FUNdamentals

Baggot, 11-12

08.28.08

Before we leave B12, what kind of therapy would you give a B12 deficient person? Only one kind of therapy – you get an injection into your arm; that is the therapy.

And, before we start amino acid metabolism (shows images) this is an example of, if you get into research, you need to run very very good controls. This guy, Goldberger, was sent out by the public health service to find the bacteria that causes pellagra, which is Niacin deficiency. It’s not a bacteria. He spent many years trying to find the bacteria and eventually became convinced that it wasn’t a bacteria at all. He conducted all these experiments where he and his group of researches tried to infect themselves with the bacteria that causes Pellagra. So they went around to the people who had pellagra and ate their feces and drank their blood. That is before IRB on human experiments. So, they never got pellagra but he actually died in 1930, I think, and his research was totally discredited in 1930 until 1940 when they figured out Goldberger was really right; it was a nutrient deficiency syndrome. His research was then accepted. And here is the crux of the matter; you take a person with Pellagra and usually in the south… now showing images.

**Pellagra hospital tangent….**

There is a Pellagra hospital; most of them were in the south; most people don’t believe there were in existence, this one was in South Carolina, but it is a US Health Service Pellagra hospital. They would take people from the hospitals, put them on a train and ship them up to Bellview(?) Hospital in NYC. Then they would treat them with antibiotics that they had because they thought it was a bacterial infection. They would treat with mercury, lead, arsenic compounds, which were the antibiotics of that time. And they would get better. People would get better in Bellview Hospital. And they would take them and out and put them back on a train to SC, GA, AL and within a couple of years, they developed Pellagra again. Remember, it is a nutrient deficiency disease. Typical person to get the disease was a farmer who ate cornbread, bacon, and collard greens. If you get shipped to Bellview Hospital in NYC, do you get fed cornbread, bacon and collard greens? No – so what they should have done was take them to Bellview Hospital, don’t treat them for anything and just let them eat the hospital diet. And then, BANG, they would have been improved. It wasn’t the arsenic, lead, zinc or mercury compounds that healed them; it was the diet.

Q: What do you feed someone with a Niacin deficiency today?

A: You have to give them Niacin.

Q: What can they eat?

A: If they have gastric bypass surgery, they need injections.

Q: I mean, back in the day, what would you have fed them [to make them healthy]?

A: Well, uh, anything except cornbread, collard greens and bacon because the 3 have very low Niacin in them and cornbread has a Niacin binder. So what little Niacin is there, it prevents the absorption of it. Any fresh fruit, vegetable, meat, egg would have enough Niacin.

Everyone thinks that quack cures are a product of recent history and of they are wrong; these are from 1920. (To image) This is easy expa? ; they had high concentrations of mercury, lead and arsenic compounds in them. $5 was a lot to pay. Here is Pellagacide. Not a whole lot of good it did a person to take toxic metals. Once food was fortified with Niacin, Pellagra disappeared as a public health problem. The cure from Pellagra was discovered when the cured black tongue disease in dogs, which a Pellagra in dogs. They fed the dogs Niacin and realized Pellagra was a nutrient deficiency disease, not a bacterial infection.

Showing images…

This is riboflavin deficiently (image) Note inflammation at the corner of the mouth of this person. This is my mom before I got her therapy. No just kidding. This is scurvy, notice the bleeding is not all the gums, its bleeding between the gums between the teeth. And if you don’t have teeth you won’t have that; so it is due to some sort of micro interaction in-between the teeth and gums. All the gums are not bleeding. It is something about Vitamin C deficiency and something about that microenvironment that causes scurvy – makes for bleeding gums. This person has a slick tongue; has folate and riboflavin deficiency and vitamin C deficiency. She has Vitamin C, foliate and riboflavin deficiency all rolled up into one. This is unusual. Her favorite thing to eat was Campbell’s soup and chocolate cake. This person has pyridoxine deficiency and riboflavin deficiency. These are the kind of things you look for; no one them is going to nail it down that you have a deficiency, but there is lots of oral signs and symptoms for vitamin deficiency and also other nutrient deficiencies like iron. This is not going to be on the test.

This is a bone marrow aspirate from someone who has megalocytic anemia. They used to take bone marrow from sternum and look at it to diagnose foliate or B12 deficiency. This look the same if you have a bone marrow aspirate or blood from circulating peripheral blood. Normal bone marrow – either foliate or b12, they look the same pathologically. These are megoloblasts here. There is not enough nucleic acid being synthesized – not enough purines and pyrimadines being synthesized to let the megoloblasts mature into normal blasts. Normal blast is a small RBC precursor with a nucleus. A megablast is a large cell with a nucleus that has expanded (not because they is plenty of purine and pyrimadines but because there is not enough to synthesize the DNA so it has expanded and swelled. It is very large in proportion to the total cell volume. It can’t mature. That would be bone marrow…

Q: (Couldn’t hear all of it; about macrolytic and megolytic anemia.)

A: Megalocytic anemia refers to the way it looks in the bone marrow aspirate; macrocytic is how it looks in peripheral blood.

Q: Couldn’t hear

A: This is what peripheral blood looks like in foliate deficiency; first of all it is an anemia deficiency, have fewer RBCs so hemocrit will be low. Strange looking cells with blobs; cells look bigger. See in peripheral blood, both with B12 or foliate deficiency. They produce identical histology and pathology in blood.

We will see why this true (B12 and foliate produce the same deficiency in blood pathology) when we study nucleic acid biosynthesis.

Amino acid Biosynthesis. We will continue with this next week.

I told you we are not looking at amino acid metabolism in yeast and bacteria, slime mold. We will study amino acid biosynthesis and catabolism in humans.

Less is known about humans that you think since many of the experiments have been done in E. coli; some in rats. More done in microorganisms than humans, probably for ethical reasons.

First, we digest and absorb proteins so we can get the amino acids from them. We have endo and exopeptidases. An endopeptidase cleaves somewhere internally on polypeptide chain; exopeptidases cleaves at the amino or carboxyl end. Both can act (?) and then we talked about zymogens. Pepsin is the one in the stomach that gets a first crack at protein; in the small intestine its trypsin, chrymotrypsin, elastase, and carboxypeptidases, which are exopeptidases that act at the carboxyl terminal.)

Then there are brush border peptidases which are associated with the membrane of the cells on the intestinal villa; absorption has a transporter for different types of amino acids; acidic, basic, hydrophilic. There is cotransport of Na++. There is transporter for di and tripeptides that transport hydrogen. The cells of the GI system love to utilize glutamic acid, glutamine and aspartic acid for energy. No one knows why.

If you have a patient who has been receiving food by mouth, when they do start receiving food by mouth, they will surely provide them with glutamic acid, glutamine and asparate. The entry site will need those to get ready. Gut will atrophy if you don’t feed it; the cells simply become quiescent and don’t divide and lose lots of their functions.

Back to transporter system – it’s wrong to think you need to digest your protein to single amino acids; lots of di and tripeptides are transported and absorbed better as di and tripeptides than single amino acids. Then you could have patients with celiac disease or cystic fibrous; both of these are not uncommon and they will have protein mal absorption that to an extent, can be treated. Celiac patients need to not eat wheat products; cystic fibrosis patients need to take pancreatic enzymes in pill form to help them digest protein.

Take N atoms away from amino acids and catabolize their carbon skeletons; we are going to make urea and biosynthesize the nonessential amino acids. Can we biosynthesize nonessential amino acids? No, because then they would be essential if we could do that. We are going to do this. We are going to deviate from your text book. We are going to do 1 carbon metabolism and biosynthesis of heme and other important compounds from amino acids.

It’s not hard but your textbook makes it look hard. Most amino acids undergo transamination; some lose their groups by deamination or elimination. That is not the preferred route; transamination is. Some will give you compounds that will undergo oxidativedecarboxylation like pyruvate and some will give compounds that look intermediates in amino acids. We will see some give compounds that give into TCA cycle (Krebs).

Let’s look at transamination.

Draw in your reaction mechanism. (Here is just the verbage of it.)

You have R1 amino acid here, and it’s going to donate amino group to R2 alpha keto analog of an amino acid. And when I say that, you know that I mean alpha-keto-amino acid analog. In a reversible reaction where the amino group (R2) the amino group ends up on R2, generating the alpha keto acid of R1. Almost all of these are reversible and all require pyridoxal phosphate or a B6 coenzyme.

What is the purpose of mother nature designing transaminases? The purpose is to keep nitrogen from appearing as ammonia. We do not want (if possible) a substrate with nitrogen on it to produce ammonia. Why don’t we want that? Because ammonia is toxic to use. The only animals that can really excrete nitrogen as ammonia are the ones that live in water. You know, they are kind of peeing in their own environment. We don’t want to do that. Ammonia raises the pH of the body. It is a terrible toxin. Transamination reactions take nitrogen in an amino group, and without it appearing as ammonia, transfer it from one amino acid to the alpha keto analog of another acid.

Starting the families (organized with bullet points to make it easier to read.)

  • Remember these things are reversible.
  • We are going to see transamination reactions a lot.
  • We are going to study the catabolism of amino acids in families. The families will overlap, but you can’t understand it any other way. You can’t go through each amino acid as a unique amino acid.
  • Questions asked are boards are not asked as single amino acids, but the questions are more conceptual.
  • One rule is that Mother Nature does not like to add or subtract carbons from the carbon skeleton when it undergoes catabolism.
  • If at all possible, it likes to use the same number of carbons and create a molecule that can be used in another metabolic pathway.
  • Includes glycolyosis and the TCA cycle (which can also be called the Krebs cycle or the citric acid cycle).
  • Want to make a substrate from the amino acid that can go into glycolysis or the TCA cycle.

First family: Glutamic acid, glutamine, arginine, histidine, proline.

  • Arginine will be discussed later in the urea cycle, but can be transformed into alpha-keto-glutarate in certain metabolism in the urea cycle. Arginine is included in this group of amino acids that are metabolized the alpha keto glutarate.
  • How many carbons does alpha-keto-glutarate have? It has five.
  • Except for His and Arg, they are all have five carbons.
  • Alpha keto glutarate will go into the TCA cycle.
  • How do we get Glutamic acid to alpha –keto- glutarate? It’s a transamination reaction. That’s all you have to know. Now you have alpha –keto- glutarate that will go into the TCA cycle.
  • Glutamine has an amide Nitrogen, so the amide Nitrogen must come off. Ammonia is produced; enzyme called glutaminase which removes the amide Nitrogen. You got glutamic acid that’s transaminated to alpha –keto- glutarate.
  • Proline: both proline and arginine can be metabolized to glutamic acid semi-aldehyde. All I want you to know. Easily oxidized to glutamic acid; just the aldehyde analog of Glutamic acid; oxidized to glutamic acid- transaminated alpha –keto- glutamate.
  • Proline & Glutamic acid, Glutamine all go to alpha –keto- glutarate.
  • Histidine, in spite of the fact that Mother Nature does not like to add or subtract carbons; histidine is a problem; It has six carbons. It has one too many; One must be gotten rid of, and the imidazole ring of Histidine is broken open giving you foramino glutamic acid.
  • What’s the difference between Glutamic acid and foriminoglutamic acid (Figlu)? The forimino group.
  • How are we going to get rid of the forimino group? Forimino has a carbon and nitrogen. A one-carbon transfer enzyme is used that requires forimino enzyme. The forimino group of forimino Glutamic acid is taken off and transfers to tetrahydrofolate producing forimino-tetrahyrofolate.
  • Figlu( foimino glutamic acid) has a foimino group and it will react with Tetrahydrofolate; this is catalyzed by an enzyme. The forimino group is taken off and will produce forimino-tetrahydrofolate while the forimino group off of figlu now becomes Glu.

Family leading to Oxaloacetate: Asp, AspNH2

  • Oxaloacetate goes to the same place—TCA cycle or the Krebs cycle.
  • How many carbons does aspartic acid and asparagines have? 4
  • Oxaloacetate has 4 carbons.
  • Asparagine has an amide nitrogen. Have seen an amide nitrogen before in glutamine.
  • We have an asparginase that takes off the amide nitrogen to produce ammonia and aspartic acid.
  • How do we get from aspartic acid to Oxaloacetate? Oxaloacetate is simply the alpha-keto analog of aspartic acid transamination, just like alpha –keto- glutarate is the alpha-keto analog of Glutamic acid.

Family leading to pyruvate: Ala, Ser, Cys

  • Where’s pyruvate going to be in metabolic pathways? Glycolysis.
  • Alanine to pyruvate is transaminiation.
  • What is this the alpha-keto analog of? All we need to do is a transamination reaction.
  • How many carbons does alanine, serine, and cysteine have? They all have three.
  • How many carbons does pyruvate have? Three.
  • Mother Nature will take three carbon amino acids and produce a three carbon metabolite that can be used in another metabolic pathway.
  • Serine goes to pyruvate. Just know this.
  • Cysteine to pyruvate.
  • This a problem. Cysteine has sulfur on it, so we need to get rid of the sulfur. One way to get rid of the sulfur is to oxidize the sulfhydral to a sulfite. Get rid of the sulfur with transamination. Get rid of the sulfur as sulfite so there’s a desulfanase enzyme to get to pyruvate. You simply oxidize it. Occurs when there is a lot of oxygen.
  • In the large intestine, there is not a lot of oxygen, this (referring to one of his diagrams where there a pathway that utilized oxygen and pathway that did not utilize oxygen) is a stinky way to get of the sulfur with the oxygen. Happens in the intestine. In the non-oxidative pathway H2S is formed and this is one reason why farts stink.
  • Both of the pathways will go on inside the body more or less dependent on the oxygen content there. If there is not a lot of oxygen, go through the non-oxidative pathway. If there is plenty of oxygen in the pathway, you will go through the oxidative pathway.

Family leading to succinyl-CoA via propionyl CoA or methylmalonyl CoA: Met, Ile, Val

  • Propionyl CoA is hard because it can be an intermediate in the oxidation of odd chain fatty acids.
  • Once propionyl CoA is produced, it is metabolized to succinyl CoA which is also in the TCA cycle.
  • Succinate also goes into the TCA cycle.
  • Reason for all the arrows (referring to the diagram)- there are a bunch of trees that are really horrible…don’t get into the trees.
  • Methionine can be metabolized to homocysteine. Will see how homcysteine can generate alpha-keto butyrate later on.
  • For now, remember that methionine can lead to propionyl CoA.
  • Isoleucine can lead to propionyl CoA.
  • Valine can lead to methylmalonyl Coa.
  • What can we do with propionyl CoA and methylmalonyl CoA? Here is where some other enzymes come into play.
  • Propionyl CoA cannot be metabolized; do not have pathways to do this, so it must be converted to succinyl-CoA.
  • To convert Propionyl CoA to Succinyl CoA, a carbon must be added. We will carboxylate it to methylmalonyl CoA. Valine already went to methylmalonyl CoA.
  • Methylmalonyl CoA then needs to be mutated to succinyl CoA. Methylmalonyl CoA is a branched chain fatty acid with a methyl branch on it; our bodies don’t like branched chain fatty acids.
  • Our bodies like straight chain fatty acids. This is where the B12 coenzyme comes into play.
  • One of the two B12 dependent enzymes in our body mutates methylmalonyl CoA to succinyl CoA. Flips groups around so it can be attached to the methyl group so the straight chain fatty acid is made.
  • Succinyl CoA then goes into the TCA cycle.
  • VERY GOOD BOARD EXAM QUESTION! What would happen since all three of these are metabolized to methylmalonyl CoA, what would happen if you had a patient that was B12 deficient? What metabolite would build up in their body in their blood or urine? Answer. Methylmalonyl Acid.
  • Looking at the trees again, all of these are methionine, Isoleucine, and Valine are metabolized the methylmalonyl CoA so by a propionyl CoA which must be mutated to succinyl CoA which can enter the TCA cycle.

Branched Chain Amino Acid Family: Leucine, Isoleucine, and Valine: