Amino acid biosynthesis and degradation

Amino acids are precursors for: Catechilamines Nucleic acids Neurotransmitters Histamine Porphorins (eg haem)

Also, amino acids are biological food sources: Can be used as an energy source Also can be converted to glucose

There are more than 20 amino acids in the body. These can be split into essential and non-essential amino acids: Essential: not made in the body and NEED to get them from the diet. Arginine can be made but not to the extent that we need in our bodies. Non-essential: can be made in the body.

There are organisms can make all of the amino acids but weve lost this ability. The liver is the main site amino acid metabolism. All tissuse have the ability to synth non essential amino acids. This can be either de novo or it can be due to amino acid interconversion. This is important in things like muscle tissue. Important for things like gluconeogenesis etc. When talking about amino acid synth we need to consider the nitrogen because it is such a toxic product in the body (in the form of ammonia). Excess nitrogen is eliminated by Transamination transfer of the amide group to another species. Deamination - Some of the amide groups need to be gotten rid of. The urea cycle When considering the carboskeleton of amino acids, an amino acid without the amide group is just a carbohydrate. This is important when considering the synthesis of things like sugars and fatty acids. amino acid deficiency is fairly rare in the west. They are usually due to some dietary protein malnutrition. Or the quality of protein is poor (eg vegetarianism). Or things like anorexia.

Deficiencies can lead to diseases like kwashiorkor (enough energy but not enough protein) and marasmus (neither energy nor protein) and cachexia(extreme wasting and severe malnutrition seen in end stage cancer and AIDS).

BIOSYNTHESIS.
You can group the amino acids into those which share similar biosynth pathways.

Amino Acid Formation by Transamination of -keto Acids

Transamination is a very common process in amino acids. But, if we consider the transamination of keto acids, = way of synth an amino acid. The door molecule gives the amide group to the reciving molecule. Eg oxaloacetateaspartate. Start with a carbon skeleton with a ketone group which is then replaced with an amide group. Alanine + -ketogluterate glutamate + pyruvate depending on the bodies needs either can be made as this is a reversible reaction

Amino Acid Formation by Amination of Amino Acid Reqires energy in the form of ATP. Eg. Aspartate asparagine Glutmate glutamine If we combine the above: Aspartate + glutamine asparagines + glutamate Glutamate can also be converted to glutamine using ATP and NH4+ by glutamine synthase.

Biosynthesis of Serine and Glycine from 3-Phosphoglycerate

Transamination reaction. Serine can also be used as a precursor for glycine biosynth. The serine undergoes multiple reduction reaction (requires water). Serine + tetrahydrofolate Glycine + N5-N10-Methylene-H4Folate

Biosynthesis of Cysteine - NON essential - Derived from both methionine and serine but if a person is methionine deficient then they will have trouble synthesising cysteine. -

Step 1: involves the activation of methionine using ATP. Step 2: formation of homocysteine Step 3: formation of cysteine via cystathionine which then undergoes a cleavage reaction. Multistep, non essential and essential aminoacids. Production of homoscysteine is the main point.

Biosynthesis of Proline from Glutamate - Glu undergoes a couple of reactions via the enzymes glutamylkinase and G-5-P dehydrogenase to become glutamate semialdehyde (linear and cyclic form exist in equilibrium) - Proline is cyclic, and derived from the cyclic form of glutamate Biosynthesis of Tyrosine from Phenylalanine - Tyrosine is non-essential. Phenylalanine and tyrosine arent very different from each other conformationally. (-OH group is the only difference) - Phenylalanine is essential which is why without this in the diet we would not produce enough tyrosine. - Phenylalanine hydroxylase with co-factor tetrahydrobiopterin - This pathway is important for tyrosine synthesis but also ph.ala degradation. Amino Acids are Precursors of Many Biomolecules - Non essential are usually derived from essential - Amino acids are imp biosynth precursors Biosynthesis of Biologically Active Amines - Histamine Vasodilator, mediator relaeased by mast cells Causes the symtoms of hayfever Controls acid secretion in the stomach Derived from histidine Decarboxylated histadine (histidine decarboxylase) Serotonin 5-hydroxytryptamine Migraine and sleep Derived from tryptophan GABA Gamma-aminebutyrate Inhibitory synapses Derived from glutamate 30% of brain synapses Catecholamines Adrenaline and dopamine derived from tyrosine Melanins Derived from tyrosine via DOPA Skin colour Different colour variaton

Haem Biosynthesis - Circular tetrapyrol - Important: co-factor; respiration etc. - B.synth is v important = occurs in mitochondria and the cytosol. - Fe2+ ions in the middle of the haem. Ferrochelatase is a catalytic antibody. - There are lots of haem assoc disease.

Porphyrias - Caused by various disoirders in the haem synth pathway. - There are lots of different types - Caused by different mutations in different genes Congenital erythropoetic porphyria - Caused by deficiency of erythroid uroporphyrinogen III synthetase (found in RBC) which leads to thee accumulation of uroporphyrinogen I and coproporphrinogen I which are both coloured compounds. Some of which expressed on the teeth. - Symptoms: Red urine + fluorescent red/brown teeth Photosenstive skin (ulceration and scarring) caused by exposure to UV which turns them into free radicals Increased hair growth on face and extremities (werewolf legend?)

Acute intermittent porphyria - Most common form - Still pretty rare - Deficiency in liver porphobilinogen deaminase which causes a build of precursors. - Symptoms: Intermittent attacks of abdominal pain Neurological dysfunction Excess excretion of ALA and PBG (red/black urine) Skin not photosensitized (different from CEP) because this happens in the liver.

Amino acids degradation and disease

You will be able to describe in detail examples of diseases caused by defects in amino acid degradation. when defects occur, you should know the molecular structure of the molecules on either side of the defect. The disease symptoms tend to be very extreme or not severe at all. An average human synthesis and degrades about 400g of protein per day coming rom recycline 100g are catabolised and then excreted. If we want to maintain the balance we need to eat ~100g each day. Amino acids can be broken down into amide groups and carbon skeletons. The amide groups are usually turned into carbomylphospate and then excreted out as urea. The carbon skeletons can be turned into glycolytic intermediates or they can be convtered to alphaketoacids fed into tca cycle and resipired. Oxaloacetate can also be made and glucose can be synthesised from this. Critically; the two halves of the catabolism of proteins (urea and TCA cycle) are joined by the aspartate-arginosuccinate shunt of the TCA cycle. You can feed in fumerate from urea cycle (converted to an intermediate of the TCA cycle). So the two things dont exist in isolation. The main thing is the TCA cycle. The amino acids all have different c.skeletons which give different intermediates for the TCA cycle.

Essentially all the carbonskeletons can be fed into the TCA cycle.

Glucogenic directly in the tca Ketogenic FFA synthesis if the body needs

Transamination key reaction; from donor a.a to receptor alpha-ketoacid

The main end point is the loss of an amide group from glutamate (and aspartate) to form a-ketogluterate (this can enter the TCA). This is done by glutamate dehydrogenase Aspartate and a-kg < oxaloacetate and glutamate by GOT enzyme Gluatamate can also be recycled from a-kg. This is done by glutamate dehydrogenase Transamiantion is important in muscle tissue to make sure the muscle doesnt run out of glucose. Muscle transaminases use pyruvate as an acceptor of keto acid. Alanine of produced. Alanine is then released into the blood stream and transported to the liver. Alanine is converted back to pyruvate and eventually to glucose (gluconeogenesis) In summary: - Pyruvate + glutamate alanine + a-kg (transamination) This is called the glucse alanine cycle During fasting. The muscle tissue contracts. Generate pyruvate. Cant use this directly. T akes other amino acids to turn the pyruvate into alanine. Alanine converted to glucose in the liver. Then this glucose transported back to the muscles. The alanine amino group is converted to urea in the liver and then to the kidneys for excretion. Essentially the muscle is getting rid of the nitrogen group.

Transamination reaction Mechanism

They all share te common feature of sharing this pyridol phosphate (Vit B6) co-factor for amino transferases. The amino transferases all have this lysine residue in the active site. This is linked covalently to the pyridol phosphate via its e-amino group. = Schiff base (-CH=N-) The N comes from lysine and C from the aldehyde in pyridol phosphate 1. Displacement 2. Formation of aldimine 3. Formation of ketimine 4. Hydrolysis (-keto acid formed) 5. New -keto acid binds 6. Fomation of ketimine 7. Formation of aldimine 8. Hydrolysis (new amino acid formed) -

Shiff base is also important for other enzymes.

Degradation of serine Serine is ultimately converted to pyruvate via serine dehyratase (has vit b6 co factor) Serine is derived from glycine Glycineserinepyruvate

Degradation of glycine Another degradation pathway = glycine cleavage system using tetrahydrofolate (also requires pyroxidal phosphate cofactor); the glycine undergoes a series of reduction reactions where the end product is N5N10-methyleneH4Folate This require NAD+ NADH + H+ Non ketoic hyperglycinemia: High levels of blood glycine Caused by defective glycine cleavage not fatal bc there is another degradation pathway. It is a single enxymes with 4 subunits and there are mutations that cause this diease linked to only one of the 4 subunits Most sufferes dont survive past infancy

Degradation of methionine Converted to cysteine and a-kbutyrate The cysteine is transaminated to pyruvate The a-kgb to propinoyl coA and then to succinyl CoA (meth made from cyst)

Deg. Of cysteine Can also be oxidised into cystseienesulfanate which can be trasaminated Cysteinesulfinte can also be coverted to non-protein amino acid taurine Hypercysteinemia: Cystothione synth definiciency Accumulation of homocystein Symp: cvd, acephaly and neural tube defect. Treatment: vit-b6 and folic acid in pregnant women Getting rid of homocysteine: recycles back to methionine in a reaction that requires h4-folate Build up of homocysteine can lead to neural defect

Deg of threonine Threonine can be met to pyruvate but also glycine and AcetylCoA Can also get succinyl coA which is converted to Acetyl CoA

Deg. Of aspartate, asparagines, glutamate and glutamine Deamination reactions occur first to the 2nd amine groups and then a transamination reaction converts : aspartate oxaloacetate glutamate a-kg the two above reactions are coupled as the second reaction is a transamination.

Deg. Of histidine Histidinase Releases NH3 TO GiVE UROCANATE Then broken down to glutmate via tetrahydrofolate enzyme Histidinemia 1/10000 instance. Most common met disease in japan. Mild and not well diagnoses Hyperactivity Speech problem and mental retardation. Restict amount of histidine in the diet

 Deg. Of arginine and proline Arginite -.> ornithine -> glutamate semi aldehyde Proline and arginine convergences They are both readily oxidised to glutamate This is then turned to a-kg Hyper prolinemia Type 1: caused by proline oxidase defect, asymptomatic, some have neural problems Type 2: defect in proline-5-carboxylate dehydrogenase. Much more serious. Seizures, convulsions and mental retardation. Both defects in the breakdown of proline increase proline in blood.

Degradation of tryptophan Glucogenic and ketogenic. Alanine and acetoacetate are end products

Degradation of valine, leucine and isoleucine They all share common enzymes for the 1st steps of deg. Long HC-chain amino acids Important thing: intitl breakdown begins with transamination reacyion. (a-kg as an acceptor) Then lots of dehydrogenation reactions. Critical thing is the same enzyme part Maple syrus urine Defect in the second step: branched-chain a-keto acid dehydrogenase First reduction step in the breakdown on these amino acids Significan excretion of these amino acids in the urine maple syrus This disease is fatal if untreated. Make sure the diet is as lot in these things as possible

Degradation dof lysine Ketogenic acetoacetate is the end product Hyperlysineuria Lysine saccharopine by saccharopine dehydrogenase (this is the first step in lysine degradation) Blood lysine and urine lysine increased. Untreated can lead to mental and physica; retardation. Treatment: restricted lysine diet.

Degradation of phelylalanine and tyrosine Phenylalanine tyrosine by phenylalanine hdroxylase Tyrosine is then converted to either fumerate/acetoacetate Fumerate TCA Acetoactate converted to AcetylCoA. Alcaptonuria: 1st human genetic disease discovered: defective homogentisate dioxygenase Homogentisate is excreted in large quantities to produce black urine Arthritic later in life but no other symptoms. Phenylketonuria (PKU): Important Most common amino acid met def dis Autosomal recessive Transamination phenylalanine = phenylpyruvate is excreted Tey cant make tyrosine Therefore lack precursors for other things; eg serotnic and melanine therefore albino Severe extreme retardation in newborn. Low phenylalanine eary life can almost cure them from mental retardation.

Aspartame and PKU People with PKU need to consume little coke etc Aspartame (artificial sweetener) turned into phenylalanine and methanol