Is the BSA a good stadard to use in the bradford assay?
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Is the BSA a good stadard to use in the bradford assay?
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- 4) A polypeptide is subjected to the following digestion procedures and the fragments were sequenced. What is the sequence of the original peptide? Cyanogen bromide Trypsin digestion Asp-lle-Lys-Gln-Met Lys-Phe-Ala-Met Tyr-Arg-Gly-Met Gln-Met-Lys Gly-Met-Asp-lle-Lys Phe-Ala-Met-Lys and Lys Tyr.Arg Sequence of original peptide:2. Given the data in the table, calculate the pl for the amino acid tyrosine. Amino Acid Glycine Alanine Valine Leucine Isoleucine Serine Threonine Methionine Phenylalanine Tryptophan Asparagine Glutamine Proline Cysteine Histidine Aspartic acid Glutamic acid Tyrosine Lysine Arginine pk₁ (-COOH) pK₂ (-NH3+) 2.34 2.34 2.32 2.36 2.36 2.21 2.63 2.28 1.83 2.83 2.02 2.17 1.99 1.71 1.82 2.09 2.19 2.20 2.18 2.17 9.60 9.69 9.62 9.60 9.60 9.15 10.43 9.21 9.13 9.39 8.80 9.13 10.60 10.78 9.17 9.82 9.67 9.11 8.95 9.04 PKR 8.33 6.00 3.86 4.25 10.07 10.79 12.484. Show exactly which peptide bonds you would expect trypsin to cleave if you set a digest with the sample below. H3N+Gly Y lle Yval YCys Giu Gin Ala (Ser Yal Pro Cys Asp Leu Arg (Lys Phe Tyr) Asn FCO0- Lys Thr Leu Y His Would you expect to form the same peptides in the trypsin digest if you pretreat this sample with reducing agent (for example DDT)? Explain
- 4. a. Give the full names of the amino acids in this peptide. НзN — CH—С-N—CH— С-N—CH—С—О ČH3 H ČH,OH H. CH2 -ОН b. Calculate the isoelectric point (pl) of a peptide with sequence SNARE. Show your work in a table, giving the pKa values of the ionizable groups, pH, and charges. Step marks are counted. Don't need to write “protonated" or “deprotonated".1. H3N a. Draw the peptide sequence, including stereochemistry (wedges and dashes) for Glu-Cys- Gly. The N-terminus is drawn for you as a starting point.2. Compare and contrast the biological roles of the following amino acids the following pairs of amino acids. Once you have documented these role state which member of the pair is most important and why (1-2 sentences) Pair #1 Ketogenic, glucogenic or both Prevalence in peptides and proteins Role in biosynthesis Role in homeostasis (e.g. ammonia) Aspartic acid Glutamic acid Important in which pathways Pair #2 Arginine Histidine Ketogenic, glucogenic or both Prevalence in peptides and proteins Role in biosynthesis Role in homeostasis (e.g. ammonia) Pair #3 Ketogenic, glucogenic or both Prevalence in peptides and proteins Role in biosynthesis Role in homeostasis (e.g. ammonia) Important in which pathways Tyrosine Phenylalanine
- 1. Using an arrow, draw the site of cleavagr for the following peptides that are reacted by: Pepsin (a- b), trypsin (c-d), and chymotrypsin (e). H H H H H NH2 а. PEPTIDE VPQFAGI H H HN, H b. PEPTIDE DLIPAE .....5. The amino acid sequences of three peptide fragments are shown below. Peptide 1: QAMGRAGDLKYLGLHSV Peptide 2: ALMALFMVMALVLVSVLFIA Peptide 3: MVEDLLKQIARYLISE (a) Circle all of the charged residues in peptide 1 (assume pH = 7.0). Box all of the aromatic residues in peptide 2. Underline all of the nonpolar residues in peptide 3. (b) Determine the net charge of the predominant form of each of the peptides at pH 4.5 and pH 11.5. Assume the ionizable groups have the pKa values listed in Table 2.1 of your text. (c) Which of these peptides would be most likely to be found as an a helix in a soluble (cytoplasmic) protein? Which would be most likely to be found as an a helix in a transmembrane protein? Which would be least likely to form an a helix of any kind? Briefly explain your answers.What is the difference between a peptide and a protein? 2. What type of bond is the peptide bond? Explain why the peptide bond is rigid. 3. The pentapeptide Gln-Tyr-Asn-Ala-Asp is present in human cerebrospinal fluid, and its concentration increases in demyelinating diseases. In these diseases, the myelin sheath of nerves is damaged and impairs the conduction of nerve signals. a. What is the N-terminal amino acid? b. What is the C-terminal amino acid? c. How many peptide bonds does this pentapeptide contain? From how many amino acids is this pentapeptide derived? d. Write the structure, the three-letter designation and the IUPAC name of this pentapeptide.
- 2. Estimate the pl of a Peptide. Estimate the pl for the following peptide: EHSLRGGA 3. Estimate the pl of a Peptide. Estimate the pl for the following peptide: GKAHHWEA6a. Using your 5 mg/mL stock solution, you wish to make 100µL of the correct concentration of protein to load. How do you make this working solution? (Yes- you would want this to be in 1x sample buffer, but that makes this question more complicated. So for this question just make the protein in water.) Volume of 10mg/ml Final Volume ! 1 100μL of protein 6b. This is a 1: A N Body* @ 2 W S dilution. #3 X E D $ 4 A C R F B I % 5 T V MacBook Pro U וכ H E U 8 N J ( 010. A new protein of unknown structure has been purified. Gel filtration chromatography reveals that the physiological protein has a molecular weight of 240,000 Daltons. Chromatography in the presence of 6 M urea yields a single peak corresponding to a protein of 60,000 Daltons. Chromatography in the presence of 6 M urea and 10 mM mercaptoethanol yields peaks for proteins of 34,000 Daltons and 26,000 Daltons. What can we learn about protein's tertiary and quaternary structure from this data?
