Purines

What is a de novo anabolic pathway in which the purine ring is assembled stepwise directly onto a ribose-phosphate scaffold provided by PRPP (5-phosphoribosyl-1-pyrophosphate), rather than being synthesized as a free base first

Purine nucleotide synthesis

The atoms of the purine ring are derived from multiple sources, including amino acids——- ___________ which donate nitrgoen atoms

glutamine and aspartate

The atoms of the purine ring are derived from multiple sources, including amino acids——- gluatmine and aspartate donate nitrgoen atoms, while _______ contributes both carbon and nitrogen and carbon units from formyl-tetrahydrofolate and Co2

glycine

This highly energy-intensive process produces inosine monophosphate (IMP), the first fully formed purine nucleotide, which then serves as: `

A branch point for the synthesis of adenosine monophoshpahte (AMP) and guanosine monophosphate (GMP)

This highly energy-intensive process produces inosine monophosphate (IMP), the first fully formed purine nucleotide, which then serves as a branch point for the synthesis of adenosine monophosphate (AMP) and guanosine monophosphate (GMP).

What happens to these nucleotides

These nucleotides are subsequently phosphorylated by ATP-dependent kinases to generate their diphosphate and triphosphate forms (ADP/ATP and GDP/GTP

This highly energy-intensive process produces inosine monophosphate (IMP), the first fully formed purine nucleotide, which then serves as a branch point for the synthesis of adenosine monophosphate (AMP) and guanosine monophosphate (GMP).

These nucleotides are subsequently phosphorylated by ATP-dependent kinases to generate their diphosphate and triphosphate forms (ADP/ATP and GDP/GTP)

What do these function as

function as essential energy carriers and substrates for DNA and RNA synthesis

Because de novo purine synthesis requires significant energy investment and multiple enzymatic steps what do cells utilize?

utilize the purine salvage pathway to recycle free bases by attaching them to PRPP, thereby conserving energy.

Purine nucleotide biosynthesis is a metabolic pathway that allows cells to construct purine nucleotides from scratch

What is this process called?

de novo synthesis

• Purine nucleotide biosynthesis is a metabolic pathway that allows cells to construct purine nucleotides from scratch, a process called de novo synthesis.

• Unlike pyrimidine biosynthesis ( via de novo synthsis) where the nitrogenous base is synthesized first and then attached to a sugar-phosphate molecule, ______

What does purine de novo biosynthesis start with

purine biosynthesis starts with PRPP (5-phosphoribosyl-1-pyrophosphate

Unlike pyrimidine biosynthesis, where the nitrogenous base is synthesized first and then attached to a sugar-phosphate molecule, purine biosynthesis starts with PRPP (5-phosphoribosyl-1-pyrophosphate).

PRPP already contains a ribose sugar with an attached phosphate group

What is important to know about the purine BASE

it is built directly onto the ribose atom by atom

PRPP already contains a ribose sugar with an attached phosphate group, and the purine base is built directly onto the ribose, atom by atom.

What does this mean in regards to the two-ring structure of purines ( the fused imidazole-pyrimidine ring)

it is constructed in a stepwise manner

Unlike pyrimidine biosynthesis, where the nitrogenous base is synthesized first and then attached to a sugar-phosphate molecule,

• purine biosynthesis starts with PRPP (5-phosphoribosyl-1-pyrophosphate).

• PRPP already contains a ribose sugar with an attached phosphate group, and the purine base is built directly onto the ribose, atom by atom.

  • This means the two-ring structure of purines (the fused imidazole-pyrimidine ring) is constructed in a stepwise manner

What is the first step within this stepwise manner?

the attachment of nitrogen from glutamine to carbon 1 of PRPP

• Unlike pyrimidine biosynthesis, where the nitrogenous base is synthesized first and then attached to a sugar-phosphate molecule (PRPP), purine biosynthesis starts with PRPP (5-phosphoribosyl-1-pyrophosphate).

• PRPP already contains a ribose sugar with an attached phosphate group, and the purine base is built directly onto the ribose, atom by atom.

• This means the two-ring structure of purines (the fused imidazole-pyrimidine ring) is constructed in a stepwise manner beginning with the attachment of nitrogen from glutamine to carbon 1 of PRPP.

Where do other atoms in the ring come from, overall?

amino acids and single carbon donors

• Unlike pyrimidine biosynthesis, where the nitrogenous base is synthesized first and then attached to a sugar-phosphate molecule, purine biosynthesis starts with PRPP (5-phosphoribosyl-1-pyrophosphate).

• PRPP already contains a ribose sugar with an attached phosphate group, and the purine base is built directly onto the ribose, atom by atom.

• This means the two-ring structure of purines (the fused imidazole-pyrimidine ring) is constructed in a stepwise manner beginning with the attachment of nitrogen from glutamine to carbon 1 of PRPP.

• Other atoms in the ring come from amino acids :________ as well as single carbon donors like ______

What are the amino acids

glycine and aspartate

• Unlike pyrimidine biosynthesis, where the nitrogenous base is synthesized first and then attached to a sugar-phosphate molecule, purine biosynthesis starts with PRPP (5-phosphoribosyl-1-pyrophosphate).

• PRPP already contains a ribose sugar with an attached phosphate group, and the purine base is built directly onto the ribose, atom by atom.

• This means the two-ring structure of purines (the fused imidazole-pyrimidine ring) is constructed in a stepwise manner beginning with the attachment of nitrogen from glutamine to carbon 1 of PRPP.

• Other atoms in the ring come from amino acids :glycine and aspartate as well as single carbon donors like _________
  

What is an example of a single carbon donor?

N10-formyl tetrahydrofolate

What is the relevence of energy in relation to the purine synthesis pathways?

it is energetically expensive, requiring multiple ATP molecules

Due to the purine synthesis de novo pathway being energetically expensive and requring multiple ATP molecules, what does the cell rely on?

the purine salvage pathway to recycle pre-exsisting bases instead of always synthesizing them de novo

The de novo purine synthesis pathway is long, involving many intermediate steps before the first complete purine nucleotide is formed.

What is the name of the first,complete purine nucleotide ?

inosine monophosphate (IMP)

The purine de novo synthesis pathway is long, involving many intermediate steps before the first complete purine nucleotide, inosine monophosphate (IMP), is formed

What happens in the early steps?

PRPP is aminated by glutamine, adding the first nitrogen, followed by the addition of atoms from glycine, formyl-tetrahydrofolate , and other donors to progressively build the two ring structure

• The purine synthesis pathway is long, involving many intermediate steps before the first complete purine nucleotide, inosine monophosphate (IMP), is formed.

• In the early steps, PRPP is aminated by glutamine, adding the first nitrogen, followed by the addition of atoms from glycine, formyl-tetrahydrofolate, and other donors to progressively build the two-ring purine structure

While many steps occur, what are they 3 main takeaways

• the pathway requires significant energy in the form of ATP

• nitrogen comes from amino acids

• single-carbon units are added via tetrahydrofolate derivative (N^10- FormylH4)

• The purine synthesis pathway is long, involving many intermediate steps before the first complete purine nucleotide, inosine monophosphate (IMP), is formed.

• In the early steps, PRPP is aminated by glutamine, adding the first nitrogen, followed by the addition of atoms from glycine, formyl-tetrahydrofolate, and other donors to progressively build the two-ring purine structure

We are going to individually repeat the 3 main takeaways:

1. What does the pathway require ?

significant energy in the form of ATP

• The purine synthesis pathway is long, involving many intermediate steps before the first complete purine nucleotide, inosine monophosphate (IMP), is formed.

• In the early steps, PRPP is aminated by glutamine, adding the first nitrogen, followed by the addition of atoms from glycine, formyl-tetrahydrofolate, and other donors to progressively build the two-ring purine structure

We are going to individually repeat the 3 main takeaways:

2. Where does nitrogen come from?

amino acids

• The purine synthesis pathway is long, involving many intermediate steps before the first complete purine nucleotide, inosine monophosphate (IMP), is formed.

• In the early steps, PRPP is aminated by glutamine, adding the first nitrogen, followed by the addition of atoms from glycine, formyl-tetrahydrofolate, and other donors to progressively build the two-ring purine structure

We are going to individually repeat the 3 main takeaways:

3. How are single carbon units added

via tetrahydrofolate derivatives and Co2

Why is step 11 of the formation of IMP critical?

this step actually PRODUCES IMP - the first nucleotide with a fully formed purine base

What does IMP contain that is essential to purines and retains the ribose-phosphate group from PRPP

the fused ring system

What is the first enzyme of the IMP pathway

glutamine-PRPP amidotransferase

what does glutamine- PRPP amidotransferase do

it is the first step in the IMP pathway and it catalyzes the transfer of NH3

What is the last enzyme of the biosynthesis of IMP

IMP synthase

What does IMP synthase do

it catalyzes the formation of IMP

What happens once IMP in synthesized

it acts as a central intermediate at a “fork in the road”

What can cells do from IMP

cells can produce either adenosine monophosphate ( AMP) or guanosine monophosphate (GMP)

From IMP what happens if a cell chooses to convert to AMP

it requires aspartate as the nitrogen donor and GTP as the energy source

If I decide to convert to AMP from IMP what does this process release as a byproduct

fumarate

What does the conversion to GMP from IMP require

glutamine as the nitrogen donor, ATP as energy, and a redox reaction via the intermediate

What is the intermediate when converting from IMP to GMP

xanthosine monophosphate (XMP)

How are the reaction of conveting to AMP from IMP regulated

AMP inhibits its own synthesis from IMP, directing IMP towards GMP and GMP similarly inhibits its own synthesi sby redirecting IMP to AMP - ensuring a balacned production of purines and avoiding excess AMP or GMP

Because de novo purine synthesis is energy-intensive, what do cells use to recycle bases from degraded nucleotides

purine salvage pathway

What does the purine salvage pathway allow the cell to do

take free purine bases from degredation and attach them back to PRPP, forming nucleotides without having to rebuild the base from scratch

What is an example of the purine salvage pathways in which - the cell takes free purine bases from the breakdown of nucleotides (DNA,RNA,ATP,GTP) and attach them back to PRPP, forming nucleotides without rebuilding the base from scratch.

Use guanine as an example

• guanine can react with PRPP via HGPRT (hypoxanthine-guanine phosphoribosyltransferase) to form GMP.

• Because de novo purine synthesis is energy-intensive, cells use the purine salvage pathway to recycle bases from degraded nucleotides.

• Salvage allows the cell to take free purine bases and attach them back to PRPP, forming nucleotides without rebuilding the base from scratch.

• For example, guanine can react with PRPP via HGPRT (hypoxanthine-guanine phosphoribosyltransferase) to form GMP.

What can adenine do in a similar fashion?

it can either be deaminated to hypoxanthine ( via adenine deaminase) , then salvaged to IMP with HGPRT

or

directly converted to AMP via APRT ( adenine phosphoribosyltransferase)

What is the purine salvage pathway most crucial in

rapidly dividing cells

The purine salvage pathway is most crucial in rapidly dividing cells- what are some examples of cells that it divides

immune cells and liver cells- this is because it acts as a highly efficient recycling system to meet the massive demand for DNA/RNA building blocks, saving significant energy and time compared to de novo synthesi

Why is the salvage pathway crucial in rapidly dividing cells

becasue it saves energy while maintaining nucleotide pools

what can defects in the salvage pathway can lead to

severe metabolic diseases due to the accumulation of free purine bases.- like cancer

• By not being able to use those free bases and place them directly on top of pyrimidine, they accumlate

After synthesis or salvage of nucleoside monophosphates (IMP, AMP, GMP) , what do cells do with them

convert them into diphosphates and triphophates

Why does the cell convert the nucleotide monophosphates (IMP , AMP, GMP) to diphosphates and triphosphates (ATP and GTP)

these are the active forms used for RNA and DNA synthesis; ATP is energy currency and DNA and RNA synthesis and GTP is for protein synthesis and signaling

which enzyme is used to go from monophosphate to diphosphate

nucleoside monophosphate kinases

which enzymes is used to go from diphosphate to triphosphate

nucleoside diphosphate kinases

Converting monophosphates to diphosphates to triphosphates generally require ATP as the phsophate donor, making it common to all nucleotides

what is this function called

housekeeping function

• After synthesis or salvage of nucleoside monophosphates (IMP, AMP, GMP), cells convert these into diphosphates and triphosphates, which are the active forms used for RNA and DNA synthesis.

• This conversion uses nucleoside monophosphate kinases to go from monophosphate to diphosphate and nucleoside diphosphate kinases to go from diphosphate to triphosphate.

• Each of these steps generally requires ATP as the phosphate donor, and this is a housekeeping function common to all nucleotides.

What is the impact of this

AMP and GMP can be phosphorylated to ATP and GTP, providing the cell with the high-energy molecules needed for nucleic acid synthesis and other cellular processes.

To synthesize DNA, what must the ribose sugar of nucleotides must be converted into

deoxyribose

To synthesize DNA, the ribose sugar of nucleotides must be converted into deoxyribose.

What enzyme is repsonsible for this?

ribonucleotide reductase

What does ribonucleotide reductase do

converts ribonucleoside diphosphates into deoxyribonucleoside diphosphates (e.g., ADP → dADP).

• To synthesize DNA, the ribose sugar of nucleotides must be converted into deoxyribose.

• This is done by ribonucleotide reductase, which converts ribonucleoside diphosphates into deoxyribonucleoside diphosphates (e.g., ADP → dADP).

What does this enzyme require to function

reducing equivalents

• To synthesize DNA, the ribose sugar of nucleotides must be converted into deoxyribose.

• This is done by ribonucleotide reductase, which converts ribonucleoside diphosphates into deoxyribonucleoside diphosphates (e.g., ADP → dADP).

• The enzyme requires reducing equivalents to function

What are these reducing equivalents derived from

NADPH

• To synthesize DNA, the ribose sugar of nucleotides must be converted into deoxyribose.

• This is done by ribonucleotide reductase, which converts ribonucleoside diphosphates into deoxyribonucleoside diphosphates (e.g., ADP → dADP).

• The enzyme requires reducing equivalents to function, which are ultimately dervied from NADPH and passed through intermediates

What are the intermediates called

glutaredoxin or thioredoxin

• To synthesize DNA, the ribose sugar of nucleotides must be converted into deoxyribose.

• This is done by ribonucleotide reductase, which converts ribonucleoside diphosphates into deoxyribonucleoside diphosphates (e.g., ADP → dADP).

• The enzyme requires reducing equivalents to function, which are ultimately dervied from NADPH and passed through intermediates such as glutaredoxin or thioredoxin.

How do these intermediates recieve electrons

they recieve them from reduced glutathione or FADH2, which in turn recieves electrons from NADPH

• To synthesize DNA, the ribose sugar of nucleotides must be converted into deoxyribose.

• This is done by ribonucleotide reductase, which converts ribonucleoside diphosphates into deoxyribonucleoside diphosphates (e.g., ADP → dADP).

• The enzyme requires reducing equivalents to function, which are ultimately derived from NADPH and passed through intermediates such as glutaredoxin or thioredoxin.

• These intermediates receive electrons from reduced glutathione or FADH2, which in turn receive electrons from NADPH

What is this electron relay essential for

reducing the 2’-hydroxyl group on the ribose, forming the deoxyribose needed for DNA synthesis

When purine nucleotides are degraded, what do they produce as their end product in humans

uric acid

During purine degredation , what are first things to be dephosphorylated to nucleosides (guanosine and adenosine)

GMP and AMP

Purine nucleotides are also degraded, producing uric acid as the end product in humans. GMP and AMP are first dephosphorylated to nucleosides (guanosine and adenosine).

What happens to guanosine

it is then converted to guanine, which is deaminated to xanthine

• Purine nucleotides are also degraded, producing uric acid as the end product in humans.

• GMP and AMP are first dephosphorylated to nucleosides (guanosine and adenosine).

• Guanosine is then converted to guanine, which is deaminated to xanthine.

What happens to adenosine

its deaminated to inosine, which loses ribose to become hypoxanthine

• Purine nucleotides are also degraded, producing uric acid as the end product in humans.

• GMP and AMP are first dephosphorylated to nucleosides (guanosine and adenosine).

• Guanosine is then converted to guanine, which is deaminated to xanthine.

• Adenosine is deaminated to inosine, which loses ribose to become hypoxanthine

What happens to hypoxanthine

Hypoxanthine is then oxidized to xanthine, and xanthine is further oxidized to uric acid.

Humans lack the enzymes to further degrade uric acid— so what happens to it

it is excreted in urine

what happens due to excess uric acid accumulation

it can lead to gout

what is gout

a condition charaterized by uric acid crystal depositon in joints

the degredation pathway also intersects with the salvage pathway- how and why

hypoxanthine and guanine can be reused to synthesize IMP and GMP via HGPRT

Purine metabolism is highly regulated at multiple points.

What is PRPP synthetase, which produces PRPP, regulated by?

ADP levels

What is the first enzyme in purine syntheisis ( glutamine PRPPamidotransferase) inhibited by

AMP, GMP, and IMP, controlling the de novo pathway.

At the fork where IMP can become AMP or GM, what does feedback inhibition ensure

balanced nucleotide production

Additionally, energy considerations dictate the choice of GTP versus ATP as the energy donor in AMP versus GMP synthesis

What is GTP used for in relation to regulation of the two

When GTP levels are high, it stimulates the pathway to form more AMP (by providing energy to adenylosuccinate synthase) while simultaneously inhibiting its own synthesis pathway (by inhibiting IMP dehydrogenase).

Additionally, energy considerations dictate the choice of GTP versus ATP as the energy donor in AMP versus GMP synthesis

What is ATP used for

ATP is the energy donor (acting as a phosphate donor to create an AMP-XMP intermediate) in the conversion of Xanthosine monophosphate (XMP) to Guanosine monophosphate (GMP).