Molecular Biology Exam 2 Flashcards
What are 3 components of PCR?
Mg2+, Primers, dNPTs
What is the origin for reverse transcriptase?
Retro- and pararetroviruses
What is the major difference between qPCR and digital PCR?
Digital PCR separates the sample into thousands of subsamples for quantitation making it more sensitive
What are 3 types of extraction techniques for nucleic acids?
Organic, Affinity, Inorganic
Why should nucleases be avoided in nucleic acid extractions?
Low nucleic acid quality, It can degrade the nucleic acids and the downstream molecular biology reactions will fail
What is a benefit that running a gel has for checking nucleic acid quality over spectrophotometry or fluorometry?
Degradation can be Assessed
What is a plasmid Ori?
The site that plasmid replication begins at
True or False: Plasmids only contain one type of gene.
False
What is an infection clone
A cDNA copy of a viral genome
True or false: Cloning is only something that humans cause
False
Why are vector constructs verified before use?
If the construct is wrong, then the downstream experiments wont work
What are examples of naturally occurring transgenic organisms
Pea aphid, humans, Sweet Potatoes
Why is it important to make recombinant proteins
To study the Protein functions, modify existing proteins and to produce enough for use in biomedical applications
What are the benefits of using affinity binding for protein purification
getting a pure extract, to have a specific tag on the protein and simplify the extraction
Why would a researcher add a fluorescent tag to a protein through genetic engineering?
To localize the protein in a cell
What is a Motif?
A conserved sequence of amino acids that has a function
What are 3 reasons to identify motifs?
To determine the function of a protein, to characterize an unknown protein and to identify related proteins
Why are software programs used to identify motifs?
The algorithms are more precise, more domains can be identified and to simplify the process
Why is maxam gilbert sequencing not used today?
It is technically challenging, it is expensive and other techniques were developed
how are dideoxynucleosides labeled?
fluorophores and radioactive phosphate
If you were sequencing the genome of an organism and don’t know any of the sequence, which method should you use?
Shotgun sequencing
Why is it essential to have the highest quality DNA for massively parallel sequencing?
low quality DNA yields low quality results, inhibitors can inhibit the sequencing reaction
cost of the reaction is much higher than sanger sequencing
What type of chemistry does Illumina sequencing use?
Reversible terminator dyes
What is the basis for the minION sequencer?
Nanopores
What involves mathematics and statistics?
Experimental Design, Preprocessing of data and structural learning
When choosing a command line bioinformatics what should be considered?
Further analysis to be performed, the application and the source of data
What types of user-interface based bioinformatic programs are there?
Proprietary fee-based programs, government funded software that is free, and proprietary freeware
What is a clade?
A cluster of branches that group together from a single point
Why is bootstrapping commonly used to test the accuracy of a tree?
It can test consistency of a clade placement, robustness of the tree placement and how efficiently a tree was made
If you were to align sequences using a web-based program, which would be the best option?
ClustalOmega
What is the benefit of using RNAseq for transcriptomics?
Transcript quantification, Identification of alternative splicing and detection of rare transcripts
True of false? Omics approaches are only used individually
False
What technological advance has made metagenomics common?
Massively parallel sequencing
