BIOCHEM 3.2 - AMINO ACIDS & NITROGEN METABOLISM

Amino Acids and Nitrogen Metabolism

Protein Degradation Mechanisms

• Protein degradation is a key part of metabolism
• Protein turnover is important for muscle development and maintenance in adults.

Amino Acids

• Essential amino acids cannot be synthesized and must be obtained through diet.
• Nonessential amino acids can be synthesized in the body.
• The need for certain amino acids in the diet is dependent on specific conditions.
• Amino acids can be connected to their source material.
• Amino acids can be identified as ketogenic or glucogenic.

Amino Acid Synthesis and Degradation

• Amino acid synthesis and degradation processes are linked to enzymatic activity and necessary cofactors.

Amino Acid Synthesis and Degradation Changes

• Changes in the synthesis or degradation of amino acids can be assessed for their causes or consequences.
• Emphasis is placed on key enzymes involved in digestion.

Urea Cycle

• The Urea cycle can be summarized and changes in the urea cycle can be assessed from the perspective of substrates, products, and enzymes.

Enzyme Changes

• The changes in enzymes required for amino acid synthesis or degradation, or in the urea cycle, can be linked to specific disorders.

Proteins: A Story of Balance

• Generation and maintenance of muscle depends on both protein and cellular turnover.
• Protein turnover is a balance between synthesis and degradation.
• Cellular turnover is a balance between generation and apoptosis.
• Turnover imbalances result in improper generation of structures.
• Regulation of mass and fiber size is predominantly due to protein turnover only in adults.
• Protein turnover imbalances can lead to atrophy.
• Muscle atrophy involves the shrinkage of myofibers due to a net loss of protein organelles and cytoplasm.
• Muscle atrophy is linked to increased proteasome activity and autophagy.

Protein Structure

• Primary structure: amino acids joined via peptide bonds.
• Secondary structure: alpha-helices and beta-pleated sheets.
• Tertiary structure: folding via side-chain interactions.
• Quaternary structure: interaction with self or other molecules.

Proteins in Metabolism

• Proteins are not typically used for energy production during normal energy times.
• Extended fasting causes muscle protein to be broken down into amino acids for new protein synthesis and keto acids for gluconeogenesis, explaining the reduction in muscle mass observed.
• Dietary proteins are needed for the amino acids that the body cannot synthesize.
• Degradation of amino acids occurs through distinct mechanisms compared to their synthesis.

Processing Proteins

• Processing of dietary proteins occurs in the oral, gastric, and intestinal phases.
• In the oral phase, salivary enzymes macerate and disintegrate food particles
• In the gastric phase, gastric pH and acid secretion facilitates pepsin activity.
• The intestinal phase involves pancreatic enzymes (trypsin, chymotrypsin, elastase, enterokinase, carboxypeptidase B) and brush border enzymes which breakdown proteins via absorption and colonic protein fermentation
• Endogenous proteins are also processed via Ub ligase, proteasomes and recycling of degradation products

Essential vs. Nonessential Amino Acids

• Essential amino acids cannot be synthesized and must be acquired through diet; these include histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine.
• Nonessential amino acids can be synthesized and include alanine, asparagine, aspartate, glutamate, and serine.
• Some amino acids are 'conditional,' in that they are made at levels that may not be sufficient for specific needs.
• Conditionally non-essential amino acids include arginine, cystine, glutamine, glycine, proline and tyrosine

Biosynthesis of Amino Acids

• Amino acid biosynthesis involves the synthesis of carbon skeletons for α-keto acids and the addition of an amino group via transamination.
• Alanine is synthesized from pyruvate via transamination.
• Aspartic acid, asparagine, arginine, glutamic acid, glutamine, and proline are synthesized from intermediates in the citric acid cycle.
• Serine is synthesized from 3-phosphoglycerate in glycolysis.
• Glycine is synthesized from serine.
• Cysteine is synthesized from serine with sulfur derived from methionine.
• Tyrosine is synthesized from phenylalanine via hydroxylation.

Amino Acid Degradation

• Glucogenic amino acids can produce glucose in the liver.
• The fumarate group results in cytoplasmic fumarate production.
• Ketogenic amino acids produce ketone bodies or acetyl CoA.

Phenylalanine Metabolism

• Dietary phenylalanine is processed into tyrosine by phenylalanine hydroxylase.
• Defects in this process can cause phenylketonuria (PKU).

Amino Acid Degradation Mechanisms

• Amino acid degradation involves three mechanisms for removing amino groups: transamination, oxidative deamination, and dehydratase-mediated removal of water.
• Transamination utilizes aminotransferases/transaminases and pyridoxal phosphate, with pyridoxamine as a reaction intermediate.
• Oxidative deamination and dehydratase-mediated removal of water are also mechanisms for amino acid degradation

Nitrogen Metabolism: Urea Cycle

• Amino acid metabolism results in excess nitrogen.
• Nitrogen is incorporated into urea from glutamate and aspartate.
• Urea generation occurs in the liver.
• Ammonia detoxification occurs via incorporation into glutamine.

Summary of Enzymes of the Urea Cycle

• Carbamoyl phosphate synthetase fixes ammonia from amino acids and requires N-acetylglutamate; deficiency leads to high blood ammonia; located in the mitochondria.
• Ornithine transcarbamoylase: a transferase, located in the mitochondria, that releases Pi and creates Citrulline
• Deficiency in ornithine transcarbamoylase leads to high blood levels of ammonia and orotic acid (due to carbamoyl phosphate shunting to pyrimidine biosynthesis).
• Argininosuccinate synthetase: A ligase, located in the cytosol, that creates argininosuccinate with high blood levels of ammonia and citrulline
• Argininosuccinate: A lyase, located in the cytosol, that cleaves argininosuccinate into fumarate and arginine with high blood levels of ammonia and citrulline
• Arginase: A hydrolase, located in the cytosol, that cleaves arginine into urea and ornithine with a moderate increase in blood ammonia and high levels of arginine

Case Study 3: Phenylketonuria (PKU)

• Autosomal recessive
• Toxic build-up of phenylalanine in blood lead to build-up in the brain and damage
• Show Variable symptoms with classic form considered most severe and skin presentations including eczema
• Pathologic mutations in PAH (phenylalanine hydroxylase) can vary
• Maternal consumption of phenylalanine particularly if the mother also has the condition can begin the damage process and cause microencephaly

Case Study 4: Urea Cycle Enzyme Deficiency, 5 month old infant

• Periodic vomiting; failure to gain weight
• Periods of irritability and lethargy
• Abnormal electroencephalogram; increased plasma ammonia
• Increased glutamine but low citrulline
• Orotate (pyrimidine nucleotide precursor) discovered in urine