Lectures 6-8

Biosynthesis of Nucleotides

• Nucleotides are precursors to DNA and RNA, serving as essential carriers of chemical energy.
• Nucleotides can be synthesized through the De Novo and Salvage pathways.
• De novo synthesis for purines and pyrimidines is identical across all organisms.
• Free bases are not intermediates in the de novo pathway but they are intermediates in the salvage process.
• PRPP is the key precursor for the de novo pathway, in which amino acids are key and glutamine is an amino group source.

De Novo - Purines

• Adenosine 5-monophosphate (AMP) and guanosine 5-monophosphate (GMP) are the parent nucleotides of nucleic acids.

Biosynthesis of AMP and GMP

• Biosynthesis regulation includes three major feedback mechanisms in regulating de novo purine nucleotide synthesis.

Pyrimidine Nucleotides

• Cytidine 5-monophosphate (CMP) and uridine 5-monophosphate (UMP) are common pyrimidine ribonucleotides, containing the pyrimidines cytosine and uracil.
• Eukaryotes use a single polypeptide consisting of three enzymes.

Pyrimidine Nucleotide Regulation

• Regulation of pyrimidine nucleotide synthesis occurs through aspartate transcarbamoylase (Atcase).
• The ATcase molecule consists of six catalytic subunits and six regulatory subunits.

Nucleoside Monophosphate → Trisphosphate

• Nucleotides convert to nucleoside triphosphate.
• AMP converts to ADP via adenylate kinase.
• ATP brings other formations, and with NMP creates ADP + NDP.
• Nucleoside diphosphates convert to triphosphates: NTPd + NDPa creates NDPd + NTPa.

Ribonucleotides precursors of Deoxyribonucleotides

• Deoxyribonucleotides are the building blocks of DNA.
• ADP converts to 2’deoxyadenosine diphosphate (dADP) in a unique reaction catalyzed by ribonucleotide reductase.
• Reduction of D-ribose.

Regulation of ribonucleotide reductase

• The regulation of ribonucleotide reductase occurs through deoxynucleoside triphosphates.

Ribonucleotides precursors of Deoxyribonucleotides (Free Radical Usage)

• The best characterized example of free radical usage.

Degradation of Purines and Pyrimidines

• The degradation of purines makes uric acid.
• The degradation of pyrimidines makes urea.

Purine and Pyrimidine recycling

• Free purine and pyrimidine bases can be recycled, for use in adenosine phosphoribosyltransferase.
• Adenine + PRPP can create AMP + Ppi.
• Another process is Hypoxanthine-guanine phosphoribosyltransferase.

Gout

• A painful form of inflammatory arthritis caused by excess uric acid in the bloodstream, leading to deposition of uric acid crystals in joints and tissues.

Cancer Targets

• Enzymes in the nucleotide biosynthesis pathways are used as targets

Thymidylate Synthesis

• In the synthesis of thymidylate from dCDP and dUMP, the process is tetrahydrofolate

Photosynthesis in vascular plants

• Photosynthesis in vascular plants takes place in chloroplasts.
• Rubisco condenses CO2 ribulose 1,5, bisphosphate, forming the unstable hexose bisphosphate, and is then split into two molecules of 3- phosphoglycereae.
• Stromal isozymes of the glycolytic cycle catalyze the reduction of 3 phosphoglycerate to glyceraldehyde-3 phosphate.
• Fixation of three CO2 into one triose phosphate is 9 ATP and 6 NADPH.
• Antiporter in the inner chloroplast membrane exchanges Pi in the cytosol for 3 phosphoglycerate or DHAP produced by CO2 assimilation.
• Four enzymes of the Calvin cycle are activated indirectly by light and can be inactive in the dark.

Carbohydrate Biosynthesis

• Anabolic pathways tend to be reductive and not oxidative.
• Plants are autotrophs.

Plastids

• Most biosynthetic activities occur in plastids.
• Plastids reproduce by binary fission.
• Chloroplasts are the area for CO2 of assimilation.
• Chloroplasts can become proplastids.
• Relative amount of each will be based upon the plant tissue type

Carbon Dioxide Assimilation

• Stage 1 - CO2 assimilation involves a carbon-fixation reaction/
• Stage 2 - 3-phosphoglycerate turns into a triose phosphate.
• Stage 3 – 5/6 triose phosphate turns into ribulose 1, 5 bisphosphate (3), which acts as the starting material.
• Fructose-6-phosphate functions as a key intermediate in stage 3 of CO2 assimilation.
• Hexose phosphate converts into pentose bisphosphate using the same reactions in the opposite direction.

Stage I: Fixation of CO2

• Photosynthetic organisms in were in 1940’s (Calvin).
• Plants that incorporate these compounds are C 3 plants compared to C 4 plants.
• Incorporation of CO2 is accomplished with the help of ribulose 1,5 bisphosphate carboxylase, also named Rubisco.
• These are two distinct forms of Rubisco.
• Two forms of Rubisco have Form I, found in vascular plants, fungi algae and cyanobacteria.
• The second Form is II and found in certain photosynthetic bacteria.

Stage I: Fixation of CO2 and Role of Mg2+

• This discusses the Role of Mg2+ in catalytic machinery
• Rubisco remains inactive until is carbamoylated on amino group of Lys201 molecule
• Ribulose 1,5bisphosphate inhibits carbamoylation.
• Rubisco activates The inhibition done via the release of ribulose 1,5
• This is a regulatory mechanism

Stage II: 3-Phosphoglycerate → Glyceraldehyde 3-phosphate

• In Cytosol, 3 phosphoglycerate is now Phosphoglycerate kinase,
• In Stroma, 3 Phosphoglycerate is converted to glyceraldehyde 3 phosphate in 2 steps, this cycle has One exception found here.
• The enzymes of Glycolytic enzymes are held in Chloraplast Stroma. There is expection, which is phophoglyerate mutase.
• Phase 1 Step for This will now be involved in Strama 3 phosphoglycerate kinase
• The 2nd Step will have Isomeric, with will utilize gkycersaldshyde 3 phosphate dyhrogenanse..
• The final Stpe this will have DhAP

Stage III: Regeneration of Ribulose I,5 Bisphosphate

• For continuous flow of CO2, ribulose 1,5 needs to be always ready
• Utilize Step 3, you will require carbon ketol group

Stage III: Transketolase and TPP Cofactor, and regeneration of Ribulose

• Transketolase helps with reactions in Calvin Cycle
• It also holds a general reaction catalyzed via transkeotolase molecule
• A cofactor is also utilized, thaimine pyrophosphate

Requirements for Synthesis

• Stage three with the call involves three ATP, the conversion will have the of cycles, the conversion is 3 CO2 to triose phosphate. Consumes 6 ATP & 6 NADPH in 2nd stage
• For every triose phosphate will require 6 NADPH and 9 for ATP.
• Animals lack Ribulose and sodoehelptose17, as well as rubisco..

Export of Triose Phosphate Cycle

• The inner membrane is not that strong towards phosphorylated components and will require light
• The P1 has to be moved to the Chloroplast and this is done with photophosphorylation
• To get phosphate to cytosol it’s gotta be converted to sucrose.
• The Secondary Function of this Is that ATM and NMDA cannot cross choloplast membrane

Export of Triose Phosphate in 2

In exporting The top components which are Triose Phosphate, DHAP, AtP and NADPH. These cannat crass membrane which are Choloplast intermennra.

Enzymes and the Light

• Reductive assimilation needs ATP and NADPH.
• Enzymes has to be efficient given Light condition.
• Fructose 1,6 bisphosphatate Will require Mg2+

Enzymes and The Light : Further Analysis

• There needs at last 4 enzymes which must regulated for Light Ribulose 5 phosphate kinase Fructose 16 bisphosphatase Gkycerldeyde 3 phosphate drhogrnes The Process to work need system as well so that there can a transfer in a way that can easily transfer electrons..

Biosynthesis of Starch and Sucrose

• Formation will be based during Light conditions
• the Synthesis and start will be in location. For this there wukk still be Production of Cabroghyoysates

How to work ADP into Glucose And to Work On Substrate For The Starch

• ADP will work as a Substrate Glucose for the start to build and to make all that has to do with Starch
• In order for the cholorcast to function, they all have to synethisxe If some of the is from non photosynthetic process must be made from amylaplast. Activated start synthesis, and will then start though adp glucose

Synthase Action And Starch Branching

• Utilizes AGpase- glucose P + ATP can be used for ADP and glucoase..
• Strsch Synthss will use a-amylose and can then transfer from ATP gluococe is can go through starch Branching Enzymes

How The Body UTlizes The Substarte For Sucroe Or UPD And Glucose Molecule

• Tryiase Molecule has to work in way which work though cycles convert to sucrose Starch
• Suorce Molecule will be synthesiized with Dhap an G3p