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A protein with a molecular weight of about 12,000 Da was isolated in elevated quantities from cells undergoing apoptosis. Researchers want to know what this protein is. It was easily purified and then was exposed to fragmentation with proteases and cyanogen bromide. The resulting pep- tides were separated on a C18 column on HPLC and then sequenced using Edman degradation. First, remind yourself of how these peptide sequences were sequenced by briefly describing how Edman degradation works. Next, examine the peptide lists that result from proteolysis (or fragmentation) of the unknown protein in handouts B through E. Use the peptide lists to compile the sequence of the protein. Your instructor may ask you to use two specific lists, three specific lists, or all of the lists. If/when you have access to the Internet, submit your final sequence to a database to identify the protein. For example, submit your sequence at the protein BLAST site of the National Center for Biotechnology Information (NCBI) by going to nih.gov and searching for "Basic Local Alignment Search Tool." What is the protein? Now, put the peptides in order by placing each one's ordinal (1st #1, 2nd #2, etc.) in the far-left column preceding each peptide sequence.

A protein with a molecular weight of about 12,000 Da was isolated in elevated quantities from cells undergoing apoptosis. Researchers want to know what this protein is. It was easily purified and then was exposed to fragmentation with proteases and cyanogen bromide. The resulting pep- tides were separated on a C18 column on HPLC and then sequenced using Edman degradation. First, remind yourself of how these peptide sequences were sequenced by briefly describing how Edman degradation works. Next, examine the peptide lists that result from proteolysis (or fragmentation) of the unknown protein in handouts B through E. Use the peptide lists to compile the sequence of the protein. Your instructor may ask you to use two specific lists, three specific lists, or all of the lists. If/when you have access to the Internet, submit your final sequence to a database to identify the protein. For example, submit your sequence at the protein BLAST site of the National Center for Biotechnology Information (NCBI) by going to nih.gov and searching for "Basic Local Alignment Search Tool." What is the protein? Now, put the peptides in order by placing each one's ordinal (1st #1, 2nd #2, etc.) in the far-left column preceding each peptide sequence.

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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This is the study of Biochemistry. This is all that was provided alongside the question. Please complete with explanations to the best of your ability 

**Activity: De-Proteolyze This!** This exercise involves analyzing peptide sequences resulting from the enzymatic digestion of proteins by different proteolytic enzymes. The image contains sequences generated by the cleavage activity of these enzymes: ### Staphylococcal Peptidase I Peptides - E - YLE - MGDVE - DTLME - RADLIAYLKATNE - KGKKIFIMKCSQCHTVE - NPKKYIPGTKMIFVGIKKKE - KGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIWGE ### Asp-N Endopeptidase Peptides - MGD - LIAYLKKATNE - TLMEYLENPKKYIPGTKMIFVGIKKKEERAD - VEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIWGED ### CNBr Peptides - M - GDVEGKKIFIM - EYLENPKKYIPGTKM - IFVGIKKEERADLIAYLKATNE - KCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIWGEDTLM ### Trypsin Peptides - K - K - K - K - K - E - HK - NK - GK - EER - GGK - ATNE - IFIMK - YIPGTK - MGDVEK - MIFVGIK - ADLIAYLK - CSQCHTVEK - TGPNLHGLFGR - TGQAPGYSYTAANK - GIIWGEDTLMEYLENPK Each section corresponds to the peptide fragments produced by one of the four enzymes: Staphylococcal peptidase I, Asp-N endopeptidase, CNBr (Cyanogen Bromide), and Trypsin. These sequences may help in understanding protein structure and the specificity of enzymatic cleavage sites.
Transcribed Image Text:**Activity: De-Proteolyze This!** This exercise involves analyzing peptide sequences resulting from the enzymatic digestion of proteins by different proteolytic enzymes. The image contains sequences generated by the cleavage activity of these enzymes: ### Staphylococcal Peptidase I Peptides - E - YLE - MGDVE - DTLME - RADLIAYLKATNE - KGKKIFIMKCSQCHTVE - NPKKYIPGTKMIFVGIKKKE - KGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIWGE ### Asp-N Endopeptidase Peptides - MGD - LIAYLKKATNE - TLMEYLENPKKYIPGTKMIFVGIKKKEERAD - VEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIWGED ### CNBr Peptides - M - GDVEGKKIFIM - EYLENPKKYIPGTKM - IFVGIKKEERADLIAYLKATNE - KCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIWGEDTLM ### Trypsin Peptides - K - K - K - K - K - E - HK - NK - GK - EER - GGK - ATNE - IFIMK - YIPGTK - MGDVEK - MIFVGIK - ADLIAYLK - CSQCHTVEK - TGPNLHGLFGR - TGQAPGYSYTAANK - GIIWGEDTLMEYLENPK Each section corresponds to the peptide fragments produced by one of the four enzymes: Staphylococcal peptidase I, Asp-N endopeptidase, CNBr (Cyanogen Bromide), and Trypsin. These sequences may help in understanding protein structure and the specificity of enzymatic cleavage sites.
### Protein Sequencing and Identification A protein with a molecular weight of about 12,000 Da was isolated in large quantities from cells undergoing apoptosis. Researchers aim to determine the identity of this protein. The protein was purified, fragmented with proteases and cyanogen bromide, and the resulting peptides were separated on a C18 column using HPLC. Sequencing was performed using Edman degradation. **Understanding Edman Degradation** Start by familiarizing yourself with how peptide sequences are analyzed using Edman degradation. ### Instructions for Sequence Compilation 1. **Examination of Peptide Lists:** - Review the peptide lists resulting from the proteolysis (fragmentation) of the unknown protein (refer to handouts B through E). - Use these lists to compile the protein sequence. Your instructor may specify whether to use two lists, three lists, or all available lists. 2. **Submitting Sequence for Identification:** - Once you have internet access, submit the compiled sequence to a protein database to identify it. - Example: Use the protein BLAST site at the National Center for Biotechnology Information (NCBI) by visiting nih.gov and searching for the "Basic Local Alignment Search Tool." - **Goal:** Identify the protein. ### Organizing Peptides Arrange the peptides by their ordinal positions (e.g., 1st #1, 2nd #2, etc.) in the column preceding each peptide sequence. This process will help you systematically piece together and identify the unknown protein.
Transcribed Image Text:### Protein Sequencing and Identification A protein with a molecular weight of about 12,000 Da was isolated in large quantities from cells undergoing apoptosis. Researchers aim to determine the identity of this protein. The protein was purified, fragmented with proteases and cyanogen bromide, and the resulting peptides were separated on a C18 column using HPLC. Sequencing was performed using Edman degradation. **Understanding Edman Degradation** Start by familiarizing yourself with how peptide sequences are analyzed using Edman degradation. ### Instructions for Sequence Compilation 1. **Examination of Peptide Lists:** - Review the peptide lists resulting from the proteolysis (fragmentation) of the unknown protein (refer to handouts B through E). - Use these lists to compile the protein sequence. Your instructor may specify whether to use two lists, three lists, or all available lists. 2. **Submitting Sequence for Identification:** - Once you have internet access, submit the compiled sequence to a protein database to identify it. - Example: Use the protein BLAST site at the National Center for Biotechnology Information (NCBI) by visiting nih.gov and searching for the "Basic Local Alignment Search Tool." - **Goal:** Identify the protein. ### Organizing Peptides Arrange the peptides by their ordinal positions (e.g., 1st #1, 2nd #2, etc.) in the column preceding each peptide sequence. This process will help you systematically piece together and identify the unknown protein.
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