Biochemistry Assignment: Metabolism of Proteins and Nucleotides

This biochemistry assignment delves into the intricate world of protein and nucleotide metabolism. It explores the roles of pyridoxamine-5'-phosphate in amino acid transfer, the transport of amino groups by glutamine and asparagine, and the alanine-mediated transport of amino groups between muscle and liver. The assignment also covers the urea cycle, including the role of the liver, the enzyme argininosuccinate lyase, and the implications of enzyme deficiencies like ornithine transcarbamylase deficiency. Furthermore, it examines nucleotide functions, the synthesis of purines and pyrimidines, and the regulatory mechanisms involved, including activators and inhibitors. The assignment provides detailed answers to questions regarding the substrates, cofactors, and processes involved in these crucial metabolic pathways, offering a comprehensive overview of the subject matter.

Running head: BIOCHEMISTRY
Name of the Student
Name of the University
Author Note

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Protein and amino acid metabolism:
Question 1:
Pyridoxamine-5'-phosphate (PMP) is the cofactor for the reaction used by
aminotransferases in the amino group transfer of amino acids (Gurr et al., 2016). It is a part of
vitamin B6 which drives 168 enzymatic processes of the body and responsible for the conversion
of essential amino acids to non-essential one.
Figure: Pyridoxamine-5'-phosphate
Source: (Gurr et al., 2016).
Question 2:
Glutamine and asparagine are responsible for the transport of amino groups in the
catabolism of amino acids. Glutamine and asparagine are the amino acids where the carboxyl
groups are replaced by an amide group which helped them to transport amine groups during

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catabolism (Cao et al., 2015).. Consequently, after transportation, they further convert into
glutamic acid and aspartic acid.
Figure: Glutamine and asparagine
Source: (Gurr et al., 2016).
Question 3:
Glutamine in the muscle is transaminated to alanine which is released into the
bloodstream. In the liver, alanine is taken up and converted into pyruvate for associated
metabolism. In this case, nitrogen is also transported as glutamine (Cao et al., 2015).

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Figure: Glutamine in the muscle is transaminated to alanine
Source: (Gurr et al., 2016).
Question 4:
Urea widely used as a potential nitrogen source and fundamental raw materials for the
chemical industry. While the body uses a different mechanism, the most frequent one is nitrogen
metabolism. The liver plays a vital role in excretion where it combines two molecules of
ammonia with one molecule of carbon dioxide in the process of the urea cycle (Afify, 2016)..
Figure: urea cycle
Source: (Afify, 2016)..

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Question 5:
Argininosuccinate lyase or argininosuccinase is an enzyme located in the cytosol of the
liver where it breaks down argininosuccinate into two amino acids such as arginine as well as
dicarboxylic acid fumarate and it occurs through E1cb elimination reaction. While arginine
breaks down into the ornithine and citrulline to continue urea cycle, fumarate after production
enters into the TCA cycle for continuing oxidation of amino acids, carbohydrate, and lipids.
Fumarate also acts as a food acidity regulator and a fundamental metabolite (Afify, 2016).
Question 6:
Urea cycle converts ammonia as a toxic product to nontoxic urea. This ATP-dependent
process occurs in hepatocytes. The regulated enzyme of the urea cycle is carbamoyl phosphate
synthetase I which requires N-acetylglutamate (N-AcGlu) as an allosteric activator. Urea is the
most important means to eliminate NH3 and is transported by the blood to the kidneys for
excretion (Offerdahl, Arneson & Byrne, 2017).
Figure: urea cycle
Source: (Afify, 2016)..

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Question 7:
In the nine old month baby, a low value of citrulline indicates the deficiency of
Ornithine transcarbamylase. The prime reason behind it is that Ornithine transcarbamylase is the
enzyme which facilitates the reaction between carbamoyl phosphate and ornithine forb
production phosphate and citrulline (Offerdahl, Arneson & Byrne, 2017).
Figure: urea cycle
Source: (Afify, 2016)..
.
Question 8:

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After the deamination reaction, amino acids are able to enter into the Krebs cycle as
pyruvate as well as acetyl CoA (Gurr et al., 2016).
Metabolism of purines and pyrimidine:
Question 1:
Nucleotides are the energy currency of cells which acts as signaling molecules and
acting like hormones and provide the monomer for genetic materials such as DNA and RNA
(Lane & Fan, 2015).
Figure: purine and pyrimidine
Source: (Afify, 2016)..

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Question 2:
Two nucleotides derived from IMP (Inosine 5'-monophosphate) are adenine and guanine
which produced as AMP (adenine monophosphate ) and GMP ( guanine monophosphate)
respectively (Lane & Fan, 2015)..
.
Question 3:
Purine is the nucleotide, synthesized as nucleotides and in particular as ribotides. The
substrate of purine synthesis is inosine monophosphate (IMP) and ATP.
Question 4:
The substrate of pyrimidine is amide nitrogen of glutamine and bicarbonate ion which
further produces carbamoyl phosphate (Aird & Zhang, 2015)..
Question 5:
In the case of pyrimidine biosynthesis, it is regulated by Carbomyolye phosphate
synthetase II, which is inhibited by UTP and UDP and activated by ATP as well as PRPP.
Another enzyme is UMP and CMP, competitive inhibitors. On the other hand, for purine
biosynthesis, inhibitors are IMP, GMP, and AMP. PRPP is the activator of the reaction (Aird &
Zhang, 2015)..

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.
Figure: purine and pyrimidine
Source: (Afify, 2016)..

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References:
Afify, H. M. (2016). Contribution of Clinical Biochemistry to Structural
Bioinformatics. American Journal of Biomedical Sciences, 8(3).
Aird, K. M., & Zhang, R. (2015). Nucleotide metabolism, oncogene-induced senescence and
cancer. Cancer letters, 356(2), 204-210.
Cao, Y., Wang, H., Ouyang, Q., & Tu, Y. (2015). The free-energy cost of accurate biochemical
oscillations. Nature physics, 11(9), 772.
Gurr, M. I., Harwood, J. L., Frayn, K. N., Murphy, D. J., & Michell, R. H. (2016). Lipids:
biochemistry, biotechnology and health. John Wiley & Sons.
Lane, A. N., & Fan, T. W. M. (2015). Regulation of mammalian nucleotide metabolism and
biosynthesis. Nucleic acids research, 43(4), 2466-2485.
Offerdahl, E. G., Arneson, J. B., & Byrne, N. (2017). Lighten the load: Scaffolding visual
literacy in biochemistry and molecular biology. CBE—Life Sciences Education, 16(1),
es1.