Biochemistry
6th Edition
ISBN: 9781305577206
Author: Reginald H. Garrett, Charles M. Grisham
Publisher: Cengage Learning
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Chapter 31, Problem 12P
Understanding the Nature of the Ubiquitin-Ubiquitin linkage Draw the structure of the isopeptide bond formed between
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Rotation about the peptide bond in glycylglycine ishindered. Draw the resonance forms of the peptide bondand explain why.
Alanine has a strong tendency to form α-helix. A biochemist synthesized a polypeptide consisting of 300 alanine residues. When this polyAla300 was suspended in buffered water, it dissolved briefly and then formed a clumped insoluble precipitate that looked like cooked egg-white.
Draw a cartoon (simple drawing) of the two different peptides, showing the structural organization of the polyAla300 as an insoluble precipitate, and the structural organization of the soluble (Ala30Gly5)10 polypeptide.
Predict the secondary and tertiary structure of the following peptide sequence:
a.) LKAENDEAARAMSEA
b.) CRAGGFPWDQPGTSN
2.) In an experiment, you somehow added cysteine so that it would covalently bond a protein complex composed of two proteins. But, the problem is you can’t detect the bridge, meaning you can’t detect covalent bond formation of cysteine in between two proteins. How do you generate disulfide bond? Give an idea to force disulfide bond formation between two proteins.
3.)Lysozyme consist of 4 disulfide bridges while Bovine Serum Albumin(BSA) is 17. However, lysozyme is more rigid compared to BSA. Why? What are the factors affecting the rigidity of their structures? Does the number of α-helixes and β-sheets matter?
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- In α-helices - what is the length of the hydrogen bonds between: TYR41H and GLU37O ALA39H and MET35O GLU38H and ILE34O THR36H and ARG32O. ARG32H and TYR28Oarrow_forwardA. Write the structure of the following peptide at pH 5.0 and calculate its net charge at this pH. Asp-His-Tyr-Arg-Lys-Leu-Thr-Gln. Based on the pKa value of the ionizable groups. B. A polypeptide consisting only of L-glutamate residues (poly-L-glutamate) may have a random coil or helical structure depending on pH. Explain this behavior by indicating at what pH values the helical structure will be favored.arrow_forwardThe Energetic Cost of Peptide Elongation How many ATP equivalents are consumed for each amino acid added to an elongating polypeptide chain during the process of protein synthesis?arrow_forward
- Amino acids have the generic structure seen below, where R represents different carbon-based side chains. Describe how the structure of amino acids allows them to be linked into long peptide chains to form proteins.arrow_forwardShape and dimension. (a) Tropomyosin, a 70-kDa muscle protein, is a two-stranded α-helical coiled coil. Estimate the length of the molecule. (b) Suppose that a 40-residue segment of a protein folds into a two-stranded antiparallel β structure with a 4-residue hairpin turn. What is the longest dimension of this motif?arrow_forwardThe enzyme creatine kinase catalyzes the ATP-dependent phosphorylation of creatine. Propose a mechanism for the reaction described using the curved arrow convention. Show the complete structure of the nucleotide.arrow_forward
- A picture of the two disaccharide repeats of hyaluronic acid are shown below. Name the two different glycosidic linkages. Are these the same linkages as those found in glycogen?arrow_forwardLeu-Trp-Phe-Met-Ala-Ile-Val- Draw the structure of the peptide at pH7.4. and Indicate the hydrogen bonds formed in the alpha helix.arrow_forwardLet’s consider histidine as a free amino acid in aqueous solution. a) Draw the most likely structure of histidine under biochemical standard state conditions. b) Given that free histidine has the following three pKa values, assign each to its corresponding acidic hydrogen or conjugate base in your structure from part a). pKa1 = 1.7; pKa2 = 6.2; and pKa3 = 9.1 c) For each pKa, give the corresponding expression for the equilibrium constant. It helps to write out the chemical equation for each. d) Create a speciation diagram for histidine by plotting Xi vs pH from pH = 4 to pH = 8 where Xi is the mole fraction of the two histidine species involved in the K2 equilibrium in part c).arrow_forward
- Draw the structure of the pentapeptide aspartic acid-serine-lysineUglutamic acidUtyrosine. Assume that thefree -NH2 group is at the aspartic acid end of the peptide chain. Would this compound be more likely to dissolve inwateror in octane? Explain.arrow_forwardDraw the structure of the tri-peptide Leu-Asn-Ser at pH 7.4. Use wedges and dashes around the alpha-carbons, and indicate charges where appropriate. Indicate which amino acid(s) has an R group that would avoid water.arrow_forwardBoth hsp60-like and hsp70 molecular chaperonesshare an affinity for exposed hydrophobic patches on pro-teins, using them as indicators of incomplete folding. Whydo you suppose hydrophobic patches serve as critical sig-nals for the folding status of a protein?arrow_forward
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