chapter 23 the metabolism of nitrogen mary k. campbell shawn o. farrell paul d. adams university of...

Chapter 23The Metabolism of Nitrogen

Mary K. CampbellShawn O. Farrellhttp://academic.cengage.com/chemistry/campbell

Paul D. Adams • University of Arkansas

Nitrogen Fixation

• Nitrogen fixation is the reduction of ____________:

• 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

• N2 to NH4+is a six-electron reduction

The Path of Electrons from Ferrodoxin to N2

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 ______ ____________

Amino Acid Biosynthesis

• Common features of amino acid biosynthesis include: _________________ & _____________________ transfers

• Glutamate is formed by reductive amination of -ketoglutarate and NH4

+

• Amidation of glutamate gives glutamine

• All amino acids are grouped into families based on their __________________________________

Amino Acid Biosynthesis

Amino Acids and The Citric Acid Cycle

Role of Pyridoxal Phosphate in Amino Acid Rxns

• The biologically active form of vitamin ______ 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 ______________________

Role of Pyridoxal Phosphate in Amino Acid Rxns

Role of Pyridoxal Phosphate in Amino Acid Rxns

• Transamination reactions switch ____________ ___________ from one amino acid to an -keto acid

A Transamination Rxn Produces Serine

Serine to Glycine

• 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

• Reduction of folic acid gives tetrahydrofolic acid (THF), the ________________ form of the coenzyme

• Tetrahydrofolate is a carrier of the one-carbon groups shown in Figure 23.11 (see next slide)

Structure and Reactions of Folic Acid

Serine to Cysteine

• In ____________ & ____________, 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

Methionine

• Methionine cannot be produced in animals, making it an _________ amino acid

• Methionine reacts with ATP to form S-adenosylmethionine (SAM)

Cysteine in Animals

• SAM is a _________________________________• The 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 ____________ and are called essential amino acids

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 end product• _________________ amino acid:_________________ amino acid: one whose carbon

skeleton is degraded to pyruvate or oxaloacetate, both of which may then be converted to glucose

• _________________ amino acid:_________________ 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

Amino Acid Catabolism

The -amino group which has been transferred to -ketoglutarate has one of two fates:

1. It may be used for biosynthesis

2. 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 nitrogen atoms come from several sources

• Steps of the cycle are outlined in Figure 23.18 (next slide)

The

Ure

a C

ycle

Fig

23.

18,

p.68

8

The

Ure

a C

ycle

Fig

23.

19,

p.69

0

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 ______________ • Others give rise to acetyl-CoA or acetoacetyl-CoA,

which can form _______________

• 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 _____________ _______________

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

Purine nucleotide biosynthesis is regulated by __________________

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 allow some purines to be reused

Purine Catabolism

Purine Salvage

Pyrimidine Biosynthesis and Catabolism

• The overall scheme of pyrimidine biosynthesis differs from that of purines because the pyrimidine ring is assembled ___________ 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 _________________ step in pyrimidine biosynthesis

Pyrimidine Biosynthesis and Catabolism

Pyrimidine Biosynthesis and Catabolism

Pyrimidine Biosynthesis and Catabolism

• Feedback inhibition in pyrimidine nucleotide biosynthesis takes place in several ways

Pyrimidine Biosynthesis and Catabolism

• 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

• _______________ is the reducing agent

Conversion of Ribonucleotides to Deoxyribonucleotides

Conversion of dUDP to dTTP

The addition of a methyl group to uracil to produce thymine requires ___________________ as the one-carbon carrier.

This process is a target for cancer chemotherapy

Thymidylate Synthase