Biological Science (6th Edition)
6th Edition
ISBN: 9780321976499
Author: Scott Freeman, Kim Quillin, Lizabeth Allison, Michael Black, Emily Taylor, Greg Podgorski, Jeff Carmichael
Publisher: PEARSON
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Chapter 3, Problem 14PIAT
Recall that proline often introduces kinks in the backbone of a polypeptide. These kinks make it difficult for enzymes in your gut to fully digest gluten. In people with celiac disease, certain proline-rich peptides left over after gluten digestion will trigger an abnormal immune response. Researchers have identified a mold enzyme called AN-PEP that effectively digests proline-rich peptides. Predict where the structural differences would occur between AN-PEP and other enzymes that do not digest the peptides.
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Consider the following peptide to answer the questions below:
A M A K K E S H I F T A I D E
What is the total charge of this peptide at pH = 5?
What is the N terminal amino acid (full name)? C terminal amino acid?
How many fragments would result if this peptide underwent proteolytic cleavage with V-8 protease and what are these fragments (list them)?
Would this peptide be a candidate to form an alpha helix? Why or why not
Once the chains of peptides that make up lysyl-tRNA synthetase protein are synthesized in ribosomes, lysyl-tRNA synthetase needs to have the proper active site in order to perform its function, explain the process of protein folding necessary to have a proper 3-D structure, include effect of thermodynamics and different states in folding, including what happen when there are prolines that form peptide bonds with other amino acids, and any disulfide bridges
Consider a short peptide that forms an alpha-helix within a larger protein structure. Suppose that one glutamate residue at some specific position in the helix were mutated to a leucine residue. The mutation could either make the helix more stable, or less stable.
i) Describe two situations in which a Glu-to-Leu mutation could make the helix more stable.
ii) Describe two situations in which the Glu-to-Leu mutation could make the helix less stable.
Explain briefly the basis for the stabilizing and destabilizing effect in all cases.
Chapter 3 Solutions
Biological Science (6th Edition)
Ch. 3 - 1. What two functional groups are bound to the...Ch. 3 - 2. What type of bond is directly involved in the...Ch. 3 - What type of information is used to direct...Ch. 3 - 4. What is an active site?
a. the location in an...Ch. 3 - Prob. 5TYUCh. 3 - Prob. 6TYUCh. 3 - 7. Why are proteins not considered to be a good...Ch. 3 - Prob. 8TYUCh. 3 - Prob. 9TYPSSCh. 3 - 10. Make a concept map (see BioSkills 12) that...
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- Considering the chemical characteristics of the amino acids valine and glutamic acid (see Figure 5.14), propose a possible explanation for the dramatic effect on protein function that occurs when valine is substituted for glutamic acid.arrow_forwardPeptides and small proteins fold spontaneously in aqueous solution at room temperature. Thus, for a small protein in water, we can say ΔG FOLD < 0. Denoting the unfolded protein as Unf and the folded protein as Fld, we can write the following equation:Unf(aq)--DELTA G FOLD----> Fld(aq)Considering the transition from the unfolded state (in which there are many possible conformations) to the folded state (only one conformation), there is clearly a decrease in the entropy of the protein. However, protein folding is (correctly) described as an entropically driven process.a) Resolve this apparent paradox by identifying the enthalpy (ΔH) and entropy (−TΔS)components involved in protein…arrow_forwardGene editing is also used to explore the structure and function ofproteins. For example, changes can be made to the coding sequenceof a gene to determine how alterations in the amino acid sequenceaffect the function of a protein. Let’s suppose that you areinterested in the functional importance of a particular glutamicacid (an amino acid) within a protein you are studying. By geneediting, you make mutant proteins in which the glutamic acidcodon has been changed to other codons. You then test the encodedmutant proteins for functionality. The results are as follows: FunctionalityNormal protein 100%Mutant proteins containingTyrosine 5%Phenylalanine 3%Aspartic acid 94%Glycine 4%From these results, what would you conclude about the…arrow_forward
- Treatment of a polypeptide by 2-mercaptoethanol yields two polypeptides that have the following amino acid sequences: Ala-Phe-Cys-Met-Tyr-Cys-Leu-Trp-Cys-Asn Val-Cys-Trp-Val-Ile-Phe-Gly-Cys-Lys Chymotrypsin-catalyzed hydrolysis of the intact polypeptide yields polypeptide fragments with the following amino acid compositions: (Ala, Phe) (Asn, Cys2, Met,Tyr) (Cys, Gly, Lys) (Cys2, Leu,Trp2,Val) (Ile, Phe,Val) Indicate the positions of the disulfide bonds in the original polypeptide.arrow_forwardTreatment of a polypeptide by 2-mercaptoethanol yields two polypeptides that have the following amino acid sequences: Ala-Phe-Cys-Met-Tyr-Cys-Leu-Trp-Cys-Asn Val-Cys-Trp-Val-Ile-Phe-Gly-Cys-Lys Chymotrypsin-catalyzed hydrolysis of the intact polypeptide yields polypeptide fragments with the following amino acid compositions: (Ala, Phe) (Asn, Cys2, Met,Tyr) (Cys, Gly, Lys) (Cys2, Leu,Trp2,Val) (Ile, Phe,Val) Indicate the positions of the disulfide bonds in the original polypeptide. I don't understand how the order of amino acids in Step 2 was arranged. Please explain. Thank you.arrow_forwardHere is a putative peptide sequence (position number on top of residues): 1 2 3 4 5 6 7 8 9 10 11 12 13 NH2- G C G N V T H N Q C V L S -COOH If expressed in a eukaryotic cell (please mark your answer in the blank space): Position(s) ___ could be N-glycosylated Position(s) ___ could be modified with myristic acid and the bond formed would be a ______________ Position(s) ______and _____ could be modified with palmiti c acid and the bond formed would be a ______________ Positio n(s) ________ could be a segment of a lipid-linked protein with a farnesyl anchor and the bond formed would be a ______________ Position(s) ________ could be a segment of an O-glycosylated protein Position(s) ________ could be modified with a glycosylphosphatidylinositol (GPI) anchor Position(s) ________ could be phosphorylatedarrow_forward
- To better understand the effects of palmitoylation on protein X, researchers want to chemically attach a palmitic acid at a specific position in this protein. The researchers first try to feed cells with palmitic acid or an amino acid with a C16 side chain. Neither of the initial experiments is successful in helping the researchers learn more about the biological role of palmitoylated protein X. Why? Suggest a strategy to specifically incorporate a palmitoylation site into protein X.arrow_forward. Give two reasons to explain why a proline residue in the middle of an ahelix is predicted to be destabilizing to the helical structurearrow_forwardMany blood clotting proteins undergo a post-translational modification in which specific glutamic acid residues (Glu) in the protein are converted to gamma-carboxyglutamic acid residues (Gla). See reaction scheme below. An example is the blood clotting protein Factor IX, which has 12 Glu in its N-terminus converted to Gla. This modification gives Factor IX the ability to bind calcium and phospholipid membranes. Bacteria do not have the enzyme required to convert Glu to Gla and therefore Factor IX proteins expressed in bacteria would not have the proper modifications. How might you engineer the translational apparatus of a bacterial cell line so that it produces Factor IX with Gla in the appropriate positions. How would you ensure that only the 12 Glu in Factor IX that are normally converted to Gla and not just all Glu (Limit 5-6 senetnces)?arrow_forward
- Propose an experimental strategy to characterize the sequence and linkages of different glycan subtypes that comprise the glycome. For example, how might protein-associated N- and O-glycans be structurally characterized?arrow_forwardConsider a mutation that results in a substitution of Cysteine (CYS) ) for Tyrosine (TYR) at position 368. What are the properties of the substituted amino acid, CYS? Does it have any special properties?arrow_forwardWhy would the mutation Ile -> Asp be likely to destabilize a protein? Why would the mutation Ile ->Val be likely to destabilize a protein? Why would the mutation Val -> Ile be likely to destabilize a protein?arrow_forward
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