Amino Acid Synthesis - General

Question 1

While the air we breathe is rich with nitrogen, we don’t absorb any of it this way. Why?

Answer 1

Nitrogen gas (N₂) is inert chemically

Question 2

What are the 3 steps of nitrogen fixation in plants and microorganisms?

Answer 2

1. The fixation of nitrogen by bacteria that reside in soil and legume root nodules into usable forms such as ammonium, nitrites, and nitrates through the Nitrogen Cycle.
2. The incorporation of ammonium into glutamate and glutamine.
3. Glutamate donates its amino group to other α-ketoacids to form most of the other amino acids that are needed in the cell

Question 3

_____ is the endpoint of nitrogen fixation; nitrates and nitrites are reduced to it, and it is used in step two of nitrogen assimilation.

Answer 3

Ammonium.

Question 4

What is the overall reaction of nitrogen fixation?

Answer 4

N₂ + 10 H⁺ + 16 ATP + 8 e- → 2 NH₄⁺ + H₂ + 16 ADP + 16 P

Question 5

How many enzyme catalyzed reactions are involved in the second step of nitrogen fixation by plants and microorganisms? What are the enzymes and what is the reaction they carry out?

Answer 5

3.

1. Glutamate dehydrogenase: a potentially reversible reaction that could be use either NADH or NADPH. The reaction catalyzed: NH₄⁺ + a-KG + NADPH + NAD⁺ <> NADP⁺ + NADH + glutamate + H⁺
2. Glutamine synthetase: Glutamate + NH₄⁺ + ATP → glutamine + ADP + P_i + H⁺
3. Glutamate synthase: (indirect reaction) α-ketoglutarate + glutamine + NADPH + H⁺ → 2 glutamate + NADP⁺

Question 6

What class of enzymes uses glutamate to donate its amino group to other α-ketoacids to form most of the other amino acids that are needed in the cell in the 3rd step of nitrogen fixation? Is the reaction reversible?

Answer 6

Aminotransferases. The reactions catalyzed by these enzymes are reversible; thus if glutamate levels are high, the reaction can flow in the opposite direction producing the various amino acids.

Question 7

​_____ is one of the major enzymes involved in assimilating nitrogen and is the primary regulatory point in nitrogen metabolism in most species.

Answer 7

Glutamine synthetase

Question 8

What reaction does glutamine synthetase catalyze?

Answer 8

Glutamate + NH₄⁺ + ATP → glutamine + ADP + P_i + H⁺

Question 9

The glutamine formed by glutamine synthetase is primarily used for what 2 purposes?

Answer 9

1. Incorporated into proteins
2. Serves as an important donor of amino groups for the synthesis of other biomolecules, which includes but is not limited to nucleotides and other amino acids

Question 10

The regulation of glutamine synthetase is highly complex and involves both _____ and _____.

Answer 10

Covalent modification, allosteric regulation

Question 11

How many allosteric inhibitors of glutamine synthetase are there? How many are nitrogen containing molecules? How many are molecules that glutamine is a provider of the nitrogen for their biosynthesis? How many are amino acids?

Answer 11

8, 8, 6, 2

Question 12

What is concerted inhibition? Describe how regulation of glutamine synthetase is a form of this.

Answer 12

A type of inhibition where there is a greater than additive effect. The degree of inhibition provided by the 8 inhibitors is more than additive, so that the cumulative effect of two, three or more is greater than the additive effect of each one individually

Question 13

Glutamine synthetase is also regulated by covalent modification, specifically by _____. What does this kind of modification refer to?

Answer 13

Adenylylation. Adenylylation refers to the linking of an AMP molecule to a tyrosine residue through the –OH group of tyrosine, forming an ester bond, using ATP as the donor of the AMP group.

Question 14

The quaternary structure of glutamine synthetase varies from species to species, but always involves multiple identical subunits that interact to form a _____.

Answer 14

Multi-subunit enzyme.

Question 15

How many identical subunits are there in human glutamine synthetase? How are these arranged? Each subunit has what? What is interesting to note about these subunits?

Answer 15

12 identical subunits arranged as two six-member “donuts” that sit on top of one another.

Each subunit has an active site.

It is interesting to note that the tyrosine residue that becomes adenylylated in each subunit is located close to the active site.

Question 16

What is the consequence of adenylation of glutamine synthetase? What does a glutamine synthetase with no adenylation show enzymatically and what can you conclude from this?

Answer 16

It acts to sensitize the enzyme to the 8 allosteric inhibitors.

Research has shown that a glutamine synthetase that is completely devoid of any adenylylation is essentially insensitive to any of the allosteric inhibitors. Thus, a combination of covalent modification and allosteric inhibition is required to control the activity of this enzyme.

Question 17

Other than glutamine synthetase, what other reaction is required to synthesize some amino acids and nucleotides? What are the two ways this reaction takes place?

Answer 17

One-carbon transfer reactions.

These are added in one of two ways; by S-adenosylmethionine (SAM), which adds methyl groups, and tetrahydrofolate, which carries a variety of one-carbon units.

Question 18

S-adenosyl methionine (SAM) donates only one type of one-carbon unit; _____.

Answer 18

Methyl groups

Question 19

Why is SAM used rather than simply methionine? Describe this chemically.

Answer 19

The methyl group in methionine is not very reactive. When adenosine is attached to the sulfur atom, this destabilizes it and becomes a positively charged sulfonium ion. This makes the methyl group subject to attack, making it very reactive.

Question 20

_____ is by far the preferred methyl group donor in the cell.

Answer 20

SAM

Question 21

Enzymes called _____ transfer the methyl group to their specific substrates. _____ is a product and is regenerated back to SAM so it can be reutilized.

Answer 21

Methyltransferases. S-adenosylhomocysteine

Question 22

Methyl groups transfered by SAM are almost always transferred to a _____ or _____ atom.

Answer 22

Nitrogen or oxygen

Question 23

_____ is synthesized from norepinephrine in a reaction that requires a methyl group transfer from SAM onto a nitrogen atom in norepinephrine. What is this enzyme termed? What would it be termed if it added to an oxygen atom?

Answer 23

Epinephrine. This enzyme is termed an N-methyltransferase, versus an O-methyltransferase which is an enzyme that transfers a methyl group onto an oxygen atom.

Question 24

A much more versatile donor of one-carbon units is the coenzyme _____.

Answer 24

Tetrahydrofolate

Question 25

Tetrahydrofolate is derived from which vitamin? Describe how this vitamin is turned into tetrahydrofolate. What enzyme catalyzes this?

Answer 25

Folate (B9). Dietary folate is reduced using NADPH to dihydrofolate, then reduced again using NADPH to tetrahydrofolate which is the active form of the vitamin in the cell.

Both reductions are catalyzed by dihydrofolate reductase.

Question 26

The terms _____ and _____ indicate the specific atoms in tetrahydrofolate to which the one-carbon units are attached; Sometimes only to one, sometimes only to the other, and sometimes to both.

Answer 26

N⁵ and N¹⁰

Question 27

The source of the one-carbon units using tetrahydrofolate is either _____ or _____, oxygen is provided by _____, and nitrogen is provided by _____. What is sometimes required for interconversions?

Answer 27

serine, formate, formate, ammonium.

ATP and/or NADPH for some interconversions.

Question 28

The synthesis of methionine from homocysteine requires a methylation reaction catalyzed by _____, which uses N⁵-methyltetrahydrofolate as the methyl donor.

Answer 28

methionine synthase

Question 29

A different form of tetrahydrofolate, N⁵-N¹⁰-methylene-tetrahydrofolate, is used in _____ synthesis from _____

Answer 29

serine, glycine

Question 30

The synthesis of asparagine from aspartate is done by what enzyme? What does this reaction require and where is it found?

Answer 30

Asparagine synthetase. The reaction requires the addition of an amino group onto aspartate, which in this case is donated by glutamine.

Question 31

The synthetic pathway for histidine in plants has both _____ and _____ act as amino group donors at different steps of the synthetic pathway.

Answer 31

Glutamine, glutamate

Question 32

All amino acids are synthesized from specific intermediates of which three metabolic pathways?

Answer 32

1. Glycolysis
2. Pentose phosphate pathway
3. Citric acid cycle

Question 33

The biosynthetic pathways for the 20 amino acids can be grouped according to which 6 metabolic precursors?

Answer 33

1. α-ketoglutarate
2. pyruvate
3. 3-phosphoglycerate
4. oxaloacetate
5. ribose 5-phosphate
6. phosphoenolpyruvate/erythrose 4-phosphate.

Question 34

The conversions of these metabolic intermediates to amino acids involve _____ as well as _____.

Answer 34

one-carbon unit transfers, amino group transfers

Question 35

Most _____ and _____ can synthesize all of the amino acids, while _____ can only synthesize some and the rest are required in the diet. The amino acids that we can synthesize are called _____ amino acids while those required in our diet are called _____ amino acids.

Answer 35

Bacteria, plants, mammals. Non-essential, essential

Question 36

There are some amino acids that are termed _____, which means that they are essential only during specific times such as during growth, such as in young, growing babies, or in individuals experiencing some specific illness which generates an increased demand for protein synthesis.

Answer 36

Conditionally essential

Question 37

Five amino acids that can be synthesized from oxaloacetate, an intermediate of _____. What are the 5?

Answer 37

The citric acid cycle.

1. Aspartate
2. Asparagine
3. Methionine
4. Lysine
5. Threonine

Question 38

Four amino acids that can be synthesized from pyruvate. What are the 4?

Answer 38

1. Alanine
2. Valine
3. Leucine
4. Isoleucine

Question 39

_____ can be synthesized from aspartate in a complex series of reactions. What is used as the amino group donor in this pathway?

Answer 39

Lysine. Glutamate is used in this pathway as an amino group donor.

Question 40

What are the 5 non-essential amino acids?

Answer 40

1. Alanine
2. Asparagine
3. Aspartate
4. Glutamate
5. Serine

Question 41

What are the 6 conditionally essential amino acids?

Answer 41

1. Arginine
2. Cysteine
3. Glutamine
4. Glycine
5. Proline
6. Tyrosine

Question 42

What are the 9 essential amino acids?

Answer 42

1. Histidine
2. Isoleucine
3. Leucine
4. Lysine
5. Methionine
6. Phenylalanine
7. Threonine
8. Tryptophan
9. Valine

Question 43

What is product inhibition? What does it prevent and why is this important?

Answer 43

A generic term that refers to a situation where the end product (let’s call it F) acts as an allosteric inhibitor of the first committed step in the pathway. This prevents unnecessary production of F when levels are sufficiently high. This is important since synthetic pathways often require the input of energy, so we don’t want to waste energy unnecessarily.

Question 44

What is sequential inhibition? What type of pathway is it present?

Answer 44

A type of inhibition where there is a sequence of events that controls the overall flux through the pathways. It is present when there is one or more branch points such that there are two or more end-products formed.

Question 45

What is concerted inhibition? What is one important feature about this type of inhibition?

Answer 45

Similar to sequential, except that the two end-products F and G both inhibit the same enzyme, the one that catalyzes the first committed step in the overall pathway.

One important feature of this type of inhibition is that the combined effect of F and G is more than additive; that is, their combined effect is greater than their effects individually if you just added them together.

Question 46

Define enzyme multiplicity feedback inhibition. What does this type of inhibition allow for?

Answer 46

The first committed step in the pathway is catalyzed by two isoenzymes, which are enzymes that catalyze the same reaction but are coded for by different genes and thus may have specific properties. This allows fine-tuning of the amount of flux through the pathways and allows inhibitors to have distinct effects on the pathway.