1. In the mechanism of action of triose phosphate isomerase, Lys12 is an essential amino acid in the flexible phosphate gripper loop that undergoes a large conformational change to trap the substrate in the active site excluding water and holding the phosphate group in the correct geometry for isomerization rather than dephosphorylation. What would be the effect of the mutation of Lys12 to the unusual amino acid shown below? Explain. w protein backbone

1. In the mechanism of action of triose phosphate isomerase, Lys12 is an essential amino acid in the flexible phosphate gripper loop that undergoes a large conformational change to trap the substrate in the active site excluding water and holding the phosphate group in the correct geometry for isomerization rather than dephosphorylation. What would be the effect of the mutation of Lys12 to the unusual amino acid shown below? Explain. w protein backbone

Biochemistry

6th Edition

ISBN:9781305577206

Author:Reginald H. Garrett, Charles M. Grisham

Publisher:Reginald H. Garrett, Charles M. Grisham

Chapter26: Synthesis And Degradation Of Nucleotides

Section: Chapter Questions

Problem 6P: Allosteric Regulation of Ribonucleotide Reductase by ATP and Deoxynucleotides Describe the...

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2. A mixture of the following amino acids (glu, leu, val, arg, ser, phe) was obtained upon complete hydrolysis of a hexapeptide. a. Edman’s reagent releases leucine b. Hexapeptide with carboxypeptidase releases serine. c. Hexapeptide with trypsin forms a tripeptide A with leucine at the N terminal and tripeptide B with valine at the N terminal. d. Tripeptide A with carboxypeptidase releases arginine and a dipeptide with glutamic acid at C terminal. e. Tripeptide B with chymotrypsin form releases serine and another dipeptide. Give: 1. the amino acid sequence of tripeptide A and B. 2. the amino acid sequence in the above hexapeptide.
1. What is the isoelectric point (pI) of lysine which has pKa values of 2.1 for the α carboxyl group, 9.7 for the α amino group and 10.5 for the side chain amino group? 2. Which of the following is most likely to be found on the exterior of a protein? A) Pro B) Trp C) Ser D) Glu 3. The type of reaction that forms a peptide bond is A) Elimination B) Hydrolysis C) Nucleophilic substitution D) Condensation
1. Consider the three-dimensional model of the tertiary structure of an enzyme below. Amino acids involved in binding are shaded blue, and amino acids involved in catalysis are shaded red. A. Suppose research has shown that amino acid 82 in the red shaded region is lysine, an amino acid with a positively-charged side chain. This lysine is critical for catalysis. Other studies have found that amino acids 12 and 62 in the blue region are both phenylalanine, an amino acid with a nonpolar side chain, and are critical for substrate binding. These amino acids are relatively close in the active site but are separated by 20-70 amino acids in the primary structure. Using what you know about protein structure, explain how amino acids separated in the primary structure can come close together in the active site. B. Use this information and figure 4.2 in your book to answer the following questions: Do you think changing amino acid 82, lysine, an amino acid with a positively-charged side…
7. During amino acid catabolism, how is amino group removed and excreted in the form of urea? Please write the reactions starting from a generic amino acid to the formation of urea. Please indicate the names of enzymes, cofactors, names of substrates, and products of each reaction and the location of the reaction i.e. whether in cytoplasm or mitochondria.
In the fungus Neurospora, some mutants were obtainedthat lacked activity for a certain enzyme. The mutationswere found, by mapping, to be in either of two unlinkedgenes. Provide a possible explanation in reference to quaternary protein structure
1 Draw a general sketch ( backbone only ) of a protein alpha- helix and a beta shet. 2 why do heat and acid denature protein 3 what rae the forces tha drive the formation of secondary and tertiary protein structure. Using your amino acid table, draw two of th epossible interactions. 4 what are enzyme and how they work? Discuss one example of how enzyme catalyze reactions. Also, provide an example of inhibition NOTE- PLEASE DO NOT EXPLAIN TOO MUCH EXPLAIN TO THE POINT EXPLAIN IN SHORT GIVE ANSWER TO THE STRAIGHT POINT.
1. Depict the structure features in the active site of cysteine protease 2. provide a step-wise reaction mechanism to show the hydrolysis of the peptide bond catalyzed by a cysteine protease
1. In a protein, why does when Ala is replaced with Ile, it loses its activity but when Lys is replaced by Arg and Leu to Ile, it only has little effect on protein structure and function? Explain. 2. Why do proteins cannot be denatured reversibly when they are chemically altered to change the chemical composition of certain side chains? Explain.
2. A group of peptides that influence nerve transmission in certain parts of the brain have been isolated from normal brain tissue. These peptides are known as opioids. Using the information below, determine the amino acid sequence of this particular opioid: ● Complete hydrolysis by HCl at 100° C followed by amino acid hydrolysis analysis indicated the presence of Gly, Leu, Phe, and Tyr, in a 2:1:1:1 ratio. ● Treatment of the peptide with FNDB followed by complete hydrolysis indicated the presence of 2,2-dinitrophenyl derivative of tyrosine. No free tyrosine could be found. ● Complete digestion of the peptide with chymotrypsin yielded free tyrosine and leucine, plus a tripeptide containing Phe and Gly in a 1:2 ratio. Instructions Make use of the table below to determine the sequence of the mystery protein:
The enzyme hexokinase adds a phosphate toD-glucose but ignores its mirror image, L-glucose. Supposethat you were able to synthesize hexokinase entirely fromD-amino acids, which are the mirror image of the normalL-amino acids.A. Assuming that the “D” enzyme would fold to a sta-ble conformation, what relationship would you expect it tobear to the normal “L” enzyme?B. Do you suppose the “D” enzyme would add aphosphate to L-glucose, and ignore D-glucose?
2 Please draw the arrow-pushing mechanism to create the polyketide backbone chain of TYLOSIN. If two or more extension rounds are exactly the same, you do not need to draw them more than once. However, please clearly indicate which steps are being repeated. Please draw the complete “business end” of any cofactors you use in a step
Which of the following statements about the allosteric site is true? a. The allosteric site is a second active site on a substrate in a metabolic pathway. b. The allosteric site on an enzyme can allow the product of a metabolic pathway to inhibit that enzyme and stop the pathway. c. When the allosteric site of an enzyme is occupied, the reaction is irreversible and the enzyme cannot react again. d. An allosteric activator prevents binding at the active site. e. An enzyme that possesses allosteric sites does not possess an active site.