Assignment Code: BBCCT-113/TMA/2023

Course Code: BBCCT-113

Assignment Name: Metabolism of Amino Acids and Nucleotides

Year: 2023

Verification Status: Verified by Professor

Part A

Q1) Give an overview of catabolism of amino acids that are converted to pyruvate.

Ans) Amino acids can be used as an energy source for the body. Amino acids can be catabolized through several pathways, one of which is the conversion of amino acids to pyruvate. The catabolism of amino acids that are converted to pyruvate occurs in three steps.

Step 1: Transamination

The first step is the removal of the amino group from the amino acid. This is accomplished by the enzyme transaminase, which transfers the amino group to α-ketoglutarate to form glutamate. The remaining carbon skeleton of the amino acid is converted to an intermediate that enters the glycolytic pathway.

Step 2: Oxidative Decarboxylation

The second step is the oxidative decarboxylation of the carbon skeleton of the amino acid. This process involves the removal of a carboxyl group as carbon dioxide and the formation of an acetyl group. The acetyl group is then combined with coenzyme A to form acetyl-CoA.

Step 3: Acetyl-CoA Enters the Citric Acid Cycle

Acetyl-CoA enters the citric acid cycle and is oxidized to produce ATP, carbon dioxide, and reduced coenzymes.

The catabolism of amino acids that are converted to pyruvate produces energy and also provides intermediates for biosynthesis.

Q2) (a) Illustrate the role of creatine and creatine phosphate as biologically active amino acid derivatives.

Ans) Creatine and creatine phosphate play important roles in cellular energy metabolism, particularly in cells with high energy demands, such as muscle cells and neurons. Creatine is a nitrogen-containing compound derived from the amino acids’ arginine, glycine, and methionine, and is primarily synthesized in the liver and kidneys. It is transported to other tissues, where it is used to synthesize creatine phosphate.

Creatine phosphate, also known as phosphocreatine, is a high-energy phosphate compound that can rapidly donate a phosphate group to adenosine diphosphate, producing adenosine triphosphate, the primary energy currency of cells. This reaction is catalysed by the enzyme creatine kinase and is important for providing a rapid source of ATP during periods of high energy demand, such as during muscle contraction or neuronal signalling.

In skeletal muscle cells, creatine phosphate serves as a reserve of high-energy phosphate that can be rapidly converted to ATP during short bursts of intense activity, such as sprinting or weightlifting. Supplementation with creatine has been shown to enhance athletic performance in certain situations by increasing the availability of creatine phosphate in muscle cells.

In the brain, creatine and creatine phosphate may play a role in neuronal energy metabolism and may be important for cognitive function. Studies have shown that creatine supplementation can improve cognitive performance in some populations, particularly in tasks requiring short-term memory or complex reasoning.

Q2) (b) What short note on Glucose-Alanine cycle?

Ans) The glucose-alanine cycle is a metabolic pathway that takes place between skeletal muscle and the liver. During periods of intense exercise, skeletal muscle produces large amounts of pyruvate, which is converted to alanine and released into the bloodstream. The alanine is transported to the liver, where it is converted back into pyruvate and used in gluconeogenesis to produce glucose. The glucose is then released into the bloodstream and transported back to the skeletal muscle, where it can be used as a source of energy.

This cycle serves to remove excess nitrogen from muscle cells, as the conversion of pyruvate to alanine requires the transfer of an amino group from glutamate. The glutamate is then converted to alpha-ketoglutarate in the liver, allowing for the removal of excess nitrogen from the body. Overall, the glucose-alanine cycle is an important metabolic pathway that allows for the efficient removal of excess nitrogen from muscle cells while also providing a source of glucose for energy production.

Q3) Explain the following disorders:

a) Hyperammonaemia Type-1 and Type-II

Ans) Hyperammonemia refers to a condition in which there is an excess of ammonia in the blood. Ammonia is a toxic compound that is produced as a by-product of protein metabolism, and it is normally removed from the body through the urea cycle, which takes place primarily in the liver. There are two main types of hyperammonemia: type 1 and type 2.

1. Type 1 hyperammonemia, also known as classic hyperammonemia or ornithine transcarbamylase deficiency, is a genetic disorder that affects the urea cycle. It is caused by a deficiency in the enzyme OTC, which is responsible for catalysing the conversion of ornithine and carbamoyl phosphate into citrulline. As a result, ammonia accumulates in the blood, leading to neurological symptoms such as lethargy, vomiting, and seizures. Type 1 hyperammonemia is typically diagnosed in infancy or early childhood and requires lifelong management, including dietary restrictions and medication.

2. Type 2 hyperammonemia, also known as citrullinemia, is a genetic disorder that affects the urea cycle. It is caused by a deficiency in the enzyme argininosuccinate synthetase, which is responsible for catalysing the conversion of citrulline and aspartate into argininosuccinate. As a result, ammonia accumulates in the blood, leading to neurological symptoms such as confusion, irritability, and seizures. Type 2 hyperammonemia can present in infancy, childhood, or adulthood, and management may involve dietary restrictions, medication, and liver transplantation.

Both types of hyperammonemia can be life-threatening if left untreated, and prompt diagnosis and management are critical.

b) Homocystinuria

Ans) Homocystinuria is a rare genetic disorder that affects the metabolism of the amino acid methionine. It is caused by a deficiency in one of several enzymes involved in the methionine metabolism pathway, which leads to the accumulation of homocysteine and its metabolites in the body. Symptoms of homocystinuria may vary depending on the specific enzyme deficiency, but common signs and symptoms include:

1. Developmental delays and intellectual disability

2. Abnormal bone development and skeletal abnormalities

3. Eye problems such as near-sightedness, lens dislocation, and glaucoma

4. Blood clotting problems and increased risk of strokes and heart attacks

5. Connective tissue disorders such as scoliosis, joint dislocations, and abnormal skin elasticity

6. Seizures and psychiatric symptoms such as depression and anxiety.

Homocystinuria can be diagnosed through a blood test that measures the levels of methionine and homocysteine. Treatment typically involves a low-methionine diet, vitamin supplements (such as vitamin B6, B12, and folic acid), and medication to lower homocysteine levels. Early diagnosis and treatment are important in preventing long-term complications and improving quality of life for individuals with homocystinuria.

Q4) Elaborate about heme degradation in porphyrin metabolism.

Ans) Heme is an iron-containing molecule found in many proteins, including haemoglobin, myoglobin, and cytochromes. Heme degradation is an important part of porphyrin metabolism, which is the process by which the body produces and breaks down porphyrins, the precursor molecules of heme. Heme degradation begins with the enzyme heme oxygenase, which cleaves the heme molecule into biliverdin, carbon monoxide (CO), and iron. Biliverdin is then converted into bilirubin by the enzyme biliverdin reductase. Bilirubin is a yellow pigment that is excreted from the body in the bile and gives feces their characteristic colour.

In addition to producing bilirubin, heme degradation also produces carbon monoxide, which can have toxic effects on the body at high concentrations. However, at low concentrations, carbon monoxide has been shown to have physiological functions, such as regulating blood vessel dilation and reducing inflammation.

The iron produced from heme degradation is either recycled or stored in the body. Iron recycling involves the transport of iron to the bone marrow for incorporation into new heme molecules, while iron storage involves the binding of iron to the protein ferritin for later use. Heme degradation plays an important role in the regulation of heme levels in the body and the production of bilirubin, carbon monoxide, and iron. Disruptions in heme degradation can lead to a range of disorders, including hemolytic anemia and disorders of bilirubin metabolism such as jaundice.

Q5) Describe glycine serine interconversion along with reactions.

Ans) Glycine and serine are two amino acids that are interconvertible through a series of biochemical reactions. This interconversion is an important part of amino acid metabolism and is essential for the synthesis of many important biomolecules in the body.

The interconversion of glycine and serine occurs through two main reactions:

1) Conversion of Glycine to Serine: This reaction is catalysed by the enzyme serine hydroxymethyltransferase (SHMT), which transfers a methyl group from tetrahydrofolate (THF) to glycine, producing serine and 5,10-methylene-THF. This reaction is reversible, and the direction of the reaction depends on the relative concentrations of glycine and serine in the cell.

2) Conversion of Serine to Glycine: This reaction is catalysed by the enzyme serine dehydratase (SDH), which removes a hydroxyl group from serine, producing glycine and an intermediate called pyruvate. This reaction is also reversible and depends on the relative concentrations of serine and glycine in the cell.

Both reactions play important roles in amino acid metabolism and the synthesis of important biomolecules. For example, serine is a precursor for the synthesis of glycine, which is then used to synthesize proteins, nucleic acids, and other important biomolecules. Glycine can also be converted to other amino acids such as serine, threonine, and purines. Furthermore, serine and glycine play important roles in the synthesis of the antioxidant glutathione, which is involved in protecting cells from oxidative stress.

Overall, the interconversion of glycine and serine is an important part of amino acid metabolism and is essential for the synthesis of many important biomolecules in the body.

Part B

Q6) How purine nucleotide synthesis is regulated?

Ans) The synthesis of purine nucleotides is a complex process that requires the coordinated regulation of several enzymes and metabolic pathways. This regulation is necessary to ensure that the production of purine nucleotides is balanced with the cellular demand for nucleic acid synthesis and other purine-containing biomolecules. There are several mechanisms by which the synthesis of purine nucleotides is regulated:

1. Feedback Inhibition: Several enzymes involved in purine nucleotide synthesis are subject to feedback inhibition by the end products of the pathway. For example, the enzyme phosphoribosyl pyrophosphate synthetase (PRPP synthetase) is inhibited by ADP and GDP, while the enzyme inosine monophosphate dehydrogenase (IMPDH) is inhibited by guanosine nucleotides (GMP and GDP).

2. Regulation of Enzyme Activity: Many of the enzymes involved in purine nucleotide synthesis are regulated by post-translational modifications, such as phosphorylation, acetylation, and ubiquitination. These modifications can alter the activity and stability of the enzymes, thereby regulating the rate of purine nucleotide synthesis.

3. Control of Gene Expression: The expression of many of the enzymes involved in purine nucleotide synthesis is regulated by transcription factors and other signalling pathways. For example, the expression of the enzyme PRPP synthetase is regulated by the transcription factor ATF4 in response to cellular stress, while the expression of IMPDH is regulated by the oncogene c-Myc in proliferating cells.

4. Availability of Substrates: The availability of substrates such as ribose-5-phosphate, amino acids, and energy sources can also regulate the rate of purine nucleotide synthesis. For example, the availability of glucose and other energy sources can affect the activity of the enzyme PRPP synthetase, which is a rate-limiting step in purine nucleotide synthesis.

Overall, the synthesis of purine nucleotides is tightly regulated to ensure that the production of nucleotides is balanced with the cellular demand for nucleic acid synthesis and other purine-containing biomolecules. Dysregulation of this pathway can lead to a range of disorders, including cancer, gout, and immunodeficiency diseases.

Q7) (a) Describe the differences in de novo pathways of purine and pyrimidine nucleotide synthesis.

Ans) Purine and pyrimidine nucleotides are two types of nucleotides that are essential building blocks of DNA and RNA. The de novo pathways of purine and pyrimidine nucleotide synthesis are different in several ways.

The de novo synthesis of purine nucleotides starts with ribose-5-phosphate, which is converted to phosphoribosyl pyrophosphate (PRPP) by the enzyme PRPP synthetase. The synthesis of purine nucleotides then proceeds through a series of reactions that add atoms and functional groups to the PRPP molecule, leading to the formation of the purine ring system. The enzymes involved in purine nucleotide synthesis are distinct from those involved in pyrimidine nucleotide synthesis. The rate-limiting step in purine nucleotide synthesis is catalysed by PRPP synthetase, while the rate-limiting step in pyrimidine nucleotide synthesis is catalysed by carbamoyl phosphate synthetase II (CPS II).

In contrast, the de novo synthesis of pyrimidine nucleotides starts with carbamoyl phosphate, which is derived from glutamine and CO2. The synthesis of pyrimidine nucleotides proceeds by the assembly of the pyrimidine ring system on a pre-existing ribose-5-phosphate molecule. The regulation of purine and pyrimidine nucleotide synthesis is also different. The synthesis of purine nucleotides is regulated by feedback inhibition by the end products of the pathway, while the synthesis of pyrimidine nucleotides is regulated by the availability of substrates such as carbamoyl phosphate and aspartate.

Q7) (b) What are Ribonucleotide reductases?

Ans) Ribonucleotide reductases are a class of enzymes that catalyse the conversion of ribonucleotides to deoxyribonucleotides, which are the building blocks of DNA. This conversion is essential for the biosynthesis and maintenance of DNA in all living organisms.

The reduction of ribonucleotides to deoxyribonucleotides is a multi-step process that involves the transfer of electrons from a reducing agent to the ribose sugar of the ribonucleotide. The reducing agent varies depending on the organism and can be a protein, a small molecule, or a metal ion. In eukaryotes, RNRs are regulated by the presence of a small molecule called dATP, which inhibits the activity of the enzyme and prevents overproduction of deoxyribonucleotides.

There are several classes of RNRs, each with different mechanisms of action and regulatory properties. Class I RNRs are found in bacteria, yeast, and mammals, and use a tyrosyl radical as a key intermediate in the reaction mechanism. Class II RNRs are found in archaea and eukaryotes and use a glycyl radical instead. Class III RNRs are found in bacteriophages and use a different mechanism altogether, involving the transfer of an electron to the ribonucleotide by a separate enzyme.

Q8) (a) Write a short note about Xanthine oxidase.

Ans) Xanthine oxidase is an enzyme that catalyses the conversion of hypoxanthine and xanthine to uric acid, a molecule that is excreted from the body in urine. It is a molybdoflavoprotein enzyme that requires oxygen and molybdenum as cofactors for its activity.

Xanthine oxidase plays a key role in purine metabolism, which is the process by which the body breaks down and recycles nucleotides, the building blocks of DNA and RNA. When purine nucleotides are broken down, hypoxanthine and xanthine are produced as intermediates, which are then converted to uric acid by xanthine oxidase. Uric acid is a waste product that is excreted by the kidneys.

Xanthine oxidase is also involved in other biological processes, including the production of reactive oxygen species and the metabolism of certain drugs and toxins. In some cases, the activity of xanthine oxidase can contribute to oxidative stress and tissue damage. Therefore, understanding the regulation and function of xanthine oxidase is important for the development of therapies for a range of diseases.

Q8) (b) Compare purine and pyrimidine nucleotide degradation.

Ans) Both purine and pyrimidine nucleotides can be degraded by a series of enzymatic reactions to produce smaller compounds that can be excreted from the body.

In purine nucleotide degradation, the first step is the deamination of the nucleotide to produce a purine base, such as hypoxanthine or xanthine. The purine base is then converted to uric acid, which is excreted by the kidneys. In humans, the enzyme responsible for the conversion of hypoxanthine to xanthine is xanthine oxidase, which requires oxygen and molybdenum as cofactors. Defects in this enzyme can lead to hyperuricemia and gout.

In pyrimidine nucleotide degradation, the nucleotide is first dephosphorylated to produce a pyrimidine base, such as uracil or cytosine. The pyrimidine base is then degraded to smaller compounds, such as beta-alanine and ammonia. The final product of pyrimidine degradation in mammals is urea, which is excreted by the kidneys.

Q9) Discuss organ specific metabolic profile of brain.

Ans) The brain has a unique metabolic profile that is essential for its proper functioning. Unlike other organs, the brain relies almost exclusively on glucose as its primary source of energy. This is because neurons require a constant supply of glucose to generate ATP, the energy currency of the cell, to maintain their membrane potentials and carry out neurotransmission.

In addition to glucose metabolism, the brain also utilizes other metabolic pathways to maintain its energy balance and support its various functions. For example, the brain has a high capacity for oxidative metabolism, which generates ATP through the process of oxidative phosphorylation in mitochondria. This is important for sustaining energy production during prolonged periods of neuronal activity.

The brain also has a high demand for lipids, which are used for the synthesis of cell membranes and myelin, the fatty substance that insulates nerve fibres. The brain can synthesize its own lipids from glucose and other precursors, but it also relies on the uptake of lipids from the blood.

Furthermore, the brain has a unique amino acid metabolism that is important for neurotransmitter synthesis and the regulation of neurotransmitter levels. For example, glutamate and GABA, two of the most abundant neurotransmitters in the brain, are synthesized from the amino acid precursor glutamine.

Q10) Briefly describe the signs and symptoms of:

i) Gout

Ans) Gout is a type of arthritis caused by the build-up of uric acid crystals in the joints, leading to inflammation and pain. The signs and symptoms of gout can include:

1. Sudden Onset of Intense Pain: Gout attacks typically occur suddenly, often at night, and are characterized by a sharp, intense pain in the affected joint. The pain may be accompanied by swelling, redness, and warmth in the joint.

2. Tenderness: The affected joint may be extremely tender to the touch, and even the slightest pressure or movement can cause significant pain.

3. Limited Mobility: As a result of the pain and swelling, the affected joint may become stiff and difficult to move.

4. Recurrent Attacks: Gout attacks may occur periodically, with periods of time between attacks varying in length.

5. Uric Acid Build-up: In addition to joint pain and inflammation, gout can also cause the build-up of uric acid crystals in other parts of the body, such as the kidneys and urinary tract, leading to kidney stones and other complications.

Overall, the symptoms of gout can be very painful and can significantly impact a person's quality of life. If you are experiencing symptoms of gout, it is important to seek medical attention to receive proper diagnosis and treatment.

ii) SCID

Ans) Severe combined immunodeficiency is a rare genetic disorder that affects the immune system, making individuals highly susceptible to infections. The signs and symptoms of SCID can include:

1. Frequent and Severe Infections: Individuals with SCID are highly vulnerable to infections and may experience recurrent or persistent infections that are difficult to treat, such as pneumonia, meningitis, and bloodstream infections.

2. Failure to Thrive: Infants with SCID may experience poor growth and development and may have difficulty gaining weight and meeting developmental milestones.

3. Chronic Diarrhoea: Chronic diarrhoea is a common symptom of SCID and can be a result of gastrointestinal infections or other underlying conditions.

4. Skin Rashes and Infections: Individuals with SCID may be prone to skin rashes and infections, such as fungal infections or persistent thrush.

5. Enlarged Lymph Nodes and Spleen: In some cases, individuals with SCID may develop enlarged lymph nodes and spleen, which can be a sign of an underlying infection or other complication.

Overall, the symptoms of SCID can be severe and can have a significant impact on a person's health and quality of life. If you suspect that you or a loved one may have SCID, it is important to seek medical attention to receive proper diagnosis and treatment.