Amino Acid Self Quiz

Match the amino acid to its correct amino acid family.

1.     Arginine                        a. 3-Phosphoglycerate

2.      Glycine                        b. Oxaloacetate

3.     Tryptophan                   c. α-ketoglutarate

4.     Alanine                         d. Phosphoenolpyruvate

5.     Threonin                       e. Pyruvate

6.     Glutamine is essential for cells because it:

a.     Incorporates oxygen into hemoglobin

b.     Allows the synthesis of ATP

c.     Incorporates inorganic nitrogen into cell material

d.     Allows the cell to cycle and excrete oxygen radicals

7.     Valine shares the same four enzymes at the end of its’ synthesis with:

a.     Methionine

b.     Leucine

c.     Isoleucine

d.     Glycine

8.      Which characteristic of leucine allows it to modulate the passage of ion through bacterial membranes and pores?

a.     Chirality on side chain

b.     Size of side chain

c.     Hydrophilic side chain

d.     Hydrophobic side chain

9.     During phenylalanine biosynthesis, what is the importance of the enzyme chorismate mutase?

a.     Hydrolysis of chorismate

b.     Catalyze a Claisen rearrangement of chorismate to form prephenate

c.     Decarboxylation of prephenate to phenylpyruvate

d.     Transamination of phenylpyruvate

10.  Which amino acid is converted into catecholmines used in the nervous system?

a.     Tryptophan

b.     Valine

c.     Tyrosine

d.     Isoleucine

11.  What additional molecule is needed in the synthesis of isoleucine in the asetolactate synthase step?

a.     Acetyl CoA

b.     Pyruvate

c.     ATP

d.     Glutamate

12.  What are the two compounds that can be interconverted with glutamate (via one conversion reaction)?

a.     Glutamine, oxaloacetate

b.     Glutamine, α-ketoglutarate

c.     Aspargine, α-ketoglutarate

d.     Aspargine, oxaloacetate

e.     None of the above

13.  Asparagine is used to:

a.     Link oligosaccharides to final protein acceptors

b.     Synthesize N-acetyl glucosamine

c.     Assimilate nitrogen

d.     Counteract free radical damage

14.  Histidine plays a physiological role in which of the following activities:

a.     Catalytic triads

b.     Proton shuffle

c.     Histidine kinases

d.     All of the above

15.  Serine is a precusor for:

a.     Glycine

b.     Cysteine

c.     Phenylalanine

d.     A and B

e.     All of the above

 16.  Cysteine is important in protein stability.

a.     True

b.     False

17.   Asp13 is the location of phosphorylation in the CheY protein in bacteria chemotaxis.

a.     True

b.     False

18.  Due to its rigidity and small loss in conformational entropy upon exposure to high temperatures, proline tends to be more abundant in thermophilic organisms.

a.     True

b.     False

19.  Methionine is in a derivative form in bacteria, called fMet, to initiate translation.

a.     True

b.     False

20.  The one letter abbreviation for Lysine is L.

a.     True

b.     False

Histidine

http://chemistry.about.com/od/imagesclipartstructures/ig/Amino-Acid-Structures/Histidine.htm

General Features
Abbreviation: His or H
Chemical Formula:C₆H₉N₃O₂
Molar Mass: 155.15 g/mol
Histidine’s codons are CAU and CAC.  Histidine is an aromatic.  It contains six pi electrons; two from a nitrogen lone pair and four from double bonds.
Physiological Roles
Histidine has many roles.  It is part of catalytic triads.  In this, the basic nitrogen of histidine removed a proton from serine, threonine, or cysteine to create a nucleophile.  Histidine can also participate in proton shuttle.  Histidine does this by using the basic nitrogen to remove a proton to make a positively charged intermediate.  It then uses another molecule to take the proton from its acidic nitrogen. Histidine also plays a role in signal transduction in the form of histidine kinases (HK).  HKs act as cellular receptors for signaling molecules.  HKs typically have an extracellular domain, transmembrane domain, and intracellular domain.  The intracellular domain contain the enzymatic activity.  The intracellular domain also has a region that can bind to secondary effector molecules that further propagate the signal within the cell.  HKs are part of a two-component signal transducation mechanism.  Below is the mechanism of histidine kinase action.

http://en.wikipedia.org/wiki/File:HK_mechanism.png

HKs transfer a phosphate group from ATP to the histidine residue within the kinase and then to an aspartate residue on the receiver domain on a different protein.  For more information, see Two-Domain Reconstitution of a Functional Protein Histidine Kinase by Heiyoung Park, Soumitra K. Saha, and Masayori Inouye.

http://www.chem.qmul.ac.uk/iubmb/enzyme/reaction/AminoAcid/His1.html

http://www.chem.qmul.ac.uk/iubmb/enzyme/reaction/AminoAcid/His2.html

Synthesis
The synthesis of histidine is complex and its pathway intertwines with nucleic acid synthesis (purine specifically).  The pathway appears to be universal in all organisms that are able to synthesize histidine.  The first steps transform phosphoribosyl pyrophosphate (PRPP) into imadiazoleglycerol phosphate.  This begins with a condensation in which the N1 of the purine ring of ATP bonds to the C1 of ribose.  PRPP provides the five carbons of histidine.  The adenine ring of ATP provides the carbon and nitrogen of the imidazole ring.  Once the imadiazole ring is formed, glutamate donates the α-amino group.  The newly formed anime is oxidized to histidine in the last step.  For more information, see Synthesis of Histidine in Escherichia coli by John Westley and Joseph Ceithaml

Ribose 5-phosphate Family

Isoleucine

Add chttp://chemistry.about.com/od/factsstructures/ig/Chemical-Structures---I/D-Isoleucine.htmaption

General Features:

Abbreviated: Ile or I
Molecular formula: C₆H₁₃NO₂
pKa: 2.36 (carboxyl), 9.60 (amino)

Physiological Roles:
Isoleucine's codons are AUU, AUC and AUA and is a non polar amino acid.  It is classified as a hydrophobic amino acid because of the hydrocarbon side chain it possess.  Its side chain is chiral (like threonine) meaning it has four possible stereoisomers, L-Isoleucine is the most common form and the form found most often in nature.  As mentioned in the post on leucine, isoleucine is an isomer of leucine. 

In eukaryotes Isoleucine is an essential amino acid, it cannot be synthesised.  Foods that are high in this amino acid include eggs, soy protein, seaweed, turkey, chicken, lamb, cheese, and fish.

Isoleucine is a helpful amino acid in catabolic pathways.  It can be converted to acetyl-CoA or acetoacetyl-CoA and from there be feed into the TCA cycle,  It can also undergo transamination followed by oxidative decarboxylation and finally a series of oxidation reactions and be converted into propionyl-CoA.  Porpionyl-CoA is a precursor for Succinyl-CoA, an essential component of the citric acid cycle (Nelson et al).
In Bacillus subtilis a gene named bkdR was found to control the utilization of isoleucine and valine as sole nitrogen sources (Debarbouille et al 1999).

When isoleucine is converted to an α-Keto acid it uses a branched chain α-keto acid dehydrogenase complex.  When this enzyme is defective it results in a disease named maple syrup urine disease   

Synthesis

Synthesis of isoleucine

There are five main steps in the synthesis of isoleucine.

Threonine dyhydratases catalyzes the first step in isoleucine biosynthesis.  It will dehydrate threonine to create ammonia and 2-oxobutyrate.  It is at this step that feedback inhibition by isoleucine itself will occur

Asetolactate synthase (Acetohydroxyacid synthase) is the next step and will catalyses the condensation of  pyruvate and 2-oxobutyrate to yield acetohydroxybutyrate.  Thiamine pyrophosphate (TPP) is a cofactor in this reaction used to stabilize pyruvate. 

Acetohydroxyacid reductoisomerase will then reduce the acetohydroxybutyrate to produce 2,3-dihydroxy-3-methylvalerate.

From there dihydroxy-acid dehydratase will dehydrate the 2,3-dihydroxy-3-methylvalerate to form 2-oxo (keto)-3-methylvalerate

The final reaction is an aminotransferase from an amino acid donor to form isoleucine. 

Threonine

General Features:
Abbreviated: Thr or T
Chemical formula: C₄H₉NO₃

pKa: 2.63 (carboxyl), 10.43 (amino)

Physiological Roles:
Threonine is a polar amino acid and is one of the three proteinogenic ("protein-building") amino acids that contains an alcohol group. Its start codons are ACU and ACA. Due to its two chiral centers, it has four possible stereoisomers. L-threonine is the most common stereoisomer (the other L-isomer, L-allo-threonine, is relatively rare). It is the only common amino acid along with isoleucine that contains a chiral carbon in its side chain.

Because of its hydrophilic nature, threonine can be found in substantial concentrations at the outer regions of soluble proteins. Its easily removed hydrogen on the hydroxyl side chain makes it a common hydrogen donor in enzymes. The exact role of threonine's hydrogen donating in enzymes remains unclear, however.

Threonine is capable of posttranslational modification. In both eukaryotic and prokaryotic cells, threonine residues are able to undergo phosphorylation, which may have different effects depending on the particular protein. Threonine is the second most commonly phosphorylated amino acid residue, following serine. Interestingly, threonine-phosphorylated proteins are the easiest to purify using antibodies and are thus the most well characterized in terms of phosphorylation effects. Phosphorylated amino acids generally lose a hydroxyl group and gain a negatively charged phosphate. This negative charge may significantly alter the biochemical properties of the entire protein. The figure below gives a good visual as to how this negative charge might affect the amino acid (note that serine and tyrosine are shown as well):

Side chain modification (phosphorylation)

A specific example of the importance of threonine phosphorylation (carried out by enzymes called threonine kinases) is the autoregulatory effects of threonine kinases in the bacterial organism Bacilus anthracis (Bryant-Hudson et al., 2011). This study shows the first hints of inhibitory phosphorylation by a prokaryotic serine/threonine kinase (STK). Within the regulatory domain/activation loop of the STK, there are specific serine and threonine phosphorylation sites that may lead to either activation or inhibition. The enzyme itself may phosphorylate these sites; thus, the enzyme is autoregulatory.

Protons may be quickly abstracted from threonine using the basic nitrogen of histidine, making threonine nucleophilic. This may have implications in downstream pathways.

Synthesis and metabolism:
Threonine is an essential amino acid in humans, meaning we are unable to synthesize it naturally and must obtain it from food sources. Plants and microorganisms are able to synthesize threonine and utilize a pathway involving aspartic acid via alpha-aspartyl-semialdehyde and homoserine.

Synthesis of threonine

The enzymes featured in this pathway are:

1. aspartokinase (AK)

2. beta-aspartate semialdehyde dehydrogenase (B-ASD)

3. homoserine dehydrogenase (HSD)

4. homoserine kinase (HSK)

5. threonine synthase (TS)

With the coupling of ATP hydrolysis, aspartokinase (AK) catalyzes the phosphorylation of aspartate to form aspartyl-beta-phosphate. It has been shown that both plant and bacterial AK are bifunctional enzymes that may contain homoserine dehydrogenase activity (Weisemann and Matthews, 1993). B-ASD subsequently removes the phosphate group. These two reactions result in the removal of an oxygen and addition of a hydrogen through the usage of an activating phosphate. HSD catalyzes the first reaction which is specific to threonine, methionine, and isoleucine biosynthesis. 

HSK is an essential branch point between threonine and methionine biosynthesis; if homoserine acetyltransferase was present instead, methionine synthesis would follow. HSK catalyzes the formation of O-phosopho-L-homoserine via O-phosphorylation of homoserine. O-phosphorylation simply implies the addition of (ortho)phosphoric acid H₃PO_4.

TS catalyzes the final step of this biosynthetic pathway and involves a hydrolysis of the phosphate group added by HSK. TS shows functional domains that share similarities with SAM-dependent methyltransferases in plants (Thomazeau et al., 2001). Many of the enzymes in this pathway are great examples of how versatile enzymes can be. This makes the organism much more energy-efficient.

Below is a more broad picture to give you an idea how threonine biosynthesis is coupled to the TCA cycle. For the purpose of this section, feel free to only pay attention to the left portion of the diagram (keeping in mind the importance of the figure as a whole, of course).

Deng et al., 2011

Metabolism of threonine may occur by two pathways: conversion to pyruvate or conversion to alpha-ketobutyrate (which enters the pathway that leads to synthesis of succinyl-CoA). Threonine may also be converted to glycine via threonine aldolase:

Jander et al., 2009

Additional resources:

If you're really excited about threonine biosynthesis, you can visit The Enzyme Database for a very comprehensive look at each point of the pathway! Or if you're feeling particularly adventurous, take a look at this original publication by Kaplan and Flavin. Or if genetics is more your thing, check out this publication by Marchenko et al.

Although we mainly focus on amino acids as they pertain to prokaryotic organisms, this site may enlighten you to all the nutritional benefits of threonine in human diets. 

Methionine

Methionine

Abbreviated: Met or M

Molecular Formula: HO₂CCH(NH₂)CH₂CH₂SCH₃

pKa: 2.28(-COOH), 9.21 (α-NH₂)

Physiological roles:

• This amino acid is coded for by the codon AUG, which is the start codon for translation. In bacteria the derivative of Methionine, N-formylmethionine (fMet) is used to initiate translation. The formation of fMet is catalyzed by the enzyme methionyl-tRNA formyltransferase.
• fMet is highly important not only for the bacterial cell itself but also for the mitochondria and the chloroplasts.
• Interestingly there has been some research looking into the possibility of methionine restriction can extend life by alternative lengthening of telomeres genes. http://www.nature.com/onc/journal/v26/n32/full/1210260a.html 
• Methionine is an intermediate in the biosynthesis of cysteine, caritine, lecithin, phosphatidylcholine, taurine, and other phospholipids.

Synthesis:

Methionine biosynthesis

The enzymes involved in this synthesis are:

1. aspartokinase
2. β-aspartate semialdehyde dehydrogenase
3. homoserine dehydrogenase
4. homoserine O-transsuccinylase
5. cystathionine-γ-sythase
6. cystathionine-β-lyase
7. Methionine sythase

First, aspartic acid is converted via β-aspartyl-semialdehyde into homoserine, introducing the pair of contiguous methylene groups. Homoserine converts to O-succinyl homoserine, which then reacts with cysteine to produce cystathionine, which is cleaved to produce homocysteine. Subsequent methylation of the thiol group by folates affords methionine. Both cystathionine-γ-sythase and cystathionine-β-lyase require pyridoxyl-5'-phosphate as a cofactor, whereas homocysteine methyltransferase  requires vitamin B12 as a cofactor. (Lehninger, Albert L.; Nelson, David L.; Cox, Michael M. (2000), Principles of Biochemistry (3rd ed.), New York: W. H. Freeman, ISBN 1-57259-153-6).

To learn more about the initiation of protein synthesis with fMet in bacteria read the article, Initiation of Protein Synthesis in Bacteria LINK: http://mmbr.asm.org/content/69/1/101.short
 
 

Asparagine

Oxaloacetate Family: Asparagine (N)

General features

R group: -CH2-C(NH2)O

MW: 132.12 g mol^-1

pKa of R group: NA

Physiological roles

Glycosylation:

Personal annotation of figure from the abstract of Larkin, Imeriali (2011)

 http://pubs.acs.org/doi/abs/10.1021/bi200346n

Within the past decade it has been confirmed that eukaryotes are not the only domain that will link glycans to large proteins during their processing in the lumen of the ER. Gram negative species have been found to bind glycan (polysaccharide groups) to proteins in the periplasm. The polysaccharide is elongated on the cytoplasmic side of the cell membrane while anchored to the cell membrane via Und-PP. When finished, the Und-PP-polysaccharide is translocated to the outer leaflet to face the periplasm where it can be linked to finished protein via an asparagines residue on that protein.

 

http://pubs.acs.org/doi/abs/10.1021/bi200346n

 

This process is very similar to peptidoglycan and LPS synthesis.

Interesting to note, is that in the context of translation, tRNA^Asn is initially loaded with aspartate, and subsequently the carboxyl group is changed by an amidotransferase (this is also the case with tRNA^Gln). In this many bacteria lack an Asn tRNA synthetase but use a Asp tRNA synthetase that has amidotransferase activitiy.   This is thought to be a potentially mechanism for future antibiotics; this mode of interference with protein synthesis has already been implemented in cancer chemotherapy treatments. Just like with cancer chemotherapy, there is limitation to the selective toxicity of this method, because mitochondrial-directed translation also uses this modified Asn/Gln tRNA charging method. For more info, one of the situation is described in the in the introduction to this article: http://nar.oxfordjournals.org/content/early/2012/02/22/nar.gks167.full  It was also described in this review article:   doi: 10.1101/gad.1187404  Genes & Dev. 2004. 18: 731-738     Also, the characterization of the ribozyme that generates this ‘different’ Asn-tRNA can be read in this paper:  http://www.ncbi.nlm.nih.gov/pubmed/18241796

Synthesis

http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=UPA00134

Two enzymes (from independent genes) are known to synthesize asparagine in bacteria: AsnA , which  catalyzes the reaction referred to as “ammonia-dependent” and can only use ammonia as the nitrogen source to convert aspartic acid to asparagines, and AsnB, whose reaction is referred to as “glutamine-dependent” can use either ammonia or glutamine as the nitrogen donor (often glutamine). AsnB  has amidotransferase activity (meaning it transfers the transfer of the amide group of one amino acid to another.) The AsnA pathway is found only in prokaryotes while the AsnB pathway exists in eukaryotes as well as prokaryotes. Because of that fact, and the efficacy of cancer chemotherapeutics effective in the AsnB directed pathway, this enzyme/pathway is better studied than that of AsnA.

Ammonia-dependent (AsnA):

ATP + L-aspartate + NH₃ = AMP + diphosphate + L-asparagine

Glutamine-dependent (AsnB):

ATP + L-aspartate + L-glutamine + H₂O = AMP + diphosphate + L-asparagine + L-glutamate