Terms and definitions from microbiology

Defined medium: Medium that contains only known (defined) ingredients.
Minimal medium: Defined medium that contains only the ingredients needed for the growth of a strain.
Batch culture (static culture): Cultivation in a closed system until harvest - examples: Shake flask or closed bottle 
In controlled fermenters, certain parameters can be measured and influenced: O 2 -input, pH, temperature, etc.
continuous culture: cultivation in a chemostat in a steady state with inflow and outflow (->dilution)
Growth phases of a batch culture: start-up (lag) phase, exponential (lg) phase, stationary phase, die-off phase
Specific growth rate: µ = (ln Nt - N0) / (t - t0)
For doublings td=doubling time: ln 2 / µ = td
Optimisation of dilution rate: dilution rate D = volume change per h

FtsZ: Bacterial tubulin that enables septum formation (process of cell division of bacteria)
MinCD: Prevents division planes at the poles in the process of cell division in bacteria
MreB: Bacterial actin that causes the rod shape of many bacteria -> positioning of the cell wall synthesis machinery
Taxis: Directed movement in response to external signal
Chemotaxis: Directed movement due to chemical substances
Aerotaxis: Directed movement due to O2/redox state
Osmotaxis: Directional movement due to ionic strength
Phototaxis: Directional movement due to light
Thermotaxis: Directional motion due to temperature
Magnetotaxis: Directional movement due to magnetic fields
Positive chemotaxis: movement in the direction of increasing concentration towards the attractor
Negative chemotaxis: Movement in the direction of falling concentration, away from the repellent
Attractant: Attractant
Repellent: attractant
Atrich: Bacteria without flagella
Monotrically Flagellated: Bacteria with one flagellum
Polytrich: bacteria with several flagella
Polytrich-Monopolar or Lophotrich: bacteria with a flagellar bundle at one of the cell poles
Polytrich bipolar or amphitrich: bacterium with flagellar bundle or single flagellum at each cell pole
Peritrich: bacterium with flagella over the entire cell body
Filament of the flagellum: main part
Hook of flagellum: Connects filament to motor complex
Basal body of the flagellum: Anchoring of the flagella in the cell envelope
Photo-energy source: light
Chemo- energy source: chemical
-organo- electron donors: organic
-litho- electron donors: onorganic
-heterotrophic Carbon source: organic
-autotrophic Carbon source: carbon dioxide
Cytoplasm Location: RNA polymerase
Periplasm Site: murein
Cytoplasmic membrane Site: ATP synthase
Outer membrane Location: Lipid-A
Cytoplasmic membrane Site: ubiquinone
Outer membrane Site: porin
Transcription: Requires DNA-dependent RNA polymerase
Replication: Requires DNA-dependent DNA polymerases
Gyrases: Important type-II topoisomerases that introduce negative supercolis into DNA
Chromosomes: Contain genes that are essential under all growth conditions
Aldolase reactions: Central role in glycolysis and Entner-Doudorff pathway.
Pentose phosphate pathway: Provides C-4 and C-5 sugars, as well as NADPH.
Glyceraldehyde phosphate dehydrogenase: Achieves substrate phosphorylation and NADH production in glycolysis through reaction.

Heterofermentative lactic acid fermentation: Generates more ATP with pentose than with hexose.
Propionic acid fermentation: lactic acid is converted to acetate and propionic acid
ATP production only by substrate chain phosphorylation: heterofermentative lactic acid fermentation
Heliobacteria: Can use light energy for photophosphorylation. But not for CO2 fixation
Calvin cycle: NADPH is needed to reduce 1,3-bisphosphoglycerate
Reductive citrate cycle: Acetyl-CoA leaves the process and can be further carboxylated to pyruvate.
Denitrification: stepwise reduction of nitrate to gaseous nitrogen
Sulphatarms: Must first activate sulphate before reduction.
Chemolithotrophic iron oxidation: Found especially in acidic environments.
Azolla caroliniana: Floating fern that forms a symbiosis with nitrogen-fixing cyanobacteria to supply nitrogen.
Phage: Virus whose host is a prokaryote.
Bacteriophage: viruses that infect bacteria
Lysogeny: State of a bacterium infected by bacteriophages in which the viral DNA is integrated into the bacterial DNA and cell proliferation occurs rather than lysis.
Lysis: State of a bacterium infected by bacteriophages in which the viral DNA is replicated and incorporated into proteins before the cell dies (lysis).
Dimorphism: Fungi can grow as a mycelium and as a yeast phase. The change in growth form is caused by an altered programme of gene expression, which is initiated either at certain stages of ontogeny or by environmental factors.
CheY: Induces the rotation of the bacterium by interacting with the flagellar switch protein FliM, thereby changing the direction of rotation of the flagella from levorotatory to dextrorotatory.
Stickland reaction: Coupled fermentation in which an amino acid is oxidised and another amino acid is reduced with the resulting electrons. Conversion to acetate. Found in clostridia
Polyhydroxybutyric acid: Synthesised during the assimilation of carbon, mainly in the form of glucose and starch as an energy source and metabolised again in the absence of other energy sources. Abbreviation PHB
What forms of energy does energy metabolism provide to performance metabolism? ATP, pmf, NAD(P)H.
 
Chemolithoautotrophic: Energy source: chemical
Electron donors: inorganic
Carbon source: carbon dioxide
Thermophilic bacteria: Require very high temperatures
Thermophilic archaea: live near very hot mineral springs on the deep sea floor
Prokaryotes: Archaea and Bacteria
Cytoplasm: Chromosomes of archaea and bacteria are located there.
Eukaryotes: Transcription and translation take place in different compartments
Archaea: do not have any compartments
Chloroplasts: Descended from symbiotic archaea
S-layer: Protein layers on the surface of many procaryotes
Ribosomal protein synthesis: Peptide bonds are formed here
Basic structure of amino acids: carboxyl group, amino group, residue
Components of bacterial phospholipids: Polar molecule (choline), phosphoric acid (phosphate), glycerine (glycerol), 2 fatty acids
L-amino acids: are the main component of amino acids
D-amino acids: Are in peptides of the bacterial cell wall
Primary structure: sequence of amino acid building blocks in proteins
Basidia: Stand fungi on which meiotic spores are formed by protrusions.
Spores on the outside of the basidia
Ascus: Often tubular cells in which 8 spores are formed after meiosis and mitosis.
Spores inside the ascus
Plasma membrane: occurrence of ATP synthase of prokaryotes
Inner mitochondrial membrane: ATP synthase of eukaryotes
Thylakoid membrane: ATP synthase of chloroplasts
ATP components: Is a nucleotide composed of adenine residue, sugar (ribose) and three phosphates
ATP is a universal and immediately available energy carrier in cells and an important regulator of energy-producing processes.
To which site does new amino acid-loaded tRNA bind: A site (acceptor)?
At which site does the peptide chain grow during translation: P-site (peptidyl)
At which site does empty tRNA detach from the ribosome: E site (exit)?
At which site of the ribisome does initiator tRNA bind and which amino acid is introduced first: P site is the inhitator tRNA and formylmethionine is the 1st amino acid. A and E sites are empty.

Amino acid that is introduced at the N-terminus of all proteins: Formylmethionine
What is the sigma factor used for in procaries: Ensures specificity of transcription
Which process competes with acetogenesis: Mathanogenesis
Acetogenesis: Hydrogen and CO2 form acetate
Compartment of the bacterial cell wall: Periplasmic space
Fumarate respiration: Fumarate can take up electrons from catabolism and be reduced to succinate.
Anaerobic respiration: Energy production (ATP synthesis) without oxygen. Oxidative energy metabolism uses other electron acceptors as oxidants instead of O2. E.g. fumarate or sulphur respiration.
Calvin cycle: cyclic CO2 assimilation pathway in cyanobacteria and procariotes.
Primases: Creates short RNA primers where needed .
Isopeptide bonds: Bonds between side chains of permanent amino and carboxyl groups. Link fibrin and confer stability.
What is a protein called that binds to an operon and thereby represses transcription: repressor?
Activator: Protein that binds to the operator binding site, thereby increasing the affinity of the polymerase.
Functions of pili: locomotion, conjugation, attachment.
Baltimore scheme classifications: 1. DNA or RNA viruses, 2. single or double stranded, 3. plus or minus RNA, 4. with or without RNA intermediate
In which membrane are LPS anchored: Outer membrane of Gram negative bacteria
How is lipid A anchored in the membrane: Directly integrated into the membrane by fatty acid chains, there it binds to the phospholipids
How are ABC transporters energised: Via the formation and hydrolysis of ATP at the ABC unit.
Glucose-specific phosphotransferase system (PTS): Glucose is phosphorylated by the PTS system as soon as it enters the cell.
How is the ATP yield reduced in the Entner-Doudorff pathway?: By KDPG aldolase, which forms pyrovate at an early stage.
Entner-Doudorff pathway: The 2nd part of glycolysis does not differ from the 2nd part of the Entner-Doudorff pathway.
Pyruvate dehydrogenase: Converts pyrovate to CO2 and acetyl-CoA, forming NADH.
What kind of fermentation is propanoic acid fermentation when it starts from lactate: A secondary fermentation.
What does propyric acid fermentation combine: substrate chain phosphorylation and electron transport phosphorylation
Mixed acid fermentation: There are serious differences in fermentation due to different representatives of Enterobacteriaceae
S-layer: Lattice-like protein layers on the surface of many prokaryotes
Negative supercoli: Reduces the number of helix turns