Biochem Ch9

protein A; maltose

Affinity chromatography is a common way to purify fusion proteins. Which of the following incorrectly matches the tag peptide with the ligand that can be used for purification? (His)6; Ni2+ protein A; maltose GST; glutathione β-galactosidase; TPEG

It catalyzes the formation of a phosphodiester bond in the DNA.

During the cloning process, what is the specific function of DNA ligase?

BACs can accommodate very long segments of cloned DNA, whereas traditional cloning vectors do not.

For which reason might a researcher choose a bacterial artificial chromosome (BAC) over a traditional cloning vector?

4096

HindIII recognizes the following sequence: (5') AAGCTT (3'). In a DNA molecule with a random sequence in which all four nucleotides were equally abundant, this sequence would be recognized by HindIII once every ___ bp.

DpnI cleaves methylated DNA; the template DNA is methylated and the newly synthesized DNA is not.

In the process of site-directed mutagenesis, how does DpnI distinguish between the parental and new DNA strand that contains the mutation?

1.05 x 10^-6 g

Starting with 1 picogram of DNA (1.00 x 10-12 g), if you were to amplify this DNA by PCR using a cycle number of 20, how much DNA would you end up with.

phenotypic function.

The effect of a protein on an entire organism is best defined as:

Primer 1: 5'-ATGCAAATGG-3' Primer 2: 5'-GGAAATCTCG-3'

The following piece of DNA was isolated from Bacillus Subtilis. The function of the gene product is unknown, but researches wanted to clone the DNA. The sequence corresponds to the coding strand of the fragment. Which pair of 10 base primers would effectively amplify the complete DNA sequence shown below? 5'-atg caa atg gaa aaa ttg atg ttt cat ccg cat ggt aaa gag ttt cat cac aat cct ttt tca gtt tta gga cga ttt aga gag gaa gag ccc att cac cga ttt gaa tta aaa cgg ttc gga gcc aca tat ccg gcc tgg tta att acc cga tac gat gat tgt atg gcc ttt tta aaa gac aat cga att aca aga gac gta aaa aat gtg atg aac caa gaa caa atc aaa atg ctc aac gtt agt gaa gat atc gat ttt gta tcc gat cat atg ctg gca aaa gac aca cct gac cat acc cgc ctg aga tca ctt gtt cat caa gca ttt act ccc cga acc att gaa aat ctg cgc ggc agc att gaa caa att gct gaa cag ctt tta gat gaa atg gaa aaa gaa aat aaa gcg gat atc atg aaa tcc ttc gct tcc cct ttg cct ttt att gtt ata tct gaa ttg atg gga atc cca aaa gaa gat cgg tca cag ttt caa atc tgg acc aat gcg atg gtt gat acc tct gaa ggt aat aga gag ctg aca aat cag gcc ctt cgt gaa ttt aaa gat tat atc gct aag ctg atc cat gac aga aga ata aag cca aaa gac gat tta atc agc aaa ctt gtg cat gct gag gaa aac ggc agc aag tta agc gaa aaa gag ctc tat tcg atg ctg ttc ttg ctc gtt gta gcc ggc ctt gaa aca act gtt aac tta ctc ggc tca ggc acc ctc gca ttg ctg cag cac aag aag gaa tgt gag aag ctc aag cag cag cct gaa atg atc gct aca gcg gtt gaa gaa ttg ctg cga tac acc tca cct gtc gtt atg atg gca aat cgg tgg gcc atc gaa gac ttt aca tat aag ggg cat tcg atc aaa aga gga gac atg att ttt ata ggc atc gga tct gcc aat cgc gac ccg aat ttt ttt gag aac ccc gaa ata tta aat ata aat cgg tcg cct aat aga cat att tct ttt ggt ttt ggc att cat ttc tgc tta gga gcg cct ctt gcc agg ctg gaa ggc cac att gca ttt aaa gca gct ttt gac gag att tcc-3'

4 fragments: 600 bp, 680 bp, 775 bp, 1895bp

The plasmid vector pTEST was used to clone a 500 bp fragment from a gene of bacterial origin at the Kpn I site. Several clones were selected and the plasmids were analyzed for insertion of the gene by restriction enzyme digestion. Assuming a single copy of the target fragment was inserted, how many DNA fragments would be produced if the plasmid was cleaved using both PstI and EcoRI, and what would their sizes be?

orthologs.

The sequencing of many genomes and the use of comparative genomics gives great insight into the relationships between species, but also can be useful for determining functions of unknown gene products in an organism. Genes that occur in different organisms but are clearly related structurally and functionally are referred to as:

It removes terminal phosphates from either the 5' or 3' end (or both).

What is the function of alkaline phosphatase with regard to its use in recombinant DNA technology?

binds the target molecule, and the secondary antibody, which carries the fluorophore, recognises the primary antibody and binds to it

What is the purpose of the secondary antibody in immunofluorescence methods?

It provides multiple recognition sequences for restriction endonucleases.

What is the role of a polylinker in a cloning vector?

2,1,3

Which of the following correctly identifies the order of events that take place during PCR? 1) anneal DNA with short primers. 2) heat denature DNA. 3) synthesize DNA. 3, 1, 2 2, 1, 3 1, 2, 3 2, 3, 1

2, 3, 1

Which of the following correctly identifies the order of events that take place during bacterial transformation? 1) growth of bacteria on an agar plate with a selectable marker. 2) incubation of plasmid DNA and bacteria at 4°C. 3) heat shock at 42°C.

All of the above

Which of the following is true of using tandem affinity purification tags for protein purification? This technique minimizes false positives. Protein interactions that persist through both steps are likely to be functionally significant. Two consecutive purification steps help to eliminate any weakly bound contaminants. All of the above.

GFP requires molecular oxygen and additional proteins and cofactors to fluoresce.

Which of the following statements about green fluorescent protein is false? A target gene fused to the GFP gene generates a fusion protein that is highly fluorescent when exposed to blue light. GFP is a protein derived from jellyfish. GFP requires molecular oxygen and additional proteins and cofactors to fluoresce. GFP can be used to visualize labeled proteins directly in a living cell.

A clone of a transformed yeast or bacteria cell in a genomic library generally contains the complete genome of the organism of interest in a cloning vector.

Which of the following statements is false regarding DNA libraries? A cDNA library only includes sequences of DNA that are expressed. To generate a cDNA library, a researcher first extracts mRNA from an organism. A genomic library is formed when fragments of a genome are cut with restriction endonucleases and inserted into cloning vectors. A clone of a transformed yeast or bacteria cell in a genomic library generally contains the complete genome of the organism of interest in a cloning vector.

Many do not undergo the covalent modifications or proteolytic cleavage that may be necessary for their activity.

Which of the following statements is incorrect regarding the use of bacteria for the expression of recombinant proteins? They require expensive media for growth. Many do not undergo the covalent modifications or proteolytic cleavage that may be necessary for their activity. They are difficult to grow in large amounts. The regulatory sequences that govern gene expression in E. coli and many other bacteria are not well understood.

Bacteria recognize eukaryotic regulatory sequences required for transcription.

Which of the following statements regarding the expression of eukaryotic proteins in bacteria is incorrect? Bacteria can be used to express the protein products of cloned eukaryotic genes at high levels. Many eukaryotic proteins aggregate into insoluble cellular precipitates called inclusion bodies. Expression of the cloned gene must be limited to the few hours before the planned harvesting of the cells because some foreign proteins can kill the host cell when expressed at high levels. Bacteria recognize eukaryotic regulatory sequences required for transcription.

The growth of mammalian cells in tissue culture is relatively inexpensive.

Which of the following statements regarding the use of mammalian cells for protein expression is false? Viruses are often employed to deliver the cloned gene of interest to these host cells. Mammalian cells can properly post-translationally modify proteins to their active form. The growth of mammalian cells in tissue culture is relatively inexpensive. Mammalian cells are generally used to test the function of a protein in vivo rather than to produce a protein in large amounts.

promoter sequences introns

Which of the following would not be found in a cDNA library? promoter sequences introns exons a and b

All of these are true statements.

Which statement regarding the use of DNA microarray analysis is NOT correct? It can be used to monitor increases or decreases in gene transcription. It can be used to compare expression patterns at different developmental stages of an organism. It cannot be used to measure changes in protein levels in response to external cellular stimuli. It cannot be used to monitor formation of specialized RNA molecules like siRNA and miRNA. All of these are true statements.

cleavage of the mRNA into smaller fragments

Which step is NOT involved in DNA microarray analysis? reverse transcription of the mRNA cleavage of the mRNA into smaller fragments hybridization of fluorescently tagged cDNA to complementary fragments on an array removal of unhybridized cDNA isolation of total mRNA from cells