Term
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Definition
| o Some (few) can make all of their nutrients from a single carbon source - and are called prototrophs (E. coli) |
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Term
| auxotrophs in biosynthesis pathway discovery |
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Definition
| o Isolation of many mutants of prototrophs that acquired a need for an amino acid (for example). These mutants are termed auxotrophs |
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Term
| What is a fastidious organism? |
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Definition
| o Bacteria that cannot make all of their nutrients (and require the presence of many amino acids and/or vitamins) are considered fastidious |
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Term
| Amino acid biosynthesis: 3-Phosphoglycerate |
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Definition
Serine
Glycine
Cystine (and selenocystine) |
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Term
| Amino acid biosynthesis: Oxaloacetate |
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Definition
Aspartate
Asparagine
Threonine
Methionine
Isoleucine (also Pyruvate)
Lysine |
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Term
| Amino acid biosynthesis: 2-Oxoglutarate |
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Definition
Glutamate
Glutamine
Arginine
Proline |
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Term
| Amino acid biosynthesis: Pyruvate |
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Definition
Alanine
Valine
Isoleucine (also oxaloacetate)
Leucine (also acetyl-CoA) |
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Term
| Amino acid biosynthesis: Erythrose-4-PO4 and phosphoenolpyruvate |
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Definition
Tyrosine
Phenylalanine
Tryptophan (also Pentose-5-PO4) |
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Term
| Amino acid biosynthesis: Pentose-5-PO4 |
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Definition
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Term
| universal nitrogen donors, universal sulfur donors |
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Definition
Glutamate and glutamine are the two ‘universal’ nitrogen donors
o Sulfur can be obtained primarily as sulfate (anion), or sulfur containing amino acids (cysteine or methionine) |
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Term
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Definition
| o Assimilatory pathways are methods for taking a nutrient in the soil, moving it into the cell and using it for biosynthesis of macromolecules |
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Term
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Definition
| o Dissimilatory pathways use the substrate as a place to dump electrons and generate energy. |
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Term
| Three methods for exchanges DNA in prokaryotes |
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Definition
o Transformation
o Transduction
o Conjugation |
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Term
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Definition
| o Horizontal gene transfer (or sometimes called lateral gene transfer) refers to events of genetic exchange between prokaryotes |
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Term
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Definition
| o Vertical transfer refers to genetic information passed strictly from mother to daughter cells (i.e. during replication) |
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Term
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Definition
| o Some bacterial have the ability to interact with exogenous DNA, take it up into the cytosol, protect it from degradation and attempt to incorporate it into their own genetic material. This is NATURAL transformation. This is limited to only a few species of bacteria (so far….) |
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Term
| Transformation: chemical or electrical |
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Definition
o Most all bacteria can be artificially transformed – usually by a process of chemical or electrical treatment to open pores in the membranes
o Common method – high calcium/magnesium treatment on ice
o Electroporation also is efficient means to get negatively charged DNA across cell membranes |
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Term
| Transduction: specialized |
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Definition
| o Specialized is due to specific recombination events that occur at specific sites in the chromosomal DNA (Lambda phage) |
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Term
| Transduction: generalized |
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Definition
| o Generalized is random insertion of host cell genes into the bacteriophage particle, and thus can be used to exchange genetic material between organisms randomly (P1 or P22 phage) |
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Term
| What does P1 phage capable of? |
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Definition
o Phage DNA is made as concatamers (rolling circle)
o DNA is cleaved based on size, and always a little longer than it needs to be
o Error in packaging occurs about 2% of the time, this is why this technique can be used by scientists to exchange chromosomal DNA between strains |
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Term
| What is Lambda phage capable of? |
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Definition
o Lambda has served as a model for phage biology
o Lambda also helped to define the response of E. coli to UV radiation, and DNA repair systems (SOS response)
o Lambda attaches preferentially at the attB site (otherwise known as Lambda attachment site)
o Lambda has also been used extensively for incorporating engineered constructs into the genome in single copy. This is important to ask questions with a physiologically relevant copy number of the gene/promoter |
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Term
| What is abortive transduction? |
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Definition
Some of the cells that acquire the DNA from the phage do not incorporate it into the genome
o This DNA is linearized in the cytosol and can be maintained, but not replicated into daughter cells
o If growth requires expression of genes in this cluster it makes a tiny colony, where all cells present require this single cell to help others survive (such as inactivation of antibiotic)
o Motility phenotype allowed solid evidence for this phenomenon |
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Term
| lambda phage – where does it integrate? |
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Definition
| o Lambda attaches preferentially at the attB site (otherwise known as Lambda attachment site) |
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Term
| How has lambda been useful? |
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Definition
o Lambda has served as a model for phage biology
o Lambda also helped to define the response of E. coli to UV radiation, and DNA repair systems (SOS response)
o Lambda has also been used extensively for incorporating engineered constructs into the genome in single copy. This is important to ask questions with a physiologically relevant copy number of the gene/promoter |
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Term
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Definition
Requires exogenous growth factor e.g. and AA or vitamin
o Bacteria that cannot make all of their nutrients (and require the presence of many amino acids and/or vitamins) are considered fastidious |
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Term
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Definition
| Unable to grow in a particular environment (E.g. high temperature) in any medium |
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Term
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Definition
| Change of one base pair for another (purine for purine or Pyrimidine for Pyrimidine) e.g. AT to GC |
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Term
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Definition
| Change of one base pair for another (purine for Pyrimidine or Pyrimidine for purine) e.g. AT to CG |
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Term
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Definition
| Change in base pair leads to a different codon = different AA |
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Term
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Definition
| in base pair leads to a stop codon = truncated protein |
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Term
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Definition
| Gain or loss of one or several base pairs designated: +1 -1 +2 -2 ect. |
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Term
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Definition
| No loss in function unless duplication lies within a single gene increases gene dose |
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Term
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Definition
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Term
| Translocation or insertion |
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Definition
| Usually causes loss of function at the insertion site |
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Term
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Definition
| Frequently causes loss of function |
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Term
| Temperature sensitive alleles |
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Definition
o Temperature sensitive alleles are generally point mutants that only display a phenotype at normal (optimal temperature), but at a lower temperature they exhibit enough ‘activity’ to allow for growth (sometimes poor growth)
o Cultures are grown at a permissive temperature (i.e. 20 degrees Celsius) and then at mid-log phase shifted to non-permissive temperature
o Some parameters are then studied to determine the role for the protein of interest (mutant vs. wild type) |
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Term
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Definition
| o Metagenomics is an emerging field (non-culturable commmunities sequenced by shotgun approach with pyrosequencing) |
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Term
| Know the overall cell cycle, with respect to the initiation (oriC and DnaA) and finishing (ter) |
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Definition
o Origin (oriC) is the site of the initiation of DNA replication
o Terminus (Ter) is the site of termination and resolving the two sister chromosomes
o DnaA protein is the first to bind to origin, and its concentration regulates when the replication is initiated
dnaA mutants can’t initiate replication, and overexpression of DnaA causes too many forks to appear |
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Term
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Definition
o FtsZ is a GTPase (homolog of tubulin) that forms a Z-ring at the cells center
o This Z-ring constricts as division progresses
o FtsZ ‘recruits’ a number of other proteins that are needed to coordinate membrane biogenesis, peptidoglycan rearrangements and ultimately cell separation (e.g. PBP3)
o These proteins together are known as a ‘divisome’ |
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Term
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Definition
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Term
| Role of MinC andMinD proteins in cell cycle |
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Definition
| o MinC and MinD are localized to the poles, and actually switch back and forth in as little as 20 seconds (measuring???) |
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