DNA is broken into small fragments and attached to small beads. Each is placed into a well on a fiber-optic plate. DNA is amplified by PCR. Each time a base is added to the DNA strand, light is released and is measured in accordance to the nucleotide that was incorporated. 1b
grow best below pH 5.5; often found in acidic thermal soils associated with volcanic activity
dependent on cytoplasmic membrane stability; pH 2 above optima will cause cell to spontaneously lyse
regulatory protein used in positive control; activator binding site can be several hundred base pairs upstream of the operon
activator protein helps RNA polymerase recognize promotor by either
changing DNA structure allowing the RNA pol to contact promotor more readily or can interact with RNA polymerase directly
grow at full oxygen tensions 6b
can tolerate and grow in the presence of O2 even though they cannot respire
-showing growth pH optima of 8 or higher; typically found in soda lakes and high carbonate soils
-some extremely alkaliphiles are also halophiles -some produce hydrolytic exoenzymes that are excreted from the cells; often added as supplements to laundry detergents to remove protein and fat stains
10aDon't forget about the age old question of What are the features of genetic code?
natural or synthetic chemical that kills or inhibits the growth of microorganisms
antimicrobial agent susceptibility assay in tubes
A series of tubes is inoculated with the test organism and a given amount of agent is added. After incubation, the tubes are scored for turbidity, and the MIC is the lowest concentration of agent that completely inhibits growth of test organism.
-chemicals that kill or inhibit the growth of microorganisms but are sufficiently nontoxic to animals to be applied to living tissues
-some are also effective disinfectants 12b
form of transcriptional control by early termination of mRNA synthesis; found in bacteria and archaea
-not possible in Eukarya due to physical distance between transcription and translation
Attenuation in Tryptophan Operon 14a
Leader sequence encodes leader peptide which contains tryptophan codons side-by-side.
-If tryptophan is plentiful, the leader peptide will be synthesized and form a stem-loop, resulting in termination of transcription of remainder of operon. -If tryptophan is scarce, causes a stalled ribosome, which results in stem-loop formation that prevents termination allowing the remainder of the operon to be transcribed. Don't forget about the age old question of What is a military alliance of western europe and the united states?
We also discuss several other topics like When does labor productivity changes?
sealed heating device that uses steam under pressure to kill microorganisms
specific signal molecule synthesized by the participating organism that freely diffuses across the cell envelope in both directions
mechanism of global control that decides between utilizing different available carbon sources
Catabolite Repression Process on Lac Operon
When glucose is present, glucose siphons cAMP out of the cell. However, when glucose levels are low, cAMP is no longer sent out of the cell leaving it to bind to CRP. CRP forms a dimer when bound to cAMP and acts as a regulator. For the operon to be translated though, the repressor must be removed by the inducer (in this case, lactose). Lactose binds to the active repressor and thence removes it from the promotor site unblocking it for transcription. Both of these processes must occur for the lac operon to be transcribed. Don't forget about the age old question of What are the types of fossilization that we covered and how do they work?
converts hydrogen peroxide to water and oxygen
Caulobacter Differentiation 20a
Swarmer= free swimming cells; cannot divide or replicate their DNA. Stalked (attached) cells- lack flagella and are attached to a surface via a stalk with a holdfast reproductive stage. Regulated by
GcrA, CtrA, and DnaA i.GcrA is critical for cell division into differentiated cells and thus is active in the daughter cells only ii. CtrA is very active in flagellation
extrachromosomal elements that are not plasmids or integrated viruses; contains clusters of genes for specialized functions that are not needed for simple survival
-ex: megnetosome island of Magnetospirillum -some carry a gene encoding an integrase enzyme to move it into a chromosome
-target site is duplicated upon insertion; an intact tRNA gene is regenerated while the chromosomal island is inserted in place of what was to be another tRNA gene 21b
kill the microorganisms; bacteriocidal, fungicidal, etc.
Closed vs. Draft Genome
gaps in the sequence annotation is found in a draft genome whereas a closed genome has no gaps
-solute that does not inhibit cellular processes in any significant way but allows halophiles to maintain a positive water balance
-typically highly water-soluble organic molecules such as sugars, alcohols, or amino acid derivatives
-maximum level of compatible solute is a genetically encoded characteristic
Connecting Unknown protein with a particular gene from genomic DNA
oligonucleotide probes or primers can locate the gene encoding the protein and then identify the gene after sequencing the DNA
Connecting unknown protein with particular gene from 2D gel system
1. elute protein from gel and sequence a portion, or
2. identify protein by use of mass spectrometry
core genome is a genome found in all strains of a given species
substance that stops enzyme synthesis (ex: arginine)
Culture Techniques for Aerobes 29a
forced aeration is necessary so the flask or tube must be vigorously shaken or have sterilized air bubbled into the medium through a fine glass tube or porous glass disk
Culture Techniques for Anaerobes 30a
-Bottles or tubes filled completely to the top with culture medium and fitted with leakproof closures and a reducing agent can remove any remaining O2
-obligate anaerobes can incubate in tubes or plates in a glass jar that is flushed with an O2- free gas or fitted with an O2 consumption system
cyclic AMP receptor protein (CRP) 31a
activator protein responsible for catabolite repression; only acts when bound to cyclic adenosine
cyclic di-guanosine monophosphate 32a
another regulatory nucleotide; provides physiological changes and expression of virulence genes necessary for biofilm formation
physical method of control that consists of treatment of an object or surface to make it safe to handle; simply removes present organisms
-fibrous sheet or mat made from random array of overlapping paper or borosilicate fibers
-important in biosafety applications such as in safety hood
Detecting Horizontal Gene Flow 35a
1. presence of genes that encode proteins typically found in distantly related species 2. presence of a stretch of DNA whose GC
content or codon bias differs significantly from the rest of the genome
3. however, as more genomes are sequenced, using horizontal gene flow as an explanation can be nulled
result of catabolite repression; cells grow first on preferred C source. Once first source is depleted, the organism undergoes a lag phase before resuming on another C source.
Difference between first-, second-, third-, and fourth-generations of DNA
First generation- Sanger Dideoxy Method; read length 700-900 bases
Second generation- 454 pyrosequencing; very large number of samples are sequenced side-by-side in the same machine requiring miniaturization and increased computing power Third generation- sequencing of single molecules of DNA based on microscopy (HeliScope Single Molecule Sequencer) or nanotechnology (Pacific Biosciences SMRT)
Fourth generation- "post light sequencing" meaning optical detection is no longer used; ion torrent method or nanopore technology
Different Classes of Autoinducers 38a
acyl homoserine lactones (AHLs), autoinducer 2, short peptides
differentiation in bacteria
formation of endospores in Gm+ Bacilli and formation of two cell types in Gm Caulobacter (flagellated cells and those stuck to a surface)
disc assay for antimicrobial agent susceptibility
Known amounts of an antimicrobial agent are added to filter-paper discs and discs arranged on surface of uniformly inoculated agar plate.
The zone of inhibition is proportional to the amount added to the disc, solubility of the agent, diffusion coefficient, and the overall effectiveness of the agent. Used to test clinically isolated pathogens for their antibiotic susceptibility.