TABLE 5.1 Properties of the common amino acids found in proteinspKa of lonizing Residue Mass OccurrencepKa ofa-COOH Group a-NH3 GrouppKa ofAbbreviations 1-and 3-letter codesName"Side Chaina(daltons)in Proteins (mol %)AlanineA, Ala2.39.771.088.7ArginineR, Arg2.29.012.5156.205.0.AsparagineN, Asn2.08.8114.114.2Aspartic acidD, Asp2.19.83.9115.095.9CysteineC, Cys1.810.88.3103.141.3GlutamineQ, Gln2.29.1128.143.7Glutamic acidE, Glu2.29.74.2129.126.6GlycineG, Gly2.39.657.067.9|HistidineН, His1.89.26.0137.152.4IsoleucineI, lle2.49.7113.175.5LeucineL, Leu2.49.6113.178.9|LysineK, Lys2.29.010.0128.185.5MethionineМ, Met2.39.2131.212.0PhenylalanineF, Phe1.89.1147.184.0ProlineP, Pro2.010.697.124.7SerineS, Ser2.29.287.085.8T, ThrW, TrpY, TyrThreonine2.610.4101.115.6Tryptophan2.49.4186.211.5Tyrosine2.29.110.1163.183.5ValineV, Val2.39.699.147.2|Approximate valuoc found for gid 4) Using the pk, data found in the supplied chart, determine the predominant charge of each aminoacid at pH 1.0, 6.0 and 12.5Arginine1.06.012.5

Amino acid is amphoteric in nature i.e it can act as both acid as well as . This property is due…

Answered: 4) Using the pK, data found in the…

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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TABLE 3-1 Properties and Conventions Associated with the Amino Acids pk, values Amino acid Phenylalanine Tyrosine Tryptophan 5.66 5.48 9.59 5.89 Abbreviation/ symbol 6.14 Phe F Tyr Y Trp W pk, M, (-COOH) 165 181 204 . 1.83 2.20 2.38 Using the table 3-1, calculate the pl of Tyrosine. Hint: Consider the structure and overall charge of the molecule between each pka. pK₂2 (-NH) 9.13 9.11 9.39 PKR (R group) 10.07
0ミレーNレ NH geometry on both cand N. Torigonal plannes CH - C-N o=), HN CH2 CH-C-OH (a- carbon) CH2 HooC Aspaxagine - Toline - Valine - Arginine - phenylalcmine - Glutamic ocid. 1.Give the name and three letter code for each amino acid in the peptide. e 2. At pH 7, approximately what charge would be on your peptide? Explain your answer. 3. Can your peptide form intra/interchain disulfide bonds? Explain why/why not. e 4. Will your peptide absorb UV and is it fluorescent? Explain why/why not. e 5. What is the probability that your peptide contains a cis peptide bond? Explain your answer.
1. The amino acid sequence for the protein lysozyme is given below. Estimate the isoelectric point for lysozyme protein. The pK, values are provided in Table 3.1. KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNT DGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKK IVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL Here's the sequence in this form: LYS VAL PHE GLY ARG CYS GLU LEU ALA ALA ALA MET LYS ARG HIS GLY Table 3.1 Typical pk, values of ionizable groups in proteins Group Acid Typical pK, Base Terminal a-carboxyl 3.1 group Aspartic acid Glutamic acid 4.1 N. Histidine 6.0 -N + H Terminal a-amino group 8.0 Cysteine 8.3 Тутosine 10.9 + H Lysine 10.8 H H. + N-H Arginine 12.5 N-H N-H Note: Values of pk, depend on temperature, ionic strength, and the microenvironment of the ionizable group. in
NAZO NHZ Ala-Cys-Glu -Tyr - Trp - Lys - Arg - His -Pro-G ly Glu pka 4.15 SH Tyr 10.10 Draw Charges Lys 10.67 Olt A3 12.10 +NH₂ Ntrm 2) Calculate net charge 3) write out I letter code 300 Ctim 3 juli of peptich (above) Ⓒ pH; 1,7,12
Based on the pK, table for amino acids (Table 1.1), draw the structures with net charge, and the equilibria representing the complete deprotonation of aspartate. Table 1.1 Name pK pk2 pKR Glycine Alanine 2.4 9.8 2.3 9.7 Valine 2.3 2.4 9.6 Leucine 9.6 Isoleucine 2.4 9.7 Methionine 2.3 9.2 Phenylalanine Proline Serine 1.8 9.1 2.0 10.6 2.1 9.2 Threonine 2.6 10.4 Cysteine Asparagine Glutamine 1.8 10.8 8.3 2.0 8.8 2.2 9.1 Tyrosine Tryptophan Aspartate Glutamate 2.2 9.1 10.9 2.4 9.4 2.0 2.2 10.0 3.9 9.7 4.3 Histidine 1.8 9.2 6.0 10.8 Lysine Arginine 2.2 9.2 1.8 9.0 12.5
1.Ala-Phe-Lys-Val-Val-Glu From the above polypeptide, what amino acid/s go/goes inside the cell after the following treatment: Chemotrypsin, thermolysin, then finally pepsin. What protein is left undigested? Write the primary structure of the undigested protein? 2.K-V-F-W-P-L-A-Y a.Chemotrypsin treatment b.Trypsin treatment c.Pepsin treatment d.Thermolysin treatment 3.Total acid hydrolysis of a pentapeptide complemented by total alkalinehydrolysis yields an equimolar mixture of 5 amino acids listed alphabetically, ala-cys,lys,phe,ser. N-terminal analysis with phenylisothiocyanate (PITC) generate PTH-ser. Trypsin digestion produces a tripeptide where N-terminal residue is cys and a dipeptide with ser as its N- terminal.Chemotrypsin digestion of the above tripeptide yields ala plus another dipeptide. A.What is the amino acid sequence of the tripeptide B.What is the amino acid sequence of the dipeptide derived from trypsin digestion? C.What is the primary structure of the original…
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
29. Amino Acid Chemistry: Using the amino acid chart provided..Ala-Lys-Cys & give the isoelectric point for the tripeptide. Table 23.2 The pK, Values of Amino Acids pk, a-COOH a-NH3* Amino acid side chain Alanine 2.34 9.69 2.17 9.04 12.48 Arginine Asparagine 2.02 8.84 3.86 Aspartic acid Cysteine 2.09 9.82 1.92 10.46 8.35 Glutamic acid 2.19 9.67 4.25 Glutamine 2.17 9.13 Glycine 2.34 9.60 1.82 9.17 6.04 Histidine 2.36 9.68 Isoleucine Leucine 2.36 9.60 2.18 $ 95 10.79 Lysine 2.28 9.21 Methionine 16 9.18 Phenylalanine 1.99 10.60 Proline 2.21 9.15 Serine 2.63 9.10 Threonine 2.38 9.39 Tryptophan Tyrosine 9.11 10.07 2.20 2.32 9.62 Valine O something else! 5.14 O 8.65 something else! 5.81 9.02 9.57
Indicate which of the amino acid residues in the following peptide sequence contains a group that has a positive charge for its most likely charge state at pH 10. Asp-Tyr-Lys-GIn-Thr-Ile-Phe-Met-Ser (If none of the amino acids fit the criterion, select "none".) Asp Tyr ооооооооо Lys Gln Thr lle Phe Met Ser none
A mixture of Aspartic Acid (pl 2.98), Histidine (pl 7.59), Lysine (pl 9.74), Phenylalanine (pl 5.48) and Threonine (pl 6.53) are separated by cation exchange chromatography. What is the order of elution of these amino acids if you use gradient buffer system from pH 10 to pH 2. v First 1. Aspartic Acid v Second 2. Histidine v Third 3. Lysine 4. Phenylalanine v Fourth 5. Threonine v Fifth 6. No separation
. The following diagram shows the biosynthesis of B12 coenzymes, starting with the vitamin. DMB is dimethylbenzimidazole. (a) What one additional substrate or cofactor is required by enzyme B? (b) Genetic deficiency in animals of enzyme C would result in exces- sive urinary excretion of what compound?
N- HO sta on e yor current pH the peptide? Explain your yor a) Based the charge state shown, what is a possible vahe amswer wsi'ng 2-3 sentences. Show the qull pH ramge yor this protonation otate 6) Hypo thesize a oingle amino acid substitution Cmutation) that wonld make Your amswer must include the which residue this lic You. peptide more hydrophi you would mutate and what new re sidue would take its place Include a 1 sentence explanation g your reasoning your

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4) Using the pK, data found in the supplied chart, determine the predominant charge of each amino acid at pH 1.0, 6.0 and 12.5 Arginine 1.0 6.0 12.5