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What is the name of the bond between phosphate and the sugar in a nucleotide?


I am slightly confused about what the name of the bond is between the phosphate and sugar within a nucleotide. All my research comes up with is a phosphodiester bond being the backbone of DNA. But within a single nucleotide, would we perhaps call it a phosphoester bond (all of my searches of phosphoester bond correct it to phosphodiester, so I don't think the term 'phosphoester' is in use… ); or maybe it would be an O-glycosidic bond as it is a sugar molecule covalently bonded to another molecule via an O atom?


Phosophoester is a valid term. There are at least a 1000 peer-reviewed articles that use this term. IUPAC Goldbook defines nucleotides as:

Compounds formally obtained by esterification of the 3 or 5 hydroxy group of nucleosides with phosphoric acid. They are the monomers of nucleic acids and are formed from them by hydrolytic cleavage."

Phosphoester or phosphoric ester means an ester of phosphoric acid.


Expanding on WIYSIWG's correct answer:

Each nucleotide contains one phosphoester bond (between a phosphate O and sugar 5'-C). Additionally, two nucleotides are connected by one phosphoester bond (between a phosphate O and sugar 3'-C). So in a polymer of multiple nucleotides (DNA, RNA), the repeating monomer unit contains two phosphoester bonds, on "top" (5') and "below" (3') the sugar. Since the repeating unit contains two phosphoester bonds, and the phosphates alternate with the sugars in the sequence, we call this a sugar-phosphate backbone held together by phosphodiester bonds/linkages.

Schematic of single nucelotide featuring vertical line as phosphoester bond (to 5' C):

$P | [sugar]-[base] $

Two nucleotides, each with an internal phosphoester bond and with a new phosphoester bond connecting them (spanning 5' of one sugar to 3' of the next):

$P | [sugar]-[base] | P | [sugar]-[base] $

Repeating unit in nucleotide polymer, with alternating sugar-phosphate backbone and one phosphodiester bond/linkage per unit/nucleotide residue (the… ellipses indicate pattern continues for the entire nucleic acid polymer, with hydroxyls capping the very ends):

$… P | [sugar]-[base] |… $


AP Biology : Understanding the Sugar-Phosphate Backbone

The most prevalent negative charge on DNA can be found on which of the following molecular components?

Hydrogen bonds between base pairs

The phosphate backbone of DNA is negatively charged due to the bonds created between the phosphorous atoms and the oxygen atoms. Each phosphate group contains one negatively charged oxygen atom, therefore the entire strand of DNA is negatively charged due to repeated phosphate groups.

Example Question #22 : Dna And Rna Structure

Please complete the analogy.

Nitrogen : Nucleic Acids :: Phosphorous : ______________.

Nitrogen is essential to create all the nucleic acids, and phosphorous is essential to create phospholipids (an obvious choice), ATP and ADP (they are the same class of molecule, and the P stands for phosphate), and DNA (for the phosphate-sugar backbone).

Example Question #21 : Dna And Rna Structure

Which of the following is not true of a DNA molecule?

A purine or pyrimidine is bound to each sugar-phosphate group

Uracil is not a component of the molecule

Adenine and thymine are held together by phosphodiester bonds

Complementary strands are held together by hydrogen bonds

Adenine and thymine are held together by phosphodiester bonds

DNA is a polymer composed of nucleotide monomers. Each nucleotide is formed from a deoxyribose sugar, a phosphate, and a nitrogenous base. There are two types of nitrogenous bases: purines and pyrimidines. The purines are adenine and guanine, while the pyrimidines are thymine and cytosine (and uracil). Adenine will always bind thymine and cytosine will always bind guanine. Uracil is only found in RNA, and is absent from DNA.

During DNA replication and synthesis, nucleotides align so that the nitrogenous bases are correctly paired. The bases bind to one other via hydrogen bonding to secure the nucleotide to the template strand. The protein DNA ligase then fuses the sugar-phosphate groups of adjacent nucleotides to create the DNA backbone. These bonds are known as phosphodiester bonds.

The only false statement concerns the identity of bonding between nitrogenous bases. Bases are held together by hydrogen bonds, and the DNA backbone is held together by phosphodiester bonds.

Example Question #4 : Understanding The Sugar Phosphate Backbone

A __________ bond between the sugar of one nucleotide and the phosphate of an adjacent nucleotide stabilizes the backbone of the DNA.

The bond formed between the sugar of one nucleotide and the phosphate of an adjacent nucleotide is a covalent bond. A covalent bond is the sharing of electrons between atoms. A covalent bond is stronger than a hydrogen bond (hydrogen bonds hold pairs of nucleotides together on opposite strands in DNA). Thus, the covalent bond is crucial to the backbone of the DNA.

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What bonds nucleotides together?

A chemical bond between the phosphate group of one nucleotide and the sugar of a neighboring nucleotide holds the backbone together. Chemical bonds (hydrogen bonds) between the bases that are across from one another hold the two strands of the double helix together.

Beside above, how are two nucleotides in a DNA molecule joined? Nucleotides form a pair in a molecule of DNA where two adjacent bases form hydrogen bonds. Strands of DNA are made by joining sugar and phosphate as backbone (by phosphodiester bonds): two such DNA strands run antiparallely forming the sides of a ladder and the paired bases act as the rungs of the ladder.

Furthermore, what type of bond is a phosphodiester bond?

In DNA and RNA, the phosphodiester bond is the linkage between the 3' carbon atom of one sugar molecule and the 5' carbon atom of another, deoxyribose in DNA and ribose in RNA. Strong covalent bonds form between the phosphate group and two 5-carbon ring carbohydrates (pentoses) over two ester bonds.

What type of bond holds nitrogenous bases together?

The nitrogen bases are held together by hydrogen bonds: adenine and thymine form two hydrogen bonds cytosine and guanine form three hydrogen bonds.


Nucleotide

As mentioned above, a nucleotide molecule consists of 2 parts&ndasha nucleoside and a phosphate group. Interlinked nucleotides form a single strand of genetic material. In the case of DNA, two strands are linked together by their nitrogenous bases to form the double-stranded structure.

The sugar molecule in RNA is a ribose sugar, which is a 5-carbon sugar molecule (C5H10O5). In DNA, the sugar molecule has one oxygen atom less, which is why it&rsquos called deoxyribose (C5H10O4). This sugar molecule is linked to the phosphate group. The phosphate group comes from phosphoric acid (H3PO4), which has lost 2 hydrogen atoms.

The attachment occurs at the 5 th carbon of the sugar molecule. The carbon atom has 2 hydrogen atoms, and a hydroxyl group (-OH group). During bond formation, the phosphate group loses a hydrogen atom, while the 5 th carbon of the sugar loses a hydroxyl group. Thus, a bond is formed between them with a water molecule, formed by the H of the phosphate group, and the OH of the sugar is released. This is an ester bond.

Nucleotide (Photo Credit : Designua/ Shutterstock)

It is important to note here that nucleotides can have one, two or three phosphate group at the 5 th carbon. However, in nucleic acids, there are three phosphate groups.


Polymerization of Nucleotides (Phosphodiester Bonds)

Nucleotides are joined together similarly to other biological molecules, by a condensation reaction that releases a small, stable molecule. Unlike proteins, carbohydrates, and lipids, however, the molecule that is released is not water but pyrophosphate (two phosphate groups bound together). When pyrophosphate is cleaved by the addition of water, a great deal of free energy is released, ensuring that the reverse process (hydrolysis of the phosphodiester bond to give free nucleotides) is very unlikely to occur.

How does releasing free energy
make the reaction go forward?

Click on the step numbers below to see the polymerization of nucleotides. Click on the mouse at left to clear the images and text.

The 5' group of a nucleotide triphosphate is held close to the free of a nucleotide chain.

The 3' hydroxyl group forms a bond to the phosphorus atom of the free nucleotide closest to the 5' oxygen atom . Meanwhile, the bond between the first phosphorus atom and the oxygen atom linking it to the next phosphate group breaks.

A new phosphodiester bond now joins the two nucleotides. A pyrophosphate group has been liberated.

The pyrophosphate group is hydrolyzed (split by the addition of water), releasing a great deal of energy and driving the reaction forward to completion.


Uracil Base

Uracil is a weak acid that has the chemical formula C4H4N2O2. Uracil (U) is found in RNA, where it binds with adenine (A). Uracil is the demethylated form of the base thymine. The molecule recycles itself through a set of phosphoribosyltransferase reactions.

One interesting factoid about uracil is that the Cassini mission to Saturn found that its moon Titan appears to have uracil on its surface.


Biology

1. What are the three parts that make up a nucleotide?

2. What is the sugar found in DNA?

3. What are the four different bases found in DNA nucleotides?

4. What two parts make up the sides of the DNA “ladder”?

5. What holds the sugars and the phosphates together?

6. What makes up the rungs of the DNA “ladder”?

7. To what part of the nucleotide are the rungs attached?

8. What is the “base-pairing” rule? How do the nucleotides pair together?

9. What holds the nitrogen bases together?

10. What best describes the shape of a DNA molecule?

11. Name three ways the RNA is chemically different from DNA.

13. What are the three steps involved in DNA replication.

14. How many strands of DNA act as a template?

15. What causes the DNA molecule to untwist and ”unzip”?

16. Where does replication occur?

17. What is true about the two new strands of DNA at the end of replication?

18. Why and when does DNA replication occur?

20. What are the four steps involved in RNA transcription?

21. How many strands of DNA act as a template?

22. What are the three different types of RNA?

23. What is the function of mRNA?

26. What are the five steps involved in translation?

27. What is made during translation?

28. What is the function of rRNA?

30. What is the function of tRNA?

32. What type of bond forms between amino acids?

33. What codon starts the process of translation? Stops it?

35. What is the difference between a point and a frameshift mutation?

36. Which is worse, point or frameshift? Explain why.

37. What is a deletion mutation?

38. What is an insertion mutation?

39. What is an inversion mutation?

40. What is a translocation mutation?

41. What causes a non-disjunction mutation?

42. What is trisomy? Monosomy?

First of all, we don't do your homework for you.

Even so, since this is not my area of expertise, I searched Google under the key word " nucleotide " to get these possible sources:

You can do the same for your other concepts. In the future, you can find the information you desire more quickly, if you use appropriate key words to do your own search.

I hope this helps. Thanks for asking.

1. phosphate sugars and a nitrogen containing base

3. Adenine thymine cytosine and guanine

This is about all i know.
1. phosphate sugars and a nitrogen containing base

3. Adenine thymine cytosine and guanine

adenine (A), cytosine (C), guanine (G), or thymine (T).

1. a phosphate group, a 5-carbon sugar, and a nitrogenous base
2. deoxyribose
3. The bases used in DNA are adenine (A), cytosine (C), guanine (G), and thymine (T).
4. The sides of the ladder are made of alternating sugar and phosphate molecules. The sugar is deoxyribose. The rungs of the ladder are pairs of 4 types of nitrogen bases. Two of the bases are purines- adenine and guanine.
5.The bond formed between the sugar of one nucleotide and the phosphate of an adjacent nucleotide is a covalent bond. A covalent bond is the sharing of electrons between atoms. A covalent bond is stronger than a hydrogen bond (hydrogen bonds hold pairs of nucleotides together on opposite strands in DNA).
6. They showed that alternating deoxyribose and phosphate molecules form the twisted uprights of the DNA ladder. The rungs of the ladder are formed by complementary pairs of nitrogen bases — A always paired with T and G always paired with C.
7. These bases make up the 'rungs' of the ladder, and are attached to the backbone where the deoxyribose (sugar) molecules are located.
8.The rules of base pairing explain the phenomenon that whatever the amount of adenine (A) in the DNA of an organism, the amount of thymine (T) is the same (Chargaff's rule). Similarly, whatever the amount of guanine (G), the amount of cytosine (C) is the same.
9. The nitrogen bases are held together by hydrogen bonds: adenine and thymine form two hydrogen bonds cytosine and guanine form three hydrogen bonds.
10. he DNA molecule is shaped like a ladder that is twisted into a coiled configuration called a double helix. The nitrogen bases form the rungs of the ladder and are arranged in pairs, which are connected to each other by chemical bonds.


What is the name of the bond between phosphate and the sugar in a nucleotide? - Biology

The building blocks of DNA are nucleotides. The important components of each nucleotide are a nitrogenous base , deoxyribose (5-carbon sugar ), and a phosphate group (see Figure 1). Each nucleotide is named depending on its nitrogenous base. The nitrogenous base can be a purine, such as adenine (A) and guanine (G), or a pyrimidine, such as cytosine (C) and thymine (T). Uracil (U) is also a pyrimidine (as seen in Figure 1), but it only occurs in RNA, which we will talk more about later.

Figure 1. Each nucleotide is made up of a sugar, a phosphate group, and a nitrogenous base. The sugar is deoxyribose in DNA and ribose in RNA.

The nucleotides combine with each other by covalent bonds known as phosphodiester bonds or linkages. The phosphate residue is attached to the hydroxyl group of the 5′ carbon of one sugar of one nucleotide and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, thereby forming a 5′-3′ phosphodiester bond.

In the 1950s, Francis Crick and James Watson worked together to determine the structure of DNA at the University of Cambridge, England. Other scientists like Linus Pauling and Maurice Wilkins were also actively exploring this field. Pauling had discovered the secondary structure of proteins using X-ray crystallography. In Wilkins’ lab, researcher Rosalind Franklin was using X-ray diffraction methods to understand the structure of DNA. Watson and Crick were able to piece together the puzzle of the DNA molecule on the basis of Franklin’s data because Crick had also studied X-ray diffraction (Figure 2). In 1962, James Watson, Francis Crick, and Maurice Wilkins were awarded the Nobel Prize in Medicine. Unfortunately, by then Franklin had died, and Nobel prizes are not awarded posthumously.

Figure 2. The work of pioneering scientists (a) James Watson, Francis Crick, and Maclyn McCarty led to our present day understanding of DNA. Scientist Rosalind Franklin discovered (b) the X-ray diffraction pattern of DNA, which helped to elucidate its double helix structure. (credit a: modification of work by Marjorie McCarty, Public Library of Science)

Watson and Crick proposed that DNA is made up of two strands that are twisted around each other to form a right-handed helix. Base pairing takes place between a purine and pyrimidine namely, A pairs with T and G pairs with C. Adenine and thymine are complementary base pairs, and cytosine and guanine are also complementary base pairs. The base pairs are stabilized by hydrogen bonds adenine and thymine form two hydrogen bonds and cytosine and guanine form three hydrogen bonds. The two strands are anti-parallel in nature that is, the 3′ end of one strand faces the 5′ end of the other strand. The sugar and phosphate of the nucleotides form the backbone of the structure, whereas the nitrogenous bases are stacked inside. Each base pair is separated from the other base pair by a distance of 0.34 nm, and each turn of the helix measures 3.4 nm. Therefore, ten base pairs are present per turn of the helix. The diameter of the DNA double helix is 2 nm, and it is uniform throughout. Only the pairing between a purine and pyrimidine can explain the uniform diameter. The twisting of the two strands around each other results in the formation of uniformly spaced major and minor grooves (Figure 3).

Figure 3. DNA has (a) a double helix structure and (b) phosphodiester bonds. The (c) major and minor grooves are binding sites for DNA binding proteins during processes such as transcription (the copying of RNA from DNA) and replication.


What is the name of the bond between phosphate and the sugar in a nucleotide? - Biology

The successive nucleotides of both DNA and RNA are covalently linked through phosphate-group "bridges." Specifically, the 5'-hydroxyl group of one nucleotide unit is joined to the 3'-hydroxyl group of the next nucleotide by a phosphodiester linkage (Fig. 12-7). Thus the covalent backbones of nucleic acids consist of alternating phosphate and pentose residues, and the characteristic bases may be regarded as side groups joined to the backbone at regular intervals. Also note that the backbones of both DNA and RNA are hydrophilic. The hydroxyl groups of the sugar residues form hydrogen bonds with water. The phosphate groups in the polar backbone have a pK near 0 and are completely ionized and negatively charged at pH 7 thus DNA is an acid. These negative charges are generally neutralized by ionic interactions with positive charges on proteins, metal ions, and polyamines.

Figure 12-7 The covalent backbone structures of 5' DNA and RNA, showing the phosphodiester bridges(one of which is shaded in the DNA) linking successive nucleotide units. The backbone of alternating 3' pentose and phosphate groups of both DNA andRNA is highly polar.

All the phosphodiester linkages in DNA and RNA strands have the same orientation along the chain (Fig. 12-7), giving each linear nucleic acid strand a specific polarity and distinct 5' and 3' ends. By definition the 5' end lacks a nucleotide at the 5' position, and the 3' end lacks a nucleotide at the 3' position (Fig. 12-7). Other groups (most often one or more phosphates) may be present on one or both ends.

The covalent backbone of DNA and RNA is subject to slow, nonenzymatic hydrolysis of the phosphodiester bonds. In the test tube, RNA is hydrolyzed rapidly under alkaline conditions, but DNA is not the 2'-hydroxyl groups in RNA (absent in DNA) are directly involved in the process. Cyclic 2',3'-monophosphates are the first products of the action of alkali on RNA, and are rapidly hydrolyzed further to yield a mixture of 2'- and 3'-nucleoside monophosphates (Fig. 12-8).

The nucleotide sequences of nucleic acids can be represented schematically, as illustrated (at right) by a segment of DNA having five nucleotide units. The phosphate groups are symbolized by (P) and each deoxyribose by a vertical line. The carbons in the deoxyribose are represented from 1' at the top to 5' at the bottom of the vertIcal line (even though the sugar is always in its closed-ring /3-furanose form in nucleic acids). The connecting lines between nucleotides (through (Pi)) are drawn diagonally from the middle (3') of the deoxyribose of one nucleotide to the bottom (5') of the next. By convention, the structure of a single strand of nucleic acid is always written with the 5' end at the left and the 3' end at the right i.e., in the 5'𔾷' direction. Some simpler representations of the pentadeoxyribonucleotide illustrated are pA-C-G-T-AoH, pApCpGpTpA, and pACGTA. A short nucleic acid is referred to as an oligonucleotide. The definition of "short" is somewhat arbitrary, but the term oligonucleotide is often used for polymers containing 50 or fewer nucleotides. A longer nucleic acid is called a polynucleotide.

Figure 12-8 Hydrolysis of RNA under alkaline conditions. The 2' hydroxyl acts as a nucleophile in an intramolecular displacement, the 2',3'-cyclic monophosphate derivative is further hydrolyzed to give a mixture of 2'- and 3'-monophosphate derivatives. DNA, which lacks 2' hydroxyls, is stable under similar conditions.

The bases have a variety of chemical properties that affect the structure, and ultimately the function, of nucleic acids. Free pyrimidines and purines are weakly basic compounds, and are thus called bases. The purines and pyrimidines common in DNA and RNA are highly conjugated molecules (see Fig. 12-2). This property has important ef fects on the structure, electron distribution, and light absorption of nucleic acids. Resonance involving many atoms in the ring gives most of the bonds a partially double-bonded character. One result is that pyrimidines are planar molecules purines are very nearly planar, with a slight pucker. Free pyrimidine and purine bases may exist in two or more tautomeric forms depending upon the pH. Uracil, for example, occurs in lactam, lactim, and double lactim forms (Fig. 12-9). The structures of the purines and pyrimidines shown in Figure 12-2 are the tautomers predominating at pH 7.0. Again as a result of resonance, all of the bases absorb UV light, and nucleic acids are characterized by a strong absorption at wavelengths near 260 nm (Fig. 12-10).

Figure 12-10 The absorption spectra of the common nucleotides and their molar absorption coefficients at 260 nm and pH 7.0 (ε260). The spectra of the corresponding ribonucleotides and deoxyribonucleotides, as well as the nucleosides, are essentially identical. When mixtures of nucleotides are present, the wavelength at 260 nm (dashed vertical lines) is used for measurements.The Properties of Nucleotide Bases Affect the Structure of Nucleic Acids

The purines and pyrimidines are also hydrophobic and relatively insoluble in water at the near neutral pH of the cell. At acidic or alkaline pH the purines and pyrimidines become charged, and their solubility in water increases. Hydrophobic stacking interactions in which two or more bases are positioned with the planes of their rings parallel (similar to a stack of coins) represent one of two important modes of interaction between two bases. The stacking involves a combination of van der Waals and dipole-dipole interactions between the bases. These base-stacking interactions help to minimize contact with water and are very important in stabilizing the three-dimensional structure of nucleic acids, as described later. The close interaction between stacked bases in a nucleic acid has the effect of decreasing the absorption of UV light relative to a solution with the same concentration of free nucleotides. This is called the hypochromic effect.

The most important functional groups of pyrimidines and purines are ring nitrogens, carbonyl groups, and exocyclic amino groups. Hydrogen bonds involving the amino and carbonyl groups are the second important mode of interaction between bases. Hydrogen bonds between bases permit a complementary association of two and occasionally three strands of nucleic acid. The most important hydrogen-bonding patterns are those defined by James Watson and Francis Crick in 1953, in which A bonds specifically to T (or U) and G bonds to C (Fig. 12-11). These two types of base pairs predominate in double-stranded DNA and RNA, and the tautomers shown in Figure 12-2 are responsible for these patterns. This specific pairing of bases permits the duplication of genetic information by the synthesis of nucleic acid strands that are complementary to existing strands, as we shall discuss later in this chapter.

Figure 12-11 Hydrogenbonding patterns in the base pairs defined by Watson and Crick.


What is the name of the bond between phosphate and the sugar in a nucleotide? - Biology

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Some molecules, such as DNA, can polymerize through phosphodiester linkage when two ester bonds, a central phosphorous atom bonded to oxygen atoms and double bonded to another are formed.

As sub-units are added, the strand continues to grow, creating its phosphate backbone.

3.9: Phosphodiester Linkages

Overview

Phosphodiester linkage is created when a phosphoric acid molecule (H3PO4) is linked with two hydroxyl groups (&ndashOH) of two other molecules, forming two ester bonds and removing two water molecules. Phosphodiester linkage is commonly found in nucleic acids (DNA and RNA) and plays a critical role in their structure and function.

Phosphodiester Bonds Link Nucleotides Together

DNA and RNA are polynucleotides, or long chains of nucleotides, linked together. Nucleotides are composed of a nitrogen base (adenine, guanine, thymine, cytosine, or uracil), a pentose sugar and a phosphate molecule (PO 3&minus 4). In a polynucleotide chain, nucleotides are linked together by phosphodiester bonds. A phosphodiester bond occurs when phosphate forms two ester bonds. The first ester bond already exists between the phosphate group and the sugar of a nucleotide. The second ester bond is formed by reacting to a hydroxyl group (&ndashOH) in a second molecule. Each formation of an ester bond removes a water molecule.

Inside the cell, a polynucleotide is built from free nucleotides that have three phosphate groups attached to the 5 o carbon of their sugar. These nucleotides are thus called nucleotide triphosphates. During the formation of phosphodiester bonds, two phosphates are lost, leaving the nucleotide with one phosphate group that is attached to the 5 o carbon by an ester bond. The second ester bond is formed between the 5 o phosphate molecule of the nucleotide and the 3 o hydroxyl group of the sugar in another nucleotide. A class of enzymes called polymerases catalyzes, or accelerates, the formation of phosphodiester bonds.

The phosphodiester bonds in a polynucleotide chain form an alternating pattern of sugar and phosphate residues, called sugar-phosphate backbone. Phosphodiester bonds impart directionality to a polynucleotide chain. The polynucleotide chain has a free 5 o phosphate group at one end and a free 3 o hydroxyl group at the other. These ends are referred to as the 5 o end and the 3 o end, respectively. The directionality of nucleic acids is essential for DNA replication and RNA synthesis.

Nakamura, Teruya, Ye Zhao, Yuriko Yamagata, Yue-jin Hua, and Wei Yang. &ldquoWatching DNA Polymerase &eta Make a Phosphodiester Bond.&rdquo Nature 487, no. 7406 (July 11, 2012): 196&ndash201. [Source]


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