The enzyme thermolysin cleaves peptide bonds on the C-terminal side of the amino acids lle. Tyr, Phe, and Trp. If thermolysin acts on the sequence below: QRYKKSHTWDPNRKLFNRYLCMA which of the figures below shows the structure of the N-terminal residue of the longest fragment? NH3 OH NH2 HO NH3 NH `NH3 CH3 H3C NH3
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- A protein in its native three dimensional conformation is cleaved with trypsin. According to the amino acid sequence, there are 9 residues where trypsin could cleave, yet only 3 fragments were produced from the digest. What conclusion can be made about protein structure that would lead to this result? The protein has multiple domains b. The protein is highly compacted, minimally accessible by solvent molecules c. The protein has quaternary structure d. The protein has a dynamic structure, highly accessible by solvent molecules e. The protein is compromised only of alpha helicesWhich of the following characterize -helix regions of proteins? (A) They all have the same primary structure. (B) They are formed principally by hydrogen bonds between a carbonyl oxygen atom in one peptide bond and the amide hydrogen from a different peptide bond. (C) They are formed principally by hydrogen bonds between a carbonyl atom in one peptide bond and the hydrogen atoms on the side chain of another amino acid. (D) They are formed by hydrogen bonding between two adjacent amino acids in the primary sequence. (E) They require a high content of proline and glycineA peptide with the sequence isoleucine1-aspartate2-valine3-lysine4-proline5-glutamate6 is located at the surface of a protein. Which residues are likely oriented toward the interior of the protein and what is the most likely secondary structure that this peptide is in? a.) Residue numbers 2, 4, 6; alpha helix b.) Residue numbers 1, 3, 5; alpha helix c.) Residue numbers 1, 3, 5; beta sheet d.) Residue numbers 2, 4, 6; beta sheet
- I-D-E-L-Y-S-Q-V-C-S-H-L-D-T-V-R This amino acid sequence forms an alpha helix. When thinking about how the helix folds into its tertiary strucutre, use entropy and enthalpy to explain what would happen energetically.Which of the following characterize -helix regions of proteins? (A) They all have the same primary structure. (8) They are formed principally by hydrogen bonds between a carbonyl oxygen atom in one peptide bond and the amide hydrogen from a different peptide bond. (C) They are formed principally by hydrogen bonds between a carbonyl atom in one peptide bond and the hydrogen atoms on the side chain of another amino acid. (D) They are formed by hydrogen bonding between two adjacent amino acids in the primary sequence. (€) They require a high content of proline and glycineWhich of the following sequences is most likely to form an unstructured loop in a protein structure? A. GPGGGGGPGGG B. VEELLSKVKQLADA C. KVDFHVNDVEVKMH
- At neutral pH, which of the following amino acids has a net positive charge, which has a net negative charge, and which is neutral? (Hint: Draw the various charged forms of each amino acid before deciding.)(a) Aspartic acid (b) Histidine (c) ValineThe structure of an alpha helix orients the oxygens of the carbonyl group of the peptide bond towards the C-terminal end of the helix while the hydrogens of the NH groups orient toward the N-terminal end, thus imparting a dipole along the length of the helix. As a result, which kinds of amino acids would favor the C-terminal end, and which would favor the N-terminal end? negatively charged, positively charged positively charged, negatively charged negatively charged, hydrophobic positively charged, hydrophobic hydrophobic, negatively charged hydrophobic, positively chargedDraw the amino acids serine and threomine bonded together with a petide bond.
- A peptide has the following amino acid composition: 2 Met, 2 Phe, 2 Glu, 1 Arg, 1 Lys, 1 Val, 1 Leu, 1 Gly, 1 Ser Reaction of the intact peptide with dansyl chloride followed by acid hydrolysis creates a derivative of Met. A specific cleavage of the intact peptide produces fragments with the following sequences: Fragment A: Glu-Gly-Lys-Phe Fragment B: Met-Ser-Leu-Arg Fragment C: Met-Val-Glu-Phe Which reagent was used for the specific cleavage? Cyanogen bromide Carboxypeptidase A Trypsin ChymotrypsinA peptide has the following amino acid composition: 2 Met, 2 Phe, 2 Glu, 1 Arg, 1 Lys, 1 Val, 1 Leu, 1 Gly, 1 Ser Reaction of the intact peptide with dansyl chloride followed by acid hydrolysis creates a derivative of Met. A specific cleavage of the intact peptide produces fragments with the following sequences: Fragment A: Glu-Gly-Lys-Phe Fragment B: Met-Ser-Leu-Arg Fragment C: Met-Val-Glu-Phe What information do this result give about the sequence of the peptide? Explain how you arrived on you answer.4. Amino acids are linked together by peptide bonds to form polypeptides. (a) Draw the structure of a tripeptide (b) draw an asterisks (*) directly beside all alpha carbons and draw a square around all peptide bonds (c) Use arrows to identify and label the N-terminus and C-terminus (d) Draw a circle around the R group of each amino acid residue in the tripeptide and classify each R group as polar, non polar, acidic, or basic (e) Using the abbreviated names of the amino acids, provide the primary structure of the tripeptide you have drawn.