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MB 302 Midterm II
Microbio Terms and Definitions
| Term | Definition |
|---|---|
| Budding | A mode of asexual reproduction in which some bacteria reproduce by forming a bud at the end of their prostheca (an extension of a bacterial cell that's narrower than the mature cell) |
| Multiple Fission | A mode of asexual reproduction in which the progeny cells are held within the cell wall of the parent cell until they are released |
| Spores | A mode of asexual reproduction in which certain bacteria form multinucleoid filaments that eventually divide to form uninucleoid spores, which are readily dispersed |
| Batch Culture | A population of microorganisms growing in a closed culture vessel containing a single batch of medium |
| Generation Time | The time required for a microbial population to double in number |
| DNA-Binding Proteins (Dps) | A type of starvation protein that is histone-like and wraps around DNA to protect it |
| Chaperone Proteins (aka "heatshock proteins" or "stress proteins") | A type of starvation protein that prevents protein denaturation |
| Viable But Nonculturable Cells (VBNC) | Microbes that are temporarily unable to grow (dormant) |
| Halophiles | A microorganism that requires high levels of sodium chloride for growth (>0.2 M NaCl) |
| Extreme Halophiles | A microorganism that requires high levels of sodium chloride for growth (2-6.2 M NaCl) |
| Halotolerant | A microorganism that can withstand large changes in NaCL |
| Osmotolerant | Organisms that grow over a wide range of water activity or solute concentration |
| Psychrophiles | A microorganism that grows well from 0-20 degrees C; optimum at 15 degrees C |
| Psychrotrophs | A microorganism that grows well from 0-35 degrees C; optimum at 22 degrees C |
| Mesophiles | A microorganism that grows well from 15-45 degrees C; optimum at 37 degrees C |
| Thermophiles | A microorganism that grows well from 45-85 degrees C; optimum at 55-65 degrees C |
| Hyperthermophiles | A microorganism that grows well from 55-130 degrees C; optimum at 85-113 degrees C |
| Aerobes | An organism that requires oxygen for respiration. Has SOD and catalase |
| Microaerophiles | An organism that only grows in low levels of oxygen ("picky"). Has SOD; may or may not have catalase |
| Facultative Anaerobes | An organism that doesn't require oxygen for respiration, but grows better with it. Has SOD and catalase |
| Aerotolerant Anaerobes | An organism that has no preference for oxygen and grows equally well with or without it. Has SOD |
| Strict/Obligate Anaerobes | An organism that is killed by oxygen. Lacks SOD and catalase |
| Barotolerant | An organism that can tolerate increased pressure |
| Barophilic/Piezophilic | An organism that grows more rapidly at higher pressures |
| Ionizing Radiation | A type of radiation found in X-rays and gamma rays; destorys DNA, primarily |
| Deinococcus radiodurans | Example of an extremely resistant bacteria to ionizing radiation |
| Oligotrophs/Oligotrophic Environment | Contains low nutrient concentrations |
| Biofilm | A growth of complex, slime-encased communities |
| Extracellular Polymeric Substances (EPS) | The formation of a matrix of biofilm |
| Quorum Sensing | The exchange of extracellular molecules that allows microbial cells to sense cell density |
| Autoinducers | With respect to quorum sensing, a small molecule that induces synthesis of the enzyme responsible for the autoinducer's synthesis |
| Acyhomoserine Lactone (AHL) | A type of autoinducer that provides information to a cell regarding its enviornment, signaling it to respond accordingly to either reach a quorum or not |
| Metabolism | The sum of all chemical reactions in a cell |
| Chemical Work | The work that is done in a cell to synthesize macromolecules |
| Transport Work | The work that is done in a cell to take up nutrients, eliminate wastes, and maintain ion balances |
| Mechanical Work | The work that is done in a cell for motility and movement of structures |
| Exergonic | A reaction that spontaneously goes forward (favorable reaction) with a delta G zero prime of negative |
| Endergonic | A reaction that spontaneously goes backwards (unfavorable reaction) with a delta G zero prime of positives |
| Standard Free Energy Change (delta G zero prime) | When the free energy change for a process is determined at carefully defined standard conditions of concentration, pressure, pH and temperature |
| Standard Reduction Potential (E prime zero) | A measure of the tendency of a chemical to lose electrons in a redox reaction |
| NAD+/NADP+ | A type of electron carrier that transports 2 electrons and 1 proton |
| FAD/FMN | A type of electron carrier that transports 2 electrons and 2 protons |
| Coenzyme Q | A type of electron carrier that transports 2 electrons and 2 protons (also called ubiquinone) |
| Cytochromes | A type of electron carrier that transports only 1 electron at a time |
| Iron-Sulfur (Fe-S) Proteins | A type of electron carrier that transports only 1 electron at a time; not to be mistaken with the redox pair |
| Ferredoxin | An example of a type of Fe-S transport proteins |
| Apoenzyme | The main part of an enzyme that is composed of protein |
| Co-factor | The non-protein component of an enzyme that's needed to function |
| Co-enzyme | The part of a co-factor that's loosely attached and can dissociate |
| Prosthetic Group | The part of a co-factor that is firmly attached to the apoenzyme |
| Holoenzyme | The complete enzyme (includes apoenzyme and co-factor) |
| Allosteric Effector | A molecule that reversibly binds to a regulatory site |
| Positive Effector | A molecule used in allosteric regulation that, when bound, causes enzyme activity |
| Negative Effector | A molecule used in allosteric regulation that, when bound, causes enzyme inactivity |
| Pacemaker Enzyme | An enzyme used in feedback inhibition |
| Autotroph | An organism that uses carbon dioxide as its sole/principal source of carbon |
| Heterotroph | An organism that uses reduced inorganice compunds as its electron source |
| Phototroph | An organism that uses light as its source of energy |
| Chemotroph | An organism that uses chemicals (either organic or inorganic) as its source of energy |
| Lithotroph | An organism that uses reduced inorganic compounds as its electron source |
| Organotroph | An organism that uses reduced organic compounds as its electron source |
| Oxidative Phosphorylation | The process by which ATP is synthesized as the result of electron transport driven by the oxidation of a chemical energy source; mechanism by which it takes place is explained by the most likely hypothesis by Peter Mitchell: the chemiosmotic hypothesis |
| Chemolithotrophy | Microbes that donate electrons to their ETCs by oxidizing inorganic molecules rather than organic nutrients |
| Ammonia Incorporation | Conversion of ammonia (NH3) to organic N |
| Nitrification | Oxidation of ammonium (NH4+) to nitrate (NO3-) |
| Assimilatory Nitrate Reduction | Reduction of nitrate (NO3-) to ammonia (NH3) to organic N |
| Nitrate Reductase | Enzyme used in assimilatory nitrate reduction that reduces nitrate (NO3) to nitrite (NO2) |
| Nitrite Reductase | Enzyme used in assimilatory nitrate reduction that reduces nitrite (NO2) to ammonia (NH3) |
| Dissimilatory Nitrate Reduction | Reduction of nitrate (NO3-) to reduced inorganic N |
| Denitrification | Reduction of nitrate (NO3-) to nitrogen gas (N2) |
| Annamox Reaction | Reaction that uses ammonium (NH4+) as an electron donor and nitrite (NO2-) as an electron acceptor to form nitrogen gas (N2) and water |
| Photophosphorylation | The synthesis of ATP from ADP + Pi using energy made available during electron transport initiated by the absorption of light energy |
| Oxygenic Photosynthesis | Photosynthesis that oxidizes water to form oxygen; characteristic of plants, protists, and cyanobacteria |
| Cyclic Photophosphorylation | The formation of ATP when light energy is used to move electrons cyclically through an electron transport chain |
| Noncyclic Photophosphorylation | The process in which light energy is used to make ATP and reducing power when electrons are moved from water to NADP+ during oxygenic photosynthesis |
| Anoxygenic Photosynthesis | Photosynthesis that does not use water as an electron donor, meaning no oxygen is produced |
| Bacteriorhodopsin/Archaeorhodopsin | A transmembranous protein to which retinal is bound; it functions as a light-driven proton pump |
| Homologous Recombination | Recombination involving two DNA molecules that are similar in nucleotide sequence |
| Site Specific Recombination | Recombination of nonhomologous genetic material with a chromosome at a specific site |
| Transposition | The movement of a piece of DNA around a cell's genome |
| Insertion Sequences (IS) | A simple, mobile genetic element that contains genes only for transposition |
| Inverted Repeats | Identical or very similar sequences of nucleotides that are on each end of an IS element in reverse orientation |
| Transposons | A mobile genetic element that carries the genes required for transposition, as well as other genes |
| Simple Transposition | Transposase-catalyzed excision of the transposable element, cleavage of a new target site, and ligation of the element into this site |
| Replicative Transposition | Original transposon remains at the parental site on the chromosome and a copy is inserted at the target DNA site |
| Competent Cell | A cell that can take up free DNA and incorporate it into its genome during transformation |
| Competence Factor | A small protein that stimulates the production of 8-10 new proteins required for transformation |
| Biotechnology | Processes in which living organisms are manipulated to form useful products |
| Vector DNA/Cloning Vector | Plasmid from bacteria or yeast that's used to transfer DNA to desired location |
| Chimera | Recombined plasmid |
| Artificial Transformation/Competency | Divalent cations, heat shocking |
| Electroporation | Exposure to high-voltage electrical pulse |
| Microinjection | DNA micropipetted into cells |
| Gene Gun | DNA coated around metallis microprojectiles |
| Oligonucleotides | Short pieces of DNA fragments that have sequences identical to those flanking the targeted sequence |
| Annealing | Subjecting nucleic acid to a process of heating and cooling in order to separate its strands |
| Extension | Creation of new strands of DNA by Taq polymerase by incorporating nucleotides that complement the template strand |
| Antisense RNA | Molecules transcribed from DNA strands complementary to those that produce normal messenger RNA |
| Gene Therapy | Replacement of malfunctioning genes with wild-type genes through viral delivery |
| Full Genome Shotgun Sequencing | Process of breaking full genomes into random fragments to be sequenced and assembled |
| Library Construction | DNA is broken into fragments and purified |
| Gap Closure | DNA fragments are sequenced |
| Single-Cell Genome Sequencing | Fragmented DNA assembled into longer stretches |
| Multiple Strand Displacement Amplification (MDA) | Uses 6 bp random primers and phage DNA polymerase |
| Bioinformatics | Management of nucleotide sequence data and other genome information; combines biology, math, computer science, and statistics |
| Genome Annotation | Determining location and nature of genes/presumed genes |
| Coding Sequences (CDS) | ORFs prsumed to encode proteins |
| Paralogues | Genes that arose form gene duplication in one organism (two of the same gene, due to transposition) |
| Orthologues | ORFs in different organisms that are predicted to have the same function |
| Functional Genomics | The analysis of genome transcripts and the proteins they encode |
| DNA Microarray | Solid supports that have DNA attached in an organized grid pattern; used to evaluate gene expression or microbial population composition |
| Probe | DNA spot representing single gene or ORF |
| Proteomics | Study of the proteome |
| Proteome | The complete collection of proteins that an organism produces |
| Functional Proteomics | Determination of the function of different cellular proteins, how they interact, and the ways they are regulated |
| Two-dimensional gel electrophoresis | Procedure that separates proteins using two different methods; sorts both pH and molecular weight |
| Structural Proteomics | Determination of a 3D protein structure |
| Protein Modeling | Prediction of likely protein shape |
| Comparative Genomics | The analysis of genomes from different organisms to look for significant differences and similarities |
| Genomic Islands | Mobile genetic elements permanently integrated into microbial genome |
| Pathogenicity Islands | Genes that contribute to virulence |
| Synteny | Similarities in organization of orthologues |
| Pseudogenes | Degraded, non-functional genes (might not be needed if depending on host, etc.) |
| Reverse Vaccinology | Use of genomics to identify target molecules for vaccine development |
| Metagenomics | The study of genomes recovered from natural samples without first isolating members of the microbial community and growing them in pure cultures |
| Phylotypes | A taxon that is characterized only by its nucleic acid sequence; generally discovered during metagenomic analysis |
| Microbiome | All the microbes that live on/in an organism or a defined environment |
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