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1. Deduce the primary structure of this polypeptide. 2. Why would cyanogen bromide not be a good choice as a cleavage reagent? 3. Can you account for the order of elution of trypsin digest peptides from gel-filtration chromatography? 4. Predict the order of elution of the tryptic peptides from a cation-exchange column eluted with pH-8.5 buffer and a salt gradient. 5. Predict the order of elution of the V8 protease peptides from an anion exchange chromatography column eluted with a pH-6.5 buffer and a salt gradient. 6. For both sets of peptides, predict the order of elution from a hydrophobic interaction chromatography column, given that the hydrophobic amino acids are V,L,I,F,A, and M.

1. Deduce the primary structure of this polypeptide. 2. Why would cyanogen bromide not be a good choice as a cleavage reagent? 3. Can you account for the order of elution of trypsin digest peptides from gel-filtration chromatography? 4. Predict the order of elution of the tryptic peptides from a cation-exchange column eluted with pH-8.5 buffer and a salt gradient. 5. Predict the order of elution of the V8 protease peptides from an anion exchange chromatography column eluted with a pH-6.5 buffer and a salt gradient. 6. For both sets of peptides, predict the order of elution from a hydrophobic interaction chromatography column, given that the hydrophobic amino acids are V,L,I,F,A, and M.

Biochemistry
Biochemistry
9th Edition
ISBN:9781319114671
Author:Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.
Publisher:Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.
Chapter1: Biochemistry: An Evolving Science
Section: Chapter Questions
Problem 1P
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Please answer part 4, 5 and 6.

**Transcription for Educational Website:** --- **Analyzing Peptides with Common Laboratory Techniques** Imagine you are in a South American rainforest, searching for naturally occurring peptides with potential as antiviral drugs. Equipped with a mobile biochemistry lab, your tools include common reagents and enzymes, an amino-acid analyzer, gel-filtration and ion-exchange chromatography, and electrophoresis. However, contamination becomes an issue, restricting you to sequencing peptides no longer than about 12 residues. During your search, you find a promising peptide from tropical orchid extracts. Here’s how you can deduce its amino-acid sequence using available tools: ### a) Molecular Weight (MW) by Electrophoresis Electrophoresis indicates the complexity of the sequencing problem. - **Result:** About 4000 ### b) Amino-Acid Analysis for Fragmentation Helps decide the fragmentation approach for sequencing. - **Result:** A₂C₂D₂E₄FG₃HKLMN₂P₂Q₂R₄S₄T₃W ### c) Peptide Fragmentation with Cleavage Reagents Determines number of peptides from cleavage: - **Cyanogen Bromide (C-side of M)** - **Staph. aureus V8 protease (C-side of D and E)** - **Trypsin (C-side of K and R)** ### d) Trypsin Cleavage and Gel-Filtration Results in six expected products, sequenced in emergence order from column: - **T-1:** ETMESSAGEFGR - **T-2:** SQTWALDHSECR - **T-3:** GPQDNK - **T-4:** TCR - **T-5:** NP - **T-6:** R ### e) Staph. aureus V8 Protease Cleavage and Gel-Filtration Results in seven expected products, sequenced in emergence order from column: - **S-1:** RSQTWALD - **S-2:** FGRPQGD - **S-3:** NKTCRNP - **S-4:** SSAGE - **S-5:** TME - **S-6:** CRE - **S-7:** HSE ### Think About It: 1. Deduce the primary structure of this polypeptide. 2.
Transcribed Image Text:**Transcription for Educational Website:** --- **Analyzing Peptides with Common Laboratory Techniques** Imagine you are in a South American rainforest, searching for naturally occurring peptides with potential as antiviral drugs. Equipped with a mobile biochemistry lab, your tools include common reagents and enzymes, an amino-acid analyzer, gel-filtration and ion-exchange chromatography, and electrophoresis. However, contamination becomes an issue, restricting you to sequencing peptides no longer than about 12 residues. During your search, you find a promising peptide from tropical orchid extracts. Here’s how you can deduce its amino-acid sequence using available tools: ### a) Molecular Weight (MW) by Electrophoresis Electrophoresis indicates the complexity of the sequencing problem. - **Result:** About 4000 ### b) Amino-Acid Analysis for Fragmentation Helps decide the fragmentation approach for sequencing. - **Result:** A₂C₂D₂E₄FG₃HKLMN₂P₂Q₂R₄S₄T₃W ### c) Peptide Fragmentation with Cleavage Reagents Determines number of peptides from cleavage: - **Cyanogen Bromide (C-side of M)** - **Staph. aureus V8 protease (C-side of D and E)** - **Trypsin (C-side of K and R)** ### d) Trypsin Cleavage and Gel-Filtration Results in six expected products, sequenced in emergence order from column: - **T-1:** ETMESSAGEFGR - **T-2:** SQTWALDHSECR - **T-3:** GPQDNK - **T-4:** TCR - **T-5:** NP - **T-6:** R ### e) Staph. aureus V8 Protease Cleavage and Gel-Filtration Results in seven expected products, sequenced in emergence order from column: - **S-1:** RSQTWALD - **S-2:** FGRPQGD - **S-3:** NKTCRNP - **S-4:** SSAGE - **S-5:** TME - **S-6:** CRE - **S-7:** HSE ### Think About It: 1. Deduce the primary structure of this polypeptide. 2.
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