CH 14: Nitrogen metabolism
Nitrogen: found in vast array of biomolecules ranging from amino acids, nitrogenous bases, porphyrins, and several lipids. In addition there are some biogenic amines and glutathione which are required in small amount also contain nitrogen.
Nitrogen fixation: useful form of nitrogen has to be converted from inert gas making the useful form scarce. Majority of nitrogen is present as inert gas. conversion of inert nitrogen to useful from (NH3) requires large amounts of energy and is carried out by only a few prokaryotuc microorganisms through this process.
rhizobium species: live in symbiosis with plants, nitrogen fixing organism.
Azotobacter vinelandii and clostridium pasteurianum: free organisms found in water, nitrogen fixing organism.
how do plants obtain their nitrogen: through the bacteria which fix atmospheric nitrogen and also absorb NH3 and NO3 from soil synthesized by soil bacteria or provided by fertilizers.
In plants, why is the amide group of the glutamine important: however plants obtain their nitrogen, it is assimilated by this group which is used to synthesize other carbon containing nitrogen compounds like amino acids, nucleotides and nucleic acids.
organisms and their amino acids: many microorganisms can synthesize all the amino acids they need. Animals on the other hand synthesize only half of the amino acids they require, known as NAA, while the other half they have to obtain from diet known as EAA.
NAA: non-essential amino acids
EAA: essential amino acids
flow of nitrogen in ecosystem: from nitrogen fixation by bacteria to plants to animals to waste to microorganisms again. This complex process of nitrogen transformation is known as ‘Nitrogen cycle’.
metabolic mechanisms for amino acids: The amino acids provided by diet are often not in correct proportion required by the body, and therefore their concentrations are adjusted by this process. excessive amounts of all NAA and EAA are degraded.
branched amino acids: concentration of certain EAA referred to as this such as Leu, Ile, and Val remain unchanged. these amino acids are used for the synthesis of many NAA.
transamination: It is a dominating chemical reaction in amino acid metabolism. This reaction is catalyzed by group of enzyme referred to as the ‘Aminotransferases’ or ‘Transaminases’. Since these reactions are readily reversible, they play important roles in both the synthesis and degradation of the amino acids.
transamination reaction process: During transamination reaction alpha-amino group is transferred from alpha-amino acid to a alpha-keto acid.
nitrogen fixation, more information: Few prokaryotic microorganisms have ability to fix atmospheric nitrogen. These include free living bacteria like A.vinelandii, C.pasteurianum and cyanobacteria (Anabaena azollae) and symbiotic bacteria (several species of Rhizobium).
what enzyme makes nitrogen fixation possible in select prokaryotes: the enzyme ‘Nitrogenase complex’. It consists of two proteins called nitrogenase (240 kD) and nitrogenase reductase (60 kD).
nitrogenase complex structure: Nitrogenase is a heterodimer that contains two Molybdenum (Mo) atoms and between 28 to 32 iron atoms, and four polypeptide subunits.
nitrogen fixation requirement: requires at least four molecules of ATP and series of electron transfers from NADH/NADPH to iron-sulfur protein ferredoxin to nitrogenase reductase to nitrogenase to nitrogen to form 2NH3.
component of oxygen in nitrogenase enzymes: both components are irreversibly inactivated by oxygen
heterocysts: in aerobic nitrogen fixing bacteria nitrogenase is contained in a specialized cells
legumes: produce oxygen-binding protein called leghemoglobin which traps oxygen before it interacts with nitrogenase complex.
amino acid biosynthesis: Plants and microorganisms can synthesize all of the amino acids required by them, while animals can synthesize some (NAA) amino acids but have to obtain some amino acids (EAA) from their diet.
amino acid functions: the building blocks of proteins. They are the source of nitrogen atoms required in various synthetic reaction pathways. The nonnitrogen parts of amino acids serve as energy source.
amino acid pool: The amino acid molecules that are immediately available for metabolic processes. derived from both the break down of dietary and tissue proteins.
amino acid functions based on body’s needs: amino acids are either synthesized or interconverted and transported to various tissue where they are used. - Transport of amino acids into cells is mediated by specific membrane bound transport proteins transporting specific amino acid.
how do synthetic reactions of amino acids occur: Once amino acids enter cells, the amino groups are available for synthetic reactions. These includes, transfer of amino group from a-amino acid to an a-keto acid (Transamination) and direct incorporation of NH4+ group into certain amino acid molecules.
type one of eukaryotic transamination: possess wide variety of aminotransferase found both in cytoplasm and mitochondria. the type of a-amino acid that donate a-amino group.
type two of eukaryotic transamination: possess wide variety of aminotransferase found both in cytoplasm and mitochondria. the type of a-keto acid that accepts the a-amino group. Most of them use ‘Glutamate’ as amino group donor.
eukaryotic transamination: Since this reaction is reversible and addition of a-amino group to a-keto glutarate produces glutamate, they are referred to as a-ketoglutarate/glutamate pair. Other such important pairs are oxaloacetate/aspartate pair and pyruvate/alanine pair.
direct incorporation of NH4: There are two principal means by which NH4 ions are incorporated into amino acids and eventually other metabolites: (1) Reductive amination of a-keto acids and. (2) formation of the amides of aspartic and glutamic acids.
synthesis of amino acids: Amino acids are synthesized via unique pathways in animals. Although they still share a common feature that, all NAA are synthesized either from glycerate-3-phosphate, pyruvate, alpha-ketoglutarate, or oxaloacetate.
exception of amino acid synthesis: tyrosine which is synthesized from essential amino acid phenyl alanine. On the basis of similarities in their synthetic pathways, they are divided in to six families: Glutamate, Serine, Aspartate, Pyruvate, the aromatics and histidine. The amino acids in each family are ultimately derived from one precursor molecule.
the glutamate family: includes in addition to glutamate,-glutamine, proline, and arginine. Glutamate is formed from alpha-ketoglutarate by reductive amination. Glutamate is very important amino acid since apart from being a part of protein, it is also used in central nervous system as an excitatory neurotransmitter.
glutamine synthase: conversion of glutamate to glutamine is catalyzed by this enzyme.
reaction of glutamate to glutamine: This is a transamination reaction where branched chain amino acids (BCAA) serve as amino group donor. Glutamine serves as part of protein as well as amino group donor in many important reactions and also serves as energy source.
proline cyclization: cyclized derivative of glutamate.
formation of proline from glutamate: negatively controlled by feed back inhibition by proline of the first enzyme g-glutamyl kinase.
arginine synthesis: begins with acetylation of a-amino group of glutamate. N-acetylglutamate is then converted to Ornithine which is converted to arginine through a part of urea cycle.
the serine family: include, serine, glycine, and cysteine. All of them are derived from glycolytic intermediate glycerate-3-phosphate. Amino acids in this family perform many important functions.
what is serine a precursor of: ethanolamine, and sphingosine.
role of glycine in serine family: is used in the purine, porphyrin, and glutathione synthetic pathways. formed from serine via a single complex reaction catalyzed by an enzyme Serine hydroxymethyltransferase. Serine is the major source of glycine. cysteine role in serine family: plays a significant role in sulfur metabolism.
role of serine in the serine family: synthesized directly from glycerate-3-Phosphate via dehydrogenation, transamination, and hydrolysis by a phosphatase. This pathway is controlled by feedback inhibition of phosphatase by cellular concentration of serine. High protein diet can also inhibit serine biosynthesis.
cytosine biosynthesis in serine family: carbon skeleton is derived from serine while sulfhydryl group is transferred from methionine.
neurotransmitters: More than 30 different substances have been proven or proposed to act as neurotransmitters. can be either excitatory or inhibitory in nature. a significant percentage of neurotransmitter molecules are either amino acids or amino acid derivatives.
biogenic amines: The amino acid derivatives are also referred to as this.
derivatives of tyrosine: The catecolamines- dopamine, norepinephrine, and epinephrine.
dopamine and norepinephrine: used as excitatory neurotransmitter in brain.
GABA: is formed by decarboxylation of glutamate acts as an inhibitory neurotransmitter in the central nervous system.
serotonine: formed from tryptophan regulates feeding and is responsible for conditions such as Bulimia, and anorexia nervosa.
histamine: produced in many cells through out the body acts as a mediator of allergic and inflammatory reactions, a stimulator of gastric acid production, and a neurotransmitter in several areas of brain. It is formed by decarboxylation of L-histidine.
nitric oxide (NO): Nitric oxide is formed in many cells and it plays role in dialation of blood vessels, inhibition of platelet aggregation and destruction of foreign or damaged cells by macrophages. In brain it is linked with the neurotransmitter function of glutamate.