Microbiology Exam 1 Flashcards
What are the three main categories of microbes?
- Prokaryotes that include virtually all bacteria/archaea
- Viruses
- Eukaryotes including yeast, most fungi, protozoa, other “higher” multicellular organisms
Louis Pasteur
It was initially thought that living organisms are “spontaneously generated” from non-living matter. Pasteur (and Lazzaro Spallanzani) debunked spontaneous microbe generation. Pasteur also developed the germ theory of disease, rabies vaccination, pasteurization, and identified yeast as an agent in the fermentation of wine
Joseph Lister
Made connection between Pasteur’s germ theory and deaths from surgery/amputations (operative sepsis). Used carbolic acid to sterilize surgical instruments and clean wounds. Using this approach sepsis deaths were significantly reduced
Robert Koch
Developed many techniques to grow microbes, pioneered streaking techniques, isolation of single bacterial colonies, and the growth of pathogens in pure culture.
What were the postulates Robert Koch used to identify M. tuberculosis as the cause of TB.
Postulate 1: Suspected pathogenic organism should be present in all cases of disease and absent from healthy animals
Postulate 2: Suspected organism should be grown in pure culture
Postulate 3: Cells from a pure culture of suspected organism should cause disease in a healthy animal
Postulate 4: Organism should be reisolated and shown to be the same as the original pathogenic organism
How were Koch’s postulates used to identify TB in particular?
A method of staining M. tuberculosis was developed, solid media was used to grow it, and guinea pigs were infected.
What is the difference between phylogeny and taxonomy?
Phylogenetic trees show the evolutionary development of a history of species while taxonomic trees classify organisms by distinguishable characteristics.
How were bacteria classified into taxonomic trees based on phenotypes?
- Growth requirements (aerobic vs anaerobic)
- Ability to be stained by a specific dye acid (gram-positive vs gram-negative)
- Lytic/reproductive properties
What are the criteria for the molecular clock based on genome sequencing to classify organisms?
It is based on the principles that all life is related, genotypes are the basis for phenotypic diversity, and classification is based on evolutionary relationships
Why was 16s rRNA useful for developing a phylogeny for life on earth?
It encodes ribosomes and is highly conserved throughout all forms of life and alignment of base pairs is also straightforward.
It is additionally universally distributed, functionally homologous, easily aligned base pair for base pair, and changes at a rate commensurate with evolutionary distance
How can Epulopiscium show why phenotype is a poor means for determining which group a given organism belongs to?
They were originally thought to be protists due to their large size (up to a million times larger than E. Coli), but they turned out to be closely related to Clostridia, an anaerobic spore organism.
Lag phase
When a fresh culture is inoculated with cells from an older or stationary phase culture cells need time to resynthesize essential components before beginning growth again. If inoculated with exponential phase cells generally no lag
Exponential phase
Population doubles in mass per unit of time (Km and Vmax measure this). Growth rate is dependent on nutrients, temperature, ionic strength (salt), etc and is plotted on a semi log scale
Stationary phase
Period which growth slows down dramatically. Occurs when cells either run out of nutrients, a waste product builds up and inhibits growth, or sometimes both
Death phase
Density of bacterial culture decreases, but a lot of times bacterial cells are still viable because they can eat each other
What are the functions of the cell membrane?
- maintains an electrochemical gradient
- key for selective import and export
- site of protein secretion
- allows for signal sensing and transduction
What tend to be the differences in the lipid bilayers of archaea and bacteria?
- Archaea tend to have a partial monolayer and ether linkages
- Bacteria tend to have a bilayer with ester linkages
What key differences are observed between gram-positive and gram-negative bacteria?
- Gram reaction: gram positive bacteria stain purple and gram negative bacteria stain pink/red due to the presence of a membrane
- Gram positive bacteria have a thicker cell wall
- Gram positive bacteria have a thick and multilayered peptidoglycan layer
- Gram positive bacteria are more rigid and less elastic
- Gram positive bacteria do not have an outer membrane but gram negative do
bactoprenol
type of riboswitch that “flips” a hydrophilic precursor molecule across a bacterial plasma membrane outside the cell in order to initiate cell wall synthesis
glycotransferase
polymerizes glycan strands to form a peptide chain that is key in producing a cell wall
transpeptidase
crosslinks peptide chains using B-Lactams to assemble the cell wall. B Lactam antibiotics like penicillin, cephalexin, and ampicillin target this step in cell wall synthesis.
Why do cell wall synthesis enzymes exhibit redundancy?
This allows for overlapping activity in order to allow robust activity even across different environmental conditions (such as salt and pH). This is why extracellular enzymes tend to be more abundant than intracellular ones.
What is the importance of the periplasm?
It contains hydrolytic enzymes, binding proteins, chemoreceptors, secretion systems
How would we know if LPS complexes contribute to cell rigidity?
Loss of LPS should be lethal at high osmolarity but tolerated at low osmolarity since water would flow outwards cell towards high osmolarity boosting the turgor pressure and lysing cells if LPS does not maintain cell rigidity.
Turgor pressure
force that pushes the cytoplasm outwards towards the cell envelope and is driven by the difference between cytoplasmic and environmental osmolarity. A cell is hypertonic when there is low turgor pressure (result of low osmolarity outside cell), isotonic when there is equal turgor pressure, and hypotonic when there is high turgor pressure (result of high osmolarity outside cell).
What did CHIR-090 treatment reveal about whether or not LPS complexes contribute to cell rigidity?
LPxC catalyzes LPS synthesis and CHIR-090 inhibits LPxC and therefore reduces the amount of LPS. At low osmolarity the cell envelope remained unchanged and at high osmolarity the cells lysed. This indicates that LPS works together with the cell wall to boost cell rigidity and prevent turgor pressure from getting too high.
magnetosomes
tiny particles of magnetite are encased in a lysosome and surrounded by a membrane. This allows A. magnetotacum to remain along a geomagnetic field line.
What kinds of compounds produce CO2 and organic compounds?
- Lithotrophs and autotrophs produce CO2 (phospho and chemo)
- Organotrophs and heterotrophs produce organic compounds (phospho and chemo)
Carboxylation (calvin cycle)
- first step of the calvin cycle, catalyzed by RuBisco
- involves the addition of CO2 to ribulose biphosphate “fixing the CO2”
- ribulose biphosphate then splits into 2 molecules of 3-phosphoglycerate using H2O
Reduction (calvin cycle)
- second step of calvin cycle
- Phosphorylate 3-phosphoglycerate becomes 1,3 biphosphoglycerate
- 1,3-biphosphoglycerate is then reduced to glyceraldehyde-3-phosphate
- One ATP and one NADPH is used
Regeneration of ribose biphosphate
pentose phosphate shunt is used to create glucose from glyceraldehyde 3P
What are the requirements for nitrogen fixation?
ATP is necessary and fixation cannot occur in the presence of O2
What is the purpose of glycolysis?
- It generates pyruvate from glucose which is important in fermentation and the generation of acetyl-coA, which is key in the citric acid cycle and lipid synthesis.
- It has a net gain of 2 ATP and 2 NADH
What are the preparatory reactions for glycolysis?
- Fructose-1,6-biphosphate is generated from glucose. 2 ATP are burned
- hexokinase and ATP is first used to produce Glucose-6-phosphate from glucose
- Isomerase is used to produce Fructose-6-phosphate
- Phosphofructokinase and ATP is used to produce Fructose-1,6-biphosphate
What happens during the oxidation phase of glycolysis?
- 2 2-phosphoglycerate becomes into pyruvate. 2 ATP and 2 NADH are gained
- Adolase is first used to produce 2 glyceraldyde-3-phosphate
- Glyceraldehyde-3-dehydrogenase is used to make 2 glyceraldehyde-3-dehydrogenase, 2 Pi, and 2 NAD+ into 2 1,3-Biphosphoglycerate, 2 NADH, and 2 electrons and protons
- Phosphoglycerokinase generates 2 ATP and 2 3-phosphoglycerate from 2 1,3-Biphosphoglycerate
