Micro Exam I: Lectures 1-10

three types of lens in light microscopy

(1) condenser lense - to (2) objective lense - from (3) ocular lens - virtual image

salmonellosis statistics

- 1.4 million cases; 400 deaths annually - associated with commercial chicken and egg production - bacteria survive in the albumin - diagnosed directly from the stool or the PCR -treatment with oral rehydration therapy

staphylococcus epidermidis

- 90% of normal skin microbiota - healthcare associated pathogen - produce biofilm on catheters - coagulase negative

methods of classifying and identifying microorganisms (2)

- Bergey's Manual of Determinative Bacteriology (identification schemes for identifying bacteria and archaea) - approved lists of bacterial names (lists species of known classification)

Two-photon microscopy

- Cells are stained with fluorochrome dyes - Two photons of long-wavelength (red) light are used to excite the dyes - Can study living cells up to 1 mm deep

confocal microscopy

- Cells are stained with fluorochrome dyes - Short-wavelength (blue) light is used to excite a single plane of a specimen - Each plane in a specimen is illuminated and a three-dimensional image is constructed with a computer

Genetics (3 types)

- DNA fingerprinting - DNA-DNA hybridization - DNA chip

Fungi (overview)

- Eukaryotic (distinct nucleus) - chitin cell walls - yeast are unicellular - molds and mushrooms are multicellular absorbs organic chemicals for energy * molds consist of masses of mycelia which is composed of filaments called hyphae

psychrotrophs

- Grow between 0°C and 20-30°C - Cause food spoilage in fridges

Hepatitis D virus (HDV)

- HepD is considered to be a subviral satellite because it can propagate only in the presence of the HepB - HepD is the only virus in the genus (deltaviridae) and it is not classified into a viral family because it is a unique virus dependent on HBV - it is linked with the hep B infection but is (-)ssRNA that is circular - there are both acute (coinfection) and chronic (superinfection) forms - if HVB infection is In a chronic stage, superinfection with HDV is often accompanied by progressive liver damage and a fatality rate several times that of people infected with HepB alone

acid-fast cell walls

- Like gram-positive - Waxy lipid (mycolic acid) bound to peptidoglycan - Mycobacterium - Nocardia - stain with carbolfuchsin

Capnophiles

- Microbes that require high CO2 conditions - the low oxygen, high-CO2 condition exist in the intestinal tract, respiratory tract

the detection of viral infection

- PCR (polymerase chain reaction) the majority of studies for the detection of HHV-8 DNA used PCR methods - immunohistochemistry - in-situ hybridization - serology (ELISA, western blot)

Pasteurization

- Pasteur demonstrated that microbial spoilage bacteria could be killed by heat that was not hot enough to evaporate the alcohol in wine - pasteurization is then the application of a high heat for a short time to kill harmful bacteria in beverages

Characteristics of Archaea cell type, cell wall, membrane lipids, first AA in protein synthesis, antibiotic sensitivity, rRNA loops, common arm of tRNA

- Prokaryote - varies in composition, contains no peptidoglycan - composed of branched carbon chains attached to glycerol by ether linkage - methionine - not antibiotic sensitive - lacks rRNA and tRNA

The First Synthetic Drugs

- Quinine from tree bark was long used to treat malaria (caused by non-motile protozoan, plasmodium species) - Paul Ehrlich speculated about a "magic bullet" that could destroy a pathogen without harming the host - 1910: Ehrlich developed a synthetic arsenic drug, salvarsan, to treat syphilis - 1930s: Sulfonamides were synthesized

gram negative cell wall

- Thin peptidoglycan - Outer membrane - Periplasmic space - 4 rings in basal body of flagella - produce endotoxins and exotoxins - not sensitive to penicillin (outer membrane) - made of lipoplysaccharides

Fluorescence microscopy

- Uses UV (short wavelength) light - Fluorescent substances absorb UV light and emit longer wavelength (visible) light - Cells may be stained with fluorescent dyes (fluorochromes) if they do not naturally fluoresce

transmission electron microscopy - define + magnification & resolution

- a beam of electrons passes through ultra thin sections of a specimen, then through an electromagnetic lens, then focused on a projector lens - specimens may be stained with heavy-metal salts for contrast - magnifies objects 10,000 - 100,000x with a resolution of 10 pm

Protista

- a catchall kingdom for a variety of organisms; autotrophic and heterotrophic - grouped into clades based on rRNA - mostly unicellular

solution, solute, solvent

- a homogenous mixture of two or more substances - substance present in the smaller amount - substance present in larger amount (usually water)

refractive index

- a measure of the light-bending ability of a medium - light may refract after passing through a specimen to an extent that it does not pass through the objective lens - immersion oil is used to keep light from refracting

chemically defined media (culture)

- a media exact chemical composition is known - fastidious organisms are those that require many growth factors provided in chemically defined media

nucleus function

- a membrane-enclosed organelle found in eukaryotic cells. - Eukaryotes usually have a single nucleus, but a few cell types, such as mammalian RBCs have no nuclei, and a few others including osteoclasts have many - contains most of the cell's genetic material, organized as multiple long linear DNA molecules In a complex with a large variety of proteins (ie histones to form chromosomes)

glycocalyx

- a sugar coat substance that is secreted on the surface of many prokaryotes - is external to the cell wall - viscous and gelatinous - made of polysaccharides and/or polypeptides - contributes to virulence due to protection of capsule to prevent bacteria from phagocytosis

the central dogma

- a theory in genetics and molecular biology subject to several exceptions that genetic information is coded in self-replicating DNA and undergoes unidirectional transfer to messenger RNAs in transcription which act as templates for protein synthesis in translation. - it was first stated by Francis Crick in 1958 replication (DNA to DNA) transcription (DNA to mRNA) translation (mRNA to protein)

function of the digestive system

- absorption of foods and nutrient (25 tons of food pass through the GI tract in a lifetime)

Viruses (overview)

- acellular - consists of DNA or RNA core - core is surrounded by a protein coat, that can be enclosed in a lipid envelope - are replicated only when they are in a living host - inert outside of living host

stages of HIV infection (3)

- acute HIV infection - chronic HIV infection - acquired immunodeficiency syndrome (AIDS)

Examples od DNA oncogenic viruses (5)

- adenoviridae (adenocarcinomas, cancer of glandular epithelial tissue) - herpesviridae (EBV - burkitt's lymphoma cells) - poxvirdiae (epithelial hyperplasia) - papovaviridae (HPV - virtually all cervical and anal cancers) - hepadnaviridae (HepB - liver cancer)

axial filaments - prokaryotic cells

- also called endoflagella - found in spirochetes - anchored at one end of a cell - rotation causes cell to move like a corkscrew

scanning electron microscopy - define + magnification & resolution

- an electron gun produces a beam of electrons that scans the surface of an entire specimen - secondary electrons emitted from the specimen produce a 3D image - magnifies object 1,000 - 10,000x with resolution of 10 nm

negative ssRNA strand

- antisense strand - viral RNA is transcribed to a + strand to serve as mRNA for protein synthesis

chronic HIV infection

- asymptomatic HIV infection or clinical latency - HIV continues to multiply in the body but at very low levels

community acquired MRSA infections are associated with (6 examples)

- athletic facilities - highly physical sports - dormitories - military barracks - correctional facilities - day care centers

the size of bacterial cells

- average size: 0.2-2.0 micrometers in diameter x 2-8 micrometers in length - most bacteria are monomorphic (single shape) - a few are pleomorphic (many shapes)

chromophore color and charge in basic/acidic dyes

- basic dye (cation) - acidic dye (anion)

plasma membrane function

- biological membrane that separates the interior of all cells from the outside environment, composed of a phospholipid bilayer - acting as a selective permeable barrier for most molecule

DNA chip

- can be manufactured to contain hundreds of thousands of synthetic single stranded DNA sequences. Assuming that each DNA sequence was unique to a different gene -tracks gene expression - tagged DNA will bind only to their complementary DNA on the chip and be fluorescent to be analyzed by a computer

falcultative anaerobes

- can survive with or without O2 - via fermentation or anaerobic respiration - bacterial growth is best where most oxygen is present but can grow regardless. can neutralize toxins via enzyme catalase and superoxide dismutase

the transformation of normal cells into tumor cells

- cancer causing alternations to cellular DNA affect parts of the genome called oncogenes - oncogenes transform normal cells into cancerous cells - oncogenic viruses become integrated into the host cell's DNA and induces tumors (proviruses) - tumor cells undergo transformation, that is, they acquire properties that are distinct from the properties of uninfected cells or from infected cells that don't form tumors - a transformed cell often harbors a tumor specific transplant antigen (TSTA) on the surface and a T antigen in the nucleus

Staphylococcus aureus

- carried in the nasal passages of 20% of population - most virulent of the staphylcocci (MRSA, antibiotic resistant) - golden yellow colonies - coagulase positive - may produce damaging toxins and cause sepsis - toxic shock syndrome (TSS) due to the secretion of TSS exotoxin (symptoms include: fevers, vomiting, shock, organ failure) - avoids host defenses in the skin (secretes protein and toxins that kill phagocytic cells)

gonorrhea general

- caused by neisseria gonorrhoeae - gram negative diplococcus - 300,000 cases in the US annually - attaches to the epithelial mucosa by the fimbriae (invades the spaces between the columnar epithelial cells (causes inflammation/form pus)

hypotonic, hypertonic, isotonic

- cells swell, too much water - cells shrink, too little water - equilibrium, unchanged

structures and functions of the nervous system (CNS, PNS, meninges, BBB)

- central nervous system: the brain and the spinal cord - peripheral nervous system: the nerves that branch from the CNS - three continuous membranes (meninges) that protect the brain and the spinal cord are the dura, arachnoid, and pia mater (the outer, middle, and innermost layers respectively) the subarachnoid space contains CSF - Blood brain barrier: certain capillaries permit some substances to pass from the blood into brain but restrict others (drugs cannot cross the BBB unless they are lipid soluble)

Acute Lymphoblastic Leukemia (ALL)

- characterized by the overproduction of WBC, particularly the B and T lymphocytes by the bone marrow - these B and T cells do not work like normal lymphocytes and are not able to fight infection well - ALL is a type of cancer in which the bone marrow makes too many immature lymphocytes (WBC)

purpose of each type of culture media (chemically defined, complex, reducing, selective, differential, enrichment)

- chemically defined: growth of chemoautotrophs and photoautotrophs; microbiological assays - complex: growth of most chemoheterotrophic organisms - reducing: growth of obligate anaerobes - selective: suppression of unwanted microbes and encourages desired microbes - differential: differentiation of colonies of desired microbes - enrichment: similar to selective media but designed to increase numbers of desired microbes to detectable levels

Culture Media - Agar

- complex polysaccharide - used as a solidifying agent for culture media in petri plates, slants, and deeps - generally not metabolized by microbes - liquifies at 100C and solidifies at 40C

bacteria and nitrogen

- component of proteins, DNA, ATP - most bacteria decompose protein material for the nitrogen course - some bacteria use NH4 or NO3 from organic materials - a few bacteria use N2 in nitrogen fixation

Plate counts

- count colonies on plats that have 30-300 colonies - to ensure that the right number of colonies are counted, the original inoculum must be diluted via serial dilutions

pour plate method

- counts are performed on a bacteria mixed into a dish with agar 1. inoculate empty plate 2. add melted nutrient agar 3. swirl to mix 4. colonies grow on and In solidified medium

culture media (culture medium, sterile, inoculum, and culture)

- culture medium: nutrients prepared for microbial growth - sterile: no living microbes - inoculum: microbes introduced into a culture medium - culture: microbes growing in or on a culture medium

2 examples of preserving bacterial cultures

- deep freezing with cryoprotectant (glycerol/dimethyl sulfoxide) -50 to -95C - lyophilization (freeze-drying): frozen (-54 to -72C) and dehydrated in a vacuum

acute HIV infection

- develops within 2-4 weeks after the infection with HIV - flu-like symptoms - HIV multiplies rapidly and spreads throughout the body - the virus attacks and destroys the infection-fighting CD4 cells of the host immune system - the level of HIV in the blood is very high

diagnosis of meningitis

- diagnosed by lumbar puncture where the CSF is analyzed for organisms. - spinal needle is inserted usually between the fourth and fifth lumbar vertebrae to access CSF

facilitated diffusion

- diffusion is facilitated by integral proteins - transports ions and larger molecules across the membrane along its concentration gradient - can be a non-specific transporter (ion transport) or a specific transporter (ie. GLUT)

penicillin

- discovered in 1928 by Alexander Fleming - derived form penicillium fungi - binds to penicillin binding protein (PBP) which is an enzyme in bacteria called DD-transpeptidase which cross-links the peptidoglycan chains to form ridge cell walls - when a bacterium multiples, small holes open up in its cell walls as the cell divides. Newly produced peptidoglycan then fill these holes to reconstruct the walls. Penicillin block the protein struts that link the peptidoglycan together which prevents the bacterium from closing the holes in its cell walls

poxviridae

- double stranded DNA (enveloped) - cause skin lesions (vaccinia and smallpox viruses (orthopoxvirus)

papovaviridae

- double stranded DNA (nonenveloped) - papillomavirus (causes warts, can transform cells and cause cancer)

adenoviridae

- double stranded DNA (nonenveloped) - respiratory infections in humans - tumors in animals

Roeviridae (2)

- double stranded RNA (nonenveloped) - reovirus (respiratory enteric orphan) - rotavirus (mild respiratory infection and gastroenteritis)

Characteristics of Eukarya cell type, cell wall, membrane lipids, first AA in protein synthesis, antibiotic sensitivity, rRNA loops, common arm of tRNA

- eukaryote - cell wall varies in composition, contains carbohydrates - methionine - not antibiotic sensitive - lacks rRNA loop but has common arm of tRNA

Protozoa (overview)

- eukaryotic - absorbs or ingests organic chemicals - may be motile via pseudopods, cilia, or flagella - free living or parasitic (derives nutrients from living host) ie. brain eating amoeba

Algae (overview)

- eukaryotic - cellulose cell wall - found in freshwater, saltwater, and soil - PHOTOSYNTHESIS for energy - produces oxygen and carbohydrates

Darkfield microscpy

- example of a compound light microscope - light objects are visible against a dark background - opaque disk placed in condenser - only light reflected off the specimen enters the objective lens

brightfield illumination

- example of a compound light microscope - makes dark objects visible against a bright background - the light reflected off the specimen does not enter the objective lens

Virulence factors of S. pyogenes (7)

- example of group A streptococci 1. streptolysins (S and O) lyse RBC and toxic for neutrophils 2. M proteins: external to the cell wall and allows adherence and immune system avoidance 3. hyaluronidase: dissolves connective tissue 4. streptokinases: dissolve blood clots 5. erysipelas: infects the dermal layer of the skin (cases local tissue destruction and sepsis) 6. necrotizing fasciitis: flesh eating disease - extotoxin A produced by S pyogenes acts as a superantigen 7. streptococcal toxic shock syndrome (TSS) similar to staphylococcal TSS

phase contrast microscope

- example of light microscope - allows examination of living organisms and internal cell structures - brings together two sets of light rays, direct rays, and diffracted rays to form an image

how can a RNA virus cause cancer if it doesn't have DNA to insert into a cell's genome?

- expression of viral oncogenes - integration that alter oncogenes/ tumor suppressors, or components of signal transduction pathways - chronic activation of inflammatory response LEADS TO INHIBITION OF APOPTOSIS (GENETIC INSTABILITY)

complex media (culture)

- extracts and digests of yeast, meats, or plants; chemical composition varies batch to batch - nutrient broth/ agar

flagella and bacteria

- filamentous appendages external of the cell - used to propel bacteria and made of protein flagellin

acquired immunodeficiency syndrome (AIDS)

- final and most severe stage of HIV infection - the body cannot fight off opportunistic infections due to severely damaged the immune system by HIV infection

stapylococcal skin infections (folliculitis, sty, furuncle, carbuncle, impetigo)

- folliculitis: infections of the hair follicles - sty: folliculitis of an eyelash - furuncle (boil) a type of abscess, localized region of pus surrounded by inflamed tissue - carbuncle: damage and inflammation of deep tissue from a spreading furuncle - impetigo: crusting (non-bullous) sores, spread by autoinoculation gram positive cocci in chains; produce hemolysins that lyse RBC, strephtococci differentiated into groups A-T based on antigenic cell wall carbohydrates

peroxide anion

- formed during reactions catalyzed by Superoxide Dismutase and other reaction - O2(-2)

Hydroxyl radical (OH)

- formed in cellular cytoplasm by ionizing radiation and cannot be eliminated by an enzymatic reaction. - it has a very short in vivo half-life of ~10(-9) seconds and a high reactivity

free-living nitrogen fixing bacteria vs symbiotic nitrogen fixing bacteria

- free-living nitrogen fixing bacteria are found in rhizosphere (azotobacter, beijerinckia, clostridium pasteurianum) - symbiotic nitrogen fixing bacteria are adapted to leguminous plants (beans and clovers of all kinds) and form root nodules (rhizobium, bradyrhizobium, frankia)

bacteria capsules and staining

- gelatinous covering that do not accept most dyes - suspension of India ink or nigrosin contrast the background with the capsule, which appears as a halo around the cell

scientific names

- genus + species - are italicized or underlined (the genus is capitalized, the specific epithet is lowercase) - are latinized and used worldwide - may be descriptive or honor a scientific

Group A Streptococcus (GAS) bacteria

- gram (+) cocci - facultative anaerobic - there are currently over 75 species under this genus - GAS lives in pairs or chains of varying lengths - infections caused by GAS are common throughout the world, result in a wide variety of illness (mild to lethal) and the most virulent GAS is S. pyogenes

neisseria meningitidis meningitis (meningococcal meningitis)

- gram negative aerobic cocci with a capsule (six serotypes associated with the disease) - 47% of people are healthy carriers - begins as a throat infection, rash, and bacteremia - mortality of 9-12% with antibiotic therapy (80% without) - outbreaks common in dorms and military barracks - vaccination protects against serogroups A, C, Y, and W but not B

crystal violet iodine complex with gram positive and gram negative stains

- gram positive bacteria: complex is trapped in the thick peptidoglycan layer; therefore turns purple - gram negative bacteria: the thin peptidoglycan layer is unable to hold the complex and the color becomes lost - therefore pink

haemophilus influenza meningitis

- gram-negative aerobic bacteria; normal throat microbiota - can enter the blood stream - pathogenicity due to capsule antigen type B - occurs mostly in children (6mts-4yr) - prevented by Hib vaccine - accounts for 45% of bacterial meningitis and 6% mortality

difference between gram positive and gram negative bacteria

- gram-positive bacteria have thick peptidoglycan cell walls - gram-negative bacteria have thin peptidoglycan cell walls and a layer of lipopolysaccharides

Phylogenetic Tree

- grouping organisms according to common properties (ie fossils, genomes) - groups of organisms evolved from a common ancestor - each species retain some characteristics of its ancestor

psychrophiles

- grow between -8C and 25C, will not grow at 25C - found mostly in the ocean's depth and polar regions - can cause food spoilage

examples of syphilis

- gummatous syphilis: gummas on many organs - cardiovascular syphilis: weans the aorta - neurosyphilis: affects the CNS; dementia - congenital: neurological damage to the fetus

general morphologies of viruses (4)

- helical virus - hollow, cylindrical capsid - polyhedral virus (many sided) - enveloped viruses - complex viruses (complicated structures)

how do viruses grow?

- in living cells (host) it must take over the host's metabolic machinery - one step growth curve - host-living cell in which a virus multiplies

eukaryotes originated from

- infoldings of prokaryotic plasma membranes - endosymbiotic bacteria developed into organelles

trace elements

- inorganic elements required in small amounts - usually as an enzyme cofactor - includes iron, copper, molybdenum, and zinc

pili (singular: pilus)

- involved in motility (gliding and twitching motility) - usually longer than fimbriae and number only two or one per cell - conjugation pili: involved in DNA transfer from one cell to another

structure and function of the lower respiratory system

- larynx, trachea, bronchial tubes, and alveoli - ciliary escalator moves particles toward the throat via ciliary action - alveolar macrophages destroy microorganisms in the lungs - respiratory mucus protects mucosal surfaces

gram negative cell walls - lipopolysaccharide

- lipid A is an endotoxin embedded in the top layer, released when bacteria die and cause fever, dilation of blood vessels, shock, blood clotting - the core polysaccharide is attached to lipid A and provides stability - O polysaccharide extends outward from the core polysaccharide and functions as an antigen

teichoic acid

- located on the surface of Gram (+) bacterial cell walls; covalently bound to peptidoglycan layers; help maintain structure for the peptidoglycan layer - carries a negative charge and regulates the movement of cations - polysaccharides and teichoic acids provide antigenic specificity

Radiation and Industrial Food Preservation

- low doses (<1 kGy) kill insects and inhibits sprouting - pasteurizing doses (1-10 kGy) reduce pathogens on meat and poultry - high doses ( >10 kGy) sterilize or greatly lower bacteria in species PRIONS ARE NOT AFFECTED (misfolded protein)

Gut-associated lymphoid tissue (GALT)

- lymph nodese - peyer's patches - the first bacteria that colonize an intestinal tract make the immune response more favorable for their own survival

bacteriophage lambda: the lysogenic cycle

- lysogeny: phage remains latent - phage DNA incorporates into host cell DNA - inserted phage DNA is known as a prophage - when the host cell replicates its chromosome, it also replicates prophage DNA - results in phage conversion - the host cell exhibits new properties

outer membrane of gram negative bacteria

- made of polysaccharides, lipoproteins, and phospholipids - porins: integral proteins that form channels through membrane - periplasm: between the outer membrane and the plasma membrane contains peptidoglycan

transmission of HIV

- mater to child (pregnancy, delivery, breast feeding) - sexual contact - needle sharing during intravenous drug use - medical injections with unsterilized equipment - transfusion of HIV-infected blood products - organ transplantation

nucleoid function

- meaning nucleus-like - is an irregularly shaped region within the cell of a prokaryote that contains all or most of the genetic material (DNA) - in contrast to the nucleus of an eukaryotic cell, it is not surrounded by a nuclear membrane

gonorrhea symptoms

- men: painful urination and discharge of pus; epididymitis - women: fewer symptoms; pelvic inflammatory disease - if left untreated, may disseminate and become systemic (endocarditis, meningitis, and arthritis) - has no adaptive immunity (anitgenic variability - the opa proteins bind to T cell receptors to prevent it from activation and immunological memory) - diagnosis with gram stain, ELISA, or monoclonal antibodies - treatment first with cephalosporins

biofilms

- microbial communities - Colonies of bacteria that adhere together and adhere to environmental surfaces (form slime or hydrogels that will adhere to the surface) - allows bacteria to survive and grow slowly in nutrient poor environments (helps shelter bacteria from harmful environmental factors) - 1000x resistant to microbicides - involved in 70% of infections (catheters, heart valves, contact lenses, dental caries)

test for syphilis and treatment

- microscopic test: direct fluorescent-antibody test (DFA-TP) with monoclonal antibodies - nontreponemal serological tests: slide agglutination VDRL test and rapid plasma reagin (RPR) test - treponemal-type serological test: enzyme immunoassay (EIA) and fluorescent treponemal antibody absorption test (FTA-ABS)

normal microbiota of the digestive system

- millions of bacteria per ml of saliva - few microorganisms in the stomach (due to HCl production, low pH) - small intestine define (paneth cells' granule-filled phagocytic cells that produce defensins) - large numbers of bacteria in the large intestine (anaerobes and facultative anaerobes) - 100 biIlion bacteria per gram of feces

pH for bacterial growth/ molds and yeast

- most bacteria grow between pH 6.5 - 7.5 - molds and yeast grow between pH 5 - 6

the spectrum of host cells a virus can infect and viral size

- most viruses infect only specific types of cells in one host (determined by specific host attachment sites and cellular factors) - bacteriophages - viruses that infect bacteria - ranges from 20 nm to 1000 nm in length

Multicellular animal parasite (overview)

- multicellular animals (eukaryotic) - not strictly microorganisms but had some microscopic stages in their life cycle * parasitic flatworms and roundworms are called HELMINTHS

the nitrogen cycle (general)

- nitrogen is required to make proteins and nucleic acids - N2 make up 80% of the atm (must be fixed into organic compounds by microorganisms)

normal microbiota of the respiratory system

- normal microbiota suppress pathogens by competing for nutrients and producing inhibitory substances - lower respiratory system is nearly sterile

structure and functions of the upper respiratory system

- nose, pharynx, middle ear, and eustachian tubes - saliva and tears protect mucosal surfaces

Molecular clock for evolution is based on

- nucleotide sequences in the genomes of organisms - mutations accumulated in genome at constant rate - comparing the number of mutations between two organisms with the expected rate of change provides of estimate of when the two diverged from common ancestor

general characteristics of viruses (5)

- obligatory intracellular parasites (require living host cells to multiply) - contain DNA or RNA - contain a protein coat - no ribosomes - no ATP generating mechanism

thermophiles

- optimum growth of 50-60C - found in hot springs and organic compost - form heat resistant endospores which can survive pasteurization

Hyperthermophiles

- optimum growth temp >80C - found in hot springs associated with volcanic activity - need sulfur for metabolism

mesophiles

- optimum growth temp of 25C to 40C - most types of microbes - adapted to live in the bodies of animals and have an optimum temperature close to their host

organic growth factors are (4 major examples)

- organic compounds obtained from the environment - vitamins (coenzymes) - amino acids - purines (A/G) - pyrimidines (C/T/U)

lysogenic cyclee

- phage DNA is incorporated in the host DNA - phage conversion (the host cell may exhibit new properties (ie the toxin produced by clostridium botulinum, which causes botulism, is encoded by prophage gene)) - specialized transduction (when a prophage is exised from the host chromosome, adjacent cell genes from either side may remain attached to the phage DNA)

phosphorus cycle

- phosphorus changes from soluble to insoluble forms and organic to inorganic forms - exists primarily as phosphate ions (PO4) - often in relation to pH (acidithiobacillus: produces acid that solubilizes phosphate in rocks) unlike the other cycles there is no volatile phosphorus containing product to return phosphorus to the atmosphere in the way CO2, N2, and SO2 are returned. Therefore, phosphorus tends to accumulate in the seas

bacteria in the carbon cycle (photoautotrophs, chemoheterotrophs, and decomposers)

- photoautotrophs: fix CO2 into organic matter using energy from the sunlight - chemoheterotrophs: use organic matter for energy (energy and CO2 are released via respiration, cycle repeats) - decomposers: oxidize organic compounds from dead plants and animals

both prokaryotes and eukaryotes are bounded by ____

- plasma membranes of similar construction that serves as a selectively permeable barrier. - both types of cells may be surrounded by a rigid cell wall that protects the cell - eukaryotic cells are much more complex, both structurally and functionally, than prokaryotic cells

peptidoglycan

- polymer of a repeating disaccharide in rows (N-acetylglucosamine (NAG) and N-actylmuramic acid (NAM) - rows of disaccharides are linked by polypeptides

stages of syphilis

- primary stage: chancre (painless ulcers in genitals) at the site of infection about 3 weeks after exposure - painless ulcer and highly infectious - disappears after 2 weeks - secondary stage: skin and mucosal rashes - palms and soles due to an inflammatory response - latent period: no symptoms - tertiary stage (appear years after latency) due to cell mediated immune reactions

Characteristics of Bacteria cell type, cell wall, membrane lipids, first AA in protein synthesis, antibiotic sensitivity, rRNA loops, common arm of tRNA

- prokaryote - cell wall contains peptidoglycan - membrane lipids: composed of straight carbon chain attached to glycerol by ester linkage - formylmethionine - antibiotic sensitivity - has rRNA and tRNA

Archaea (overview)

- prokaryotic - lack peptidoglycan cell walls - often found in extreme conditions - includes: methanogens (CO2 to methane), extreme halophiles, and extreme thermophiles

Bacteria (overview)

- prokaryotic (prenucleus) - single celled - peptidoglycan cell walls - divide by binary fission - energy and nutrient from organic or inorganic chemicals and photosynthesis

gram positive pleomorphic rods that are are associated with the skin

- propionibacterium acnes inhabits hair follicles - anaerobic (produce acids that maintain low skin pH) - corynebacterium xerosis occupy the skin surface - aerobic yeast - malassezia furfur causes dandruff

extreme or obligate halophiles

- require high osmotic pressure (high salt) - organisms from such saline waters as Dead Sea often require nearly 30% salt in solution

obligate aerobes

- require oxygen - can neutralize toxins via enzyme catalase and superoxide dismutase

Microaerophiles

- require oxygen concentration lower than air - produce lethal amounts of toxic forms of oxygen if exposed to normal atmospheric oxygen

inclusions (define + 7 examples)

- reserve deposits; stored nutrients - metachromatic granules (volutin) phosphate reserves - polysaccharide granules - energy reserve - lipid inclusions - energy reserve - sulfur granules - energy reserves - carboxysomes - contains RuBisCO enzyme for CO2 fixation during photosynthesis - gas vacuoles - protein covered cylinders that maintain buoyancy - magnetosomes - iron oxide inclusions that destroy H2O2

normal microbiota of the skin

- resistant to drying and high salt concentrations - often grouped into small clumps - microorganisms remaining in hair follicles and sweat glands after washing will soon reestablish the normal populations - large number of gram (+) cocci -- staphylcocci and micrococci - ares with moisture have higher populations (metabolize sweat and contribute to body odor)

endospore

- resistant, dormant structures inside some cells that cannot be stained by ordinary methods - resting cells, produced when nutrients are depleted - resistant to desiccation, heat, chemicals, and radiation - produced by bacillus and clostridium

symbiosis examples between animals and microbes

- ruminants (sheep/cows) and digestive bacteria in the rumen - mycorrhizae: relationship between plant roots and fungi that extend the root surface area (endomycorrhizae and ectomycorrhizae)

salmmonellosis define

- salmonella gastroenteritis - gram negative, facultative anaerobe, nonendospore-forming rod - normal inhabitant of the human intestinal tract (2000 serotypes) - invades intestinal mucosa and multiplies (passes through the M cells and enters the lymphatics (replicates in macrophages) - incubation of 12-36 hrs - fever, nausea, pain, cramps and diarrhea

positive ssRNA stand

- sense strand - viral RNA serves as mRNA for protein synthesis

Differential interference contrast (DIC) microscopy

- similar to phase contrast - uses two light beans and prisms to split light beams, giving more contrast, and color to the specimen

picornaviridae (2)

- single stranded RNA (+ strand) non-enveloped - enterovirus (poliovirus - causative agent of poliomyelitis) and coxsackievirus - rhinovirus (common cold) - hepatitis A virus

filtration for microbial growth

- solution passed through a filter that collects bacteria - filter is transferred to a petri dish and grows as colonies on the surface

specialized transdunction

- specific bacterial genes transferred to another bacterium via a phage - changes genetic properties of the bacteria 1. prophage exists in galactose - using host (containing the gel gene) 2. phage genome excises, carrying with it the adjacent gal gene from the host 3. phage matures and cell lyses, releasing phage carry gal gene 4. phage infects a cell that cannot utilize galactose (lacking gal gene) 5. along with the prophage, the bacterial gal gene becomes integrated into the new host's DNA 6. Lysogenic cell can now metabolize galactose

Staphylococci (general define)

- spherical gram(+) bacteria that forms irregular clusters - normal flora of the skin, mouth, nose, and throat - unless the skin barrier is broken (by burns or trauma) staphylococci are normally harmless - cause of purulent (pus containing) skin lesions - pimples, bullae, pustules - many produce coagulase (enzyme that clots fibrin in the blood; used to identify type of staph) there is a high correlation between the bacterium's ability to form coagulase and its production of damaging toxins

togaviridae (2)

- ssRNA (+ strand) - enveloped - alphavirus (transmitted by arthropods; includes chikungunga - rubivirus (rubella)

Rhabdoviridae

- ssRNA (- strand) one RNA strand - lyssavirus (rabies) - numerous animal diseases

stages of pertussis (3), vaccination, treatment

- stage 1: catarrhal stage, like the common cold - stage 2: paroxysmal stage, violent coughing, gasping for air - stage 3: convalescence stage, may last for months - prevented by DTaP vaccine - treated with erythromycin and other macrolides (class of abx) before vaccines, 6000 people died annually in the US from the pertussis

Carbon for bacterial growth (autotrophs and chemoheterotrophs)

- structural backbone of organic materials - autotrophs use CO2 - chemoheterotrophs use organic molecules as energy

energy sources using microbes - biofuels (ethanol creation)

- sugars are fermented by microorganisms to ethanol - cellulose in plants are digested by cellulase to make ethanol

bacteria and sulfur

- sulfur is used in AA, thiamine, and biotin - most bacteria decomposes protein for sulfur source - some bacteria uses SO4 or H2S (hydrogen sulfide)

mycorrhizae

- symbiotic relationships between fungal hyphae and plant roots - help plants absorb nutrition, especially phosphorus - which is not very mobile in the soil

generation time of bacteria

- the time required for a cell to divide is roughly about 20 minutes to 24 hours - binary fission doubles the number of cells each generation - exponential growth (total number of cells is two to the number of generations) - growth curves are represented logarithmically

Louis Pasteur (1861)

- theory of biogenesis - he demonstrated that microorganisms are present in the air via his experiments and that life did not arise spontaneously form nonliving matter - his discoveries included the relationship between microbes and disease, immunity, and antimicrobial drugs - also showed that microbes are responsible for fermentation

Flat sour spoilage

- thermophilic spoilage without gas - often caused by geobacillus stearothermophilus

facultative halophiles

- those that do not require, but can tolerate high salt concentrations, tolerate high osmotic pressure - these microorganisms can grow at salt concentrations up to 2% and a few species can tolerate even 15% salt

aerotolerant anaerobes

- tolerate but cannot use oxygen - many are lactic acid producers - growth occurs evenly as oxygen has no effect - can partially neutralize harmful forms of oxygen

obligate anaerobes

- unable to use oxygen and are harmed by it - O2 is toxic to them - lacks enzymes to neutralize harmful forms of oxygen, cannot tolerate

Reducing media culture

- used for the cultivation of anaerobic bacteria - contain chemicals (sodium thioglycolate) that combine O2 to deplete it - heated to drive off O2

phosphorus and bacteria

- used in DNA, RNA, ATP - found in membranes - (PO4)-3 is a source of phosphorus

electron microscopy

- uses electrons instead of light - the shorter wavelength of electrons gives greater resolution - used for images too small to be seen with light microscopes (ie. viruses)

what are microbial diseases of the skin? (vesicles, bullae, macules, papules, pustules, exanthem, enanthem)

- vesicles: small, fluid-filled lesions - bullae: vesicles larger than 1 cm in diameter - macules: flat, reddened lesions - papules: raised leisons - pustules: raised lesions with pus - exanthem: skin rash arising from a disease - enanthem: rash on mucous membranes arising from a disease

family names end in ___ (for viruses)

- viridae

viral structures - virion - nucleic acid - capsid - envelope - spikes

- virion is a complete, fully developed viral particle - nucleic acid (DNA or RNA) can be single or double stranded (linear or circular) - capsid: protein coat made of capsomeres (subunits) - envelope: lipid, protein, and carbohydrate coating on some viruses - spikes: projections from outer surface, carbohydrate-protein complexes, can provide viral attachment and hemagglutination (influenza virus)

how to grow animal viruses in embryonated eggs ? (influenza virus)

- virus injected into the egg - viral growth is signaled by changes or death of the embryo

direct microscopic count

- volume of a bacterial suspension placed on a slide - average number of bacteria per viewing field is calculated via the petroff-hausser cell counter # of bacteria per ml = #cells counted/ volume of area counted

structure of plasma membrane

-Fluid mosaic model -Membrane is as viscous as olive oil -Proteins move freely for various functions -Phospholipids rotate and move laterally -Self-sealing

plasma (cytoplasmic) membrane

-Phospholipid bilayer that encloses the cytoplasm -Peripheral proteins on the membrane surface -Integral and transmembrane proteins penetrate the membrane - hydrophilic heads and hydrophobic tails

Endospore staining (primary stain, decolorizing, counterstain)

-Primary stain: malachite green, usually with heat -Decolorize cells: water -Counterstain: safranin -Spores appear green within red or pink cells

gram positive cell walls

-Thick peptidoglycan -Teichoic acids -2-rings in basal body of flagella -Produce exotoxins -High sensitive to penicillin -Disrupted by lysozyme

Knowledge of microorganisms allows humans to (3)

-prevent food spoilage -prevent disease -understand causes and transmission of disease to prevent epidemics

Thermophilic anaerobic spoilage

-spoilage from thermophilic bacteria that survive in low-acid canned foods (thermophilic species of clostridium) -can swells with gas; food has a lowered pH and a sour odor

simple stains

-use of a single basic dye - highlights the entire microorganism to visualize cell shape and structures

genus name end for viruses

-virus

Koch's Postulates

1) Pathogen must be present in all disease cases 2) Isolate pathogen, cultivate in pure culture 3) Inoculate into susceptible animal, initiate disease symptoms 4) Re-isolate pathogen, confirm it's the same pathogen

Three principles of cell theory

1. All organisms are composed of one or more cells 2. The cell is the structural unit of life 3. All cells arise only by division from preexisting cells

1. DNA dependent DNA polymerase 2. RNA dependent RNA polymerase 3. DNA dependent RNA polymerase 4. RNA dependent DNA polymerase

1. DNA replicase (copies DNA into DNA) 2. RNA replicase (copies RNA into RNA) 3. Transcriptase (copies DNA into RNA) 4. Revertase (copies RNA to DNA)

influenza virus genetic mutations (2)

1. antigenic drift: minor antigenic changes in hemaagulation spikes (viral attachment and entry) and neuraminidase spikes (enzyme for viral release from infected host), allows the virus to elude some host immunity 2. antigenic shifts: changes great enough to evade most immunity. Recombination of the genomes of two or more viral strains and formation of new subtype of the virus which has mixture of the surface antigens of the two or more original strains

gram staining procedure (4)

1. application of crystal violet (purple dye) 2. application of iodine (mordant) 3. alcohol wash (decolorization) 4. application of safranin (counterstain)

T-Even Bacteriophages: The Lytic Cycle

1. attachment: phage attaches to host cell 2. penetration: phage penetrates host cell and injects its DNA 3. biosynthesis: phage DNA directs synthesis of viral components by the host cell 4. maturation: viral components by the host cell 5. release: host cell lyses, and new virions are released

multiplication of animal viruses

1. attachment: viruses attach to the cell membrane 2. entry by receptor mediated endocytosis or fusion 3. uncoating by viral or host enzyme 4. biosynthesis: production of nucleic acid and proteins 5. maturation: nucleic acid and capsid proteins assemble 6. release by budding (enveloped viruses) or rupture

the shape of bacterial cells (3 basic shapes + 2 other examples)

1. bacillus (rod shaped) 2. coccus (spherical) 3. spiral (vibrio, spirillum, and spirochete) 4. start shaped 5. rectangular

3 examples of special stains used to distinguish parts of a microorganism

1. capsule stain 2. endospore stain 3. flagella stain

what are three possible side effects of CART-cell therapy

1. cytokine-release syndrome (CRS) large amount of cytokines produced during the activation of the immune system which causes flu-like symptoms 2. B-cell aplasia: deficiency in normal lymphocytes (B cells). can be countered with intravenous immunoglobulin administration 3. Tumor lysis syndrome (TLS) can occur as a complication during the treatment of cancer, where large amounts of tumor cells are killed off (lysed) at the same time by the treatment, releasing their content into the bloodstream

Baltimore classification classes and their method of replication with examples

1. ddDNA virus; adenovirus, herpesvirus, and poxvirus 2. +ssDNA virus; parovirus 3. dsRNA virus; reovirus 4. +ssRNA virus; picornavirus and togavirus 5. -ssRNA virus; orthomyxovirus and rhabdovirus 6. +ssRNA that replicate through a DNA intermediate; retrovirus 7. dsDNA virus that replicate through a ssRNA intermediate; hepadnavirus

PCR steps (3)

1. denaturation: the reaction is heated to 94-98C to break the H bonds between the strands 2. annealing: the reaction temp is lowered to 50-65C for 20-40 s to allow primers to anneal to the template strands 3. Elongation: the temp is increased to 75-78C (Taq polymerase) to allow for the addition of dNTPs. the amount of target sequence doubles with each thermal cycle which leads to an exponential amplification

the four phases of bacterial growth

1. lag phase: intense activity preparing for population growth, but no increase in population (little or no cell division) 2. log phase: exponential increase in population (binary fission) 3. stationary phase: period of equilibrium, microbial 4. death phase: population is decreasing at an exponential rate

how to count colonies (CFU) on original plate 1? (3 steps)

1. make serial dilution of bacterial culture (original inoculum) 2. count CFUs on plate 3 (1:1000 dilutions) 3. number of colonies on plate 3 x dilution of sample = number of bacteria/ml

bacteria vs viruses 1. intracellular parasite 2. plasma membrane 3. binary fission 4. pass thru bacteriological filters 5. posses both DNA and RNA 6. ATP generating metabolism 7. ribosomes 8. sensitive to antibiotics 9. sensitive to interferon

1. no; yes 2. yes; no 3. yes; no 4. no; yes 5. yes; no 6. yes; no 7. yes; no 8. yes; no 9. no; yes

examples of antiviral treatments for HIV/AIDs (7)

1. nucleoside analog (zidovudine) 2. nucleotide analog (tenofovir) 3. non-nucleoside inhibitor (nevirapine) 4. protease inhibitors (atazanavir) 5. integrase inhibitors (raltegravir) 6. entry inhibitors (miraviroc) 7. fusion inhibitors (enfuvirtide) chronic, life-threatening, but not immediately fatal

5 different types of arrangements of bacterial cells and examples

1. pairs (diplococci and diplobacilli) 2. clusters (staphylococci) 3. chains (streptococci, streptobacilli) 4. groups of four (tetrad) 5. cubelike groups of eight (sarcinae)

3 methods of direct measurement of microbial growth

1. plate count 2. filtration 3. direct microscopic count

herpes simplex life cycle

1. primary lytic infection of epithelial or mucosal cells 2. progeny viral particles are transported to nerve cell bodies and virus can be spread to the CNS 3. viral genome can persist as a latent episome within the neurons 4. upon stimulation virus can reactivate and travel to neuron termini 5. virus initiates productive recurrent infection upon encountering an epithelial/ mucosal cell

transfer/ packaging/ and envelope vector

1. regulatory signals (LTR and psi) promoter and insert gene 2. structural and packaging gene (may already be present in the packaging line - to create the infectious viral particles) 3. viral envelope protein alters host range of the viral vector

characteristics of proteins by western blot

1. separate proteins by weight 2. transfer to nitrocellulose membrane 3. detect the protein of interest with specific antibodies western blot = protein immunoblot

the skin is inhospitable place for most microorganisms because

1. the secretion of the skin is acidic 2. most of the skin contains little moisture a few microbes that colonize skin can cause disease (staphylococcus aureus)

herpes gladiatorum herpetic whitlow herpes encephalitis

1. vesicles on the skin 2. vesicles on the fingers 3. virus spreads to the brain (treated with acyclovir)

How many nanometers are in 10 micrometers?

10,000 nanometers

Golden Age of Microbiology (years)

1857-1914

A Fortunate Accident—Antibiotics

1928: Alexander Fleming discovered the first antibiotic Fleming observed that Penicillium fungus made an antibiotic, penicillin, that killed S. aureus 1940s: Penicillin was tested clinically and mass produced

the discovery of reverse transcriptase

1970 Howard Temin and David Baltimore

most organisms grow best between what pH

6.5 - 8.5

_____% of the immune system is located in the intestinal tract, especially the ______________

80; small intestine

Which of the following statements about viruses is false? a. they can only be found associated with animal and bacterial cells b. they are smaller than bacteria c. they are responsible for numerous human diseases d. some of them can become integrated into the DNA of the host's cell

A

Acute vs Chronic HBV

Acute - often subclinical, infected person is often entirely unaware - similar symptoms to HAV, gradually recovers - fulminant hepatitis in 1% of cases (sudden massive liver damage, fatal) Chronic (HBeAg) - involves 10% of infected pts - may lead to liver cirrhosis or liver cancer - presence of HBeAg indicates a vigorously replicating virus - treated with interferons and nucleoside analogs

safranin stain

Added as the counter/secondary stain in a Gram Stain which color the gram negative bacteria pink-red and have no effect on gram positive bacteria.

antigenic

Any substance that can stimulate the production of antibodies and combine specifically with them

contrary to viruses, bacteria: a. contain genetic material in the form of DNA or RNA b. can be infected by bacteriophages c. have only 3-4 genes d. are microscopic

B

7 types of microorganisms

Bacteria Archaea Fungi Protozoa Algae Viruses Multicellular animal parasites

how do bacteriophages get nucleotides and amino acids if they do not have any metabolic enzymes

Bacteriophages propagate themselves by hijacking the metabolic enzymes of bacteria they infect and using amino acids and nucleotides etc already present in the cytoplasm.

acid fast stain

Binds only to bacteria that have a waxy material in their cell walls, which is not Electrons have a smaller wavelength than visible light, leading to higher resolution. and is not decolorized by acid-alcohol - Used for the identification of Mycobacterium && Nocardia

To kill tumor cells we need to construct new T killer cells known as _____

CART cells (chimeric antigen receptor therapy)

when describing a polymerase enzyme, the terms _______ or ______ may be used to indicate the type of nucleic acid template that he enzyme uses

DNA - dependent RNA - dependent

Recombinant DNA

DNA produced by combining DNA from different sources (1960) Paul Berg inserted animal DNA into bacterial DNA and then the bacteria produced an animal protein

Baltimore classification

Developed by David Baltimore, a virus classification system that groups viruses into families, depending on their type of genome (DNA/RNA/ss/ds) and method of replication - broken down into 7 classes

Why do electron microscopes have greater resolution than light microscopes?

Electrons have a smaller wavelength than visible light, leading to higher resolution.

Carl Woese (1978)

Found that there are three domains based on cellular organization (BAE) - bacteria (cell wall with peptidoglycan) - archaea ( cell wall if present without peptidoglycan) - Eukarya (protist: slime mold, protozoa, algae)(fungi: unicellular yeast, multicellular molds, mushrooms) (plants: mosses, ferns, conifers, flowering plants) (Animals: sponges, worms, insects, vertebrate)

macromolecules (4)

Four main classes of large biological molecules - carbohydrates - protein - lipids - nucleic acid (polysaccharides, proteins, and nucleic acids consists of monomers (subunits) that are linked together by covalent bonds)

you discovered a new multicellular, nucleated, heterotrophic, organism with cell whats. What kingdom does it belong to?

Fungi

structures of the digestive tract an the accessory structures

GI tract: - mouth - pharynx (throat) - esophagus - stomach - small intestine - large intestine Accessory structures: - teeth and tongue - salivary glands - liver - gallbladder - pancreas

differential staining

Gram staining, acid-fast staining; not useful for bacteria without cell walls

Spontaneous generation

Hypothesis stating that life could arise from nonliving matter.

Western blotting

Identifies antibodies in a patient's serum; confirms HIV infection

Vibrio Cholerae produces toxin and is capable of causing cholera only when it is lysogenic. What does this mean?

Its only capable of causing cholera when the viruses incorperate their DNA into the host cells DNA and begin the lysogenic cycle.

enzyme-linked immunosorbent assay (ELISA)

Known antibodies and an unknown type of bacterium are added to a well; a reaction identifies the bacteria

Classification of viruses

Not a part of any domain; not composed of cells; require a host cell

what are the requirements for bacterial growth? (physical and chemical requirements)

PHYSICIAL - temperature - pH - osmotic pressure CHEMICAL - carbon - nitrogen - sulfur - phosphorous - oxygen - trace elements - organic growth factors

Compare DNA, histones, first AA, ribosomes, and reproduction in prokaryotic, eukaryotic, and eukaryotic organelles

PROKARYOTE - circular/some linear - histones only in archaea - (b) formylmethionine (a) methionine - 70S - binary fission EUKARYOTE - linear DNA - has histones - methionine - 80S - mitosis EUKARYOTIC ORGANELLES - circular DNA - no histones - formylmethionine - 70S - binary fission

Venn diagram compare and contrast prokaryotes and eukaryotes

PROKARYOTES - oldest cell type - small and simple - lack nucleus - lack organelles - single celled single circular chromosomes BOTH - have DNA - have ribosomes - have cytoplasm - have plasma membrane EUKARYOTE - evolved from prokaryote - larger and more complex - contain nucleus - contains organelles - single celled or multicellular - multiple linear chromosomes

what are the main features that distinguishes prokaryotes from eukaryotes?

PROKARYOTES - one circular chromosome, not in a membrane - no histones - no organelles - bacteria: peptidoglycan cell walls - archaea: pseudomurein cell walls - divides by binary fission EUKARYOTES - paired chromosomes, in nuclear membrane - histones - organelles - polysaccharide cell walls, when present - divides by mitosis

Theory of Biogenesis

Pasteur's S-shaped flask kept microbes out but let air in - the broth in flasks showed no signs of life but the neck of the flask trapped the microbes - proved that microorganisms originate in air or fluids, not mystical forces

nucleic acids for viral identification

RFLPs and PCR

viruses multiple in the host cell's cytoplasm using

RNA-dependent RNA polymerase

Taxonomy

The science of classifying organisms - shows the degree of similarity among organisms

Immunology

The study of immunity. Vaccines and interferons are being investigated to prevent and cure viral diseases

retroviridae

Viral RNA is transcribed to DNA (using reverse transcriptase), which can integrate into host DNA HTLV-1 and HTLV-2 cause adult T-cell leukemia and lymphoma

archaea cell walls

Wall-less, or Walls of pseudomurein (lack NAM and D-amino acids)

how would one determine whether a microbe is a strict anaerobe?

You can tell by the way it grows. If its a strict anaerobe then it will only grow at the BOTTOM where there is NO O2

normal microbiota (microbiome)

a community of microorganisms (such as bacteria, fungi, virus) that inhabits a particular environment and especially the collection of microorganisms living in or on the human body - your body is home to about 100 trillion bacteria = microbiome (Carl Zimmer) - preventing the overgrowth of harmful bacteria - producing vitamin K and some vitamin B - can cause some disease if resistance of body is low

Bacterial strain

a group of genetically identical bacteria derived from a single cell

cell wall function

a layer located outside the cell membrane, composed of disaccharides and amino acids. They give bacteria structural support

Rebecca Lancefield (1933)

a major advance in immunology where she classified streptococci based on their cell wall components

Agar plate

a petri dish that contains a solid growth medium, typically agar plus nutrients, used to culture small organisms such as microorganisms

bacterial capsule function

a polysaccharide layer that lies outside the cell wall. It is considered a virulence factor because it enhances the ability of bacteria to cause disease (ie. prevents phagocytosis)

colony

a population of cells arising form a single cell or spore or form a group of attached cells (bacterial) - often called a CFU - colony forming unit

In an antiserum,

a solution of antibodies is tested against an unknown bacterium

smear for staining

a thin film of a material containing microorganisms spread over a slide

Resolution on a microscope

ability to separate two adjacent objects. (ie) A microscope with a resolving power of 0.4 nm can distinguish between two points at least 0.4 nm apart (shorter wavelength of light provides greater resolution)

nondairy fermentations - vinegar

acetobacter and gluconobacter aerobically convert ethanol to acetic acid

what can be used to preserve foods and can increase the osmotic pressure?

addition of salts (other solutes)

bioaugmentation

addition of specific microbes (specifically adapted) to degrade a specific pollutant (degradation of chlorinated ethene, such as tetrachlorethylene and trichloroethylene, petroleum cleanup)

Additive and synergistic effects

additive effects of two or more concurrent different treatments are simply the SUM of that treatment, if they were used separately, whereas, if the effects of different treatments are MORE than the sum of individual effect, there is synergistic effect

How are brightfield, darkfield, phase-contrast, and fluorescence microscopy similar?

all examples of light microscopy

differential media culture

allows to grow and distinguish colonies of different microbes on the same plate (some media have both selective and differential characteristics)

Reverse transcriptase

also called RNA-depended DNA polymerase, an enzyme encoded from the genetic material of retroviruses that catalyzes the transcription of retrovirus RNA into DNA

metabolic activity and bacteria

amount of metabolic product is proportional to the number of bacteria

Is reassortment of the RNA segments of the influenza virus the cause of antigenic shift or antigenic drift

antigenic shift

light microscopy simple definition and 6 examples

any kind of microscope that uses visible light to observe specimen - compound light microscopy - phase contrast microscopy - differential interference contrast (DIC) microscopy - fluorescence microscopy - confocal microscopy - STED (stimulated emission depletion)

xenobiotics

are resistant to degradation - made of chemicals that do not naturally occur in nature

composting

arranging organic waste to promote microbial degradation by thermophiles and converts plant remains into the equivalent of natural humus

what is the main source of the carbon in the cellulose forming the mass of a forest?

atmosphere

quorum sensing bacteria produce and release chemical signal molecules called __________ that increase in concentration as a function of cell density

autoinducers

slide agglutination test

bacteria agglutinate when mixed with antibodies produced in response to the bacteria (serology example) - agglutination is the clumping of particles

dry weight

bacteria are filtered, dried, and weighed - used for filamentous organisms

why do glycocalyx contribute to virulence?

bacteria that possess capsules are considered to be encapsulated and generally have greater pathogenicity (ability to cause disease) because the capsule protects the bacteria

syphilis

bacterial disease of the reproductive system - caused by treponema pallidum - gram negative spirochete and grows slowly in cell culture - invades the mucosa or through skin breaks and enters the bloodstream - stable incidence in the US

bacterial culture

bacterial grown in laboratory media

nitrogen fixation (nitrogen cycle)

bacterial process that converts nitrogen gas to ammonia - uses nitrogenase enzyme

Lynn Margulis

believed that certain organelles of a eukaryotic cell (mitochondria, chloroplast) had evolved from smaller prokaryotic cells that had taken up residence in the cytoplasm of a larger host cell

how do bacteria divide

binary fission (increase in number of cells not cell size) 1. cell elongates and DNA is replicated 2. cell wall and plasma membrane begin to constrict 3. cross wall forms, completely separating the two DNA copies 4. cell separates

because of the crucial importance of the nervous system, it is strongly protected from accident and infections by the ____________________

blood brain barrier (BBB) - pathogens capable of causing disease of the nervous system often have a special virulence characteristics that enables them to penetrate this defense - protozoan naegleria fowleri can enter the brain from the olfactory nerve in the nose (brain eating amoeba)

sectional diagram through a compound light microscope has what kind of lens

both an objective and an ocular lens

nondairy fermentations examples (~10)

bread dough beer sake wine vinegar sauerkraut pickles olives chocolate coffee

Hepatitis E virus (HEV)

caliciviridae - (+) ssRNA, nonenveloped - spread by fecal oral transmission (similar to HepA) - endemic in areas with poor sanitation - HEV does not cause chronic liver disease, but for some unexplained reason, it is responsible for a mortality rate in excess of 20% pregnant women

what bacteria is recognized as one of the main causes of bacterial food-borne disease in many developing countries

campylobacter jejuni

serological testing

can differentiate between species and strains within species

sarcoma

cancer of the connective tissue

adenocarcinomas

cancers of glandular epithelial tissue

two types of glycocalyx

capsule: neatly organized and firmly attached to the cell wall slime layer: unorganized and loose

what kind of stain stains every cell?

carbolfuschin (basic)

SDS-PAGE

carries out in the presence of a charged detergent, sodium docdecyl sulfate (SDS) -SDS denatures the protein molecules into a similar shape and then proteins become separated solely by mass

Antibiotics

chemicals produced by bacteria and fungi that inhibit or kill other microbes

Fungi

chemoheterotrophic; unicellular or multicellular; cell walls of chitin; develop from spores or hyphal fragments

stains consists of a positive and negative ion, one of which is colored known as ________

chromophore

gram stains

classifies bacteria into gram-positive and gram-negative

symbiosis

close association between two unlike organisms that is beneficial to one or both of them

psychrophiles, psychrotrophs, mesophiles, thermophiles,

cold-loving cold-resistant moderate-temp loving heat-loving

CART cell therapy

collecting, engineering, and using patient's own immune cells to treat cancer

energy sources using microbes - biomass

collective organic matter produced by living organisms

objective lens

collects light from the specimen

microbes that are growing are increasing in number, accumulating into _______ of hundreds of thousands of cells or population of cells

colonies

Color of acid fast vs non-acid fast for (1) primary stain: carbolfuchsin (2) decolorizing agent: acid-alcohol, and (3) counterstain: methylene blue

color of acid fast - red, red, red color of non-acid fast - red, colorless, blue

staining

coloring microorganisms with a dye that emphasizes certain structures

ribosome function

complex molecule machine, found within all living cells, that serves as the site of biological protein synthesis (translation) - made of protein and ribosomal RNA - in bacteria are 70S made of 50S and 30S subunits

in a _____________ microscope, the image from the objective lens is magnified by the ___________ lens

compound; ocular

pure culture

contains only one species or strain

energy sources using microbes -bioconversion

converting biomass into alternative energy sources

magnification on a microscope

creates an optical image of the object which appears to be enlarged

role of microorganisms in food production - cheese

curd: made of the protein casein and formed by the action of an enzyme (rennin) and lactic acid bacteria

bacteria of the genus pseudomonas, in the absence of oxygen, will use fully oxidized nitrogen as an electron acceptor, a process in the nitrogen cycle that is given what name?

denitrification

Biochemical test

determines presence of bacterial enzymes

osmosis

diffusion of water across a selectively permeable membrane - water moves from areas of low solute concentration to ares of higher solute concentration bc water is the solvent

condenser lens

directs light to the specimen

Dmitri Iwanowski (1892) and Wendell Stanley (1935)

discovered the cause of mosaic disease of tobacco as a virus

mitochondria function

double membrane bound organelle found in most eukaryotic organisms that generate most of the cell's supply of ATP as a source of chemical energy

herpesviridae and how - many times (?)

double stranded DNA (enveloped) - HHV-1/HHV-2 (simplexvirus, cause cold sores) - HHV3 (varicellovirus, causes chickenpox) - HH4 (lymphocryptovirus, causes mononucleosis) - HH5 - cytomegalovirus - HHV6/HHV7 - roseolovirus - HHV8 -(rhadiovirus, causes kaposi sarcoma)

mordant

dye fixative that is used to hold the stain or coat the specimen to enlarge it

are truffles an ecto/endo-mycorrhizae?

ectomycorrhiza

if lyme disease is suspected in a patient, _________ is used to separate the borrelia burgdorferi proteins

electrophoresis

biogeochemical cycles

elements are oxidized and reduced by microorganisms to meet their metabolic needs

Recombinant DNA technology

enables bacteria and fungi to produce a variety of proteins, vaccines, and enzymes - missing or defective genes in human cells can be replaced in gene therapy - genetically modified bacteria are used to protect crops from insects and from freezing

enrichment culture

encourages the growth of a desired microbe by increasing very small numbers of a desired organism to detectable levels (usually a liquid)

structures and functions of the skin (epidermis, keratin, dermis)

epidermis: thin outer portion of skin, composed of layers of epithelial cells keratin: waterproofing protein coating outer layer of epidermis dermis: inner, thick portion of skin, composed mainly of connective tissue

Stanley Prusiner

explained the cause of bovine spongiform encephalopathy (mad cow disease) he coined the term prion, which comes from the word (proteinaceous and infectious) to refer to a previously undescribed form of infection due to protein misfolding

endosymbiotic theory

explains how eukaryotic cells may have evolved from prokaryotic cells through the symbiosis (close relationship between two or more simpler organisms). Through millions of years of evolution, the aerobic bacteria became mitochondria and the photosynthetic bacteria became chloroplasts

glycocalyx that helps cells in biofilm attach to their target environment and to each other is called ______

extracellular polymeric substance (EPS)

Carolus Linnaeus (1735)

father of taxonomy who developed the system of scientific nomenclature of two names: genus and species (specific epithet)

role of microorganisms in food production - kefir

fermented milk beverages made with lactic acid producing bacteria and lactose fermenting yeast

characterization of proteins by western blot (protein immunoblot)

first need to run PAGE electrophoreses and separate proteins based on weight. Then, transfer the proteins to a nitrocellulose membrane which will then detect the protein of interest with specific antibodies

Robert Hooke (1665)

first reported that living things are composed of little boxes (cells) and marked the beginning of cell theory: all living things are composed of cells

during preparation of smears, microorganisms are _________ to the slide, which kills the microorganism

fixed (attached)

Hepatitis C virus (HCV) 9

flaviviridae - (+) ssRNA that is enveloped (often transfusion transmitted) - destroys the liver by using genetic variation to evade the immune response system - kills more in the US than AIDs - 85% of the cases become chronic and 25% develops liver cirrhosis or cancer - treated with peginterferon and ribavirin - Hep C is probably the major reason for liver transplantations - no vaccines available at the time - sharing items such as razors, toothbrushes, or nail clippers can be dangerous, in more than 1/3 of the cases, a mode of transmission - by contaminated blood, sexual contact, or other means - cannot be idenitified

role of microorganisms in food production - butter

flavor and aroma are from diacetyl (organic molecule) produced by lactic acid bacteria

superoxide radicals

form during incomplete reduction of oxygen in aerobic and anaerobic respiration

ocular lens

forms an enlarged, virtual image

water movement across membrane

from an area of lower solute concentration to higher solute concentration - through lipid layer - water channels are known as aquaporins

Are skin bacteria more likely to be gram-positive or gram-negative?

gram-postive

Kilogray (kGy) - 1000 gray

gray is defined as the absorption of one joule of ionizing radiation by one kilogram of matter (ie human tissue)

Human immunodeficiency virus (HIV) identifications- group, family, subfamily, genus, species

group VI: ssRNA retroviridae family orthoretrovirinae subfamily lentivirus genus HIV-1 and HIV-2 species

acidophiles

grow in acidic environments (<pH 5) - acidophiles in acid mine drainage oxidize sulfur to form sulfuric acids and can survive at pH 1

bacteriophages

grown in bacteria - form plaques (which are clearings on a lawn of bacteria on the surface of agar) - each plaque corresponds to a single virus: can be expressed as plaque-forming units (PFU)

2 examples of bacterial meningitis

haemophilus influenzae and meisseria meningitidis - initial symptoms of fever, headache, and a stiff neck; followed by nausea and vomitting - may progress to convulsions and coma or death from shock and inflammation (due to endotoxin and cell wall release) - viral meningitis is more common and mild

Fimbriae (singular: fimbria)

hairlike appendages that are shorter, straighter, and thinner than flagella. have a tendency to adhere to each other and to the surface (biofilm formation

pilus function

hairlike structure especially on the surface of a cell or microorganism

Hepatitis B virus (HBV)

hepadnaviridae - dsDNA, enveloped - resembles retroviruses - transmitted via the blood and bodily fluids (up to 1 billion viruses per ml blood) - the complete virions are called Dane particles - spherical particles and filamentous particles are the unassembled components of the virion (lacks DNA and contains HBV surface antigens (HBsAg) - prevented by a vaccine and can be treated with hepatitis B immune globulin (HBIG) - birth transmission can be prevented by administration HBIG to the newborn immediately after birth

shingles

herpes zoster - reactivation of the latent varicella zoster virus that moves along peripheral nerves to the skin (due to stress or lower immunity) - follows the distribution of affected cutaneous sensory nerves and limited to one side of the body - postherpetic neuralgia - prevention via the zoster vaccine - and antiviral drugs may lessen symptoms

neonatal herpes

herpesvirus crosses the placental barrier and infects the fetus (damages the CNS, developmental delays, blindness, hearing loss) - survival rate is 40% - newborns infected with HSV exposure during delivery - diagnosed by PCR test and fluorescent antibody test - treated with intravenous acyclovir

pascalization

high-pressure food preservation - pre-wrapped, precooked foods submerged into pressurized water tanks (87,000 psi) - kills many pathogens and non-pathogens - preserves food, color, and flavor

herpes simplex 1 & 2

human herpesvirus 1 and 2 (HSV-1)(HSV-2) - HSV-1 is spread primarily by oral or respiratory routes - HSV-2 is spread via sex 90% of the population is infected - usually develop as cold sores or fever blisters BUT NOT THE CAUSE OF CANKER SORES - HSV-1 remains latent in trigeminal nerve ganglia (outbreaks are triggered by the sun, stress, or hormonal changes - HSV-2 remains latent in sacral nerve ganglia near the spine

the sulfur cycle

hydrogen sulfide(H2S) forms under anaerobic conditions - source of energy for autotrophic bacteria - converted to elemental sulfur granules and sulfates (SO4) (ie. beggiatoa uses light for energy and H2S reduces CO2; plants incorporate sulfates into AA)

high osmotic pressures in ____________ environments causes __________

hypertonic; plasmolysis

_______ is used to keep light from refracting

immersion oil

how do animal viruses grow in the lab?

in cell cultures - tissues are treated with enzymes to separate cells - virally infected cells are detected via their deterioration, known as cytopathic effect (CPE) - continuous cell lines are used

where are biofilms found?

in digestive system and sewage treatment systems - can clog pipes

where do DNA viruses replicate their DNA?

in the nucleus of the host using viral enzymes - they synthesize capsid in the cytoplasm using host cell enzyme

microbial growth

increase in number of cells, not cell size

encephalitis

inflammation of the brain

Meningoencephalitis

inflammation of the brain and meninges

meningitis

inflammation of the meninges

Influenza

influenzavirus (orthomixovirus influenzae) - contains 8 RNA segments and an outer lipid bilayer - symptoms contain chills, fever, headache, and muscle aches (no intestinal symptoms) - 30,000-50,000 death in the US annually - types include: avian, swine, and mammalian strains (swine serve as mixing vessels for new strains) - 1% mortality rate - usually the very young and the very old - multivalent vaccine for the most important strains (composition of the vaccine determined annually by the id of circulating viruses) labor-intensive to produce and doesn't provide long term immunity - difficult to diagnose from clinical symptoms and treated with zanamivir (Relenza) and oseltamivir (tamiflu) which inhibits neuraminidase

Edward Jenner (1796)

inoculated a person with cowpox virus, who was then protected from smallpox - vaccination is derived from the latin word, vacca, meaning cow - protect is called immunity

bacterial flagellum function

is a lash-like appendage that protrudes from the cell body of a certain bacterial and eukaryotic cells. The primary role is locomotion, but also functions as a sensory organelle, being sensitive to chemicals and temperature outside the cell

flagellin

is a protein subunit of the flagellum that carries H antigens and distinguish among serovars

Polyacrylamide gel electrophoresis (PAGE)

is based on the migration of proteins in an electric field (to separate proteins) western blotting

the prion protein

is encoded by a gene within the cell's own chromosomes prpC: prion protein cellular normal form of protein NORMAL prpSc: prion protein scrapie-infectious form of protein (solubility and protein structure) DISEASED

cytoskeleton function

is present in all cells of all domains of life. It is a complex network of interlinking filaments and tubules (microtubules) that extend throughout the cytoplasm, from the nucleus to the plasma membrane

Fermentation

is the microbial conversion of sugar to alcohol in the absence of air

Serology

is the science that studies serum and immune response in serum

in clinical microbiology, ___________ are used to note types of specimens collected and tests to be conducted

lab requisition forms

mycoplasmas cell walls

lacks cell wall sterols in plasma membrane

smooth endoplasmic reticulum function

lacks ribosomes and functions in lipid manufacture and metabolism, the production of steroid hormones and detoxification

nondairy fermentations - sake

made by converting rich starch to sugar by aspergillus

nondairy fermentations - wine

made form fermented plant sugars; bacteria conduct malolactic fermentation to make wine less acidic

Identification

matching characteristics of an "unknown" organism to lists of known organisms (clinical lab identification)

Cytoplasm function

material within a living cell, excluding the cell nucleus substance inside the plasma membrane - 80% water plus proteins, carbs, lipids, and ions (cytoskeleton)

turbidity

measurement of cloudiness with a spectrophotometer (light sensitive detector)

temperature for bacterial growth (minimum/ optimum/ maximum growth temp define)

microbes can be classified according to the range of temperature at which they grow - minimum growth temp is the lowest temperature at which a species will grow - optimum growth temp is the best temp at which the species grows - maximum growth temp is the highest temperature at which growth is possible

what are microorganisms measured in? && give example of conversion

micrometers and nanometers

role of microorganisms in food production - yogurt

milk inoculated with strephtococcus thermophilus and lactobacillus delbrueckii

soil microbiology

millions of bacteria per gram of soil - most cannot be cultured and the largest populations are in the top few centimeters

simple diffusion

movement of molecules or ions from an area of high to low concentration

Plantae

multicellular; cellulose cell walls; undergo photosynthesis

Animalia

multicellular; no cell walls; chemoheterotrophic

industrial food canning (industrial microbiology) - 4 examples

must kill endospore-forming anaerobic bacteria (clostridium botulinum) 1. commercial sterilization 2. 12D treatment 3. thermophilic anaerobic spoilage 4. flat sour spoilage - mesophilic bacteria can spoil food In leaking cans (external bacteria introduced during the sealing process - causes putrefaction) - most acidic foods can be preserved by processing at less than 100C (heat resistant fungi: byssochlamys fulvus and aspergillus)

acid fast organisms cell wall is nearly impermeable, it contains ...

mycolic acid and large amounts of fatty acids, waxes, and complex lipids

the degradation of synthetic chemicals in soil and water (4 examples)

natural organic matter is easily degraded by microbes - composting - xenobiotics - bioremediation - bioaugmentation

staining the background instead of the cell is called

negative staining

Emerging infectious diseases (EIDs)

new diseases and diseases increasing in incidence - COVID-19 Coronovirus - H1N1 influenza (swine flu) pandemic - Avian Influenza A (H5N1) bird flu, sickened 242 people in 2008 - MRSA - methicillin resistant S aureus endemic in hospitals - VISA - vancomycin intermediate S aureus reported in 1990

denitrificiation (nitrogen cycle)

nitrite used as an electron acceptor by microbes in the absence of oxygen - produces nitrogen gas (lost to the atmosphere) - NO3 > NO2> N2O > N2

Based on the cell theory, do you think viruses are cells

no bc no preexisting cell, a cellular

singlet oxygen

normal molecular oxygen that has been boosted into a higher-energy state and is extremely reactive

the role of molecular chaperones

not all proteins can assume their final tertiary structures - molecular chaperones are known as helper proteins bind to short stretches of hydrophobic AA to hep unfolded proteins achieve their proper 3D conformation larger polypeptides are transferred to a different type of chaperone called chaperonin, a cylindrical protein complex that provides a folding environment

brownian movement

not true movement, is the continuous random movement of small particles suspended in a fluid, which arises from collisions with the fluid

total magnification formula

objective lens x ocular lens

Anton van Leeuwenhoek

observed the first microbes in 1623-1673 -- stated that animalcules were viewed through magnifying lenses using single-lensed microscopes of his own design

persistent viral infection

occurs gradually over a long period, generally fatal (subacute sclerosing panencephalitis) measles virus

Through what lenses does light pass in a compound microscope?

ocular, objective, and condenser

how to phage type test?

on a plate, clearings called plaques appear where phages infect and lyse bacterial cells - bacteriophages are highly specialized, in that way usually infect only membranes of a particular species or particular strain within a species

Chloroplast function

organelles, specialized compartments, in plant and algae cells that conducts photosynthesis

Microoraganisms

organisms that are too small to be seen with the unaided eyes

nitrificiation (nitrogen cycle)

oxidation of ammonium ions to produce nitrate - nitrate used by plants for protein synthesis

aseptic packaging

packages made of materials that cannot tolerate heat (sterilized) - paper and plastic sterilized with hot hydrogen peroxide or UV light - metal containers sterilized with super-heated steam or high-energy electron beams

Rapid identification methods

perform several biochemical tests simultaneously (ie. the picture of tube with media for multiple tests is inoculated with an unknown bacteria via needle to observe results (color bands)

Joseph Lister

performed surgery under aseptic conditions using phenol (antiseptic) to prevent surgical wound infections. Proved that microbes caused surgical wound infections

structure and functions of the skin (perspiration, lysozyme, antimicrobial peptides, oily secretions (sebum))

perspiration: provides moisture and nutrients for growth, contains salt that inhibits microorganism lysozyme: breaks down bacterial cell walls oily secretion (sebum): oil glands contains fatty acids that inhibit pathogens perspiration and sebum are nutritive for many microorganisms

lytic cycle of bacteriophages

phage causes lysis and death of the host cell

capsules prevent bacteria from ________

phagocytosis (only encapsulated bacillus anthracis causes anthrax) phagocytosis is the process in which a cell engulfs a particle, digest it, and expels the waste product

Hepatitis A virus (HAV)

picornaviridae - (+)ssRNA, lacks an envelope - entry via the oral route and multiples in the epithelial lining of the intestinal tract (spreads to the liver, kidneys and spleen) - symptoms include: anorexia, malaise, nausea, diarrhea, fever and chills which then turns into jaundice and dark urine - symptoms last 2-21 days with a low mortality rate of 0.3-0.6% - detected via IgM anti-HAV (appears in blood 4 weeks after infection) - treated with immune globulins - inactivated vaccine for prevention

Classification

placing organisms in groups of related species - lists of characteristics of known organisms

monomers and polymers form and break via

polymerization and hydrolysis

Bacteria clone

population of cells derived from a single parent cell

12D treatment

population of endospores decreased by 12 logarithmic cycles (1 survivor in 10^12 endospores)

viral species

population of viruses with similar characteristics (morphology, genes, enzymes) that occupies a particular ecological niche

RNA - positive and negative sense

positive sense chain (+ side) is sequence translated or tanslatable to protein. negative sense chain (- strand) chain is complementary to the mRNA

two methods of preparing plates for plate counting

pour plate method and spread plate method

osmotic pressure

pressure that must be applied to prevent osmotic movement across a selectively permeable membrane

cell wall of bacteria

prevents osmotic lysis and protects the cell membrane; made of peptidoglycan in bacteria and contributes to pathogenicity

four levels of protein folding

primary: AA sequence of protein secondary: alpha helix and beta pleated sheets folding (H bonds) tertiary: 3D shape of protein In which one single polypeptide chain (backbone) with one or more protein secondary structures (protein domains) quaternary: composed of subunits (ie hemoglobin)

Oxygen is so pervasive in the environment that it would be very difficult for a microbe to always avoid physical contact with it. What, therefore, is the most obvious way for a microbe to avoid damage?

produce enzymes to neutralize them against toxicity

energy sources using microbes - methane

produced form waste in landfills; produced by methanogenic microorganisms (archaea) in a process of anaerobic respiration

dissimilation - sulfur cycle

protein decomposition releases H2S into the sulfur cycle

If bacterial cells were given a sulfur source containing radioactive sulfur (35S) in their culture media, in what molecules would the 35S be found in the cells?

proteins

Robert Koch (1876)

proved that a bacterium causes anthrax and provided the experimental steps, Koch's postulates, to prove that a specific microbe causes a specific disease [established experimental steps for directly linking a specific microbe to a specific disease]

Peroxisomes function

provides the breakdown of very long chain fatty acids through beta oxidation and converts the long fatty acids to medium chain fatty acids, which are subsequently shuttled to the mitochondria where they are broken down to CO2 and H2O.

Bacteria communicate cell-to-cell via

quorum sensing

CART 19 receptor

receptor which recognizes B cell antigens CD19 we can deliver CART19 gene and incorporate it to T cells genome using HIV virus as a delivery vector

ammonification (nitrogen cycle)

release of ammonia by bacteria and fungi 1. microbial decomposition: break down proteins into AA 2. deamination: amino groups removed and converted to ammonia (NH3)

latent virus

remains in asymptomatic host cell for long periods and may reactivate due to changes in immunity (cold sores, shingles)

flagella staining

requires a mordant to make the flagella wide enough to see - flagella are structures of locomotion and uses a mordant and carbolfuchsin

nondairy fermentations - bread dough and beer

saccharomyces cerevisiae (baker yeast) produces ethanol anaerobically

a single strand of DNA - sense or antisense?

sense (postive +) if an RNA version of the same sequence is translated or translatable into protein

to ensure the right number of colonies are being counted, the original inoculum must be diluted via

serial dilution

________ ________ bacteria may form biofilms on urinary catheters or on contact lenses

serratia marcescens

Reye's Syndrome symptoms

severe complications of chickenpox - vomiting and brain dysfunction (aspirin use increase risk)

is shingles a persistent or latent infection?

shingle is active phase of latent chickenpox virus

__________ wavelength of light provides _______ resolution

shorter; greater

Peyer's patches

small masses of lymphatic tissue found throughout the ileum region of the small intestine

viroids

smallest pathogens, each consisting of a small, naked circular RNA molecule, without its protein coat. All known viroids are inhabitants of higher plants. causes potato spindle tuber disease (PSTV)

order for preparing smears for staining (3)

smear, fix, stain

A series of subdivisions developed by Linnaeus to classify plants and animals

species genus family order class phylum kingdom domain

endospore formation and return to vegetative state terms

sporulation; germination

spread plate method

spread on the surface of a plate 1. inoculate plate containing solid medium 2. spread inoculum over surface evenly 3. colonies grow only grow on surface of medium

commercial sterilization

steam under pressure in a retort; not as rigorous as complete sterilization

rough endoplasmic reticulum function

studded with ribosomes that are the sites of protein synthesis

Bacteriology

study of bacteria

Mycology

study of fungi

Parasitology

study of protozoa and parasitic worms

Virology

study of viruses electron microscopes have made it possible to study the structure of viruses in detail

Genomics

study of whole genomes, including genes and their functions - has provided new tools for classifying microorganisms

passive processes of membrane transport

substances move from high concentration to lower concentrations; no energy expended

Active processes of membrane transport

substances move from low concentration to high concentration; energy expended (ATP) - against concentration gradient

selective media culture

suppresses unwanted microbes and encourages desire microbes - contains inhibitors to suppress growth

what is the common name for the group of microbes that oxidize soil nitrogen into a form that is mobile in soil and likely to be used by plants for nutrition

symbiotic nitrogen fixing bacteria

polymerase enzymes

synthesizes copies of nucleic acid molecules and are used in many genetic engineering procedures

food preservation temperature

temps greater than 60 destroy most microbes, danger zone of bacterial growth is between 15-50F and there is no significant growth of bacteria below freezing

Phage Typing

test for determining which phages a bacterium is susceptible to

the concept of pH

the concentration of H+ in a solution is expressed as pH (pH = -log[H+]) - increasing [H] = increasing acidity - increasing [OH] = increasing alkalinity

DNA-DNA hybridization

the experimental determination of genomic similarity by measuring the extent of hybridization of DNA from one organism with that of another (picture)

what is a provirus

the genetic material of a virus as incorporated into, and able to replicate with, the genome of a host cell

Biogenesis

the hypothesis that living organisms arise from preexisting life

Escherichia coli is found in

the large intestine/ colon

Staphylococcus aureus is found on

the skin

what is the body's first line of defense against pathogens?

the skin, which covers and protects the body - microbes can enter when the skin breaks - larval forms of few parasites can penetrate intact skin

molecular biology

the study of how DNA directs protein synthesis

microbial genetics

the study of how microbes inherit traits

Systematics (phylogeny)

the study of the evolutionary history of organisms

Germ Theory

the theory that infectious diseases are caused by certain microbes

Biotechnology

the use of microbes for practical applications, such as producing foods and chemicals

Design of replication incompetent lentiviral vectors (3rd gen)

the viral vector is "gutted"as much as possible to create room for the insert gene and to divide the viral genome into cis and tran s acting regions - three types of vectors: transfer vector, packaging vector, and envelope vector

how are prokaryotes and eukaryotes distinguished from each other?

their size and type of organelles they contain - because of their common ancestry, both types of cells share an identical genetic language, a common set of metabolic pathways, and many common structural features

India ink or Nigrosin stain

these two stains help contrast the background of the bacterial capsule which then appears as a halo around the cell

treatment for streptococcal TSS and necrotizing fasciitis

they are both life-threatening infections that are fatal in 30-40% of the cases - treatment includes antibiotics, skin grafts, amputations, hyperbaric oxygen therapy

Microorganisms are antigenic (foreign substances that triggers immune response)

they stimulate the body to form antibodies in the serum

flagella allow bacteria to move ______

towards or away from stimuli (taxis) - ie. light (phototaxis) or chemicals (chemotaxis) - flagella rotate to "run" or "tumble"

Chemotherapy

treatment of disease with chemicals

microtubules function

tubular polymers of tubulin that form part of the cytoskeleton. They provide platforms for intracellular transport and are involved in a variety of cellular processes, including the movement of secretory vesicles, organelles, and intracellular macromolecular assemblies. Also makes up the internal structure of cilia and flagella

estimating bacterial numbers by indirect methods (3)

turbidity, metabolic activity, and dry weight

HIV virus structure

two identical ssRNA molecules - proviral DNA is generated by the reverse transcription of the viral RNA genome into DNA

bioremediation

use of microbes to detoxify or degrade target pollutants; enhanced by nitrogen and phosphorus fertilizer

transport media

used to collect and transport pathogens to a laboratory

examples of differential stains

used to distinguish between bacteria (gram stain and acid fast stains)

streak plate method

used to isolate pure cultures (loop must be sterilized after each streak series)

Chemotherapeutic agents

used to treat infectious disease can be synthetic drugs or antibiotics

binomial nomenclature

used worldwide to consistently and accurately name organisms - genus + specific epithet

Morphological characteristics

useful for identifying eukaryotes; tell little about phylogenetic relationships (ie. presence of endospores or flagella)

chickenpox

varicella - herpes virus varicella-zoster (human herpes virus 3) - transmitted via the respiratory route and is caused by pus filled vesicles - virus becomes latent in the central nerve ganglia and is prevented by a live attenuated vaccine (breakthrough varicella can occur if previously vaccinated)

how does a virus species different from a bacterial species?

virus species need a host to survive

if you would like to detect proteins from the mixture of different types of proteins you will perform a ______

western blot

serological testing for viral identification

western blotting - reaction of the virus proteins with antibodies

pertussis

whooping cough, disease of upper and lower respiratory systems - caused by bordetella pertussis (gram negative coccobacillus) - produces a capsule which allows attachment to ciliated cells in the trachea (destroys ciliated cells and shuts down the ciliary escalator) - tracheal cytotoxin of cell wall damages ciliated cells - pertussis toxin enters the bloodstream

treatment for syphilis

with benzathine penicillin

How to deliver new CART19 receptors to the T cells

with the HIV virus

Microbes in our lives (6)

• A few are pathogenic (disease-producing) • Decompose organic waste • Generate oxygen by photosynthesis (70-80% algae) • Produce chemical products such as ethanol, acetone, and vitamins • Produce fermented foods such as vinegar, cheese, and bread • Produce products used in manufacturing (e.g., cellulase) and disease treatment (e.g., insulin)

Biosynthesis of RNA viruses that use DNA

• Single-stranded RNA, produce DNA • Use reverse transcriptase to produce DNA from the viral genome • Viral DNA integrates into the host chromosome as a provirus • Retroviridae • Lentivirus (HIV) • Oncoviruses