exam # biol 2042

alkaliphile Bacillus

adaptation: derives the energy for transport reactions and motility from a Na+ ion gradient rather than a proton motive force

reduction reactions

add electrons to acceptor molecules, leaving them reduced

β-Propionolacton

alkylating agent binds to DNA clear liquid with a strong odor and has the ability to kill endospores metabolized by animals and humans to lactic acid. disadvantages: - irritant, - permanent damage to the eyes, kidneys, or liver - carcinogenic

Which of the following are found only in prokaryotes? a. anoxygenic photosynthesis b. nitrogen fixation c. methanogenesis d. all of the above

all of the above

most probable cell number (MPN

allows estimation of cell numbers in cultures without using solid media

sodium dichloroisocyanurate (NaDCC)

alternative for drinking water disinfection.

Pentose Phosphate Pathway (PPP)

alternative pathway to glycolysis, has both oxidative and non-oxidative branches and the purpose is to make NADPH and five-carbon sugars products: ribose-5-phosphate (the five-carbon sugar that gives this pathway its name) NADPH 1 ATP 1 pyruvate PPP does not replace glycolysis some of the glucose in the cell enters the pentose phosphate pathway instead of glycolysis who uses this: bacteria (Bacillus subtilis and Escherichia coli.)

prokaryotes cell cycle

always asexual genetic recombination in the form of horizontal gene transfer

sterile field

an area that is set up for certain procedures and is free from all organisms how: - packaging and drapings, - strict procedures for washing and application of sterilants

Apoenzyme

an enzyme lacking a necessary cofactor or coenzyme and is inactive

Holoenzyme

an enzyme with the necessary associated cofactor or coenzyme

The final electron acceptor in fermentation is:

an organic molecule

early prokaryotic life on earth was

anaerobic cynobacteria evolved to perform oxygenic photosyntheis

coenzyme A (CoA)

bind to the enzyme's active site, aiding in the chemistry of the transition of a substrate to a product

How do enzymes lower activation energy?

binding to the reactant molecules and holding them in such a way as to speed up the reaction

noncompetitive (allosteric) inhibitor

binds to the enzyme at an allosteric site and still manages to block substrate binding to the active site by inducing a conformational change that reduces the affinity of the enzyme for its substrate

high-energy phosphate bonds

bonds between phosphate groups (one in ADP and two in ATP)

Alkaliphiles example #2

bright pink archaean Natronobacterium pH of 10.5

chlorhexidine

broad-spectrum activity against yeasts, gram-positive bacteria, and gram-negative bacteria, with the exception of Pseudomonas aeruginosa, which may develop resistance on repeated exposure disrupts cell membranes and is bacteriostatic at lower concentrations or bactericidal at higher concentrations, in which it actually causes the cells' cytoplasmic contents to congeal. poorly effective against Mycobacterium tuberculosis and nonenveloped viruses, and it is not sporicidal. more persistent than iodophors, providing long-lasting antimicrobial activity.\

taxonomical hierarchy

broadest group is the domain and the narrowest is the species

Entner-Doudoroff pathway

can be used instead of glycolysis and pentose phosphate in some bacteria products: 2 pyruvates 2 NADPH 1 ATP found in: Pseudomonas, Rhizobium, Agrobacterium, and other bacteria.

Halotolerant (Osmotolerant)

can grow in up to 10% NaCl ex. Halomonas spp found in : salt marshes

Obligate anaerobes

cannot grow in the presence of oxygen They depend on fermentation and anaerobic respiration using a final electron acceptor other than oxygen

internal indicators types

#1) heat-sensitive autoclave tape - white stripes that turn black when the appropriate temperature is achieved during a successful autoclave run - inexpenisve - gives no indication of length of exposure - not for sterility #2) biological indicator spore test - strip of paper or a liquid suspension of the endospores of Geobacillus stearothermophilus to determine whether the endospores are killed by the process - obligate thermophilic bacterium G. stearothermophilus are the gold standard used for this purpose because of their extreme heat resistance Test effectiveness of: - sterilization - ethylene oxide - dry heat - formaldehyde - gamma radiation - hydrogen peroxide plasma sterilization use: G. stearothermophilus, Bacillus atrophaeus, B. subtilis, or B. pumilus spores. #3) Diack tube - glass ampule containing a temperature-sensitive pellet that melts at the proper sterilization temperature - used periodically to ensure the autoclave is functioning properly

mesophiles temp range

("middle loving") moderate temperatures optimal growth temperatures: - 20 °C - 45 ° C core temperature of the human body, 37 °C (98.6 °F) ex. normal human microbiota and pathogens (e.g., E. coli, Salmonella spp., and Lactobacillus spp.

how can baceria cause gastroenteritis?

(inflammation of the stomach and intestinal tract) either by colonizing and replicating in the host, which is considered an infection, or by secreting toxins, which is considered intoxication.

BLS 2

- Moderate risk - indigenous = commonly found in that geographical area. ex. Staphylococcus aureus and Salmonella spp ex. viruses like hepatitis, mumps, and measles viruses precautions: 1. add to BLS1 2. restricted access; 3. required PPE = face shields in some circumstances 4. biological safety cabinets for procedures that may disperse agents through the air (called "aerosolization") modifications: 1. self-closing doors 2. eyewash station 3. autoclave

Biological Methods control microorganisms

- antibiotic produced by microorganisms kills or inhibits the growth of other microorganisms - probiotics helps you maintain normal microbiota and that this normal healthy state can help prevent disease

Unique biodegradation in prokaryotes

- breakdown of hydrocarbons (oil, spills) - degradation of complex molecules (ex. Benzene, toluene)

BSL-3 agents

- can cause lethal infection by inhalation - either indigenous or "exotic" precautions: 1. require restricted access. 2. Laboratory workers are under medical surveillance, possibly receiving vaccinations for the microbes with which they work 3.PPE 4. wear a respirator 5. work with microbes and infectious agents in a biological safety cabinet at all times modifications: 1. hands-free sink 2. eyewash station near the exit 3. two sets of self-closing and locking doors at the entrance 4. directional airflow - air cannot be recirculated, so a constant supply of clean air is required. directional airflow = meaning that clean air is pulled through the lab from clean ares to potentially contaminated areas

indirect method: measuring dry weight of a culture

- cell suspension used for weighing must be concentrated by filtration or centrifugation, washed, and then dried before the measurements are taken - degree of drying must be standardized to account for residual water content. useful for: - filamentous microorganisms, which are difficult to enumerate by direct or viable plate count

Physical Methods to Control Microorganisms: HEAT

- cooking - canning - temperature or radiation to control growth - Heat can kill microbes by altering their membranes and denaturing proteins cold temp = slow or stop microbial growth Temperature microbial control? - Refrigerating food - Freezing food - Cooking food - Keeping food hot on a buffet line - Autoclaving media or canning food - Sanitizing dishes using heat in a dishwasher Radiation? - UV = kill microorganisms - UV light can be absorbed by DNA to form pyrimidine dimers, which are covalent bonds between adjacent thymines or cytosines covalent bonds are not supposed to be there, and they interfere with DNA replication pyrimidine dimers, it cannot successfully copy its DNA and will be killed - Ionizing radiation, like gamma rays causes double-stranded DNA breaks, which will also prevent the cell from copying its DNA.

Measurement of bacterial growth: Direct cell count

- counting individual cells simplest way to count bacteria is: direct microscopic cell count: - involves transferring a known volume of a culture to a calibrated slide and counting the cells under a light microscope - Petroff-Hausser chamber: the calibrated slide - similar to a hemocytometer used to count red blood cells process: 1. central area of the counting chamber is etched into squares of various sizes 2. sample of the culture suspension is added to the chamber under a coverslip that is placed at a specific height from the surface of the grid 3. It is possible to estimate the concentration of cells in the original sample by counting individual cells in a number of squares and determining the volume of the sample observed 4. Cells in several small squares must be counted and the average taken to obtain a reliable measurement. advantages: - method is easy to use, relatively fast, and inexpensive disadvantage: - counting chamber does not work well with dilute cultures because there may not be enough cells to count - not always possible to distinguish between live cells, dead cells, and debris of the same size under the microscope

Measurement of bacterial growth: Indirect cell count

- depend on the measurement of cell presence or activity without actually counting individual cells - are commonly used to estimate and compare cell densities in a culture approaches: - turbidity (cloudiness) - of a sample of bacteria in a liquid suspension

MALDI-TOF methods

- determining the specimen's mass spectrum and then comparing it to a database that contains known mass spectra for thousands of microorganisms - based: on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF) and uses disposable MALDI plates on which the microorganism is mixed with a specialized matrix reage sample/reagent mixture is irradiated with a high-intensity pulsed ultraviolet laser, resulting in the ejection of gaseous ions generated from the various chemical constituents of the microorganism. plot of detector signal versus m/z yields a mass spectrum for the organism that is uniquely related to its biochemical composition. permits identification of the unknown

BSL-4 agents are the most dangerous and often fatal

- exotic microbes - easily transmitted by inhalation - cause infections for which there are no treatments or vaccinations ex. Ebola virus and Marburg virus= cause hemorrhagic fevers, and smallpox virus precautions: - addition to BLS- 3 - change their clothing on entering the laboratory - shower on exiting - decontaminate all material on exiting - wear a full-body protective suit with a designated air supply OR - conduct all work within a biological safety cabinet with a high-efficiency particulate air (HEPA)-filtered air supply and a doubly HEPA-filtered exhaust. If wearing a suit, the air pressure within the suit must be higher than that outside the suit, so that if a leak in the suit occurs, laboratory air that may be contaminated cannot be drawn into the suit location of lab: - separate building OR - isolated portion of a building and have its own air supply and exhaust system as well as its own decontamination system

plant cells also produce an enzyme called

- laeghemoglobin - which is an oxygen scavenging protein some nitrogen fixation work with plants - infect the root nodule, the bacteria can fix nitrogen and provide nitrogen to the host plant - plant feed the bacteria, giving them the ATP and NADPH needed for nitrogen fixation

Reactions of type: superoxide dismutase (SOD)

- mediated by the enzyme - breaks down the powerful superoxide anions generated by aerobic metabolism: (2)2O2−+2H+→H2O2+O2

direct counting technique: electronic cell counting device (Coulter counter)

- to detect and count the changes in electrical resistance in a saline solution 1. glass tube with a small opening is immersed in an electrolyte solution 2. first electrode is suspended in the glass tube. 3. second electrode is located outside of the tube. 4; cells are drawn through the small aperture in the glass tube, they briefly change the resistance measured between the two electrodes and the change is recorded by an electronic sensor 5. each resistance change represents a cell advantage: 1. rapid and accurate within a range of concentrations disadvantage: 1. if the culture is too concentrated, more than one cell may pass through the aperture at any given time and skew the results. 2. does not differentiate between live and dead cells. need to know: 1. important to know the number of live, or viable, cells

Chemical Methods of Microbial Control

-Halogens - Includes chlorine, iodine, fluorine. Oxidize cellular materials. - Alcohols - Ethanol, isopropanol. Disrupt membranes. Cause dehydration. - Acids - Acetic acid. Lower pH. - Detergents - Sodium dodecylsulfate. Disrupt membranes. - Salts - Sodium chloride. High concentrations cause dehydration of cells. - Sugars - Dextrose. High concentrations cause dehydration of cells.

semilogarithmic graph

-uses only one axis logarithmic in which it increases by 10 times -each division is 10 times larger than the preceding one -Solves problem of having too little or too many bacteria

Name a genus for following:

1. Anaerobic photosynthesis - Nostoc 2. Aerobic photosynthesis - Limnohabitans 3. Free-living bacterial cell nitrogen fixation - Azotobacter 4. Cyanobacterium with heterocysts - Anabaena 5. Bacterium fixing nitrogen in plant root nodules - Rhizobium 6. Denitrification - Pseudomonas 7. Sulfur oxidation - Thioalkalivibrio 8. Sulfide oxidation - Thiomicrospira 9. Sulfate reduction - Desulfobacter 10. Methanogenesis - Methanosarcina

membrane filtration technique (direct cell count)

1. Known volumes are vacuum-filtered aseptically through a membrane with a pore size small enough to trap microorganisms. 2. The membrane is transferred to a Petri plate containing an appropriate growth medium 3. Colonies are counted after incubation 4. Calculation of the cell density is made by dividing the cell count by the volume of filtered liquid ex. A very dilute sample—drinking water, for example—may not contain enough organisms to use either of the plate count methods described. In such cases, the original sample must be concentrated rather than diluted before plating

cells are unable to carry out respiration because of one or more of the following circumstances::

1. The cell lacks a sufficient amount of any appropriate, inorganic, final electron acceptor to carry out cellular respiration. 2.The cell lacks genes to make appropriate complexes and electron carriers in the electron transport system. 3.The cell lacks genes to make one or more enzymes in the Krebs cycle.

2 factors influence cleanliness for a diff fornite

1. application for which the item will be used ex. invasive applications that require insertion into the human body require a much higher level of cleanliness than applications that do not 2. the level of resistance to antimicrobial treatment by potential pathogens ex. foods preserved by canning often become contaminated with the bacterium Clostridium botulinum, which produces the neurotoxin that causes botulism. Because C. botulinum can produce endospores that can survive harsh conditions, extreme temperatures and pressures must be used to eliminate the endospores.

quorum sensing steps

1. binding of the autoinducer to its specific receptor only when a threshold concentration of signaling molecules is reached 2. a cascade of signaling events leads to changes in gene expression. 3. result is the activation of biological responses linked to quorum sensing, notably an increase in the production of signaling molecules themselves, hence the term autoinducer.

laboratory or clinic sterilization

1. dry-heat sterilization 2. moist-heat sterilization

factors affect disinfecting agent effectiveness

1. length of time of exposure 2. susceptibility of the agent to that disinfecting agent or protocol 3. concentration of disinfecting agent or intensity of exposure ex. higher temperatures and higher concentrations of disinfectants kill microbes more quickly and effectively.

ex of measure out each component media

E. coli minimal media

Phenol Coefficient

1.0 means: that the chemical agent has about the same level of effectiveness as phenol. less than 1.0 is less effective than phenol ex. formalin, with phenol coefficients of 0.3 (S. aureus) and 0.7 (S. enterica serovar Typhi) greater than 1.0 is more effective than phenol ex. chloramin is no longer commonly used because the conditions and organisms used were arbitrarily chosen.

Krebs Cycle/Citric Acid Cycle/Tricarboxylic Acid Cycle PRODUCTS

2 CO2 1 ATP/GTP produced by substrate level phosphorylation 3 NADH 1 FADh2

glycolysis products

2 pyruvate, 2 ATP, 2 NADH

atp overall

38 ATP 4 from substrate level phosphorylation 34 from oxidative phosphorylation

nitrogen fixation

80% nitrogen in atm nitrogen gas = dinitrogen which cannot be incorporated into living cells Lightning is one source of a limited amount of these compounds Lightning can break the bonds between N2 and convert small amounts of nitrogen in the air to ammonia and nitrates, but this is only a fraction of what is needed by life on the planet enzymes used: nitrogenase nitrogenous is destroyed in the presence of oxygen enzymes utilizes a lot of energy in the form of ATP in order to break the triple bond of dinitrogen Nitrogen fixation can only occur in anaerobic environments because nitrogenase is destroyed in the presence of oxygen

Fermentation

A catabolic process that makes a limited amount of ATP from glucose without an electron transport chain and that produces a characteristic end product, such as ethyl alcohol or lactic acid. final electron acceptor: organic molecule (commonly pyruvate) does not: involve an electron transport system and does not directly produce any additional ATP beyond that produced during glycolysis by substrate-level phosphorylation. recycling NADH to NAD+ - reduction using NADH as the electron donor and pyruvate - NADH is oxidized to NAD+ - used for glycolysis - pyruvate is reduced to form lactic acid Simplest type of fermentation: lactic acid fermentation is reversible (NADH electron donor, Pyruvate is electron acceptor) ATP made: max 2

prokaryotic species definition

A collection of strains that share many stable properties and differ significantly from other groups of strains OR collection of organisms that share the same sequences in their core housekeeping genes DNA comparisons can also be used to group prokaryotes into species - 98% DNA similarity as the cutoff for two bacteria to be considered part of the same species

Acidity (pH)

Acidity is the measure of Hydrogen ions in a substance. The acidity of a substance can be measured using the pH scale. Numbers 0-6 = acidic 7 = neutral, 8-14 = alkaline or base, the opposite of acidic. Scientists find the pH of lakes, rain, water, and environment to determine how healthy they are. The pH of a lake is always changing, but scientists use the pH of a lake to know if it is a healthy acidity for life in that area.

Detoxification of Reactive Oxygen Species

Aerobic respiration constantly generates reactive oxygen species (ROS), byproducts that must be detoxified

-efficiency particulate air (HEPA) filters

Air filtered through HEPA filters have effective pore sizes of 0.3 µm, small enough to capture bacterial cells, endospores, and many viruses, as air passes through these filters,

Bacteriorhodopsin (BR)

An archaeal membrane-embedded protein that contains retinal and acts as a light-driven proton pump; it is homologous to the bacterial proteorhodopsin. similar to eye pigment rhodopsin.

in science a "theory" is

An explanation that is well-supported by evidence

spectrophotometer

An instrument that measures the proportions of light of different wavelengths absorbed and transmitted by a pigment solution. 1. light beam is transmitted through a bacterial suspension 2. light passing through the suspension is measured by a detector 3. the amount of light passing through the sample and reaching the detector is converted to either percent transmission or a logarithmic value called ABSORBANCE (optical)DENSITY numbers of bacteria in a suspension increase, the turbidity also increases and causes less light to reach the detector ADVANTAGE: - fast method to estimate cell density as long as there are enough cells in a sample to produce turbidity - correlate turbidity readings to the actual number of cells by performing a viable plate count of samples taken from cultures having a range of absorbance values.

common approach for determining the genus and the species of the bacterium

Analyzing the nutritional and metabolic capabilities of the bacterial isolate

dry-heat sterilization

Aseptic technique involved direct application of high heat sterilizing inoculating loops Incineration at very high temperatures kill all microorganisms Dry heat can also be applied for relatively long periods of time (at least 2 hours) at temperatures up to 170 °C by using a dry-heat sterilizer, such as an oven

Budding (asexual)

Asexual reproduction in which a part of the parent organism pinches off and forms a new organism species may form a long narrow extension at one pole in a process The tip of the extension swells and forms a smaller cell, the bud that eventually detaches from the parent cell common in: yeast seen in: prosthecate bacteria and some cyanobacteria

three classes of BSCs I, II, and III

BSC II and III: protect the materials or devices in the cabinet BSC I - protect person, enviro - low to moderate risk for exposure to biological agents - Air is drawn into the cabinet and then filtered before exiting through the building's exhaust system. BSC II - Protect person, enviro, product - directional air flow and partial barrier systems to contain infectious agents BSC III - used in suit, Protect person, enviro, product - working with highly infectious agents like those used in BSL-4 laboratories - gas tight, and materials entering or exiting the cabinet must be passed through a double-door system, allowing the intervening space to be decontaminated between uses.

selective media example

EMB/MacConkey agar - has bile salts and crystal violet, which interfere with the growth of many gram-positive bacteria and favor the growth of gram-negative bacteria, particularly the Enterobacteriaceae Sabourauds/Salmonella Shigella called ENTRICS

common glycolysis in microbes

Embden-Meyerhof-Parnas (EMP) pathway

Domains of Life

Bacteria, Archaea, Eukarya described by Carl Woese - based on his analysis of ribosomal RNA sequences - 16S rRNA from prokaryotes or the 18S rRNA in eukaryotes Sequences from biolodical molecules can be used sd 'molecular clocks" - more diff more time difference d - ribosomes are very specialized, they change very little over and give us good indicators of long evolutionary histories between organisms - since both have genome = also have the ability to transcribe mRNA and to translate those messages into protein, so they also contain ribosomes

example of a microaerophile and is grown under low-oxygen conditions

Campylobacter jejuni gastrointestinal infections

sterilants

Can destroy all microorganisms, including endospores and viruses. Chemicals that can be used to achieve sterilization

carbon cycle

Carbon is one of the most important elements to living organisms Carbon is exchanged between heterotrophs and autotrophs within and between ecosystems primarily by way of atmospheric CO2 a fully oxidized version of carbon that serves as the basic building block that autotrophs use to build multicarbon, high-energy organic molecules such as glucose. constant exchange of CO2 between the heterotrophs (which produce CO2 as a result of respiration or fermentation) and the autotrophs (which use the CO2 for fixation) Autotrophs also respire or ferment, consuming the organic molecules they form

induced fit

Caused by entry of the substrate, the change in shape of the active site of an enzyme so that it binds more snugly to the substrate

why do pathogens within a biofilm have more resistance?

Cells in the deep layers of a biofilm are metabolically inactive and may be less susceptible to the action of antibiotics that disrupt metabolic activities. The EPS may also slow the diffusion of antibiotics and antiseptics, preventing them from reaching cells in the deeper layers of the biofilm. Phenotypic changes may also contribute to the increased resistance exhibited by bacterial cells in biofilms.

metabolic pathways.

Cellular processes such as the building or breaking down of complex molecules occur through series of stepwise, interconnected chemical reactions

disinfectants in the food processing and restaurant industries to reduce the spread of foodborne diseases

Chlorine gas, sodium hypochlorite, and calcium hypochlorite

__________________ are maps that show evolutionary relationships among organisms.

Cladograms

Growth Curve: Stationary Phase

Closed environment - cells remains relatively constant - cell division rate equaling the death rate slowing factors: reach a plateau 1. Waste products accumulate 2. nutrients are gradually used up 3. gradual depletion of oxygen begins to limit aerobic cell growth number of new cells created by cell division is now equivalent to the number of cells dying; thus, the total population of living cells is relatively stagnant culture density: stationary is constant cells switch to a survival mode of metabolism growth slows, so too does the synthesis of peptidoglycan, proteins, and nucleic-acids; thus, stationary cultures are less susceptible to antibiotics that disrupt these processes. bacteria able to produce ensopores undergo SPORULATION what is synthesized here? - Secondary metabolites, including antibiotics certain pathogenic bacteria, - associated with the expression of virulence factors, products that contribute to a microbe's ability to survive, reproduce, and cause disease in a host organism - ex. quorum sensing in Staphylococcus aureus initiates the production of enzymes that can break down human tissue and cellular debris, clearing the way for bacteria to spread to new tissue where nutrients are more plentiful.

Growth Curve: Death Phase

Closed environment culture medium accumulates toxic waste and nutrients are exhausted, cell dies dying cells exceeds the number of dividing cells exponential decrease in the number of cells Many cells lyse and release nutrients into the medium, allowing surviving cells to maintain viability and form endospores persisters: - few cells are characterized by a slow metabolic rate - associated with certain chronic infections, such as tuberculosis, that do not respond to antibiotic treatment.

Growth Curve: Lag Phase

Closed environment inoculum: beginning of the growth curve represents a small number of cells - bacterial cells are adjusting to their new environment cells are added to a fresh CULTURE MEDIUM, a nutritional broth that supports growth lag phase: number of cells does not change during - cells grow larger and - cells are metabolically active - synthesizing proteins needed to grow within the medium -repair takes place during the lag phase duration: - determined by many factors: 1. the species 2. genetic make-up of the cells 3. the composition of the medium 4. the size of the original inoculum.

Growth Curve: log phase

Closed environment logarithmic (log) growth phase/ exponential growth phase - rapid increase in the cell number - cells are fully adjusted to their new environment and are growing at their best possible rate. - cells are actively dividing by binary fission - cell number increases exponentially intrinsic growth rate - generation time under specific growth conditions (nutrients, temperature, pH, and so forth) is genetically determined relationship between time and number of cells is not linear but exponential plotted on semilogarithmic graph

Chemical Food Preservatives

Commonly used: 1. sorbic acid 2. benzoic acid 3. propionic acid 4.their more soluble salts potassium sorbate 5. sodium benzoate 6. calcium propionate control the growth of molds in acidic foods. nontoxic and readily metabolized by humans. Sorbic and benzoic acids exhibit increased efficacy as the pH decreases. Sorbic acid- inhibiting various cellular enzymes, including those in the citric acid cycle, as well as catalases and peroxidases

What group on the tree of life does the molecular evidence show as the ancestro of mitochondria

Cyanobacteria

Which of the following was responsible for the initial rise of oxygen levels in the Earth's atmosphere?

Cyanobacteria

taxonomic levels

Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species

Other glycolytic pathway

Entner-Doudoroff (ED) pathway - prokaryotes use alternative glycolytic pathways - some bacteria, including the opportunistic gram-negative pathogen Pseudomonas aeruginosa, contain only the ED pathway for glycolysis, other bacteria, like E. coli, have the ability to use either the ED pathway or the EMP pathway.

alkylating agent that is used for gaseous sterilization.

Ethylene

Cell type comparison

Eukaryotes - Chromosomes: linear - ribosomes: 80s - first amino acid: methionine - cell division: Normal cell division, mitosis Bacteria - chromosomes: circular - ribosomes: 70s - first amino acid: formylmethionine - cell division: divide binary fission Mitochondria - chromosomes: circular - ribosomes: 70s - first amino acid: fMet - cell division: binary fission Chloroplast - chromosomes: circular - ribosome : 70s - first amino acid: fMet - cell division: binary fission

Sonication

Exposure to high frequency sound waves to disrupt cell structure UV = change pressure w/in intracellular liquid = cavitation (form bubbles) = disrupt cell structures = cause the cell to lyse or collapse used: lysing cells to release their contents for further research cleaning surgical instruments, lenses, and a variety of other objects such as coins, tools, and musical instruments.

A prokaryotic species is defined as a group of closely related organisms that breed among themselves

False

A prokaryotic species is defined as a group of closely related organisms that breed among themselves.

False

Fermentation requires an electron transport chain

False

Viruses are classified as prokaryotes

False

in a complex grow medium, we know exactly how much of each medium is present

False

Biofilm Structure

Filamentous biofilms called streamers - anchored to the substrate by a "head" and the "tail" floats downstream in the current still or slow-moving water - biofilms mainly assume a mushroom-like shape biofilms under confocal laser and scanning electron microscopes - matrix interspersed with open water channels extracellular matrix: - extracellular polymeric substances (EPS) secreted by the organisms in the biofilm - represents a large fraction of the biofilm, accounting for 50%-90% of the total dry mass

Filamentous biofilms called Streamers are the ________________

Filamentous biofilms called streamers form in rapidly flowing water, such as freshwater streams, eddies, and specially designed laboratory flow cells that replicate growth conditions in fast-moving fluids.

membrane filtration

Filtration can also be used to remove microbes from liquid samples remove bacteria have an effective pore size of 0.2 µm, smaller than the average size of a bacterium (1 µm) ex. antibiotic solutions and vitamin solutions. small volumes, syringe filters

entrics

Found in the intestine, and are adapted to the presence of bile salts

Lyophilization (freeze-drying)

Frozen (-54° to -72°C) and dehydrated in a vacuum rapidly frozen ("snap-frozen") and placed under vacuum so that water is lost by sublimation combines both exposure to cold temperatures and desiccation, making it quite effective for controlling microbial growth items may be stored at room temperature

binomial nomenclature

Genus and species names used together developed Carolus Linnaeus genus is always capitalized, and species is never capitalized

most common pathway for catabolism of glucose for bacteria, eukarytes and archaea?

Glycolysis

quorum sensing belong to two major classes

Gram-negative bacteria communicate mainly using N-acylated homoserine lactones, gram-positive bacteria mostly use small peptides

oxygenic photosynthesis

H2O is split and supplies the electron to the reaction center. byproduct: O2 and is released. Produce: ATP and NADPH

Filtration in Hospitals

HEPA filters are also commonly used in hospitals and surgical suites to prevent contamination and the spread of airborne microbes through ventilation systems

Mercury

Heavy metal treat syphilis. mercury bind to sulfur-containing amino acids within proteins, inhibiting their functions. mercury toxic to central nervous system, digestive and renal system at high conc. negative environmental effects - bioaccumulation in fish

human impact on nitrogen cycle

Human activity releases nitrogen into the environment by the use of artificial fertilizers that contain nitrogen and phosphorus compounds, which are then washed into lakes, rivers, and streams by surface runoff major effect from fertilizer runoff is saltwater and freshwater eutrophication

cyclic photophosphorylation

If a cell's need for ATP is significantly greater than its need for NADPH, it may bypass the production of reducing power

noncyclic photophosphorylation

If the cell requires both ATP and NADPH for biosynthesis the lost electron from the PSII reaction center is replaced by the splitting of water The excited PSI reaction center electron is used to reduce NADP+ to NADPH and is replaced by the electron exiting the ETS

pour plate method (direct cell count)

In the pour plate method of cell counting, the sample is mixed in liquid warm agar (45-50 °C) poured into a sterile Petri dish and further mixed by swirling. This process is repeated for each serial dilution prepared. The resulting colonies are counted and provide an estimate of the number of cells in the original volume sampled

spread plate method (direct cell count)

In the spread plate method of cell counting, the sample is poured onto solid agar and then spread using a sterile spreader. This process is repeated for each serial dilution prepared. The resulting colonies are counted and provide an estimate of the number of cells in the original volume samples.

what happens to lipids with extreme basic pH

Lipids are hydrolyzed by an extremely basic pH

how to have bacteria for long-term storage as stocks

Liquid cultures of bacteria are mixed with sterile glycerol solutions and frozen to −80 °C Cultures can withstand freeze drying (lyophilization) and then be stored as powders in sealed ampules to be reconstituted with broth when needed

who developed pasteurization?

Louis Pasteur

differential fermentation of lactose can be observed on _______

MacConkey agar lactose fermenters produce acid, which turns the medium and the colonies of strong fermenters hot pink The medium is supplemented with the pH indicator neutral red, which turns to hot pink at low

Macromolecules structural differences in thrmophiles, hyperthermophiles, mesophiles.

Macromolecules in thermophiles and hyperthermophiles show some notable structural differences from what is observed in the mesophiles The ratio of saturated to polyunsaturated lipids increases to limit the fluidity of the cell membranes Their DNA sequences show a higher proportion of G-C nitrogenous bases, which are held together by 3 H- bonds in contrast to A & T, which are connected in the double helix by 2 hydrogen bonds.

phospholipid-derived fatty acids (PLFA) analysis

Membranes are mostly composed of phospholipids, which can be saponified (hydrolyzed with alkali) to release the fatty acids. The resulting fatty acid mixture is then subjected to FAME analysis, and the measured lipid profiles can be compared with those of known microorganisms to identify the unknown microorganism.

low temperatures of macromolecules

Membranes lose their fluidity and are damaged by ice crystal formation Chemical reactions and diffusion slow considerably Proteins become too rigid to catalyze reactions and may undergo denaturation

Decimal Reduction Time (DRT) or D-value

Minutes to kill 90% of a population at a given temperature time it takes for a specific protocol to produce a one order-of-magnitude decrease in the number of organisms

moist-heat sterilization

Moist heat denatures proteins more effective protocol because it penetrates cells better than dry heat does

neutrophiles

Most bacteria grow between pH 6.5 and 7.5 grow optimally at a pH within one or two pH units of the neutral pH of 7 ex. Escherichia coli, staphylococci, and Salmonella

Which of the following is the oxidized form of nicotinamide adenine dinucleotide?

NAD+

used in energy extraction from sugars during catabolism

NAD+/NADH FAD/FADH2

Which of the following is the reduced form of nicotinamide adenine dinucleotide?

NADH

role in anabolic reactions and photosynthesis

NADP+/NADPH

microaerophiles bacteria

Need oxygen to grow less that 21% require a minimum level of oxygen for growth, about 1%-10%, well below the 21% found in the atmosphere. Have superoxide dismutase and peroxidase they have peroxidase, they are not able to handle large amounts of oxygen Habitats: - oxygen gradient between normal atmospheric oxygen levels and an anaerobic environment ex. areas like mud where the oxygen levels decrease with depth

Natural Chemical Food Preservatives

Nisin: is an antimicrobial peptide produced by the bacterium Lactococcus lactis and is particularly effective against gram-positive organisms. works: disrupting cell wall production, leaving cells more prone to lysis. It is used to preserve cheeses, meats, and beverages. Natamycin: is an antifungal macrolide antibiotic produced by the bacterium Streptomyces natalensis

nitrates food preservation

Nitrites are added to processed meats to maintain color and stop the germination of Clostridium botulinum endospores Nitrites are reduced to nitric oxide, which reacts with heme groups and iron-sulfur groups Nitrosamines disadvantage? - are carcinogenic and can be produced through exposure of nitrite-preserved meats (e.g., hot dogs, lunch meat, breakfast sausage, bacon, meat in canned soups) to heat during cooking.

Sterilization

The process that completely destroys all microbial life, including spores. extreme protocols killing of all vegetative cells, endospores, and viruses from the targeted item or environment where: - reserved for laboratory, medical, manufacturing, and food industry

aerobic respiration final electron acceptor at the end of the ETS is

O2 that becomes reduced to water (H2O) final electron acceptors: Pseudomonas and sulfate in Desulfovibrio Electron carrier: cytochrome oxidase - differs between bacterial types needs to recycle the NADH back to NAD+ still make ATP through the electron transport chain and chemiosmosis, but they make fewer of total ATP. still uses the Krebs cycle. It still has an electron transport chain, but it cannot use all the same steps as aerobic respiration because oxygen is not the final electron acceptor.

identify plants

Observations such as these can be part of methods like dichotomous keys, which are quite commonly used in botany to identify plants

In _______________ typing, bacteria are classified based on the types of viruses that can infect them.

Phage

light for growth bacteria

Photoautotrophs, such as cyanobacteria or green sulfur bacteria, and photoheterotrophs depend on sufficient light intensity at the wavelengths absorbed by their pigments to grow and multiply light is captured by pigments and converted into chemical energy that drives carbon fixation and other metabolic processes

Which of the following is an organism that gets its carbon from pre-formed organic molecules and its energy from light?

Photoheterotrophs

types of proteins

Proteins in: psychrophiles - rich in hydrophobic residues - display an increase in flexibility - have a lower number of secondary stabilizing bonds when compared with homologous proteins from mesophiles Antifreeze proteins and solutes: - decrease the freezing temperature of the cytoplasm are common. lipids in the membranes tend to be unsaturated to increase fluidity Growth rates are much slower than those encountered at moderate temperatures

chemical reaction of lactic acid fermentation

Pyruvate + NADH↔lactic acid + NAD+

exergonic reactions

Reactions that are spontaneous and release energy

oxidation reactions

Reactions that remove electrons from donor molecules, leaving them oxidized

Species, interbreeding

Reproduction between similar species like horses and donkeys can produce mules, but mules are sterile. For eukaryotic species this definition works well

the most plentiful enzyme on earth

Rubisco composing 30%-50% of the total soluble protein in plant chloroplasts

water activity ex

Salted meats and fish, like ham and cod, respectively, were critically important foods before the age of refrigeration

what is in bleach?

Sodium hypochlorite

sulfur cycle

Sulfur is an essential element for the macromolecules of living organisms Anoxygenic photosynthetic bacteria as well as chemoautotrophic archaea and bacteria use hydrogen sulfide as an electron donor, oxidizing it first to elemental sulfur (S0), then to sulfate (SO42−).(SO42−). Many bacteria and plants can use sulfate as a sulfur source Decomposition dead organisms by fungi and bacteria remove sulfur groups from amino acids, producing hydrogen sulfide, returning inorganic sulfur to the environment.

Surfactants (chemical method)

Surface-active agents lower the surface tension of water major ingredients in soaps and detergents interact with nonpolar oils and grease to create emulsions in water, loosening and lifting away dirt and microbes from surfaces and skin. soap = no antiseptic or disinfectant

circumstances under which aerobic respiration

The cell lacks genes encoding an appropriate cytochrome oxidase for transferring electrons to oxygen at the end of the electron transport system. The cell lacks genes encoding enzymes to minimize the severely damaging effects of dangerous oxygen radicals produced during aerobic respiration, such as hydrogen peroxide (H2O2) or superoxide (O2-).(O2-). The cell lacks a sufficient amount of oxygen to carry out aerobic respiration.

catalase

The enzyme catalase converts hydrogen peroxide to water and oxygen as shown in Reaction 3. (3)2H2O2→2H2O+O2

maximum growth pH

The highest pH value that an organism can tolerate

maximum permissive oxygen concentration

The highest tolerated concentration of oxygen

optimum oxygen concentration

The ideal concentration of oxygen for a particular microorganism fastest growth rate

minimum growth pH

The lowest pH value that an organism can tolerate

Quorum sensing in bacteria

The mechanism by which cells in a biofilm coordinate their activities in response to environmental stimuli which can occur between cells of different species within a biofilm—enables microorganisms to detect their cell density through the release and binding of small, diffusible molecules called AUTOINDUCERS When the cell population reaches a critical threshold (a quorum), these autoinducers initiate a cascade of reactions that activate genes associated with cellular functions that are beneficial only when the population reaches a critical density

Ecosystem

is a community of organisms and their physical and chemical environment that function as an ecological unit

water activity

The water content of foods and materials can be lowered without physical drying by the addition of solutes such as salts or sugars. high concentrations of salts or sugars, the amount of available water in microbial cells is reduced dramatically because water will be drawn from an area of low concentration (inside the cell) to an area of high solute concentration (outside the cell

theory

Theory has a lot of scientific evidence that supports taht explanation

Thermophiles (heat loving) examples

Thermus aquaticus and Geobacillus spp.

fatty acid methyl ester (FAME) analysis

To identify a microbe by its lipid composition, the fatty acids present in their membranes are analyzed. fatty acids are extracted from the membranes of microorganisms, chemically altered to form volatile methyl esters, and analyzed by gas chromatography (GC). The resulting GC chromatogram is compared with reference chromatograms in a database containing data for thousands of bacterial isolates to identify the unknown microorganism

Anaerobic respiration requires an electron transport chain.

True

Catalysts are not used or changed during chemical reactions and, therefore, are reusable.

True

Most bacterial cells divide by binary fission. Generation time in bacterial growth is defined as the doubling time of the population

True

Polymerase chain reaction can be used to identify microorganisms even when it is not possible to culture the organisms in the lab.

True

Polymerase chain reaction can be used to identify microorganisms even when nit is not possible to culture the organisms in the lab

True

Viruses are not classified as part of any of the three domains.

True

a eukaryotic species is defined as a group of closely related organisms that breed among themselves.

True

cells are continually balancing catabolism with anabolism

True

each transfer of an electron through the ETS, the electron loses energy, but with some transfers, the energy is stored as potential energy by using it to pump hydrogen ions (H+) across a membrane

True prokaryotic cells H+ is pumped to the outside of the cytoplasmic membrane (called the periplasmic space in gram-negative and gram-positive bacteria) eukaryotic cells they are pumped from the mitochondrial matrix across the inner mitochondrial membrane into the inter membrane space.

how to thaw frozen foods

USDA: only safe ways that frozen foods can be thawed are in the refrigerator, immersed in cold water changed every 30 minutes OR in the microwave, keeping the food at temperatures not conducive for bacterial growth In addition, halted bacterial growth can restart in thawed foods, so thawed foods should be treated like fresh perishables.

Alkaliphiles example

Vibrio cholerae, the pathogenic agent of cholera, grows best at the slightly basic pH of 8.0 survive pH values of 11.0 but is inactivated by the acid of the stomach

Radiation to sterilize many packaged materials

X-rays and gamma rays easily penetrate paper and plastic

Reactions of type: catalyzed by peroxidases

X−(2H+)+H2O2→oxidiz X+2H2O - electron donor oxidizes hydrogen peroxide, or other peroxides to water enzymes play an important role by limiting the damage caused by peroxidation of membrane lipids.

chemically defined medium

a medium whose exact chemical composition is known ex. EZ medium - all individual chemical components are identified and the exact amounts of each is known

bisphenol hexachlorophene

a phenolic a disinfectant is the active ingredient in pHisoHex, a topical cleansing detergent widely used for handwashing in hospital settings.

cresols

a phenolic active ingredients in various formulations of Lysol since its invention in 1889

Triclosan

a phenolic bisphenol compound that has seen widespread application in antibacterial products used in hand soaps and is frequently impregnated into a wide variety of other products, including cutting boards, knives, shower curtains, clothing, and concrete, to make them antimicrobial. against gram-positive bacteria on the skin, as well as certain gram-negative bacteria and yeasts.

pHisoHex

a phenolic effective against gram-positive bacteria, including those causing staphylococcal and streptococcal skin infections. hexachlorophene can lead to neurological problems.

carbolic acid

a phenolic skin irritant, antiseptic mouthwashes

FtsZ

a protein that forms a ring along the mid-cell division plane to initiate cell division

active site

a region on an enzyme that binds to a protein or other substance during a reaction.

Cyanobacterium

a type of bacterium that is a photosynthetic autotroph photoautotrophs: light for energy and obtain their carbon from carbon dioxide

Asepsis

absence of significant contamination

Halobacterium spp.

accumulates large concentrations of K+ and other ions in its cytoplasm proteins are designed for high salt concentrations and lose activity at salt concentrations below 1-2 M

Prions,

acellular, misfolded proteins responsible for incurable and fatal diseases such as kuru and Creutzfeldt-Jakob disease resistant to heat, chemicals, and radiation extremely infectious and deasly

Copper, Nickel, and Zinc

antimicrobial activity Copper sulfate is a common algicide used to control algal growth in swimming pools and fish tanks Copper linings in incubators help reduce contamination of cell cultures copper pots for water storage in = combat diarrheal diseases Copper coatings - frequently handled objects such as doorknobs, cabinet hardware, and other fixtures in health-care facilities in an attempt to reduce the spread of microbes. Nickel and zinc coatings - Zinc chloride is quite safe for humans and is commonly found in mouthwashes, substantially increasing their length of effectiveness

halogen fluorine

antimicrobial properties that contribute to the prevention of dental caries (cavities) Fluoride is the main active ingredient of toothpaste and is also commonly added to tap water to help communities maintain oral health Fluoride also enhances the uptake of calcium and phosphate ions in tooth enamel, promoting remineralization

Silver

antiseptic. Silvadene cream is commonly used to treat topical wounds and is particularly helpful in preventing infection in burn wounds Silver nitrate drops: - once applied to the eyes of newborns to protect against ophthalmia neonatorum, eye infections that can occur due to exposure to pathogens in the birth canal, but antibiotic creams are more now commonly used. often combined with antibiotics, making the antibiotics thousands of times more effective. incorporated into catheters and bandages, rendering them antimicrobial

Antisepsis

applying an antiseptic

Disk-Diffusion Method

applying different chemicals to separate, sterile filter paper disks disks are then placed on an agar plate that has been inoculated with the targeted bacterium and the chemicals diffuse out of the disks into the agar where the bacteria have been inoculated As the "lawn" of bacteria grows, zones of inhibition of microbial growth are observed as clear areas around the disks larger zones typically correlate to increased inhibition effectiveness of the chemical agent zone is measured in millimeters

Standard operating temperatures for autoclaves are

are 121 °C some: 132 °C pressure: 15 to 20 pounds per square inch (psi) exposure time: depends on the volume and nature of material being sterilized, - typically 20 minutes or more,

Coenzymesn enzyme helper molecule

are organic helper molecules that are required for enzyme action they are not consumed and, hence, are reusable. ex. dietary vitamins

Chloroplast

arose in eukaryotes by endosymbiosis of a photosynthetic bacterium - eukaryotic cells did not evolve until 1.4 billion years ago - enclosed by a double membrane with inner and outer layers Within the chloroplast is a third membrane that forms stacked, disc-shaped photosynthetic structures called thylakoids thylakoid membranes or other photosynthetic bacterial: molecules organized into one or more photosystems, granum: stack of thylakoids stroma: space surrounding the granum within the chloroplast

Alternative Patterns of Cell Division in prokaryotes

asymmetrical division (as in budding) production of spores in aerial filaments ex. cyanobacteria, many nucleoids may accumulate in an enlarged round cell or along a filament, leading to the generation of many new cells at once - fragmentation: new cells often split from the parent filament and float away

quaternary ammonium salts (quats)

ationic detergents include an important class of disinfectants and antiseptics cationic detergents have a positively charged cation instead at one end attached to a long hydrophobic chain, quats have properties similar to phospholipids, having hydrophilic and hydrophobic ends. advantages: - ability to insert into the bacterial phospholipid bilayer and disrupt membrane integrity. - stable, nontoxic, inexpensive, colorless, odorless, and tasteless active against fungi, protozoans, and enveloped viruses, but endospores are unaffected.

SERIAL DILUTION EXAMPLE (direct cell count)

average of 50 colonies was counted on the plates obtained from the 1:10,000 dilution. Because only 0.1 mL of suspension was pipetted on the plate, the multiplier required to reconstitute the original concentration is 10 × 10,000 number of CFU per mL is equal to: - 50 × 10 × 10,000 = 5,000,000. number of bacteria in the culture is estimated as 5 million cells/mL. colony count obtained from the 1:1000 dilution was 389, well below the expected 500 for a 10-fold difference in dilutions. This highlights the issue of inaccuracy when colony counts are greater than 300 and more than one bacterial cell grows into a single colony.

endosymbiosis

bacterial cell entered a eukaryotic cell as a symbiont and eventually became an organelle Endosymbiotic theory states that some of the organelles were once free-living bacteria ribosomal RNA, so we can use their rRNA sequences to see where they fall on the Tree of Life Mitochondria match Proteobacteria contains a diverse group of bacteria, including E. coli, and gram neg E. coli = chemoheterotrophs aerobic respiration Kreb cycle: Mitochondria are the organelle in eukaryotes where aerobic respiration occurs are the site of the electron transport chain chloroplast evidence: organelle is the site of photosynthesis in eukaryotic cells, so before the sequence was analyzed we could hypothesize that the most likely match would be to the cyanobacteria, which are the only group of bacteria that can do oxygenic photosynthesis. E Eukaryotic cells contain membrane bound organalles

Biochemical tests

bacterial classification We can identify which enzymes and biochemical pathways an organism contains, and those biochemical pathways are often associated with certain families or genera.

Pressure optimums

barophile: - organism that grows best at higher pressures

Phylogenetic classification systems

based on actual evolutionary relationships look at how DNA has changed over time

proteomic analysis

based on the proteins produced under specific growth conditions within the human body proteins from the pathogen are first separated by high-pressure liquid chromatography (HPLC), and the collected fractions are then digested to yield smaller peptide fragments These peptides are identified by mass spectrometry and compared with those of known microorganisms to identify the unknown microorganism in the original specimen.

allosteric activators

bind to locations on an enzyme away from the active site, inducing a conformational change that increases the affinity of the enzyme's active site(s) for its substrate(s).`

supercritical fluids

carbon dioxide is brought to approximately 10 times atmospheric pressure has physical properties between those of liquids and gases Supercritical carbon dioxide works by penetrating cells and forming carbonic acid, thereby lowering the cell pH considerably. effective against vegetative cells and is also used in combination with peracetic acid to kill endospores Benefits of scCO2: - nonreactive, nontoxic, and nonflammable of CO2 - preserves the object's integrity and is commonly used for treating foods (including spices and juices) and medical devices such as endoscopes

granules within their cytoplasm: poly-β-hydroxybutyrate (PHB)

carbon- and energy-storage compound found: in some nonfluorescent bacteria of the genus Pseudomonas

alkylating agents disadvantages

carcinogenic, highly explosive

Molecular energy stored in the bonds of complex molecules is released in _______ pathway

catabolic

binary fission

cell replication in bacteria 1. Before dividing, the cell grows and increases its number of cellular component 2. replication of DNA starts at a location on the circular chromosome called the origin of replication, where the chromosome is attached to the inner cell membrane. 3. Replication continues in opposite directions along the chromosome until the terminus is reached. each offspring receives a complete copy of the parental genome and a division of the cytoplasm ( cytokinesis) FtsZ: - cytokinesis and cell division is directed by a protein - assembles: into a Z ring on the cytoplasmic membrane - Z ring is anchored by FtsZ-binding proteins and defines the division plane between the two daughter cells. - Additional proteins required for cell division are added to the Z ring to form a structure called the divisome - divisome activates to produce a peptidoglycan cell wall and build a septum that divides the two daughter cells. - daughter cells are separated by division of the septum

Phenolics

chemical compounds found in antiseptic mouthwashes and throat lozenges inhibit microbial growth by denaturing proteins and disrupting membranes phenol consists of a benzene ring with an -OH group, ex. thymol and eucalyptol occur naturally in plants ex. derived from creosote, a component of coal tar stable, persistent on surfaces, and less toxic than phenol

Sulfur dioxide

chemical preservatives - prevents browning of foods and is used for the preservation of dried fruits - dissolves in water readily, forming sulfites sulfites degrade thiamine, an important nutrient in some foods.

substrates

chemical reactants to which an enzyme binds

Alcohols (chemical method)

chemicals commonly used as disinfectants and antiseptics how? - rapidly denaturing proteins, which inhibits cell metabolism, and by disrupting membranes, which leads to cell lysis. - Once denatured, the proteins may potentially refold if enough water is present in the solution used at concentrations of about 70% aqueous solution and, in fact, work better in aqueous solutions than 100% alcohol solutions. why? - alcohols coagulate proteins. In higher alcohol concentrations, rapid coagulation of surface proteins prevents effective penetration of cells. - The most commonly used alcohols for disinfection are ethyl alcohol (ethanol) and isopropyl alcohol (isopropanol, rubbing alcohol) can alcohol kill: - bactericidal and fungicidal, but may also be viricidal for enveloped viruses only - not sporicidal, they do inhibit the processes of sporulation and germination. used to make tinctures with other antiseptics, such as the iodine tinctures disadvantages: - high volatility, limiting their effectiveness to immediately after application.

E. coli

chemoorganoheterotroph metabolically versatile chemoheterotroph grown on a variety of substrates, under various oxygen concentrations with fumarate or nitrate, replacing oxygen as the terminal electron acceptor under anaerobic conditions

Energy source types

chemotroph: energy from chemical compound Phototroph: source of energy is light chemoorganotroph; organism that gets its energy from the oxidation of reduced organic molecules Chemoorganotrophs are always heterotrophs Organotrophic obtain metabolic energy from the oxidation of organic compounds chemolithotroph: energy from inorganic chemical sources

Lithotrophs

chemotrophs that get energy from inorganic compounds, including hydrogen sulfide (H2S) and reduced iron. unique to the microbial world

Chemical disinfectants ex.

chlorine bleach or products containing chlorine, are used to clean nonliving surfaces such as laboratory benches, clinical surfaces, and bathroom sinks

Phylogenetic Trees

circular tree of the domain Bacteria: - Each branch point indicates where two groups diverged as they evolved from the last common ancestor of all bacteria bacteria are on branches that came off that original center point fairly early and are thus what we call the deep branches of the bacterial tree

Maps that show evolutionary relationships among organisms

cladogram

chloramines

class of chlorinated relatively stable, releasing chlorine over long periods derivatives of ammonia used for disinfection of drinking water, and chloramine tablets are frequently used by the military for this purpose

Phylogeny

classification of organisms based on their evolutionary relatedness

Taxonomic Tools

classifying organisms based on characteristics that we can view or measure 1. Morphology 2. Differential Staining 3. Biochemical Tests 4. Serology

sanitization

cleansing of fomites to remove enough microbes to achieve levels deemed safe for public health ex. 1. commercial dishwashers used in the food service industry typically use very hot water and air for washing and drying; the high temperatures kill most microbes, sanitizing the dishes 2. Surfaces in hospital rooms are commonly sanitized using a chemical disinfectant to prevent disease transmission between patients

what happens within a biofilm?

different species of microorganisms establish metabolic collaborations in which the waste product of one organism becomes the nutrient for another ex. aerobic microorganisms consume oxygen, creating anaerobic regions that promote the growth of anaerobes occurs in many polymicrobial infections that involve both aerobic and anaerobic pathogens

protocol level of cleanliness:

clinically: - categorized: critical: - must be sterile because they will be used inside the body - often penetrating sterile tissues or the bloodstream ex of critical items: - surgical instruments - catheters - intravenous fluids. semicritical - contact mucous membranes or nonintact skin but do not penetrate tissues. ex. of semicritical items: - Gastrointestinal endoscopes - various types of equipment for respiratory therapies noncritical: - contact but not penetrate intact skin ex. noncritical items: - bed linens, furniture, crutches, stethoscopes, and blood pressure cuffs

enzyme helper molecules

cofactors and coenzymes

Morphology

color, shape, and texture this can narrow down the possibilities

A ____________________ inhibitor binds at the active site of an enzyme.

competitive

light-harvesting complex

consists of multiple proteins and associated pigments that each may absorb light energy and, thus, become excited. eventually (after about a millionth of a second) it is delivered to the reaction center. only energy—not electrons—has been transferred between molecules. Different kinds of light-harvesting pigments absorb unique patterns of wavelengths (colors) of visible light.

reaction-center complex

contains a pigment molecule that can undergo oxidation upon excitation, actually giving up an electron It is at this step in photosynthesis that light energy is converted into an excited electron - Once the light harvesting complex transfers the energy to the reaction center - reaction center delivers its high-energy electrons, one by one, to an electron carrier in an electron transport system - electron transfer through the ETS is initiated Produce: NADH or NADPH, ATP by chemiosmosis through photophosphorylation

enriched media

contains growth factors, vitamins, and other essential nutrients to promote the growth of fastidious organisms

Soap form

contains high concentrations of calcium and magnesium mineral salts

enzymes

controlling cellular metabolism enzyme functions by lowering the activation energy

autotrophs

convert inorganic carbon dioxide (CO2) into organic carbon compounds ex. Cyanobacteria, plants

Dunaliella spp.

counters osmotic pressure of the environment with a high cytoplasmic concentration of glycerol and by actively pumping out salt ions

4 classification levels " biological safety levels" (BSLs)

created by: The Centers for Disease Control and Prevention (CDC) and the National Institutes of Health (NIH) who uses similar to it: (WHO), European Union (EU) BLS is determined by the agent's infectivity, ease of transmission, and potential disease severity, as well as the type of work being done with the agent Each BSL requires a different level of biocontainment to prevent contamination and spread of infectious agents to laboratory personnel and, ultimately, the community.

preserving foods by using salts and sugars work by

creation a hypertonic enviornment brines and layering meat and fish in salt are time-honored methods of preserving food

Indirect methods measure

culture density by measuring turbidity of a culture or live cell density by measuring metabolic activity

4 major classes of electron carriers involved in both eukaryotic and prokaryotic electron transport systems are?

cytochromes, flavoproteins, iron-sulfur proteins, and the quinones

where does glycolysis take place in prokaryotes and eukaryotes?

cytoplams

microbial death curve

degree of microbial control describe the progress and effectiveness of a particular protocol Death curves are often plotted as semilog plots just like microbial growth curves because the reduction in microorganisms is typically logarithmic

At higher temperatures, enzymes are:

denatured which can irreversibly destroy function

Obligate aerobes

depend on aerobic respiration and use oxygen as a terminal electron acceptor. They cannot grow without oxygen

exotic

derived from a foreign location, include pathogens such as: - Mycobacterium tuberculosis - Bacillus anthracis - West Nile virus - human immunodeficiency virus (HIV)

metabolism

describe all of the chemical reactions inside a cell growth of microorganisms depends on metabolic characteristics

In-Use Test

determine whether an actively used solution of disinfectant in a clinical setting is microbially contaminated 1-mL sample of the used disinfectant is diluted into 9 mL of sterile broth medium that also contains a compound to inactivate the disinfectant. 1. Ten drops, totaling approximately 0.2 mL of this mixture, are then inoculated onto each of two agar plates 2. One plate is incubated at 37 °C for 3 days and the other is incubated at room temperature for 7 days 3. plates are monitored for growth of microbial colonies. Growth of five or more colonies on either plate suggests that viable microbial cells existed in the disinfectant solution and that it is contaminated.

Joseph Lawrence

developed listerine an alcohol-based mixture of several related compounds that is still used today as an oral antiseptic

_________________________ are used in identification through a series of questions that have two possible answers each.

dichotomous key

2 types of autoclaves

differ in the way that air is removed from the chamber 1. gravity displacement autoclaves - steam is introduced into the chamber from the top or sides - Air, which is heavier than steam, sinks to the bottom of the chamber, where it is forced out through a vent - Complete displacement of air is difficult, especially in larger loads, so longer cycles may be required for such loads 2. prevacuum sterilizers - air is removed completely using a high-speed vacuum before introducing steam into the chamber - Because air is more completely eliminated, the steam can more easily penetrate wrapped items. Many autoclaves are capable of both gravity and prevacuum cycles, using the former for the decontamination of waste and sterilization of media and unwrapped glassware, and the latter for sterilization of packaged instruments.

Measurement of bacterial growth

direct counts, plate count methods, indirect methods - estimating # bacterial cells in a sample - in clinical sample serves as an indication of the extent of an infection

Use-Dilution Test

disinfection effectiveness on an inanimate surface 1. cylinder of stainless steel is dipped in a culture of the targeted microorganism and then dried 2. The cylinder is then dipped in solutions of disinfectant at various concentrations for a specified amount of time 3. the cylinder is transferred to a new test tube containing fresh sterile medium that does not contain disinfectant, and this test tube is incubated Bacterial survival is demonstrated by the presence of turbidity in the medium, whereas killing of the target organism on the cylinder by the disinfectant will produce no turbidity. minimum of 59 of 60 replicates must show no growth in such a test to achieve a passing result, and the results must be repeatable from different batches of disinfectant and when performed on different days.

o-phthalaldehyde (OPA)

disinfection of medical equipment two reactive aldehyde groups, but they are linked by an aromatic bridge less irritating to skin and nasal passages, produces a minimal odor, does not require processing before use, and is more effective against mycobacteria.

PH effect on proteins

disrupt hydrogen bonding, which, in turn, promotes changes in the folding of the molecule, promoting denaturation and destroying activity

Actinobacteria

diverse group of high G+C gram-positive organisms

Aerotolerant anaerobes what enzymes do they have?

do have SOD but no catalase.

suffix -stat or -stasis

do not kill organisms but, instead, stop their growth, making their population static less toxic to humans and other animals, and may also better preserve the integrity of the item treated reduced toxicity - allows them to be impregnated safely into plastics to prevent the growth of microbes on these surfaces

Commercial sterilization is a limited heat treatment to destroy

does not eliminate the presence of all microbes; rather, it targets those pathogens that cause spoilage and foodborne diseases, while allowing many nonpathogenic organisms to survive.

glycolysis portion of metabolism

does not require oxygen and neither do the pentose phosphate or Entner-Doudoroff pathways

Desiccation

drying, dehydration; the process of being rendered free from moisture preserve food: -raisins - prunes - jerky how it works? all cells require water for their metabolism and - might not kill all microbes or their endospores how dried? - sun - freeze- drying

began in prokaryotes is photosynthesis

earliest form of photosynthesis by bacteria did not produce oxygen and is known as anoxygenic or cyclic photosynthesis does not involve the splitting of water Instead, the same electrons are excited from the photosystems over and over, returning to the photosystem after passing down an electron transport chain.

NADPH

electron carrier for anabolic pathways

NADH

electron carrier in catabolic pathways

oxidation-reduction reactions, or redox reactions

electrons can move from one molecule to another, oxidation and reduction

anabolism

endergonic metabolic pathways involved in biosynthesis, converting simple molecular building blocks into more complex molecules, and fueled by the use of cellular energy.

Activation energy

energy needed to form or break chemical bonds and convert reactants to products

glycolysis and the subsequent pathways in the catabolism of glucose provide the cell with

energy stored in molecules such as NADH and ATP energy for intermediates of these pathways, including pyruvate and others, can serve as building blocks for other molecules the cell needs for growth

which of the following pathways is used in some bacteria which do not have glycolysis?

entner- doudrorff

what geologic processes are involved in the cycling of elements on earth

erosion, water drainage, the movement of the continental plates, and weathering

nitrogen cycle

essential role by: Prokaryotes nitrogen = 78% of atmosphere nitrogen fixation: - reduction of atmospheric nitrogen to ammonia - redction catalyzed by the enzyme nitrogenase Nitrogen enters the living world through free-living and symbiotic bacteria ex. Cyanobacteria in aquatic ecosystems fix inorganic nitrogen (from nitrogen gas) into ammonia (NH3) that can be easily incorporated into biological macromolecules. nitrogen that enters living systems by nitrogen fixation is eventually converted from organic nitrogen back into nitrogen gas by microbes through 3 steps: 1. ammonification - bacteria and fungi convert nitrogenous waste from living animals or from the remains of dead organisms into ammonia (NH3). 2. nitrification - ammonia is then oxidized to nitrite (NO−2),(NO2−), then to nitrate (NO−3),(NO3−) - by nitrifying soil bacteria such as members of the genus Nitrosomonas 3. denitrification - whereby soil bacteria, such as members of the genera Pseudomonas and Clostridium, use nitrate as a terminal electron acceptor in anaerobic respiration- - converting it into nitrogen gas that reenters the atmosphere.

generation time

eukaryotic organisms: - Generation time: time between the same points of the life cycle in two successive generations - ex. typical generation time for the human population is 25 years definition is not practical for bacteria - reproduce rapidly or remain dormant for thousands of years prokaryotes (Bacteria and Archaea) -Generation time: doubling time: defined as the time it takes for the population to double through 1 round of binary fission - Bacterial doubling times vary enormously - Escherichia coli can double in as little as 20 minutes under optimal growth conditions in the laboratory

Ethylene

highly penetrating and can sterilize items within plastic bags such as catheters, disposable items in laboratories and clinical settings (like packaged Petri dishes), and other pieces of equipment. oxide exposure is a form of cold sterilization, making it useful for the sterilization of heat-sensitive item

obligate anaerobe ex.

ex. C. tetani - causes gas gangrene - infection starts in necrotic tissue (dead tissue that is not supplied with oxygen by blood circulation). ex. Clostridium spp - gram-positive, rod-shaped - ability to form endospores allows them to survive in the presence of oxygen - health-acquired infections is C. difficile, known as C. diff. - health-acquired infections is C. difficile, known as C. diff. - Antibiotic treatment disrupts the balance of microorganisms in the intestine and allows the colonization of the gut by C. difficile, causing a significant inflammation of the colon.

microorganisms contribute to nutrient cycles

ex. chemolitrophic bacteria use sulfur compounds to provide energy for an ecosystem that exist at the bottom of the ocean chemosynthesis maybe how early life survived

Biofilms and Human Health

ex. intestinal and respiratory the layers of normal microbiota lining the intestinal and respiratory mucosa play a role in warding off infections by pathogens. However, other biofilms in the body can have a detrimental effect on health. ex. form in plaque that form s on teeth is a biofilm ex. in wounds, sometimes causing serious infections that can spread ex. Pseudomonas aeruginosa often colonizes biofilms in the airways of patients with cystic fibrosis, causing chronic and sometimes fatal infections of the lungs. ex. Pathogens embedded within biofilms exhibit a higher resistance to antibiotics than their free-floating counterparts biofilms provide an ideal environment for the exchange of extrachromosomal DNA, which often includes genes that confer antibiotic resistance.

NADH and ATP

ex. of coenzymes that provide high-energy electrons or phosphate groups, respectively, which bind to enzymes, thereby activating them.

Refrigeration and Freezing

exception of psychrophiles Refrigerators: temperatures between 0 °C - 7 °C. - inhibits microbial metabolism Freezing below −2 °C may stop microbial growth and even kill susceptible organisms Bacterial cultures and medical specimens requiring long-term storage or transport are often frozen at ultra-low temperatures of −70 °C or lower HOW? - storing specimens on dry ice in an ultra-low freezer or in special liquid nitrogen tanks, which maintain temperatures lower than −196 °C

catabolism

exergonic pathways that break down complex molecules into simpler ones

Transient anaerobic conditions

exist when tissues are not supplied with blood circulation they die and become an ideal breeding ground for obligate anaerobes.

high-temperature short-time (HTST) pasteurization

exposes milk to a temperature of 72 °C for 15 seconds

complex media

extracts and digests of yeasts, meat, or plants don't know exactly how much of each chemical is actually present. ex. Nutrient broth, tryptic soy broth, and brain heart infusion Nutrient broth has two main components, beef extract and yeast extract These extracts are made from dehydrated tissue, from beef in the first one and from yeast in the second mixed with water, you have all the nutrients needed to grow many bacteria

a prokaryotic species is defined as a group of closely related organisms that breed among themselves

false

anaerobic respiration requires electron transport chain

false

disinfectants

fast acting, stable, easy to prepare, inexpensive, and easy to use. ex. vinegar; its acidity kills most microbes disinfection does not lead to sterilization because endospores tend to survive even when all vegetative cells have been killed

many types of biochemical test

fermentation pathways or oxygen metabolism or many other specific metabolic pathways

lactic acid bacteria

fermentative bacteria that produce lactic acid, are found in the Firmicutes, and are important in the production and preservation of many foods vaginal microbiota is composed largely of lactic acid bacteria, but when these bacteria are reduced, yeast can proliferate, causing a yeast infection. important: maintaining the health of the gastrointestinal tract and, as such, are the primary component of probiotics.

which of the following is an example of physical control of microbial growth?

filtering with a 0.22 micron filter

serial dilution (direct cell count)

first step before proceeding to either the pour plate or spread plate method goal: - obtain plates with CFUs in the range of 30-300 - usually involves several dilutions in multiples of 10 to simplify calculation dilution factor of 10, or 1:10, compared with the original culture: 1st dilution- fixed volume of the original culture, 1.0 m, is added to and thoroughly mixed with the first dilution tube solution, which contains 9.0 mL of sterile broth. 2nd dilution - same volume, 1.0 mL, is withdrawn and mixed with a fresh tube of 9.0 mL of dilution solution. The dilution factor is now 1:100 compared with the original culture process continues until a series of dilutions is produced that will bracket the desired cell concentration for accurate counting each tube, a sample is plated on solid medium using either the POUR PLATE METHOD OR SPREAD PLATE METHOD plates are incubated until colonies appear Two to three plates are usually prepared from each dilution and the numbers of colonies counted on each plate are averaged

Bisbiguanides

first synthesized in the 20th century are cationic (positively charged) molecules known for their antiseptic properties ex. chlorhexidine

Ribose

five-carbon sugar found in RNA

chemiosmosis

flow of hydrogen ions across the membrane use: channel membrane via a membrane-bound enzyme complex called ATP synthase Process by which a Hydrogen pump pumps protons into the thylakoid membrane. H+ passively flows through the ATP synthase which leads to the creation of ATP prokaryotic cells: H+ flows from the outside of the cytoplasmic membrane into the cytoplasm eukaryotic mitochondria: H+ flows from the intermembrane space to the mitochondrial matrix

Most organisms could not survive the powerful oxidative properties of reactive oxygen species (ROS)

highly unstable ions and molecules derived from partial reduction of oxygen that can damage virtually any macromolecule or structure with which they come in contact ex. of ROS - Singlet oxygen (O2•), superoxide (O2−),(O2−), peroxides (H2O2), hydroxyl radical (OH•), and hypochlorite ion (OCl−), the active ingredient of household bleach, are all examples of ROS.

direct counting technique: fluorescence staining techniques

fluorescence staining techniques: - distinguish viable and dead bacteria. - viability stains (or live stains) bind to nucleic acids - the primary and secondary stains differ in their ability to cross the cytoplasmic membrane - Primary staining: - fluoresces green, can penetrate intact cytoplasmic membranes, staining both live and dead cells - secondary staining: - fluoresces red, can stain a cell only if the cytoplasmic membrane is considerably damaged. thus, live cells fluoresce green because they only absorb the green stain, whereas dead cells appear red because the red stain displaces the green stain on their nucleic acids

Pressure

food industry: - high-pressure processing/ pascalization used to: kill bacteria, yeast, molds, parasites, and viruses in foods while maintaining food quality and extending shelf life. high pressure between 100-800 MPa (sea level atmospheric pressure is about 0.1 MPa) is sufficient to kill vegetative cells by protein denaturation, but endospores may survive these pressures.

commercial sterilization

food sterilization protocol heat at a temperature low enough to preserve food quality but high enough to destroy common pathogens responsible for food poisoning, ex. C. botulinum - found in soil, they may easily contaminate crops during harvesting, and these endospores can later germinate within the anaerobic environment once foods are canned They assume an impossibly large population of endospores (1012 per can) and aim to reduce this population to 1 endospore per can to ensure the safety of canned foods. how: - low- and medium-acid foods are heated to 121 °C for a minimum of 2.52 minutes= which is the time it would take to reduce a population of 1012 endospores per can down to 1 endospore at this temperature.

bacterial cell cycle

formation of new cells through the replication of DNA and partitioning of cellular components into two daughter cells. bacteria : single circular chromosome exception bacteria: of Lyme disease, has a linear chromosome

enrichment cultures

foster the preferential growth of a desired microorganism that represents a fraction of the organisms present in an inoculum

Benzoic acid

found naturally in many types of fruits and berries, spices, and fermented products It is thought to work by decreasing intracellular pH, interfering with mechanisms such as oxidative phosphorylation and the uptake of molecules such as amino acids into cells. Foods preserved with benzoic acid or sodium benzoate include : - fruit juices, jams - ice creams, pastries - soft drinks - chewing gum - pickles.

fungi pH

fungi thrive at slightly acidic pH values of 5.0-6.0

products of Lipid catabolism

glycerol and fatty acids can it be further degarades? yes - Glycerol can be phosphorylated to glycerol-3-phosphate and easily converted to glyceraldehyde 3-phosphate, which continues through glycolysis - fatty acids are catabolized in a process called β-oxidation, which sequentially removes two-carbon acetyl groups from the ends of fatty acid chains, reducing NAD+ and FAD to produce NADH and FADH2, respectively, whose electrons can be used to make ATP by oxidative phosphorylation.

earliest biochemical pathways

glycolysis: found in the cytoplasm of cells in all domains does not require an organelle and does not require oxygen so it predates the oxygen atmosphere

Listeriosis monocytogenes

gram-positive short rod found in soil, water, and food classified as a psychrophile and is halotolerant it often contaminates food such as meat, fish, or dairy products.

Psychrophiles (cold loving)

grow at 0 °C and below optimum growth temperature close to 15 °C not survive at temperatures above 20 °C found in permanently cold environments such as the deep waters of the oceans psychrophiles and psychrotrophs are important decomposers in cold climates

Thermophiles (heat loving)

grow at optimum temperatures of 50 °C - a maximum of 80 °C do not multiply at room temperature found: widely distributed in hot springs, geothermal soils, and manmade environments such as garden compost piles where the microbes break down kitchen scraps and vegetal materia

Acidophiles

grow in acidic environments pH= less than 5.55 ex. sulfur-oxidizing Sulfolobus spp.

study of obligate anaerobes

grown under conditions devoid of oxygen anaerobic jar - include chemical packs that remove oxygen and release carbon dioxide (CO2) anaerobic chamber - enclosed box from which all oxygen is removed

the growth curve

growth pattern Closed environment Microorganisms grown in closed culture (also known as a batch culture), in which no nutrients are added and most waste is not removed ex. small number of cells grown in a pond - Infections of the body do not always follow the growth curve, but correlations can exist depending upon the site and type of infection.

Hyperthermophiles

growth ranges from 80 °C to a maximum of 110 °C Extreme examples: survive temperatures above 121 °C, the average temp of an autoclave ex. hydrothermal vents at the bottom of the ocean 340 °C

Chlorine

halogen chlorine gas is mixed with water, it produces a strong oxidant called hypochlorous acid enters cells easily Chlorine gas used for: municipal drinking water and wastewater treatment plants, with the resulting hypochlorous acid producing the actual antimicrobial effect

Salt optimums

halophiles: - growing best in high salt concentrations

Thioglycolate medium

has strong reducing properties and autoclaving flushes out most of the oxygen

High-level germicides

have the ability to kill vegetative cells, fungi, viruses, and endospores, leading to sterilization, with extended use.

heat temperature affect macromolecules

heat denatures proteins and nucleic acids. Increased fluidity impairs metabolic processes in membranes

carbon sources

heterotroph: organism obtains its carbon from pre-formed organic molecules that it obtains from external sources autotroph: takes in carbon dioxide from its environment and incorporates that carbon into its molecules through the process of carbon fixation

Inorganic Phosphate (Pi)

high-energy bonds are broken to release one phosphate

sterilization: Plasma

hot, ionized gas, described as the fourth state of matter, is useful for sterilizing equipment because it penetrates surfaces and kills vegetative cells and endospores Peracetic acid can be used as a liquid or plasma sterilant insofar as it readily kills endospores, is more effective than hydrogen peroxide even at rather low concentrations, and is immune to inactivation by catalases and peroxidases.\ breaks down to environmentally innocuous compounds; in this case, acetic acid and oxygen.

Temperature Optimums

human body = lower than 37°C = Mesophile= middle loving - optimum= 20°C and 40°C - will not grow much below 15 or 20°C - killed above 42-45°C. temperature gets above the enzyme's optimum the protein may begin to denature Below the optimum temperature of the organism's enzymes, the enzymes work slowly or become inactive psychrophile = cold-loving - optimum = 15°C - 30°C. thermophiles = heat-loving - optimums around 65°C hyperthermophiles - optimums above 90°C - microorganisms that grow in places like the hot springs of Yellowstone or the volcanic vents in the mid-ocean ridges

granules within their cytoplasm: do not accumulate PHB granules.

human pathogen P. aeruginosa and the plant pathogen P. syringae are two examples of fluorescent Pseudomonas species that do not accumulate PHB granules.

extracellular polymeric substances (EPS)

hydrated gel composed primarily of polysaccharides and containing other macromolecules such as proteins, nucleic acids, and lipids key role in maintaining the integrity and function of the biofilm Channels in the EPS allow movement of nutrients, waste, and gases throughout the biofilm. This keeps the cells hydrated, preventing desiccation. EPS also shelters organisms in the biofilm from predation by other microbes or cells (e.g., protozoans, white blood cells in the human body).

Serological tests

identified by the carbohydrates attached to proteins (glycoproteins) in the plasma membrane or cell wall. Antibodies and other carbohydrate-binding proteins can attach to specific carbohydrates on cell surfaces, causing the cells to clump together.

quorum sensing ex

in some pathogens, synthesis of virulence factors only begins when enough cells are present to overwhelm the immune defenses of the host in bacterial populations quorum sensing takes place between bacteria and eukaryotes and between eukaryotic cells such as the fungus Candida albicans, a common member of the human microbiota that can cause infections in immunocompromised individuals.

Disinfection

inactivates most microbes on the surface of a fomite by using antimicrobial chemicals or heat

Fomites

inanimate objects that are contaminated by direct contact with a reservoir objects contaminated with infectious material that contains the pathogens

Ionizing radiation

includes X-rays, gamma rays, and high-energy electron beams includes X-rays, gamma rays, and high-energy electron beams introduces double-strand breaks in DNA molecules directly cause DNA mutations to occur, or mutations may be introduced when the cell attempts to repair the DNA damage lead to cell death used to sterilize materials that cannot be autoclaved, such as plastic Petri dishes and disposable plastic inoculating loops. ex clinical use: ionizing radiation is used to sterilize gloves, intravenous tubing, and other latex and plastic items used for patient care.

aerotolerant anaerobes

indifferent to the presence of oxygen do not perform aerobic respiration most test negative for the enzyme catalase They do not use oxygen because they usually have a fermentative metabolism, but they are not harmed by the presence of oxygen as obligate anaerobes are ex. lactobacilli and streptococci, both found in lactobacilli and streptococci, both found in the oral microbiotathe oral microbiota

Propionic acid

inhibit enzymes and decrease intracellular pH, working similarly to benzoic acid effective preservative at a higher pH naturally produced by some cheeses during their ripening and is added to other types of cheese and baked goods to prevent mold contamination added to raw dough to prevent contamination by the bacterium Bacillus mesentericus, which causes bread to become ropy

bacteriostatic

inhibits bacterial growth

Confactors. enzyme helper molecule

inorganic ions such as iron (Fe2+) and magnesium (Mg2+) that help stabilize enzyme conformation and function ex. enzyme that builds DNA molecules, DNA polymerase, which requires a bound zinc ion (Zn2+) to function.

hyperbaric oxygen therapy

involves breathing pure oxygen in a special chamber that allows air pressure to be raised up to three times higher than normal place patient inside hyperbaric chamber or by supplying the pressurized oxygen through a breathing tube treat infections Hyperbaric oxygen therapy helps increase oxygen saturation in tissues that become hypoxic due to infection and inflammation. enhances immune response by increasing the activities of neutrophils and macrophages, white blood cells that fight infections. Increased oxygen levels also contribute to the formation of toxic free radicals that inhibit the growth of oxygen-sensitive or anaerobic bacteria like as Clostridium perfringens, a common cause of gas gangrene reduce secretion of a bacterial toxin that causes tissue destruction.

iodophor

iodine complexed with an organic molecule, thereby increasing iodine's stability and, in turn, its efficacy. ex. povidone-iodine, which includes a wetting agent that releases iodine relatively slowly. Betadine is a brand of povidone-iodine commonly used as a hand scrub by medical personnel before surgery and for topical antisepsis of a patient's skin before incision

Halogens (chemical method)

iodine, chlorine, and fluorine Iodine works by oxidizing cellular components, including sulfur-containing amino acids, nucleotides, and fatty acids, and destabilizing the macromolecules that contain these molecules.

how to protect from X-rays and gamma irradiation?

ionizing irradiation cannot penetrate thick layers of iron or lead, so these metals are commonly used to protect humans who may be potentially exposed.

other biogeochemical cycles involve redox chemistry

iron (Fe), manganese (Mn), and chromium (Cr) cycles

chlorinated compounds disadvantages?

irritate the skin, nose, or eyes of some individuals not completely eliminate certain hardy organisms from contaminated drinking water ex, protozoan parasite Cryptosporidium - protective outer shell that makes it resistant to chlorinated disinfectants.

Glycolysis (Embden-Meyerhof pathway)

it produces energy, reduced electron carriers, and precursor molecules for cellular metabolism Cellular respiration begins when electrons are transferred from NADH and FADH2—made in glycolysis, Part of glycolysis catabolism every organism carries out glycolysis Glycolysis does not use Oxygen generate ATP by substrate-level phosphorylation. can be coupled with additional metabolic processes aerobic or anaerobic 6 carbon glucose and 3 carbon sugar(pyruvate) Pyruvate broken down further after glycolysis to get more Energy but many organisms, including many microbes, may be UNABLE TO BREATH; for these organisms, glycolysis may be their only source of generating ATP. reduced NAD+ to NADH availability of NAD+ is crucial to continuing the process of extracting energy from glucose - NADH must be recycled back to NAD+

bactericides

kill bacteria

fungicides

kill fungi

Heavy Metals

kill microbes by binding to proteins, thus inhibiting enzymatic activity are oligodynamic, meaning that very small concentrations show significant antimicrobial activity Ions of heavy metals bind to sulfur-containing amino acids strongly and bioaccumulate within cells, allowing these metals to reach high localized concentrations. This causes proteins to denature. not selectively toxic to microbial cells They may bioaccumulate in human or animal cells, as well, and excessive concentrations can have toxic effects on humans.

viricides

kill or inactivate viruses

homolactic fermentation

lactic acid is the only fermentation product ex. Lactobacillus delbrueckii and S. thermophiles used in yogurt production.

growth curve phases

lag phase, log phase, stationary phase, death phase how? -collecting cell counts in a culture of bacteria growing in a culture flask begin: 1. inoculate a flask of culture media with a sample of the bacteria ex. by touching a sterile loop to an isolated bacterial colony on a plate and then transferring bacteria to our flask 2. culture flask is then placed in a shaking incubator at an appropriate temperature for the bacterium we are growing 3. Samples are taken and cell number measured at time intervals up to about 48 hours 4. Samples are taken and cell number measured at time intervals up to about 48 hours

retorts

large industrial autoclaves allow for moist-heat sterilization on a large scale

environmental conditions influence the potency of an antimicrobial agent and its effectiveness.

length of exposure concentration of the chemical Temperature pH

Thermal death time (TDT)

length of time needed to kill all microorganisms in a sample at a given temperature parameters = describe sterilization procedures that use high heat ex. autoclaving

Intermediate-level germicides

less effective against endospores and certain viruses, and low-level germicides kill only vegetative cells and certain enveloped viruses, and are ineffective against endospores

photosynthetic pigments

light energy is actually converted into chemical energy Photosynthetic pigments within the photosynthetic membranes are organized into photosystems photosystems composed of: a light-harvesting (antennae) complex and a reaction center.

Thiomicrospira

lives near volcanic vents in deep ocean rifts oxidizes sulfur compounds for energy and fixes carbon dioxide chemolithoautotroph

allosteric site

location other than the active site,

in which phase are the cells dividing at their maximum rate for the given condition?

log

sustaining microbial growth

logarithmic phase of growth - chemostat: used to maintain a continuous culture in which nutrients are supplied at a steady rate - controlled amount of air is mixed in for aerobic processes - Bacterial suspension is removed at the same rate as nutrients flow in to maintain an optimal growth environment

Thermal death point (TDP)

lowest temperature at which all microbes are killed in a 10-minute exposure.

differential media

make it easy to distinguish colonies of different bacteria how? change in the color of the colonies or the color of the medium. what causes color change? result of end products created by interaction of bacterial enzymes with differential substrates in the medium or, in the case of hemolytic reactions, the lysis of red blood cells in the medium.

indirect counting methods

measure cell activity by following the production of metabolic products or disappearance of reactants - Adenosine triphosphate (ATP) formation - biosynthesis of proteins - nucleic acids, - consumption of oxygen can all be monitored to estimate the number of cells

agar

media solidifying agent Agar is a polysaccharide that comes from the red algae agar into solution, the temperature of the media must be heated to close to boiling Once dissolved, the media is cooled and becomes solid below about 45°C Once solid, agar does not melt again until you heat it close to boiling. Prior to using agar, microbiologists used gelatin, similar to what you use in foods like Jello

peculiar watermelon snow is caused by

microalga Chlamydomonas nivalis a green alga rich in a secondary red carotenoid pigment (astaxanthin) which gives the pink hue to the snow where the alga grows.

Pasteurization

microbial control for food that uses heat but does not render the food sterile - kills pathogens - reduces the number of spoilage-causing microbes while maintaining food quality.

Bioremediation

microbial metabolism to remove xenobiotics or other pollutants Xenobiotics are compounds synthesized by humans and introduced into the environment in much higher concentrations than would naturally occur EX. adhesives, dyes, flame retardants, lubricants, oil and petroleum products, organic solvents, pesticides, and products of the combustion of gasoline and oil xenobiotics resist breakdown, and some accumulate in the food chain after being consumed or absorbed by fish and wildlife, which, in turn, may be eaten by humans

Fannie Hesse is credited with giving ________ the idea to use agar as a solidifying agent

microbiological media

Biofilm found where

microorganisms grow mainly in biofilms form on a variety of environmental surfaces, from industrial conduits and water treatment pipelines to rocks in river beds not restricted to solid surface substrates Almost any surface in a liquid environment containing some minimal nutrients will eventually develop a biofilm biofilms are NOT RANDOM collections of microorganisms; rather, they are highly structured communities that provide a selective advantage to their constituent microorganisms.

ultra-high-temperature (UHT) pasteurization

milk is exposed to a temperature of 138 °C for 15 + 2 or more seconds. stored for a long time in sealed containers without being refrigerated high temperatures alter the proteins in the milk, causing slight changes in the taste and smell

minimum permissive oxygen concentration

minimum permissive oxygen concentration

Z scheme

model of how photosystems I and II interact electrons Upon passing of the PSII reaction center electron to the ETS that connects PSII and PSI, the lost electron from the PSII reaction center is replaced by the splitting of water. The excited PSI reaction center electron is used to reduce NADP+ to NADPH and is replaced by the electron exiting the ETS.

Charles Chamberland (1851-1908)

modern autoclave in 1879 while working in the laboratory of Louis Pasteur

Extreme alkaliphiles have adapted

modification of lipid and protein structure compensatory mechanisms to maintain the proton motive force in an alkaline environment.

electron carriers

molecules that bind to and shuttle high-energy electrons between compounds in pathways

six most common elements associated with organic molecules

molecules—carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur

oxidative phosphorylation

most ATP produced here Occurs: cellular respiration (begins in glycolysis) Product: - water final inorganic electron acceptor: - either oxygen in aerobic respiration - non-oxygen inorganic molecules in anaerobic respiration). energy of the electrons is harvested to generate an electrochemical gradient across the membrane, which is used to make ATP by oxidative phosphorylation. Toxic Byproducts: - superoxide radical, O2 - damages cellular materials, including proteins and lipids, so a cell using aerobic respiration must quickly detoxify the superoxide radical if it is going to survive how to detoxify? - enzyme: superoxide dismutase - Superoxide dismutase takes the superoxide radical plus water to produce hydrogen peroxide, H2O2 - Hydrogen peroxide can also damage cellular materials, but it is less damaging than the superoxide radical - Cells still need to detoxify this molecule in order to protect their components from damage and have two strategies for doing so. These options are either catalase or peroxidase Catalase: hydrogen peroxide and water to produce water and O2 - ex. hydrogen peroxide= bubbles, O2 gas being produced by catalase in skin cells - production of Oxygen gas from catalase as biochemical test called the catalase test - Catalase if very efficient at detoxifying hydrogen peroxide so does a very good job of protecting cells from this destructive compound. For cells with superoxide dismutase and catalase, the toxic byproducts of aerobic respiration are removed other option for detoxifying hydrogen peroxide is the enzyme peroxidase. - Peroxidase catalyzes a reaction between hydrogen peroxide with the product of water - No oxygen gas is produced. Peroxidase is not able to detoxify hydrogen peroxide as quickly as catalase can, so cells with peroxidase instead of catalase are more sensitive to oxygen - They can survive only in lower oxygen concentrations

nicotinamide adenine dinucleotide NAD

most common mobile electron carrier used in catabolism Oxidized: NAD+ Reduced: NADH

optimum growth pH

most favorable pH for the growth of an organism

microorganisms Osmotic and Barometric Pressure

natural environments tend to have lower solute concentrations than the cytoplasm of most microorganisms Rigid cell walls protect the cells from bursting in a dilute environment

pH Optimums

neutrophiles: - optimum pH of between 6.5 - 7.5 acidophiles - lower pH basophiles - pH up to a maximum of about 10

Official Names of Bacteria

new bacterial name is considered to be official when it has been accepted and published in the International Journal of Systematic and Evolutionary Microbiology submission is reviewed by other scientists through peer review and, if the evidence meets the requirements to show that this organism is different from anything that is known, then the paper would be published

B vitamin are derivatives of nucleotides easily reduced or oxidized.

nicotinamide adenine dinucleotide nicotine adenine dinucleotide phosphate flavin adenine dinucleotide

At low temperatures, enzymes are:

not able to function due to lack of energy for chemical reactions

Photosynthetic membranes in prokaryotes

not organized into distinct membrane-enclosed organelles they are infolded regions of the plasma membrane. thylakoid membranes or other photosynthetic bacterial: molecules organized into one or more photosystems, ex. cyanobacteria these infolded regions are also referred to as thylakoids.

Eutrophication

nutrient runoff causes the overgrowth and subsequent death of aquatic algae, making water sources anaerobic and inhospitable for the survival of aquatic organisms

Oxygen Requirements of Microorganisms

observe molecular oxygen by growing in thioglycolate tube cultures A test-tube culture starts with autoclaved thioglycolate medium containing a low percentage of agar to allow motile bacteria to move throughout the medium - The tubes are inoculated with the bacterial cultures to be tested and incubated at an appropriate temperature. - Over time, oxygen slowly diffuses throughout the thioglycolate tube culture from the top. - Bacterial density increases in the area where oxygen concentration is best suited for the growth of that particular organism.

Organotrophs

obtain electrons from organic compounds - humans - fungi - many prokaryotes

Chemotrophs

obtain energy for electron transfer by breaking chemical bonds.

Boiling

oldest methods of moist-heat control of microbes it is typically quite effective at killing vegetative cells and some viruses less effctive killing endospores endospores are able to survive up to 20 hours of boiling. boiling may be less effective at higher altitudes, where the boiling point of water is lower and the boiling time needed to kill microbes is therefore longer. boiling water, a method that allows endospores of Clostridium botulinum to survive. C. botulinum produces botulinum toxin, a neurotoxin that is often deadly once ingested.

optimum growth and minimum pH of Salmonella spp.

optimum growth pH of Salmonella spp. is 7.0-7.5, the minimum growth pH is closer to 4.2.

capnophile

organism that requires a higher than atmospheric concentration of CO2 to grow

phototrophs

organisms that get energy from light

Biofilms

organized ecosystem within which many cells, usually of different species of bacteria, fungi, and algae, interact through cell signaling and coordinated responses. provide a protected environment in harsh conditions and aids colonization by microorganisms To study: - req. new approaches Why? cells' adhesion properties, many of the methods for culturing and counting cells

2 types of chemotrophs

organotrophs lithotrophs

In __________________________ phosphorylation, ATP is generated through use of an electron transport chain with oxygen as the final electron acceptor and chemiosmosis.

oxidative

flavin adenine dinucleotide (FAD)

oxidized: FAD Reduced: FADH2

Nicotine adenine dinucleotide phosphate (NADP+),

oxidized: NAD+ variant that contains an extra phosphate group, is another important electron carrier Reduced: NADPH

Oxygen Tolerance

oxifying these destructive byproducts of oxygen metabolism 1.Aerobes - have both superoxide dismutase and catalase. They are able to live and grow in normal oxygen levels. 2. Anaerobes - cannot grow in the presence of oxygen - lack the enzymes needed to detoxify the byproducts of oxygen metabolism and are damaged by these molecules in an oxygen environment

"Goldilocks" culture

oxygen level has to be just right for growth

hyperbaric oxygen therapy risks?

oxygen toxicity and effects on delicate tissues eyes, middle ear, and lungs, which may be damaged by the increased air pressure

The source of this electron (H2A) differentiates who

oxygenic photosynthesis for plants and cyanobacteria anoxygenic photosynthesis for other types of bacterial phototrophs

filamentous cyanobacteria have developed a different strategy

oxygenic photosynthesis, a cell photosynthesizing would not be able to also fix nitrogen cells: heterocysts - cells have a specialized cell wall that helps to exclude oxygen, and they are able to fix nitrogen even though adjacent cells are photosynthesizing - cells in the filament can exchange nutrients with one another so fixed nitrogen leaves the heterocyst while the heterocyst benefits from the photosynthesis occurring in the other cells ex. Anabaena

Alkaliphiles

pH between 8.0 and 10.5

archaean genus Ferroplasma pH

pH values of 0-2.9

Enzymes are subject to influences by

pH, substrate concentration, and temperature

pH of Lactobacillus bacteria

part of normal microbiota of the vagina pH values 3.5-6.8 contribute to the acidity of the vagina through their metabolic production of lactic acid

Growth Optimum curve

peak in the middle = optimum optimum= where the condition under which the organism is growing best Anything that is less than the optimum is going to be a lower growth rate

gamma-irradiated

penetrate paper, plastic, thin sheets of wood and metal, and tissue

unique metabolic pathways found in bacteria

pentose phosphate and Entner-Doudoroff pathways - Nitrogen fixation is a process that is done only by bacteria - methanogenesis can be done only by archaea

third type of glycolytic pathway that occurs in all cells

pentose phosphate pathway (PPP) OR phosphogluconate pathway or the hexose monophosphate shunt PPP may be the most ancient universal glycolytic pathway may be favored when the cell has need for nucleic acid and/or protein synthesis, respectively

Genus Streptococcus

permanently incapable of respiration, even in the presence of oxygen.

Carbamide peroxide,

peroxygen that combats oral biofilms that cause tooth discoloration and halitosis (bad breath).

Benzoyl peroxide

peroxygen that used in acne medication solutions. kills the bacterium Propionibacterium acnes

ozone gas

peroxygen with disinfectant qualities and is used to clean air or water supplies.

in ____ typing, bacteria are classified based on the types of viruses that can infect them

phage

methods to characterize and identify microorganisms

phenotypic biochemical characteristics, while others use genotypic identification.

other biogeochemical cycles DO NOT involve redox chemistry

phosphorus (P), calcium (Ca), and silica (Si) cycles The cycling of these elements is particularly important in oceans because large quantities of these elements are incorporated into the exoskeletons of marine organisms. fluctuations in the solubility of compounds containing calcium, phosphorous, and silica.

anoxygenic photosynthesis

photosynthesis in which O2 is not produced Product: only ATP ex of other electron donor: Hydrogen sulfide (H2S) or thiosulfate (S2O2−3)(S2O32−) bacteria , including some cyanobacteria Unique catabolic pathways in bacteria - entner- doudoroff - pentose phosphate

Photosystems have been classified into two types:

photosystem I (PSI) photosystem II (PSII) Cyanobacteria and plant chloroplasts have both photosystems anoxygenic photosynthetic bacteria use only one of the photosystems.

How to achieve sterilization

physical means: 1. exposure to high heat, pressure OR 2. filtration through an appropriate filter OR 3. by chemical means

Filtration

physically separating microbes from samples

Biofilms occurs when

planktonic cells attach to a substrate and become sessile. Cells in biofilms coordinate their activity by communicating through quorum sensing.

Biofilm formation

planktonic: - Free-floating microbial cells that live in an aquatic environment formation of a biofilm essentially involves the attachment of planktonic cells to a substrate, where they become sessile (attached to a surface occurs in stages: 1. attachment of planktonic cells to a surface coated with a conditioning film of organic material -attachment to the substrate is reversible, but as cells express new phenotypes that facilitate the formation of EPS, they transition from a planktonic to a sessile lifestyle 2. 1st colonizers become irreversibly attached ( second, minutes) 3. growth and cell division ( hours, days) 4. develop: extensive matrix and water channels - Appendages such as fimbriae, pili, and flagella interact with the EPS, and microscopy and genetic analysis suggest that such structures are required for the stablishment of a mature biofilm 5. attachement of secondary colonizers and dispersion of microbes to new sites (days, months) dispersal - cells on the periphery of the biofilm revert to a planktonic lifestyle

whyc can Selective and differential media can be combined

play an important role in the identification of bacteria by biochemical methods

aseptic technique

precautions taken to prevent contamination of a surgical wound clinical purposes maintain sterility, or asepsis

how do microbes contribute to ecosystem

primary production and decomposition - Primary production is the synthesis of new organic matter from carbon dioxide and other inorganic compounds - Decomposition is the breakdown of accumulated organic matter Microbes are an important part of nutrient cycling in the environment

biogeochemical cycle

process in which elements, chemical compounds, and other forms of matter are passed from one organism to another and from one part of the biosphere to another

heterolactic fermentation

producing a mixture of lactic acid, ethanol and/or acetic acid, and CO2 as a result, because of their use of the branched pentose phosphate pathway instead of the EMP pathway for glycolysis.

Methanogenesis

production: methane (CH4) can be done only by mehtanogenic archaea final electron acceptor in anaerobic respiration: carbon dioxide Others can ferment acetate to release carbon dioxide and methane (anaerobic conditions) ex. genus Methanococcus ex. location: swamps have stagnant water with lots of decaying organic matter, landfills

Unique Biodegradations

prokaryotes have unique biodegradations bacteria can take complex carbohydrates or other complex organic molecules such as oil or benzene rings and degrade them

protein catabolism

protease enzymes breakdown protein Extracellular proteases cut proteins internally at specific amino acid sequences - breaking down to peptides that cn then be taken up by cells - Some clinically important pathogens can be identified by their ability to produce a specific type of extracellular protease. ex. the production of the extracellular protease gelatinase by members of the genera Proteus and Serratia can be used to distinguish them from other gram-negative enteric bacteria.

Acidophilic adaptations to strong acidic environments

proteins show increased negative surface charge that stabilizes them at low pH Pumps actively eject H+ ions out of the cells changes in the composition of membrane phospholipids probably reflect the need to maintain membrane fluidity at low pH

biochemical characteristics of a bacterium

provide many traits that are useful for classification and identification

a bacterium with a growth optimum around 115 C is called

psychrophile

an organism with optimal growth temperature of 10 degrees C would be considered to be a ___

psychrophile

Psychrotrophs

psychrotolerant prefer cooler environments, high temperature of 25 °C - 4°C responsible for the spoilage of refrigerated foods

thermoenzymes

purified from thermophiles ex. amplification of nucleic acids in the polymerase chain reaction (PCR) depends on the thermal stability of Taq polymerase, an enzyme isolated from T. aquaticus. Degradation enzymes from thermophiles are added as ingredients in hot-water detergents, increasing their effectiveness.

Another differential stain is the acid-fast stain

quickly identifies a specific genus because only organisms such as Mycobacterium that have mycolic acids in their cell wall will be positive for this staining method endospore stain would quickly narrow down the choices to a few genera if positive

organism will not grow outside the _____

range of oxygen levels found between the minimum and maximum permissive oxygen concentrations

products of chemiosmosis

regenerates ATP from ADP and inorganic phosphate by oxidative phosphorylation ATP generated vaires

Why is allosteric control important?

regulation of metabolic pathways involved in both catabolism and anabolism.

Autoclaves

rely on moist-heat sterilization raise temperatures above the boiling point of water to sterilize items such as surgical equipment from vegetative cells, viruses, and especially endospores air in the chamber of an autoclave is removed and replaced with increasing amounts of steam trapped within the enclosed chamber, resulting in increased interior pressure and temperatures above the boiling point of water. internal indicators: ensure proper sterilization

heterotrophs

rely on more complex organic carbon compounds as nutrients; these are provided to them initially by autotrophs. ex. Escherichia coli

mechanical methods of microbial control

remove microbial cells from samples or locations -washing your hands - Brushing your teeth - Filtration filters with pore sizes of 0.22 microns can be used to remove all bacteria from a liquid sample However, most viruses would still be able to pass through those pores

for photosynthesis to continue, the electron lost from the reaction center pigment must be ______

replaced

endergonic reactions

require energy to proceed.

barophiles

require high atmospheric pressure for growth The bacteria that live at the bottom of the ocean must be able to withstand great pressures.

halophiles ("salt loving")

require high salt concentrations for growth found: in marine environments where salt concentrations hover at 3.5%. Extreme halophilic: - ex. red alga Dunaliella salina and the archaeal species Halobacterium - grow in hypersaline lakes such as the Great Salt Lake, which is 3.5-8 times saltier than the ocean, and the Dead Sea, which is 10 times saltier than the ocean ex. staphylococci, micrococci, and corynebacteria that colonize our skin tolerate salt in their environment.` Halotolerant pathogens are an important cause of food-borne illnesses because they survive and multiply in salty food ex. S. aureus, Bacillus cereus, and V. cholerae = food poision

BLS 1

requires the fewest precautions lowest risk for microbial infection generally do not cause infection in healthy human adults include: - noninfectious bacteria ex. nonpathogenic strains of Escherichia coli and Bacillus subtilis - viruses known to infect animals other than humans ex. baculoviruses precautions: - standard aseptic technique - may work with these agents at an open laboratory bench or table - wearing personal protective equipment (PPE) such as a laboratory coat, goggles, and gloves, as needed. modifications needed: - sink - door to separate lab from rest of building

pathogenic strains of E. coli, S. typhi, and other species of intestinal pathogens pH?

resistant to stomach acid

what is the primary molecule used by woese to place organisms into domains?

ribosomal RNA

At _________________________, an enzyme's reaction rate can no longer increase because all active sites are already in use.

saturation

Fragmentation

seen in: Actinomycetes - gram-positive, anaerobic bacteria commonly found in soil - grow in long filaments divided by septa, similar to the mycelia seen in fungi, resulting in long cells with multiple nucleoids - Environmental signals, probably related to low nutrient availability, lead to the formation of aerial filaments. seen in: - Epulopiscium Several daughter cells grow fully in the parent cell, which eventually disintegrates, releasing the new cells to the environment.

In ______________ testing, microbial strains can be differentiated based on different antigens

serological serology

Light Independent Reactions (Calvin Cycle)

set of reactions in photosynthesis that do not require light; energy from ATP and NADPH is used to build high-energy compounds such as sugar; also called the Calvin cycle for long-term energy storage carbon comes from CO2, the gas that is a waste product of cellular respiration. biochemical pathway used for fixation of CO2, is located within the cytoplasm of photosynthetic bacteria and in the stroma of eukaryotic chloroplasts.

Most Probable Number (MPN) (direct cell count)

sets of five lactose broth tubes 10 mL sample five lactose broth tubes with 1 mL of sample, and five lactose broth tubes with 0.1 mL of sample, are inoculated with three different volumes of pond water: 1. 10 mL 2. 1 mL 3. 0.1mL. Bacterial growth is assessed through a change in the color of the broth from red to yellow as lactose is fermented. - lactose broth tubes contain a pH indicator that changes color from red to yellow when the lactose is fermented. a statistical procedure for estimating of the number of viable microorganisms in a sample Often used for water and food samples, the MPN method evaluates detectable growth by observing changes in turbidity or color due to metabolic activity ex. estimation of the number of coliforms in a sample of pond water coliforms: gram-negative rod bacteria that ferment lactose - coliforms in water is considered a sign of contamination by fecal matter

facultative anaerobes

shows heavy growth at the top of the tube and growth throughout the tube organisms that thrive in the presence of oxygen but also grow in its absence by relying on fermentation or anaerobic respiration if there is a suitable electron acceptor other than oxygen and the organism is able to perform anaerobic respiration In aerobic environments, they can grow more quickly by using aerobic respiration contain both superoxide dismutase and catalase, so they are able to grow in the presence of oxygen ex. Staphylococci and Enterobacteriaceae Staphylococci -found the skin and upper respiratory tract Enterobacteriaceae - found primarily in the gut and upper respiratory tract but can sometimes spread to the urinary tract, where they are capable of causing infections

competitive inhibitor

similar enough to a substrate that it can compete with the substrate for binding to the active site by simply blocking the substrate from binding ex. Sulfa drugs provide a good example of competitive competition.

Bioremediation processes can be categorized as in situ or ex situ.

situ: - Bioremediation conducted at the site of contamination - does not involve movement of contaminated material ex situ removal of contaminated material from the original site so that it can be treated elsewhere typically in a large, lined pit where conditions are optimized for degradation of the contaminant. bacteria of the genera Rhodococcus and Pseudomonas are known for their ability to degrade many environmental contaminants

Hypochlorite salts

sodium and calcium hypochlorites, are used to disinfect swimming pools

antiseptics

solutions that destroy microorganisms or inhibit their growth on living tissue ex. hydrogen peroxide and isopropyl alcohol must also be selectively effective against microorganisms and able to penetrate tissue deeply without causing tissue damage

Glutaraldehyde

two reactive aldehyde groups used as a 2% solution for sterilization brand name Cidex. disinfect a variety of surfaces and surgical and medical equipment. irritates the skin and is not used as an antiseptic.

general media

some media: all purpose and support large variety of organisms ex. tryptic soy broth (TSB) needs to provide those elements, carbon, hydrogen, oxygen, nitrogen, phosphorus, and sulfur, in larger quantities add quantities of grams per liter of chemicals containing the major elements, such as sugars for carbon along with nitrogen-containing molecules For trace elements that are necessary, but potentially toxic, you will usually find them added in microgram per liter quantities. This would include things like zinc

laboratory instrument used to measure turbidity is called a _________

spectrophotometer

in which phase does the number of cell dividing equal the number of cells dying

stationary

fermentation pathways: ethanol fermentation FINISH THIS

steps 1. carboxyl group is removed from pyruvate and released in as carbon dioxide, producing a two-carbon molecule called acetaldehyde 2. NADH passes electrons to acetaldehyde, regenerating \text{NAD}^+NAD+start text, N, A, D, end text, start superscript, plus, end superscript and forming ethanol intermediates products: ethanol what the final what the electron acceptor? NADH fully reversible NADH donates its electrons to a derivative of pyruvate, producing ethanol.

fermentation pathways: lactic acid fermentation FINISH THIS

steps 1. glycolysis 2. NADH regeneration intermediates: byproducts: lactate what the final what the electron acceptor: Pyruvate fully reversible used on: red blood cells and in skeletal muscle that has an insufficient oxygen supply to allow aerobic respiration to continue Oxidizes: NADH regenereat NAD+ anaerobic fermentation Pyruvate + NADH ↔ lactic acid + NAD+

Autoclave

sterilizing materials with pressurized steam before use or disposal

alkylating agents

strong disinfecting chemicals that act by replacing a hydrogen atom within a molecule with an alkyl group (CnH2n+1), thereby inactivating enzymes and nucleic acids formaldehyde (CH2OH) used at a concentration of 37% (known as formalin) or as a gaseous disinfectant and biocide kill bacteria, viruses, fungi, and endospores leading to sterilization at low temperatures, which is sometimes a convenient alternative to the more labor-intensive heat sterilization methods cross-links proteins and has been widely used as a chemical fixative inactivate infectious agents in vaccine preparation Formaldehyde is very irritating to living tissues and is also carcinogenic; therefore, it is not used as an antiseptic.

Peroxygens

strong oxidizing agents that can be used as disinfectants or antiseptics most used: hydrogen peroxide breakdown into: - water and oxygen gas decomposition is accelerated in the presence of light, so hydrogen peroxide solutions typically are sold in brown or opaque bottles disadvantage: - damage to skin that may delay healing or lead to scarring how does it work? - producing free radicals that damage cellular macromolecules - working against gram-positive and gram-negative bacteria, fungi, viruses, and endospores. - no associated environmental hazard. ex. Benzoyl peroxide

catalyst

substance that helps speed up a chemical reaction

In __________________________ phosphorylation, ATP is generated when a high-energy phosphate is directly transferred to ADP.

substrate level substrate-level

ATP molecules produced during the energy payoff phase of glycolysis are formed by _______

substrate-level phosphorylation - phosphate group is removed from an organic molecule and is directly transferred to an available ADP molecule, producing ATP. During glycolysis, high-energy phosphate groups from the intermediate molecules are added to ADP to make ATP.

converted from organic nitrogen back into nitrogen gas by microbes through 3 steps: ammonification, nitrification, and denitrification. 1. In terrestrial systems, the first step is: ammonification: - in which certain bacteria and fungi convert nitrogenous waste from living animals or from the remains of dead organisms into ammonia (NH3) 2. ammonia is then oxidized to nitrite (NO−2),(NO2−) 3. then to nitrate (NO−3),(NO3−), by nitrifying soil bacteria such as members of the genus Nitrosomonas 4..denitrification: whereby soil bacteria, such as members of the genera Pseudomonas and Clostridium, use nitrate as a terminal electron acceptor in anaerobic respiration, converting it into nitrogen gas that reenters the atmosphere. A similar process occurs in the marine nitrogen cycle, where these three processes are performed by marine bacteria and archaea.

summary later

Obligate anaerobes lack what enzymes?

superoxide dismutase, peroxidase, and catalase

Three main enzymes break down those toxic byproducts

superoxide dismutase, peroxidase, and catalase each one catalyzes a different reaction

selective media

suppress unwanted microbes and encourage desired microbes support the growth of the organism of interest by supplying nutrients and reducing competition

archea pH

survive pH= of 2.5-3.5

How to determine the effectiveness of a chemical agent?

swabbing surfaces before and after use to confirm whether a sterile field was maintained during use - Phenol Coefficient

Prior to our use of phylogeny what was the primary method for classifying organisms?

taxonomy

effect on enzyme with change in temperature?

temperature outside of an optimal range can affect chemical bonds within the active site, making them less well suited to bind substrates High temperatures will eventually cause enzymes, like other biological molecules, to denature, losing their three-dimensional structure and function.

optimum growth temperature

that at which growth rate is highest

bacteria are obligate (strict) aerobes

that cannot grow without an abundant supply of oxygen. #1

production of ATP in cellular respiration depends on ____

the concentration gradient of H+ across the plasma membrane

what determines if - cidal or -static

types of microorganisms targeted: 1. the concentration of the chemical used 2. the nature of the treatment applied.

electron transport system (ETS)

the final metabolic pathway, which proceeds as a series of chemical reactions in the mitochondria that transfer electrons from the hydrogen atom carriers NAD and FAD to oxygen; water is formed as a by-product the electrochemical energy released by the hydrogen ions is coupled to the formation of ATP from ADP and Pi electrons move from electron carriers with more negative redox potential to those with more positive redox potential.

ethanol fermentation

the first reaction, the enzyme pyruvate decarboxylase removes a carboxyl group from pyruvate, releasing CO2 gas while producing the two-carbon molecule acetaldehyde. The second reaction, catalyzed by the enzyme alcohol dehydrogenase, transfers an electron from NADH to acetaldehyde, producing ethanol and NAD+

maximum growth temperature

the highest temperature at which growth is possible

minimum growth temperature

the lowest temperature at which the species will grow

Degerming

the mechanical removal of microbes from a limited area microbial # r reduced by gently scrubbing living tissue, most commonly skin, with a mild chemical (e.g., soap) to avoid the transmission of pathogenic microbes ex. handwashing, wiping skin with alcohol swap

Culture Density

the number of cells per unit volume - closed environment: culture density is also a measure of the number of cells in the population.

Lipid catabolism (lipolysis)

the process of splitting/ broken down triglycerides into fatty acids and glycerol- triglycerides: catalyzed by lipases phospholipids: catalyzed by phospholipases Triglycerides are a form of long-term energy storage in animals. made of : glycerol and three fatty acids Phospholipids compose the cell and organelle membranes of all organisms except the archaea

taxonomy

the science of biological classification

Plasmolysis (plant cells)

the shrinking of the protoplasm away from the intact cell wall) and cell death following concentration gradient, flows out of the cell high osmotic pressure

Biolog's system identifies cells based on . . .

their ability to metabolize certain biochemicals and on their physiological properties - including pH and chemical sensitivity - It uses all major classes of biochemicals in its analysis. Identifications can be performed manually or with the semi- or fully automated instruments

fastidious organisms

those that require many growth factors provided in chemically defined media

Calvin Cycle

three basic stages: fixation, reduction, and regeneration Fixation: The enzyme ribulose bisphosphate carboxylase (RuBisCO) catalyzes the addition of a CO2 to ribulose bisphosphate (RuBP). This results in the production of 3-phosphoglycerate (3-PGA). Reduction: Six molecules of both ATP and NADPH (from the light-dependent reactions) are used to convert 3-PGA into glyceraldehyde 3-phosphate (G3P). Some G3P is then used to build glucose. Regeneration: The remaining G3P not used to synthesize glucose is used to regenerate RuBP, enabling the system to continue CO2 fixation. Three more molecules of ATP are used in these regeneration reactions. used by: plants and photoautotrophic bacteria nonphotosynthetic chemoautotrophs to fix CO2 other bacteria and archaea use alternative systems for CO2 fixation

Pyruvate in the transition reaction OR Bridge reaction

to enter the next oxidative pathway, it must first be decarboxylated by the enzyme complex pyruvate dehydrogenase to a two-carbon acetyl group electrons are also transferred to NAD+ to form NADH two-carbon acetyl must be attached to a very large carrier compound called coenzyme A (CoA) Where? Eukaryotes: mitochondrial matrix Prokaryote: cytoplasm

suffix -cide

to kill Physical and chemical methods of microbial control that kill the targeted microorganism are identified

argyria

too much silver accumulates in the body - skin turns irreversibly blue-gray

Sepsis

toxic inflammatory condition arising from the spread of microbes, especially bacteria or their toxins, from a focus of infection Failure to practice aseptic sepsis: systemic inflammatory response to an infection that results in high fever, increased heart and respiratory rates, shock, and, possibly, death

fungistatic

treatment inhibit fungal growth

Organisms can also be identified by the energy source they use.

true

a eukaryotic species is defined as a group closely related organisms that breed among themselves

true

if respiration does not occur, NADH must be reoxidized to NAD+ for reuse as an electron carrier for glycolysis,

true

Pigments reflect or transmit the wavelengths they cannot absorb, making them appear the corresponding color

true ex. bacteriochlorophylls (green, purple, or red) carotenoids (orange, red, or yellow) chlorophylls (green) phycocyanins (blue) phycoerythrins (red). photosynthetic bacteria is optimized for harvesting the wavelengths of light to which it is commonly exposed, leading to stratification of microbial communities in aquatic and soil ecosystems by light quality and penetration.

Extreme pH affects the structure of all macromolecules

true - hydrogen bonds holding together strands of DNA break up at high pH

pyrophosphate (PPi)

two connected phosphate groups

Embden-Meyerhof-Parnas (EMP) pathway

two distinct phases: 1. investment phase uses energy from 2 ATP molecules to modify a glucose molecule so that the 6-carbon sugar molecule can be split evenly into 2 phosphorylated 3-carbon molecules called (G3P). 2. energy payoff phase extracts energy by oxidizing G3P to pyruvate, producing four ATP molecules and reducing 2 molecules of NAD+ to 2 molecules of NADH, using electrons that originated from glucose.

electrochemical gradient

uneven distribution of H+ across the membrane that establishes an electrochemical gradient because H+ ions are positively charged (electrical) and there is a higher concentration (chemical) on one side of the membrane. proton motive force (PMF). - accumulation of H+ (also known as a proton) on one side of the membrane potential energy of this electrochemical gradient generated by the ETS causes the H+ to diffuse across a membrane (the plasma membrane in prokaryotic cells and the inner membrane in mitochondria in eukaryotic cells).

Methanotrophs

use methane as their carbon source bacteria adn archaea Some methanogens also ferment acetate (two Carbons) to produce methane and CO2. methane accumulation = green house effect Methane accumulation due to methanogenesis occurs in both natural anaerobic soil and aquatic environments; methane accumulation also occurs as a result of animal husbandry because methanogens are members of the normal microbiota of ruminants.

nonionizing radiation

used for disinfection and uses less energy than ionizing radiation. does not penetrate cells or packaging ex. ultraviolet light (UV) - causes thymine dimers to form between adjacent thymines within a single strand of DNA ex. UV lights - purify water from natural environments before drinking ex. Germicidal lamps - used in surgical suites, biological safety cabinets, and transfer hoods, typically emitting UV light at a wavelength of 260 nm

Specialized media

used in the identification of bacteria and are supplemented with dyes, pH indicators, or antibiotics ex. enriched media

differential staining

used is the Gram stain stain immediately eliminates approximately half of the bacteria because the results are generally either gram-positive or gram-negative small number of bacteria are known as gram-variable, but most fall into one of the first two categories

Membrane filtration

used to count live cells in dilute solutions

pour plate and spread plate methods

used to plate serial dilutions into or onto, respectively, agar to allow counting of viable cells that give rise to colony-forming units

Biological Safety Cabinets (BSCs)

used to remove particulates in the air either entering the cabinet (air intake), leaving the cabinet (air exhaust), or treating both the intake and exhaust. Use of an air-intake HEPA filter prevents environmental contaminants from entering the BSC, creating a clean area for handling biological materials

Serology

uses antibodies to identify certain types of organisms allows us to identify those different strains from one another Antibodies are made as a result of the interaction between the immune system and a foreign antigen Each antibody is very specific to a particular antigen

direct counting technique: plate count method

viable plate count based on the principle that viable cells replicate and give rise to visible colonies when incubated under suitable conditions for the specimen 2 APPROACHES: 1. pour plate 2. Spread plate method final inoculation procedure differs between these two methods, they both start with a serial dilution of the culture. COLONY- FORMING UNITS per milimiter (CFU/mL) - samples of bacteria that grow in clusters or chains are difficult to disperse and a single colony may represent several cells Some cells are described as viable but nonculturable and will not form colonies on solid media DISADVANTAGE: 1. viable plate count is considered a low estimate of the actual number of live cells. FOR: - 30-300 colonies TOO FEW COLONIES: - <30 - do not give statistically reliable numbers OVERCROWDED: - >300 colonies

Microorganisms depend on available _____ to grow

water

how is moisture measured as?

water activity (aw): which is the ratio of the vapor pressure of the medium of interest to the vapor pressure of pure distilled water; therefore, the aw of water is equal to 1.0 Bacteria require high aw (0.97-0.99) fungi ( drier enviro): range of aw ex. Aspergillus spp. is 0.8-0.75. decrease water: dry or freeze (incr osmotic pressure) to prevent spoilage

oxygenic photosynthesis splits what?

water is split to release oxygen while the electrons are excited by a photon of light and passed down an electron transport chain to a second photosystem. After excitation by another photon of light, the electrons travel down another electron transport chain before being used to reduce NADP+ to NADPH. Oxygenic photosynthesis produces both ATP and NADPH, while anoxygenic photosynthesis produces only ATP

Photosynthetically Active Radiation (PAR)

wavelengths of light between 400 and 700 nm that photosynthetic organisms use as a source of energy portion of the electromagnetic spectrum that is absorbed by these organisms accessory pigments: fucoxanthin in brown algae and phycobilins in cyanobacteria, widen the useful range of wavelengths for photosynthesis and compensate for the low light levels available at greater depths of water

Humans are a combination of...

we are heterotophs and organotrophic

Krebs Cycle/Citric Acid Cycle/Tricarboxylic Acid Cycle

where? Eukaryotes: mitochondrial matrix prokaryotes: Cytoplasm Part of glycolysis catabolism generate ATP by substrate-level phosphorylation. Named after: Hans Adolf Krebs - citric acid has three carboxyl groups in its structure last part of the pathway regenerates the compound used in the first step some cellular molecules use (acids, chlorophylls, fatty acids, and nucleotides) to synthesize

obligate anaerobes

which are killed by oxygen Found: anaerobic conditions - deep sediments of soil - still waters - bottom of the deep ocean = no photosynthetic life - intestinal tract of animals ex. Bacteroidetes - microbes in the human gut. ex. Mycobacterium tuberculosis causative agent of tuberculosis and Micrococcus luteus, a gram-positive bacterium that colonizes the skin. Neisseria meningitidis, the causative agent of severe bacterial meningitis, and N. gonorrhoeae, the causative agent of sexually transmitted gonorrhea, are also obligate aerobes

can BSL 1 laboratories have an autoclave?

yes

do most forms of fermentation besides homolactic fermentation produce gas (CO2/H)

yes

is anaerobic photosynthesis evolved first and is found only in prokaryotes

yes

does substrate concentration influence enzyme activity

yes Enzyme activity is increased at higher concentrations of substrate until it reaches a saturation point at which the enzyme can bind no additional substrate.