Nucleotide- Definition, Characteristics, Biosynthesis, Functions

What is a Nucleotide?

A nucleotide is a pentose sugar linked to a nitrogenous base and a phosphate molecule. Nucleotides are the building blocks of DNA.

• The nitrogenous bases are derived from two-parent compounds – purines and pyrimidines.
• DNA中存在的核苷酸含有2` - 脱氧 - D-核糖糖和RNA中的核苷酸含有D-核糖糖。
• The main difference is seen at the second position of the pentose structure, in the case of 2` – deoxyribose there is an absence of an alcohol group/ oxy group/ -OH group at the second position, hence the name.
• 在D - 核糖五核的情况下，–OH组存在于第二个位置。
• In both types, the pentoses are present in their β-furanose form which is a close five-membered ring structure.

核苷酸的特征

1. The nitrogenous base is linked covalently to pentose sugar by an N- glycosidic bond (N-1 in the case of pyrimidines and N-9 in the case of purines is linked to the C-1 carbon atom of the pentoses.)
2. DNA和RNA中存在的主要嘌呤碱是腺苷（A）和鸟嘌呤（G）。DNA中的主要嘧啶碱是胸腺嘧啶（T）和胞嘧啶（C），RNA胸腺氨酸中的尿胺（U）代替尿嘧啶（U）作为主要嘧啶碱。

• DNA和RNA中的连续核苷酸通过磷酸 - 二烯键连接，一个核苷酸的5`磷酸基团与另一种核苷酸的3`羟基相关，辅助核苷酸与氢键连接。
• Adenosine and Thymine are bonded by two hydrogen bonds and Guanine and Cytosine are bonded by three hydrogen bonds.
• The backbone of the DNA is composed of the chain of nucleotides linked to each other.

核苷酸的生物合成

核苷酸由两种途径合成：

1. 从头综合
2. 打捞路径

A. de从核苷酸的从头合成

In this pathway, complex nucleotides are synthesized using simple molecules such as sugars and amino acids. The pathway for synthesis of Purines and Pyrimidines is different and requires different precursors.

嘧啶核苷酸的合成

该合成涉及两个主要步骤

1. 嘧啶环的形成是6个成员环结构
2. Attachment of the pentose sugar (ribose – 5 – phosphate) to the ring structure

• Formation of the pyrimidine ring involves Aspartate, PRPP (5-phosphoribosyl-1-pyrophosphate) and, Carbamoyl Phosphate.
• 尿嘧啶和胞嘧啶是嘧啶合成中形成的核苷酸。这些核苷酸是在不同阶段形成的。
• 参与此过程的酶是：
  • Aspartate transcarbamoylase (ATCase)
  • Carbamoyl phosphate synthetase (Type II)
  • Dihydroorotate dehydrogenase
  • Orotate phosphoribosyltransferase
  • Orotidine -5-磷酸羧化酶
• Glutamine, Aspartate, ATP and, CO₂are required for the synthesis of pyrimidines.
• Carbamoyl phosphate required in the biosynthesis of pyrimidine is formed in the cytosol by the enzyme carbamoyl phosphate synthetase II.
• The first step of pyrimidine synthesis is the reaction between carbamoyl and aspartate to form N-carbamoyl aspartate. This reaction is catalyzed by the enzyme Aspartate transcarbamoylase.
• 从N-喀巴马酰基天冬氨酸中除去一个H2O分子以形成L-二羟基苯二酸盐，并由二氢烯酶进行该反应。
• This L-dihydroorotate in presence of dihydroorotate dehydrogenase forms orotate. Orotate is the most important compound to which the ribose-5-phosphate sugar is added further.
• Orotate in presence of enzyme orotate phosphoribosyltransferase forms Orotidylate. In this step the sugar, ribose-5-phosphate is provided by Phosphoribosyl pyrophosphate (PRPP). The sugar attaches to the orotate to form orotidylate.
• This Orotidylate further undergoes decarboxylation in presence of orotidylate decarboxylase to form Uridylate (UMP) also known as Uridine 5`-monophosphate.
• 该尿苷磷酸化以进一步的步骤磷酸化，形成尿苷5`-三磷酸（UTP）。
• Cytidine 5`- triphosphate (CTP) is formed by the enzyme cytidine synthetase from UTP. In this conversion the nitrogen donor is glutamine.
• In this way, the biosynthesis of pyrimidines takes place.

Synthesis of Purine nucleotides

• Unlike in biosynthesis of pyrimidine nucleotides, purine synthesis initiates with PRPP and then the purine ring is built around the sugar.
• 参与此过程的酶是：
  • Glutamine phosphoribosylpyrophosphate amidotransferase (Glutamine-PRPP)
  • 糖酰胺核糖核苷酸合酶（GAR合酶）
  • Gylcinamide ribotide transforamylase (GAR transformylase)
  • 甲基乙酰酰胺合酶
  • 氨基咪唑核苷酸合酶
  • 氨基咪唑核苷酸羧化酶
  • 琥珀酰胺氨基二唑烷酰胺核苷酸合酶
  • Adenylosuccinate lyase
  • Aminoimidazole carboxamide ribotide transformylase
  • IMP环氢酶
• The first process involves the formation of Inosinate (IMP) ad further from the IMP ring the purine monophosphates are synthesized.

1. Phosphoribosyl pyrophosphate (PRPP) in presence of enzyme Glutamine-PRPP forms Phosphoribosyl amine (PRA). The amino group donated by Glutamine is attached to the C1 of the PRPP complex.

2. GAR synthase acts upon PRA to form glycinamide ribonucleotide (GAR). Here three atoms from the glycine molecule are added to the nitrogen atom.

3. GAR forms Formylglyacinamide ribonucleotide (FGAR) in presence of the enzyme GAR transformylase. The added glycine molecule is formylated by N¹⁰- 甲基四氢叶酸盐。

4.在存在酶FGAM合酶的情况下，FGAR形成甲基甘氨酸（FGAM）。

5. FGAM is catalyzed by enzyme AIM synthase to form Aminoimidazole ribonucleotide, which is further converted to Carboxyaminoimidalzole ribonucleotide (CAIR) by enzyme AIR carboxylase.

6. CAIR in presence of SAICAR synthase forms complex succinylaminoimidazole ribonucleotide. Here Aspartate donates its amino group.

7.在存在酶腺苷糖酸酯裂解酶的情况下，SAICAR转化为氨基咪唑羧酰胺核糖核苷酸（AICAR）。

8.在存在酶AICAR转录纤维化酶的情况下，AICAR被转换为FAICAR。第二个嘌呤环的最终碳由N贡献¹⁰- 甲基四氢叶酸盐。

9. Finally the second ring is closed to form the complete purine ring in presence of enzyme IMP cyclohydrolase to form Inosinate (IMP).

10. Now from the IMP AMP and GMP are synthesized using enzymes Adenylosuccinate synthetase and Adenylosuccinate lyase (for AMP) and IMP dehydrogenase and GMP synthetase (for GMP).

这完成了从头合成嘧啶的合成。

B. Salvage pathway of Purine nucleotides

• Adenine is catalyzed by the enzyme adenosine phosphoribosyltransferase (APRT) from purine bases ad purine核苷。
• Guanine and hypoxanthine are salvaged by the enzyme Hypoxanthine-guanine phosphoribosyltransferase (HGPRT) through the process of phosphoribosylation.
• Through other processes such as deamination, adenosine deaminase can be converted to adenosine which can further be converted to hypoxanthine.

打捞路径of Pyrimidine nucleotides (Thymine)

• The enzyme thymidine kinase can salvage the dTTP (deoxythymidine triphosphate) from thymidine or deoxyuridine.

嘧啶生物合成调节

• The Biosynthesis of pyrimidines is regulated at different levels. This is majorly controlled by the enzyme ATCase (Aspartate transcarbamoylase).
• ATCASE是一种具有6个活性位点的多生育变构酶。它在嘧啶的生物合成中起重要作用。ATP充当激活剂，CTP充当Atcase的抑制剂。
• This enzyme brings about the conversion of aspartate to carbamoyl aspartate. Hence, when the biosynthesis of pyrimidines is to be regulated CTP binds to ATCase to stop the synthesis. This is known as feedback inhibition, where the last product of the pathway inhibits the first enzyme to regulate the synthesis. This is achieved when high levels of CTP are present in the cell.
• 嘧啶的生物合成也可以在PRPP（磷酸磷酸磷酸磷酸）形成下受到调节。高水平的PRPP表示高水平的嘧啶合成。因此，将UTP转换为CTP的CTP合成酶被CTP抑制。该酶可以被GTP激活。
• These mechanisms regulated the biosynthesis of pyrimidines.

嘌呤生物合成调控

• The biosynthesis of purines is regulated at 3 different levels. PRPP synthetase is the first regulatory point in the pathway. Feedback inhibition is exerted by AMP and GMP over PRPP synthetase.
• PRPP酰基转移酶是一种变构酶和GTP，ATP，GDP，ADP，GMP和AMP结合酶变构并调节生物合成。
• 最后一个调节点是小鬼的分支点。过量的ATP加速GMP的合成，反之亦然。

Functions ofNucleotide

• Nucleotides act as energy reserves in the body and are involved n many important processes.
• ATP（三磷酸腺苷）被认为是细胞的货币，在各种途径中起着至关重要的作用，并且是磷酸组供体。
• 水解ATP产量large amount of energy which can be utilized by the cell of different functions.
• Nucleotides are a part of many co-factors for many enzymes.

示例 - 乙酰二氧化碳，NAD⁺(Nicotinamide adenine dinucleotide), FAD (Flavin adenine dinucleotide)

• cAMP (adenosine cyclic monophosphate) is a common second messenger produced in response to hormones and various chemical signals. cAMP is formed during a reaction of ATP catalyzed by adenylyl cyclase.
• CGMP（鸟苷循环单磷酸）在细胞中也具有许多调节功能。
• 在氨基酸饥饿条件下，在细菌细胞中观察到PPGPP（鸟苷四磷酸）功能，这响应于蛋白质产生的放缓。

References

1. Moffatt BA，Ashihara H.嘌呤和嘧啶核苷酸合成和代谢。拟南芥书。2002; 1：e0018。doi：10.1199/tab.0018。
2. Zimmermann H. (2016). Extracellular ATP and other nucleotides-ubiquitous triggers of intercellular messenger release.Purinergic signalling,12（1），25-57。https://doi.org/10.1007/s11302-015-9483-2
3. Lehninger生物化学原理 - 第六埃德 - C2013
4. Cell Biology, T Devasena, Oxford University Press.
5. https://www.genome.gov/genetics-glossary/nucleotide
6. https://uh.edu/dtu/19-nuc%20mata-1-08.htm
7. http://www2.csudh.edu/nsturm/CHEMXL153/NucleotidesCompandStruc.htm
8. https://knowgenetics.org/nucleotides-and-bases/