BIOCHEMISTRY

YUSRON SUGIARTO

Amino Acid OxidationProduction of Urea

• Metabolic Fates of Amino Groups• Nitrogen Excretion and the Urea Cycle• Pathways of Amino Acid Degradation

Key topics:

Oxidation of Amino Acids is a Significant Energy-Yielding Pathway in Carnivores

• Not all organisms use amino acids as the source of energy

• About 90% of energy needs of carnivores can be met by amino acids immediately after a meal

• Only a small fraction of energy needs of herbivores are met by amino acids

• Microorganisms scavenge amino acids from their environment for fuel

Metabolic Circumstances of Amino Acid Oxidation

Amino acids undergo oxidative catabolism under three circumstances:

• Protein amino-acid residues from normal turnover are recycled to generate energy and molecular components

• Dietary amino acids that exceed body’s protein synthesis needs are degraded

• Proteins in the body are broken down to supply amino acids for catabolism when carbohydrates are in short supply (starvation, diabetes mellitus),

Dietary Proteins are Enzymatically Hydrolyzed

• Pepsin cuts protein into peptides in the stomach

• Trypsin and chymotrypsin cut proteins and larger peptides into smaller peptides in the small intestine

• Aminopeptidase and carboxypeptidases A and Bdegrade peptides into amino acids in the small intestine

Enzymatic Degradation of Dietary Proteins

• (a) gastrin -> secretion of HCl by parietal cells and pepsin by chief cells

• (b) exocrine cells synthesize zymogens

• zymogen granules fuse with plasma membrane

• zymogens released into the lumen of the collecting duct

• collecting ducts -> pancreatic duct -> small intestine.

• (c) Amino acids -> villi -> capillaries

OVERVIEW OF AMINO ACID CATABOLISM

THE AMINO GROUP IS REMOVED FROM ALL AMINO ACIDS FIRST

Fates of Nitrogen in Organisms• Plants conserve almost all the nitrogen• Many aquatic vertebrates release ammonia to their environment

• Passive diffusion from epithelial cells• Active transport via gills

• 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 to conserve water

• Humans and great apes excrete both urea (from amino acids) and uric acid (from purines)

Excretory Forms of Nitrogen

Enzymatic Transamination• Typically, -ketoglutarate

accepts amino groups

• L-Glutamine acts as a temporary storage of nitrogen

• L-Glutamine can donate the amino group when needed for amino acid biosynthesis

• All aminotransferases rely on the pyridoxal phosphate cofactor

Structure of Pyridoxal Phosphate and Pyridoxamine Phosphate

• Intermediate, enzyme-bound carrier of amino groups

• Aldehyde form can

react reversibly with

amino groups

• Aminated form can

react reversibly with

carbonyl groups

Pyridoxal Phosphate is Covalently Linked to the Enzyme at Rest

• The linkage is made via an nucleophilic attack of the amino group an active-site lysine side chain

• After dehydration, a Schiff base linkage is formed

• The covalent complex is called internal aldimine because the Schiff base connects PLP to the enzyme

Internal Aldimine in Aspartate Aminotransferase (Lys258-purple)

PLP (red) bound to one ofthe two active sites of the dimericenzyme aspartate aminotransferase,a typical aminotransferase

another close-up view of the active site,with PLP linked to the substrate analog 2-methylaspartate (green) via aSchiff base (PDB ID 1AJS).

Chemistry of the Amino Group Removal by the Internal Aldimine

• The external aldimine of PLP is a good electron sink, allowing removal of -hydrogen

PLP Also Catalyzes Racemization of Amino Acids

• The external aldimine of PLP is a good electron sink, allowing removal of -hydrogen

PLP Also Catalyzes Decarboxylation of Amino Acids

• The external aldimine of PLP is a good electron sink, allowing removal of -carboxylate

Ammonia in Transported in the Bloodstream Safely as Glutamate

• Un-needed glutamine

is processed in

intestines, kidneys

and liver

Glutamate can Donate Ammonia to Pyruvate to Make Alanine

• Vigorously working muscles

operate nearly anaerobically

and rely on glycolysis for

energy

• Glycolysis yields pyruvate that

muscles cannot metabolize

aerobically; if not eliminated

lactic acid will build up

• This pyruvate can be

converted to alanine for

transport into liver

Excess Glutamate is Metabolized in the Mitochondria of Hepatocytes

The Glutamate Dehydrogenase Reaction

• Two-electron oxidation of glutamate followed by hydrolysis

• Net process is oxidative deamination of glutamate

• Occurs in mitochondrial matrix in mammals

• Can use either NAD+ or NADP+ as electron acceptor

Ammonia is Re-captured via Synthesis of Carbamoyl Phosphate

• This is the first nitrogen-acquiring reaction

Nitrogen from Carbamoyl Phosphate Enters the Urea Cycle

The Reactions in the Urea Cycle

• 1 ornithine + carbamoyl phosphate => citrulline • (entry of the first amino group).• citrulline passes into the cytosol.

• 2a citrulline + ATP => citrullyl-AMP + PPi• 2b citrullyl-AMP + Aspartate => argininosuccinate + AMP

• (entry of the second amino group).

• 3 argininosuccinate => arginine + fumarate• fumarate enters the citric acid cycle.

• 4 arginine => urea + ornithine• Ornithine passes to the mitochondria to continue the cycle

UREA CYCLE N-2 FROM ASPARTATE

Aspartate –Arginosuccinate Shunt Links Urea Cycle and Citric Acid Cycle

Not All Amino Acids can be Synthesized in Humans

• These amino acids must be obtained as dietary protein

• Consumption of a variety of foods (including vegetarian only diets) well supplies all the essential amino acids

Fate of Individual Amino Acids• Seven to acetyl-CoA

• Leu, Ile, Thr, Lys, Phe, Tyr, Trp

• Six to pyruvate• Ala, Cys, Gly, Ser, Thr, Trp

• Five to -ketoglutarate• Arg, Glu, Gln, His, Pro

• Four to succinyl-CoA• Ile, Met, Thr, Val

• Two to fumarate• Phe, Tyr

• Two to oxaloacetate • Asp, Asn

Summary of Amino Acid Catabolism

Summary of Amino Acid Catabolism

Summary

• Amino acids from protein are an important energy source in carnivorous animals

• Catabolism of amino acids involves transfer of the amino group via PLP-dependent aminotransferase to a donor such as -ketoglutarate to yield L-glutamine

• L-glutamine can be used to synthesize new amino acids, or it can dispose of excess nitrogen as ammonia

• In most mammals, toxic ammonia is quickly recaptured into carbamoyl phosphate and passed into the urea cycle

In this chapter, we learned that: