MICROBIOLOGY 2051 BRINNINSTOL Characteristics of Cells: true of all living cells * Communicate with environment * Molecules being exchanged—recognized by other cells—causes cell to do something (releasing toxins; move) * Growing—one cell divides and becomes two cells (binary fisson) * Some form appendages—form differently, look dfrnt, function dfrnt—spores, cysts, flagella * Evolve—ancestral cell Microbial Communities Table 1.1 More water than land Most microbes in soil Origin of Earth * 3.8 billion years ago—evidence of microbial cells Agriculture * Bacteria in plant (soybean plant) fixes nitrogen to usable nitrogen for environment * Cows have microbes in digestive tract to digest grass into sugar Energy—biofuels (methane, ethanol—from sugar cane) produced from microbial Disease—Cause & Treatment * More death-causing bacteria in 1900’s than today (in US!) Food—Microbes make food—bread, beer, cheese, 1665—Hooke; first to describe microorganisms through primitive microscope; drew picture of sprouting bodies 1676—Leeuwenhoek; first to describe bacteria; tiny microscope; drew multiple pictures of dfrnt kinds Four Types of Light Microscopy: 1. Brightfield: simplest; stained and illuminated, 10x 100x 1000x 2. Phase Contrast: cast shadow; shows depth 3. Darkfield: black background; light refracted 4. Fluorescent: fluorescent stained; naturally fluorescent; *requires UV light source

Compound Light Microscope: all listed above * Limit of resolution: ~0.2microns *e.coli smallest cells in see in lab; two can be so close they look like one Electron microscopes * PURPOSE: to magnify specimen; higher resolution with transmission * Scanning: outside viewing purposes; scans surface characteristics: i.e. cilia * Transmission: better to view inside of cell and see details; but must be cut with glass blade: have to embed cell in resign Mycobacterium leprae: leprosy: Hanson’s disease: treatable with antibiotic; naturally associated with armadillos Smaller cells grow faster than bigger cells do. Bacteria cells grow faster than eukaryotes. BECAUSE cell size to volume ratio; there’s less to do; takes in less food (less surface area) and its easier to rid waste (less volume to travel thru) *STRUCTURE is the most missed question on the exam

*STRUCTURE is the most missed question on the exam

Basic components of ALL microbial cells: * Cytoplasm, cytoplasm membrane, and ribosomes, DNA Prokaryotic Microbes * Nucleoid: is SPACE where the DNA is found; can be anywhere in the cell; usually found together BUT NOT forced to be together * Cytoplasm, cytoplasm membrane, ribosomes, plasmid * *Can have cell wall Eukaryotic Microbes * Cytoplasm, cytoplasmic membrane, ribosomes * Endoplasmic reticulum, golgi * Nucleus, nucleolus, nuclear membrane * *Can have mitochondrion, chloroplast (photosynthetic) * *Can have cell wall Cytoplasmic Membrane: “fluid” membrane, lipid and protein layer STRUCTURE: * Have transport proteins—some highly selective * Phospholipid bilayer: hydrophobic, fatty acids inside: hydrophilic, gylerical heads on outside * Archae lipid monolayer: glyerical heads and continuous fatty acid “legs” * *Much more resistant to peeling apart than BILAYERS because of molecular difference * Other lipids: add flexibility and help strengthen * Sterols and hopaniods FUNCTION: * Permeability barrier—rid of waste; take in nutrients * Energy conversion occur on site –very important for PROKARYOTES b/c they do not have mitochondria * Protein anchor—allows cell to detect environment, to move or such

Some can be prokaryotic and eukaryotic—organelle-like structures Peptidoglycan Layer: * Acetylglucosamine (sugar) * Acetylmuramic acid (sugar) beta 1: 4 bond—glycosidic linkage (covalent linkage) * Both sugars repeat following one another over and over again; string of sugars * Tetrapeptide Crosslink: 4 amino acids linked together * *Always connected to the Acetlymuramic acid (sugar) * *Crosslink holds peptidoglycan layers together through peptide bond * Four amino acid linkage on both sides of the peptidoglycan layer Lysozyme: one of the first line in defense against bacteria * Must be able to access the glycosidic linkages and weakens it (breaks beta 1:4 walls) –now flexible * Allows water to get inside cell and it proliferates Gram Positive Peptidoglycan is on the outside of the membrane Figure 3.15 – * Smooth, dark straight, outside line is peptidoglycan layer (made of strong amino acids) * Wavy, thin, light line on the inside is the fatty acid cell membrane (fat is fluid) Teichoic Acid—help support the peptidoglycan layers Proteins also Gram Negative Wavy, outside to show that it is a membrane—all layers Have 3 lines, two thicker outer layers with thin cell membrane on the inside Periplasm LPS—embedded in the outer membrane with strings of sugars reaching out Lipid A anchors the membrane Our bodies recognizes these sugars to detect bacteria Archae cell walls Pseudomurein (aka Pseudopeptidoglycan) Can have protein cell walls, glycoproteins (mainly sugar), .. Acetltalosaminuronic* is what differs from peptidoglycan & there’s a Beta 1: 3 Halococcus are Archae that have cell walls…NOT Puesdo.^^^ S-Layer—made up of protein; selective sieve Fimbriae—used for attachment to…surface—they’re SHORT Flagella are the LONG filaments Pili: Pilus: functions as a tube; will exchange DNA; copies of its own plasmids NOT its genome Capsules—are used for attachment; are sticky (because covered in sugar or protein) * Many human pathogens are in capsules * Sugars/proteins on outside of capsule can trick body into not realizing its foreign Slime Layer—glide by slime layer Gliding—slow (snail) for movement * Twitching motility—erratic movement * Ratchet-protein mechanism ‘walking’ by proteins Eukaryotic Movement—flagella and cilia * MOVEMENT back and forth/ fanning * *9 pairs of microtubules surrounding 2 central Bacteria Movement—much more COMPLEX than eukaryotic (NOTHING ALIKE) * Made of different proteins which form rings to anchor * Filament—flagella (much diversity among different species) * Hook * Motor: Mot proteins take in protons which creates a force and allows for the hook to turn (rotate) ***MOVES IN CIRCLES (rotating) * 60 cell lengths/ second possible—motor is powerful Archae Flagella [**NOT IN 12th ED**] * Multiple proteins make up filament * Smaller diameter flagellum less torque, slower speeds * Powered by ATP not protons (not mot proteins—its different) Location of Flagella—characteristic of a certain species * Polar—faster * Peritrichous—‘hair-like’ cover entire cell Movement How to determine where to go Taxes Many bacteria are photosynthetic and they are not limited to being green* Absorb different wavelengths of light depending on what pigments they have. Bacteria need oxygen—detect it (areo..)—and move toward it

Gas Vesicles * Bacteria with these are usually photosynthetic and move in response of light with the use of oxygen * Vesicles will release/take in gas to move throughout aquatic environment * Need to be in water to avoid radiation –UV rays Microcystic example of bacteria with gas vesicles Magnetosomes: acts as weight to pull down cell to sediment; keep it oriented; to metabolize (magnets) Carboxysome—*organelle found in prokaryotes—use these synthesize part of photosynthesis Needs to bind CO2 to make sugar—less oxygen interference Cell Inclusion Bodies Phospahte—polyphosphate granules Why would a cell need so much phosphate? * DNA has a phosphate backbone Sulfur—stored in periplasm (gram-negative) 1876: Cohn: described life cycle of Bacillus subtilis vegetative cellendospor vegetative cell Endospore Formation: sporulation * Vegetative cell encounters harsh conditions; such as: *nutrients, lack of water * Series of events cell will form a spore inside the cell; contains all essential macromolecules; such as: * DNA, lipids, carbohydrates, proteins, tiny bit of water * Calcium dipicolinic acid & small acid soluble proteins **only found in endospores * Spore must contain enough to start a whole new vegetative cell * Spore location formation is specific to the species * Terminal: end of the spore * Subterminal: close to the middle * Central: right in the middle; looks as if whole cell is spore Layers of an Endospore * DNA is in middle surrounded by fatty, lipid layer: Cortex Spores are resistant to heat, many chemicals, radiation (UV, cosmetic), dessication (dry it out) * Thought to be able to survive for infinite amount of times Germination—needs nutrients and water; makes genetically identical organism that can last for billion of years

Virus—virion—virus particle * Have no metabolism * Exist in 2 forms—and all reliable on host cell * Extracellular: outside of host; inert * Intracellular: replicates inside host by taking over metabolic machinery of host Table 9.2 THE BALTIMORE CLASSIFICATION SYSTEM OF VIRUSES * Cellular organisms have doubled stranded DNA genome * *DO not have to know chart just understand how viruses are classified Viruses do not need a lot—do not need enzymes; no metabolic abilities—may have a few enzymes: functioned to protect the virus Tobacco mosaic plant virus—plant virus; not as typically specific Viron linear or circular talking about chromosome structure (humans have linear) Capsid is what gives virus its shape * Made of an arrangement of proteins—can be same repeating protein * Capsomere is the protein that makes up capsid and *protects the nucleic acid inside the the capsid * The fewer the proteins the more rigid and geometric capsid will look—more proteins: rounder appearance Enveloped: lipid bilayer *important because *virus gets that lipid bilayer from host cell (when it leaves host cell it wraps itself in the hosts membrane through *budding) * Not all viruses are enveloped Complex—docking mechanism through tail pins and tail fibers –only some viruses Viriods and Prions—oddities—non-cellular microbes Viriod: infectious RNA particle—repeated fragment; host cell makes more for the virus * *ONLY infect plants; spread easily between plants; can spread through pollen * No membrane; no proteins Prions: protein; no nucleic acid; * Humans have the genes to code for this protein and we produce it Prion mechanism of action: Mad Cow Disease; Parks Field Jacob * Prion protein is produced—normal prion protein; stays like that: not harmful * If in production of protein it folds incorrectly; then it can be harmful. * Will form aggregates with other proteins—makes cell unable to rid of it—build up—cause neurological problems * Will others like it * Happens through digesting these mutant prions; through mutation in the prion gene in the neuronal cell (appears later on); through inheriting defective gene (appear early onset; can be passed on) Key Processes involving genetic information: Replication: independent process; makes a copy of the genome Transcriptions: synthesis of RNA from DNA; transcribes parts of the genome at once—process can end here; does not HAVE to be translated Translation: always proceeds transcription (as in alphabet); reads RNA to assembly amino acids and make proteins Prokaryotes have to do it a little differently because its chromosomes are circular –just one circular chromosome Plasmids—unique to prokaryotes; not needed; extra chromosomal information; much smaller than host circular chromosome

Replication: **Semiconservative—original strains are the parent strains—new strands will be complementary (A—T & C—G ) three prime hydroxal—indicator to add nucleotides to the END complementary to the parent sequence leading strand never has to stop—bottom strand: helicase unwinds DNA and work in fragments: owaski fragments *online tutorials 3’ prime 5’ prime adds complementary nucleotides –hydrogen bonded two replicated pieces of double-stranded DNA; each with a parent strand Terminarion of Replication: * In Bacteria: one side of DNA will have origin of sequence: three nucleotides and across TER sites * Eukaryotes: linear chromosome: end primers (certain sequence) gets put on and removes: have telomerase to recognize this sequence and adds nucleotides to end the strand TRANSCRIPTION: RNA synthesis: all kinds of RNA: important ones: * mRNA, tRNA, rRNA mRNA: complementary sequence of DNA promotor will indicate RNA polymerase where to go ( transcription start site) polymerase add ribonuceotides RNA polymerase reads bottom strand 35 and makes replication that is 53? Only one gene at a time

Must splice out introns and leave only the exons in mature RNA molecule Must be capped—special bonding nucleotide: 5 prime methanol cap Must have a string of A’s : poly-A tail ALL this before it leaves the nucleus IF this does NOT happen then it will be degraded prematurely; as soon as it leaves nucleus BACTERIA Single sigma factor- binds to sequence in promotor and positions RNA polymerase at start site—without it cannot indicate where to start When it binds, it no longers needs the sigma factor—it will get recycled Bottom 35 No introns in prokaryotic genes. No cap and no tail; not necessary. Can transcribe MORE THAN ONE gene at a time * produces a polycestron gene (gene A and gene B) now linked together * *more efficient than eukaryotes Termination of Transcription: * Rho dependent – wont have a row of inverted repeat * Intrinsic terminators – Operon: several genes transcribed together—within the same promoter and terminator * Exception not the rule for bacteria * Have spaces * Will end up as separate genes—some processing but not as complex as other Regulation of Transcription:
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TEST TWO MATERIAL Metablolism: Energy source—organic/ inorganic compounds, iron, light Used to do things (produce ATP); some energy used to make things (catabolism)-making cell wall Catabolic—energy producing Anabolic—biosynthetic: energy using Redox Reactions: leo the lion goes ger Donor is oxidized and acceptor is reduced *Most of the time donors do not freely give up their electrons to acceptors—they use electron carriers Electron carriers: can be in the cell membrane, cytoplasm, i.e. NAD+/NADH * NAD+: oxidized form: willing and able to accept electron * **Subscript plus is “holding the place” of the ‘H’ * NADH: reduced form Reaction 1 NAD+ and substrate bind to enzyme (enzyme-substrate complex) NAD+ took electron from substrate NADH is reduced; substrate oxidized Rection 2 NADH binds to substrate and enzyme NADH gives electron to substrate NAD+ is oxidized; substrate reduced

Catabolism: Purpose: to produce ATP: any energy (*anything with –TP) Many of many pathways: *none possible without redox reactions Energy will be made for cell * **Need to know * What comes in and what comes out and * Where they go.. Anhydride bonds: cleavage of phosphate bond: energy is released Thioester bond: cleavage of this bond releases energy but not as much anhydride Long term source because can be broken off in small amounts as needed * Glycogen, Poly-B-hydroxybutyrate, elemental.. **Chemoorganotroph: carbon based molecules; organic molecules * Aerobic/ Anaerobic Respiration, fermentation **Chemolithotroph: inorganic compounds * Primarily aerobic respiration; some anaerobic respiration Types of Phosphorylation: 1. Substrate Level: Substrate giving a phosphate group to ADP to make ATP 2. Oxidative: free moving inorganic phosphate (Pi) added to ADP with the help of ATP synthase to make ATP 3. Photophosphorylation: light-mediated oxidative phosphorylation (photosynthetic) **LOOK AT POWERPOINT FOR PATHWAYS; not at book*** GLYCLOYSIS: purpose: break down glucose *major pathway * Glucose (1) comes into glycolysis and pyruvate (2) and ATP (2) comes out * Use 2 ATP to start process and 4 are produced but only 2 usable ATPs * Requires some NAD+; produces some NADH * Substrate level phosphorylation

Fermentation vs. Respiration: purpose: both make ATP for cell * Respiration: will occur is electron acceptor is present * Fermentation: will occur with no acceptor; last option for cell * Does not require oxygen but can occur in the presence of oxygen * Usually occurs only when there is no oxygen Fermentation: start with an organic molecule: sugars, alcohol, purines/pyrimidines, organic acids, proteins—many fermentation pathways * Organic intermediates—that give ADP to make ATP * *Substrate level phosphorylation

Electron Transport Chain: * Better at accepting electrons at the top/beginning of the chain and those less capable at the end of the chain * Substrates, NAD/NADH, flavoprotein… * Oxygen is at the bottom of the chain= last (terminal) electron acceptor * Takes electron and becomes water NADH gives up electron and starts process Protons entering system FMN takes electrons/protons and pushes protons out and passes electron along to FE/SQHQH2/Q FE/ScytO2 (H2O) Protons accumulate outside of membrane, and create an acidic/positive charge; Electrons on inside create alkaline/negative charge * *Required to make ATP (the force) * NAD/NADH create proton motive force Easier to account for protons of cell has cell wall; not all do *In eukaryotes, happens in the inter membrane of mitochondria (matrix) * Protons accumulate in between layers Electron transport in E.cole Aerobic respirationuse cyt to produce oxygen Anaerobic respiration use nitrate reductase to produce nitrate * Aerobic respiration is always the first one E.coli will try to do because it produces more ATP---why? Because there is a greater proton motive force (more protons on the outside of the cell) Chemiosmosis: * Use ATP synthase (ATPase) * To send protons back into cytoplasm * And creates rotation * In the cytoplasm there is a pool of phosphate and … and this rotation sends the phosphate moving—takes 3 phosphate to make 1 ATP 1 glucose 38 ATP (aerobic respiration) Fermentation vs. Respiration * Respiration is more efficient; more evolved; more complex * Fermentation is less evolved; more simple; but very few ATP *Bacteria do photosynthesis Photosynthetic microbes need: Pigments: located in: membranes * Eukaryotes= chloroplasts * Prokaryotes= chlorosomes (sole purpose to hold pigment); cytoplasmic membrane; thylakoid membranes (freely floating) Chloroplasts: * Contain outer membrane, inner membrane, thylakoid membranes (grana) Chlorosomes: * Membrane structure full of bacteriachlorophyll Chlorophylls/ Bacteriochlorophylls Antenna chlorophylls/=transfer light energy to reaction center Reaction Center chlorophyll * Complexes of pigment and protein; bigger Carotenoids—organisms will contain these to absorb more light energy * More variety of light waves to be absorbed for organisms * Found in organisms not photosynthetic * Photoprotective role * Act as toxic oxygen species * Like pigments in our skin protect us from UV rays Phycobilins Types of Photosynthesis: * All about it oxygen produced Anoxygenic: no oxygen Oxygenic: oxygen Electron transport in Anoxygenic Photosynthesis Passing along electrons and as it does so it pushes protons outside of the membrane All inorganic molecules—no glucose, no carbon * Eat hydrogen sulfide to start process * Light starts the process; inorganic molecules donating * Cyclic Electron transport in Oxygenic Photosynthesis * Two reaction centers * Start with Photosystem II * Once chlorophyll absorbs enough energy it takes an electron from WATER (never another molecule) initiates electron transport chain * Releases oxygen as a byproduct (this is the oxygen we breathe) * Terminal electron acceptor NADH * NOT CYCLIC Why would a cell want to do cyclic photophosphorylation? Water is not the issue Wavelengths of light... Review of Photosynthesis: Oxygenic: Two electron transport chain Two photosystems—different wavelengths (what is available) Purpose of making ATP is for biosynthesis Autotrophs: Carbon fixation many pathways * Calvin-Benson cycle (what trees use) Some organisms can be autotrophs and heterotrophs—versatile Calvin-Benson Cycle: * *RibuloseRubisCO3-Phospho- * We want rubisco to bind one molecule CO2 and one molecule ribulose.. and it could combine them and then splits them apart to get 2 molecules phosphor-glycerate * CO2 molecules to get taken up by rubisco for the organism to produce 1 molecule of sugar (a 6 phosphate)—ATP * Uses NADH (which came from last acceptor in electron transport chain) * *Occurs in chloroplast stroma (autotrophic prokaryotes) * *Carboxysomes—can also occur here * aka “Dark Reaction” can happen if light is there or not * Oxygen acts as an inhibitor to process * This might be why it is carried out in concentrated areas (carboxysomes) of rubisco where there is less oxygen to interfere Do not need to know bacteria on bottom of slides or intermediates Reverse Citric Acid Pathway: Called a pathway because there will be an end product All enzymes used in citric acid cycle are reversible * Get Acytel-CoA out * Takes CO2 and connects it to another molecule to build bigger organic molecules * Yields sugar—requires CO2 and ATP Hydroxypropionate Pathway: Acetyl-CoA Pathway: acetogens * Acetate is made and turn around and used * Substrate-level phosphorylation at the end * *Sodium motive force (Na+ instead of H+) *Pathway used by organisms depends on what they are genetically able to do. Halobacterium—grows on salt—needs high salt concentration for sodium motive force to make ATP for itself Methanogenisis: Uses Co2 & some H2 and produces methane (CH4) Occurs in cows gut microbes and bottoms of the ocean Methanocaldococcus jannaschii: archaea *majority of organisms that do methanogenisis are Archaea Methanotrophs use methane to initiate electron transport chain * Take in and fix carbon (from environment) into methane to donate electron to transport chain and produce ATP and products which fix carbon (biosynthesis) Chemoliotrophic hydrogen oxidation * Starts with H2 (inorganic) and ATP to make cell material * Oxygen accepts last electron to make water—Aerobic respiration *Most chemoliotrophs do aerobic respiration *Most are autotrophs Many non-photosynthetic organisms can fix carbon. Biosynthesis of Sugars and Polysaccharides * Glucose can be made from many different other molecules Pentose Polysaccharides * Activated forms of glucose—when attached to glucose act as energy; * When bondage of UDPG is cleaved, energy is released, and another glucose can be added on (UDP provides the energy) *Those organisms that do fermentation are chemoorganotrophs. * Need organic molecules to start fermentation Phototroph * Anoxygenic * Oygenic—water is ALWAYS the electron donor. * Once water gives up its electron is releases oxygen Archaea, Prokarya, Eukarya all contain: * Phototrophs * ------------------------------------------------- Chemoorganotrophs

----MATERIAL FOR TEST THREE---- Macronutrients Oxic/ Anoxic *Aerobic respiration is the only metabolic pathway that must have oxygen to occur. Our stomach, gut, is an anoxic environment Aerobes: three kinds 1. Obligate: must have oxygen; can only perform aerobic respiration 2. Facultative: prefer using oxygen; but have other options (yeast) 3. Microaerophilic: require oxygen, but lower than atmospheric levels Anaerobes 1. Aerotolerant: tolerate oxygen; do not use it 2. Obligate: cannot have oxygen (or just wont grow in presence/ some O2 actually kills organism); fermentation/anaerobic respiration *Metabolism is the reason why they are classified as they are.

PROKARYOTES Cell Wall Synthesis In order to put new cell wall material in, small holes must be made in the existing cell wallcertain protein placesquickly filled in with new material * Autolysins * Autolysis: too many holes that are not filled in * Penicillin could cause lysis 1. Peptidoglycan Precursor—5 amino acids (pentapeptide) 2. Transpor 3. Bactrophenol: attaches to precursor and attached it to hole * Needs bactrophenl to get sugar (hydrophilic) through hydrophobic inside membrane; bactrophenol has no preference to –phillic –phobic Transpeptidation- bond between I. Equal parts do not need to know bacteria on slide except two below Hycomicrobium and Cor Budding from hyphae cell elongation; dna at polar end; pinches off (swarmer cell) ; Septum: where cell wall is laid down; gets flagella and then can swim away; once that cell wants to divide it will loose its flagella and start process over again * Hyphomicrobium Cell division in stalked bacteriastalk is attached to a surface=purpose=anchor cell to surface (rock, ect.); new cell will come from other side (not stalk extension); two extensions from each side; can keep releasing swarmer cells; time is dependent on organism * Calobacter

EUKARYOTES * Bacteria cannot do sexual reproduction Sacchromyces * Two different mating types: type A and type alpha * Can fuse together (opposites) sexual reproduction: nucleous will fuse together two haploid cells become one diploid cell * Saccromyces does not prefer sexual reproduction; only when conditions are bad; good for variation however * In good conditions; undergo meiosis (4 haploid cells: 2 a and 2 alpha) * Once diploid can reproduce as diploid Can also occur in green algae Chlamydomonas * Nutrient deprovation: low nitrogen * Have + and – and only opposites can fuse; fuse a flagella * Syngamy: creates hard encrusted zygote until conditions are good * *Would prefer asexual reproduction The Growth Cycle Lag Phase: cell is accessing environment; nutrients in culture medium; figuring out what it needs to do; time dependent on organism and Exponential: cells start growing; exponentially Stationary: plateau growth; nutrients run out; growth waits; could be caused by build up of toxic wastemust live in their own waste Visible to naked eye at 1000 cells in one colony: a millimeter

Halo.. Vibrio natrigens: needs high salt concentration; found in salt-water environments; * Fastest growing-reproduces in 6 minutes Exponential Growth:

Biofilms: groups of cells (depth of microbes) packed in together and form on a solid surface; sticky; form for many reasonsby chance, nutrients, defense, ect. * Protist come along and eat surface but not likely to remain there and continue eating down * **Review article on biofilms * Forms capsules (slime layer)—gooey matrix * Cells signal one another and biofilm grows in 3 dimensionsdeveloping spaces, water channelsmore complex (with many species joining the mix) * *Not like colonies on a plate (those are pure cultures); biofilms are typically not pure cultures * Once big, it will not stay in ‘place’it will start breaking off and spreadingescaping bacterial cells Ouorum Sensing: cells communicate with moleculeshomoserine lactone (AHL): * Very powerful messenger that assembles other cells & tells them what to do * Molecules secreted by cells when their concentration is at a certain thresh hold (number) Those with diseases, such as Cystic Fibrosis, cannot remove microbes and lungs are not sterile biofilm forms in lungs and kills host Periodontal disease: biofilm that forms on teeth and in between teeth Infections with implants opening body up allows inside of body to be vulnerable to bacteria where it normally never would Pipelines contain a lot of hydrocarbon (food for microbes); attach to surface; form a biofilm and secrete acid which corrode pipe (weakens it) Boats ***found out molecule that forms from bacteria on boat and degrade it *** Intra species communicationmolecules are similar in part of but have a different ending (different words but species specific) AHL Inter species communication Bacteria are multilingual generic enzymetrade language; universal communication molecule: 5 carbon molecule ***FOUND OUT MOLECULE IN ARTICLE***

1. Virulent Virus Attachment, Penetration, Rejection, Leaving Virus highjacks host cells machinery and force the host cell to recognize its genes. * Modifies RNA polymerase; viral promoterssynthesize of more viral protein Viruses cannot make their own proteins—must make host cell transcribed for them. Proteins can leave through lysing or through budding (leaving as vesicle enclosed in host membrane). * Better for virus to leave by budding then the host could be infected forever, now acting as a virus factory. Virus will go through process within 20 minutesfairly rapid * One cell could have multiple viruses attached to it. * Animals are more commonly to be infected by say pig, horse, and bird flu all at the same time. T4 takes capsids and puts them together and fills it with nucleic acid as much will fit—one long single string (one linear piece)—nucleic acid string 9 genes long cut by enzyme 2. Temperate Virus—goes through 5 steps BUT have alternative pathway: lysogeny Lysogenic Pathway: virus becomes prophagehost has no idea it has viral DNA in its genome; virus stays dormantwill get out of prophage stage and go into the lytic pathwayand proceed C1 (lambda repressor) Cro: intergrase cuts hosts DNA to allow viral DNA to be added in If Cro is in greater amount than C1, then you get the lytic pathway—there is no turning back—it will compete to lysis **When Lysogeny** Exponential is when replication takes place—active; lots of However, not in stationary stage—therefore virus will go into lysogeny If endospore is formed in lag stage, then viral DNA will be part of that genome. **When Lysis** DNA damage—virus does not want to incorporate into dying host. -Protease flip proteins (break down old ones into amino acids to build new proteins)—all cells produce this naturally -Amounts and proportions of CI and Cro are what matter
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Test 4 Material Chemotherapeutic … Antibiotics made by BACTERIA effective against other Bacteria **known first two columns** Aminoglycosides---binds to ribosomes and inhibits protein synthesis; stops growing Tetracyclines— Macrolides- Vancomycin Daptomycin Platensimycin—Methocilin resistance (semi-synthetic penicillin) Antibiotic resistance—predates humans and is not caused by humans ***following slide has a lot of information need to know*** Table 26.8 *Chlamydia and …. Do not have cell walls (penicillin is worthless on infection—penicillin has no target) Reduced permeability—do not absorb/take up antibiotics * Gram negative has outer, selective membrane which makes it harder to treat than gram positive * Weaken cell wall Inactivation of antibiotic * Alter antibitotic (beta lactamase) * Cut enzymes (these enzymes are already existing in organism, which uses enzymes for other reasons also). Inhibiting Precursor—folic acid ------------------------------------------------- Antimicrobial Drug Resistance Planet Earth: ~ 4.5 billion years old Oldest Dated Rocks: ~ 3.86 billion years old First Microbes: ? 3.5 billion years old Early Earth: anoxic; lots of Co2 As Earth cooled, there was so much water; it was all covered whole area Under water, just the right elements montmorillonite plates * RNA can form on plates Stromatolites: first; photosynthetic; precipitated minerals which build rock Shift from anoxic to oxic environment: Banded Iron formation -Organisms started using oxygen (oxygenic prototroph) and over hundreds of millions of years, oxidize watermillions of years after atmosphere becomes oxygenated -Oxygen reacts with UV and creates the ozone layershields Earth and allows organisms & bacteria to move from aquatic habitat to land Endosymbiosis Theory: -Mitochondria and chloroplasts are the only organelles which have their own genome; ribosomes (70S= same as bacteria); respond the antibiotics; similar rRNA sequences -Look like bacteria The Hydrogen Hypothesis-how first eukaryotic was formed? -Engulfment of H2 producing cell of Bacteria by a H2 consuming cell of Archaea beneficial relationship was stable and continued Mitochondria can no longer be independent of a host cell. Oxygenic phototroph must of engulfed a cyanobacteria cellchloroplast (membrane bound from the host cell)later bacterial cells, now chloroplasts, have many membranes (thylakoids) and are already ‘double bound’ Taxonomic Hierarchy D.P.C.O.F.G.S. (strains) Proteobacteria: biggest phylum; all gram negative Phylogeny: ribosomal RNAs= the best and first used to test if organism is new * Sequencing 16s (prokaryotes) & 18s (eukaryotes) * Sequence gene which transcribes for ribosomes above Ribosomal RNA Sequencing Table 16.2 Molecular taxonomy 1. GC ratio-higher the temperature (tm) = higher the GC ratio contenttriple bonded 2. DNA:DNA hybridization- nearly perfect match=same species (70-100%)16s 3. Multilocus Sequence Typing: house-keeping genes (i.e. gyrase in bacteria) 4. ------------------------------------------------- Fatty Acid Methyl Ester (FAME) Analysis- fatty acids differ within domains-graphs with ‘peaks’ relay amounts of kinds of fatty acids (composition); however it does depend on diet Immunology Leukocytes- ‘white blood cells’- phagocytes and lymphocytes are leukocytes * Phagocytes: forefront of immune response * Lymphocytes: * T Cells (Killer T’s): mature in the thymus * B Cells: mature in bone marrow Circulatory and Lymphatic Systems: function together; swap cells, molecules, ect * One system Non-Specific/ Innate Immunity -NK circulate in blood all the time searching for foreign cells (virus, bacterial, tumor) -Bind to foreign cell and release enzymes to kill foreign cell -Phagocytes * Toll-like receptors (TLRs): recognition molecules; specific * TLR 1-2: recognize lipopeptides * TLR 4: recognize gram negative * TLR 3: recognizes viruses, double stranded RNA * Recognition sets a series of steps Neutrophils: in highest concentration always; first phagocyte to respond Chemokines: proteins; signaling molecules; signal for help Adaptive (Specific) Immunity Specificity, Immunity, Tolerance

Natural Killer Cells—Innate Immunity -MHC protein embedded in normal cells -NK cell is introduced to MHC and deactivates itself cell is licensed -NK cell look for cells that do no have the MHC protein or cells that do not have a lot of MHC Cell Mediated Immunity -T-cytotoxic cells: MHC I -T-helper cells: MHC II: signals for helpreleases cytokinesprompts series of events, such as, inflammation (opens blood vessels to allow more blood cells to get to site of infection) and phagocytosis T-Cell Tolerance * Positive: must interact with MHC proteins and if they don’t, then they die. * Now with MHC protein, they can recognize self and move on. * Negative: t cells interact with self and hold on too tightly and if they do, they die because you want it to recognize self and move on. If it holds too tightly it means its activated when recognized self, and that is not good= autoimmune disease Antibody Mediated/ Antibodies/ Immunoglobulin (Ig)proteins with 4 polypeptide -Variable region interacts with antigen *Need to Know 5 Classes * IgG: major antibody * IgA: antibody in secretions; deals with respiratory pathogens (flu) * IgM: first to infection elsewhere (besides mouth and respiratory) * IgD: similar to IgM * IgE: allergic reactions *parasitic infection B Cells Plasma Cells Memory Cells Secondary Immune Response IgMIgG : class switiching * Light chain stays the same