Consider a protein with a beta conformation sequence EAGQVHRGP a) Which residue(s) can be substituted by N without affecting the conformation? b) Which residue(s) can be substituted by D without affecting the conformation? c) Which residue(s) cannot be substituted without affecting the conformation?
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Chemistry
Consider a protein with a beta conformation sequence EAGQVHRGP a) Which residue(s) can be substituted by N without affecting the conformation? b) Which residue(s) can be substituted by D without affecting the conformation? c) Which residue(s) cannot be substituted without affecting the conformation?
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- E. PROTEIN PRIMARY STRUCTURE ELUCIDATION. 1. Determine the primary structure of the protein described below. Write the final sequence using the corresponding three-letter code for each amino acid. Example: M-F-Y-R should be written as Met-Phe-Tyr-Arg Treatment with cyanogen bromide and sequencing yields the following peptide fragments: o D-M o R-A-Y-G-N o L-F-M Chymotrypsin digestion and sequencing yields the following peptide fragments: o G-N D-M-L-F o M-R-A-Y o o01 Description Please draw the structure of the 19 L-a-amino acids and proline in any form, as you prefer. You may want to use a letter-size sheet or larger, it's up to you. Guiding principle: You want to understand the differences among amino acids. Although you may want to only draw the R-group it's preferable to draw it along with the rest of the molecule (i.e., the Ca, the amino group and the carboxyl group). Here are some examples (your drawings should not limited to the following styles): NH₂ OH Alanine H H O OH Proline lysine alarmy stock płwłos Tryptophan OH COOH | H₂N-C-H CH₂ Phenylalanine arginineGTTTTCACTGGCGAGCGTCATCTTCCTACT 10. Generate a secondary structure prediction for one identified protein.
- Chymotrypsin digestion, separation of peptides, and Edmann technique give the sequences for peptide fragments as follows: C-1 G-A-E-A-T-E C-2 G-K-V-G-A-H-A-G-E-Y C-3 V-L-S-P-A-K-T-N-V-K-A-A-W What is the sequence for the peptide? NOTE: Label the fragments when reconstructing the peptide chain e.g. for trypsin T-1, T-2 etc...GT 3 A. Write the structure of the pentapeptide GLDSC. B. What is the complete name of this pentapeptide? Show a tertiary structure of ACGGC after a disulfide bond forms. A sample of an unknown peptide was divided into two aliquots. One aliquot was treated with trypsin; the other was treated with cyanogen bromide. Given the following sequences (N-terminal to C- terminal) of the resulting fragments, deduce the sequence of the original peptide. Trypsin treatment Asn-Thr-Trp-Met-lle-Lys Gly-Tyr-Met-Gln-Phe Val-Leu-Gly-Met-Ser-Arg Cyanogen bromide treatment Gln-Phe Val-Leu-Gly-Met lle-Lys-Gly-Tyr-Met Ser-Arg-Asn-Thr-Trp-Met11. Below is a folding energy funnel describing folding energy landscape of a protein. The width of the funnel indicates the entropy of the protein, and the height corresponds to the free energy. A) If A is the native fold structure, which state is a molten globule? How does this state differ from A in term of structures. B) Does this protein have multiple folding pathways or just one? C) which state has the lowest free energy? D) According to the width of the funnel, the native state B of the protein has the lowest entropy. If the protein fold A spontaneously to this state, does it violate the 2nd law of thermodynamics? Why or why not? (Hint: in the folding funnel, only the entropy of the protein alone is considered). E) Does the native state also have the lowest enthalpy. What makes the enthalpy decrease as the protein folds? 12. List four methods by which a protein can be denatured and briefly describe how these methods act to disrupt protein structure.
- Two peptide segments are shown below. Predict which one would have the most negative AG when going from an unfolded to a folded structure. Justify your choice. (i) Gly-Ala-Asn-lle-Val-Trp-Leu-Glu-Met-Phe-Val-Pro OR (ii) Ala-Gly-Lys-lle-Arg-Tyr-Thr-Cys-Val-Glu-Met-SerLoop regions play important roles in the secondary structure of protein. Define loop region and give three (3) of the rolesAmino acids have the generic structure seen below, where R represents different carbon-based side chains. Describe how the structure of amino acids allows them to be linked into long peptide chains to form proteins.
- Predict the protein 3° structure of the following protein sequence. Provide detail from 2° structure principles Nterm – SLDVTFSPGAEITFKWNPGSFNSLKDTIRQVTDK – Cterm8. Multiple choice. Which of the following is not a method that can be used to determine the 3° structure of proteins? (2 pts) a) Protein X-ray crystallography b)) Circular dichroism c) Cryogenic electron microscopy d) Protein NMR 9. Multiple choice. Approximately what overall yield can you expect from the solid phase peptide synthesis (SPPS) of a "10-mer" (a 10 amino acid peptide), if the yield from each step is 85%? (2 pts) 23% b) 20% c) 85% d) 71% 10. Multiple choice. Which protein purification method is best for an experiment in which you want to purify a monomeric form of a protein away from a tetrameric form? (2 ptrs) (-His a) Affinity chromatography S b) High pressure liquid chromatography c) lon exchange chrommatography d) Size exclusion chromatography 2. I1. Short answer. What is the Edman degradation experiment useful for? (3 pts) purdinate an for prry structers steps .GT 3 A. Write the structure of the pentapeptide GLDSC. B. What is the complete name of this pentapeptide? 1. Show a tertiary structure of ACGGC after a disulfide bond forms. A sample of an unknown peptide was divided into two aliquots. One aliquot was treated with trypsin; the other was treated with cyanogen bromide. Given the following sequences (N-terminal to C-terminal) of the resulting fragments, deduce the sequence of the original peptide. 2. 3. Trypsin treatment Asn-Thr-Trp-Met-lle-Lys Gly-Tyr-Met-GIn-Phe Val-Leu-Gly-Met-Ser-Arg Cyanogen bromide treatment Gln-Phe Val-Leu-Gly-Met lle-Lys-Gly-Tyr-Met Ser-Arg-Asn-Thr-Trp-Met