1. Amino acid side chains act as nucleophiles and proton donor/acceptors in various enzymaticreactions. We will use them frequently in reactions during 40B and therefore the purpose of thisexercise is to review the properties of amino acid side chains you have learned in 40A.Ozempic is a medication used for the treatment of type 2 diabetes and an anti-obesity treatment.Ozempic is a modified peptide that mimics the structure of the natural hormone GLP-1.a.Gay-The Phe-The-Ser Asp-Val-Ser-Ser-Tyr-Leu-Glu-Gily Gin-Ala-Ala-auhe-sNHC.For example: -Ser- will be represented byGu Phe-lle Ala-Trp -Leu-Val-Arg-Gly Arg Gly-OHAdd above the tree-letter code of each amino acid the relevant functional group on its side chain.OHSerThe protonation state of each functional group depends on the pH of the solution. Assume thatOzempic is in a solution at pH=7. Draw the functional groups at their correct protonation form.OGu Phe-le- Ala-Trp Leu-Val- Arg-Gly Arg-Gly-OHQuay Thr Phe Thr-Ser Asp-Val-Ser-Ser-Tyr-Leu Glu-Gly Gin-Ala Ala-M/C CH₂gethoraNHNHWhat will be the protonation state of the long non-peptide side chain at pH=7?

Peptides are composed of amino acids. Some amino acids have ionizable side chains while others do…

Answered: 1. Amino acid side chains act as…

Biochemistry

9th Edition

ISBN:9781319114671

Author:Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.

Publisher:Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.

Chapter1: Biochemistry: An Evolving Science

Section: Chapter Questions

Problem 1P

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E Threonine 6. You have identified some intermediates in threonine synthesis: A, B, C, D and E. You grow a few of your mutants in the presence of these different intermediates to determine the order in which the gene products act. Below are your results. A (+) means growth and a (-) means no growth. Given these data, draw the best possible pathway for the synthesis of threonine. The diagram should use arrows to indicate one intermediate being changed to another intermediate. Indicate which gene produces the product responsible for the conversion by listing the mutant in that gene above the arrow. Mt1 Mt2 Mt4 Mt7
One of the reasons for oxidizing the disulfide bonds in RNase A before removing the urea in the Anfinsen experiment was to demonstrate that ... Urea promotes disulfide bond exchange O Incorrectly-folded proteins lose their enzymatic activity. Urea prevents disulfide bond formation. Urea forms thio-esters with reduced cysteines at pH 8.2 Disulfide bonds are required for enzyme activity.
Help filling in the blanks: Pyridoxal phosphate, PLP, is produced from pyridoxine or vitamin B6. PLP is considered a/an [1C/2C/acyl/amino/carboxyl] carrier. In transaminases, PLP forms a [Schiff base/acetal/phosphoanhydride/condensation] with an amino acid and causes the [a- amino/a-carbon/a-carboxyl] to become [electrophilic/nucleophilic] allowing replacement of the amino group on the amino acid with a ketone. PLP is also used by several other enzymes that work on amino acids because in forming a covalent bond with amino acids it provides for an opportunity for nucleophilic attack and because PLP is conjugated, the cofactor is able to [delocalize/transfer/reduce/stabilize] pi electrons in the substrate and thus [stabilize/delocalize/transfer/reduce] the transition state of the reaction. Production of citrulline occurs in the [cytosol/mitochondrial matrix] while the rest of the urea cycle occurs in the [cytosol/mitochondrial matrix]. Urea is produced in the…
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ymes change their conformation after each reaction, therefore they can only be used once. OEnzymes can be proteins that can be denatured by changes in pH or temperature. D Question 37 A major difference between purine and pyrimidine biosynthesis is that pyrimidine: O are attached to the ribose sugar while being synthesized O are completely synthesized prior to attaching to the ribose sugar O are partially synthesized, the sugar is added, then synthesis is completed O do not have a sugar moiety Question 38 Which of the following is produced in largest numbers by the TCA cycle?
Part B Some nonessential amino acids are synthesized in the body by a simple transamination. The transamination between oxaloacetate, an a-keto acid, and glutamate, a amino acid with the side chain -CH₂CH₂COO proceeds according to the following reaction: OOC-CH₂-C-COO + OOC-CH₂CH₂CH COO OOC-CH₂CH₂-C-COO + amino acid 2 NH₂+ Predict the structure of the amino acid product, indicated by amino acid 2, for the reaction. Draw the molecule on the canvas by choosing buttons from the Tools (for bonds), Atoms, and Advanced Template toolbars. The single bond is active by default. Include all hydrogen atoms and formal charges.
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Amino acids are linked through peptide bonds to form proteins. This linkage of amino acids in the formation of proteins accomplished by [ Select ] reaction V [ Select ] Hydrolysis Fission Condensation Fusion
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4. Below is a Michaelis-Menten plot for a wild-type (WT) and mutant (V105A) enzyme isolated from the bacterium Staphylococcus aureus. The enzyme is involved in carbohydrate metabolism and is a potential biocatalyst for the large-scale production of rare sugars. (8) mg V₂ μmol s1 1.50- 1.25- 1.00- 0.75- 0.50- 0.25- 0.00 0 100 200 300 [s], mM 400 500 WT (a) Estimate the KM and Vmax for the wild-type and mutant enzyme from the graph. V105A (b) Calculate the keat and keat/KM for the wild-type and mutant enzyme based on your estimated values in (a) if the total enzyme concentration is 0.5 µmol/mg. (c) Is the mutant enzyme a more or less efficient catalyst than the wild-type enzyme? Briefly explain.
a. Suppose that you have the peptide Ala-Gly-Tyr-His-Leu and you treat it with FDNB and then 6M HCl. Draw the structures of all the products that you will have in solution (assume all reactions to go to completion).
Small molecules are used as inhibitors of protein action - as drugs. They most often do this by blocking the active site within the protein. Potential drugs can be screened computationally to determine if they are strongly bound to the protein. Figure 1 shows a possible conformation of a candidate drug molecule, 4-bromo-2- carboxymethylamide-pyrrole (abbreviation: BCMAP) at the active site of a protein (abbreviation: PR). Figure 2 shows the full protein structure whilst figure 3 shows a known inhibitor of the protein at the site, overlayed with another calculated conformer of BCMAP. (a) Explain what types of interactions, both intermolecular and intramolecular, that a molecular mechanics forcefield must be able to describe in order to be able to accurately determine the geometry of BCMAP in the protein. Identify which interactions will be the most important to describe accurately. Figure 1.4-bromo-2-carboxymethylamide-pyrrole (BCMAP) (C, N, O, and Br atoms in yellow, blue, red, and…

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