Chapter Twenty-Three The Metabolism of Nitrogen

Nitrogen Fixation Nitrogen fixation is the reduction of N 2 to NH 3 : Bacteria are responsible for the reduction and typically form symbiotic relationships that result in nodules on the roots of leguminous plants Reduction is catalyzed by the nitrogenase enzyme complex N 2 to ammonium ion is a six-electron reduction

The Path of Electrons from Ferrodoxin to N 2

Summary Nitrogen enters the biosphere by the process of nitrogen fixation. Atmospheric nitrogen is converted to ammonia in its conjugate acid form, ammonium ion. The nitrogenase enzyme found in root nodules of leguminous plants catalyzes crucial reactions in nitrogen fixation

Feedback Inhibition in Nitrogen Metabolism If there is a high level of end product amino acid or nucleotide, the cell saves energy by not making the compound through a feedback mechanism In summary, because the biosynthetic pathways for many nitrogen-containing compounds are long and complex, feedback inhibition helps save energy

Amino Acid Biosynthesis Common features of amino acid biosynthesis include: transamination and one-carbon transfers Glutamate is formed by reductive amination of  -ketoglutarate and NH 4 + Amidation of glutamate gives glutamine All amino acids are grouped into families based on their biosynthetic pathways

Amino Acid Biosynthesis (Cont’d)

Amino Acids and The Citric Acid Cycle

Role of Pyridoxal Phosphate in Amino Acid Reactions The biologically active form of vitamin B 6 is pyridoxal phosphate (PyrP) PyrP participates in the catalysis of a wide variety of reactions of amino acids, including transaminations and decarboxylations Pyridoxal phosphate forms an imine (a Schiff base) with the  -amino group of an amino acid Rearrangement gives an isomeric imine Hydrolysis of the isomeric imine gives an  -ketoacid and pyridoxamine All reactions are reversible

Role of Pyridoxal Phosphate in Amino Acid Reactions (Cont’d)

Transamination reactions switch amino groups form one amino acid to an  -keto acid

A Transamination Reaction Results in Generation of Serine

Serine to Glycine Involves the Transfer of a One-Carbon Unit Serine to glycine is an example of a one-carbon transfer The one-carbon acceptor is tetrahydrofolate, which is derived from folic acid

Serine to Glycine Involves the Transfer of a One-Carbon Unit (Cont’d) Reduction of folic acid gives tetrahydrofolic acid (THF), the reactive form of the coenzyme Tetrahydrofolate is a carrier of the one-carbon groups shown in Figure (see next slide)

Structure and Reactions of Folic Acid

Serine to Cysteine In plants and bacteria, serine is acetylated to form O- acetylserine The source of sulfur in plants and bacteria differ from that in animals Sulfur donor comes from PAPS (3’-Phospho- 5’adenylylsulfate)

Serine to Cysteine (Cont’d)

Methionine Methionine cannot be produced in animals, making it an essential amino acid Methionine reacts with ATP to form S- adenosylmethionine (SAM)

Cysteine in Animals SAM is a methyl group carrier and this methyl group can be transferred to a number of acceptors producing S-adenosylhomocysteine

Summary Two of the most important classes of reactions in the biosynthesis of amino acids are transamination reactions and one-carbon transfers The amino acids glutamate and glutamine are the principal donors of amino groups in transamination reactions Carriers of one-carbon groups include biotin, SAM, and derivatives of folic acid

Essential Amino Acids The biosynthesis of proteins requires the presence of all the constituent amino acids Some species, including humans, cannot produce all of the amino acids and they must come from the diet, and are called essential amino acids In Summary: Humans cannot produce some amino acids in sufficient quantities to meet their metabolic needs. These are called essential amino acids The essential amino acids must come from other dietary sources

Amino Acid Catabolism First step is removal of the  -amino group by transamination  -amino group is transferred to  -ketoglutarate to give glutamate and an  -ketoacid The breakdown of carbon skeletons follows two pathways, depending on the type of endproduct Glucogenic amino acid: Glucogenic amino acid: one whose carbon skeleton is degraded to pyruvate or oxaloacetate, both of which may then be converted to glucose Ketogenic amino acid: Ketogenic amino acid: one whose carbon skeleton is degraded to acetyl-CoA or acetoacetyl-CoA, both of which may then be converted to ketone bodies

Amino Acid Catabolism (Cont’d)

The  -amino group which has been transferred to  - ketoglutarate has one of two fates: It may be used for biosynthesis It may be excreted as a part of a nitrogen- containing product

The Urea Cycle The urea cycle is the central pathway in nitrogen metabolism The nitrogens come from several sources Steps of the cycle are outlined in Figure (see next slide)

The Urea Cycle (Cont’d)

Summary The carbon skeleton has two fates in the breakdown process. Some carbon skeletons give rise to pyruvate or oxaloacetate, which can be used in gluconeogenesis. Others give rise to acetyl-CoA or acetoacetyl-CoA, which can form lipids The urea cycle, which has links to the citric acid cycle, plays a central role in nitrogen metabolism. It is involved in both the anabolism and the catabolism of amino acids

Purine Biosynthesis Where do the atoms of purines come from?

How is IMP converted to AMP and GMP IMP is the precursor to AMP and GMP, and the conversion takes place in 2 stages

Regulation of ATP and GTP by Feedback Inhibition Purine nucleotide biosynthesis is regulated by feedback inhibition In Summary: The growing ring system of purines is attached to ribose phosphate during the synthesis process The biosynthesis of nucleotides requires considerable expenditures of energy by organisms in long and complex pathways. Feedback inhibition at all stages plays a key role in regulating the pathway

Purine Catabolism The catabolism of purine nucleotides proceeds by hydrolysis to the nucleoside and subsequently to the free base, which is further degraded Salvage reactions are important in the metabolism of purine nucleotides because of the amount of energy required for the synthesis of the purine bases In Summary: Purines are degraded to uric acid in primates and are further degraded in other organisms. Overproduction of uric acid causes gout in humans Salvage reactions exist so that some purines can be reused

Purine Catabolism (Cont’d)

Purine Salvage

Pyrimidine Biosynthesis and Catabolism The overall scheme of pyrimidine biosynthesis differs from that of purines because the pyrimidine ring is assembled before it is attached to ribose-5- phosphate Carbon and Nitrogen atoms of the pyrimidine ring come from carbamoyl phosphate and aspartate The production of N-carbamoylaspartate is the committed step in pyrimidine biosynthesis

Pyrimidine Biosynthesis and Catabolism (Cont’d)

Feedback inhibition in pyrimidine nucleotide biosynthesis takes place in several ways

Pyrimidine Biosynthesis and Catabolism (Cont’d) Pyrimidine catabolism involves the breakdown of the molecule first to the nucleoside, and then to the base This is similar to what happens in purine catabolism

Summary The ring system of pyrimidines is assembled before it is attached to ribose phosphate During breakdown, the nucleoside is formed first, then the base. Ring-opening reactions of the base complete the degradation

Conversion of Ribonucleotides to Deoxyribonucleotides Ribonucleoside diphosphates are reduced to 2’- deoxyribonucleoside diphosphates in all organisms NADPH is the reducing agent

Conversion of Ribonucleotides to Deoxyribonucleotides (Cont’d)

Conversion of dUDP to dTTP The addition of a methyl group to uracil to produce thymine requires tetrahydrofolate as the one-carbon carrier. This process is a target for cancer chemotherapy

Thymidylate Synthase

Problem set 4, 6, 7, 10, 11, 12, 13, 16, 17, 20, 31, 33, 35, 38, 39, 40, 41, 45, 48, 49, 51 No homework!!