MBS326M Exam 1 UGCA Review PDF

MBS326M Exam 1 Review Presented by your Teaching Assistants ☺ Agenda ► Go through each chapter’s learning objectives ► Address any content questions for each chapter ► Quick reminder: While this review is going over all of the learning objectives, it is not meant to be a substit...

MBS326M Exam 1 Review Presented by your Teaching Assistants ☺ Agenda ► Go through each chapter’s learning objectives ► Address any content questions for each chapter ► Quick reminder: While this review is going over all of the learning objectives, it is not meant to be a substitute for properly studying for the exam. What we are presenting today is not a review of what will explicitly be on the exam, rather, it is a review of the content we have covered in class so far. The level of detail that you are expected to know is presented in Dr. Kim’s slides and in her problems. EXAM FORMAT ► Next Wednesday (2/5) In-Class ► 60 Minutes ► 40 Multiple Choice Questions Chapter 1 Learning Objectives 1. Describe how we define a microbe. 2. List several ways in which microbes affect our lives. 3. Define cells. 4. Recognize the system of scientific nomenclature that uses two names: a genus and a specific epithet. 5. Describe the three major domains of life: archaea, bacteria, and eukarya. Explain what the three domains have in common and how they differ. 6. Which groups of microbes are prokaryotes? Which are eukaryotes? 7. How are viruses different from living organisms? 8. Explain how microbial diseases have changed human history. 9. Explain the importance of observations made by Hooke and van Leeuwenhoek. 10. Compare spontaneous generation and biogenesis. 11. How was spontaneous generation disproved? 12. Define the germ theory of disease. 13. Explain how Koch’s postulates can show that a specific kind of microbe causes a disease. Explain the problems in interpreting Koch’s postulates in practice. 14. Identify the contributions to microbiology made by Jenner, Pasteur, Semmelweis, Lister, and Fleming. 15. Explain how mitochondria and chloroplasts evolved by endosymbiosis. 16. Read Scenario- Half a Lung is better than none. What is the causative agent for this disease? 1) Describe how we define a microbe. 6) Which groups of microbes are prokaryotes? Which are eukaryotes? - Microbes are commonly defined as “living organisms that require a microscope to be seen - Not all microbes are living! - Microbes can be prokaryotic, eukaryotic, or some category outside of this - Prokaryotic cells have no nucleus and include organisms from the domain Bacteria and Archaea - Eukaryotic microbes can include fungi, protozoa, and algae - Not much specifically about these species are required to be known yet - Microbes which belong in this category since they do not fit anywhere else includes viruses and prions 2) List several ways in which microbes affect our lives. - Microbes are some of Earth’s earliest lifeforms - Microbes can partake in the following roles - Nitrogen fixation - Producing vitamins - Serving as primary producers - This is not the whole list but these are the main three for the environment you should be aware of - Some but not all microbes can be pathogenic (Our course focuses on the pathogenic ones but this is an important distinction!) - These pathogenic microbes have also had profound effects through history, being an unknown cause of disease until the 1850s 3) Define cells. - A cell is the basic unit of life - Cells are enclosed by a membrane complex - Generally all cells have: - Some kind of genetic material - Cell membrane - Ribosomes - Cytoplasm - Living organisms are composed of at least one cell 4) Recognize the system of scientific nomenclature that uses two names: a genus and a specific epithet. - Scientific nomenclature is written like this: Genus species - The genus is capitalized and proceeds the lowercase epithet/species name - Making sure this is italicized is very important - Some examples :) - Staphylococcus aureus - Staphylococcus epidermidis - Streptococcus pyogenes - While this is a smaller topic, make sure you keep this in mind for your presentations too! 5) Describe the three major domains of life: archaea, bacteria, and eukarya. Explain what the three domains have in common and how they differ. Archaea: - No true nucleus - Lives in more extreme conditions (pH, temperature, etc…) - Generally not thought of as pathogenic Bacteria: - No true nucleus - Unicellular Eukarya: - Can be multicellular or unicellular (multiple kingdoms within) - Has membrane bound organelles - Has a true nucleus 7) How are viruses different from living organisms? - Viruses are not considered living organisms - Viruses are unable to reproduce independently - Invade host cells in order to have access to machinery to replicate and spread - They are generally composed of a protein capsule and some kind of genetic material (DNA or RNA) - We may get more into this later but focus on why we do not classify viruses as living - Viruses have no cellular matter and are non metabolic 9) Explain the importance of observations made by Hooke and van Leeuwenhoek. - Robert Hooke - Built the first compound microscope - Observed cells in the microscope, coining the term after corkscrews - van Leeuwenhoek - Was able to successfully observe the first microbe - Known as the father of microbiology An important distinction to make between Robert Hooke and Antonie van Leeuwenhoek is that Hooke built the first compound microscope and observed the first cells. Leeuwenhoek was able to successfully see microbes, revealing a new world of lifeforms. 10) Compare spontaneous generation and biogenesis. 11) How was spontaneous generation disproved? - Spontaneous generation - life can suddenly appear - Biogenesis - the rise of new lifeforms come from preexisting life - Spontaneous generation was disproved by Pasteur’s famous swan-neck experiment 12) Define the germ theory of disease. 13) Explain how Koch’s postulates can show that a specific kind of microbe causes a disease. Explain the problems in interpreting Koch’s postulates in practice. - Germ disease is the idea that diseases are caused by specific microscopic “germs” - Koch’s postulates can help identify the pathogen causing a disease - Pathogens are isolated from a diseased host and given to another organism - If the organism develops the same disease then we have determined the cause of disease - These postulates cannot always be practiced - Some diseases do not ALWAYS cause disease for the host - Some pathogens only have humans as a host - Focus more on what Koch’s postulate is instead of ethics for exam 1 14) Identify the contributions to microbiology made by Jenner, Pasteur, Semmelweis, Lister, and Fleming. - Jenner - Vaccination - Found that cowpox could be used as a vaccine for smallpox - Pasteur - Biogenesis experiment (see earlier) - Found that exposure to attenuated/weak strains of bacteria can give a person immunity without subjecting them to extreme disease - Semmelweis - First pioneer of antiseptic techniques in hospitals - Lister - Developed chemical treatment to clean surgical tools - Led to aseptic operating rooms - Fleming - Discovered penicillin on accident, the first discovered antibiotic 15) Explain how mitochondria and chloroplasts evolved by endosymbiosis. - There is evidence that mitochondria and chloroplasts were prokaryotic cells engulfed by a bigger cell - Mitochondrias are from aerobic prokaryotic cells - First engulfing event - Chloroplasts are from photosynthetic organisms - Second engulfing event - Independent replication, independent genome, genetic structures, ribosomes, double membrane, etc… - (Covered a bit more in depth in Chapter 5) 16) Read Scenario- Half a Lung is better than none. What is the causative agent for this disease? - Mycobacterium tuberculosis can be the causative agent of tuberculosis - Infection is caused by the inhalation of the bacteria - Symptoms can include coughing, fatigue, and weight loss - More extreme cases can include the degradation of biological tissue - M. tuberculosis is an acid-fast bacteria - Layer of waxy mycolic acid outside the cell wall - Needs acid-fast stain to be identified Chapter 2 Learning Objectives 1. Describe differences between “normal” microbiota and pathogens. 2. Explain colonization, adhesins, parasites, and pathogenicity. 3. Discuss the relationship between infection and disease and between virulence and pathogenicity. 4. Differentiate between primary pathogens and opportunistic pathogens. 5. Differentiate between acute infection and chronic infection. 6. Differentiate between infectious dose and lethal dose. 7. Discuss the fundamental attributes of a successful pathogen. 8. Explain host range. 9. Distinguish between the signs and symptoms of a disease. 10. Explain the role of immunopathogenesis in infectious disease. 11. Describe the five basic stages of infectious disease. 12. Describe complex versus simple infection cycles. 13. Differentiate between endemic, epidemic, and pandemic disease. 14. Explain animal reservoirs and incubators. 15. Describe the various portals of entry and exit for microbial pathogens. 16. Discuss concepts of biosafety and biocontainment. 17. Define the biological features of human hosts that influence the course of an infection. 18. Explain how host behavior can impact susceptibility to disease. 19. Read Scenario- The broker's secret. What is the causative agent for this disease? 1) Describe differences between “normal” microbiota and pathogens. “Normal” human microbiota: the collection of all microbes that live in and on the human body without causing disease under normal conditions Pathogen: is any bacterium, virus, fungus, protozoan, or worm (helminth) that causes diseases in humans 2) Explain colonization, adhesins, parasites, and pathogenicity. Colonization: the ability of the microbe to stay attached to the body surface and replicate => adhesins - special proteins that organisms use to attach to receptors on host cells - allow the microbiota (collection of microbes) to attach to host cells Parasites: are microbes that cause harm-inducing infections - Ectoparasites: reside on surface of host’s body (fleas, ticks, lice) - Endoparasites: reside inside of host’s body (worm) Pathogenicity: is the ability of the organism to cause disease 3) Discuss the relationship between infection and disease and between virulence and pathogenicity. Infection: occurs when a pathogen or parasite enters and begins to grow on the host => most infections do NOT cause symptoms/can go unnoticed Disease: occurs when the patient develops symptoms Virulence vs Pathogenicity Virulence describes the level of harm caused by a pathogen FOLLOWING INFECTION (severity) while Pathogenicity is the ability of the organism to CAUSE DISEASE  4) Differentiate between primary pathogens and opportunistic pathogens. Primary pathogens: likely to cause disease after infection in a HEALTHY HOST - deadly pathogens -> higher chance pathogen will cause disease - rapidly reproduce/increase in number - moderate to high virulence Opportunistic pathogens: LESS likely to cause disease in a healthy host - low virulence Know these terms! (Table 2.1) **We will only go into depth with some of these terms but make sure to know what all of these terms mean 5) Differentiate between acute infection and chronic infection. Acute Infection: symptoms develop and resolve RAPIDLY i.e common cold Chronic Infection: symptoms develop GRADUALLY and resolve SLOWLY i.e Tuberculosis, HIV *diseases can be both ACUTE & CHRONIC => i.e Hepatitis A & B starts off with an acute infection and can develop into liver infection Focal vs. latent infection Focal Infection: initial site of infection from which organisms can travel via the bloodstream to another area of the body i.e paper cut to the skin can be the initial site Latent Infection: - infection may occur after an acute episode with symptoms resolving BUT organism remains dormant in the host - disease can reappear at a later time when the host’s immune system is more vulnerable i.e Herpesvirus 6) Differentiate between infectious dose and lethal dose. Virulence can be measured by: - Lethal dose 50% (LD50): the number of bacteria or virions required to kill 50% of an experimental group of hosts - Infectious dose 50% (ID50): the number of bacteria or virions required to cause disease symptoms in 50% of an experimental group of hosts 7) Discuss the fundamental attributes of a successful pathogen. Aspects of the pathogen that contribute to virulence: (the terms sound similar but describe different things) - Invasion: the entry of a pathogen into a living human or nonhuman cell, where it then lives i.e Salmonella (cause of diarrhea) live inside small, membrane-enclosed structures called vacuoles within the host cell - Invasiveness: the ability of a bacterial pathogen to RAPIDLY SPREAD THROUGH TISSUE i.e Streptococcus pyogenes secrete enzymes that degrade host tissues 8) Explain host range. Host Range: the animals a pathogen can infect and produce disease in - Narrow Host Range => Salmonella enterica serovar Typhi infects humans ONLY - Broad Host Range => Salmonella enterica serovar Typhimurium infects other animals IN ADDITION to humans 9) Distinguish between the signs and symptoms of a disease. Signs can be observed by EXAMINATION (objective marker of disease) examples: fluid-filled rash, fever of 102 degrees F, high blood pressure, swelling Symptoms are EXPERIENCED BY THE PERSON (subjective indicator of disease) examples: pain, fatigue, headache, nausea 10) Explain the role of immunopathogenesis in infectious disease. Immunopathology: signs and symptoms of disease caused by the host’s response to the infection *Organ and tissue damage caused by most infectious diseases is typically caused by immunopathology 11) Describe the five basic stages of infectious disease. 1. Incubation phase: the time after a microbe first infects; no symptoms 2. Prodromal phase: mild symptoms (no major symptoms yet) 3. Illness phase: symptoms & signs of the disease appear and the pathogen reaches peak numbers 4. Decline phase: immune response gets stronger and symptoms subside 5. Convalescence: symptoms have completely disappeared; recovery Know these terms! (Table 2.2) **We will only go into depth with some of these terms but make sure to know what all of these terms mean 13) Differentiate between endemic, epidemic, and pandemic disease. Endemic: disease that is always present in a community at a low rate, often in an animal reservoir ○ Ex: Malaria is always present in areas in Africa Epidemic: number of cases of a disease increases in a community in a short time ○ Ex: Sudden outbreak of measles in a country Pandemic: epidemic that spreads worldwide ○ Ex: COVID-19 ** You don’t need to know these examples but they might help you understand the definitions! Disease transmission terms Horizontal transmission: infectious agent transferred from one person/animal to another Vertical transmission: infectious agent transferred from parent to offspring ○ Ex: Listeria can cross the placenta Direct transmission: organism spread from person to person Indirect transmission: organism spread indirectly through air, fomites, vehicles, or vectors ○ Fomites -> inanimate objects such as tissues & clothing ○ Vehicles -> food, water, or air ○ Vectors -> ticks & mosquitoes Vehicle transmission: includes transmission via fomites or vehicles Disease transmission terms (cont.) Reservoir: animal, human, or environment that normally harbors the pathogen Asymptomatic carrier: harbors the potential disease agent but does not have the disease Zoonotic diseases: infections of animals that can be transmitted to humans ○ The pathogen may or may not cause disease in the animal reservoir 15) Describe the various portals of entry and exit for microbial pathogens. Most of these are very straight forward! Portals of entry/exit: ○ Fecal-oral -> Mucosa of G.I. tract ○ Skin -> Skin epithelium ○ Respiratory -> Mucosa of the respiratory tract ○ Urogenital -> Mucosa of the genital and urinary tracts ○ Parenteral: Breaks in the skin (needle injections & insect bites) ○ Entry via the eye -> Conjunctiva 17) Define the biological features of human hosts that influence the course of an infection. 18) Explain how host behavior can impact susceptibility to disease. Biological: ○ Age ○ Host genetic makeup ○ Pre-existing conditions such as chronic infection ○ Immune status (immunocompromised or not) Behavior: ○ Hand washing ○ Proper cooking of food ○ Sexual activity ○ Nutrition & exercise ○ Occupation 19) Read Scenario- The broker's secret. What is the causative agent for this disease? The patient was diagnosed with syphilis (a STI) Causative agent: Treponema pallidum ○ Shape -> Spirochete (thin, flexible, corkscrew-shaped) Chapter 3 Learning Objectives 1. List the units used to measure microorganisms. 2. Define magnification and resolution. 3. A light microscope can be used in both brightfield and darkfield. What are the differences between these? 4. What are the advantages of brightfield, darkfield, phase-contrast, and fluorescence microscopy? 5. What are the common shapes of bacteria? 6. List four ways of light interacts with an object - Figure 3.9 7. Why is immersion oil necessary? 8. List types of light microscopy. 9. Diagram the path of light through a compound microscope. 10. Describe how to observe an object in focus by using a compound microscope. 11. Explain how to calculate total magnification. 12. Explain how electron microscopy differs from light microscopy. 13. Explain why fixation is required before staining. 14. What are the differences between basic dyes and acidic dyes? 15. Describe a simple stain. 16. What are the differential stains? List a few examples. 17. Describe how the Gram stain distinguishes two classes of bacteria and describe the appearance of Gram-positive and Gram-negative cells after each step. 18. How can the Gram reaction be useful in prescribing antibiotic treatment? 19. Explain why each of the following is used and explain each step for this stain: acid-fast stain, endospore stain, and negative stain. 20. How do TEM and SEM images of the same organism differ? 21. Read Case Scenario- Pathogens in a Can. 1) List the units used to measure microorganisms. Microbe size is usually measured in micrometers (bacteria) and nanometers (viruses) In general, eukaryotes > prokaryotes > viruses in terms of size ○ Exception is Thiomargarita magnifica (largest bacterium) 2) Define magnification and resolution. Magnification: increases the apparent size of an image Resolution: smallest distance by which two objects can be separated and still be distinguished 3) A light microscope can be used in both brightfield and darkfield. What are the differences between these? Brightfield: ○ Dark object against bright background ○ Object absorbs light Darkfield: ○ Light object against dark background ○ Light scatters in all directions from the object 5) What are the common shapes of bacteria? Bacillus (rod-shaped) Coccus (sphere-shaped) Vibrio (comma-shaped) Spirillum (corkscrew-shaped, thick, rigid) Spirochete (corkscrew-shaped, thin, flexible) 6) List four ways of light interacts with an object - Figure 3.9 A. Absorption: object blocks light & gains energy a. This is how brightfield microscopy works B. Reflection: light bounces off object at the same angle as incident angle a. This is how we capture surface details of microbes in microscopy C. Refraction: light slows as it enters an object and bends in toward an object a. This is how magnification works D. Scattering: most of light passes through an object while the rest scatters away from the object in all directions a. This is how darkfield microscopy works 7) Why is immersion oil necessary? At higher magnification (100x), the objective lens is closer to the slide containing the microbes Light will refract after passing from the glass slide to the air between the slide and the objective lens The light can refract far enough that it doesn’t enter the objective lens, and you won’t be able to observe the specimen Immersion oil prevents light from refracting so that it can enter the objective lens 8) List types of light microscopy. Light Microscopes: Any kind of microscope that uses visible light to observe specimens ► Compound light microscopy (brightfield) ► Multiple lenses ► Easier to observe stained, dead specimens ► Darkfield microscopy ► Needed to observe spirochetes ► Phase-contrast microscopy ► Can observe unstained, live specimens ► Fluorescence microscopy ► UV light and fluorescent substances to stain ► Specific microbes and subcellular structures ► Also, Confocal and DIC microscopy (not important) ► Can observe live or dead specimens with all of these 9) Diagram the path of light through a compound microscope. Path of light: light source → diaphragm → condenser → specimen / sample → objective lens → ocular lens → eye 10) Describe how to observe an object in focus by using a compound microscope. Compound Microscope uses a system of multiple lenses designed to correct or compensate for aberration ► The condenser lens focuses light rays from the light source onto small area of the slide ► The image from the objective lens is amplified by a secondary focusing step through the ocular lens (10x) 11) Explain how to calculate total magnification. Important Equation: Total Magnification = Objective lens x Ocular lens ► Objective lens (ex: 10x, 40x, 100x) ► Ocular lens (10x) 12) Explain how electron microscopy differs from light microscopy. Light Microscope ► Source of Illumination: visible light ► Type of Sample: Can be alive or dead (depending on type of light microscopy) ► Resolution: Differs, but less than electron microscopes Electron Microscope ► Source of Illumination: a beam of electrons ► Type of Sample: Dead ► Resolution: High magnification and resolution 13) Explain why fixation is required before staining. Before staining, fixation (aka smear preparation → can be heat of chemical fixation) must occur to kill the cells and stabilize the sample on the slide 14) What are the differences between basic dyes and acidic dyes? Basic Dyes are positively charged ► Therefore, they bind to negative charges on bacterial cell compartments ► ex: Methylene blue, Crystal violet Acidic Dyes are negatively charged ► Therefore, they bind to positive charges ► ex: nigrosine ► nigrosine is an acidic dye that carries a negative charge and bacterial cell surfaces also carry negative charge (like charges repel), so it leaves the bacterial cell clear → stains the background instead 15) Describe a simple stain. ► Use of a single dye ► most common is methylene blue (basic dye) ► A simple stain adds a dark color to cells, but not the background ► Highlights the entire microorganism to visualize cell shapes and structures 16) What are the differential stains? List a few examples. Differential stain: stains two different kinds of cells in a distinguishable manner ► Most popular is gram-staining → explained in depth during the next slide Even though gram-staining helps distinguish between gram-positive and gram-negative bacteria → There are Exceptions! ► Gram variable bacteria ► Do not consistently stain as either gram-positive or gram-negative ► ex: Mycobacterium (acid-fast staining needed) ► No Gram Reaction ► Do not respond to the Gram staining process at all ► ex: Mycoplasma (no cell wall) 17) Describe how the Gram stain distinguishes two classes of bacteria and describe the appearance of Gram-positive and Gram-negative cells after each step. End results: ► Gram-positive bacteria: retains the crystal violet (purple appearance) ► Gram-negative bacteria: retains the safranin (pink appearance) 18) How can the Gram reaction be useful in prescribing antibiotic treatment? If we are able to differentiate between Gram-Negative and Gram-Positive bacteria ► knowing the classification of a microbial species in the case of a bacterial infections can help clinicians decide an appropriate treatment plan. ► Certain antibiotics only impact either Gram-negative or Gram-positive ► ex: penicillin works against mainly gram-positive, but not as much gram-negative ► Avoid unnecessary broad-spectrum antibiotic use ► Improve patient outcomes initiating timely, targeted therapy ► ex: gram-negative releases endotoxins that can cause shock 19) Explain why each of the following is used and explain each step for this stain: acid-fast stain, endospore stain, and negative stain. ► Acid-fast stain (used to identify Mycobacterium) ► Stains mycolic acids (waxy, lipid) in cell walls of acid-fast bacteria ► Smear preparation → Primary Stain: Carbofuchsin with head → Decolorizer: Acid-Alcohol → Counterstain: Methylene Blue ► Results: Acid-fast bacteria is red while non-acid fast bacteria is blue ► Endospore Stain (used to identify endospore-forming bacteria like Bacillus and Clostridium) ► Smear preparation → Primary stain: Malachite green with heat → Decolorizer: Water → Counterstain: Safranin ► Results: Endospores are green while vegetative cells are red ► Negative Stain of Capsules ► Uses acidic dyes, such as nigrosine, to visualize capsules ► Capsules are extracellular polysaccharides that some bacteria produce as a form of protection and also help them adhere to the surface ► A capsule appears as a clear halo around a stained cell. 20) How do TEM and SEM images of the same organism differ? Transmission Electron Microscopy (TEM) ► Electron beams penetrate a very thin slice of tissue with very high resolution ► Mainly used to observe internal structures and organelles Scanning Electron Microscopy (SEM) ► Electron beams scan the specimen and are reflected by the stain molecules to reveal the contours of its 3D surface (outside) ► Mainly observes shape and morphology 21) Read Case Scenario- Pathogens in a Can. Organism: ► Clostridium botulinum ► Endospore forming bacilli Illness: ► Canning factory did not properly can their goods, so it caused contamination ► Botulinum toxin A released by this species that ultimately caused the harm Chapter 5 Learning Objectives 1. Compare the cell structure of prokaryotes and eukaryotes. 2. Describe the key parts of a bacterial cell. 3. Explain the function of a bacterial cell’s parts. 4. Describe the structure and function of the bacterial cell and how it differs from the cell of a eukaryote. 5. Describe the functions of a cell membrane. 6. Explain how nutrients are transported and how energy is spent to drive transport. 7. Describe how pathogens use ion gradients and ATP to obtain nutrients from the host. 8. Compare passive transport with active transport. 9. Describe the cell wall structure, and explain how it protects bacteria from osmotic shock. 10. Explain the function of the Gram-positive cell wall and teichoic acids. 11. Explain the function of the Gram-negative outer membrane, LPS, and periplasm. 12. List the components outside of the bacterial cell wall. 13. Describe how DNA is organized within the bacterial cell. 14. Describe the envelope of mycobacteria, mycoplasma, and archaea. 15. What are endospores? Which genera produce endospores? 16. Explain how DNA replication is coordinated with cell growth and division. 17. Explain bacterial cell division and septation during division - slide 26 and 27 18. Describe the function of pili, fimbriae, and flagella. 19. Explain how flagellar motility and chemotaxis enable bacteria to respond to environmental change. 20. Describe the patterns of flagella distribution. 21. Explain other types of motility of bacteria. 22. Describe the key parts of a eukaryotic cell. 23. Explain the structure and interconnection of membranous organelles in the endomembrane system. 24. Which types of eukaryotic cells possess cell walls? 25. What are the structural differences between prokaryotic and eukaryotic ribosomes? 26. Explain how the evolutionary process of endosymbiosis led to mitochondria and chloroplasts. 27. Describe the structure of eukaryotic flagella and cilia. 28. Read Case Scenario. 1) Compare the cell structure of prokaryotes and eukaryotes. (Siona) Prokaryote Eukaryote ► One circular chromosome, not in a ► Paired chromosomes, in nuclear membrane membrane ► Some linear, multiple ► Histones ► No histones ► Organelles ► No organelles ► Polysaccharide cell walls, when present ► Bacteria: peptidoglycan cell walls ► Divides by mitosis ► Archaea: pseudomurein cell walls ► Divides by binary fission 2) Describe the key parts of a bacterial cell (Siona) ► Cell Wall ► Made of peptidoglycan ► Outside the membrane of the cell body ► Cell membrane ► Cytoplasm of bacterial cell ► Gel-like network of proteins and other macromolecules ► Outer Membrane ► Outside the cell wall in gram-negative bacteria ► Cell Envelope ► Cell membrane ► Cell wall ► Outer membrane (for gram-negative species) ► Nucleoid ► Chromosomes organized as a system of looped coils within the cytoplasm 2) Describe the key parts of a bacterial cell (cont.) (Siona) ► Cytoplasm ► Gel-like substance inside a bacterial cell ► Containings various cellular components like ribosomes, the nucleoid (bacterial DNA), plasmids, enzymes, and nutrients ► Ribosomes ► 70S Ribosome ► Large subunit = 50S ► Small subunit = 30S ► Membrane Proteins ► Make up external structures like capsule + flagella 3) Explain the function of a bacterial cell’s parts (Siona) ► Cell Wall ► Acts like a molecular cage, protecting the cell membrane from osmotic shock ► Prevents osmotic lysis (bursting due to increasing volume) ► Cell Membrane ► Defines a cell ► Separates the cytoplasm from the outside environment ► Outer Membrane ► Protects Gram-negative bacteria against a harsh environment ► Cell Envelope ► Protects the cell from its environment by providing structural integrity, maintaining cell shape, and acting as a barrier against harmful substances ► Also allows for necessary nutrient uptake and waste removal 3) Explain the function of a bacterial cell’s parts (cont.) (Siona) ► Nucleoid ► Regulates the growth, reproduction, and function of the prokaryotic cell ► Cytoplasm ► Primary site for metabolic activity ► Ribosomes ► Site of protein synthesis ► Membrane Proteins ► Transport of substances in and out of the cell across the membrane ► Selective Permeability = allows the passage of some molecules but not others ► Support for structures that extend out from the cell (flagella, pili) ► Signaling and communication ► Export of toxins and other virulence factors ► Establishment of concentration gradients for energy transfer  4) Describe the structure and function of the bacterial cell and how it differs from the cell of a eukaryote. (Siona) Feature Bacterial (Prokaryotic) Cell Eukaryotic Cell Nucleus No true nucleus; DNA is in the nucleoid True nucleus with a nuclear envelope DNA Single circular chromosome Multiple linear chromosomes Organelles No membrane-bound organelles Membrane-bound organelles Ribosome Smaller (70S) Larger (80S) Cell Wall Contains peptidoglycan (in most bacteria) Made of cellulose (plants) or chitin (fungi), or absent in animal cells Reproduction Asexual (binary fission) Sexual or asexual (mitosis and meiosis) Size Generally smaller Larger Motility May have flagella May have cilia or flagella 5) Describe the functions of a cell membrane. (Siona) ► Defines a cell ► Separates the cytoplasm from the outside environment ► Phospholipid bilayer with proteins ► Contains bacterial membrane proteins ► Transport of substances in and out of the cell across the membrane ► Selective permeability ► Support for structures that extend out from the cell (flagella, pili) ► Signaling and communication ► Export of toxins and other virulence factors ► Establishment of concentration gradients for energy transfer 6) Explain how nutrients are transported and how energy is spent to drive transport Passive Processes ► Simple Diffusion ► Movement of a solute from an area of high concentration to an area of low concentration ► Continue until molecules reach equilibrium ► Facilitated Diffusion ► Solute combines with a transporter protein in the membrane ► Osmosis ► the movement of water across a selectively permeable membrane from an area of high water to an area of lower water concentration Active Processes ► Group Translocation ► Requires a transporter protein and substance is altered as it crosses the membrane ► Example: Glucose → Glucose-6- phosphate (observed in many bacteria) 7) Describe how pathogens use ion gradients and ATP to obtain nutrients from the host (Siona) Both use the energy from ATP hydrolysis to move substances against their concentration gradients. ABC (ATP-Binding Cassette) Transporters These transporters use ATP hydrolysis to power the uptake of sugars, peptides, vitamins, and ions. Many bacteria use ABC transporters to import siderophore-bound iron. Siderophores = molecules that bind iron with high affinity. 7) Describe how pathogens use ion gradients and ATP to obtain nutrients from the host (cont.) (Siona) Use the energy from ATP hydrolysis to move substances against their concentration gradients. Siderophores and an ABC Transporter Iron is essential for many pathogens but is tightly regulated by the host. Pathogens produce siderophores The siderophore-iron complexes are then transported back into the pathogen using ion-gradient-powered transporters (such as the ABC transporter) 8) Compare passive transport with active transport. (Siona) ► Passive Transport ► Does not require energy (no ATP usage). ► Substances move down their concentration gradient (from high to low concentration). ► Active Transport ► Requires energy, typically from ATP hydrolysis or ion gradients. ► Substances move against their concentration gradient (from low to high concentration). 9) Describe the cell wall structure, and explain how it protects bacteria from osmotic shock. (Siona) ► The cell wall is a single, interlinked molecule that encloses the entire cell. ► Peptidoglycan (murein) consists of parallel polymers of disaccharides called glycan chains. ► The glycan chains are crosslinked with short peptides ► The bacterial cell wall acts like a molecular cage, protecting the cell membrane from osmotic shock 10) Explain the function of the Gram-positive cell wall and teichoic acids. (Siona) ► Gram-Positive Cell Wall = thick cell wall, multiple layers of peptidoglycan ► Gram-Positive cell wall includes: ► Thick peptidoglycan ► Teichoic Acids ► Provide flexibility to the cell-wall by attracting cations such as calcium and potassium ► Found exclusively in gram-positive bacteria ► Function ► Gram-Positive Cell Wall ► Provides structural support, prevents lysis, and retains Gram stain ► Teichoic Acids ► Stabilize the cell wall, mediate adhesion, regulate ion flow, and contribute to pathogenicity 11) Explain the function of the Gram-negative outer membrane, LPS, and periplasm (Siona) ► Outer membrane ► Outer membrane provides additional protection ► Porins (proteins) form channels through outer membrane ► Lipopolysaccharide (LPS) = outer leaflet of the outer membrane ► Made of Lipid A + Polysaccharide chains ► Lipid A acts as an endotoxin in lysed cells, so antibiotic treatment can kill cells but can also cause endotoxic shock in patients 11) Explain the function of the Gram-negative outer membrane, LPS, and periplasm (cont.) (Siona) ► Periplasmic Space ► Gel-like compartment in bacteria that's located between the inner and outer membranes ► Present in both Gram-positive and Gram-negative bacteria, but is larger in Gram-negative bacteria ► Periplasm between the outer membrane and the plasma membrane contains peptidoglycan 12) List the components outside of the bacterial cell wall. (Siona) Outermost layer in the cell envelope ► Capsules ► Well-organized layers made of polysaccharides that are covalently bonded and difficult to wash away. ► Slime Layers ► Polysaccharide layers that are unorganized and easily washed away ► Glycocalyx ► Polysaccharide extension that aids in attachment to solid surfaces. ► S-layers ► Geometric pattern made of protein that aid in protecting from ion and pH fluctuations 13) Describe how DNA is organized within the bacterial cell. (Siona) ► Nucleoid ► DNA containing region of the bacteria cell ► Not membrane bound ► Contains supercoiled DNA and DNA-binding proteins ► The Bacterial Chromosome ► The DNA of most bacteria is contained in a single circular molecule 14) Describe the envelope of mycobacteria, mycoplasma, and archaea. (Siona) ► Mycobacteria ► Contain a unique envelope ► Complex cell wall with peptidoglycan and mycolic acid ► Resistant to staining ► Include human pathogens: ► Mycobacterium tuberculosis ► Mycobacterium leprae ► Mycoplasma ► Lack cell walls ► Sterols in plasma membrane ► Resistant to antibiotics that interfere with cell wall synthesis (Penicillins) ► Archaea ► Walls made of pseudomurein ► Similar to bacterial peptidoglycan in function and physical structure ► Has a different chemical structure → lack NAM and D-amino acids 15) What are endospores? Which genera produce endospores? ► Allow bacteria to survive in harsh conditions (starvation, freezing, boiling water, UV light, and extreme desiccation) ► Produced by Bacillus and Clostridium ► These are dormant structures that persist until ample nutrients are available for growth to continue 16) Explain how DNA replication is coordinated with cell growth and division. ► DNA replication ALWAYS occurs before cell division ► ensures both daughter cells have a complete copy of the genome ► As the DNA replicates the cell elongates 17) Explain bacterial cell division & septation during division ► Bacteria replicate by binary fission (know the steps) ► 1. DNA replication occurs bidirectionally ► 2. Protein synthesis and expansion of cytoplasm causes cell to elongate ► 3. Septum forms and the cell divides ► Septation- pattern of septation causes differences in the appearance of cells ► Rod (bacilli)- elongate their cell wall BEFORE septation ► Cocci- Form chains when they septate in parallel planes; Form grape clusters when they septate in random orientations 18) Describe the function of pili, fimbriae, and flagella. ► Pili- used for DNA transfer, motility (movement), longer, thicker, less numerous (10/cell) ► Fimbriae- hairlike appendages used to attachment cells to surfaces, shorter, thin, numerous (1,000/cell) ► Flagella- used for motility in a liquid environment and attachment to surfaces ► swimming ► swarming: on a semi-solid environment 19) Explain how flagellar motility and chemotaxis enable bacteria to respond to environmental change. ► Chemotaxis- involves rotation of the flagella that propels the cell in response to stimuli ► Movement toward a chemical attractant or away from a chemical repellent using flagella ► Counterclockwise (CCW) rotation- moves cell towards attractant ► Clockwise (CW) rotation- cell stops forward movement, causing a tumbling motion and direction change 20) Describe the patterns of flagella distribution. ► Monotrichous—one flagellum on one pole ► Amphitrichous—one flagellum at each end of cell ► Lophotrichous—a cluster of flagella at one or both ends ► Peritrichous—spread over entire surface of cell 21) Explain other types of motility of bacteria. ► Spirochete Motility ► Axial Filaments ► Flagella remain inside the cell wall: Endoflagella ► Corkscrew shape exhibits flexing and spinning movements ► Twitching Motility ► Pili at ends of the cell, extends, attaches to the surface, and drags the cell ► ONLY occurs on solid surfaces, NO flagella ► Gliding motility ► cell rotates and motor proteins involved ► Smooth movements that do not require appendages. ► ONLY occurs on solid surfaces, NO flagella 22) Describe the key parts of a eukaryotic cell. ► Key parts of Eukaryotic cell ► Nucleus ► Ribosomes ► Rough endoplasmic reticulum (rough ER) ► Smooth endoplasmic reticulum (smooth ER) ► Lysosomes ► Golgi apparatus ► Mitochondria ► Chloroplasts ► Typically much larger than prokaryotic cells ► Compartmentalization ► enhances the efficiency and regulation of cellular processes 23) Explain the structure and interconnection of membranous organelles in the endomembrane system. ► The Endomembrane system- system of interconnected membrane-bound organelles that work together to organize uptake, package, digest, and transport lipids and proteins in a cell ► Consists of: ► Rough endoplasmic reticulum (rough ER) ► Smooth endoplasmic reticulum (smooth ER) ► Lysosomes ► Golgi apparatus 24) Which types of eukaryotic cells possess cell walls? ► Photosynthetic algae ► Cell wall consists of: cellulose, pectin, silica ► Fungal cells ► Cell wall consists of: chitin, glucan ► Plant cells ► Cell wall consists of: cellulose, pectin 25) What are the structural differences between prokaryotic and eukaryotic ribosomes? ► Prokaryotes- 70s ► consists of 50S (large subunit) + 30S (small subunit) ► Eukaryotes- 80s ► consists of 60S (large subunit) + 40S (small subunit) 26) Explain how the evolutionary process of endosymbiosis led to mitochondria and chloroplasts. ► Endosymbiotic Theory- Larger bacterial cells engulfed smaller bacterial cells, developing the first eukaryotes ► Ingested photosynthetic bacteria became chloroplasts ► Ingested aerobic bacteria became mitochondria ► Evidence supporting this theory ► Have their own circular DNA ► Have a 70s ribosome ► Reproduce by binary fission ► Have a double membrane 27) Describe the structure of eukaryotic flagella and cilia. ► Flagella and cilia are constructed of microtubules (9+2 arrangement) ► Flagella ► longer, fewer appendages ► Cilia ► small, numerous appendages ► ONLY in eukaryotes ► Pili are ONLY in prokaryotes 28) Read case scenario- An Upscale Tick Bite Organism ► Borrelia burgdorferi ► spirochete bacteria Illness ► Lyme disease which is characterized by a “bull’s eye” type of rash ► Causes Lyme diseases which when left untreated can lead to more serious symptoms such as crippling arthritis, neurological symptoms,