Lectures 27/28: Amino Acid Metabolism Flashcards
Nitrogen
Essential element found in amino acids, nitrogenous bases and many other molecules
Biologically available nitrogen is scarce
Nitrogen Fixation
Reduction of N2 by prokaryotic microorganisms to form NH3
Often rate limiting factor in plant growth
High energy requirement
Nitrogen often rate limiting factor in plant growth
Conversion into amide group of glutamine
Catalyzed by nitrogenase complex
Free-living cyanobacteria
Most prominent nitrogen-fixing species
Symbiotic bacteria
Most prominent nitrogen-fixing species
Nitrogen assimilation
Incorporation of inorganic nitrogen compounds into organic molecules
Roots in plants
NH4+ or NO3- incorporated into amino acids
NO3
As nitrogen source, two step reaction is used to convert it to NH4+ by nitrite reductase
Glutamine synthetase
Catalyzes ATP-dependent reaction of glutamate with NH4+ to form glutamate
Found in all organisms
Entry point in microorganisms for fixed nitrogen
Uses ATP
Glutamate + ammonium to glutamine: formation of irreversible amide bond
Phytoplankton bloom
Can trigger dead zone formation
Decomposition carried out by aerobic bacteria: increased oxygen use by bacteria, O2 levels drop, hypoxic conditions for fish
Glutamate synthase
Produces glutamate from glutamine and alpha-ketoglutarate
Only bacteria and plants
Together with glutamine synthase leads to assimilation
Does not use ATP
2 Glutamate yield: Can enter glutamine synthetase reaction
Only in plants and microorganisms
Glutamine
Acts as amino group carrier
Synthesis in peripheral tissues and transport to liver also transports amino groups
Amino acids
Protein monomeric units
Energy metabolites: can be converted into pyruvate, oxaloacetate, or TCA intermediates
Some can only be converted into acetyl CoA, ketone bodies or fatty acids
Precursors for many biologically active nitrogen-containing compounds
Signalling molecules
Essential and non-essential
Essential amino acids
Must be taken up with diet
Non-essential amino acids
Can be synthesized by body
Plants and microorganisms have enzymes for the synthesis of all 20 amino acids
Transamination
Catalyzed by aminotransferase (transaminase)
Reaction with alpha-ketoacid to yield another amino acid and alpha-ketoglutarate
Transaminase
All have pyridoxal phosphates as prothetic group
Pyritical phosphate
Derived from pyridoxine VitB6
Aspartate aminotransferase
alpha-ketoglutarate + aspartate = glutamate + oxaloacetate
Malate-Asparate shuttle
Relies on transamination of aspartate and oxaloacetate
Indirectly transfers NADH into mitochondrial matrix
Malate in exchange for KG, Asp in exchange for Glu
Amination/deamination
Catalyzed by glutamate dehydrogenase in mitochondrial matrix
Degradation of amino acid to give KG: reversible
Direction determined by reactant concentrations
Amidation
Formation of amide bond: irreversible
Glutamine synthetase converts glutamate + NH4+ to glutamine
Costs ATP
Deamidation
Catalyzed by glutaminase
Conversion of glutamine to glutamate
Reverse of glutamine syntheses reaction
Amino acid synthesis
Animals synthesize from intermediates of glycolysis and citric acid cycle
Bacteria and plants synthesize with sulfur, branched chains, aromatic groups, histidine, lysine and threonine
Cysteine synthesis
Can be made from methionine
Not sufficient: essential aa
Glutamate formation
From KG by reductive lamination or transamination
Neurotransmitter in brain: conversion to glutamine prevents overstimulation and neurotoxicity
Glutamine-glutamate shuttle
In brain
Neurons secrete glutamate as NT: too much extracellular is toxic
Astrocytes (surrounding neutrons) take up glutamate and convert it to glutamine
Glutamine is secreted and taken up by neurons and converted back
Aspartate
Synthesized from oxaloacetate by transamination
Asparagine, methionine, threonine, lysine and isoleucine are synthesized from aspartate
Asparagine synthetase
Synthesizes aspartate into asparagine
Serine
Derives carbon skeleton from glycolytic intermediate 3-phosphoglycerate
Served from 3-phosphoglycerate via dehydration, transamination and hydrolysis
Precursor for sphingolipids and phospatidylserine
Enantiomer D-serine is neuromodulator
Glycine
Hydromethyl group transfer reaction from serine
Neurotransmitter
Cysteine
Serine plus sulphur group from another amino acid
Thiol group is redox active
Precursor for glutathione
Glutathione
Antioxidant
Tripeptide of glutamate of cysteine and glycine
Cysteine is lease abundant: supply is rate limiting
reacts with peroxide to give non-reactive thiols
GSSG in oxidized form
One-Carbon metabolism
Describes metabolic pathways that are connected to reactions involving the transfer of single carbons: methyl groups of different oxygen states equivalent of methanol, formaldehyde and formate
Includes folate metabolism, methylation cycle and transsulfuration
Most important carriers of 1-C groups: folic acid and S-adenosylmethionine
Folic Acid
B vitamin (B9) Once absorbed by the body, converted to tetrahydrofolate (THF) One of most important carriers of 1-C groups Very important during development Decreased prevalence of neural tube defects following folate fortification of flour
S-adenosylmethionine
Derivative methionine
One of most important carriers of 1-C groups
Tetrahydrofolate
Synthesized from folic acid/folate/vitamin B9, requires NADPH
Carrier of 1-C units in several reactions of amino acids and nucleotide metabolism: carrier of methyl groups in different oxidation states
Accepts methyl group from serine to convert serine to glycine
Serine hydroxymethyltransferase
Catalyzes transfer of methyl-group from serine to tetrahydrofolate to convert serine to glycine
Folate metabolism
Required for serine to indirectly supply methyl groups for methionine synthesis, B6 and B12 are also required
Methylation requires 3 phosphates
Methionine synthase
Works with B12
Synthesizes methionine from homocysteine by taking methyl group from 5-methyl-THF to convert it to THF
Methionine
Converted from homocysteine by accepting methyl group from 5-methyl-THF
Converted into S-adenosyl-methionine by using 3 phosphates
S-adenosyl-methionine
Converted from methionine
Methylated into S-adenosyl-homocysteine
S-adenosyl-homocysteine
Addition of H2O and release of adenosine to give homocysteine
DNA methylation
Methylation of cytosine to 5-methyl cytosine
Catalyzed by DNA transferases
Regulates transcription without changes in DNA sequence
Epigenetics
DNA methylation
Importance of methylation reactions
DNA methylation (epigenetic)
Phosphatidylcholine synthesis (from phosphatidylethanolamine)
Thymidine synthesis (dTMP from dUMP)
Purine synthesis
Synthesis of carnitine, creatine, epinephrine and other products
Amino acids and signalling molecules
Glutamate and glycine as neurotransmitters
Other neurotransmittedrs/neuromodulators derived form amino acids
Catecholamines
Nitric oxide
GABA
NT derived from glutamate
Dopamine
From tyrosine
Serotonin
From tryptophan
Melatonin
From tryptophan
D-Serine
NT
By racemizaton of L-serine
D-aspartate
NT
By racemizaton of L-aspartate
Catecholamines
Epinephrine, norepinephrine, dopamine
Derivatives of tyrosine
Nitric Oxide
From precursor arginine
Nitric oxide synthase
Reacts with arginine and NADPH and oxygen to citrulline, NO, NADP+ and water
Purine synthesis
AMP and GMP
Requires glutamine, glycine, aspartate, bicarbonate and methyl groups
ATP promotes GMP synthesis
GTP promotes AMP synthesis: two purine will be present in roughly equal amounts
Pyrimidine synthesis
UMP and CMP
Requires glutamine, aspartate, bicarbonate
dUMP is methylated to generate dTMP
CTP inhibits pyrimidine synthesis (negative feedback)
ATP is feedforward activator for pyrimidine synthesis
Deoxyribonucleotide synthesis
ATP, GTP, CTP and UTP are dephosphorylated, then reduced to deoxyribonucleotides by ribonucleotide reductase and phosphorylated again: requires NADPH
Ribonucleotide reductase
Reduces dephosphorylated ATP, GTP, CTP and UTP to deoxyribonuceotides
Two regulatory sites: 1 to regulate overall activity, and one to regulate substrate specificity (overall synthesis and relative amount of the different dNTP)
Activated by ATP
dATP decreases activity
Binding of purine ATP: reductase prefers pyrimidines
Binding of pyrimidine dTTP: reductase prefers purine GDP
Protein degradation
By proteasome or lysosomal proteases
Each protein has a biological half-life
Most amino acids are degraded to precursors for gluconeogenesis: carbon skeleton of amino acids resemble energy metabolites and can be oxidized for energy
Lysosomes
Internal vesicular organelles that have very low pH
Contain many different proteases
Usually takes place after endocytosis of extracellular and membrane material
Intracellular material and whole organelles can also be packaged into large double-membrane vesicles which fuse with lysosomes for degradation: autophagy
Autophagy
Intracellular material and whole organelles can be packaged into large double-membrane vesicles which fuse with lysosomes for degradation
Proteasomal degradation
Breaks down single proteins
Proteins are tagged with small 76aa protein ubiquitin and degraded by large multi protein complex proteasome
Important quality control mechanism: breaks down misfiled and damaged proteins
Both glycogenic and ketogenic amino aicds
Isoleucine Phenylalanine Threonine Tryptophan Tyrosine
Ketogenic amino acids
Leucine
Lysine
Branched chain amino acids catabolism
First two steps for all are transamination and decarboxylation
BCKD
Maple Urine Syrup Disease
Caused by defects in BCKD
Degradation of aa carbon skeleton
Carbon skeleton of glycogenic amino acids are used for pyruvate of TCA cycle intermediates: useful for anaplerosis and glucogneogenesis
Of ketogenic amino acids: converted to acetyl-CoA energy substrate but not for gluconeogenesis or anapldrotic reactions
Negative N balance
Nin less than Nout
Starvation
Serious illness
Insufficient essential amino acids
Postitive N balance
Nin less than Nout
Growth
Pregnancy
Recovery illness or starvation
Excretion of excess nitrogen
Amino acid transamination does not eliminate nitrogen form the body
Some reactions set free ammonium, which can be directly eliminated form the body
High ammonium concentrations are cytotoxic (especially for the brain)
Terrestrial animal secrete nearly 80% excess N as urea
Some eliminated as ammonium salts or uric acid
Purines are broken down to uric acid
Lysine
Only amino acid that cannot be transaminated
Urea
Highly water soluble
Non-Toxic
pH neutral
Eliminates two amino groups per molecule urea
Highly efficient nitrogen disposal
Terrestrial animal secrete nearly 80% excess N as urea
Direct precursor is arginine
Arginine
Direct precursor of urea
Intermediate in urea cycle
Direct substrates of urea cycle
Aspartate and carbamoyl phosphate
Products of urea cycle
Urea and fumarate
Fumarate is covered to oxaloacetate through TCA cycle reactions
Carbamoyl phosphate synthesis
Investment of energy to generate a transferable amino group
Controls urea production
Carbamoyl phosphate synthetase
Controls the urea cycle and is activated by N-acetylglutamate: controls urea production
N-acetylglutamate
Allosteric activator
Formed when degradation of amino acids lead to high concentration of acetyl-CoA and glutamate
Urea
Formed from cyclic pathway in liver
Intermediates are not used up
One amino group stamps from ammonia, one from aspartate, carbon comes from bicarbonate
Enters blood stream and is filtered out by kidney into urine: requires large quantities of water to be excreted
