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

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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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)?
The following data describe the catalysis of cleavage of peptide bonds in small peptides by the enzyme UTSAse (the arrow indicates the peptide bond cleaved in each case). Substrate Km(mM) kcat(s-1) PAPA↓G 4.0 26 PAPA↓A 1.5 37 PAPA↓F 0.64 18 what features of amino acid sequence dictate the specificity of the proteolytic cleavage? Large hydrophilic R-groups Large hydrophobic R-groups Neutral R-groups Small hydrophilic R-groups Large hydrophobic R-groups Negatively charged R-groups Positively charged R-groups
Here is a putative peptide sequence (position number on top of residues): 1 2 3 4 5 6 7 8 9 10 11 12 13 NH2- G C G N V T H N Q C V L S -COOH If expressed in a eukaryotic cell (please mark your answer in the blank space): Position(s) ___ could be N-glycosylated Position(s) ___ could be modified with myristic acid and the bond formed would be a ______________ Position(s) ______and _____ could be modified with palmiti c acid and the bond formed would be a ______________ Positio n(s) ________ could be a segment of a lipid-linked protein with a farnesyl anchor and the bond formed would be a ______________ Position(s) ________ could be a segment of an O-glycosylated protein Position(s) ________ could be modified with a glycosylphosphatidylinositol (GPI) anchor Position(s) ________ could be phosphorylated
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?
The synthesis of a protein requires that the amino acids that constitute the growing polypeptide chain be covalently linked to the amino acid attached to the tRNA at the aminoacyl site of the ribosome. Which of the following catalyses this reaction? Options: the aminoacyl tRNA synthetase eEF2 eEF1-GTP a large ribosomal RNA the initiator tRNA met
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.
Ribonuclease A cannot catalyze the hydrolysis of DNA. which of the following statements explains it. a. Ribonuclease requires two active site histidines to be active but the nucleobase of DNA will form hydrogen bonds with these histidines and block their acid-base catalysis. b. DNAs have thymidine that is more stable than the uracil in RNAs c. DNAs are double-stranded and the nucleobases are protected while RNAs are single stranded d. DNAs does not have hydroxyl group at 2' position of the sugar ring to support the catalysis
Which of the following statements comparing the synthesis of pyrimidines vs. purines is correct? (A) Both types of nucleotides are formed by constructing the nitrogenous base step-by-step on a phosphorylated ribose foundation.(B) Aspartate serves as a nitrogen donor only for purines, while pyrimidines use only glutamine as a nitrogen donor. (C) Both pathways require the synthesis of 5-phophoribosyl-1-pyrophosphate.(D) During the de novo synthesis of both types of nucleotides, nucleosides are formed first and then phosphates are added to the 5’ carbon of ribose.(E) Ribonucleotide reductase is used to form dNTPs from pyrimidine NTPs but not purines.
Why might it be advantageous to add a preassembled block of 14 sugar residues to a protein in the er, rather than building the sugar chains step-by-step on the surface of the protein by the sequential addition of sugars by individual enzymes?
Which of the following would be a good chemotherapy approach: blocking formationof the ribonucleotide GTP or blocking formation of the deoxyribonucleotide dGTP?Why? Please explain the chemical differences between each of the two nucleotides. Use the specific processes below to support your choice by explaining how either GTP or dGTPare related to these and how loss of the particular molecule would affect each process. *PEP carboxykinase in gluconeogenesis*Succinyl-CoA synthetase in the TCA Cycle*Glucagon signal transduction
In studies using repeating copolymers, AC . . . incorporates threonine and histidine, and CAACAA . . . incorporates glutamine, asparagine, and threonine. What triplet code can definitely be assigned to threonine?
When performing his experiments on protein refolding, Christian Anfinsen obtained a quite different result when reduced ribonuclease was reoxidized while it was still in 8 M urea and the preparation was then dialyzed to remove the urea. Ribonuclease reoxidized in this way had only 1% of the enzymatic activity of the native protein. Why were the outcomes so different when reduced ribonuclease was reoxidized in the presence and absence of urea?