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How does the position of hydroxyl group in a nucleotide monomer affect the dehydration synthesis of nucleotides?

How does the position of hydroxyl group in a nucleotide monomer affect the dehydration synthesis of nucleotides?


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In dehydration synthesis of nucleotides, the hydrogen atom from the 3' carbon on the deoxyribose sugar of one nucleotide reacts with the hydroxyl group on the phosphate group of another nucleotide to form water. As the water molecule forms, a new covalent bond comes into existence between the two nucleotides.

Hydroxyl group can be in different positions within the phosphate group, for example:

I'm wondering if different positions of the hydroxyl group have an impact on the dehydration synthesis between nucleotide monomers. For example, when the hydroxyl group is at the bottom, will the dehydration synthesis occur at all? Also, when the hydroxyl group is on the left, does the spatial structure of the sugar-phosphate backbone have a spatial shape different from when the OH group is on the top?


Wherever the hydroxyl group is; the result is the same I think. The phosphate has oxygen arranged in a tetrahedron around it.

In cells the hydrogen is not attached most of the time. For example the triphosphate on ATP is a weak base with a pKa of about 6.6. Cytoplasm usually has a pH of about 7.2, so an ATP molecule is only protonated (very approximately) 15% of the time.

https://en.wikipedia.org/wiki/Polyphosphate#Acid-base_and_complexation_properties


An alcohol can be converted to a corresponding thiol using Lawesson's reagent (LR 2,4-bis(4-methoxyphenyl)-1,3,2,4-dithiadiphosphetane 2,4-disulfide). However, the reaction is messy and could give you a mixture of products in addition to intended thiol, including eliminated product, alkene (Ref.1). For example, treatment of acyclic 1,4-diols with LR gives the 1,3-dienes (Ref.1).

However, the substitution versus elimination outcome with LR is depends on the structural features of the substrate (Ref.2), and hence, worth considering. The computational mechanism is depicted below:

Alternatively, you can use highly efficient Mitsunabu type reaction with diisopropyl azodicarboxylate (Ref.3). The abstract summerize the reaction as:

Various alcohols were converted to their corresponding thiolacetates by treatment with triphenylphosphine and diisopropyl azodicarboxylate in the presence of thiolacetic acid. The overall conversion was both highly efficient (89–99% yields) and stereoselective (99.5% inversion).


The DNA Double Helix

The DNA double helix looks like a twisted staircase, with the sugar and phosphate backbone surrounding complementary nitrogen bases.

Learning Objectives

Describe the structure of DNA

Key Takeaways

Key Points

  • The structure of DNA is called a double helix, which looks like a twisted staircase.
  • The sugar and phosphate make up the backbone, while the nitrogen bases are found in the center and hold the two strands together.
  • The nitrogen bases can only pair in a certain way: A pairing with T and C pairing with G. This is called base pairing.
  • Due to the base pairing, the DNA strands are complementary to each other, run in opposite directions, and are called antiparallel strands.

Key Terms

  • mutation: any error in base pairing during the replication of DNA
  • sugar-phosphate backbone: The outer support of the ladder, forming strong covalent bonds between monomers of DNA.
  • base pairing: The specific way in which bases of DNA line up and bond to one another A always with T and G always with C.

DNA is a Double Helix: Native DNA is an antiparallel double helix. The phosphate backbone (indicated by the curvy lines) is on the outside, and the bases are on the inside. Each base from one strand interacts via hydrogen bonding with a base from the opposing strand.

A Double-Helix Structure

DNA has a double-helix structure, with sugar and phosphate on the outside of the helix, forming the sugar-phosphate backbone of the DNA. The nitrogenous bases are stacked in the interior in pairs, like the steps of a staircase the pairs are bound to each other by hydrogen bonds. The two strands of the helix run in opposite directions. This antiparallel orientation is important to DNA replication and in many nucleic acid interactions.

Antiparallel Strands: In a double stranded DNA molecule, the two strands run antiparallel to one another so one is upside down compared to the other. The phosphate backbone is located on the outside, and the bases are in the middle. Adenine forms hydrogen bonds (or base pairs) with thymine, and guanine base pairs with cytosine.

Base Pairs

Only certain types of base pairing are allowed. This means Adenine pairs with Thymine, and Guanine pairs with Cytosine. This is known as the base complementary rule because the DNA strands are complementary to each other. If the sequence of one strand is AATTGGCC, the complementary strand would have the sequence TTAACCGG.

DNA Replication

During DNA replication, each strand is copied, resulting in a daughter DNA double helix containing one parental DNA strand and a newly synthesized strand. At this time it is possible a mutation may occur. A mutation is a change in the sequence of the nitrogen bases. For example, in the sequence AATTGGCC, a mutation may cause the second T to change to a G. Most of the time when this happens the DNA is able to fix itself and return the original base to the sequence. However, sometimes the repair is unsuccessful, resulting in different proteins being created.


DNA Packaging

DNA packaging is an important process in living cells. Without it, a cell is not able to accommodate the large amount of DNA that is stored inside.

Learning Objectives

Describe how DNA is packaged differently in prokaryotes and eukaryotes

Key Takeaways

Key Points

  • In eukaryotic cells, DNA and RNA synthesis occur in a different location than protein synthesis in prokaryotic cells, both these processes occur together.
  • DNA is “supercoiled” in prokaryotic cells, meaning that the DNA is either under-wound or over-wound from its normal relaxed state.
  • In eukaryotic cells, DNA is wrapped around proteins known as histones to form structures called nucleosomes.

Key Terms

  • nucleosomes: The fundamental subunit of chromatin, composed of a little less than two turns of DNA wrapped around a set of eight proteins called histones.
  • histones: The chief protein components of chromatin, which act as spools around which DNA winds.

A eukaryote contains a well-defined nucleus, whereas in prokaryotes the chromosome lies in the cytoplasm in an area called the nucleoid. In eukaryotic cells, DNA and RNA synthesis occur in a separate compartment from protein synthesis. In prokaryotic cells, both processes occur together. What advantages might there be to separating the processes? What advantages might there be to having them occur together?

Eukaryotic and prokaryotic cells: A eukaryote contains a well-defined nucleus, whereas in prokaryotes, the chromosome lies in the cytoplasm in an area called the nucleoid.

The size of the genome in one of the most well-studied prokaryotes, E.coli, is 4.6 million base pairs (approximately 1.1 mm, if cut and stretched out). So how does this fit inside a small bacterial cell? The DNA is twisted by what is known as supercoiling. Supercoiling means that DNA is either under-wound (less than one turn of the helix per 10 base pairs) or over-wound (more than 1 turn per 10 base pairs) from its normal relaxed state. Some proteins are known to be involved in the supercoiling other proteins and enzymes such as DNA gyrase help in maintaining the supercoiled structure.

Eukaryotes, whose chromosomes each consist of a linear DNA molecule, employ a different type of packing strategy to fit their DNA inside the nucleus. At the most basic level, DNA is wrapped around proteins known as histones to form structures called nucleosomes. The histones are evolutionarily conserved proteins that are rich in basic amino acids and form an octamer. The DNA (which is negatively charged because of the phosphate groups) is wrapped tightly around the histone core. This nucleosome is linked to the next one with the help of a linker DNA. This is also known as the “beads on a string” structure. This is further compacted into a 30 nm fiber, which is the diameter of the structure. At the metaphase stage the chromosomes are at their most compact, approximately 700 nm in width, and are found in association with scaffold proteins.

Eukaryotic chromosomes: These figures illustrate the compaction of the eukaryotic chromosome.

In interphase, eukaryotic chromosomes have two distinct regions that can be distinguished by staining. The tightly packaged region is known as heterochromatin, and the less dense region is known as euchromatin.

Heterochromatin usually contains genes that are not expressed, and is found in the regions of the centromere and telomeres. The euchromatin usually contains genes that are transcribed, with DNA packaged around nucleosomes but not further compacted.


Summary

Proteins, carbohydrates, nucleic acids, and lipids are the four major classes of biological macromolecules&mdashlarge molecules necessary for life that are built from smaller organic molecules. Macromolecules are made up of single units known as monomers that are joined by covalent bonds to form larger polymers. The polymer is more than the sum of its parts: it acquires new characteristics, and leads to an osmotic pressure that is much lower than that formed by its ingredients this is an important advantage in the maintenance of cellular osmotic conditions. A monomer joins with another monomer with the release of a water molecule, leading to the formation of a covalent bond. These types of reactions are known as dehydration or condensation reactions. When polymers are broken down into smaller units (monomers), a molecule of water is used for each bond broken by these reactions such reactions are known as hydrolysis reactions. Dehydration and hydrolysis reactions are similar for all macromolecules, but each monomer and polymer reaction is specific to its class. Dehydration reactions typically require an investment of energy for new bond formation, while hydrolysis reactions typically release energy by breaking bonds.


Most people are familiar with carbohydrates, especially when it comes to what we eat. Carbohydrates are an essential part of our diet grains, fruits, and vegetables are all natural sources. More generally, carbohydrates are one of the four classes of macromolecules that compose all cells. While we may be most familiar with the role carbohydrates play in nutrition, they also have a variety of other essential functions in humans, animals, plants, and bacteria. In this section, we will discuss and review basic concepts of carbohydrate structure and nomenclature, as well as a variety of functions they play in cells.

In their simplest form, carbohydrates can be represented by the stoichiometric formula (CH2O)n, where n is the number of carbons in the molecule. For simple carbohydrates, the ratio of carbon to hydrogen to oxygen in the molecule is 1:2:1. This formula also explains the origin of the term &ldquocarbohydrate&rdquo: the components are carbon (&ldquocarbo&rdquo) and the components of water (hence, &ldquohydrate&rdquo). Simple carbohydrates are classified into three subtypes: monosaccharides, disaccharides, and polysaccharides, which will be discussed below. While simple carbohydrates fall nicely into this 1:2:1 ratio, carbohydrates can also be more complex, structurally. For example, many carbohydrates contain functional groups (remember them from our basic discussion about chemistry) besides the obvious hydroxyl. For example, carbohydrates can have phosphates or amino groups substituted at a variety of sites within the molecule. These additional groups can provide additional properties to the molecule and will alter its overall function. However, even with these types of substitutions, the basic overall structure of the carbohydrate is retained and easily identified.

Nomenclature

One issue with carbohydrate chemistry is the nomenclature. Here are a few quick and simple rules:

  1. Simple carbohydrates, such as glucose, lactose, or dextrose, end with an ". ose."
  2. Simple carbohydrates can be classified based on the number of carbon atoms in the molecule, as with triose (three carbons), pentose (five carbons), or hexose (six carbons).
  3. Simple carbohydrates can be classified based on the functional group found in the molecule, such as a ketose or aldose.
  4. Polysaccharides are often organized by the number of sugar molecules in the chain, such as in a monosaccharide, disaccharide, or trisaccharide.

For a short video on carbohydrate classification, see the 10-minute Khan Academy video by clicking here.

Monosaccharides

Monosaccharides (mono- = &ldquoone&rdquo sacchar- = &ldquosweet&rdquo) are simple sugars, the most common of which is glucose. In monosaccharides, the number of carbons usually ranges from three to seven. If the sugar has an aldehyde group (the functional group with the structure R-CHO), it is known as an aldose, and if it has a ketone group (the functional group with the structure RC(=O)R'), it is known as a ketose.

Figure 1. Monosaccharides are classified based on the position of their carbonyl group and the number of carbons in the backbone. Aldoses have a carbonyl group (indicated in green) at the end of the carbon chain, and ketoses have a carbonyl group in the middle of the carbon chain. Trioses, pentoses, and hexoses have three, five, and six carbons in their backbones, respectively. Attribution: Marc T. Facciotti (own work)

Glucose versus galactose

Galactose (part of lactose, or milk sugar) and glucose (found in sucrose, glucose disaccharride) are other common monosaccharides. The chemical formula for glucose and galactose is C6H12O6 both are hexoses, but the arrangements of the hydrogens and hydroxyl groups are different at position C4. Because of this small difference, they differ structurally and chemically (and are known as chemical isomers) because of the different arrangement of functional groups around the asymmetric carbon both of these monosaccharides have more than one asymmetric carbon (compare the structures in the figure below).

Fructose versus both glucose and galactose

A second comparison can be made when looking at glucose, galactose, and fructose (the second carbohydrate that with glucose makes up the disaccharide sucrose, and is a common sugar found in fruit, hence the name). All three are hexoses however, there is a major structural difference between glucose and galactose versus fructose: the carbon that contains the carbonyl (C=O). In glucose and galactose, it is on the C1 carbon, forming an aldehyde group in fructose, it is on the C2 carbon, forming a ketone group. The former are called aldoses based on the aldehyde group that is formed the latter are designated as ketoses based on the ketone group. Again, this difference gives fructose different chemical and structural properties from those of the aldoses, glucose, and galactose, although fructose, glucose, and galactose all have the same chemical composition: C6H12O6.

Figure 2. Glucose, galactose, and fructose are all hexoses. They are structural isomers, meaning they have the same chemical formula (C6H12O6) but a different arrangement of atoms.

Linear versus ring form of the carbohydrates

Monosaccharides can exist as a linear chain or as ring-shaped molecules in aqueous solutions, they are usually found in ring forms (Figure 3). Glucose in a ring form can have two different arrangements of the hydroxyl group (OH) around the anomeric carbon (C1 that becomes asymmetric in the process of ring formation). If the hydroxyl group is below C1 in the sugar, it is said to be in the alpha (&alpha) position, and if it is above the plane, it is said to be in the beta (&beta) position.

Figure 3. Five and six carbon monosaccharides exist in equilibrium between linear and ring forms. When the ring forms, the side chain it closes on is locked into an &alpha or &beta position. Fructose and ribose also form rings, although they form five-membered rings as opposed to the six-membered ring of glucose.

Disaccharides

Disaccharides (di- = &ldquotwo&rdquo) form when two monosaccharides undergo a dehydration reaction (also known as a condensation reaction or dehydration synthesis). During this process, the hydroxyl group of one monosaccharide combines with the hydrogen of another monosaccharide, releasing a molecule of water and forming a covalent bond. A covalent bond formed between a carbohydrate molecule and another molecule (in this case, between two monosaccharides) is known as a glycosidic bond. Glycosidic bonds (also called glycosidic linkages) can be of the alpha or the beta type.

Figure 4. Sucrose is formed when a monomer of glucose and a monomer of fructose are joined in a dehydration reaction to form a glycosidic bond. In the process, a water molecule is lost. By convention, the carbon atoms in a monosaccharide are numbered from the terminal carbon closest to the carbonyl group. In sucrose, a glycosidic linkage is formed between the C1 carbon in glucose and the C2 carbon in fructose.

Common disaccharides include lactose, maltose, and sucrose (Figure 5). Lactose is a disaccharide consisting of the monomers glucose and galactose. It is found naturally in milk. Maltose, or malt/grain sugar, is a disaccharide formed by a dehydration reaction between two glucose molecules. The most common disaccharide is sucrose, or table sugar, which is composed of the monomers glucose and fructose.

Figure 5. Common disaccharides include maltose (grain sugar), lactose (milk sugar), and sucrose (table sugar).

Interactions with carbohydrates

We have just discussed the various types and structures of carbohydrates found in biology. The next thing to address is how these compounds interact with other compounds. The answer to that is that it depends on the final structure of the carbohydrate. Because carbohydrates have many hydroxyl groups associated with the molecule, they are therefore excellent H-bond donors and acceptors . Monosaccharides can quickly and easily form H-bonds with water and are readily soluble. All of those H-bonds also make them quite "sticky." This also true for many disaccharides and many short-chain polymers. Longer polymers may not be so readily soluble.

Finally, the ability to form a variety of H-bonds allows polymers of carbohydrates or polysaccharides to form strong intramolecular and intermolocular bonds. In a polymer, because there are so many H-bonds, this can provide a lot of strength to the molecule or molecular complex, especially if the polymers interact. Just think of cellulose, a polymer of glucose, if you have any doubts.

Polysaccharides

A long chain of monosaccharides linked by glycosidic bonds is known as a polysaccharide (poly- = &ldquomany&rdquo). The chain may be branched or unbranched, and it may contain different types of monosaccharides. The molecular weight may be 100,000 daltons or more, depending on the number of monomers joined. Starch, glycogen, cellulose, and chitin are primary examples of polysaccharides.

Starch is the stored form of sugars in plants and is made up of a mixture of amylose and amylopectin (both polymers of glucose). Plants are able to synthesize glucose, and the excess glucose, beyond the plant&rsquos immediate energy needs, is stored as starch in different plant parts, including roots and seeds. The starch in the seeds provides food for the embryo as it germinates and can also act as a source of food for humans and animals. The starch that is consumed by humans is broken down by enzymes, such as salivary amylases, into smaller molecules, such as maltose and glucose. The cells can then absorb the glucose.

Starch is made up of glucose monomers that are joined by 1-4 or 1-6 glycosidic bonds the numbers 1-4 and 1-6 refer to the carbon number of the two residues that have joined to form the bond. As illustrated in Figure 6, amylose is starch formed by unbranched chains of glucose monomers (only 1-4 linkages), whereas amylopectin is a branched polysaccharide (1-6 linkages at the branch points).

Figure 6. Amylose and amylopectin are two different forms of starch. Amylose is composed of unbranched chains of glucose monomers connected by 1-4 glycosidic linkages. Amylopectin is composed of branched chains of glucose monomers connected by 1-4 and 1-6 glycosidic linkages. Because of the way the subunits are joined, the glucose chains have a helical structure. Glycogen (not shown) is similar in structure to amylopectin but more highly branched.

Glycogen is the storage form of glucose in humans and other vertebrates and is made up of monomers of glucose. Glycogen is the animal equivalent of starch and is a highly branched molecule usually stored in liver and muscle cells. Whenever blood glucose levels decrease, glycogen is broken down to release glucose in a process known as glycogenolysis.

Cellulose is the most abundant natural biopolymer. The cell wall of plants is mostly made of cellulose this provides structural support to the cell. Wood and paper are mostly cellulosic in nature. Cellulose is made up of glucose monomers that are linked by &beta 1-4 glycosidic bonds.

Figure 7. In cellulose, glucose monomers are linked in unbranched chains by &beta 1-4 glycosidic linkages. Because of the way the glucose subunits are joined, every glucose monomer is flipped relative to the next one, resulting in a linear, fibrous structure.

Cellulose is not very soluble in water when it is in a crystalline state this can be approximated by the stacked cellulose fiber depiction above. Can you suggest a reason for why (based on the types of interactions) it might be so insoluble?

As shown in the figure above, every other glucose monomer in cellulose is flipped over, and the monomers are packed tightly as extended, long chains. This gives cellulose its rigidity and high tensile strength&mdashwhich is so important to plant cells. While the &beta 1-4 linkage cannot be broken down by human digestive enzymes, herbivores such as cows, koalas, buffalos, and horses are able, with the help of the specialized flora in their stomach, to digest plant material that is rich in cellulose and use it as a food source. In these animals, certain species of bacteria and protists reside in the rumen (part of the digestive system of herbivores) and secrete the enzyme cellulase. The appendix of grazing animals also contains bacteria that digest cellulose, giving it an important role in the digestive systems of ruminants. Cellulases can break down cellulose into glucose monomers that can be used as an energy source by the animal. Termites are also able to break down cellulose because of the presence of other organisms in their bodies that secrete cellulases.


Nucleotides

DNA and RNA are made up of monomers known as nucleotides. The nucleotides combine with each other to form a polynucleotide: DNA or RNA. Each nucleotide is made up of three components:

Each nitrogenous base in a nucleotide is attached to a sugar molecule, which is attached to one or more phosphate groups.

Figure (PageIndex<1>): DNA and RNA: A nucleotide is made up of three components: a nitrogenous base, a pentose sugar, and one or more phosphate groups. Carbon residues in the pentose are numbered 1&prime through 5&prime (the prime distinguishes these residues from those in the base, which are numbered without using a prime notation). The base is attached to the 1&prime position of the ribose, and the phosphate is attached to the 5&prime position. When a polynucleotide is formed, the 5&prime phosphate of the incoming nucleotide attaches to the 3&prime hydroxyl group at the end of the growing chain. Two types of pentose are found in nucleotides, deoxyribose (found in DNA) and ribose (found in RNA). Deoxyribose is similar in structure to ribose, but it has an H instead of an OH at the 2&prime position. Bases can be divided into two categories: purines and pyrimidines. Purines have a double ring structure, and pyrimidines have a single ring.


Monosaccharide Structure

All monosaccharides have the same general formula of (CH2O)n, which designates a central carbon molecule bonded to two hydrogens and one oxygen. The oxygen will also bond to a hydrogen, creating a hydroxyl group. Because carbon can form 4 bonds, several of these carbon molecules can bond together. One of the carbons in the chain will form a double bond with an oxygen, which is called a carbonyl group. If this carbonyl occurs at the end of the chain, the monosaccharide is in the aldose family. If the carboxyl group is in the middle of the chain, the monosaccharide is in the ketose family.

Above is a picture of glucose. Glucose is one of the most common monosaccharides in nature, used by nearly every form of life. This simple monosaccharide is composed of 6 carbons, each labeled in the image. The first carbon is the carbonyl group. Because it is at the end of the molecule, glucose is in the aldose family. Typically, monosaccharides with more than 5 carbons exist as rings in solutions of water. The hydroxyl group on the fifth carbon will react with the first carbon. The hydroxyl group gives up its hydrogen atom when it forms a bond with the first carbon. The double bonded oxygen on the first carbon bonds with a new hydrogen when the second bond with the carbon is broken. This forms a fully connected and stable ring of carbons.


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.

Subsequently, question is, 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.

Subsequently, one may also ask, 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.


Fate of DNA Sugar Radicals

Amanda C. Bryant-Friedrich , in Advances in Molecular Toxicology , 2010

Publisher Summary

Oxidative damage to nucleic acids occurs at the nucleobase and at the sugar-phosphate backbone. While base damage dominates in frequency, the attack of oxidants at sugars in the nucleic acid backbone often leads to strand breaks that ultimately leave gaps or nicks that carry modified or “dirty” ends. When the damage is focused on the 2'-deoxyribose component of DNA, hydrogen atoms are abstracted from one of the five unique carbons of the pentose ring to deliver a highly reactive radical intermediate. Another important factor, which should be considered while attempting to make such predictions, is the identity of the oxidant. One of the most significant species to consider when discussing DNA oxidants is the hydroxyl radical. This reactive oxygen species is produced endogenously through cellular metabolism, at higher levels under conditions of oxidative stress, as a part of chronic inflammation and as a major outcome of the exposure of cells to ionizing radiation. The hydroxyl radical is small, highly diffusible, reactive, and capable of hydrogen atom abstraction at any position of 2'-deoxyribose moiety in DNA. Finally, the position of the Cɵ-radical relative to the nucleobase of DNA renders its reactivity toward the heterocyclic nucleic acid moieties very distinct as compared to the four other positions.