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Chapter 12: Genomics, Proteomics, and Transgenics
Chapter 12: Genomics, Proteomics, and Transgenics Notecards
42
Biology
Undergraduate 3
12/16/2012
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Term
__________ __________ are endonucleaes produced by bacteria to degrade any foreign DNA.
 Definition
1) Restriction enzymes
Term
How far apart the cuts will be depends on the probability of finding the __________ sequence.
 Definition
1) Recognition
Term
A __________ __________ molecule is created when the restriction enzyme generated DNA from one species is joined by DNA ligase to another piece of DNA from a different species.
Usually the second piece is a self-replicating molecule called a __________ __________.
 Definition
1) Recombinant DNA
2) Cloning vector
Term
The first cloning vectors used were small double-stranded circular molecules found in bacteria called __________.
 Definition
1) Plasmids
Term
When DNA is introduced back into cells, very few cells pick up any DNA; those that are transformed gain only __________ recombinant molecule.
When grown, each colony contains a different recombinant DNA clone.
Since only a rare cell picks up the DNA, use is made of a selectable marker to kill all the __________ cells and only cells that have picked up a __________ will survive in the presence of an antibiotic.
 Definition
1) One
2) Untransformed
3) Plasmid
Term
What three features must a cloning vector have?
 Definition
1) Origin of replication
2) Selectable marker gene (drug-resistant gene)
3) Unique cutting site for restriction nuclease, which can be used to open up the plasmid and insert foreign DNA into the vector
Term
Bacteriophage __________ derived vectors can often accept large pieces (__________-__________ kb).
 Definition
1) Lambda
2) 12-20
Term
__________ are plasmids that have the cohesive end of phage lambda; a typical one is about __________ kb.
 Definition
1) Cosmid
2) 5
Term
__________ __________ __________ have been created by manipulation of the sex plasmid (F-factor) of E. coli and there is no limit to the size of __________ that can be accepted.
 Definition
1) Bacterial artificial chromosome (BAC)
2) DNA
Term
DNA larger than __________-__________ kb is hard to keep intact in a BAC.
 Definition
1) 150-200
Term
Some vectors called __________ also carry the origin of replication for a single-stranded DNA phage, in addition to the plasmid origin of replication.
 Definition
1) Phagemids
Term
Knowledge of yeast chromosome structure and cloning of replication origins, centromere, and telomere sequences has permitted the creation of vectors called __________ __________ __________ which can also take very large inserts.
 Definition
1) Yeast artificial chromosomes (YAC)
Term
An __________ __________ should be used when trying to overproduce the product of a cloned gene.
 Definition
1) Expression vector
Term
__________ __________ have a strong promoter and a strong ribosome-binding site next to the cloning site.
 Definition
1) Expression vector
Term
__________ __________ carry two replication origins, one for E. coli and another for a second host.
 Definition
1) Shuttle vector
Term
It was discovered that E. coli cells will take up foreign DAN provided that they are pretreated with __________ __________.
 Definition
1) Calcium chloride
Term
__________ is a technique inn which a high voltage and very brief pulse of electric current is applied to a suspension of cells. The current causes the formation of short-lived holes in the __________ __________ which DNA is able to enter through.
 Definition
1) Electroportation
2) Cell membrane
Term
The use of intragenic complementation with the __________-__________ (Z) gene was made to develop plasmid vectors that permitted a color-based discrimination between recombinant and intact plasmids.
 Definition
1) B-galactosidase
Term
The Z' gene produces a small polypeptide (the __________ __________) with no B-galactosidase activity.
 Definition
1) Alpha peptide
Term
When the alpha peptide and the full size polypeptide with a small deletion are present together in the same E. coli cell, one gets a functional B-galactosidase enzyme (a process called __________ __________).
 Definition
1) Alpha complementation
Term
__________ __________ contains every sequence present in a cell; it is used when one wants to gain information about the whole genome.
 Definition
1) Genomic DNA
Term
When creating genomic libraries, one uses partially cut DNA (often with a __________ __________ that recognizes a __________ nucleotide sequence every 256 nucleotides on average).
 Definition
1) Restriction enzyme
2) 4
Term
__________ __________ do not provide any information about which genes are being expressed under any particular condition.
 Definition
1) Genomic libraries
Term
__________ clones are useful in overproducing the protein products of eukaryotic genes in heterologous organisms since the introns have been removed.
 Definition
1) cDNA
Term
__________ __________ are enzymes that can make a DNA copy of an RNA molecule.
 Definition
1) Reverse transcriptase
Term
__________ activity destroys the RNA strand in a DNA-RNA hybrid.
 Definition
1) RNaseH
Term
What can you do with a cloned gene?
 Definition
1) Use it to analyze the state of the gene in different situations
2) Overproduce protein
3) Use in forensics
4) Localize the gene on a chromosome
5) Sequence the DNA
6) Mutagenize the DNA
7) Amplify the PCR
8) Attach to glass and make DNA microarrays
Term
In __________ blotting, DNA fragments are separated in an agarose gel, the pattern transferred to a membrane filter and then probed for a particular DNA sequence using a radioactive DNA probe.
 Definition
1) Southern
Term
In __________ blotting, mRNA mixture is fractionated in an agarose gel, the pattern is transferred to a membrane filter, and a particular RNA sequence size and quantity is measured using a radioactive DNA probe.
 Definition
1) Northern
Term
In __________ blotting, a mixture of proteins is size-fractionated in a polyacrylamide gel, transferred to a membrane and a particular protein is quantitated by binding to radioactive antibody specific for that protein
 Definition
1) Western
Term
In __________ __________, cells and organisms are treated with mutagens and then selected for desired mutants.
 Definition
1) Forward genetics
Term
In __________ __________, you decide what mutant you want and create it.
 Definition
1) Reverse genetics
Term
__________ __________ is when you try to find the clone by looking at the overlapping clones.
 Definition
1) Chromosome walking
Term
A __________ __________ is a long continuous DNA sequence derived by joining shorter overlapping sequences.
 Definition
1) Sequence contig
Term
A __________ __________ occurs by joining shorter overlapping clones.
 Definition
1) Clone contig
Term
Short sequences derived from cDNA clones that have been mapped to particular chromosome locations are called __________ __________ __________.
 Definition
1) Expressed sequence tags
Term
__________ __________ allows the analysis of expression of thousands of genes at a time which would have required hundreds of Northern blots in the past.
 Definition
1) DNA microarrays
Term
In the __________ __________ __________, DNA from thousands of clones (or PCR products) are spotted on glass using a robotic spotting device.
 Definition
1) Spotting DNA microarrays
Term
In the __________ __________ __________, many thousands of small oligonucleotides (typically __________ nucleotides long) are synthesized directly on the glass surface.
 Definition
1) Synthesis DNA microarrays
Term
__________ __________ is the study of sequences, gene organizations of whole genomes.
 Definition
1) Structural genomics
Term
__________ __________ is the study of gene function for the entire genome.
 Definition
1) Functional genomics
Term
__________ is the study of all proteins that an organism can produce.
 Definition
1) Proteomics
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