Interpretation:
The two types of bonding which will occur in the bonding of the enzyme-substrate complex should be given with dotted lines.
Concept Introduction:
Enzyme:
- It is a protein or a molecule which can act as a catalyst for a biological reaction.
- Does not affect the equilibrium point of the reaction.
- Active site of the enzyme is the region where the reaction takes place.
- Enzyme’s activity can be specific which means the activity is limited to a certain substrate and a certain type of reaction and it is referred to as specificity of the enzyme.
Hydrogen bonding: It is an unusual strong intermolecular force occurs between a hydrogen atom and an electronegative atom like nitrogen, oxygen or fluorine. It occurs in both water and ammonia
Answer to Problem 19.24UKC
Explanation of Solution
Enzymes are three dimensional molecule with a catalytic site into which the substrate can fit. The enzymes are said to be so specific in their action because the activity is limited to a certain substrate and a certain type of reaction and it is referred to as specificity of the enzyme. It can be said that few molecules have the appropriate shape and functional groups to fit into the catalytic site.
Given in the diagram a dipeptidase enzyme and the substrate to form the enzyme-substrate complex. Different types of bonding may occur between the enzyme and the substrate to form the enzyme-substrate complex.
Hydrogen bonding is the attraction between a hydrogen atom and an electronegative atom and it can be considered as a special type of dipole-dipole interaction. The oxygen atom in the substrate can make hydrogen bond with hydrogen in the enzyme.
Salt bridges are formed between oppositely charged residues that are nearby to experience electrostatic attraction. Here, salt bridge is formed between the anionic carboxylate ion
The bonding is shown below:
The two types of bonding which will occur in the bonding of the enzyme-substrate complex is given with dotted lines.
Want to see more full solutions like this?
Chapter 19 Solutions
Fundamentals of General, Organic, and Biological Chemistry (8th Edition)
- b) Why might the compound shown below act as a transition state analog of phosphoglucose isomerase? A drawing of the normal transition state for this enzyme is needed. HO- OH T .N -OH -OH CH₂OPO₂²-arrow_forwardRuBP carboxylase is by no means an ideal enzyme. Describe some of the problems with its active site and its substrate specificity. If we compare the amino acid sequences of this enzyme from many different species, they are almost identical. What is the significance of this uniformity?arrow_forwardParts of the mechanism for lysozyme are shown below. The catalytic lysozyme residue side chains can be identified as being above and below the polysaccharide chain shown at point A. Complete the missing structures (points B and E) and curly arrows (points A, B, C, D and E) in the mechanism, as well as from the knowledge you have gained, label the catalytic amino acids at point A in your mechanism with their correct name and residue number. A OH R OH O-R H₂C- HO NHAC NHAC E R D OH B R C H RO H3C- ° H₂C- NHAC Y R OH NHAC R Rarrow_forward
- The following reaction coordinate diagram charts the energy of a substrate molecule (S) as it passes through a transition state (X‡) on its way to becoming a stable product (P) alone or in the presence of one of two different enzymes (E1 and E2). How does the addition of either enzyme affect the change in Gibbs free energy (ΔG) for the reaction? Which of the two enzymes binds with greater affinity to the substrate? Which enzyme better stabilizes the transition state? Which enzyme functions as a better catalyst?arrow_forwardHow is it possible to determine the structure of an enzyme substrate complex by x ray crystallography when the reaction is over so quickly and the x ray analysis takes at least several minutes?arrow_forwardSome of the following four amino acids : alanine, arginine, histidine, aspartic acid would provide a side chain for acid-base catalysis at physiological pH (assume pK of each amino acid is equal to pK value for the free amino acid in solution). Explain for each amino acid how and why each would or would not provide the side chain residue to support acid-base catalysis at physiological pH.arrow_forward
- Consider the oligopeptide whose structure is shown below: How many peptide bonds are there? Give the complete name of the oligopeptide What is the net charge of the oligopeptide at pH 7? Explain. If you were asked to fragment the oligopeptide with just one enzyme or one chemical reagent, what enzyme or chemical reagent will you use to give the most number of fragments? Show where the peptide bond cleavage will occur.arrow_forwardBeginning with the 1st tetrahedral intermediate, show the complete steps in chymotrypsin mechanism that occurs to form the 2nd chymotrypsin intermediate in the chymotrypsin active site. The substrate for chymotrypsin to be used is Ala-Tyr-Gly. Further, name the amino acid(s) that would be released as a result of the reactions you'd illustrated above.arrow_forwardThe following are structural diagrams of a selection of newly discovered amino acids. OH -の-CHs NH HO C-OH NH, AN-CH CH2 CH2 OH Ho NH, C=0 a) Select 1 amino acid. Redraw it. Label the alpha carbon and circle/highlight the entire backbone of the amino acid. b) The amino acids are part of a channel protein embedded in the cell membrane. Choose 2 amino acids (from above) that you would expect to find within the interior/middle of the cell membrane. Draw the formation of the dipeptide using the 2 amino acids you selected. Identify the other products formed in the reaction.arrow_forward
- The diagram below shows the substrate binding cleft for a protease, providing the substrate structure, and indicating the residues (using one-letter code) that line the four specificity pockets. 1 M F H₂N K R IZ 2 3 P F S W оо E 4 The protease is known to cleave the amide linkage between W and E residues for substrates containing the WEFD sequence. Using 3-letter code with amino acids linked by a "dash" (ex. GLY-ALA), the N-terminal product is A and the C-terminal product is Aarrow_forwardWhat type of bonds in the tertiary structure of the enzyme break at high temperatures? Which ones will not break?arrow_forwardThe active site of an enzyme that uses a general acid-base catalytic mechanism contains a Glu and an Asp residue (both of which are essential for catalysis) with pKa values of 5.9 and 4.5, respectively. If the enzyme is found in the lysosome (pH = 5.2), which residue will act as the general acid and which will act as the general base during the initial steps of the reaction?arrow_forward
- BiochemistryBiochemistryISBN:9781319114671Author:Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.Publisher:W. H. FreemanLehninger Principles of BiochemistryBiochemistryISBN:9781464126116Author:David L. Nelson, Michael M. CoxPublisher:W. H. FreemanFundamentals of Biochemistry: Life at the Molecul...BiochemistryISBN:9781118918401Author:Donald Voet, Judith G. Voet, Charlotte W. PrattPublisher:WILEY
- BiochemistryBiochemistryISBN:9781305961135Author:Mary K. Campbell, Shawn O. Farrell, Owen M. McDougalPublisher:Cengage LearningBiochemistryBiochemistryISBN:9781305577206Author:Reginald H. Garrett, Charles M. GrishamPublisher:Cengage LearningFundamentals of General, Organic, and Biological ...BiochemistryISBN:9780134015187Author:John E. McMurry, David S. Ballantine, Carl A. Hoeger, Virginia E. PetersonPublisher:PEARSON