Term
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Definition
| In protein translocation, what term describes trafficking proteins from cytosol to cell membrane |
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Term
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Definition
| In protein translocation, what term describes trafficking proteins from cytosol to milieu (environmental medium) |
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Term
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Definition
| In protein translocation, what term describes the extracellular transport of non-proteinaceous compounds |
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Term
| Export, Secretion, Excretion |
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Definition
| Name three terms that would describe the different methods of protein translocation. |
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Term
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Definition
| Name the 3 translocation pathways |
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Term
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Definition
[image]
What protein translocation pathway is this? |
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Term
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Definition
[image]
What protein translocation pathway is this? |
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Term
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Definition
[image]
What protein translocation pathway is this? |
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Term
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Definition
| In Eukarya, which part of the cell contains all 3 types of the protein translocation pathways? |
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Term
| Euarchaeota does, Cren does not have YidC |
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Definition
| In Archaea, specifically between Euryarcheaota and Crenarcheaota, out of the two, which contains all 3 types of the protein translocation pathways? |
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Term
| All three: YidC, Sec, and Tat |
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Definition
| Which protein translocation pathways does Bacteria contain? |
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Term
| Bacteria, Euryarcheaota, and Cholorplasts in Eukarya |
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Definition
| Which Domain of life contains all 3 translocation pathways (YidC, Sec and Tat)? |
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Term
| Crenarcheaota and the cytosol in Eukarya |
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Definition
| Which domain of life lacks the YidC pathway? |
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Term
| The mitochondria of Eukarya |
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Definition
| Which domain of life lacks the Sec pathway? |
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Term
| The mitochondria and Cytosol of Eukarya |
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Definition
| Which domain of life lacks the Tat pathway? |
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Term
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Definition
| A set of all mRNA and sRNA molecules in one cell or a population of cells is referred to as? |
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Term
| By RNA sequencing or DNA microarrays |
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Definition
| Name two ways transcriptomes can be measured? |
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Term
| RNA sequencing (old term: whole transcriptome shotgun sequencing) |
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Definition
| An emerging method of choice for measuring transcriptomes using next generation sequencing and software to infer transcripts directly from short sequence reads and can reveal the quantity and presence of RNA in a sample at a given moment is called? |
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Term
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Definition
| An older hybridization-based technique that maps transcripts onto a reference genome, either of the organism itself or one closely related is called? |
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Term
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Definition
| The collection of metabolites in a biological tissue, organ or organism synthesized under a specific condition at a given time is referred to as? |
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Term
Gas chromatography
High performance liquid chromatography (HPLC)
Capillary electrophoresis (CE)
Mass spectrometry (MS)
Nuclear magnetic resonance (NMR) |
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Definition
| Name some current in situ methods that are underdevelopment to measure metabolomes? |
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Term
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Definition
| What does gas chromatography do? |
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Term
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Definition
| The global (genome wide) analysis of proteins synthesized in a cell or any biological sample under specific conditions at a certain time is called? |
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Term
The transcriptome alone does not present a complete picture of cell biology
Proteins are active players in the cell that determine its function
Post-translational modifications of effect of protein function
Metabolomics is also important |
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Definition
| Name 4 reasons why studying proteomics is important |
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Term
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Definition
| What test method separates protein mixtures by using a 2D gel electrophoresis, separating the protein by two properties. |
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Term
In the first dimension, by their isoelectric focusing or IEF)
In the second dimension, by their mass (SDS-PAGE) |
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Definition
| What are the two properties proteins are separated into during 2D-PAGE? |
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Term
| Cleave with proteases such as trypsin that cleaves after basic residues such as lysine and arginine |
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Definition
During digestion of proteins, in a gel or shotgun, you need to cleave the proteins with what?
Give a specific example too. |
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Term
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Definition
[image]
What test method does this represent? |
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Term
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Definition
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Term
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Definition
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Term
| Immobilized metal affinity chromatography |
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Definition
| What does IMAC stand for? |
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Term
| Metal Oxide Affinity Chromatography |
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Definition
| What does MOAC stand for? |
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Term
| High Performance Liquid Chromatography |
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Definition
| What does HPLC stand for? |
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Term
| Multidimensional Protein Identification Technology |
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Definition
| What does MudPIT stand for? |
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Term
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Definition
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Term
Electron Ionization
Formly known as electron impact ionization or electron bombardment ionization |
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Definition
| A hard ionization method that uses high energetic electrons to produce ions that leads to extensive fragmentation which is helpful for structure determination of unknown compounds is called? |
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Term
| Matrix assisted laser desportion/ionization tiem of flight mass spectrometry |
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Definition
| What does MALDI-TOF stand for? |
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Term
| Electrospray Ionization Tandem Mass Spectrometry |
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Definition
| What does ESI MS/MS stand for? |
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Term
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Definition
| Name two methods that are relatively soft ways of obtaining ions of large molecules (very little fragmentation) in the gas phase. |
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Term
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Definition
| When comparing MALDI vs ESI, which produces ions using an electrospray i nwhich a high voltage is applied to a liquid to create an aerosol? |
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Term
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Definition
| When comparing MALDI vs ESI, which mixes the sample with a matrix material and applied to a metal plate, where a pulsed laser is used to irradiated and trigger the ablation and desorption of the sample and the matrix material (basically vaporized from the surface). |
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Term
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Definition
| When comparing MALDI vs ESI, which produces more charged ions? |
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Term
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Definition
| When comparing MALDI vs ESI, which has analyte molecules that are ionized (deprotonated or protonated_ in the ablated gases enabling their acceleration into the mass spectrometer |
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Term
Grows on defined medium
Genome sequence is complete
Genetic tools established
Organism studied for biotechnology applications |
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Definition
| Name some key features for a model archaeon |
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Term
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Definition
| Name a model archaeon studied for biotechnology applications |
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Term
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Definition
| Where was Sulfolobus solfataricus first isolated? |
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Term
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Definition
| What phylum does Sulfolobus solfataricus belong to? |
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Term
| It is a thermoacidophilic obligate aerobe that has an optimal temp of 80 degrees celsius and a pH of 2-3 |
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Definition
| What are some key characteristics of Sulfolobus solfataricus? |
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Term
sugars (celluose, D-glucose, D-xylose, and cellobiose)
Alcohols, aldehydes, amino acids and peptides |
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Definition
| What kind of organic compounds does Sulfolobus solfataricus utilize as carbon and energy sources? |
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Term
| Sulfolobus turreted icosahedral virus |
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Definition
| What does STIV stand for? |
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Term
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Definition
| Name the 7 DNA Polymerase families |
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Term
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Definition
| Which of the 7 DNA Pol families are found in Archaea? |
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Term
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Definition
| Which Archaeal DNA Pol family is used for high fidelity PCR, DNA sequencing and site directed mutagenesis |
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Term
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Definition
| Which Archaeal DNA Pol family has more potential for error prone PCR and random mutagenesis because of their low fidelity and strong thermostability? |
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Term
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Definition
| Which type of DNA Pol is from Thermus aquaticus and used for PCR? |
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Term
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Definition
| Which family of DNA Pol lack 3' to 5' exonucleases proofreading activity, making them low fidelity enzymes? |
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Term
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Definition
| Pfu DNA polymerase for PCR is isolated from what? |
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Term
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Definition
| RNase P processes what end of the pre-tRNAs? |
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Term
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Definition
| What is essential for most archaea, including the precise hybridization of nucleic acids? |
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Term
| They directly encode the mature 5' end of the tRNA |
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Definition
| What do nanoarchaea do that is different than other archaea that involve RNase P? |
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Term
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Definition
| What is a native RNA-mediated adaptive immune system that protects bacteria and bacteria from viruses or plasmids? |
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Term
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Definition
| What can act as safe vaccine adjuvants in mammals? |
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Term
| They impart long lasting CD8 and T cell immunity as well as antibody repsonses |
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Definition
| How do archaeosomes work in vaccines? |
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Term
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Definition
| What is composed of archaeal polar lipid mixtures hydrated to form lipid membrane vesicles with bilayer or monolayer structures? |
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Term
1) Use of temperature downshift to regulate recombinant enzyme activity
2) high temp growth minimizes contamination risk, even though the possibility of viral contamination can occur, there has not been a virus discovered that can affect hyperthermophilic euryarchaeaon. CRISPR system can be used to 'immunize' these industrial strands |
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Definition
| Discuss two advantages to using hyperthermophiles as engineering platforms. |
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