Nucleotides And Nucleic Acids

Nucleotides and Nucleic Acids

Nucleotides have three characteristic components:

(1) a nitrogenous (nitrogen-containing) base, (2) a pentose, and (3) a phosphate. The molecule without the phosphate group is called a nucleoside. The nitrogenous bases are derivatives of two parent compounds, pyrimidine and purine. The bases and pentoses of the common nucleotides are heterocyclic compounds. The carbon and nitrogen atoms in the parent structures are conventionally numbered to facilitate the naming and identification of the many derivative compounds.

The pentoses of nucleotides and nucleosides the carbon numbers are given a prime (‘) designation to distinguish them from the numbered atoms of the nitrogenous bases. The base of a nucleotide is joined covalently (at N-1 of pyrimidines and N-9 of purines) in an N--glycosyl bond to the 1 carbon of the pentose, and the phosphate is esterified to the 5 carbon. The N--glycosyl bond is formed by removal of the elements of water (a hydroxyl group from the pentose and hydrogen from the base), as in O-glycosidic bond formation.

Both DNA and RNA contain two major purine bases, adenine (A) and guanine (G), and two major pyrimidines. In both DNA and RNA one of the pyrimidines is cytosine (C), but the second major pyrimidine is not the same in both: it is thymine (T) in DNA and uracil (U) in RNA. Only rarely does thymine occur in RNA or uracil in DNA. Nucleic acids have two kinds of pentoses. The recurring deoxyribonucleotide units of DNA contain 2-deoxy-D-ribose, and the ribonucleotide units of RNA contain D-ribose. In nucleotides, both types of pentoses are in their -furanose (closed five-membered ring) form. The pentose ring is not planar but occurs in one of a variety of conformations generally described as “puckered.” Specific long sequences of A, T, G, and C nucleotides in DNA are the repository of genetic information.

Phosphodiester Bonds

The successive nucleotides of both DNA and RNA are covalently linked through phosphate-group “bridges,” in which the 5-phosphate group of one nucleotide unit is joined to the 3-hydroxyl group of the next nucleotide, creating a phosphodiester linkage.Thus the covalent backbones of nucleic acids consist of alternating phosphate and pentose residues, and the nitrogenous bases may be regarded as side groups joined to the backbone at regular intervals. The backbones of both DNA and RNA are hydrophilic. The hydroxyl groups of the sugar residues form hydrogen bonds with water. The phosphate groups, with a pKa near 0, are completely ionized and negatively charged at pH 7, and the negative charges are generally neutralized by ionic interactions with positive charges on proteins, metal ions, and polyamines.

All the phosphodiester linkages have the same orientation along the chain, 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. 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, non enzymatic 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-monophosphate nucleotides 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 mono phosphates. A short nucleic acid is referred to as an oligonucleotide. The definition of “short” is somewhat arbitrary, but polymers containing 50 or fewer nucleotides are generally called oligonucleotides. A longer nucleic acid is called a polynucleotide.

DNA Molecules Have Distinctive Base Compositions

A most important clue to the structure of DNA came from the work of Erwin Chargaff and his colleagues in the late 1940s. They found that the four nucleotide bases of DNA occur in different ratios in the DNAs of different organisms and that the amounts of certain bases are closely related. These data, collected from DNAs of a great many different species, led Chargaff to the following conclusions:

1. The base composition of DNA generally varies from one species to another.

2. DNA specimens isolated from different tissues of the same species have the same base composition.

3. The base composition of DNA in a given species does not change with an organism’s age, nutritional state, or changing environment.

4. In all cellular DNAs, regardless of the species, the number of adenosine residues is equal to the number of thymidine residues (that is, A= T), and the number of guanosine residues is equal to the number of cytidine residues (G =C). From these relationships it follows that the sum of the purine residues equals the sum of the pyrimidine residues; that is, A+ G= T +C.

These quantitative relationships, sometimes called “Chargaff’s rules,” were confirmed by many subsequent researchers. They were a key to establishing the three dimensional structure of DNA and yielded clues to how genetic information is encoded in DNA and passed from one generation to the next.

DNA Is a Double Helix

To shed more light on the structure of DNA, Rosalind Franklin and Maurice Wilkins used the powerful method of x-ray diffraction to analyze DNA fibers. They showed in the early 1950s that DNA produces a characteristic x-ray diffraction pattern. From this pattern it was deduced that DNA molecules are helical with two periodicities along their long axis, a primary one of 3.4 Å and a secondary one of 34 Å. The problem then was to formulate a three-dimensional model of the DNA molecule that could account not only for the x-ray diffraction data but also for the specific A= T and G=C base equivalences discovered by Chargaff and for the other chemical properties of DNA.

In 1953 Watson and Crick postulated a three dimensional model of DNA structure that accounted for all the available data. It consists of two helical DNA chains wound around the same axis to form a right handed double helix. The hydrophilic backbones of alternating deoxyribose and phosphate groups are on the outside of the double helix, facing the surrounding water. The furanose ring of each deoxyribose is in the C-2’ endo conformation. The purine and pyrimidine bases of both strands are stacked inside the double helix, with their hydrophobic and nearly planar ring structures very close together and perpendicular to the long axis. The offset pairing of the two strands creates a major groove and minor groove on the surface of the duplex. Each nucleotide base of one strand is paired in the same plane with a base of the other strand. Watson and Crick found that the hydrogen-bonded base pairs illustrated in G with C and A with T, are those that fit best within the structure, providing a rationale for Chargaff’s rule that in any DNA, G = C and A = T. It is important to note that three hydrogen bonds can form between G and C, symbolized G=C, but only two can form between A and T, symbolized A=T. This is one reason for the finding that separation of paired DNA strands is more difficult the higher the ratio of G=C to A=T base pairs. Other pairings of bases tend to destabilize the double-helical structure. When Watson and Crick constructed their model, they had to decide at the outset whether the strands of DNA should be parallel or anti parallel—whether their 5,3-phosphodiester bonds should run in the same or opposite directions. An anti parallel orientation produced the most convincing model, and later work with DNA polymerases provided experimental evidence that the strands are indeed anti parallel, a finding ultimately confirmed by x-ray analysis.

Watson-Crick model for the structure of DNA. The original model proposed by Watson and Crick had 10 base pairs, or 34 Å (3.4 nm), per turn of the helix; subsequent measurements revealed 10.5 base pairs, or 36 Å (3.6 nm), per turn. (a) Schematic representation, showing dimensions of the helix. (b) Stick representation showing the backbone and stacking of the bases. (c) Space-filling model

To account for the periodicities observed in the X ray diffraction patterns of DNA fibers, Watson and Crick manipulated molecular models to arrive at a structure in which the vertically stacked bases inside the double helix would be 3.4 Å apart; the secondary repeat distance of about 34 Å was accounted for by the presence of 10 base pairs in each complete turn of the double helix. In aqueous solution the structure differs slightly from that in fibers, having 10.5 base pairs per helical turn.

The two anti parallel polynucleotide chains of double-helical DNA are not identical in either base sequence or composition. Instead they are complementary to each other. Wherever adenine occurs in one chain, thymine is found in the other; similarly, wherever guanine occurs in one chain, cytosine is found in the other. The DNA double helix, or duplex, is held together by two forces: hydrogen bonding between complementary base pairs and base-stacking interactions. The complementarity between the DNA strands is attributable to the hydrogen bonding between base pairs. The base-stacking interactions, which are largely nonspecific with respect to the identity of the stacked bases, make the major contribution to the stability of the double helix. The important features of the double-helical model of DNA structure are supported by much chemical and biological evidence. Moreover, the model immediately suggested a mechanism for the transmission of genetic information. The essential feature of the model is the complementarity of the two DNA strands.

RNA

We now turn our attention to RNA, which differs from DNA in three respects. First, the backbone of RNA contains ribose rather than 2-deoxyribose. That is, ribose has a hydroxyl group at the2’-position. Second, RNA contains uracil in place of thymine. Uracil has the same single-ringed structure as thymine, except that it lacks the 5’- methyl group. Thymine is in effect 5’-methyl-uracil. Third, RNA is usually found as a single polynucleotide chain. Except for the case of certain viruses, RNA is not the genetic material and does not need to be capable of serving as a template for its own replication. Rather, RNA functions as the intermediate, the mRNA, between the gene and the protein-synthesizing machinery. Another function of RNA is as an adaptor, the tRNA, between the codons in the mRNA and amino acids. RNA can also play a structural role as in the case of the RNA components of the ribosome. Yet another role for RNA is as a regulatory molecule, which through sequence complementarity binds to, and interferes with the translation of, certain mRNAs. Finally, some RNAs (including one of the structural RNAs of the ribosome) are enzymes that catalyze essential reactions in the cell. In all of these cases, the RNA is copied as a single strand off only one of the two strands of the DNA template, and its complementary strand does not exist. RNA is capable of forming long double helices, but these are unusual in nature.

Difference between DNA and RNA

DNA		RNA
Difference:	1.Found in nucleus 2. sugar is deoxyribose 3. Bases are A,T,C,G	1.Found in nucleus and cytoplasm 2.sugar is ribose. 3. Bases are A,U,C,G
Bases & Sugars:	DNA is a long polymer with a deoxyribose and phosphate backbone and four different bases: adenine, guanine, cytosine and thymine	RNA is a polymer with a ribose and phosphate backbone and four different bases: adenine, guanine, cytosine, and uracil
Definition:	A nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms	RNA, single-stranded chain of alternating phosphate and ribose units with the bases adenine, guanine, cytosine, and uracil bonded to the ribose. RNA molecules are involved in protein synthesis and sometimes in the transmission of genetic information.
Job/Role:	Medium of long-term storage and transmission of genetic information	The main job of RNA is to transfer the genetic code need for the creation of proteins from the nucleus to the ribosome. this process prevents the DNA from having to leave the nucleus, so it stays safe. Without RNA, proteins could never be made.
Stands for:	DeoxyriboNucleicAcid	RiboNucleicAcid
Predominant Structure:	Typically a double- stranded molecule with a long chain of nucleotides	A single-stranded molecule in most of its biological roles and has a shorter chain of nucleotides
Pairing of Bases:	A-T(Adenine-Thymine), G-C(Guanine-Cytosine)	A-U(Adenine-Uracil), G-C(Guanine-Cytosine)
Stability:	Deoxyribose sugar in DNA is less reactive because of C-H bonds. Stable in alkaline conditions. DNA has smaller grooves where the damaging enzyme can attach which makes it harder for the enzyme to attack DNA.	Ribose sugar is more reactive because of C-OH (hydroxyl) bonds. Not stable in alkaline conditions. RNA on the other hand has larger grooves which makes it easier to be attacked by enzymes.
Unique Features:	The helix geometry of DNA is of B-Form. DNA is completely protected by the body i.e. the body destroys enzymes that cleave DNA. DNA can be damaged by exposure to Ultra-violet rays	The helix geometry of RNA is of A-Form. RNA strands are continually made, broken down and reused. RNA is more resistant to damage by Ultra-violet rays.

Gene

A gene is the molecular unit of heredity of a living organism. It is used extensively by the scientific community as a name given to some stretches of deoxyribonucleic acids (DNA) and ribonucleic acids (RNA) that code for a polypeptide or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains. Genes hold the information to build and maintain an organism's cells and pass genetic traits to offspring. All organisms have genes corresponding to various biological traits, some of which are instantly visible, such as eye color or number of limbs, and some of which are not, such as blood type, increased risk for specific diseases, or the thousands of basic biochemical processes that comprise life.

Genes that are expressed usually have introns that interrupt the coding sequences. A typical eukaryotic gene, therefore, consists of a set of sequences that appear in mature mRNA (called exons) interrupted by introns. The regions between genes are likewise not expressed, but may help with chromatin assembly, contain promoters, and so forth. Intron sequences contain some common features. Most introns begin with the sequence GT (GU in RNA) and end with the sequence AG. Otherwise, very little similarity exists among them. Intron sequences may be large relative to coding sequences; in some genes, over 90 percent of the sequence between the 5′ and 3′ ends of the mRNA is introns. RNA polymerase transcribes intron sequences. This means that eukaryotic mRNA precursors must be processed to remove introns as well as to add the caps at the 5′ end and polyadenylic acid (poly A) sequences at the 3′ end.

The Central Dogma

 

Transcription of DNA to RNA to protein: This dogma forms the backbone of molecular biology and is represented by four major stages.

1. The DNA replicates its information in a process that involves many enzymes: replication.

2. The DNA codes for the production of messenger RNA (mRNA) during transcription.

3. In eucaryotic cells, the mRNA is processed (essentially by splicing) and migrates from the nucleus to the cytoplasm.

4. Messenger RNA carries coded information to ribosomes. The ribosomes "read" this information and use it for protein synthesis. This process is called translation.

Proteins do not code for the production of protein, RNA or DNA.

They are involved in almost all biological activities, structural or enzymatic.

Replication

DNA replication is the process of producing two identical replicas from one original DNA molecule. This biological process occurs in all living organisms and is the basis for biological inheritance. DNA is made up of two strands and each strand of the original DNA molecule serves as template for the production of the complementary strand, a process referred to as semiconservative replication. Cellular proofreading and error-checking mechanisms ensure near perfect fidelity for DNA replication

When DNA replicates, many different proteins work together to accomplish the following steps:
 

1. The two parent strands are unwound with the help of DNA helicases.
2. Single stranded DNA binding proteins attach to the unwound strands, preventing them from winding back together.
3. The strands are held in position, binding easily to DNA polymerase, which catalyzes the elongation of the leading and lagging strands. (DNA polymerase also checks the accuracy of its own work!).
4. While the DNA polymerase on the leading strand can operate in a continuous fashion, RNA primer is needed repeatedly on the lagging strand to facilitate synthesis of Okazaki fragments. DNA primase, which is one of several polypeptides bound together in a group called primosomes, helps to build the primer.
5. Finally, each new Okazaki fragment is attached to the completed portion of the lagging strand in a reaction catalyzed by DNA ligase

Transcription

Before the synthesis of a protein begins, the corresponding RNA molecule is produced by RNA transcription. One strand of the DNA double helix is used as a template by the RNA polymerase to synthesize a messenger RNA (mRNA). This mRNA migrates from the nucleus to the cytoplasm. During this step, mRNA goes through different types of maturation including one called splicing when the non-coding sequences are eliminated. The coding mRNA sequence can be described as a unit of three nucleotides called a codon.

Transcription proceeds in the following general steps:

1 One or more sigma factor protein binds to the RNA polymerase holoenzyme, allowing it to bind to promoter DNA.

2 RNA polymerase creates a transcription bubble, which separates the two strands of the DNA helix. This is done by breaking the hydrogen bonds between complementary DNA nucleotides.

3 RNA polymerase adds matching RNA nucleotides to the complementary nucleotides of one DNA strand

4 RNA sugar-phosphate backbone forms with assistance from RNA polymerase to form an RNA strand.

5 Hydrogen bonds of the untwisted RNA-DNA helix break, freeing the newly synthesized RNA strand.

6 If the cell has a nucleus, the RNA may be further processed. This may include polyadenylation, capping, and splicing.

7The RNA may remain in the nucleus or exit to the cytoplasm through the nuclear pore complex

 Translation

The ribosome binds to the mRNA at the start codon (AUG) that is recognized only by the initiator tRNA. The ribosome proceeds to the elongation phase of protein synthesis. During this stage, complexes, composed of an amino acid linked to tRNA, sequentially bind to the appropriate codon in mRNA by forming complementary base pairs with the tRNA anticodon. The ribosome moves from codon to codon along the mRNA. Amino acids are added one by one, translated into polypeptidic sequences dictated by DNA and represented by mRNA. At the end, a release factor binds to the stop codon, terminating translation and releasing the complete polypeptide from the ribosome.