution/WWT 16 F Mar 9 23 Microbial Genetics 16 Discussion #4 post due 10 M Mar Industrial/Agricultural Microbiology 10, 14, 16 W Mar Food/Food Safety Discussion #4 closed F Mar Special Topics 11 M Mar Cumulative review for final exam Special Topics W Mar 21 Final Exam vi

9 Course Policies Electronics: Use of electronics in the classroom is prohibited, other than those used for course related activities. I may sometimes ask you to use an electronic device to look up something related to class, which is an approved use. If you are observed using cell phones, pagers, laptops, tablets, or any other device non-course related activities (texting, social media, , etc.) during class, you may be asked to leave the class and you will forfeit any reading quiz points you have earned that day. Clickers: The Turning Technologies clicker system is used for in-class reading quizzes as well as other in-class activities. It is your responsibility to ensure their clicker is in working order (this includes full batteries). Accommodations for broken or forgotten clickers will not be made. Anyone found operating more than one clicker during class will turn in both remotes to the instructor, and everyone involved will receive a zero for all points based on clicker responses. Grades: You are responsible for ensuring grades have been added and entered properly into the Canvas gradebook. Please check my manual entry of your grades. It is in your interest to make sure that your grade is accurately represented in Canvas. You have one (1) week from the time an assignment is handed back to you to contest a score. If a score is contested, I reserve the right to regrade the assignment in its entirety. Any grade adjustments made after the 1-week period are at my discretion. In order to contest a score on an answer, you should submit a request via . I may ask you to provide additional information as to your rationale or ask you to explain something before coming to a decision regarding your request. Alternative assignments to make up points lost elsewhere in the class will not be offered. Academic Integrity: In any situation of academic dishonesty, I will document the incident, permit the You to provide an explanation, advise you of possible penalties, and take action. I may impose any academic penalty up to and including an F grade in the course after consulting with the department chair and informing you of the action taken. See the above material under the Student Code of Conduct for additional information about academic integrity. If you ask for points at the end of the term, you will lose ALL extra credit points and any points that were added back to exams. Classroom Environment The University, and this laboratory, should be a safe and comfortable working environment for all students. The expectation is that no one should feel awkward, embarrassed, unwelcome, or uncomfortable engaging in classroom activities or discussions. Please be conscious of your own language and behavior it should be respectful to the other students and your instructors. If you are having any problems or need help, please bring it to my attention. It is my job to facilitate your education. vii

10 GUIDED LECTURE NOTES Table of Contents Unit 1 General Microbiology... 1 Basics of Microbiology... 1 History of Microbiology... 3 Genes and Information Flow... 4 Growth and Metabolism... 6 Chemical Principles and Metabolism... 9 Nutritional Classification Unit Taxonomy and Nomenclature Cell Structure Prokaryotic Microbes: Bacteria & Archaea Eukaryotic Microbes: Protists and Fungi Acellular Entities Unit 3 Medical Microbiology Microorganisms & Human Health Immunology Microorganisms & Human Disease Viral Pathogens Bacterial Pathogens Eukaryotic Microbial Pathogens Unit 4 Environmental & Applied Microbiology Global Cycles & Microorganisms Microbes and Pollution Microbial Genetics & Genetic Engineering Industrial & Agricultural Microbiology Food and Food Safety

11 Basics of Microbiology Unit 1 General Microbiology Terms & Concepts Acellular Cell Theory Eukaryotic Gene Theory Germ Theory Macroscopic Microbiology Micrometer (Micron) Microorganism (Microbe) Microscopic Multicellular Nanometer Prokaryotic Unicellular Guided Lecture Notes Microbiology includes the study of these four major microbial groups: Louis Pasteur and spontaneous generation are associated with: Robert Koch and his postulates are associated with: Alfred Hershey and Martha Chase are associated with: What do all microbes have in common? When measuring microorganisms, what measurements are typically used for bacteria? What about for viruses? Which microorganisms are ONLY unicellular (except for the exceptions, of course)? Which microorganisms can be unicellular or multicellular? 1

12 What are the five groups of microorganisms? Answer Later: How does this list of five groups compare to the list of four groups on the previous page? Of the five groups, which are eukaryotic and which are prokaryotic? Eukaryotic: Prokaryotic Which group is neither eukaryotic nor prokaryotic? 2

13 History of Microbiology Terms & Concepts Anton van Leeuwenhoek Cell Theory Cell Gene Theory of Inheritance Gene Germ Theory of Disease Alfred Hershey and Martha Chase Robert Koch Koch s Postulates Louis Pasteur Spontaneous Generation Swan-necked Flask Virus (Virion) Guided Lecture Notes Theory: evidence. Fact: Hypotheses: A comprehensive explanation of some aspect of nature that is supported by a vast body of Things which can be observed and/or measured repeatedly. Educated guesses based on observations (facts). Hypotheses should be testable. Cell Theory Cell theory took over 100 years to become a formal written scientific theory. What was the big fight that took place all about? Who performed the final experiment with swan-necked flasks that definitively disproved the idea of spontaneous generation? Cell Theory Revised All cells have the same basic chemical composition. Cells contain hereditary information (DNA) which is passed on from cell to cell during division. Energy flow (metabolism) occurs within cells. Answer Later: Would it be correct to refer to spontaneous generation as the Theory of Spontaneous Generation? Why or why not? Answer Later: What does it mean when a scientific theory is modified? Germ Theory (of Infectious Disease) 3

14 Koch s Postulates The microorganisms must be found in all organisms suffering from the disease, but should not be found in healthy organisms. The microorganism must be isolated from a diseased organism and grown in pure culture. The cultured microorganism should cause disease when introduced into a healthy organism. The microorganism must be re-isolated from the inoculated, diseased experimental host and shown to be the same as the original microorganism. Limitations to Koch s Postulates Some microbes which cause disease are also found in asymptomatic carriers. Some microbes cannot be isolated in pure culture. Some microbes are deadly and no animal model exists for them. Gene Theory (of Inheritance) Traits are passed from parent to offspring in packets of information called genes. The Central Dogma of Science states that: Hershey and Chase Experiments Used (a virus which infects bacteria). These viruses are composed of: Experiment #1 Labeled Viral Proteins Did the viral protein get into the bacterial cell? Did the bacterial cell produce more virions? Experiment #2 Labeled Viral DNA Did the viral DNA get into the bacterial cell? Did the bacterial cell produce more virions? Conclusion: What part of the virus was required to make new virions inside of the bacterial cells? Genes and Information Flow Terms & Concepts A, T, C, G, U Amino acid Anticodon Base Codon DNA 4

15 DNA polymerase Double helix Gene Genetic code mrna Mutation Nucleotide Peptide Protein Replication Ribosome RNA polymerase rrna Sugar-phosphate backbone Transcription Translation trna Guided Lecture Notes Every cell needs to: Form enzymes, cellular machinery, cellular scaffolding etc. Be able to double cellular contents in preparation for cell division. Make a duplicate copy of the cell s blueprints. Provide,, and for all of these processes. Proteins make up a bulk of the functional parts of every cell. The instructions for producing any cellular protein are contained in DNA in information packets called. To produce proteins, information in DNA needs to be from DNA to a temporary form (RNA). Then the information needs to be from the nucleic acid language (4 letters in groups of three) to the amino acid language (twenty letters in groups of variable size). DNA structure is very complicated, but the two very general parts are the the bases. and RNA is similar to DNA. One of the biggest differences is: TRANSCRIPTION The first step in producing a protein is to produce mrna. To put an RNA molecule together, which of the following are needed? DNA polymerase DNA strand Nucleotides: ATCG Nucleotides: AUCG Ribosome RNA polymerase mrna strand amino acids At the end of the TRANSCRIPTION process what has been formed? TRANSLATION The second step to producing a protein is to...produce the protein. To put a protein molecule together, which of the following are needed? DNA polymerase DNA strand Nucleotides: ATCG Nucleotides: AUCG Ribosome RNA polymerase mrna strand amino acids trna 5

16 Label the required components (listed above) on the diagrams below. A B C REPLICATION The process of making a copy of DNA from an existing DNA strand occurs only when a cell needs to divide. Which of the following are required for replication? DNA polymerase DNA strand Nucleotides: ATCG Nucleotides: AUCG Ribosome RNA polymerase mrna strand amino acids trna At the beginning of replication, there is one double-stranded DNA chromosome. At the end of replication, there are two identical double-stranded DNA chromosomes. Answer Later: Replication and Where did the original two strands of DNA end up? transcription seem very similar. How are Where do the two double-stranded DNA chromosomes end up? they different? Mutation Mistakes that happen during. Do mutations occur naturally? Answer Later: Why are mistakes made during replication so important? Growth and Metabolism Terms & Concepts Acidophile Aerotolerant Anaerobe Alkaliphile Barophile Closed System Death Phase Facultative Anaerobe Growth Curve Halophile Halotolerant 6 Lag Phase Log Phase Mesophile Microaerophile Neutrophile

17 Non-halophile Obligate Aerobe Obligate Anaerobe Guided Lecture Notes Psychrophile Radiophile Stationary Phase Thermophile Generation Time Doubling Time A closed system has: Because of these two things, it is possible to create a, which has four phases: During the log phase of a closed system growth curve, the organism will double according to its generation time or doubling time. For instance, if you have 3 million bacteria at the start of the log phase and the organism s doubling time is 20 minutes, after the first 20 minutes (1 generation) you will have 6 million bacteria. After the second 20 minutes (40 minutes total, 2 generations), you will have 12 million bacteria. If you know two things (variables) you can calculate the number of organisms at any time during the log phase. These variables are summarized here: (# of starting organisms) x 2 ^ (# of generations) In order of being adapted to hot/warm temperatures to being adapted to cold/freezing temperatures: Hot: Location Examples: Moderate: Location Examples: Cold: Location Examples: In order of preferred oxygen presence from oxygen required to oxygen detrimental: 7

18 Oxygen toxicity is caused by: (ROSs) Microorganisms with enzymes such as are protected from these toxic effects of oxygen. and In order of preferred ph (acidity vs. alkalinity): Organisms that prefer or require high salt concentrations are prefer lower concentrations of salt are.. Organisms that can tolerate, but. Everything else is Barophiles: Radiophiles: 8

19 Chemical Principles and Metabolism Terms & Concepts Amino Acid Anabolism ATP Carbohydrate Carbon Catabolism Guided Lecture Notes Which theory deals with Metabolism? Cell Theory Germ Theory Gene Theory Metabolism: Catabolism: energy, electrons and carbon*. Anabolism: energy, electrons and carbon*. Metabolism = Catabolism + Anabolism Electrons Energy Enzyme Hydrogen Lipid Metabolism Nucleic Acid Organic Carbon Oxygen Peptide Protein Saccharide chemical reactions in a cell. reactions. reactions. CARBON* (Organic Molecules/Organic Carbon) Organic molecules are composed primarily from these three elements: The four major groups of organic molecules are: 1 carbon:2 hydrogen:1 oxygen ratio made from amino acids genetic information molecules carbon, hydrogen and oxygen, but no ratio ELECTRONS Electrons are used to chemical bonds between atoms. When two or more atoms are connected by these chemical bonds, the result is called a molecule. Molecules can be as small as two bonded (connected) atoms or as large as hundreds or thousands of bonded atoms. ENERGY Energy in all living systems is packaged into molecules of (adenosine triphosphate). During, energy is harvested and stored in this molecule. During, energy stored in this molecule is used to power cellular reactions. This molecule is the same in bacteria, humans, plants and all other living organisms. 9

20 Nutritional Classification Terms & Concepts acid alcohol ATP autotroph carbon dioxide (CO 2 ) carbon fixation carbon source chemoorganotroph chemotroph dark reaction electron source electron transport chain energy source fermentation glucose glycolysis heterotroph light reaction lithotroph organotroph photolithoautotroph photosynthesis phototroph pyruvate respiration water (H 2 O) Guided Lecture Notes Organisms that get their ENERGY from sunlight are: Organisms that get their ENERGY from a chemical (inorganic or organic) are: Organisms that get their ELECTRONS from inorganic chemicals are: Organisms that get their ELECTRONS from organic chemicals are: Organisms that get their CARBON atoms from carbon dioxide (CO 2 ) are: Organisms that get their CARBON atoms from anything else are: 10

21 Photolithoautotrophs get their energy from electrons from carbon atoms from The process that photolithoautotrophs use to harvest their energy, electrons and carbon is called:. PHOTOSYNTHESIS: A process combining catabolism of water and carbon dioxide and collecting light energy to form (anabolize) simple sugars (carbohydrates). Light Reactions of photosynthesis Collects light energy phototrophy; catabolism Harvests electrons from water (H 2 O) lithotrophy; catabolism Oxygen (O 2 ) is a waste product from this process. Dark Reactions of photosynthesis Collects carbon from carbon dioxide (CO 2 ) autotrophy; catabolism Carbon Fixation: converting inorganic carbon (CO 2 ) into organic carbon (carbohydrates) Forms carbohydrates from C, e - and energy anabolism The processes that chemoorganoheterotrophs can use to harvest their energy, electrons and carbon are called: and RESPIRATION: A process collecting energy, electrons and carbon by using the following catabolic reactions: Krebs (TCA) Cycle don t worry about remembering this line FERMENTATION: A process collecting energy, electrons and carbon by using the following catabolic reactions: Both respiration and fermentation use GLYCOLYSIS to break down carbohydrates to release energy, electrons and carbon. Is glycolysis a catabolic or anabolic reaction? What is the toxic molecule produced at the end of glycolysis? After glycolysis is complete, the differences between respiration and fermentation become apparent. RESPIRATION uses... Krebs (TCA) Cycle to produce lots and lots of... 11

22 FERMENTATION uses... acid-producing fermentation or alcohol-producing fermentation or other types of fermentation Waste products from RESPIRATION include: water (H 2 O) carbon dioxide (CO 2 ) Waste products from FERMENTATION include: acids, alcohols or other things carbon dioxide (CO 2 ) or other gases to produce a little... ATP and acid or ATP and alcohol or ATP and other things Answer Later: What do you use to harvest energy, electrons and carbon from food you eat? Where does all the CO 2 come from that you breathe out of your body? Some things to think about! Most organisms which use respiration use aerobic respiration, meaning that they require oxygen in order to perform their respiration reactions. A very few organisms can use anaerobic respiration, meaning that they do not require oxygen to perform their respiration reactions. What type of respiration do you use? What type of respiration do plants use? Depending on the organism, fermentation will be a strictly anaerobic process (only occurs when oxygen is not present) or can occur regardless of oxygen (doesn t need oxygen, but oxygen doesn t get in the way). Consider the oxygen usage terms (aerobe, anaerobe, facultative anaerobe) in relation to respiration (aerobic and/or anaerobic) and fermentation (anaerobic or indifferent to oxygen). Some organisms can use both respiration and fermentation, depending on the environmental conditions. Which of the two processes would the organism prefer to use? Why? Can you think of a scenario where the organism would be forced to use the less-desirable process? Why are humans required to breathe in oxygen (O 2 ) and breathe out carbon dioxide (CO 2 ) in order to live? 12

23 Unit 2 Taxonomy and Nomenclature Terms & Concepts Archaea Bacteria Binomial Nomenclature Class Domain Eukarya Family Genus Kingdom Order Phylum Species Strain Taxonomy Guided Lecture Notes Taxonomy, or classification, of living organisms is constantly being updated, modified and rearranged. The Five Kingdom classification shown on the left has been replaced by the newer Three Domain classification on the right. The three domains of life are: To think about later: Notice that four kingdoms seem to have survived mostly intact. What happened to the kingdom Monera? When we discuss protists, we will talk about a subset of organisms called algae. Algae is a very generic term, relating to eukaryotic photosynthetic marine organisms. Some algae are protists; some algae are plants; some algae are neither protists nor plants, such as the kelps and seaweeds. These organisms need to be put somewhere...where would you put them? Scientific Names Binomial Nomenclature 13

24 Every organism has a name. This is called binomial (two-part) nomenclature (naming). The binomial nomenclature consists of a: genus name + species-specific designation = full name The first word (genus name) is ALWAYS capitalized. The second word (species-specific designation) is ALWAYS lower-case. The full name is ALWAYS italicized OR underlined. Examples of binomial nomenclature: Escherichia coli Escherichia coli a species of bacteria Lactobacillus acidophilus Lactobacillus acidophilusa species of bacteria Homo sapiens Homo sapiens humans Felis catus Felis catus the species of common cats Felis sylvestris Felis sylvestris the species of wildcats Canis lupus Canis lupus the species of grey wolves You can be even more specific when talking about organisms by referring to subspecies, serovars, morphovars and/or STRAINS. In microbiology, talking about specific strains is very, very common. Examples of binomial nomenclature plus more specific designations: Escherichia coli O157:H7 a pathogenic E. coli strain which causes hemorrhagic colitis (bloody diarrhea) Canis lupus lupus a subspecies of grey wolves, the Eurasian grey wolves Canis lupus familiaris a subspecies of grey wolves, the domesticated dog Salmonella enterica enterica Typhi Ty2 a very specific strain of the Salmonella enterica species of bacteria associated with typhoid fever One of the best definitions of a STRAIN: A group of organisms of the same species, sharing certain hereditary characteristics not typical of the entire species, but minor enough not to warrant classification as a separate species. For instance, most humans have a lot of Escherichia coli (a bacterium) living in our intestines all the time. Most E. coli living in our intestines all the time don t cause disease in us (non-pathogenic E. coli). Escherichia coli O157:H7 is the same species as these other E. coli, but it does cause disease. It is similar in all other ways to these non-pathogenic E. coli, but because it can cause disease we distinguish it from the others by its STRAIN name, the O157:H7 following the species name. 14

25 Cell Structure Terms & Concepts Cell Cell Wall Chloroplast Cilium (Cilia) Cytoplasm Eukaryotic Flagellum (Flagella) Mitochondrion (Mitochondria) Nucleus Plasma Membrane Prokaryotic Ribosome Guided Lecture Notes Which scientific theory is directly related to cell structure? Cells are: Definition of a cell: An autonomous self-replicating unit that may exist as a functional independent unit of life (as in the case of a unicellular organism), or as a subunit in a multicellular organism (such as in plants and animals) that is specialized in carrying out particular functions toward the cause of the organism as a whole. The general parts of a EUKARYOTIC CELL are: the perimeter of the cell the fluid insides of the cell the information center of the cell Endoplasmic Reticulum don t worry about remembering this line Golgi (Golgi apparatus, Golgi process etc) don t worry about remembering this line the protein-making machines of the cell the energy-producing organelles Endosomes, Lysosomes don t worry about remembering this line Cytoskeleton don t worry about remembering this line a special EUKARYOTIC structure in photosynthetic cells Where do the following processes occur in EUKARYOTIC CELLS? Glycolysis Respiration Fermentation Transcription Translation Replication Photosynthesis Some eukaryotic cells have additional external cellular features: Cell Wall an additional perimeter layer just external to the plasma membrane 15

26 Flagella long, whip-like structures which some cells use for movement (picture a sperm cell) Cilia short, hair-like structures which some cells use for movement, some use for nutrient collection Compare and contrast EUKARYOTES with PROKARYOTES eukaryote a cell with a true nucleus Size Range: prokaryote a cell which existed before Size Range: Cross off the general parts of a EUKARYOTIC CELL which are NOT present in a PROKARYOTIC CELL Plasma Membrane the perimeter of the cell Cytoplasm the fluid insides of the cell Nucleus the information center of the cell Endoplasmic Reticulum don t worry about remembering this line Golgi (Golgi apparatus, Golgi process etc) don t worry about remembering this line Ribosomes the protein-making machines of the cell Mitochondria the energy-producing organelles Endosomes, Lysosomes don t worry about remembering this line Cytoskeleton don t worry about remembering this line Chloroplast a special EUKARYOTIC structure in photosynthetic cells The general parts of a PROKARYOTIC CELL: the perimeter of the cell the fluid insides of the cell the protein-making machines of the cell Where do the following processes occur in PROKARYOTIC CELLS? Glycolysis Respiration Fermentation Transcription Translation Replication Photosynthesis What is the relative size of prokaryotic cells to eukaryotic cells? 15

27 Prokaryotic Microbes: Bacteria & Archaea Terms & Concepts Acid-fast bacteria Amphitrichous Archaea Bacillus Bacteria Binary Fission Biofilm Capsule Coccus Endospore Guided Lecture Notes Flagellum (Flagella) Glycocalyx Gram Negative Gram Positive Lipopolysaccharide Lophotrichous Monotrichous Mycobacteria Mycoplasma Outer Membrane Peptidoglycan Periplasmic Space Peritrichous Pilus (Pili) Plasmid S-Layer Slime Layer Staphylo- Strepto- Teichoic Acid The two domains which contain ALL of the prokaryotes are: BACTERIA and EUKARYA BACTERIA and ARCHAEA Things which are unique to BACTERIA ; e.g. DNA polymerase, RNA polymerase and ribosomes Bacterial cell walls (almost) always contain ; only (some) bacteria can form these ARCHAEA and EUKARYA Synthesis Enzymes (e.g. DNA polymerase, RNA polymerase and ribosomes) ARCHAEA and BACTERIA Things which are unique to ARCHAEA Unique plasma membrane structures Archaeal cell walls are extremely diverse and can contain a lot of different things, but NEVER contain peptidoglycan. There are no known archaeal pathogens, so we won t talk about these any more. 16

28 The general parts of a PROKARYOTIC CELL: the perimeter of the cell the fluid insides of the cell the protein-making machines of the cell Where do the following processes occur in PROKARYOTIC CELLS? Glycolysis Respiration Fermentation Transcription Translation Replication Photosynthesis What is the relative size of prokaryotic cells to eukaryotic cells? Additional Interior Bacterial Cellular Structures PLASMIDS: extrachromosomal DNA; contains extra genes that can benefit the bacterium, but are not necessary for the bacterium to survive. ENDOSPORE: a special multi-layer covering which can protect the dormant bacterium from very harsh environments The Bacterial Cell Envelope (the plasma membrane AND all surrounding layers) Plasma Membrane (almost) all bacteria have this extra layer, but there are different types only some bacteria have this layer made of polysaccharides a term for an ordered layer of polysaccharides a term for a disordered and diffuse layer of polysaccharides only some bacteria have this rigid layer made from protein The bacterial CELL WALL (a part of the cell envelope) helps determine shape of bacterium helps protect the bacterium contributes to pathogenicity (ability to cause disease) Distinct cell wall structures between Gram positive bacterial cells: 18

29 The peptidoglycan (PDG) layer IS the entire cell wall. Teichoic acid is a special molecule found only in Gram positive bacterial cells. The periplasmic space (if it exists) is found between the plasma membrane and the PDG layer. There are only TWO parts found in all Gram positive cell envelopes: Plasma Membrane Cell Wall (PDG Layer) Gram negative bacterial cells: The cell wall consists of: Peptidoglycan Layer Outer Membrane Lipopolysaccharide (LPS) is a special molecule found only in Gram negative bacteria. The periplasmic space is found between the plasma membrane and the outer membrane. There are THREE parts found in all Gram negative cell envelopes: Plasma Membrane Two-Part Cell Wall: PDG Layer Outer Membrane The term Gram positive and Gram negative comes from a special staining procedure used constantly by microbiologists. During the stain, some bacterial cells will be stained purple (Gram positive outcome) and others will be stained pink (Gram negative outcome). As we improved our microscopy, we were able to see the actual cellular layers 19

30 and found that bacteria with a single, but thick, layer of PDG seemed to stain purple (Gram positive) and that bacteria with an outer membrane and a thin PDG layer seemed to stain pink (Gram negative). Acid-fast bacteria (e.g. Mycobacterium species [Mycobacterium tuberculosis or Mycobacterium leprae]) have a Gram positive cell wall (no outer membrane) don t stain purple during the gram stain because of presence of waxy lipids which repel the staining dye If you use a special acid staining technique, these bacteria will retain the dye and other bacteria will not; hence the name Acid-Fast. Bacteria with no cell wall (e.g. Mycoplasma bacteria [Mycoplasma pneumoniae]) extremely small bacteria (as small as the largest viruses) obligate intracellular bacteria (must live within another cell) some can cause disease Additional Exterior Bacterial Cellular Structures Pilus (Pili sometimes also called fimbriae) short, hair-like structures often used for movement, but some are specialized: Sex Pilus involved in a process called conjugation (we ll take about this process in unit 3) Flagellum (Flagella) long, whip-like structures often used for movement, but can also be used for attachment or for virulence factors Flagellar Arrangement Types: one, hair one flagellum on one end of the bacterium on both sides, hair one flagellum on each end of the bacterium tufts, hair clumps of flagella on one end of the bacterium around, hair flagella cover the bacterium BINARY FISSION How bacteria reproduce Asexual Reproduction One cell becomes two cells. The two cells are identical to the original cell. The time it takes the bacterium to undergo binary fission is called its generation time or doubling time. Shapes of Bacterial Cells Coccus Bacillus Spiral Vibrio Spirilla Spirochete Arrangements of Bacterial Cells Staphylo- Strepto- 20

31 Eukaryotic Microbes: Protists and Fungi Terms & Concepts amoeba ascocarp ascospore ascus aseptate (coenocytic) basidiocarp basidiospore basidium binary fission budding chlorophyll chloroplast ciliate diatom dinoflagellate Endosymbiotic Theory eyespot (stigma) flagellate fragmentation fruiting body fungus (fungi) hypha (hyphae) lichen mitochondrion (mitochondria) mold mycelium mycorrhizae nucleus organelle photosynthetic pigment phytoplankton plasmodium protist protozoan Red Tide saprophytic septate spore spore formation (asexual) spore formation (sexual) sporozoan unicellular algae yeast zygosporangium zygospore Guided Lecture Notes Endosymbiotic Theory: Mitochondria and chloroplasts arose from an ancient symbiotic relationship where a small bacterial cell lived within a larger cell. The small bacterial cell devolved into a non-living organelle within the larger cell. By some currently unknown process, these cells also enveloped their DNA chromosomes within a nucleus and became EUKARYOTIC cells. What are the two EUKARYOTIC microbial groups? PROTISTS have two characteristics: They differ from bacteria and archaea because: They differ from fungi because: 21

32 Taxonomy of protists is very, very difficult and constantly changing, so rather than talk about protists by taxonomical groups, we use the following three generic groups: protozoans unicellular algae slime and water molds PROTOZOANS (animal-like protists) These can be further divided based on their MOVEMENT TYPE: ALGAE: Some definitions (Can you find how each definition contradicts another?) A simple non-flowering plant of a large group that includes the seaweeds and many single-celled forms. Algae contain chlorophyll, but lack true stems, roots, leaves and vascular tissues. Primitive, chlorophyll-containing, mainly aquatic, eukaryotic organisms lacking true stems, roots and leaves. Any of many aquatic photosynthetic organisms, whose size ranges from a single cell to giant kelps and whose form is very diverse; some are eukaryotic and some are prokaryotic. Algae can be divided into three large groups: Blue-green algae: photosynthetic bacteria (Which definition above includes this group?) Unicellular eukaryotic algae: photosynthetic protists (Which definitions above include this group?) Multicellular eukaryotic algae: photosynthetic organisms (Which kingdom do these belong to?) Which of these groups are microbial groups? Which is not? UNICELLULAR ALGAE (plant-like protists) Algae are classified into taxonomic groups based on their PHOTOSYNTHETIC PIGMENTS Pyrrophyta aka or fire algae The cause of. Chrysophyta Includes the and golden algae. Euglenophyta Contain to detect light. Chlorophyta The most of all the unicellular algae. 22

33 FUNGUS-LIKE PROTISTS The weirdest ones; some can form a PLASMODIUM, a massive multi-nucleate protoplasmic mass (one plasma membrane surrounding hundreds of nuclei) Includes the slime molds and water molds. True molds are fungi; slime and water molds are right on the border between protists and fungi. FUNGI eukaryotic non-motile o o Cell walls made of chitin can be: o unicellular (yeast) o multicellular (molds) Fungal Classification Groups yeasts, truffles, morels, mildews mushrooms, toadstools, rusts bread molds * fungi with no recognized sexual reproduction Fungal Terminology A: B: C: D: E: F: 23

34 Fungi can reproduce in a variety of ways. Asexual Reproduction (the progeny are identical to the parent fungus) Sexual Reproduction (the progeny are a mix of two different fungi) Notice that SPORE FORMATION is found under both asexual and sexual reproduction. These are NOT the same process. Fungi are classified based on their method of SEXUAL SPORE FORMATION. Ascomycota sexually-produced spores result from formation of: Ascoscarp (fruiting body) which contains o Asci (plural of ascus) which are small sacs that contain Ascospores which are the sexually-produced spores. Basidiomycota sexually-produced spores result from formation of: Basidiocarp (fruiting body) which contains o Basidia (plural of basidium) which are small clubs that contain Basidiospores which are the sexually-produced spores. Zygomycota sexually-produced spores result from formation of: Zygosporangium (fruiting body) which produces Zygospores which are the sexually-produced spores. Deuteromycota no one has ever seen sexual reproduction in these fungi, but when we do, we ll move them to one of the other groups! Fungi that hang out with other organisms: LICHEN a relationship of a fungus with a photosynthetic microbe. The fungus gets carbohydrates from the photosynthetic microbe. The photosynthetic microbe gets safety and security from the fungus. MYCORRHIZAE a relationship of a fungus with a plant. The fungus gets carbohydrates from the photosynthetic plant. The plant gets hard-to-reach nutrients from the soil via the fungus. 24

35 Acellular Entities Terms & Concepts acute assembly (packaging) attachment (adsorption) bacteriophage budding cancer capsid chronic complex endocytosis entry (penetration) envelope exit (release) fusion helical icosahedral injection latent lysis lysogenic lytic oncogene prion prophage (provirus) spike protein (glycoprotein) synthesis (replication) virion viroid virus Guided Lecture Notes All viruses have at least two parts: All viruses are obligate intracellular pathogens, meaning that: Viruses are extremely small: The average range for viruses is: Viruses are not living organisms and therefore they are NOT classified anywhere in the three domains of life. Instead they are classified in their own taxonomic system using the following characteristics: Dimensions of the virion and the capsid don t worry about remembering this line Genetic Relatedness don t worry about remembering this line The viral nucleic acid is either or. The symmetry of the viral capsid is either: 25

36 Some viruses are surrounded by a lipid membrane called an. Some viruses have structures extending out from their capsid or their envelope; these structures are called or and can help in viral attachment to a host cell. Of all the organisms in the three domains of life, are there any that are not able to be infected with a virus? The Viral Replication Cycle All viruses go through five basic steps to replicate, or make copies of, new progeny virions. These steps are: There are three major routes of entry (penetration) that viruses use to get into a cell: There are two major routes of exit (release) that viruses use to get out of a cell: Viruses which infect bacteria are called. When these viruses infect a bacterial cell, they can undergo the normal virus replication cycle called a LYTIC INFECTION or they can become momentarily side-tracked when the viral genome becomes integrated into the bacterial chromosome. This infection cycle is called a LYSOGENIC INFECTION and the viral genome inside of the bacterial chromosome is called a PROPHAGE. Viruses which infect eukaryotic cells can also have variations in their replication cycles. There are three major types: : A typical lytic infection where destruction of the host cell occurs. : Similar to lysogenic infections of bacteria, this infection results in the virus becoming latent, dormant or hidden within the host cell; no virions are produced and the host cell does not die. : An ongoing infection where the host cell is (usually) not killed and the virus remains in the body for extended periods (often life-long). Some viruses can contribute to the development of cancer by turning on host cell genes called ONCOGENES which promote cancerous growth or by turning off host cell genes called TUMOR SUPPRESSOR genes which prevent cancerous growth. VIROIDS made of NUCLEIC ACID (RNA) only. Infect plants. PRIONS made of protein only. Cause a variety of deadly diseases in animals, including humans. 26

37 Unit 3 Medical Microbiology Microorganisms & Human Health Terms & Concepts colonization commensalism disease gastrointestinal system genitourinary system indigenous microbiota infection integumentary system lower respiratory tract mutualism opportunistic pathogen parasitism pathogen resident microbiota respiratory system sterile symbiosis transient microbiota upper respiratory tract Guided Lecture Notes Symbiosis: Types of Symbioses: Competition Neutralism Indigenous Microbiota: All humans have an indigenous microbiota, made up of commensal microorganisms. In fact, we have more bacterial cells in/on our bodies than we have human cells in our body! Host Indigenous microbiota are RESIDENT microorganisms. These microorganisms are more or less always present. These populations do have some variation in actual numbers and specific species, thus our resident microorganisms can change 27

38 over periods of time, e.g. the indigenous microbiota that were present when we were infants were different from the ones we had as children and are different from the ones we have as adults. TRANSIENT microorganisms are NOT part of our indigenous microbiota. These are microbes: OPPORTUNISTIC PATHOGENS: (can be resident or transient microorganisms) Medical Treatment Antibiotics: directly cause loss of indigenous of microbiota; indirectly cause outgrowth of indigenous microbiota Anti-inflammatories/Immunosuppressors: cause suppression of immune system Injury Burns, wounds, surgery etc: cause breakdown of immune protection Where are indigenous microbiota found on the human body? Anywhere your body Body Systems COMPLETELY covered Body Systems PARTIALLY covered Nervous System This system includes the conjunctiva of the eye. There is some debate about whether the conjunctiva is normally covered or sterile. 28

39 Integumentary System (Skin) Dry, Salty Extreme Temperatures Inhibitory substances Gram positive bacteria are the most common, but a few Gram negative bacteria and fungi are also present. The diversity of microorganisms on the skin is LOW, because of the required specialization to live here. The concentration of microorganisms on the skin is HIGH. First barrier encountered by microorganisms. Answer Later: What is meant by required specialization to live on the skin? Why do you think the concentration of microorganisms on the skin is high? Respiratory System Excellent Environment for Many Microorganisms Can find Gram positive, Gram negative and fungi Upper Respiratory Tract (mouth, nose, throat) Indigenous Microbiota? Yes or No Lower Respiratory Tract (trachea, bronchus, bronchioles, lungs) Indigenous Microbiota? Yes or No Gastrointestinal System (mouth, esophagus, stomach, small and large intestines) Can find Gram positive and Gram negative bacteria (including lactic acid bacteria (LAB) and coliforms we will talk about both of these groups in unit 3). More than 90% of your fecal matter is microbial biomass. You defecate about 100 billion bacteria every day. The diversity of microorganisms in the gastrointestinal tract is HIGH. The concentration of microorganisms in the gastrointestinal tract if HIGH. Answer Later: Why are the diversity and concentration of bacteria in the gastrointestinal tract both high? 29

40 Genitourinary System Urinary System Sterile Indigenous Microbiota Genital System Indigenous Microbiota Other Components Exposed Surfaces: Other Components Interior Surfaces: Excellent Environment for Many Microorganisms Can find Gram positive, Gram negative bacteria and fungi (including lactic acid bacteria (LAB)). The diversity of microorganisms in the genitourinary tract is LOW/MODERATE. The concentration of microorganisms in the genitourinary tract is LOW/MODERATE. Answer Later: Why is it not surprising that the diversity and concentration of the genitourinary tract are low/moderate rather than high? Body Systems WITHOUT indigenous microbiota (i.e. STERILE body systems) Nervous System This system includes the conjunctiva of the eye. There is some debate about whether the conjunctiva is normally covered or sterile. In a body system which has indigenous microbiota, does the presence of microorganisms mean that the person has been infected with a pathogen? Why or why not? In a body system which is normally sterile, does the presence of microorganisms mean that the person has been infected with a pathogen? Why or why not? 30

41 Immunology Terms & Concepts adaptive immunity antibody antigen antigen-presenting cell (APC) attenuated vaccine autoimmunity B cell B cell receptor (BCR) CD4 + T cell (helper T cell) CD8 + T cell (cytotoxic T cell) clonal expansion cytokine degranulation dendritic cell effector T cell Fc receptor Fc region fever hypersensitivity immune immunodeficiency inactivated vaccine inflammation innate immunity leukocyte lymphocyte lysozyme macrophage major histocompatibility complex (MHC) memory B cell memory T cell mucus membrane naïve B cell naïve T cell non-specific immunity peristalsis phagocytosis plasma cell specific immunity T cell T cell receptor (TCR) toxoid vaccine vaccination variable region antibiotic antibacterial antiviral resistance (antibiotic) sensitivity (antibiotic) probiotic Guided Lecture Notes The human immune system is divided into two parts: A non-specific response: a generic response generally effective against groups of pathogens. An innate response, meaning it exists and functions from birth (congenital). A specific response: a response tailored to destroy pathogens which produce specific ANTIGENS. An adaptive response: over time, the specific immune response learns and adapts to new pathogens. This arm of the human immune system makes vaccination possible. Cells of the Immune System: All cells of the immune system are derived from hematopoetic stem cells. Cells of the innate (non-specific) immunity (leukocytes [aka white blood cells]) neutrophils macrophages dendritic cells 31 mast cells basophils eosinophils Cells of the adaptive (specific) immunity (lymphocytes a subset of leukocytes) T cells B cells Professional Antigen-Presenting Cells (Professional APCs)

42 macrophages dendritic cells neutrophils B cells INNATE IMMUNITY: a non-specific immunity which exists and functions at birth which includes: Barriers Barriers Skin Acid Production Mucous Membranes Digestive Enzymes Cytokines (e.g. Fever) Barriers Coughing/Sneezing Ciliary Motion Peristalsis The four characteristics of INFLAMMATION are: Processes Inflammation Phagocytosis Degranulation PHAGOCYTOSIS: Devouring by a cell Famous phagocytes: DEGRANULATION: Vomiting by a cell Famous granulocyte: Major Histocompatibility Complex (MHC) Molecules Used to present antigens (produced by innate immune response) to adaptive immune response MHC I Presents only antigens which arose from inside of the cell on which the MHC molecule is found (endogenous antigens). MHC II Presents only antigens which arose from outside of the cell on which the MHC molecule is found (exogenous antigens). Professional Antigen-Presenting Cells (Professional APCs) have both MHC I and MHC II molecules on their surfaces. macrophages neutrophils dendritic cells B cells ADAPTIVE IMMUNITY: a specific immunity which must first be activated by an infection before becoming effective. Antigens: Bits and pieces of anything that can cause an immune response. 32

43 Examples: Answer Later: After we finish talking about the immune system, consider this list in terms of autoimmunities and hypersensitivities. What is the connection? Cells of the Adaptive Immune Response: The LYMPHOCYTES T cells CD4 + T cells (helper T cells) CD8 + T cells (cytotoxic T cells): the primary component of cell-mediated adaptive immune response B Cells antibody-producing cells: the primary component of antibody-mediated adaptive immune response To activate any of the lymphocytes (T cells or B cells), ANTIGENS are required. These lymphocytes recognize and respond to specific antigens by using their antigen-specific surface receptors: (TCR) found on T cells (BCR) found on B cells Each receptor recognizes a different, specific antigen. MHC Molecules MHC I present endogenous antigens to CD8 + T cells MHC II present exogenous antigens to CD4 + T cells. To activate T cells, TWO SIGNALS are required: T cell Activation Signal #1 MHC presents antigen to TCR (T cell receptor) T cell Activation Signal #2 Cytokines produced by innate immune cells Once a T cell is activated, it becomes an EFFECTOR T cell and will perform functions based on the type of T cell that it is: CD4 + T cells (helper T cells) will help activate other lymphocytes (B cells and CD8 + T cells) CD8 + T cells will begin targeted destruction of infected cells or other cells showing abnormal features. After clearance of the source of the antigen(s), most effector T cells will die; a few, however, will change and become Memory T Cells which are long-living, more easily activated and produce more efficient effector T cells when activated. 33

44 Stages of T cells and... B cells To activate B cells, TWO SIGNALS are required: B cell Activation Signal #1 Antigen binds to BCR (B cell receptor) B cell Activation Signal #2 Cytokines produced by CD4 + T cells Once a B cell is activated, it becomes a PLASMA CELL which will begin producing one of five types of ANTIBODY, Ab (aka immunoglobin, Ig). IgA: secretory antibody found at mucosal surfaces; can be transmitted through breast milk from mother to infant. IgG: most common Ab; can cross the placenta from mother to fetus. IgE: anaphylactic Ab; can bind to Fc receptors on granulocytes and result in allergies. IgD: found as part of the BCR IgM: can form pentameric/hexameric Ab immune complexes. 34

45 Parts of the Antibody Variable regions determine the antigen specificity. Fc regions determine antibody type and Fc binding. IgG antibodies bind to IgG Fc receptors on phagocytes and trigger phagocytosis. IgE antibodies bind to IgE Fc receptors on granulocytes and trigger degranulation. Memory T and B cells Memory cells respond faster and are more productive than naïve cells. Vaccination mimics an infection and causes your body to produce memory T and B cells. Types of Vaccines Inactivated vaccines: Attenuated vaccines: Toxoid vaccines: Subunit/Conjugate/GE Produced by growing/culturing the real pathogen and then killing the pathogen. Produced by growing/culturing the real pathogen in a non-ideal environment which weakens the pathogen. Produced by chemically modifying a microbial toxin causing the toxin to become inert (toxoid. The person will only make antibodies against the toxoid antigens which should mimic the toxin antigens. Produced by combining pieces of a pathogen with other molecules or organisms. 35

46 Destructive Immune Responses Activation of self-reactive T and B cells which result in tissue damage. Type I IgE-mediated release of histamines causing allergies and localized/systemic anaphylaxis. Type II IgG/IgM and complement causes cytolytic reactions. Type III IgG immune complex formation causes excessive localized or systemic inflammation. Type IV Delayed CD8 + T cell-mediated immune reaction. Defects in one or more components of the immune system. Some are congenital, others are acquired. Chemotherapy Antibiotics: Antibacterial: Can target important processes such as: example: example: example: Antiviral Example: Antifungal Example: Drug Resistance & Being Too Clean? Probiotics: Herbal Remedies: 36

47 Microorganisms & Human Disease Terms & Concepts airborne blood-borne direct transmission disease droplet-borne endemic epidemic epidemiology Fomite food-borne high infectivity high pathogenicity high virulence indirect transmission infection infectious disease infectious dose infectivity invasiveness low infectivity low pathogenicity low virulence non-infectious disease nosocomial outbreak pandemic pathogen pathogenicity reservoir sexual transmission toxin transmissibility transmission event transmission route vector-borne virulence virulence enzyme virulence factors water-borne Guided Lecture Notes Pathogens can infect which body systems? Circulatory Endocrine Gastrointestinal Genitourinary Pathogens are: Epidemiology is the study of Pathogen-Related Terms Integumentary Lymphatic Muscular Nervous in human populations. Respiratory Skeletal TRANSMISSIBILITY: The ability to be transmitted from one host to another host. Transmission Routes Answer Later: How can airborne and fecal-oral be considered both direct and indirect e.g. physical contact, airborne, fecal-oral transmission? Where would sexual transmission be placed? e.g. fomites, food/water-borne, vector-borne, airborne, fecal-oral 37

48 INFECTION INFECTIVITY: The minimal infectious dose required to allow the organism to establish a population within a host. High Infectivity Example: Hepatitis B Virus (HBV) minimal infectious dose is less than 10 virions. Low Infectivity Example: Klebsiella pneumoniae minimal infectious dose is more than 100,000 bacteria. DISEASE: A detrimental change in health. Disease is caused by pathogenic microbes or acellular entities or their products. Disease is NOT caused by pathogenic microbes or acellular entities or their products. PATHOGENICITY: The ability of a microorganism to cause a detrimental change in health (i.e. disease). High Pathogenicity Low Pathogenicity No Pathogenicity VIRULENCE: The severity of pathogenicity. High Virulence Infected, diseased host has Low Virulence Infected, diseased host has Virulence Factors mechanisms, substance or other microbial components which contribute to the severity of disease. Invasiveness: ability to spread from one tissue to another. Virulence Enzymes: microbial enzymes with detrimental effects on body functions. Toxins: small molecules that cause a variety of detrimental effects on the body. Answer Later: What would indigenous microbiota be considered? What about the indigenous microbiota which are opportunistic pathogens? 38

49 Comparing PATHOGEN characteristics. Pathogen pathogenae Transmissibility: Infectivity: Pathogenicity: Virulence: Pathogen infectae Transmissibility Infectivity: Pathogenicity: Virulence: 39

50 Epidemiology-Related Terms OUTBREAK: Occurrence of a health-related event in excess of the normal level or baseline for a population. EPIDEMIC: Occurrence of a health-related event in excess of the normal expectancy or pattern for a population. Epidemics always involve outbreaks; Outbreaks aren t always epidemics. PANDEMIC: Spread of an epidemic to several people. countries (often worldwide), affecting many ENDEMIC: Permanence of a disease in a defined geographical area or population group. Examples: RESERVOIR: Technical, but not practical, definition: Host organisms which are not adversely affects by parasites of other organisms. Practical definition: Organism or location where the pathogen is commonly found. Technical Examples: Rats infected with Yersinia pestis do not develop disease. Humans infected develop plague. Bats infected with Rabies Virus do not develop disease. Humans develop rabies. Practical Examples: Rats, Bats, Environment, Nosocomial Sources, Humans 40

51 Viral Pathogens Terms & Concepts Acquired Immunodeficiency Syndrome (AIDS) chickenpox (disease) common cold (disease) gastroenteritis (disease) hepatitis (disease) hepatitis A virus (HAV) hepatitis B virus (HBV) herpesvirus Human Immunodeficiency Virus (HIV) influenza (disease) influenza virus rhinovirus rotavirus shingles (disease) stomach flu (disease) varicella-zoster virus Guided Lecture Notes 41

52 Bacterial Pathogens Terms & Concepts Anthrax Atypical Pneumonia Bacillus anthracis Borrelia burgdorferi Chlamydia Chlamydia trachomatis hemolytic (,, ) Lyme Disease Mycobacterium tuberculosis Mycoplasma pneumoniae Pneumonia Streptococcal Infections Streptococcus pneumoniae Streptococcus pyogenes Tuberculosis Typical Pneumonia Guided Lecture Notes Bacterial Pneumonia Pneumonia is a general term referring to inflammation of the lower respiratory tract. This inflammation is often caused by the presence of microorganisms (viruses, bacteria, fungi or protists). The most common pneumonia-causing microorganisms are bacteria. 42

53 Eukaryotic Microbial Pathogens Terms & Concepts asymptomatic athlete s foot (disease) Candida albicans candidiasis (disease) cryptococcosis (disease) Cryptococcus neoformans cyst gametocyte Giardia intestinalis giardiasis (disease) immunocompromised jock itch (disease) malaria (disease) merozoite Plasmodium spp. sporozoite thrush (disease) Toxoplasma gondii toxoplasmosis (disease) Trichophyton rubrum trophozoite Guided Lecture Notes 43

54 Unit 4 Environmental & Applied Microbiology Global Cycles & Microorganisms Terms & Concepts ammonia ammonification carbon cycle denitrification eutrophication inorganic carbon nitrate nitrification nitrite nitrogen cycle nitrogen fixation nitrogenase organic carbon organic nitrogen Guided Lecture Notes Global Cycles Nitrogen is used in which of the following biological molecules? amino acids (which means every single protein) nucleic acids (which means all DNA and RNA) enzymes (a very special and important group of proteins) vitamins etc. Nitrogen Cycle converts nitrogen gas into organic nitrogen. converts organic nitrogen into ammonia. converts ammonia into nitrate. converts nitrate into nitrogen gas. 44

55 Nitrogen Fixation Conversion of: Requires the enzyme. Nitrogenase uses a LOT of energy (ATP) and electrons to convert a single N 2 (nitrogen gas) molecule into organic nitrogen. The presence of oxygen interferes with nitrogenase; therefore nitrogenase needs to be in an anaerobic environment. Only bacteria have this enzyme. Free-living nitrogen-fixing bacteria e.g. cyanobacteria (photoautotrophs) Aerobic bacteria with specialized Heterocysts create an anaerobic microenvironment where nitrogen fixation can take place. Plant-associated nitrogen-fixing bacteria e.g. Rhizobium spp. (chemoheterotrophs) Aerobic bacteria which live in an anaerobic environment (root nodules). The plant supplies oxygen to the bacteria in a controlled way (via ) so that it will not interfere with nitrogenase. Ammonification Conversion of: Ammonia is toxic to many things at high concentrations. Nitrification Conversion of: First Step: Ammonia Oxidation converts into Second Step: Nitrite Oxidation converts into Denitrification Conversion of: An anaerobic process which often occurs in wetlands and other riparian (water) regions and in waste water treatment facilities. This process can become overwhelmed if there is a large amount of nitrates in the environments (e.g. from fertilizer usage) Eutrophication Excess of nitrate causes algal bloom, followed by bacterial bloom which causes loss of oxygen in water and death of plants and animals in/near water. 45

56 Carbon Cycle At which part(s) of the carbon cycle are microorganisms important? At which part(s) of the carbon cycle do plants get all of the credit when, in reality, microorganisms out-produce plants? How do human activities influence the balances of the carbon cycle? 46

57 Microbes and Pollution Terms & Concepts acid mine drainage (AMD) acid rock drainage (ARD) Acidithiobacillus ferrooxidans activated sludge active biomass aerobic microbes anaerobic microbes biochemical oxygen demand (BOD) bioleaching bioreactor bioremediation chlorination coliforms Dehalococcoides ethenogenes Deinococcus radiodurans denitrifying microbes Desulfovibrio desulfuricans dissolved oxygen (DO) fecal coliforms heavy metals indicator organism primary settling tank primary sludge primary treatment radioactivity reductive dechlorination secondary settling tank secondary treatment sulfur-reducing bacterium tertiary treatment Guided Lecture Notes Heavy metals present in soils can naturally cause high levels of acidity and formation of soluble heavy metals. This process is called Acid Rock Drainage (ARD). Mining causes an increase of soluble heavy metals formation and increased acidity. This is called Acid Mine Drainage. Bacteria can increase the rate of soluble heavy metal ion formation and increased acidity in both ARD and AMD. Mining 1. Ores are unburied. 2. Ores are collected into a vat where they are treated with chemicals (leaching) or with bacteria (bioleaching) to produce metals which will settle out of the liquid debris (tailings). 3. Metals are then smelted to remove any remaining impurities (slag). Acid Drainage causes an accumulation of: 47

58 The most common bacterium involved in ARD/AMD and bioleaching is: Bioremediation: Bioremediation of ARD/AMD involves sulfur-reducing bacteria which cause heavy metals to become insoluble reducing acidity and heavy metal concentrations in water. The most common bacterium in this sulfur-reducing bacterial group is: Acidithiobacillus ferrooxidans chemolithoautotroph aerobic Gram positive sulfur-oxidizing bacterium Desulfovibrio desulfuricans chemoorganoheterotroph anaerobic Gram negative sulfur-reducing bacterium Other Examples of Bioremediation Polychlorinated Biphenols (PCBs) removed by Dehalococcoides ethenogenes Radioactivity removed by sulfur-reducing bacteria (potentially by Deinococcus radiodurans in the future?) Petroleum/Oil removed by oil-degrading bacteria can cause algal blooms (eutrophication) as an undesirable side effect Water Safety The most dangerous contamination of water is fecal contamination and pathogens present in fecal material. How can you detect these pathogens (red) when they represent such a small part of the microbial content of the water? Indicator Organisms Easily distinguishable Easily detected Associated with pathogen Able to survive in a way similar to pathogen 48

59 Fecal Coliforms Indicator organisms for fecal contamination of water EPA Standard: ZERO coliforms present in 100 ml of water sample Wastewater Treatment (removing waste from water) Biochemical Oxygen Demand (BOD) The more organic matter in the water, the more microbes are able to be present resulting in more oxygen being used (oxygen demand). Low BOD means: High BOD means: BOD is calculated by measuring and subtracting the oxygen present in the water (dissolved oxygen, DO) before incubation (initial) and after incubation (five days later). DO initial DO 5 days = BOD If a water sample starts out with 100 ppm of dissolved oxygen (DO initial ) and, after incubation, the water sample ends with 5 ppm of dissolved oxygen (DO 5 days ). It means that 95 ppm of dissolved oxygen was used by microorganisms present. That is a lot of oxygen, which means there was enough food (aka waste) in the water on which the microorganisms could feed. Our calculation would be 100 ppm 5 ppm = 95 ppm BOD. This is much higher than 10 and the water sample is of extremely poor quality! What would the BOD be if the original water sample had 5 ppm and, after incubation, had 1 ppm? What about an initial BO of 500 ppm and a five day DO of 499 ppm? 49

60 Wastewater Treatment Steps Primary Treatment 1. Wastewater filtered and placed in primary settling tank. 2. Primary sludge removed and digested by: 3. Liquid portion (primary) moved to: Secondary Treatment 1. Liquid portion from primary treatment mixed with in the. 2. The active biomass moved to secondary settling tank. 3. Activated sludge removed and sent one of two places: o o 4. Liquid portion (secondary) moved to: Tertiary Treatment 1. Water from secondary treatment undergoes to remove nitrogen. 2. Water chemically treated with and released into waterways. Further techniques for purifying water: Coagulation/Flocculation Filtration Chlorination UV Irradiation 50

61 Microbial Genetics & Genetic Engineering Terms & Concepts bacteriophage competence factor conjugation F plasmid gene of interest genetic engineering genetic recombination horizontal gene transfer ligase restriction endonuclease restriction enzyme sex pilus sticky ends transduction transformation vector DNA vertical gene transfer Guided Lecture Notes Vertical Gene Transfer Recombination of parental genes (traits) Horizontal Gene Transfer Recombination of shared genes Addition of shared genes to current genetic material Types of Horizontal Gene Transfer in Bacteria Conjugation Direct transfer of DNA from one bacterium to another involving the F plasmid. The F plasmid contains: genes required to transcribe/translate the proteins for the sex pilus. genes required to transfer replicated F plasmid DNA through the sex pilus. Bacteria which contain the F plasmid are called and these bacteria can initiate. Bacteria which do not contain the F plasmid are called and these bacteria initiate conjugation. 51

62 Transformation Naked DNA is picked up from the environment by a bacterium. This process involved competence factors which enable the DNA to enter the bacterial cell. Transduction Transfer of DNA from one bacterium to another bacteria by a bacteriophage. Copy and cut the following squares from the page, then put them in the correct order: ^ ~ #! $ & * 52

63 Genetic Engineering: deliberate genetic recombination Basic Step of Genetic Engineering Restriction Endonucleases (Restriction Enzymes) cut DNA at VERY specific DNA sequences and produce sticky ends. The red arrows indicate exactly where the restriction endonuclease cuts the sugar phosphate backbone within the DNA strand. Why are the ends of the DNA called sticky ends? Why are these enzymes called restriction enzymes? Based on the roots and ending of the word, why are these enzymes called endonucleases? Combining the Pieces: What does GOI stand for? How do you choose your vector DNA? What enzyme is added to the second picture to combine the two pieces in order to form the complete circle in the third picture? In order to make the protein(s) from your GOI, what do you need to do with your new genetically engineered DNA? 53

64 Industrial & Agricultural Microbiology Terms & Concepts Agrobacterium tumefaciens Bacillus thuringiensis composting Crown Gall Disease ensiling Guided Lecture Notes GE microbial products genetically engineered (GE) Golden Rice lactic acid natural microbial products ruminant animal silage Ti plasmid tumor -carotene DO NOT ATTEMPT TO MEMORIZE the lists on this page. These are solely for the purpose of seeing the vast number of connections microbiology has with industry. Any product(s) which you need to know will be discussed again later. Products humans use that are naturally produced by microorganisms (many of which are ONLY produced by microbes): Enzymes and their uses : : : : Vitamins and their alternate names : : Organic acids and their uses : : : : Other products and their uses : : Products which humans have genetically engineered microorganisms to mass produce to save money, resources and/or to produce in a safer, more controlled manner: Health Products: Commercial Products: Potential Future Products: Food products which all require active microbial growth in order to be produced: Agricultural products which require microorganisms to be produced: 54

65 Naturally-Occurring Agricultural Microbiology Composting: What is so important about the temperature increase of composting materials? What causes the temperature increase? Are human pathogens mesophiles or thermophiles? Mutualistic Symbiosis between Ruminant Animals and Microorganisms What is a mutualistic symbiosis? What benefit does the ruminant animal receive from the microorganism? What benefit does the microorganism receive from the ruminant animal? Engineered Agricultural Microbiology (NOT genetically engineered what s the difference?) Silage (ensiling: the process of producing silage) Preservation of livestock feed by adding microorganisms. Microorganisms feed on (ferment) starch and simple sugars in the livestock feed, producing lactic acid. A build-up of causes a very acidic environment to develop and prevents further microbial growth and prevents further breakdown of the livestock feed. Compare and contrast composting and ensiling: Purpose: Ensiling Composting Microorganisms Used: Fermentation results in: Products of Process: 55

66 Genetically Engineered Agricultural Microbiology (How is this different from engineered agricultural microbiology?) Agrobacterium tumefaciens and Crown Gall Disease: plasmid with a GOI: Genetic modification of the Ti Why is it significant that the GOI is inserted into the gene for tumor induction? Genetically engineered Agrobacterium tumefaciens and genetically engineered plants: 56