Biological Science, Loose-leaf Edition (7th Edition)
7th Edition
ISBN: 9780135272800
Author: Scott Freeman, Kim Quillin, Lizabeth Allison, Michael Black, Greg Podgorski, Emily Taylor, 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 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.
Consider the hypothetical serine protease in the image, which shows the specificity pockets. The S1 pocket is small and hydrophobic, the S2
pocket is deep and hydrophobic, and the S1' pocket has an aspartate residue in the bottom. If the amino acids involved are K, W, and G,
which pair is joined by the peptide bond that will be cleaved by the protease? MAKE SURE YOUR CHOICE REFLECTS THE S1-S ORDER
DESCRIBED.
S1
Rs
R1
Ri
H.
S2
S
OGK
OKAN
OwG
IZ
IZ
Many 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)?
Chapter 3 Solutions
Biological Science, Loose-leaf Edition (7th Edition)
Ch. 3 - 1. What two functional groups are bound to the...Ch. 3 - What type of information is used to direct...Ch. 3 - Prob. 5TYUCh. 3 - Prob. 6TYUCh. 3 - 7. Why are proteins not considered to be a good...Ch. 3 - Prob. 9TYPSSCh. 3 - Prob. 12PIATCh. 3 - Prob. 13PIATCh. 3 - Recall that proline often introduces kinks in the...Ch. 3 - SOCIETY Based on the experiment in question 15,...
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- Imagine a globular protein with a histidine that is involved in a salt bridge to an aspartic acid, in an internal (hydrophobic) region of the protein. What would happen to the pKa of that histidine R group if the protein was mutated, and the aspartic acid was replaced with an alanine? (i.e., would the pKa increase, decrease, or stay the same?). Assume that the location of the histidine stays the same. Explain your answer clearlyarrow_forwardMost animals cannot use wool for nourishment. An exception is the clothes moth: it can derive nourishment from eating clothing made of natural fibers such as wool (which is rich in a-keratin). The digestive tract of the larvae of clothes moths provides a highly reducing environment. Why is this beneficial to the larvae? The reducing environment will reduce the disulfide linkages, making it easier to digest the proteins. The reducing environment will hydrolyze the peptide bonds. The reducing environment will interfere with the H-bonding between the tropocollagen molecules, making the type of protein found in most natural fibres easier to digest. The reducing environment will help to kill bacterial pathogens. The reducing environment will detoxify the carcinogenic dyes used in the textile industry.arrow_forwardConsider 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)arrow_forward
- I'm conducting an experiment concerned with the binding affinity of tretinoin (all trans retinoic acid) and beta lactoglobulin. This can be accomplished by monitorization of fluorescence quenching of a tryptophanyl residue that resides in a hydrophobic pocket known as a calyx inside the protein. Generally, fluorescence quenching is classified as static or dynamic. Would fluorescence quenching be a result of amide bond formation to tryptophan from tretinoin or through another mechanism (ie FRET: Forester resonance energy transfer)? Could it be both?arrow_forwardTwo proteins are discovered, and both are shown to have a potential in treating fatty liver disease. The structural differences of the proteins require them to be delivered using spherical nanoparticles made of different polymers. The scientists are trying to decide which protein will be more efficient to use in applications where a faster drug release is more favorable. Protein 1 is loaded into spherical nanoparticles made of polymer 1 which has R=100 nm at a concentration of 50 nM. Protein 2 is loaded into spherical nanoparticles made of polymer 2 which has R=250 nm, at a concentration of 50 nM. The partition coefficient of polymer 1 is 0.01 and is known to be half of partition coefficient of polymer 2. The diffusion coefficient of protein 1 in polymer 1 is 2x10-6 cm2/s, and diffusion coefficient of protein 2 in polymer 2 is 3.4x10-6 cm2/s. Determine which treatment will be selected for treatment of fatty liver disease.arrow_forwardConsider the hypothetical serine protease in the image, which shows the specificity pockets. The S1 pocket has a glutamic acid in the bottom, the S2 pocket is small and hydrophobic, and the S1' pocket is deep and hydrophobic. Suggest a 3-amino acid sequence that this protease would cleave and indicate between which sites the peptide bond would be broken. S2 Which sequence would this protease cleave? O Leu-Val-Arg Arg-Val-Leu Val-Leu-Arg Val-Arg-Leu O Leu-Arg-Val O Arg-Leu-Val W Ma étv N 894arrow_forward
- Remembering that the amino acid side chains projecting from each polypeptide backbone in a β sheet point alternately above and below the plane of the sheet, consider the following protein sequence: Leu-Lys-Val-Asp-Ile-Ser-Leu-Arg- Leu-Lys-Ile-Arg-Phe-Glu. Do you find anything remarkable about the arrangement of the amino acids in this sequence when incorporated into a β sheet? Can you make any predictions as to how the β sheet might be arranged in a protein?arrow_forwardTo 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_forwardOrnithine is structurally similar to lysine except ornithine’s side chain is one methylene group shorter than that of lysine. Attempts to chemically synthesize and isolate ornithinyl-tRNA proved unsuccessful. Propose a mechanistic explanation. (Hint: Six-membered rings are more stable than sevenmembered rings.)arrow_forward
- Some types of tumors express cell-surface receptors that are specific for unique peptide sequences. Development of modified peptides that target cancerous cells specifically is an area of active research. One peptide that has been studied extensively is luteinizing hormone-releasing hormone. A portion of the peptide sequence is: HWSYKLRPG. a. Of the nine amino acid sidechains in HWSYKLRPG, how many carry a positive charge at pH 4? at pH 7.4? at pH 11? b. What is the net charge on the peptide HWSYKLRPG at pH 7? c. (optional) For extra practice, draw the structure of HWSYKLRPG in its predominant form at pH 7.4.arrow_forwardA tridecapeptide yields the following fragments when partially hydrolized. Determine the sequence of amino acids in the tridecapeptidedrolyzed. Determine the sequence of the tri decapeptide. tridecapeptide à lys-arg + gly-phe-pro + phe-ser-asp-lys + pro-phe-ser + asp-lys-arg-val + gln-ala-tyr + val-trp-gln. Determine the sequence of amino acids in the tridecapeptidearrow_forwardWild-type E. coli cells can synthesize all 20 common amino acids, but some mutants, called amino acid auxotrophs, are unable to synthesize a specific amino acid and require its addition to the culture medium for optimal growth. Besides their role in protein synthesis, some amino acids are also precursors for other nitrogenous cell products. Consider the three amino acid auxotrophs that are unable to synthesize glycine, glutamine, and aspartate, respectively. Match each nitrogenous product with the mutant or mutants that would fail to synthesize it. Each mutant may fail to synthesize more than one nitrogenous product, and some nitrogenous products may fail to be synthesized by more than one mutant. glycine auxotrophs glutamine auxotrophs aspartate auxotrophs Answer Bank adenine nucleotides cytosine nucleotides guanine nucleotides uridine nucleotidesarrow_forward
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