MIP 300 Exam 1 Review - Lecture notes 1-6 PDF

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MIP 300 Exam 2 Key Concepts...

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Lecture 8 Wrap-Up A. Bacterial Mechanisms of Antibiotic Resistance 1. Some bacteria are just inherently resistant (not entirely but kind of) e.g. some antibiotics have a hard time penetrating a mycolic acid layer 2. Types of ACQUIRED mutations a) Spontaneous mutations b) Horizontal gene transfer B. HOW BACTERIA CAN BECOME RESISTANT TO ANTIBIOTICS 1. Number 1 in diagram: altered antibiotic target spontaneous mutation that changes the antibiotics target site so the antibiotic won’t be able to bind to target anymore--likely due to SPONTANEOUS mutation 2. 2-4: genes acquired through horizontal gene transfer a) Probably on a plasmid is how they acquired the gene b) Three different genes in plasmid (orange, white, green) (1) Orange gene codes for enzyme that degrades antibiotic (2) Green gene changes enzyme (3) White gene encodes for efflux pump, pumping out antibiotics out of cell; these pumps can kick out MULTIPLE antibiotics C. ANTIBIOTICS DO NOT INDUCE RESISTANCE THEY ARE SAFE D. PEOPLE SHOULDN’T OVERUSE ANTIBIOTICS BECAUSE THE ANTIBIOTICS INDUCE RESISTANCE: FALSE 1. THEY ARE NOT MUTAGENS, THEY ARE NOT CARCINOGENIC E. PENICILLIN HAS WHICH MODE OF ACTION: NEED TO KNOW THIS ONE INHIBITS BACTERIAL CELL WALL SYNTHESIS F. What affects whether an antimicrobial works??? a) Think EtOH should be 70%, if more than gets evaporated before doing anything How does soap clean? Many people buy soaps with antibacterial drugs in them A. A soap micelle has a HYDROPHILIC head that is in contact with the water and a center of hydrophobic tails which can be used to isolate and remove oil, soil particles, microbes B. Soap is antibacterial by nature, no need to get soap with antibacterials with them C. Micelles form this shape because of hydrophobic forces 1. Creates spot that can trap gross stuff When is it appropriate to use antibiotics? A. Common bacterial infections 1. Bladder infections definitely caused by bacteria 2. Staph infections (wound and skin infections)

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3. Severe sinus infections 4. Some ear infections 5. Strep throat B. Common viral infections 1. Bronchitis 2. Colds 3. Flu 4. Most coughs 5. Most ear infections 6. Most sore throats 7. Stomach flu (viral gastroenteritis) C. Under both lists 1. Food borne infections D. When do you for sure want antibiotics? 1. Rash with headache and fever 2. Really bad sore throat that doesn’t get better in a week a) Not getting antibiotics can cause causing and tissue damage after immune system complications b) Heart damage later in life due to strep throat! c) Get in your bloodstream, become septisemic 3. Infections of the skin that get red and swollen with pus quickly 4. Bladder infections 5. Mucus (yellow, red, orange) E. Viral infections more white-ish and green, bacterial is yellow due to pus gets a bit orange because of red blood cells Anti-fungals and Anti-protozoals A. What if you have fungi infeciton?? These are eukaryotes! 1. Difficult to achieve selective toxicity since eukaryotes not many major differences Anti-virals A. Difficult to achieve toxicity because most viruses use host cells to replicate themselves 1. Obligate intracellular parasites 2. Use many of host’s functions to reproduce--use our ribosomes, our DNA and RNA polymerase so difficult to reproduce

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By blocking quorum sensing, the researchers found, they can decrease the virulence of P. aeruginosa and its ability to form films of bacteria on surfaces, such as those inside the body.

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Trillion human cells but ten trillion bacterial cells in you or on you; 30,000 genes, 100x more bacterial genes in you or on you

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Keep us alive, digest our food, make vitamins, educate I.S. to keep bad microbes out Seems that they would have no impact if they just acted as individuals, they don’t live unicellularly, they live in communities Fibrio fischierae A. Bacteria that makes light, naturally bioluminesce 1. Don’t make light when alone 2. Make light when they grew to a certain number 3. How can bacteria tell when they are alone and when they are in a community and decide what to do together? a) Via COMMUNICATION (1) Bacteria make and secrete molecules (2) When alone, the molecules just float away--no light (3) When together, secrete molecules, these molecules increase in proportion to cell number; when certain cell number reached, recognize molecule and they all turn on light in synchronicity! B. This bacteria lives in a certain type of squid 1. Squid is nocturnal, at night it needs to hunt a) At night the stars and light can penetrate the water and the squid has developed a shutter so it can open and close the light that is shining from the moon/stars and THE BACTERIA CAN EXACTLY MATCH THIS LIGHT SO THE OCTOPUS DOESN’T MAKE A SHADOW; USES THE LIGHT TO COUNTER ILLUMINATE ITSELF SO PREDATORS CAN’T EAT IT b) During the day: thick dying culture of bacteria, can’t sustain it (1) When sun comes up, has a pump that pumps out the bacteria, the bacteria are dilute, not making light because signals too far but then at night cycle repeats Quorum Sensing A. Ex: fibrio fischerae have an enzyme (signal producing protein) that creates the molecule; as cells grow, all releasing the molecules in the environment B. The molecules will bind to a signal receptor protein C. When molecule increases to a certain amount (indicating large number of bacteria), signals collective behavior of making light D. ALL bacteria have systems like this Antibiotics A. Virulent behavior as an example of behavior they all launch to overcome a host B. Say bacterial virus enters your body, its not like they immediately start releaing toxins 1. The bacteria get in you, wait, start growing, recognize when they all have large enough cell number, all start signaling the molecule 2. Thus bacteria always control pathogenicity with quorum sensing C. Intra-Species Communication

1. Red triangles: molecules (the words the bacteria talk with) 2. The molecules are related a) Half of the molecular structure is identical in all the species, but the other half is a little different in every species, conferring species specificity, allowing each molecule to fit in a specific receptor (1) This is for INTRA species communication, allowing bacteria to count their OWN siblings (2) But in reality...bacteria live in diverse communities, many different species in one neighborhood (a) Can’t just talk within your own species, have to be able to take a census with all the different types (i) Discovered that bacteria are multi-lingual (a) Second enzyme that makes a second signal with its own receptor used by all bacteria allowing for INTER species (i) Allows for counting how many of me, how many of you (ii) This mechanism of counting allows for deciding what tasks to carry out depending on who is in the minority and who is in the majority (b) THERE IS A UNIVERSAL COMMUNICATION MOLECULE used for inter-species communication D. Implications 1. Some bacteria use this communication for pathogenicity so what if we inhibited them from talking and listening? Couldn’t these be new types of antibiotics? a) All the antibiotics we use kill bacteria by popping membrane or stop DNA replication; all the antibiotics we are currently using traditional antibiotics which SELECTS FOR resistant mutants 2. So why not stop communication to prevent synchronized virulent behavior a) Target intra-species system (1) Make similar looking molecules that lock the receptors that the signal molecule would normally bind to (a) Made species-specific anti-quorum sensing molecules

(b) Make antagonists of inter-species universal molecules to act as BROAD SPECTRUM antibiotics 3. Strategy a) Bacteria gets in mouse b) Doesn’t initiate virulence right away, starts growing, secretes molecule until communicate synchronized message c) Give mouse virulent bacteria but give it in conjunction with anti-uorum sensing molecules (look like real thing but a little different) (1) If you treat with a multi-drug resistant pathogenic bacteria AND anti-quorum sensing molecule at the same time, the animal lives! 4. Bacteria can distinguish self from others--me vs you 5. Also make PRO-quorum sensing bacteria to enhance good conversations VIII. IX.

Biofilms Lecture 4 handout A. Describe the internal structural features of prokaryotic cells and how these differ from eukaryotic cells 1. Both eukaryotes and prokaryotes have a cytoskeleton and cytoplasm; however, the cytoskeleton of eukaryotes is much more sophisticated, prokaryotes have homologues with similar functions: cell shape, division, and mobility 2. While both eukaryotes and prokaryotes have ribosomes, bacteria have FREE FLOATING ribosomes that can be targeted by antibiotics a) 70s 3. Unique to bacteria: inclusion bodies a) Inclusion bodies can be granules, crystals, or globules b) Some inclusion bodies are free in the cytoplasm c) Others are enclosed by a single membrane (1) Although bacteria do not have MBOs, they can use their inclusion bodies to store necessary nutrients 4. Types of inclusion bodies a) Organic (1) Glycogen granules: store glycogen (2) Cyanophycin granules: contain nitrogen, long chain of amino acids (3) Carboxysomes: found in PSS bacteria to fix CO2 b) Inorganic (1) Magnetosomes: inclusion bodies that store Fe3+ which acts as a magnetic, align bacteria with earth’s magnetic field to optimize growth

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(2) Polyphosphate granules: store phosphate needed for ATP, DNA, phospholipids Differences in prokaryotic and eukaryotic internal structures a) Prokaryotes have inclusion bodies, free floating ribosomes, nucleoids, plasmids, and endospores Spore layers a) Core: this is where nuceloid is, essentials; calcium dipicolinic acid enters and stabilizes the DNA, core is dehyrated b) Core wall c) Cortex = peptidoglycan d) Spore protein coat Sporogenesis (sporulation): how and why spore are formed a) Spore are formed when times get tough: lack of food, bad temperature, exposure to UV light, gamma radiation b) How spores are formed: (1) Undergo cell division, double the DNA (2) Axial filament formation (3) Septum formation i (4) Engulfment of forespore (5) Cortex formation (6) Coat synthesis (7) Completion of coat synthesis, increase in heat resistance c) How spores go from metabolically inactive to vegetative state: GERMINATION--a SURVIVAL mechanism not a REPRODUCTIVE ONE (1) Activation: heat (2) Germination: food (3) Outgrowth: protoblast able to grow out of spore, vegetative cell formed Medical Importance of Spore-Containing Bacteria that Cause Disease a) Most bacteria that contain endospores are gram positive bacilli (1) Exception: sporosarcina (2) Clostridium bacteria (a) Botulism (i) Cannot contract muscles (ii) Droopy eyes (iii) Babies can’t eat honey for this reason; they are unable to digest the spores in time so they vegetate (b) Tetanus (i) Spores in soil, ingested or get in wound

(ii) Uncontrollable muscle contractions (c) Gas gangrene (i) Spores in soil (ii) Explosions, bombs (iii) Toxins cause tissue to melt, bad smell (d) C. diff disease (i) Spores in feces (ii) Hospital settings (iii) Horrible diarrhea, can be deadly (3) Bacillus bacteria (a) Anthrax (i) Spores get inhaled (ii) Nausea, cough up blood, tightness in chest, fever, sore throat, spread to liver and kidneys deadly (b) Food poisoning X.

Lecture 5 Handout A. Describe the different ways in which bacteria can produce motility 1. Motility via flagella a) Axial filament: Flagella = largest hair like appendages that function to give bacteria motility (monotrichous/polar, amphitrichous, lophotrichous, peritrichous) (1) Structure of flagella: (a) Axial Filament: long part of flagella that extends out of cell (b) Basal body: embedded in the cell (c) Hook: links basal body and filament (d) Note: spirilla have tufts of flagella 2. Axial Filament motility via spirochetes: internal flagella 3. Twitching and gliding a) Type 4 fimbriae can twitch for mobility (fimbriae are the smallest/shortest hair like appendages) 4. Slime Production can allow for motility via gliding 5. Brownian Motion: NOT a type of motility but water will hit the cells B. If a bacterium is non-motile, can it ever change locations? Why or why not? 1. Yes it can due to brownian motion (caused just by bacteria getting hit by water) 2. A motile bacteria has the ability to propel itself forward via e.g. flagella movement (axial filament -- spirochete internal), gliding via slime production, twitching via type 4 pili tiny appendage C. Under a microscope, non-motile bacteria often appear to shake. Why is this? 1. Brownian motion D. Describe the process of chemotaxis. How do the bacteria know where to go?

1. Chemotaxis is achieved through bacteria that are motile and have chemoreceptors a) Chemotaxis occurs when bacteria move towards food (Attractants) or away from toxins (repellants) b) The bacteria know where to move because they have chemoreceptors (1) The chemoreceptors, which are proteins found in the plasma membrane or periplasmic space, are what detect attracts and repellants 2. Understanding the chemoattractant test a) Testing whether bacteria exhibit chemotaxis (1) If motile and have chemoreceptors, will move towards attractant b) Experiment (1) Take agar and fill it with nutrients before the agar hardens (2) Place three different types of bacteria on the plate: 1) non-motile bacteria 2) motile bacteria without chemoreceptors 3) motile bacteria with chemoreceptors (3) When you see large dot: indicates the bacteria moved, ate what was below them, moved more and kept eating (4) Less large dot: motile bacteria that don’t have bacteria so they move randomly (5) TIny tiny dot: non-motile bacteria with chemoreceptors E. How would chemotaxis provide a selective advantage to motile bacteria? 1. Allow bacteria to move toward nutrients to grow and move away from repallants to survive F. What are the functions of a bacterial capsule? 1. Capsule = polysaccharide layer that is well organized and not easily removed 2. The bacterial capsule protects bacteria from dehydration because the capsule contains water, protects from toxins, and protects from getting attacked by the immune system a) Considered a virulence factor because it protects cells from getting phagocytosed by macrophages b) Example of capsule being a virulence factor:

(1) Streptococcus pneumoniae: h  as two strains (a) Harmless strain: does not contain a capsule so complement can bind, season the bacteria to make it look yummy to the macrophage

(b) Dangerous strain: the strain that HAS A CAPSULE (i) CAPSULE PREVENTS COMPLEMENT FROM BEING ABLE TO SEASON THE BACTERIA SO IT DOES NOT LOOK YUMMY! G. What components found outside the bacterial cell wall can a bacterium possess? What are each of these components made of? How do these components help the bacteria that possess them? 1. The components found outside the bacterial cell wall that a bacteria can possess include: a) SUGAR (POLYSACCHARIDE) LAYERS (1) 1) capsule 2) slime layer 3) glycocalyx (2) Capsule is a WELL ORGANIZED layer of polysaccharides difficult to remove: virulence factor (3) Slime layer: less organized layer of polysaccharides, diffuse and easily removed (4) Glycocalyx = “sugar shell” comprises the capsule and slime layer (a) The capsule, slime layer, glycocalyx and biofilms are all made up of or protected by polysaccharide layers b) ADVANTAGES OF SUGAR LAYERS: (1) Not required for survival but can confer growth advantages (2) Help adhere to host (3) Help avoid immune system phagocytosis (4) Help avoid chemicals, detergents, viruses (5) Avoid dehydration (6) Allow for formation of BIOFILMS (a) Communities of bacteria that stick together through polysaccharide layers (i) Able to amplify message of signal molecule to exhibit a synchronized behavior e.g. virulence (b) Within biofilm, diverse bacteria communicate through quorum sensing, allowing them to: (i) Upregulate polysaccharide gene expression

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Upregulate antibiotic gene expression Downregulate flagella gene expression q

c) PROTEIN LAYERS (1) Archaea typically have S layers -- patterned like floor tiles d) ADVANTAGES OF PROTEIN LAYERS (1) help give cell shape, protects against changes in pH, osmotic pressure, protect against antibacterial enzyme (2) Just like polysaccharide layers aiding in virulence, S layers aid in virulence since they adhere to your host cells e) MYCOLIC ACID LAYER (FATTY ACID LAYER) (1) Waxy layer in mycobacterium f) ADVANTAGES OF MYCOLIC ACID LAYER (1) Somewhat resistant to dehydration, antibiotics phagocytosis g) There are mycobacterium that can cause TB and leprosy H. If polysaccharide layers, protein layers, and mycolic acid layers are helpful why don’t all bacteria have them? 1. Not required for reproduction/growth I. Describe pili/ fimbriae (pili = fimbriae) 1. Small, short hair-like appendages that are usually not involved in motility; however, some type 4 fimbriae can twitch to cause motility 2. Fimbriae are able to adhere to host cells LECTURE 6 HANDOUT A. How do prokaryotes and eukaryotes differ in structure? 1. Eukaryotes are characterized by membrane bound organelles 2. The cytoplasmic matrix and cytoskeleton is more complex in eukaryotes 3. 80s ribosomes (AND 70s ribosomes bc mitochondria and chloroplast) 4. Some eukaryotes have cilia and flagella 5. Eukaryotes have a less complicated cell wall a) Just need to know some eukaryotes have cell wall (fungi and algae) and some don’t (protozoa) 6. Pellicle: rigid structure beneath the cell membrane, kind of like a cell wall--found in many protozoa and some algae

B. Fungi are composed of molds, mildews, and yeast. Molds and mildews are found in our bread. Molds and mildews are made of hyphae and fruiting bodies that produce spores 1. Bread mold - rhizopus stolonifer a) Dangerous to those who are immunosuppressed or on chemotherapy C. What role do fungi play in the environment? 1. The association of fungi to plants is called mycorrhizae; this association improves nutrient uptake! ¾ of all plants need mycorrhizae 2. Thus, fungi play a major role as decomposers of organic matter 3. Fungi are spore forming but they do not do this for survival purposes like we see in bacteria, spore-forming in this case is a reproductive process 4. Fungi are molds, mildews, and yeast 5. They are ubiquitous 6. Don’t have chlorophyll so they don’t photosynthesize, instead have enzymes that break down foot 7. Mycoses are fungal diseases a) Mycoses can be subcutaneous or systemic (inhaled infections) D. What are some of the ways that fungi cause disease or disease symptoms? 1. Fungal diseases = mycoses 2. Fungi can cause disease via direct and indirect contact mycoses (superficial, cutaneous, subcutaneous; infections of skin, hair, nails); healthy people get these 3. Fungi can cause disease via systemic mycoses: spores usually inhaled then disseminate to organs 4. Opportunistic mycoses: tend to be system (inhaled); affect people who have been immunocompromised E. Name and describe one systemic and one opportunistic fungal disease of humans. 1. Systemic type of mycoses: histoplasmosis a) A heavily encapsulated yeast, found worldwide in soil containing bird and bat poop b) TB like--skin test, infect lung macrophages F. What is the role of algae in the environment?

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1. The primary role of algae is to function as a primary food source in water environments a) Algae have chlorophyll, can be unicellular or multicellular, are found in water and moist areas, and are a major component of phytoplankton Are there algae that cause diseases? If so, how? 1. There are algae that can cause disease by releasing toxins or when they are depleted of oxygen and nutrients in water during overgrowth 2. Algae are not parasitic Discuss how bacterial endospores and protozoal cysts are similar 1. Both are r...