9. The T conformation of the hemoglobin tetramer is stabilized (in part) by a salt linkage between the side chain of the lysine residue at position 40 in the a-chain of one aß dimer and the C-terminal carboxylate group of the ß-chain of the opposing aß dimer. Draw a diagram of this salt linkage (show complete side chains).
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- 2. The diagram to the right shows the change in the structure of the C-terminal portion of each of the ẞ-subu- nits of human hemoglobin (HbA) in the oxyHb to deox- yHb or R-to-T transition. The hydrogen bonding interac- tion of the C-terminal ẞHis 146 residue with the side chain of Asp94, highlighted by the red ellipse, has been shown to be responsible for a major portion of the proton uptake associated with the Bohr effect. Treatment of HbA with the enzyme carboxypeptidase A (CPA) results in loss of the C-terminal ẞHis 146 and ẞTyr145 residues of the ẞ- subunits. (a) ( ) Draw a Hill plot [log(Y/[1-Y]) vs. log(pO2), Y = fraction of heme groups occupied by O2] to compare the values of the Hill coefficient nн and the O2-binding affinity at pH 7.4 of normal HbA before and after treat- ment of with CPA. (b) (' ) How will the plot for CPA-digested HbA change at pH 7.2? (c) 1 Hi5146 HN- ✓ Low PK B-chain. CH2 CH-NH-CO-CH-NH- CH₂ Tyr145 он HbO2 or R state Туг145 CH-CH2- OH co NH CH CH₂ His…1. The human hemoglobin molecule, like all mammalian he- moglobins, is comprised of two a-chains and two ß-chains con- ₂ taining 141 and 146 amino acid residues, respectively. Be- cause the molecule possesses two-fold symmetry, there are a1-a2, B1-B2, and a1-B2 interfaces formed by amino acid sidechains through which structural changes are transmitted underlying ligand binding. The most important of these is the a1-B2 interface that is illustrated in the diagram on the right. All of the sidechain interactions across the a1-B2 interface are hydrophobic except for that between Asp(a94) and Asn- (B102). This is the only polar interaction across the α1-³2 in- terface and it helps to stabilize the oxy- or R-conformation. Its approximate location in the Hb molecule is represented by the red double arrow in the diagram on the right. His FG4 97 Asp G1 (99) Tyr C7 (42) Hb mutant (a) T State (deoxy) 95 The C6 41 (a) The diagram below on the right-hand side illustrates the polar Asp(a94). . . Asn…1. A pentapeptide has the sequence of H2N-Glu-His-Leu-Arg-Gly-COOH. a) What is the net charge of the peptide at pH 3, 8, and 11? (Use pka values for side chains and terminal amino and carboxyl groups in the table provided.) peptide. b) Estimate the pl for this pK, values Abbreviation/ symbol pk, M, (-COOH) (-NH5) (R group) pK; pKR Hydropathy Occurrence in index* proteins (%)* Amino acid pl Nonpolar, aliphatic R groups Glycine Alanine Proline Valine 2.34 -0.4 Gly G Ala A Pro P 75 9.60 5.97 7.2 89 115 2.34 9.69 10.96 6.01 6.48 5.97 1.8 1.6 4.2 3.8 4.5 7.8 5.2 1.99 117 131 Val V 2.32 2.36 9.62 9.60 6.6 9.1 Leucine Leu L 5.98 Isoleucine lle I 131 2.36 2.28 9.68 6.02 5.3 Methionine Met M 149 9.21 5.74 1.9 2.3 Aromatic R groups Phenylalanine Tyrosine Tryptophan 2.8 -1.3 3.9 3.2 Phe F 165 1.83 9.13 9.11 9.39 5.48 2.20 Tyr Y Trp W 181 10.07 5.66 204 2.38 5.89 -0.9 1.4 Polar, uncharged R groups Serine Ser S 105 2.21 6.8 9.15 9.62 5.68 5.87 5.07 5.41 5.65 -0.8 Threonine Thr T 119 2.11 -0.7 5.9…
- The following amino acids that are often found inside globulin molecules are () A, Tyr B, Phe C, Asn D, Glu True of false 1. In the de novo synthesis of purine nucleotides and pyrimidine nucleotides, base rings are first synthesized and then corresponding nucleotides are formed with phosphoribose. () 2. Transcription is the process of transferring genetic information from DNA to RNA. DNA is synthesized under the catalysis of RNA polymerase, and the direction of synthesis is from the 5 'end to the 3' end. () 3. The change of protein conformation is caused by the breaking of covalent bonds within the molecule. () 4. In very high and very low pH solutions, amino acids exist mainly in non-ionic form. () 5. The active center of an enzyme usually consists of several amino acid residues adjacent to each other in the primary structure. ()you have the following peptide Arg-Ile-Pro-Leu-Asp-Lys-Glu The net charge on this peptide at pH 7.0 is ?. The net charge on this peptide at 1M HCl is ?.1. At pH 7, draw the structure of Arg-Tyr-Gln-Glu-Lys. 2. What’s the charge of this peptide at pH 12? Explain.
- 1. Cysteine is an important amino acid that stabilizes the structure of peptides and proteins by the formation of disulfide bond with another cysteine residue. Illustrate the titrimetric profile of cysteine and calculate its isoelectric pH. [Hint: The sulfhydryl group is titratable] 2. The tripeptide Glu-Pro-Arg (EPR) which is a product of Lactobacillus casei fermentation of milk was found to have potent blood pressure lowering properties. Draw the structure of the tripeptide, give its systematic name, show its titration profile, and determine its isoelectric pH.1. Amino acid analysis of the peptide gave the following residues: Asp Leu Lys Met Phe Tyr. The following facts were observed: Trypsin treatment had no effect. The phenylthiohydantoin released by Edman degradation was C-C-CH2. Brief chymotrypsin treatment yielded several products including a dipeptide and a tetrapeptide. The tetrapeptide contained Leu, Lys and Met is some order. Cyanogen bromide treatment afforded a dipeptide, a tetrapeptide and a free Lys. What is the amino acid sequence for this heptapeptide?27. Draw palmitic acid, identify a, B and w carbons, write out its short hand notation 28. Examine the peptide sequence below and then answer the questions: H2N-Gly- Leu- Ala-Asp-Cys-Asn-Trp-lle-Ser-Phe-Lys-Cys-Arg-Pro-coOH a. Circle the asparagine residue b. A possible intramolecular disulfide bond can be formed within this peptide between which two residues? c. Circle one residue which has a positively charged side chain under pH 7.4 d. Circle one residue which has a negatively charged side chain under pH 7.4 e. Circle the residue which can be phosphorylated
- Given the peptide Val-Ser-Gln-Lys The lateral chain of one of these amino acids can be modified by N-acetylation. Write the semi‐developed form of the lateral chain of this modified amino acid at pH 7 The lateral chain of one of these amino acids can be modified by phosphorylation. Write the semi‐developed form of the lateral chain of this modified amino acid at pH 7.c) A lysine residue in the active site of UstD is involved in forming a covalent Schiff base linkage with the PLP cofactor. In order for this linkage to form, the lysine residue must be in its deprotonated form. Draw the structure of the R group of lysine in this neutral form. What is the ratio of the concentration of this form to that of its conjugate acid form at neutral pH? ( )Consider the peptide Asp-Lys-Phe-Glu-Asn-Tyr-Gln-Val-Cys. In a single beaker, you treat this peptide with 2 proteases. One protease cleaves at the N-terminus of aromatic R groups and the other cleaves at the C-terminus of polar, non-ionizable R groups. Following the enzymatic digestion, you want to separate your peptide fragments so that you can identify them. You choose to separate the fragments using an anion exchange column. Beginning at pH=6 you apply your peptide fragments to the column and you gradually decrease the pH of the column stopping the separation when the pH of the column equals 4. Omitting chemical structures, write the amino acid sequence of the peptide fragments that are produced from this digest. Write the order that these fragments will elute from the column (if at all). (Relevant pKa values are: 2.1, 3.8, 4.3, 8.3, 9.6, 10.1, and 10.5)