Biochemistry - Chapter 30: Amino Acid Degradation and the Urea Cycle

Amino acids

Amino acids are obtained from the diet when proteins are digested. Cellular proteins are degraded to amino acids because of damage or for regulatory purposes. The first priority for use of amino acids is as precursors for proteins or other biomolecules. Amino acids are not stored, so any excess amino acids are degraded. Amino acids are the source of nitrogen in our body

Overview of Amino Acid Catabolism Diagram

An early step in the catabolism of amino acids is the separation of the amino group from the carbon skeleton. Removed amino groups produce ammonia, and ammonia is removed through Urea cycle. Carbon skeletons may be used for ATP production.

You are making a chemical modeling kit to make amino acids. What elements should be included in this kit?

C, O, H, N, S

Urea synthesis in mammals takes place primarily in tissues of the

Liver

Many aquatic animals release ammonia to their environment.

passive diffusion from epithelial cells active transport via gills

Removing Amino Groups: Two Steps

1. Transamination: Amino groups from amino acids are funneled to glutamate 2. Oxidative deamination of glutamate to form NH4+. Aminotransferases (transaminases) transfer amino groups from an amino acid to α-ketoglutarate to generate glutamate.

The Glucose-Alanine Cycle Diagram

During extensive exercise or prolonged fasting, muscles use brunched amino acids for energy, and NH4+ formed as a byproduct. NH4+ is toxic, so it must be disposed. In the liver it is processed through urea cycle. But Urea cycle enzymes are not available in muscles, it is a liver-specific process. So NH4+ should be transferred to the liver to go through Urea cycle. One of the ways to get rid of NH4+ in the muscle is a Glucose-Alanine Cycle. Ammonia is combined with pyruvate to make glutamate, and glutamate is transformed to the alanine, Alanine is to be transported out of the cell into the bloodstream and to be absorbed by hepatocytes. Alanine in the liver undergoes this pathway, but in reverse. We get pyruvate and ammonia. Liver uses the urea cycle to get rid of toxic ammonia. Also liver is the place where gluconeogenesis runs. So pyruvate is used to make glucose and to e transported back to muscles through bloodstream. Alanine serves as a carrier of ammonia and of the carbon skeleton of pyruvate from skeletal muscle to liver. The ammonia is excreted and the pyruvate is used to produce glucose, which is returned to the muscle.

PATHWAY INTEGRATION: The glucose-alanine cycle.

During prolonged exercise and fasting, muscle uses branched-chain amino acids as fuel. The nitrogen removed is transferred (through glutamate) to alanine, which is released into the bloodstream. In the liver, alanine is taken up and converted into pyruvate for the subsequent synthesis of glucose.

The Urea Cycle

Excess NH4+ is converted into urea by the urea cycle. Organisms that excrete excess NH4+ as urea are called ureotelic organisms. In humans, the urea cycle occurs in the liver.

Amino group catabolism

Excretory forms of nitrogen. Excess NH4+ is excreted as ammonia (microbes, bony fishes), urea (most terrestrial vertebrates), or uric acid (birds and terrestrial reptiles). Notice that the carbon atoms of urea and uric acid are highly oxidized; the organism discards carbon only after extracting most of its available energy of oxidation.

Fates of the carbon skeletons of amino acids.

Glucogenic amino acids are shaded red, and ketogenic amino acids are shaded yellow. Several amino acids are both glucogenic and ketogenic. The carbon skeletons of the amino acids are metabolized to seven major metabolic intermediates: pyruvate, acetyl CoA, acetoacetyl CoA, α-ketoglutarate, succinyl CoA, fumarate, and oxaloacetate. Amino acids metabolized to acetyl CoA and acetoacetyl CoA are called ketogenic amino acids because they can form fats but not glucose. Amino acids degraded to the remaining major intermediates are called gluconeogenic amino acids because they can be used to synthesize glucose. Only leucine and lysine are solely ketogenic.

Urea cycle: Steps 3 to 5

In the cytoplasm Citrulline condenses with Aspartate to form Argininosuccinate. Aspartate is the donor of the second amino group in the urea molecule. Then argininosuccinate is cleaved into Arginine and Fumarate. Finally , Arginine is hydrolyzed to generate urea and ornithine. Ornithine is transported back to mitochondria. Fumarate is the link between urea cycle and gluconeogenesis. Carbon skeleton of Aspartate is reutilized as Fumarate Urea: O came from water; C from CO2; one N from free NH3, and another N from the Aspartate. Urea is not very toxic. It is transported into the blood and removed by kidneys.

Overview of Amino Acid Catabolism

Once broken down to amino acid, all types of protein are treated the same way dependent on the organism's energy needs: 1. Recycled into new proteins 2. Oxidized for energy - removal of amino group (urea cycle) - entry into central metabolism (glycolysis, citric acid cycle) The major site of amino acid degradation in mammals is liver.

Ammonia Collected in Glutamate Is Removed by Glutamate Dehydrogenase

Oxidative deamination occurs within mitochondrial matrix in liver cells. This reaction is catalyzed by glutamate dehydrogenase. It is the only enzyme that can use either NAD+ or NADP+ as electron acceptor Ammonia is processed into urea for excretion (liver-specific reaction). The a-ketoglutarate formed can be used in the CAC and for glucose synthesis

Excretory Forms of Nitrogen

Plants conserve almost all the nitrogen. Many aquatic animals release ammonia to their environment. Many terrestrial vertebrates and sharks excrete nitrogen in the form of urea. Some animals such as birds and reptiles excrete nitrogen as uric acid. Humans and great apes excrete both urea (from amino acids) and uric acid (from purines).

Enzymatic Transamination to Glutamate

Release of free ammonia is toxic. Ammonia is captured by a series of transaminations. Transaminations allow transfer of an amine to a common metabolite (e.g., α-ketoglutarate) and generate a trafficable amino acid (e.g., glutamate).

Step 1: Removal of the Amino Group

Release of free ammonia is toxic. Ammonia is captured by a series of transaminations. Transaminations allow transfer of an amine to a common metabolite (e.g., α-ketoglutarate) and generate a trafficable amino acid (e.g., glutamate).

Carbamoyl Phosphate Reacts with Ornithine to Begin the Urea Cycle

The carbamoyl group is transferred to ornithine by ornithine transcarbamolyase to form citrulline. Citrulline is transported out of the mitochondria into the cytoplasm in exchange for ornithine. Ornithine and citrulline are amino acids, but these amino acids are not building blocks of proteins. Citrulline is transported into cytoplasm in exchange for ornithine.

Reaction catalyzed by glutamate dehydrogenase

The glutamate dehydrogenase of mammalian liver has the unusual capacity to use either NAD+ or NADP+ as cofactor. The glutamate dehydrogenases of plants and microorganisms are generally specific for one or the other. The mammalian enzyme is allosterically regulated by GTP and ADP. The reason for toxic ammonia to be produced inside of mitochondria is to keep it away from cytoplasm.

Deamination of Branched-Chain Amino Acids

The liver cannot deaminate the branched-chain amino acids Branched-Chain Amino Acids: Isoleucine, Leucine, Valine Other tissues, mostly muscles, use brunched amino acids as a source of fuel

The metabolic context of nitrogen metabolism

The urea cycle, citric acid cycle, and the transamination of oxaloacetate are linked by fumarate and aspartate.

Enzymatic Transamination

Transamination is a common way to move amines from one molecule to another. Transamination is catalyzed by aminotransferases. Typically, a-ketoglutarate accepts amino groups. Transfer of one amine to a-ketoglutarate results in synthesis of glutamate (e.g., transamination). Glutamate is transported to liver mitochondria

Ammonia is safely transported in the bloodstream as glutamine

l-Glutamine acts as a temporary storage of nitrogen. l-Glutamine can donate the amino group when needed for amino acid biosynthesis Excess of ammonia in tissues is added to glutamate to form glutamine, a process catalyzed by glutamine synthetase. After transport in the bloodstream, the glutamine enters the liver and NH4+ is liberated in mitochondria by the enzyme glutaminase.

Urea cycle: Steps 1 and 2

Urea cycle occurs mostly in hepatocytes, in the liver, but also in kidneys. Urea cycle includes 5 steps: Steps 1-2 are in the matrix of mitochondria; steps 3-5 are in the cytoplasm; Step 1: coupling of free NH4+ with CO2 in the form of bicarbonate to form carbamoyl phosphate (ATP required). It is the committed reaction of the urea cycle. Carbamoyl synthetase is a key regulatory enzyme of the urea cycle. Step 2: Carbamoyl phosphate is passed to Ornithine to form Citrulline

Many terrestrial vertebrates and sharks excrete nitrogen in the form of urea.

Urea is far less toxic that ammonia. Urea has very high solubility

Some animals such as birds and reptiles excrete nitrogen as uric acid.

Uric acid is rather insoluble. Excretion as paste allows the animals to conserve water.

The Glucose-Alanine Cycle

Vigorously working muscles operate nearly anaerobically and rely on glycolysis for energy. Glycolysis yields pyruvate. If not eliminated, lactic acid will build up. This pyruvate can be converted to alanine for transport into the liver.

All enzyme-catalyzed aminotransferase reactions remove amino groups from amino acids, producing what byproduct?

an α-ketoacid