1. Opine dehydrogenases (ODH) have evolved in invertebrate marine organisms with wide-rangingphysiological roles. The first class of this family of enzymes provides an alternative pathway for thelactate dehydrogenase pathway in anaerobic energy production. The lactate dehydrogenase pathwayis found in higher organisms and in mammals including humans. One class of opine dehydrogenasescatalyzes the reductive coupling of pyruvate to N-a-carboxyalkyl-L-amino acids represented by the re-action below:དང་NH₂ODHསHO Sམིནྟཱ ཨཱར པ 'ནཔི ཏཏྭཱ ཡཾ དསྨཱ ཨབྷིནྡནྟི ཨཱR₂OHNAD(P)H NAD(P)*R OHR₁ R₂where R1 is the side chain of the amino acid, R2 represents the alkyl group of the a-keto acid that iscoupled to the amino acid, and NAD(P)H/NAD(P)* are the reduced/oxidized forms of nicotinamide ad-enine dinucleotide phosphate, a cofactor of the enzyme that catalyzes oxidation-reduction reactions.(a).: The product of the reaction has two chiral centers as shown: The Ca atom of the aminoacid containing the R₁ side chain has an S or L configuration while the Ca atom containing the R2 sidechain has an R or D configuration. Using any of the representations of a tetrahedral carbon illustratedbelow, draw the configurations of the substituents attached to the tetrahedral carbon atoms if both theR1 and R2 side chains are methyl groups. Name the amino acid.(b)Of the twenty naturally occurring L-amino acids, 18 exhibit S chirality with respect to theCa atom. Which L-amino acid amino acid does not hold to this relationship? Explain with diagramswhy this is the case. Is R-cysteine of the L or D configuration?

To determine the L/D configuration of amino acids, place the alpha carbon () in the center, the…

(a). The product of the reaction has two chiral centers as shown: The Ca atom of the amino acid containing the R₁ side chain has an S or L configuration while the Ca atom containing the R2 side chain has an R or D configuration. Using any of the representations of a tetrahedral carbon illustrated below, draw the configurations of the substituents attached to the tetrahedral carbon atoms if both the R1 and R2 side chains are methyl groups. Name the amino acid. (b) Of the twenty naturally occurring L-amino acids, 18 exhibit S chirality with respect to the Ca atom. Which L-amino acid amino acid does not hold to this relationship? Explain with diagrams why this is the case. Is R-cysteine of the L or D configuration?

(a). The product of the reaction has two chiral centers as shown: The Ca atom of the amino acid containing the R₁ side chain has an S or L configuration while the Ca atom containing the R2 side chain has an R or D configuration. Using any of the representations of a tetrahedral carbon illustrated below, draw the configurations of the substituents attached to the tetrahedral carbon atoms if both the R1 and R2 side chains are methyl groups. Name the amino acid. (b) Of the twenty naturally occurring L-amino acids, 18 exhibit S chirality with respect to the Ca atom. Which L-amino acid amino acid does not hold to this relationship? Explain with diagrams why this is the case. Is R-cysteine of the L or D configuration?

Biochemistry

6th Edition

ISBN:9781305577206

Author:Reginald H. Garrett, Charles M. Grisham

Publisher:Reginald H. Garrett, Charles M. Grisham

Chapter25: Nitrogen Acquisition And Amino Acid Metabolism

Section: Chapter Questions

Problem 16P: A Deficiency on 3-Phosphogtycerate Dehydrogenase Can Affect Amino Acid Metabolism Although serine is...

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1. Opine dehydrogenases (ODH) have evolved in invertebrate marine organisms with wide-ranging physiological roles. The first class of this family of enzymes provides an alternative pathway for the lactate dehydrogenase pathway in anaerobic energy production. The lactate dehydrogenase pathway is found in higher organisms and in mammals including humans. One class of opine dehydrogenases catalyzes the reductive coupling of pyruvate to N-a-carboxyalkyl-L-amino acids represented by the re- action below: NH₂ ི་ ODH HO R 요 OH སྨིཾནྟཱ ར པ དརཱ ཨཱཋཏྭཱ… … ཨཱསྨིཾ ཏྟཏྟིནྡནྟི ཨཱ HO NAD(P)H NAD(P)* S R₁ R₂ where R1 is the side chain of the amino acid, R2 represents the alkyl group of the a-keto acid that is coupled to the amino acid, and NAD(P)H/NAD(P)* are the reduced/oxidized forms of nicotinamide ad- enine dinucleotide phosphate, a cofactor of the enzyme that catalyzes oxidation-reduction reactions. (a). The product of the reaction has two chiral centers as shown: The Ca atom of the amino acid…
1. Prostaglandins are a class of eicosanoids, fatty acid derivatives with a variety of extremely potent actions on vertebrate tissues. They are responsible for producing fever and inflammation and its associated pain. Prostaglandins are derived from the 20- carbon fatty acid arachidonic acid in a reaction catalyzed by the enzyme prostaglandin endoperoxide synthase. This enzyme, a cyclooxygenase, uses oxygen to convert arachidonic acid to PGG2, the immediate precursor of many different prostaglandins. (a) The kinetic data given below are for the reaction catalyzed by prostaglandin endoperoxide synthase. Focusing here on the first two columns, determine the Vmax and Km of the enzyme. (b) Ibuprofen is an inhibitor of prostaglandin endoperoxide synthase. By inhibiting the synthesis of prostaglandins, ibuprofen reduces inflammation and pain. Using the data in the first and third columns of the table, determine the type of inhibition that ibuprofen exerts on prostaglandin endoperoxide…
2B. Calculate the total number of ATP that will be generated from the complete B-oxidation of oncobic acid (CH:(CH,),CH=CH(CH,),COOH; 15:1 cis-A9) in an organism that has all the standard required enzymes for metabolism but which pumps only 2 H" in complex I, 0 H' in complex II, 2 H* in complex III and 4 H' in complex IV. The F,F, ATPase is composed of 3 a/ß subunits and 10 c subunits. Show all of your calculations. HO
2. The mechanism of HMG-CoA reducatse enzyme activity involves several stages. For the catalytic reaction to proceed, another substrate known as NADPH, which acts as a reducing agent is required. The kinetics of enzyme activity with NADPH at non-limiting amounts of HMG-CoA in the absence or presence of compactin is shown below. a) Based on the description above, which of the six types of enzymes does HMG-CoA reductase belong to? b) What is the Km for the reaction with no inhibitor present? Do NOT forget the units. Answers can be expressed either as a fraction or in decimals. c) What happens the measured Km with increasing amounts of compactin? (select one) increases decreases does not change d) What happens to the measured Vmax with increasing amounts of compactin? (select one) increases decreases does not change e) Based on your answers above, what type of inhibitor is compactin relative to its effects on enzyme activity NADPH? with -60 -40 1/V, (nanomoles/min)-1 -20 0.2 0.18 0.16…
6. Phosphofructokinase is an allosteric enzyme that catalyzes the conversion of fructose 6-phosphate to fructose 1,6-bisphosphate and represents the key control point in mammalian glycolysis. The enzyme is a homotetramer that is inhibited by ATP binding, activated by AMP binding, negatively regulated by phosphorylation, and competitively inhibited by 2,5-anhydro-D-glucotiol-1,6-diphosphate. (a) Would you expect a plot of the initial rate of fructose 1,6-bisphosphate formation as a function of substrate concentration to show a sigmoidal or hyperbolic curve in the absence of any regulators? (b) How would each of the regulators above affect the dynamics of the T state to R state equilibrium of phosphofructokinase? Briefly explain your reasoning. (c) If it were possible to isolate phosphofructokinase monomers in an active form, how would you expect the kinetics in (a) to be affected? How would the rate of the reaction be affected by ATP, AMP, and 2,5-anhydro-D-glucotiol-1,6-diphosphate?…
3. Answer the following questions about the metabolic pathway shown below: glutamate dehydrogenase e NH3 0-C-C-cH2-CH2-C- 0-C-CH-CH2-CH2-C-O + H,O + NAD + NH + NADH + H (a) Label the correct substances as the substrate, enzyme, and co-enzyme. (b) Which of the six classes does the enzyme of this reaction belong to? Why? (c) What is the name of the first molecule in this reaction? (d) Which metabolic pathway is this reaction likely to be a part of? A. glycolysis B. deamination C. beta-oxidation D. fermentation
11. Refer to the figure below. нн Н `NH2 NH2 N' N- 2e-+H* R NAD+ NADH NAD+ functions as a coenzyme in many enzyme-catalyzed reactions. The changes that take place in this coenzyme are the same for all of these reactions and are illustrated in the figure. It is likely that, in these reactions, NAD+ functions as an electron acceptor (reducing agent) in redox reactions. functions as an electron donor (oxidizing agent) in redox reactions. functions as a base in acid-base catalytic mechanisms. functions as an electron donor (oxidizing agent) in redox reactions. functions as an electron acceptor (oxidizing agent) in redox reactions. +Z-
1) In aerobic conditions in animal cells, oxidative decarboxyliation release CO2 by eliminating the methyl (—CH3) group. : True / False 2) All enzymes of the cycle are located in the cytoplasm, except succinate dehydrogenase, which is bound to the inner mitochondrial membrane: True / False 3) Malonate is a competitive inhibitor of the enzyme succinate dehydrogenase. In the presence of malonate, one would expect succinate to accumulate: True / False
1. The diagram to the right illustrates in panel A the N- acetyl-glutamate content of rat livers as a function of time after intraperitoneal injection of a load of amino acids containing glutamate (1.5 g/kg body weight). The lower panel B illustrates the activity of carbamoyl phosphate synthetase I activity isolated from intact rat liver mitochondria similarly as a function of time after intraperitoneal injection of a load of amino acids (1.5 g/kg body weight). Virtually identical data were generated when only L- glutamate was injected intraperitoneally instead of the load of amino acids containing glutamate. It was also shown that the liver content of endogenous arginine and ornithine remained constant when arginine was omitted from the amino acid mixture. (a) (b) (c) (d) Write the reactions using structural formulas underlying the observations in the two diagrams to the right (one for each panel). Include all the reactants, enzymes and cofactors. Make sure the chiral centers are…
4. (a) courses (such as this one) that NADH produced through glycoly- °H °H! sis in the cytosol can be used to generate ATP in the mitochon- dria. Yet, if 7-(14C)-NADH (in which the nicotinamide C-7 position is radioactively labeled; see diagram on the right) is added to rat hepatocytes, no radioactivity appears in the mitochondrial matrix while, if 4-(H)-NADH is added to hepatocytes, the tritium label soon appears in the mitochondrial matrix. Explain. It is generally stated and taught in biochemistry H H `NH2 NH2 R R [4-°H]NADH [7-14C]NADH
2. Prokariotic aldolase are mediated by a Zn2+ and are inhibited by EDTA, eukaryotic aldolases though are inactivated by sodium borohydride. A) Draw out the mechanism of the eukaryotic aldolase and propose a parallel mechanism for the zinc catalyzed prokaryotic reaction. B) Propose a strategy that could be could be used to specifically inhibit prokaryotic aldolases and not eukaryotic?
The following diagram shows reaction curves for aspartate transcarbamoylase (ATCase) with carbamoylphosphate and different concentrations of aspartate, in the absence of ATP (curve 1) and presence of ATP (curve 2). What do the shapes of the curves tell us about the ATCase enzyme? 2 جر [aspartate] It binds substrate through a sequential mechanism. It binds substte cooperatively. It obeys Michaelis-Menten kinetics. It binds substrate through a concerted mechanism.