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What types of information can be retrieved from a protein sequence database?

Short Answer

Expert verified

The protein sequence database retrieve protein sequence records by gene name, organism, author name, accession number and a variety of other text terms.

Step by step solution

01

Protein database

Protein databaseis a collection of sequences from several sources, including translations from annotated coding regions in GenBank. They are an important resource because proteins mediate most biological functions.

02

SWISS-PROT database

It is acurated protein sequence database which strives to provide a high level of annotations like protein function, domain structure, modifications observed after translation, variants and so on.

03

Accuracy

A minimal level of repetition and high level of integration with other database.

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Most popular questions from this chapter

Consult Table 5-1 to complete the following: (a) On a plot of absorbance at 280 nm versus elution volume, sketch the results of gel filtration of a mixture containing human cytochrome c and bacteriophage T7 RNA polymerase and identify each peak. (b) Sketch the results of SDS-PAGE of the same protein mixture showing the direction of migration and identifying each band.

What fractionation procedure could be used to purify protein 1 from a mixture of three proteins whose amino acid compositions are as follows?

1. 25% Ala, 20% Gly, 20% Ser, 10% Ile, 10% Val, 5% Asn, 5% Gln, 5% Pro

2. 30% Gln, 25% Glu, 20% Lys, 15% Ser, 10% Cys

3. 25% Asn, 20% Gly, 20% Asp, 20% Ser, 10% Lys, 5% Tyr

All three proteins are similar in size and pI, and there is no antibody available for protein 1.

Explain how you would use salting out to prepare a more concentrated solution of a protein.

Question: Purification tables are often used to keep track of the yield and purification of a protein. The specific activity is a ratio of the amount of the protein of interest, in this case Mb, obtained at a given step (μmol or enzyme units) divided by the amount (mg) of total protein. The yield is the ratio of the amount of the protein of interest obtained at a given step (μmol or enzyme units) divided by the original amount present in the crude extract, often converted to percent yield by multiplying by 100. The fold purification is the ratio of the specific activity of the purified protein to that of the crude preparation.

(a) For the purification table below, calculate the specific activity, % yield, and fold purification for the empty cells.

(b) Which step—DEAE or affinity chromatography—causes the greatest loss of Mb?

(c) Which step causes the greater purification of Mb?

(d) If you wanted to use only one purification step, which technique would you choose?

You are trying to purify a protein that is soluble in a solution of 2 M ammonium sulfate. After centrifugation to remove other proteins that have precipitated at this high salt concentration, you recover the supernatant to assay the target protein’s activity in a cell culture system.

(a) Explain why the cells die when incubated with the supernatant.

(b) What procedure could you perform to correct the problem? (Hint: See Section 2-1D).

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