Purine Biosynthesis

Sections

Full-Length Text

Here, we will draw the process of purine biosynthesis.

Overview

Denote that purine biosynthesis occurs via two key pathways:

De Novo synthesis

• The base, itself, is synthesized from scratch
  • from such components as: ATP, key amino acids, N10-formyltetrahydrofolate, CO2).
• Then attached to the activated (phosphorylated) ribose (sugar) to form the desired nucleotide.

Salvage pathway

• The base is reattached to the phosphorylated ribose (ribose phosphate) to form the nucleotide.

Nucleoside vs. Nucleotide

Let's remind ourselves, now, of some key nucleic acid terminology:

• A nucleoside is a BASE + SUGAR
• A nucleotide is a BASE + SUGAR + PHOSPHATE

PRPP (5-phosphoribosyl-1-pyrophsophate)

Before we jump into the purine ring formation, we need to understand the formation of 5-phosphoribosyl-1-pyrophsophate (aka 5'-phosphoribosyl-1'-pyrophosphate), commonly abbreviated: PRPP or activated ribose (meaning it's activated to accept nucleic bases).

• Indicate that Ribose 5-Phosphate (R5P) converts to PRPP via PRPP synthetase, which catalyzes the addition of 2 phosphate (a pyrophosphate) from ATP, which then converts to AMP.

The Liver & Purine Ring Formation

For reference, we now show the liver produce a standard purine ring, so we can refer to it throughout the production of the ring we will build during this tutorial.

• The liver is the primary organ that produces nucleic acids – we can remember this because it manages ammonia, and as we'll see ammonia is a key component of purine biosynthesis.

Purine vs Pyrimidine

• What should be noted is the semantic confusion that comes from the reality that "purine" is a short-sounding name for the larger of the two bases whereas pyrimidine is the longer-sounding name for the smaller of the two bases: don't let this confuse you.

purine biosynthesis

3 Key Parts

We divide purine biosynthesis into 3 parts:

• Part 1: Formation of 5-Phosphoribosyl-1-amine from ribose-5-phosphate
• Part 2: Formation of the Purine Ring
• Part 3: Derivation of adenosine monophosphate (AMP) and guanosine monophosphate (GMP) from inosinate (IMP).

Part 1

Formation of 5-Phosphoribosyl-1-amine from ribose-5-phosphate

• Draw out Ribose 5-Phosphate (R5P), which allows us to review what we learned in the Nucleic Acids tutorial.

Ribose

• To draw ribose, draw a pentagon with an oxygen atom inserted at the top.
• Label carbons 1' through 4' going clockwise from the oxygen atom.
• Add carbon 5' as an attachment to carbon 4'.
• Finally, add hydroxyl groups to carbons 1', 2', and 3'.
  • Now, add a phosphate to the 5' carbon: hence, Ribose (the sugar), 5-Phosphate).
  • We leave the 5' and 3' in different colors, so we can already tell the 5' to 3' orientation of the sugar/phosphate backbone.

PRPP

• Now, redraw the R5P but, here, at the 1' hydroxyl add a pyrophosphate.
• Indicate that this is PRPP: 5-phosphoribosyl-1-pyrophsophate (aka 5'-phosphoribosyl-1'-pyrophosphate) via PRPP synthetase, which catalyzes the addition of 2 phosphate (a pyrophosphate) from ATP, which then converts to AMP.

5-Phosphoribosyl-1-amine

Now, let's draw the first step in the De Novo formation of the purine ring. Draw 5-Phosphoribosyl-1-amine (aka 5'-Phosphoribosyl-1'-amine) as follows:

• Redraw PRPP but here show that
  • The pyrophosphate (PPi) leaves.
  • In its place add an amine.
• Indicate that glutamine hydrolysis produces ammonia, which provides the amine group, which adds the N9 nitrogen of the Purine Ring.
  • This is why nucleotide production occurs in the liver, because it is the organ that can best handle nitrogen (ammonia) waste – so it makes sense that if nucleotide synthesis relies on ammonia formation, it ought to occur in a body organ that can best manage ammonia!
  • So if we think about why we would want nucleotide biosynthesis to occur in the liver, again, one reason is that it's where the management of ammonia occurs!
    So, now, show that we have N9 in place and attached to the ribose-5-phosphate backbone.

Part 2

We're ready to build the rest of the purine ring! Note that below is a simplification with a goal of learning where each of the key molecules of the ring come from, rather than learning the structural rearrangements that create the ring, itself.

Formation of the Purine Ring

• Show that Glycine, then, provides C4, C5, N7.
• N10-Formyltetrahydrofolate (THF) provides C8 (via a formyl group).
• Glutamine hydrolysis adds N3 (via ammonia).
  • Thus, although the purine ring is large, it has some key repetitions in its formations, which make its biosynthesis easier to remember.
• CO2 provides C6
• Aspartate provides N1
• N10-Formyltetrahydrofolate (THF) provides C2, adjacent to N3 (in the same way that C8 was added adjacent to N9).

Part 3

We've built the purine ring, specifically show that we've built:

Derivation of adenosine monophosphate (AMP) and guanosine monophosphate (GMP) from inosinate (IMP).

Draw Inosinate (IMP) as follows:

• Redraw the purine ring:
  • N9 (from glutamine hydrolysis) (with the ribose-5-phosphate attached).
  • C4, C5, N7 (from Glycine)
  • C8 (from THF)
  • N3 (from glutamine hydrolysis)
  • C6 (from CO2)
  • N1 (from Aspartate)
  • C2 (from THF)
  • Show double bonds between C8 and N7, C4 and C5, and C2 and N3.
  • And show that the C6 carbon is double-bonded to oxygen.

Adenosine Monophosphate (AMP)

• Now, show that with the addition of aspartate and the phosphorylation by GTP, IMP forms AMP, by passing through adenylosuccinate.
• Indicate that the GTP is the phosphoryl-group donor (and converts to GDP in the process).

Guanosine Monophosphate (GMP)

• Then, show that once again, an amine group is added via ammonia produced from glutamine hydrolysis in the process of IMP conversion to GMP.
• However, show that this actually happens AFTER inosinate is oxidized to xanthylate (XMP) with NAD+ acting as the hydrogen acceptor.
• And indicate that this time it is ATP, which serves as the phosphoryl-group donor (which converts to ADP) (rather than GTP).
• Cross-regulation & end-product inhibition maintain a balanced production of these end-products.
  • Cross-regulation means that: GMP (the building-block of GTP) is necessary for the formation of AMP & vice-versa: AMP (the building-block of ATP) is necessary for the formation of GMP.

Purine nomenclature

As a final check on our understanding of purine biosynthesis and the full breadth of its impact on molecular biochemistry, let's run through nomenclature of the purines:

• The bases are:
  • Adenine and guanine
• The ribonucleosides (meaning the sugars + bases) are:
  • Adenosine and guanosine
• The ribonucleotides (meaning the sugars + bases + 5'-monophosphates) are:
  • Adenylate (AMP) and guanylate (GMP)
• The diphosphates are:
  • Adenosine diphosphate ADP and Guanosine diphosphate GDP
• The triphosphates are:
  • Adenosine triphosphate ATP and Guanosine triphosphate GTP

Full-Length Text

• Here, we will draw the process or purine biosynthesis.

• To begin, start a table.

• Denote that purine biosynthesis occurs via two key pathways:
  • De Novo synthesis, which means the base, itself, is synthesized from scratch (from such components as: ATP, key amino acids, N10-formyltetrahydrofolate, CO2), and then attached to the activated (phosphorylated) ribose (sugar) to form the desired nucleotide.
  • Salvage pathway, which means the base is reattached to the phosphorylated ribose (ribose phosphate) to form the nucleotide.

Let's remind ourselves, now, of some key nucleic acid terminology:

• A nucleoside is a BASE + a SUGAR.

• A nucleotide is a BASE + a SUGAR + PHOSPHATE

Before we jump into the purine ring formation, we need to understand the formation of 5-phosphoribosyl-1-pyrophsophate (aka 5'-phosphoribosyl-1'-pyrophosphate), commonly abbreviated: PRPP or activated ribose (meaning it's activated to accept nucleic bases).

• Indicate that Ribose 5-Phosphate (R5P) converts to PRPP via PRPP synthetase, which catalyzes the addition of 2 phosphate (a pyrophosphate) from ATP, which then converts to AMP.

• For reference, we now show the liver produce a standard purine ring, so we can refer to it throughout the production of the ring we will build during this tutorial.
  • The liver is the primary organ that produces nucleic acids – we can remember this because it manages ammonia, and as we'll see ammonia is a key component of purine biosynthesis.

What should be noted is the semantic confusion that comes from the reality that "purine" is a short-sounding name for the larger of the two bases whereas pyrimidine is the longer-sounding name for the smaller of the two bases: don't let this confuse you.

• We divide purine biosynthesis into 3 parts:
  • Part 1: Formation of 5-Phosphoribosyl-1-amine from ribose-5-phosphate
  • Part 2: Formation of the Purine Ring
  • Part 3: Derivation of adenosine monophosphate (AMP) and guanosine monophosphate (GMP) from inosinate (IMP).

Part 1:

• To begin, draw out Ribose 5-Phosphate (R5P), which allows us to review what we learned in the Nucleic Acids tutorial.

Ribose

• To draw ribose, draw a pentagon with an oxygen atom inserted at the top.
  • Label carbons 1' through 4' going clockwise from the oxygen atom,
  • Add carbon 5' as an attachment to carbon 4'.
  • Finally, add hydroxyl groups to carbons 1', 2', and 3'.

• Now, add a phosphate to the 5' carbon: hence, Ribose (the sugar), 5-Phosphate).
  • We leave the 5' and 3' in different colors, so we can already tell the 5' to 3' orientation of the sugar/phosphate backbone.

• Now, redraw the R5P but here, at the 1' hydroxyl add a pyrophosphate.
  • Indicate that this is PRPP: 5-phosphoribosyl-1-pyrophsophate (aka 5'-phosphoribosyl-1'-pyrophosphate) via PRPP synthetase, which catalyzes the addition of 2 phosphate (a pyrophosphate) from ATP, which then converts to AMP.

Now, let's draw the first step in the De Novo formation of the purine ring.

• Draw: 5-Phosphoribosyl-1-amine (aka 5'-Phosphoribosyl-1'-amine). To do so, redraw PRPP but here show that:
  • The pyrophosphate (PPi) leaves.
  • In its place add an amine.

• Indicate that glutamine hydrolysis produces ammonia, which provides the amine group, which adds the N9 nitrogen of the Purine Ring.
  • This is why nucleotide production occurs in the liver, because it is the organ that can best handle nitrogen (ammonia) waste – so it makes sense that if nucleotide synthesis relies on ammonia formation, it ought to occur in a body organ that can best manage ammonia!
  • So if we think about why we would want nucleotide biosynthesis to occur in the liver, again, one reason is that it's where the management of ammonia occurs!

• So, now, show that we have N9 in place and attached to the ribose-5-phosphate backbone.

Part 2:

We're ready to build the rest of the purine ring! Note that below is a simplification with a goal of learning where each of the key molecules of the ring come from, rather than learning the structural rearrangements that create the ring, itself.

• Show that Glycine, then, provides C4, C5, N7.

• N10-Formyltetrahydrofolate (THF) provides C8 (via a formyl group).

• Glutamine hydrolysis adds N3 (via ammonia).

Thus, although the purine ring is large, it has some key repetitions in its formations, which make its biosynthesis easier to remember.

• CO2 provides C6

• Aspartate provides N1

• N10-Formyltetrahydrofolate (THF) provides C2, adjacent to N3 (in the same way that C8 was added adjacent to N9).

Now, for Part 3.

• We've built the purine ring, specifically show that we've built:
  • Inosinate (in-o-sinate) (IMP)

Draw it as follows:

• Redraw our purine ring:
  • N9 (from glutamine hydrolysis) (with the ribose-5-phosphate attached).
  • C4, C5, N7 (from Glycine)
  • C8 (from THF)
  • N3 (from glutamine hydrolysis)
  • C6 (from CO2)
  • N1 (from Aspartate)
  • C2 (from THF)
  • Show double bonds between C8 and N7, C4 and C5, and C2 and N3.
  • And show that the C6 carbon is double-bonded to oxygen.

• Now, show that with the addition of Aspartate and the phosphorylation by GTP, IMP forms AMP, by passing through adenylosuccinate.

• Indicate that the GTP is the phosphoryl-group donor (and converts to GDP in the process).

• Then, show that once again, an amine group is added via ammonia produced from glutamine hydrolysis in the process of IMP conversion to GMP.
  • However, show that this actually happens, AFTER inosinate is oxidized to xanthylate (XMP) with NAD+ acting as the hydrogen acceptor.

• And indicate that this time it is ATP, which serves as the phosphoryl-group donor (which converts to ADP) (rather than GTP).

• Write out that: Cross-regulation & end-product inhibition (which we are already familiar with) maintain a balanced production of these end-products.
  • What's meant by cross-regulation is that: GMP (the building-block of GTP) is necessary for the formation of AMP & vice-versa: AMP (the building-block of ATP) is necessary for the formation of GMP.

As a final check on our understanding of purine biosynthesis and the full breadth of its impact on molecular biochemistry, let's run through nomenclature of the purines:

• The bases are: adenine and guanine

• The ribonucleosides (meaning the sugars + bases) are: adenosine and guanosine

• The ribonucleotides (meaning the sugars + bases + 5'-monophosphates) are: adenylate (AMP) and guanylate (GMP)

• The diphosphates are: adenosine diphosphate ADP and guanosine diphosphate GDP

• The triphosphates are: adenosine triphosphate ATP and guanosine triphosphate GTP