Question

Walk through the the process for how nucleotides and ribose are made and show how these come together to make ATP used for DNA replication

Walk the class through ATP production and regeneration (ATP synthase).

Answer 1

Dear student

Synthesis of nucleotides :-

Nucleotides can be synthesized by a variety of means both in vitro and in vivo.

In vitro, protecting groups may be used during laboratory production of nucleotides. A purified nucleoside is protected to create a phosphoramidite, which can then be used to obtain analogues not found in nature and/or to synthesize an oligonucleotide.

In vivo, nucleotides can be synthesized de novo or recycled through salvage pathways.The components used in de novo nucleotide synthesis are derived from biosynthetic precursors of carbohydrate and amino acid metabolism, and from ammonia and carbon dioxide. The liver is the major organ of de novo synthesis of all four nucleotides. De novo synthesis of pyrimidines and purines follows two different pathways. Pyrimidines are synthesized first from aspartate and carbamoyl-phosphate in the cytoplasm to the common precursor ring structure orotic acid, onto which a phosphorylated ribosyl unit is covalently linked.

Purines, however, are first synthesized from the sugar template onto which the ring synthesis occurs. For reference, the syntheses of the purineand pyrimidine nucleotides are carried out by several enzymes in the cytoplasm of the cell, not within a specific organelle. Nucleotides undergo breakdown such that useful parts can be reused in synthesis reactions to create new nucleotides

Synthesis of ribose :-

Ribose is a type of sugar normally made in the body from glucose. Ribose plays important roles in the synthesis of RNA, DNA, and the energy-containing substance adenosine triphosphate (ATP).

The pentose phosphate pathway (also called the phosphogluconate pathway and the hexose monophosphate shunt) is a metabolic pathway parallel to glycolysis. It generates NADPH and pentoses (5-carbon sugars) as well as ribose 5-phosphate, the last one a precursor for the synthesis of nucleotides.

Now,

Glycolysis - begins glucose metabolism in all cells to produce 2 molecules of pyruvate. Occurs outside of mitochondria, usually in cytoplasm. Cellular Respiration - uses oxygen from the environment and converts each pyruvate to three molecules of carbon dioxide while trapping the energy released in this process in ATP.

Most of the ATP produced by aerobic cellular respiration is made by oxidative phosphorylation. This works by the energy released in the consumption of pyruvate being used to create a chemiosmotic potential by pumping protons across a membrane.

ATP is a nucleotide that consists of three main structures: the nitrogenous base, adenine; the sugar, ribose; and a chain of three phosphate groups bound to ribose. The phosphate tail of ATP is the actual power source which the cell taps.

ATP synthase is an enzyme that creates the energy storage molecule adenosine triphosphate(ATP). ATP is the most commonly used "energy currency" of cells for all organisms. It is formed from adenosine diphosphate (ADP) and inorganic phosphate (Pi). The overall reaction catalyzed by ATP synthase is:

ADP + Pi + H+out ⇌ ATP + H2O + H+in

ATP is a nucleoside triphosphate (ribose sugar, adenine base and three phosphate groups), where a high-energy bond attaches the third phosphate group to the molecule.  This bond is highly unstable, and when it is hydrolysed it releases a substantial amount of free energy (approximately 7 kcal/mole).  In addition to providing energy, ATP has other essential roles within cells:  it is one of the four nucleotides required for the synthesis of DNA (replication) and RNA (protein synthesis); it regulates certain biochemical pathways; in mammals it is released from damaged cells to elicit a pain response; and in photosynthetic organisms it drives carbon fixation.  However, as it is unstable (cannot be stored for long) and is used for almost every conceivable process, each cell in the body must constantly produce ATP to supply its needs.  In total, an organism’s requirement for ATP is substantial: the average human body generates over 100 kg of ATP per day.  ATP synthase is the prime producer of ATP in cells, catalysing the combination of ADP (adenosine diphosphate) with inorganic phosphate to make ATP:

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