FUNDAMENTALS 1: 10:00-11:00
TUESDAY, AUGUST 31, 2010
PROFESOR:DeLucas
AMINO ACID SYNTHESIS
I. How Do Organisms Synthesize Amino Acids?
Scribe: CALVIN SIMS
Proof: FARAH BUTT
Page 1 of 6 a. Plants and microorganisms can make all the 20 essential amino acids and as a result, if you look at mammals, there are amino acids that we cannot make without ingesting food or something to help us make them. b. There are 10 amino acids that we make. The ones we cannot make are known as the essential amino acids.
II. Amino Groups for Amino Acids are Derived from Glutamate in Transamination Rxns a. In all these organisms, Glutamate is the source of nitrogen and it’s via transamination rxns. b. With all the amino acids, there are different ways we can group them with one being by the intermediate form of the molecule that the amino acid is created from. c. For example, α-Ketoglutarate family is grouped based on the precursor from where these groups of molecules are made. α-Ketoglutarate is the precursor molecule.
III. Amino Groups for Amino Acids are Derived from Glutamate in Transamination Rxns a.In transamination reactions involving glutamate, there is a colored group with an Rgroup , a C=O, and a carbonyl group. If you notice, the α-Carbon has a carbonyl group that is being replaced by the Nitrogen group, which becomes a leaving group. b. This takes place because of the enzyme Pyridoxal Phosphate-dependent aminotransferase. To be specific, it is an aminoglutamine transferase. c. The amino group leaves the glutamine section and a new amino acid is created based on what the R group might be. It cran be any of the amino acids that are a part of the
Glutamate Family (Glu, Gln, Pro, and Arg) d. The fundamental equation: AA
1
(Amino Acid 1) + αK
2
(alpha ketoacid 2) -> αK
1
(alpha ketoacid 1) + AA
2
(Amino Acid 2). The amine group is transferred to make a new amino acid from the α-ketoacid and the other amino acid becomes the new α-ketoacid because it loses the –NH
2
group.
IV. Slide 4
V. Amino Acids are Synthesized From a Limited Number of Precursors. a. This table shows how the amino acids are grouped into families. Each amino acid is named based on the precursor for the type of amino acid it is.
VI. Humans Can Synthesize Only 10 of the 20 Common Amino Acids

FUNDAMENTALS 1: 10:00-11:00
TUESDAY, AUGUST 31, 2010
PROFESOR:DeLucas
AMINO ACID SYNTHESIS
Scribe: CALVIN SIMS
Proof: FARAH BUTT
Page 2 of 6 a. As previously said, humans can only make 10 of the 20 amino acids. The others must be made by ingesting plants. b. There are 10 essential amino acids we cannot make. c. Looking back in evolution, why is it that bugs can make all these and we can’t? It turns out that one thing you can look at is how badly we need them and how difficult it is to make them. d. We do not need any of them because we cannot get them all from what we eat. There was no constraint evolution wise as for why we should keep making them. There is a possibility, but no proof that if we were to go back a thousand years, that we could have made all of our amino acids. e. Why would we choose to make some and not others? The abundance of protein; Even though some amino acids were available, the body chose to make its own for more of the amino acids. Therefore, there was no push for production of certain amino acids to cease. f. Another factor could have been the number of steps involved in making the amino acids. g. Tyrosine is a nonessential amino acid because if you have Phenylalanine present, you can make Tyrosine.
VII. The Difference Between Essential and Nonessential Amino Acids a. The essential amino acids (listed in red) require many more steps to synthesize. This is a possible reason we chose not to make these because we could get them from what we eat instead doing so much to make the amino acids. There is more energy needed and more enzymes involved for this process. For those two reasons, the body may have chosen not to make certain amino acids, but to ingest them.
VIII. The Mechanism of Aminotransferase a. The mechanism starts with a Pyridoxal Phosphate that is hooked on the Lysine portion of the aminotransferase enzyme. b. The aminotransferase enzyme has a Lysine group with a Pyridoxal Phosphate on it. c. Along comes amino acid and ketoacid, where it hooks on the Nitrogen with a double bond on the Carbon on the phosphate group. This forms a partial bond known as a Schiff base. d. The Schiff base can move around but it is deprotonated and has a carboxylic acid group, which becomes the leaving group. It goes from a ketamine state to an aldimine state, transferring hydrogen atoms where the enzymes play a role in forming a complex again.

FUNDAMENTALS 1: 10:00-11:00
TUESDAY, AUGUST 31, 2010
PROFESOR:DeLucas
AMINO ACID SYNTHESIS
Scribe: CALVIN SIMS
Proof: FARAH BUTT
Page 3 of 6 e. Know how the Pyridoxal Phosphate plays a role in the mechanism and how enzymes play a role in shifting amine groups.
IX. The α-Ketoglutarate Family of Amino Acids Includes Glu, Gln, Pro, Arg, and Lys a. The routes for Glu and Gln synthesis were described when we talked about the ammonia assimilation pathways. b. There are similarities with ornithine pathways and the proline pathways. c. The CPS-1 is the rate-limiting step in the urea cycle and has some feedback inhibitors.
The enzyme is found in mitochondria.
X. The α-Ketoglutarate Family of Amino Acids Includes Glu, Gln, Pro, Arg, and Lys a. Shows how proline is made from α-Ketoglutarate. b. There are three essential enzymes in this process. c. In Step 1, ƴ-glutamyl kinase phosphorylates glutamate and it gets reduced. d. Then you have glutamate-5-semialdehyde dehydrogenase, which aids in NADPH of organic molecules. A Hydrogen atom replaces the O
-
. e. In Step 3, Hydrolysis of water occurs without enzymatic help, which creates a cyclic structure. (Forming a double bonded N) f. This is then reduced with Δ-pyrroline-5-carboxylate reductase, which adds on two hydrogen atoms.
XI. Slide 11 a. If we talk about the bacterial pathway of ornithine, this is how it is synthesized. b. A critical component is the first step where carbamoyl group is added to the Nitrogen of Glutamate. It is the rate-limiting step. The substituent then serves as a feedback inhibitor. c. The phosphate then comes in the replaces the O . The phosphate is then reduced, leaves, and is replaced with a hydrogen. d. N-acetylglutamate-5-semialdehyde then converts glutamate to α-Ketoglutarate and replace the COO
-
group with an –NH
3
group. e. Finally, the last substituent is pulled off and ornithine is created. f. Ornithine is important for synthesis of arginine, degradation of arginine, and plays many different roles in the Citric Acid Cycle. It also detoxifies body when too much
Nitrogen is present.
XII. Slide 12

FUNDAMENTALS 1: 10:00-11:00
TUESDAY, AUGUST 31, 2010
PROFESOR:DeLucas
AMINO ACID SYNTHESIS
Scribe: CALVIN SIMS
Proof: FARAH BUTT
Page 4 of 6 a. Carbomoyl phosphate synthetase-1 is the rate-limiting step in the urea cycle.
b. Has important role of taking excess biocarbonate in the body (which is unhealthy) and combining with an ATP group to make Carbomoyl-P Intermediate. Inorganic phosphate becomes a leaving group forming Carbamate.
c. Carbamate is ATP phosphorylated and a Carbamoyl Phosphate group is formed. (1 st group hooked onto ornithine in urea cycle as it comes into mitochondria) d. CPS-1 eliminates bicarbonate and ammonia, which are both toxic in abundance.
e. Also leads to amino acid synthesis of amino acids that work in the tricarboxylic acid cycle. (It produces energy)
XIII. Slide 13 a. Urea cycle takes place in the cytosol of the cell. b. The reaction of CPS-1 takes place in the mitochondria. c. The ornithine has to hook onto the mitochondrial membrane and go in and out of it.
Ornithine transcarboxylase assists in this process. It also transports citriline and different isoenzymes in and out of mitochondria. d. Diseases can result from problems with this. Problems with this usually are fatigue and sleepiness due to lack of ATP from the mitochondria. e. Two of the related diseases are Citrilinia and Ornithinia. f. If there is a high level of dietary ornithine, it is not critical for mitochondria to make more ornithine and continue operating in the urea cycle. g. The next group aspartate and argininosuccinate synthetase, which is called synthetase because we are using energy producers (AMP). C=N and substituents from aspartate are joined creating a new substituent. So the Nitrogen came from the α Carbon of aspartate and the next step is to break off from argininosuccinase and you are left with arginine.
You now have two Nitrogens bonded to a Carbon. h. If you take a look at where the Nitrogen came from, you’ll see it came from ammonia, that gets incorporated and as a result arginase is broken, urea is created, and we get rid of the ammonium ion. The other Nitrogen is used to break down another amino acid, aspartate. So one Nitrogen comes from the α-Carbon of aspartate and the other comes from ammonia. (Ornithine can also be made from glutamate) The cycle continues to repeat itself.
XIV. The Urea Cycle Acts to Excrete Excess N Through Arg Breakdown a. Breakdown of Arg in the urea cycle releases two N and one C as urea. b. Urea cycle is linked to the TCA by fumarate.
XV. Pumping Iron vs. Eating Amino Acids and Proteins

FUNDAMENTALS 1: 10:00-11:00
TUESDAY, AUGUST 31, 2010
PROFESOR:DeLucas
AMINO ACID SYNTHESIS
Scribe: CALVIN SIMS
Proof: FARAH BUTT
Page 5 of 6
XVI. Slide 16
XVII. Slide 17 a. Increase in the amino acid catabolism lead to elevated glutamate levels and a rise in Nacetylglutamate, the allosteric activator of CPS-1. b. There is a feedback inhibitor of glutamate that regulates CPS-1. c. Stimulation of CPS-1 increases the overall urea cycle activity because the remaining urea cycle enzymes work on the carbamylated ornithine if there is some present . d. The whole rate of the urea cycle is determined in the mitochondria, creating the substituent citriline, which comes out with the carbamoyl group hooked to it. e. The removal of potentially toxic ammonium ions by CPS-1 is an important aspect for overall regulation of the urea cycle. f. The urea cycle is linked to the citric acid cycle through fumarate, a byproduct of argininosuccinase.
XVIII. Slide 18
XIX. Slide 19
XX. The Aspartate Family of Amino Acids Includes Asp, Asn, Lys, Met, Thr, Ile a. Glutamate transfers the Nitrogen group to oxaloacetate to form Aspartate. You then get
α-Ketoglutarate from that and the Aspartate is the other molecule.
XXI. The Aspartate Family of Amino Acids Includes Asp, Asn, Lys, Met, Thr, Ile a. Asparagine is formed with two steps. In the first step, you phosphorylate Aspartate. In the second step, asparagine synthetase in bacteria creates a Nitrogen group, which is added to make asparagine.
XXII. Asparagine and Leukemia a. Both are linked to diseases. b. Leukemia is a cancer of bone marrow that affects the production of lymphocytes. c. Two types of leukemia: Acute lymphoblastic and acute myoblastic, which are caused by overproduction of immature lymphocytes. d. Lymphocytes are highly dependent on the uptake of asparagine. One chemotherapeutic approach of treating this is getting an enzyme from bacteria that break down asparagine. e. This technique has been tried and is somewhat helpful. However, eventually the body will reject the protein because it is a foreign protein.

FUNDAMENTALS 1: 10:00-11:00
TUESDAY, AUGUST 31, 2010
PROFESOR:DeLucas
AMINO ACID SYNTHESIS
Scribe: CALVIN SIMS
Proof: FARAH BUTT
Page 6 of 6 f. Another approach would be to inhibit its substrate, aspartyl-AMP Intermediate. The problem is that asparagine synthetase doesn’t get into the cell that easily.
XXIII. Biosynthesis of Thr, Met, and Lys Proceed From Aspartate a. Thr, Met, and Lys can be synthesized from aspartate.
XXIV. Slide 24 a. Chorismate is a precursor for aromatic amino acids like phenylalanine, tryptophan, and tyrosine. b. It is common to the cell compounds having benzene rings like Vitamin E and K, folic acid, Lignin, and other substituents.
XXV. Slide 25
Acids. a. Know how important Chorismate is and how it takes pathways to synthesize Amino
XXVI. Tyrosine is Made From Phenylalanine a. Alternate pathway for getting Tyrosine. b. Instead of taking in foods with Tyrosine, it can be created. c. Phenylalanine-4-monoxygenase, also known as phenylalanine hydroxylase, is important in this process.
XXVII. The Active Sites of Tryptophan Synthase Are Connected by a Hydrophobic Tunnel a. An example of tunneling shown in Tryptophan Synthetase b. Molecules have 50:50 chance of ending up in specific areas on molecules with tunneling. c. This happens because of charge sharing.
XXVIII. Amino Acid Biosynthesis Inhibitors as Herbicides a. If you want to make a drug, you have to look at what it has and how it affects us. b. If making herbicides, we have to pick out proteins/amino acids that we do not have because it could be unhealthy for us to target amino acids that we share.
XXIX. Amino Acid Biosynthesis Inhibitors as Herbicides a. Since we don’t make 10 amino acids, there has to be enzymes/amino acids that plants and microbes have that we don’t have. Those are amino acids we should target when

FUNDAMENTALS 1: 10:00-11:00
TUESDAY, AUGUST 31, 2010
PROFESOR:DeLucas
AMINO ACID SYNTHESIS
Scribe: CALVIN SIMS
Proof: FARAH BUTT
Page 7 of 6 making herbicides to get rid of plants/microbes. This makes the herbicide less toxic to us.
b. Although we may not have some of the amino acids we target, we still must be cautious because it can contaminate other proteins in our body if enough is taken in.
XXX. Slide 30 a. Shows how things are shuttled into the Citric Acid Cycle.
b. Shows hoe Acetyl-CoA and Acetoacetate plays a role in the cycle.
c. α-Ketoglutarate and Fumarate plays a role in the cycle.
d. Amino acids enter in the cycle to create energy.
e. Pyruvate goes to acetyl-CoA, which then goes into the citric acid cycle.
XXXI. Slide 31
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