The text states that in E. coli ribonucleotide reductase Tyrosine-122 was identified as the source of the catalytically essential free radical. Describe experimental evidence that would support this conclusion.
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The text states that in E. coli ribonucleotide reductase Tyrosine-122 was identified as the source of the catalytically essential free radical. Describe experimental evidence that would support this conclusion.
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- The objective is to study a novel protease P isolated from the digestive tract of an Amazonian insect. This protease can exist into two forms Pi and Pa which have identical amino acid sequences (both of 80 kDa). However, only Pa shows proteolytic activity. To better understand the activation mode of Pi (inactive form) in Pa (active form), the following experiment was done using DIPF. DIPF (diisopropylphosphofluoridate) is a well-known irreversible inhibitor of serine proteases. It reacts with the catalytic serine residue of the active site of proteases as shown below: Enzyme -CH₂OH + CH(CH3)2 O F-P=0 O CH(CH3)2 Diisopropylphospho- fluoridate (DIPF) Enzyme -CH,—O CH(CH3)2 O <=0 O CH(CH3)2 DIP-Enzyme Both proteases Pa and P₁ were incubated with 32P-DIPF for 30 min at 37°C, and then dialysed to remove excess of unreacted radiolabelled reagent. The two proteases were then analyzed in Sodium Dodecyl Sulphate-Polyacrylamide Gel Electrophoresis (SDS-PAGE), with and without 2-mercaptoethanol.…Human ribonucleotide reductase has two allosteric sites, the S site and the A site. What is the function of each? How does this compare with the E. Coli enzyme discussed in the text?Certain glutamine analogs irreversibly inactivate enzymes that bind glutamine. Identify the nucleotide biosynthetic intermediates that accumulate in the presence of those compounds.
- Which of the following statements regarding Anfinsen's denaturing experiments with ribonuclease A are valid? (i) Exposing the denatured protein to air oxidation and then dialysis to remove urea restored the protein to its original functionality. (ii) Removing urea by dialysis and then allowing air oxidation of the denatured protein restored the protein to its original functionality. (iii) Denaturing the protein with both urea and β-mercaptoethanol yielded an inactive protein. (iv) Protein folding is determined by its primary sequence.The majority of bacterial mutations that need isoleucine also require valine for growth. Why? Which enzyme or process would be deficient in a mutant that requires solely isoleucine for growth (rather than valine)?The 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.
- Explain why RNase A cannot catalyze the hydrolysis of DNA.What would be the effect on the activity of phosphofructokinase of the mutation of Asp103 to the unusual amino acid shown below? Explain in terms of actual structures of the side chains of Asp and this unusual amino acid.In the case of normal RNase A, Anfisen found that oxidizing the Cys residues before slowly removing the urea gave a very different result than oxidizing the Cys after slowly removing the urea. When the urea was removed first, Anfisen recovered 100% of the catalytic activity. When the urea was removed after oxidation, only about 1% of the activity (1/105) was recovered. The conclusion was that 104 of every 105 molecules was misfolded, and therefore catalytically inactive. Let's say someone raises an objection to this interpretation, and says that perhaps, instead, something chemically happens to the active site of RNase A when it is oxidized before refolding, and that the ~1% activity measured represents the residual and greatly reduced enzyme activity of all of the molecules, and the number is just coincidently similar to 1/105. (In other words, instead of 104 completely inactive molecules for every 1 completely active molecule, all molecules are equally damaged, and only function at…
- Most bacterial mutants that require isoleucine for growth also require valine.Why? Which enzyme or reaction would be defective in a mutant requiringonly isoleucine (not valine) for growth?(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…Escherichia coli Fpg protein is responsible for removing damaged DNA base pairs such as C8-oxoguanine (8-oxoG). The catalytic mechanism is believed to involve the formation of a transient Schiff base intermediate formed between DNA base the N-terminal proline residue. Draw the structure of PTH-derivative that is formed after Fpg is subjected to one cycle of Edman degradation.