5. E. coli ribonuclease H1 is an enzyme that catalyzes the hydrolysis of phosphodiester bonds in RNA. Its proposed mechanism involves a 'carboxylate relay,' as shown below. His124 Asp70 || -HN-CH-C -HN-CH-C- CH2 CH2 c=0 RNA substrate HN H. H. (1) Fill the blanks. In the reaction scheme above, His124 acts as a ( ). The purpose of this relay system is to deprotonate the water molecule (II) so that it becomes a better ( :0

5. E. coli ribonuclease H1 is an enzyme that catalyzes the hydrolysis of phosphodiester bonds in RNA. Its proposed mechanism involves a 'carboxylate relay,' as shown below. His124 Asp70 || -HN-CH-C -HN-CH-C- CH2 CH2 c=0 RNA substrate HN H. H. (1) Fill the blanks. In the reaction scheme above, His124 acts as a ( ). The purpose of this relay system is to deprotonate the water molecule (II) so that it becomes a better ( :0

Biochemistry

6th Edition

ISBN:9781305577206

Author:Reginald H. Garrett, Charles M. Grisham

Publisher:Reginald H. Garrett, Charles M. Grisham

Chapter30: Protein Synthesis

Section: Chapter Questions

Problem 2P

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What is the role of his119 in the RNase-catalyzed hydrolysis of RNA, as indicated in the Figure below? RNA -0-CH₂ Q Base His 119 H H NH His 12 -P-0-CH₂ a Base H H 3' H O 2' O-H OH O -0-P=0 It acts as a general base, abstracting a proton from the 2' hydroxyl in order to increase its nucleophilicity. It forms an H-bond with his12 in order to stabilize the transition state. It serves as a general acid, donating a proton to improve the quality of the leaving group. It works through concerted general acid-base catalysis with his 12 in order to favour the products of the reaction. Two of the above are true.
The figure shows an example of a thermal denaturation plot. The melting temperature (T) is the midpoint of the temperature range over which denaturation occurs. Percent unfolded 100 80 60 40 20 0 20 Tm E 40 60 Temperature (°C) 80 100 Suppose that a Met residue buried in the folded, hydrophobic core of T4 lysozyme is replaced by mutation with a Lys residue.
(c) On the right is a diagram of the ac tive site of E. coli aspartate aminotrans- ferase illustrating the cofactor pyridoxal phosphate (labeled PLP) with the dicar- boxylic acid maleate (labeled MAL) bound in the active site. The structural formula of maleate is shown on the right. Am 194 MAL Arg292 Arg386 Ilx17 Lauf 'coo- H get H Coo- Maleate (c1) Draw the structure of L-aspartate and draw a border around the atoms in the amino acid that maleate simulates. (c2) Identify the active site residues that make hydrogen bonds and electrostatic interac- tions with the oxygen atoms of the carboxylate groups of maleate in the diagram above. Identify the carboxylate groups according to the numbering in the diagram of maleate above. Indicate the hydrogen donor groups of the active site residues. (C3) Compare and draw the structures of L-Arg and L-Lys. On the basis of the diagram why does replacement of an arginine for a lysine have an effect on substrate binding to AspAT? (c4) Of the mutant…
A ribonuclease reaction containing 0.50µM RNASE A will hydrolyze RNA at a maximal rate of 5µM/s in the presence of 40mM RNA at 37°C. What is the turnover number, kcat, for the enzyme (per second).
Cell wall bullding block D-Ala-D-Alal-Lys-tail NH,Me Heptapeptide backbone R1 R. R2 ii) With the aid of the figure above showing the important features of the binding of Vancomycin (lower part) to a bacterial cell wall peptia discuss the antibiotic effect of Vancomycin. i) Vancomycin resistant strains often have a mutation in which one of the D-Ala moieties is exchanged to a D-lactate moiety. Discuss why this mutation makes the strain Vancomycin- resistant but still viable. iv) Glycoconjugate vaccines based on bacterial capsular polysaccharides have been used for 30 years without any need for changes in their structures, while the flu vaccine, based on attenuated or killed virus particles, requires many different structures and a check each time when there is an epidemic that the right vaccine is used. Discuss the reason behind this.
Match the ribosome antibiotics with their binding sites and activities Puromycin [ Choose ] Macrolides (azithromycin, i.e., Z-pak) [ Choose ] Aminoglycosides (kanamycin) [ Choose ] Chloramphenicol V[Choose ] Binds the 30S subunit at the decoding site, interferes with decoding, leading to mis-reading andproduction Binds the E site and prevents de-acylated tRNAs from exiting. This drives pt'ase activity backwards and Binds the A site and mimics an aa-TRNA, is added onto the growing peptide chain by the pt'ase activity of Binds the peptidyltransferase site and blocks pt'ase activity, may also block the TRNAS from entering the A
Can you please describe the specific components that each of these structures are comprised of ( alpha helices and beta sheets) in more detail? Also, what do the different colors represent? Your reply will be greatly appreciated. The ligand that was assigned to me is tadalafil.
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Xylose racemase is a bacterial enzyme that converts the sugar D-xylose to L-xylose, which is needed in small amounts for the bacterial cell wall. The active site of xylose racemase includes a Y residue with a pKa = 7.2. The altered pKa of this residue, compared to its pKa in bulk water, is due largely to the presence of a nearby charged amino acid residue in the active site. Which is a likely explanation for the shift in the Y residue pka? The negative charge in a nearby E residue could stabilize a deprotonated Y residue. The negative charge in a nearby D residue could destabilize a protonated Y residue. The positive charge in a nearby K residue could stabilize a deprotonated Y residue. The positive charge in a nearby R residue could destabilize a deprotonated Y residue.
What is the role of his 12 in the RNase-catalyzed hydrolysis of RNA, as indicated in the Figure below? 5' His 119 RNA CH₂ H H 3 O Base 1' 12' 8-H His 12 -P-0-CH₂ a Base H H O -0-P=O H OH NH It acts as a general base, abstracting a proton from the 2' hydroxyl in order to increase its nucleophilicity. It forms an H-bond with his119 in order to stabilize the transition state. It donates a proton to improve the quality of the leaving group. It works through concerted general acid-base catalysis with his119 in order to favour the products of the reaction. Two of the above are true.