Untitled Flashcards Set

Positive control: a condition or sample in an experiment that is expected to produce a detectable result (effect) in the response variable. If it provides negative results, your experiment is NOT working correctly and all results are invalid. 

Negative control: a condition or sample in an experiment that is NOT expected to produce an effect in the response variable. If it provides positive results your experiment is NOT working correctly and all results are invalid. 

Experimental sample/condition: an unknown variable in an experiment that serves to answer a hypothesis. 

Bacterial strain: genetic variants or subtypes of an organism that may exhibit different genotypes and phenotypes.

Control: a known variable group that remains unchanged or unaffected to compare experimental results to and to ensure experiment is working correctly.  

Positive Control: a condition or a sample in an experiment that is expected to produce a detectable result (effect) in the response variable. If it provides negative results your experiment is NOT working correctly and all results are invalid.   

Negative Control: a condition sample in an experiment that is NOT expected to prouce an effect in the response variable. If it provides results your experiment is NOT working correctly and all results are invalid. 

Manipulated Variable: a variable in an experiment that is intentionally changed to examine outcomes. 

Response Variable: variable in an experiment that is measured as a result of a change in the manipulated variable.   

Controlled Variable: variables held constant within an experiment to prevent interference with experimental outcomes.   

Antibiotic sensitivity: assay to determine which antibiotics are most effective in killing a specific bacteria by testing which antibiotics cause the highest amount of cell death.  

Culture (bacteria): the cultivation and growth of a microorganism in a laboratory setting under ideal physiological conditions. 

Bacterial lawn: abundant bacterial growth on a petri dish agar plate where individual colonies do not appear and growth appear as a homogenous layer on the agar surface. 

Solid culture: the growth of bacteria on a solid medium containing nutrients and potentially other essential compounds. 

Liquid culture: the growth of bacteria in a liquid medium/broth that contains nutrients and potentially other essential compounds. 

Viability assay: estimation of the size of a microbial population based on the number of viable colonies formed from a diluted sample onto an agar plate   

Growth curve assay: the determination of the amount of bacterial population growth numbers over time by taking viable cell timepoints to determine growth dynamics under different conditions.  

Colony: A visible population of microorganisms living in one place is an aggregation of cells arising from a single parent cell. 

Colony forming unit (CFU): a single cell or group of related cells that produce a colony 

Generation time (doubling time): time required for a parent cell to grow and divide into two identical daughter cells.  

Binary fission: method of asexual reproduction in prokaryotes where a parental cell disappears due to formation of progeny a parent cell grows and divides into two identical daughter cells. 

Lag phase: the phase in a growth curve in which the organisms are adjusting to their environment and preparing for growth to occur, synthesizing essential metabolic components for the current conditions.  

Log (Exponential) Phase: phase in a growth curve where the population is most actively growing, population increases exponentially over time. 

Stationary Phase: phase in a growth curve where cell growth is equal to cell death. Population numbers level off as time goes on.   

Death Phase: phase in a growth curve where cell death is occurring faster than cell growth. Cell population numbers begin to decrease over time. 

Disk-diffusion Susceptibility (Kirby-Bauer): an antibiotic-soaked disk is placed in an agar plate with a bacterial lawn to allow the antibiotic to diffuse into the agar/surrounding lawn to begin to kill bacterial cells making up the lawn. The zone of inhibition around the disk is measured to quantify the bacteria’s susceptibility to the antibiotic. 

Polymerase Chain Reaction (PCR): a laboratory technique that allows for the production of large amounts of identical DNA molecules in vitro. 

Quantitative polymerase chain reaction (qPCR): a laboratory technique that allows for a quantification of DNA and RNA levels within a cell. 

cDNA: DNA synthesized from an mRNA template using reverse transcriptase polymerase.   

Enzyme Assay: a laboratory assay that functions to measure enzymatic activity. 

Macronutrients: substances used for biosynthesis and energy production that require for microbial growth and are needed in large amounts. 

Micronutrients: substances used for biosynthesis and energy production that are required for microbial growth which are needed in a very small amounts. Also known as trace elements, these are often used as cofactors of enzymes. 

Nutrient Availability: the presence of necessary nutrients ready be obstained and used by microorganisms for growth. 

Cell mass: amount of total matter present in a cell

Dry mass: the amount of matter present in a cell that is not taken up by water (carbon, nitrogen, oxygen)

Culture medium: a semi solid or liquid preparation used to grow microorganisms that contains all required nutrients of the organism to be cultivated. 

Defined medium: a semi-solid or liquid preparation used to grow microorganisms where all exact chemical species are known in their exact concentrations.

Complex medium: a semi solid or liquid preparation used to grow microorganisms where ingredients containing unknown chemical compositions are used. 

Agar: gel-like polysaccharide isolated from seaweed that is often used as a thickening agent in media. 

Tryptone: trypsin digest of casein protein that serves as a cheap, reproducible carbon and nitrogen source when added to growth media. Used often as a component of complex/undefined media. 

Peptone: pepsin digest of casein protein that serves as a cheap reproducible carbon and nitrogen source when added to growth media. Used often as a component of complex/undefined media. 

Yeast extract: cells are grown, killed, and dried to provide carbon and nitrogen when added to growth media. Used often as a component of complex/undefined media. 

Casein

Casamino acids: amino acids from degraded casein proteins used in complex/defined media to assist in microbial biosynthesis and growth. 

Growth rates: the speed in which microbial growth and division is capable of occurring. Frequently determined by nutrient availability and abundance. 

Minimal medium: a nutrient media where only the lowest amount of nutrients possible for growth are present. Forces cells to synthesize all proteins, nucleic acids, lipids, and vitamins itself, slowing growth rate 

Enriched medium: a nutrient media that contains many essential microbial building blocks pre-made, such that the cell does not have to produce these molecules on its own (easier to culture fastidious microorganisms), leading to faster growth rate. 

Fastidious: in terms of microorganisms, one that requires a specific added nutrient in order to grow. 

De novo synthesis: the synthesis of essential biomolecules from smaller molecules by the cell itself. 

Blood agar: common diagnostic underdefined growth media that includes nutrients for growth along with blood, allowing for visualization of bacteria capable of hemolysis (lysis of blood cells) 

Sterilization: killing of organisms and spores. 

Autoclave: pressure-cooker-like machine used for sterilization of growth media and other items through the usage of heat. High pressure is used to prevent media from boiling (pressure does not sterilize). 

Filtration: passage of air or liquid through a material that traps and removes microbes.  

Selective medium: a growth medium that has ingredients that inhibit growth of some organisms while others are capable of growth use to isolate a certain type of organism. 

Differential medium: a growth medium that contains an indicator that allows microbes to be visually distinguished by chemical differences. 

API 20: diagnostic test for identification of bacteria type. Sample is taking from a patient and struck out on an agr nutrient plate for cell isolation. Cells are added to different diagnostic chambers containing different chemicals and ingredients that will change color based on the bacteria added. Color chart can then be used to identify bacterium based on what colors were present. 

Vitamins: organic compounds that can be water soluble that are necessary for growth. 

Eukaryote cell: a single-celled organism containing a nucleus that contains genetic material and other membrane-bound organelles. 

Bacterial cells (prokaryotic cell): a unicellular organism that does not contain a nucleus or membrane-bound organelles. 

The central dogma of molecular biology: the fundamental process of protein synthesis. DNA encodes genetic information that is converted into RNA (transcription) which is then translated into protein (translation). 

Genotype: an organism’s genes present within its genome. 

Phenotype: the observable traits and features of an organism caused by genes being expressed in the genotype. 

Transcription: the process by which genetic information stored in DNA is copied into RNA nucleotide sequences. 

Translation: the process by which genetic information carried in mRNA is used by ribosomes to construct polypeptide chains based on specific amino acid sequences present in the mRNA. 

Nucleic acid (DNA & RNA): a macromolecule that function in storage and expression of genetic information. Made up of a pentose sugar (5C), phosphate group, and nitrogenous base. 

Polypeptide: a polymer chain of amino acids linked by peptide bonds. Make up proteins. 

Lipid: an organic macromolecule that is not composed of monomers and is insoluble in water. 

• Fatty acid: hydrocarbon chains of differing lengths that contain a carboxylic acid. Can be either saturated or unsaturated. 

• Phospholipids: phosphate-containing lipids made up of molecules with two fatty acid chains. Make up the cell membrane. 

Carbohydrate: an organic macromolecule that consists of carbon, hydrogen, and oxygen. Function in structural support and energy storage within organisms. 

Protein/enzyme: an organic macromolecule that can consist of carbon, hydrogen, oxygen, nitrogen, and sulfur that have diverse essential functions in cellular processes. These serve to catalyze reactions in the cell. 

Wildtype: a typical cell/strain commonly found in nature

Mutant: a cell/strain that arises due to unrepaired mutations, sometimes leading to a change in observable phenotype. 

Catabolic pathway: a chemical pathway that results in the release of energy by the breaking down of a compound/polymer into smaller components for an essential purpose. 

Anabolic pathway: a chemical pathway that requires energy input to build large compounds and polymerase from smaller molecules (such as DNA and proteins) 

Energy source: an energy source that is necessary for living organism to survive. Can be deprived chemically or from light. 

Carbon source: a source of carbon that is necessary for living organisms to survive. Can be obtained via inorganic sources (CO2) or organic sources (proteins, carbohydrates, ect…) 

Chromosome: a molecule of DNA associated with protein in which genetic information is stored in prokaryotes, it is typically circular. 

Cytoplasmic membrane: the phospholipid and protein membrane that surrounds all cells. 

Nucleoid: a region within the prokaryotic cytosol that contains the cell’s chromosome. NOT a membrane-bound organelle. 

Membrane potential: potential energy built across a membrane due to an electrochemical gradient. 

Proton motive force: 

Aerobic (cellular) respiration: a metabolic process that involves the complete oxidation of substrate molecules and production of ATP via redox reactions that require the use of oxygen as the terminal electron acceptor. 

Anaerobic respiration: metabolic process that involves the complete oxidation of substrate molecules and production of ATP via redox reactions that requires the use of the terminal electron acceptor that is not oxygen. 

Fermentation: the partial oxidation of sugar (such as glucose) to generate ATP energy by using an endogenous organic molecule as a terminal electron acceptor. 

Growth curve: a graph that plots bacterial population numbers over time. 

Escherichia coli (E. coli)A bacillus-shaped bacterial organism that can be pathogenic. One of the most common and well-studied bacteria. It’s found in the gut. 

Staphylococcus aureus (S. aureus) Normal inhabitants of the human microbiota and present commonly on the skin. Can be opportunistic pathogens that cause serious disease. 

Differential stains: use of multiple stains to distinguish different types of microorganisms. 

• Gram stain: differential stain that establishes gram status of microorganisms through the usage of crystal violet and safranin stains. Gram neg bacteria appear red/pink, while gram pos appear purple. 

  • Gram Negative: cell wall composition – thin, protected peptidoglycan layer with few cross-links, connected to the outer membrane via lipoproteins. 

  • Gram Positive: cell wall composition – thick, exposed peptidoglycan layer with many cross links reinforced to the cytoplasmic membrane by teichoic acids. 

Pleomorphic: does not contain a cell wall, can be flexible with no set defined shape. 

Cell Wall: structural boundary of a cell composed of proteins and polysaccharide chains that provide shape and support against osmotic pressure. 

Semi-rigid: this characteristic of the cell wall maintains cell integrity by being stuff but not flexible. 

Peptidoglycan: polymer of glycan tetrapeptide repeating units that makes up a part of bacterial cell walls. Made by crosslinked N-acetylglucosamine and N-acetylmuramic acid disaccharides. 

• Gram positive (in terms of Cell wall composition): bacteria that have exposed, thick layer of peptidoglycan on top of the cytoplasmic membrane. Does not have an outer membrane. 

• Gram negative (in terms of Cell wall composition): bacteria that have an outer membrane and a thin interior peptidoglycan layer on the top of the cytoplasmic membrane. Does not have an exposed peptidoglycan layer. 

Polymer: 

Monomer: a subunit that can be linked together to form polymers. 

Glycosidic Bond: a covalent chemical bond that links carbohydrate/sugar molecules together. 

Murein Sacculus: term for massive mesh-like peptidoglycan layer that surrounds the entire cell. 

Glycan: carbohydrate polymer 

Outer membrane: lipid membrane containing proteins and carbohydrates that surrounds the exterior of gram neg bacterial cells. Contains lipopolysaccharides (LPS)

Teichoic Acids: polymers of repeating ribitol or glycerol connected by negatively charged phosphate groups linked to the peptidoglycan layer. Only found in gram-positive bacterial cell walls. 

Lipoteichoic Acids: polymers of repeating ribitol or glycerol connected by negatively charged phosphate groups linked to the cell membrane and spanning the entire peptidoglycan layer. 

Lipopolysaccharide (LPS): molecule composed of lipid A and polysaccharide found in the outer membrane of gram neg cell walls. 

Endotoxin: lipopolysaccharides composed of lipid A and other polysaccharide that are released from dead gram negative cells are toxic and can cause disease. 

Lipid A: component of lipopolysaccharides that are composed of disaccharides with fatty acids responsible for endotoxin. 

Core polysaccharide: connects lipid A and O-specific polysaccharides in lipopolysaccharides, composed of various 6 carbon sugars

O-specific polysaccharide: a component of lipopolysaccharides that is a major antigen that is used for bacterial identification (serotyping) 

Lipoprotein: lipid-protein that links the outer membrane to the peptidoglycan layer to help with the formation of the periplasmic space in gram-negative bacteria. 

Porins: trimeric tube-like proteins that span the outer membrane bilayer that assist in nutrient transport. 

Trimeric: in the context of proteins, a complex of proteins made up of three individual proteins working together as one complex. 

Serotype: an identifiable strain of bacteria

Antigen: molecules capable of triggering an immune response. Inclusions intracellular structures composed of stored nutrients, proteins or energy. May or may be surrounded by a membrane. 

Aggregation cells are capable of adherence to each other 

Storage polymers polymers of molecules that store carbon and energy for when the cell needs it 

Depolymerize the breakdown of a polymer to release carbon and energy for usage by the cell 

Gas Vesicles a small membrane bilayer that provides photosynthetic aquatic prokaryotes buoyancy 

Bilayer a two-layered structure formed by lipids with a hydrophobic tail and hydrophilic head when in water 

Endospores highly differentiated forms of bacterial cells that are extremely resistant to external stressors such as temperature, drying, and chemicals 

Carboxysomes internal structures that provide a proton gradient across an internal membrane 

Anammoxosome An example of an internal inclusion that is involved in energy production? (converts ammonium (NH₄⁺) and nitrite (NO₂⁻) into dinitrogen gas (N₂) under anaerobic conditions, producing energy for the cell.)

Supercoils the coiling of DNA into a tight conformation to take up less space within a cell

Topoisomerases enzymes that break one strand of DNA, rotate one end around the helix, and reseal to coil DNA over itself 

Nucleoid an aggregated structure of genomic DNA and specific proteins that is not surrounded by a membrane, a highly twisted and compact chromosome 

Flagellum

Endoflagella a special internal flagellum utilized by spirochetes that allows the entire cell to rotate to grant motility 

Motility the ability for a cell to move

Glycogen a large branched polymer of glucose used for energy storage 

Polyphosphate granules linear polymer of high-energy inorganic phosphate esters used to store phosphate and energy, High-energy bonds are broken to release energy 

Sulfur granules a storage polymer made of sulfur that can be metabolized by some bacteria to provide energy 

Sporulation formation of endospores, often induced due to stress conditions 

Vegetative an active cell capable of growing and dividing; no spore is formed 

Germination the induction of an endospore to reform into a growing, vegetative cell once favorable conditions are met 

B. thuringiensis spore-forming bacterium that produces a biological insecticide toxin that kills larvae by allowing insects to ingest spores, where they germinate and infect

B. subtilis a well-studied spore-forming bacterium frequently used to study endospores in laboratory research settings 

B. anthracis also known as anthrax, a spore-forming bacterium that produces lethal toxins 

C. perfringens spore-forming bacterium that causes gas gangrene

C. tetani spore-forming bacterium that leads to tetanus, releasing a toxin that produces uncontrolled muscle contraction 

C. botulinum spore-forming bacteria that leads to botulism, releasing a toxin that causes muscle paralysis 

Prespore formed during the early development of endospores after the cells commitment to spooulation

Septum the division that separates the prespore from the cell

Exosporium outermost layer of an endospore; incorporates calcium ions, acid-soluble proteins and dipicolinic acid to protest genomic material against stressors 

Cortex protective coating that makes up the endospore, protected by the exterior coat layer 

Spore coats makes up the endospore coat to protect the cell genome, RNA, and ribosomes from environmental stressors 

Core the center of the endospore that houses RNA, DNA, ribosomes, and dipicolinic acid 

Dipicolinic Acid compound in bacterial endospores that plays a crucial role in the resistance and the stability of the endospores under extreme conditions 

Spore acid-soluble proteins proteins used in endospores that are stable to heat, chemicals, and radiation

Adhesion bacteria that can have the ability to attach to each other and other surfaces 

Capsule semi-rigid matrix that surrounds the cell made from polysaccharide(glycocalyx)

Slime Layer non-rigid, easily deformed layer that surround the outside of the cell 

India Ink a stain that uses fine carbon particles to stain background of bacterial cells to see unstained external cell features such as capsule 

Glycocalyx the general term for the polysaccharide that forms the capsule 

Flocculation term for the ability of bacteria to aggregate together 

Desiccation drying, lack of hydration 

Fimbriae protein filaments that aid in attachment of bacteria. allow bacteria to adhere to host cells, surfaces, and each other 

Adhesins proteins attached to fimbriae that allows for specific binding of bacteria to a certain host type cell 

Host specificity

Tissue Tropism term for adhesion/binding of a bacteria only occurring in a specific target host 

Pili protein tubes that function in adhesion and genetic exchange between bacterial cells 

Type IV pili protein tube that allows bacteria to utilize twitching motility through extension, binding via adhesins, and retraction of protein tube to pull the cell 

Conjugative Pili protein tube that allows for genetic exchange between two bacteria via direct contact 

Twitching Motility movement by a cell using a type IV pilus to repeatedly extend forward, bind a surface using adhesins, and retract, pulling the cell forwards 

Conjugation the transfer of genetic material between a host and recipient cell through direct contact with pilus 

Flagella 

• Peritrichous numerous flagella are located all around the cell 

• Polar a single flagellum or multiple flagella are located at one or both ends of the bacterial cell 

• Lophotrichous numerous flagella are located at one end of the bacterial cell 

Monotrichous types of flagella: one flagellum is located on one end of the bacterial cell 

Basal Body the membrane-bound portion of the flagella, made up of the mot proteins and ring proteins that power movement 

Hook the flexible, curved protein that connects the filament tail to the basal body 

Filament the long and hollow primary component of the flagella, made of flagellin 

Proton Motive Force (PMF): the usage of the electrochemical gradient derived from the high proton concentration outside of the cell moving down their proton gradient across the cell membrane back into the cell to power the cellular process. 

Mot Protein proteins in the basal body that convert proton motive force into energy for rotation 

Stator

Rotor the rotating component of the flagellar motor 

MS/C ring rings a part of the flagellar motor that are found in both Gram-positive and Gram-negative bacteria, anchor the flagella in the cytoplasmic membrane 

P ring flagellar ring that can be found only in Gram-negative bacteria, anchors the flagella in the peptidoglycan layer within the periplasmic space 

L ring flagellar ring found only in Gram-negative bacteria, anchors the flagella in the outer membrane 

Forward Run term for the flagella rotation to form a bundle in order to rotate as a unit to move in a single direction 

Tumble term for flagella pushing apart out of its rotating unit to reorient itself in order to being a forward run in a new direction 

Binary fission method of asexual reproduction in prokaryotes where a parental cell disappears due to the formation of progeny, a parent cell grows and divides into identical daughter cells

Cell elongation a growing cell expands on length to the length of two cells to divide into two identical cells 

Partition/septum the constriction point that occurs in the middle of a cell as it being s to pinch off and divide into two cells 

Generation time

Divisome proteins group of proteins responsible for septum formation and cell division

MinC forms a dimer protein with MinD to help assemble divisome at the center of the cell 

MinE protein in the divisome that assists in finding the center of the cell as it divides 

MinD forms a dimer protein with MinC to help assemble divisome at the center of the cell 

FtsZ protein ring that forms in the middle of the cell; functions by inward constriction of the cell through depolymerization of the ring t create a septum and pinch off a cell into two identical cells 

MreB protein that forms helical filaments on the inner surface of the cytoplasmic membrane that is found in non-coccoid bacteria, establishing rod shape morphology of bacteria

Non-coccoid bacteria bacteria that do not have a coccoid (circular/spherical) morphology 

Growth zone narrow area present in dividing Gram-positive bacteria where peptidoglycan and cell wall synthesis occurs (synthesis only occurs in this narrow zone) 

Precursor units name for building blocks of peptidoglycan, made in the cytoplasm. consists of N-acetylmuramic acid and N-acetylglucosamine with an amino acid chain 

Bactoprenol peptidoglycan precursor unit carrier molecule that transfers precursor unit from inside the cytoplasmic membrane to the outside (to the peptidoglycan)

Transglycosylase enzyme used during peptidoglycan synthesis, connects N-acetylmuramic acid and N-acetylglucosamine sugars to link the precursor unit to existing peptidoglycan layer

Transpeptidase enzyme used during peptidoglycan synthesis, connects amino acid chains to crosslink to surrounding peptidoglycan 

Bacitracin antibiotic that targets peptidoglycan synthesis by inhibiting bactoprenol. inhibits bactoprenol function to prevent precursor units from moving across cytoplasmic membrane to be added to the growing peptidoglycan layer, preventing peptidoglycan synthesis, leading to cell death

Penicillin antibiotic that targets peptidoglycan synthesis by inhibiting transpeptidase. transpeptidase is unable to crosslink amino acid chains, thus preventing peptidoglycan synthesis, leading to cell death 

Penicillin binding protein 

Direct Slide count method of determining cell population number through directly counting cells from a sample on a coverslip and calculating the number of cells present on the slide

Viable Cell Count measure the number of viable cells in a sample by using agar growth medium and counting colonies 

• Spread-plate method method of determining the amount of viable cells in a culture by spreading a known dilution of bacteria onto a plate and counting subsequent colonies once grown to estimate the number of viable cells in the original samples by counting colonies grown on the surface of agar 

• Pour-plate method melted nutrient agar that can be added in with a bacteria sample and solidified to determine viable cell count of the original bacterial sample

• Molten agar method of determining the amount of viable cells in a culture by aliquoting a samples of bacteria into molten agar that is then poured into an agar plate and allowed to solidify to estimate the number of viable cells in the original sample by counting calories 

Autolysin enzyme used during peptidoglycan synthesis, cuts peptidoglycan to create holes where new precursor units can be inserted 

Turbidity light scattering that occurs from cells suspended in a liquid culture or suspension 

Spectrophotometers machine that can be used to determine cell density in a liquid cultures/suspension based on ratio of light entering the samples and light exiting the sample  

Optical density the log ratio of light entering the liquid culture samples over the light leaving the liquid culture sample. used to estimate the number of cells present in the original sample 

Standard curve the usage of a known concentration of cells to determine a known optical density to compare a taken sample to. allows for a quantitative estimation of how many cells are present in an unknown sample 

Metabolism: the sum of all chemical reactions within an organism.  

Catabolism: a chemical pathway that results in the release of energy by the breaking down of a compound/polymer into smaller components for an essential purpose. 

Anabolism: a chemical pathway that requires an energy input to build large compounds and polymers from smaller structures.  

Protein: an organic macromolecule that can consist of carbon, hydrogen, oxygen, nitrogen, and sulfur that have diverse essential functions in cellular processes.  

Enzyme: proteins that catalyze chemical reactions within the cell.  

Oxidation: chemical reactions that result in the loss of an electron/hydrogen OR a gain of oxygen.  

Reduction: chemical reactions that result in the gain of an electron/hydrogen OR the loss of oxygen 

Half-reaction: term for one of two reactions during oxidation-reduction (often seen as two different reactions  occurring simultaneously to complete one task). 

Redox couple: a compound in its reduced and oxidized form that would appear on opposite sides of a redox reaction.  

Redox potential: the likelihood of a specific molecule to act as a good electron donor or electron acceptor. 

Redox/electron tower: tool used to measure energy yield from the movement of electrons down from different redox couples.  

Reactants:  the atoms, ions, or molecules that exist at the beginning of a chemical reaction. 

Products: the atoms, ions, or molecules that remain once a chemical reaction is complete.  

Activation energy: the amount of input energy required in order to catalyze a reaction to occur.  

Enzyme-Catalyzed  

Electron donor: a molecule that is capable of being oxidized to donate an electron to an electron acceptor. 

Electron acceptor 

Electron Carriers: compounds capable of moving electrons in biological system sthat can act as substrates or cofactors of enzymes or proteins. 

NAD: (in its oxidized form) an electron carrier used during metabolism, capable of carrying two electrons and two protons that can act as a substrate or cofactor of enzymes. 

ATP: a high energy molecule used to power cellular activities through the breaking of bands between its phosphate groups to generate chemical energy. 

High energy bond: chemical bonds that are capable of storing large amounts of energy that can be broken to yield energy.  

Glucose 

Glycolysis: the oxidation of glucose to produce 2 pyruvate, 2 NADH, and 2 net ATP through the usage of substrate level phosphorylation. 

Substrate-level phosphorylation: the physical transfer of phosphate to ADP from another phosphorylated organic compound.  

Fermentation: the process of recycling NAD+ from NADH for glycolysis through the usage of an endogenous organic molecule rather than an external molecule as a final electron acceptor.  

Pyruvate: a three carbon sugar that is a product of glycolysis. 

Lactic Acid: product of the fermentation pathway using glucose as a substrate to recycle NAD+ from NADH, has importance in food production. Rapid production of this product is why humans get sore after sprinting long periods of time. 

• Flavins: a vitamin derived electron carrier capable of carrying two electrons and two protons that  has ribitol tail in its oxidized form. 

Quinones: an electron carrier that is capable of carrying two electrons and two protons that has a long hydrocarbon tail embedded in the membrane.  

Fe-S clusters: essential protein cofactor that function to assist in electron transfer without the usage of heme. 

Heme: an iron containing porphyrin compound containing a centralized iron compound bound by 4 nitrogen molecules that is used by proteins to transfer electrons. 

cytochrome: proteins that contain and use heme to transfer electrons  

Electron acceptor: a molecule that is capable of being reduced in order to gain an electron from an electron donor.  

Terminal electron acceptor: the final electron acceptor at the end of an electron transport chain or a series of reactions. 

Terminal oxidase: proteins in an electron transport chain that transfer electrons from an electron donor to the terminal electron acceptor.  

Electron transport chain: a series of redox reactions passing electrons from one membrane-bound electron carrier to another until it reaches a terminal electron acceptor, coupled with the pumping of protons across the membrane to form an electrochemical gradient, with the goal of producing high levels of ATP.  

Proton motive force (PMF): the energy generated by the electrochemical gradient derived from high proton concentrations outside of the cell moving down their proton gradient across the cell membrane back into the cell, used to power cellular processes. Powers oxidative phosphorylation. 

Energized membrane: term for high concentrations of protons pumped outside of the cell membrane to create chemical potential energy to be used to create PMF. 

Aerobic respiration 

Oxidative phosphorylation: the use of energy from redox reactions and proton motive force generated by an electron transport chain in order to attach inorganic phosphate to ADP. 

ATP synthase (ATPase): protons outside the cell flow down their concentration gradient through this membrane spanning protein complex to catalyze synthesis of ATP in an electron transport chain. 

Branched respiratory chain 

Alternative terminal electron acceptor: compound capable of accepting electrons at the end of an electron transport chain that is not oxygen. 

Nitrate reduction: nitrate accepts an electron to become its oxidized form nitrite.  

Nitrate reductase: the enzyme that facilitates the reduction of nitrate to nitrite.  

Anaerobic respiration: metabolic process that involves the complete oxidation of substrate molecules and production of ATP via redox reactions that requires the use of a terminal electron acceptor that is not oxygen.  

Minimum temperature: the lowest temperature required for bacterial growth. At temperatures too low, membranes can gel and enzymes required for growth may fail due to inability to catalyze reactions. 

Optimal temperature: the ideal temperature for a bacterial to grow, bacteria will row at the max growth rate possible leading to the shortest generation time. Enzymes will work at a max rate with membranes working the best at this temperature. 

Maximum temperature: the highest temperature possible for bacterial growth. At temperatures too ghih, proteins and enzymes will denature and membranes will fail, leading to cell death. 

Psychrophile: a category of microorganisms that grow best at temperatures within the temperature ranges of 5C to 15C

Mesophile: a category of microorganisms that grow best at temperatures within the temperature range of 15C to 45C. This category includes Escherichia coli and other common human pathogens. 

Thermophile: a category of microorganisms that grow best at temperatures within the temperature range of 45C to 80C. 

Hyperthermophile: a category of microorganisms that grow best at temperatures above 80C. 

Decimal Reduction Time: the time required to reduce viable cell numbers by 10-fold. Increasing temperature and exposure time to kill bacteria will result in a decreased amount of time required to reduce by 10-fold. 

Aerobic respiration: metabolic process that involves the complete oxidation of substreate molecules and production of ATP via redox reactions that requires the use of oxygen as the terminal electron acceptor. Typically leads to the production of 38 ATP. 

Aerobic Microorganisms: microorganisms that require oxygen for growth in some capacity. 

Obligate aerobe: microorganisms that must have oxygen in order to grow. 

Microaerophile: microorganisms that only grow when oxygen is in low concentrations. 

Facultative: microorganisms that prefer oxygen to grow if available but can utilize other metabolism pathways for growth if there is no oxygen. 

Anaerobic microorganisms: microorganisms that do not need to utilize oxygen in order to grow. 

Obligate anaerobe: microorganisms that only grow when there is no oxygen present. 

Aerotolerant anaerobe: microorganisms that are capable of growing when oxygen is present but does not utilize oxygen for growth. 

Superoxide dismutase: enzyme used by the cell to rid itself of toxic byproducts such as radical oxygen ions produced by aerobic respiration. 

Thioglycolate agar medium: nutrient medium that can be used to determine oxygen requirements of a microorganism based on the formation of oxygen gradient and observing where in the tube bacteria most optimally grow. 

Sodium thioglycolate: ingredient in thioglycolate agar medium that reacts with oxygen to create an oxygen gradient within the tube where oxygen is in high concentrations at the top of the agar and in low concentrations at the bottom of the agar. 

Resazurin: ingredient in thioglycolate agar medium that reacts with oxygen to turn red. 

Oxic zone zone in tube with thioglycolate agar medium where there is a high concentration of oxygen and is red

Anoxic zone: zone in tube with thioglycolate agar medium where there is no oxygen/low concentrations of oxygen is not red (no oxygen to react with resazurin)