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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Using Fig. as a guide, draw the complete structure of a nucleoside triphosphate before and after it becomes incorporated into a polynucleotide chain. Draw the structure that would result if the newly formed phosphodiester bond were hydrolyzed.
Choose if it's true or false
Different from RNA since in the latter the internucleotide linkages are between C-2’ and C-5’
A long chain polymer in which the internucleotide linkages are of the diester type between C-3’ and C-5’
Usually present in tissues as a nucleoprotein and cannot be separated from its protein component
Hydrolyzed by weak alkali (pH 9 to 100°C)
Leu-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.
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- i. A schematic structure of the subunit of hemerythrin (an oxygen-binding protein from invertebrate animals) is shown to the right. (a) It has been found that in some of the a-helical regions of hemerythrin, about every third or fourth amino acid residue is a hydrophobic one. Suggest a structural reason for this finding. (b) What would be the effect of a mutation that placed a proline residue at point A in the structure?arrow_forwardUnderstanding the Relevance of Chaperones in Protein Folding Protein molecules, like all molecules, can be characterized in terms of general properties such as size, shape, charge, solubility/hydrophobicity. Consider the influence of each of these general features on the likelihood of whether folding of a particular protein will require chaperone assistance or not. Be specific regarding just Hsp7O chaperones or Hsp7O chaperones and Hsp60 chaperonins.arrow_forwardRemembering 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_forward
- Let's consider a protein with two surface-exposed histidine residues: • Hisa is a "typical" histidine residue with pKa = 6.2 Hisg is involved in a stabilizing interaction (His-NH* --- -02C-Glu) with a neighboring glutamic acid residue. For Hisg, the Gibbs free energy of deprotonation at pH = 7.0 and T = 293 K is AG'° = +15 kJ mol-1. If you had a solution, at pH = 7.0 and T = 293 K, containing this protein: a) What fraction of Hisa residues are protonated? b) What fraction of Hisg residues are protonated? c) What is the pK, of Hisg?arrow_forwardLoop regions play important roles in the secondary structure of protein. Define loop region and give three (3) of the rolesarrow_forwardIdentify three true statments about the structure of keratinarrow_forward
- Consider a protein with two surface-exposed histidine residues: HisA is a “typical” histidine residue with a pKa = 6.2 HisB is involved in a stabilizing interaction (His-NH+ ..... -O2C-Glu) with a neighboring glutamic acid residue. For HisB, the Gibbs free energy of deprotonation at pH = 7.0 and T = 293K is ΔG'o = +15 kj mol-1. If you had a solution, at pH = 7.0 and T = 293K, containing this protein: a) What fraction of HisA residues are protonated? b) What fraction of HisB residues are protonated? c) What is the pKa of HisB?arrow_forwardUsing the pKa data in as shown and the Henderson-Hasselbalch equation,calculate the approximate net charge on each of the four common ribonucleoside 5′-monophosphates (rNMPs) at pH 3.8. If a mixture of these rNMPs was placed in an electrophoresis apparatus, as shown, draw four bands to predict the direction and relative migration rate of each.arrow_forwardWhich statements are true? Explain why or why not.1 Each strand in a β sheet is a helix with two aminoacids per turn.2 Intrinsically disordered regions of proteins can beidentified using bioinformatic methods to search genes forencoded amino acid sequences that possess high hydro-phobicity and low net charge.3 Loops of polypeptide that protrude from the sur-face of a protein often form the binding sites for other mol-ecules.4 An enzyme reaches a maximum rate at high sub-strate concentration because it has a fixed number ofactive sites where substrate binds.5 Higher concentrations of enzyme give rise to ahigher turnover number.6 Enzymes that undergo cooperative allosteric tran-sitions invariably consist of symmetric assemblies of mul-tiple subunits.7 Continual addition and removal of phosphatesby protein kinases and protein phosphatases is wastefulof energy—since their combined action consumes ATP—but it is a necessary consequence of effective regulation byphosphorylation.arrow_forward
- eading list Cells have oligosaccharides displayed on their cell surface that are important for cell-cell recognition. Your friend has discovered a transmembrane glycoprotein, GP1, on a pathogenic fungal cell that is recognized by human immune cells. He decides to purify large amounts of GP1 by expressing it in bacteria. To his purified protein he then adds a branched 14-sugar oligosaccharide to the asparagine of the only Asn-X- Ser sequence found on GP1. Unfortunately, immune cells do not seem to recognize this synthesized glycoprotein. What's a likely explanation for this problem? O The oligosaccharide needs to be further modified before it's mature. O The oligosaccharide should've been added one sugar at a time. O The oligosaccharide needs a disulfide bond. O The oligosaccharideehould've been added to the serine instead of the asparagine.arrow_forwardSuggest a reasonable strategy for the specific phosphorylation of the5’ –OH group of a nucleoside.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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