Term
| What are the 4 types of temperature classifications based on optimal temperatures? |
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Definition
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Term
| Barophile definition, adaptation |
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Definition
| Pressure-loving, adapted membranes and amino acid sequences |
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Term
| Typical optimal environment for microbes |
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Definition
20-40 degrees C
near-neutral pH
salt concentration of .9%
ample nutrients |
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Term
| Halophile definition, adaptation |
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Definition
| Salt-loving, additional sodium ion pumps to maintain osmotic balance |
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Term
| Acidophile, Neutrophile, Alkaliphile definitions, adaptation |
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Definition
| Acid-tolerant, Neutral pH-loving, Alkaline-loving, pump protons (H+) in or out of the cell to maintain a neutral pH |
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Term
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Definition
| Cannot survive in O2 environments |
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Term
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Definition
| Only survives in O2 environments |
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Term
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Definition
| Prefers low O2 environments |
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Term
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Definition
| Prefers O2 environments but can resort to anaerobic environments |
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Term
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Definition
| Doesn't use O2 but can survive in any amount/lack of O2 |
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Term
| Reactive oxygen species (ROS) |
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Definition
| byproduct of aerobic respiration, damages DNA, proteins, membranes, ect. |
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Term
| Superoxide dismutase (SOD) + Catalase, which kind of microbe doesn't have either? |
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Definition
| Enzymes that break down ROS, strict anaerobes |
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Term
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Definition
| Microbe requiring external supplements of essential nutrients |
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Term
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Definition
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Term
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Definition
| Synthetic mix of chosen nutrients |
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Term
| How do most bacteria reproduce? |
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Definition
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Term
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Definition
1. DNA replication
2. Protein synthesis + expansion of cytoplasm
3. Septum forms, cell division |
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Term
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Definition
| Time it takes for a population to double (generations) |
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Term
| 4 phases of bacterial growth |
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Definition
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Term
| What does a continuous culture do? |
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Definition
| Prolongs the log (exponential growth) phase |
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Term
| What is the only direct form of measuring growth in the lab? |
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Definition
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Term
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Definition
| Polymer-encased community of microbes |
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Term
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Definition
| Regulates secretion of extracellular polymeric substances (EPS) in high population density |
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Term
| Matrix provides protection, facilitates movement of nutrients, diverse communities |
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Definition
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Term
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Definition
| A cell's resting state, high resistance to heat, chemicals, dehydration, ect. |
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Term
| Sporulation vs. Germination |
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Definition
Sporulation: process of forming a endospore
Germination: process of endospore returning to its vegetative (normal) state |
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Term
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Definition
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Term
| Methanotrophy vs. Methanogenesis |
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Definition
Methanotrophy: Uses methane as an energy source to produce CO2
Methanogenesis: Produces methane from CO2 |
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Term
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Definition
| NH4+ or NO3- turns into biomass |
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Term
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Definition
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Term
| Nitrogen fixation definition |
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Definition
| N2 gas turns into NH4+ in the soil |
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Term
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Definition
| NH4+ turns into NO3- within the soil |
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Term
| Denitrification definition |
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Definition
| NO3- turns into N2 gas in the air |
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Term
| Nitrogenase definition, what is it sensitive to? |
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Definition
| Enzyme that catalyzes nitrogen fixation, sensitive to O2 |
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Term
| Biochemical oxygen demand (BOD) |
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Definition
| The amount of O2 removed from the water through aerobic respiration |
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Term
| Eutrophic definition, what is it caused by? |
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Definition
| Environment that is deprived of oxygen and kills aerobes. Caused by high densities of heterotrophic microbes that eat C and N |
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Term
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Definition
| Large eutrophic marine environments |
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Term
| 4 Benefits of fermentation |
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Definition
| Preservation, digestibility, nutrition, flavor |
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Term
| Food spoilage vs. Food contamination |
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Definition
Food spoilage: microbial changes/metabolism affect the food in an unpalatable way
Food contamination: presence of pathogens or harmful microbes, could lead to foodborne illness |
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Term
| What does preservation do? |
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Definition
| Slows or inhibits microbial growth |
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Term
| What are the 3 types of chemical preservation? |
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Definition
1. Organic acids: microbial fermentation
2. Other organic compounds: plant-based
3. Inorganic compounds: e.g. salts |
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Term
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Definition
| Removal of water to prevent microbial growth |
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Term
| Modified atmosphere preservation |
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Definition
| Packaging food in low O2 or high N2 or CO2 environments |
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Term
| Cold temperature preservation |
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Definition
| Slows or inhibits microbial growth based on optimal temperature |
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Term
| Pasteurization preservation |
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Definition
| Moderately high heat for a short time to kill bacteria (doesn't sterilize) |
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Term
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Definition
| Cooking under high pressure destroys most microbes |
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Term
| Food irradiation preservation |
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Definition
| Damages cells and DNA with rays, can be bactericidal |
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Term
| What is Polymerase chain reaction? |
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Definition
| Synthetic DNA replication in a lab setting |
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Term
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Definition
| several genes on the same mRNA molecule that are turned on/off by the same promoter |
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Term
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Definition
| mRNA molecule with multiple genes |
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Term
| What is a Sigma factor and what does it do? |
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Definition
| A part of RNA polymerase, responsible for recognizing promoters |
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Term
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Definition
| Signal, Sensor, Regulator, Response |
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Term
|
Definition
Activator: proteins promote transcription when bound to DNA
Repressor: proteins block transcription when bound to DNA |
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Term
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Definition
Induced: expression is turned on by presence of a signal
Repressed: expression is turned off by presence of a signal |
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Term
| Quorum sensing: signal, and response |
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Definition
Signal: autoinducers (population density)
Response: positive feedback loop for autoinducers, expression of genes needed for things involving more than once cell |
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Term
| 3 types of Base substitutions |
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Definition
Silent mutation: codes for same amino acid
Missense mutation: codes for different amino acid
Nonssense mutation: codes for stop codon |
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Term
| Additions and Deletions cause... |
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Definition
| Frameshift mutation: changes the reading frame |
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Term
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Definition
| A gene product that is nonfunctional (can be any mutation except silent) |
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Term
| Spontaneous vs. Induced mutation |
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Definition
Spontaneous: base substitutions and add./del. are random mistakes by DNA polymerase
Induced: a mutagen causes increased mutation rate |
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Term
| What do chemical mutagens do? |
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Definition
| Can damage or alter DNA bases, or reassemble DNA subunits and cause wrong pairings |
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Term
| What do radiation mutagens do? |
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Definition
UV radiation: causes thymine dimers
Ionizing radiation: damages bases or breaks DNA backbone |
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Term
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Definition
| Single damaged base is recognized and removed by DNA glycosylase, and replaced by DNA polymerase |
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Term
| Nucleotide excision repair |
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Definition
| Distorted DNA is recognized, surrounding nucleotides are removed, and replaced by DNA polymerase |
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Term
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Definition
| Mismatch is recognized, part of new strand (hasn't received CH3 yet) is removed, and replaced by DNA polymerase |
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Term
| Photolyases (light repair) |
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Definition
| Thymine dimer (T=T) is recognized, an enzyme uses light to reverse/break the bond |
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Term
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Definition
| Extensive damage is recognized, DNA recombination and Error-prone DNA polymerase repair (increases mutation rate for survival) |
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Term
| What is the main benefit of mutation? |
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Definition
| Genetic diversity, leads to new strains with new resistances or metabolism |
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Term
| Vertical gene transfer vs. Horizontal gene transfer |
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Definition
Vertical gene transfer: genome copies are passed to daughter cells
Horizontal gene transfer: cell picks up new DNA |
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Term
| What of 2 conditions must DNA have to be "maintained"? |
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Definition
| Have its own origin of replication (plasmid) OR be recombined into the existing genome (chromo. or plasmid) |
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Term
| (HGT) Transformation definition |
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Definition
| A competent cell imports free DNA (usually from lysed bacteria or biofilms) |
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Term
| (HGT) Conjugation definition |
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Definition
| Donor cells transfer DNA via cell-to-cell contact to recipient cells, conjugation pilus is used to brings cells together |
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Term
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Definition
| DNA sequence containing genes needed to facilitate conjugation |
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Term
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Definition
F-: genotype lacking F factor (recipient)
F+: genotype containing F factor (donor)
Hfr: genotype containing F factor in its chromosome (donor) |
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Term
| Chromosomal vs. Plasmid conjugation |
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Definition
Chromosomal (rare): part of DNA is cut and transferred to recipient cell, recipient remains F-
Plasmid (common): one strand of DNA helix is transferred, each cell replicates the single strand, both cells end F+ |
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Term
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Definition
| DNA sequence in the F factor that is cut |
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Term
| What are the 5 stages of biofilm formation? |
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Definition
[image]
Flagella attach to the monolayer, microcolonies form, cells produce EPS, biofilm matures, biofilm dissolves |
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Term
| What do mobilizable plasmids have, what do they lack? |
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Definition
| They have oriT, but no conjugation genes; can "hitchhike" if in a donor cell when other genes are transferred. |
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Term
| (HGT) Transduction definition |
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Definition
| Viruses that infect bacteria cells (bacteriophage or phage) transfer DNA from one bacteria cell to another |
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Term
| Generalized vs. Specialized transduction |
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Definition
Generalized: phage capsid is mistakenly filled with bacterial DNA instead of phage DNA (packaging mistake)
Specialized: prophage is cut out of the chromosome along with some bacterial DNA (excision mistake) |
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Term
| Transducing particle definition |
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Definition
| Phage capsid filled with bacterial DNA |
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Term
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Definition
| Phage integrated into host cell's genome |
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Term
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Definition
| A swap-out of DNAs that have sequence homology in the genome (similarity) |
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Term
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Definition
| A bacterial protein that facilitates homologous recombination |
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Term
| Site-specific recombination |
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Definition
| A short DNA sequence is recognized by a recombination enzyme and inserted into the genome |
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Term
| Mobile genetic elements definition |
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Definition
Gene segments moved via horizontal gene transfer
Ex. Plasmids, Phage DNA, Transposons, Genomic islands |
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Term
| Core genes vs. Accessory genes |
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Definition
| Core genes are common among species, accessory genes differ between strains |
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Term
| Genomic islands definition |
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Definition
| Large strands of DNA that add beneficial functions to a cell's genome (ex. virulence factors) |
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Term
| What are Transposons, what can they cause? |
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Definition
| Segments of DNA that can "jump" across different parts of the genome. Insertion site is usually random, cause knock-out if it lands in a gene |
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Term
|
Definition
| Enzyme that facilitates insertion of transposons |
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Term
| Insertion sequence definition |
|
Definition
| A simple transposon, consists of transposase gene and inverted repeats |
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Term
| Composite transposons definition |
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Definition
| Transposons that contain other genes in addition to the insertion sequence (ex. resistance genes) |
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|
Term
|
Definition
|
|
Term
|
Definition
| A substance required for growth in cells, must either be synthesized by cells or readily available in a cell's environment |
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Term
| When do endospores form? What can form endospores? |
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Definition
| When environmental conditions become unfavorable, only some species of gram-positive bacteria |
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Term
| Primary vs. Secondary metabolites |
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Definition
Primary metabolites: compounds needed for essential physiological processes (ex. growth, development, reproduction)
Secondary metabolites: compounds needed for non-essential but beneficial ecological processes (ex. defense) |
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Term
| Why are microbes important in the Carbon and Nitrogen cycles? |
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Definition
| They convert them into forms that can be used by other living things |
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Term
| Two component system definition |
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Definition
| A membrane-bound kinase sensor, and a response regulator |
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Term
|
Definition
| It targets a known sequence and replicates it to synthesize millions of copies of the desired sequence. |
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Term
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Definition
| The physiological state in which a cell can import new DNA and be transformed |
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|
Term
| What steps of gene regulation can be regulated? |
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Definition
| Transcriptional, post-transcriptional, translational, post-translational |
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|
Term
| Why are transposons considered both mutation and HGT? |
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Definition
| Transposons introduce new genetic material into the genome (causing mutations) and can facilitate genetic transfer between different organisms |
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|
Term
| Which HGT events would need to be followed by recombination in order for the new DNA to be maintained/passed on? |
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Definition
| Transformation, conjugation, transduction |
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