Compare and contrast the structure of DNA and RNA and ...



Introduction

The scientific world focused on the structure of DNA, soon after it was discovered that DNA is the prime genetic molecule which carries all the hereditary information within chromosomes. During the late 1940s and early 1950s, several research groups in the United States and in Europe engaged in serious efforts to understand how the atoms of DNA are linked together by covalent bonds and how the resulting molecules are arranged in three-dimensional space. When the fundamental DNA structure was found to be the double helix, it was known to the scientific world that genes have roughly the same three-dimensional form and that the differences between two genes exist in the order and number of their four nucleotide building blocks along the complementary strands. Till now studies and experiments are ongoing in the structure and properties of DNA, but the simple description of its structure as the double helix has not altered much.

Later studies have realized that the structure of DNA is not quite as uniform as it was observed earlier. For instance, the chromosomes of some small viruses have single-stranded, not double-stranded, molecules. Also it was later found out that some DNA sequences permit the double helix to twist in the left-handed sense, as opposed to the right-handed sense originally formulated for DNA’s general structure. Also while some DNA molecules are linear, others are circular. Now it is realized that RNA, which at first look appears to be very similar to DNA, has its own characteristic structural features. Though the basic structure remains the same as it was first discovered, the richness and complexities of these structures were later revealed in consequent studies. This paper tries to describe them in brief and the process of gene expression from DNA sequence to protein synthesis.

Structure of DNA

DNA stands for Deoxyribonucleic acid. DNA is a linear macromolecule found in all living cells. It is build up of only four different types of building blocks, called nucleotides. Nucleotides are composed of a base, being either a purine or pyrimidine group, or a 2'-deoxyribosyl-tri-phosphate. The four types of bases composing the sequence of DNA are: Adenine A,   Guanine G, Thymine T and Cytosine C.  

B-DNA or Watson and Crick double helix

Single DNA strands are not constant. They combine with a second strand to form a double helix structure. In this structure, both strands interweave around each other. The four bases are H-bonded to each other at the center of the helix in a very specific way. The bases point toward the helix center and H-bond is such that   G with C 3 H-bonds and A with T 2 H-bonds. The rigidity and linear geometry of the H-bonds limits base pair formation. The plane of the base pair falls perpendicular to the helix axis. The right handed B-DNA form is the physiological form of the DNA double helix which was first illustrated by Watson and Crick in 1953. The sequence of the bases in the polymer encodes the genetic information for the synthesis of proteins. The B-DNA is a right handed, anti-parallel double helix with 2nm in diameter and the B-DNA helix of these parameters represents an idealized helix. The fundamental DNA structure deviates slightly from the B form in a sequence dependent manner as well as depending on the interaction with DNA-binding proteins. The minor and major grooves, winding along the helix surface are the important features of the double helix. Parts of the aromatic ring structures of the purines and pyrimidines are exposed to the surface of the helix in those grooves. Most protein-DNA interactions occur in the major groove.

A-DNA and Z-DNA

Although only B-DNA and Z-DNA have been directly observed in functional organisms, the conformation that DNA adopts depends on the hydration level, DNA sequence and the amount and direction of super coiling. It also depends on chemical modifications of the bases, the type and concentration of metal ions, as well as the presence of polyamines in solution. The A-DNA form is a wider right-handed spiral, with a shallow, wide minor groove and a narrower, deeper major groove in comparison to B- DNA. The A form occurs under non-physiological conditions when the relative humidity of the sample is lowered below 75%. In the cell it may be produced in hybrid pairings of DNA and RNA strands, as well as in enzyme-DNA complexes. Segments of DNA where the bases have been chemically modified by methylation may undergo a larger change in conformation and adopt the Z form. Here, the strands turn about the helical axis in a left-handed spiral, the opposite of the more common B form. These unusual structures can be recognized by specific Z-DNA binding proteins and may be involved in the regulation of transcription. The biological significance for both A and Z helices is not well understood. Structural studies of Z-DNA are derived from synthetic oligonucleotides rather than long stretches of DNA extracted from cells.

DNA super coiling

The helix is often wound up in a super-coiled form because of the large size of circular DNA. The combination of super coiling and helix conformation has an effect on the recognition of DNA binding proteins. DNA can be twisted like a rope in a process called DNA super coiling. If the DNA is twisted in the direction of the helix, this is positive super coiling, and the bases are held more tightly together. If they are twisted in the opposite direction, this is negative supercoiling, and the bases come apart more easily. In nature, most DNA has slight negative supercoiling that is introduced by enzymes called topoisomerases. These enzymes are also needed to relieve the twisting stresses introduced into DNA strands during processes such as transcription and DNA replication.

RNA Structure

Each nucleotide in RNA contains a ribose sugar, with carbons numbered 1' through 5'. A base is attached to the 1' position, generally adenine (A), cytosine (C), guanine (G) or uracil (U). Adenine and guanine are purines, cytosine and uracil are pyrimidines. A phosphate group is attached to the 3' position of one ribose and the 5' position of the next. The phosphate groups have a negative charge each at physiological pH, making RNA a charged molecule (polyanion). The bases may form hydrogen bonds between cytosine and guanine, between adenine and uracil and between guanine and uracil. However other interactions are possible, such as a group of adenine bases binding to each other in a bulge, or the GNRA tetraloop that has a guanine–adenine base-pair.

Chemical structure of RNA

An important structural feature of RNA that distinguishes it from DNA is the presence of a hydroxyl group at the 2' position of the ribose sugar. The presence of this functional group causes the helix to adopt the A-form geometry rather than the B-form most commonly observed in DNA. This results in a very deep and narrow major groove and a shallow and wide minor groove. A second consequence of the presence of the 2'-hydroxyl group is that in conformationally flexible regions of an RNA molecule (that is, not involved in formation of a double helix), it can chemically attack the adjacent phosphodiester bond to cleave the backbone.

RNA is very similar to DNA in that is made of four different building blocks, the ribonucleotides. The pyrimidine base thymine is modified in that it lacks a methyl group and the resulting uracil takes its place in base pairing. The ribose comes in its fully hydroxylated form. Together, the presence of uracil in place of thymine, and the 2'-OH in the ribose constitute the two chemical differences between RNA and DNA.

RNA differs, however, from DNA because it does not form an analogous double helical structure. RNA does, however, form base pairs with DNA resulting in a heteromeric double helix consisting of one DNA and one RNA strand. This annealing of an RNA strand to its complementary DNA strand is called hybridization and plays a crucial role in the transcription and translation of genetic sequences into protein sequences. RNA does, in contrast to DNA, form short double strand structures on itself, thereby forming so called stem and loop structures. Both DNA/RNA double helices and RNA/RNA double strands have an A-DNA like conformation, also called A-RNA or RNA-II. .There is three major RNA species that can be distinguished both on their ability to form stem and loop structures as well as their functional role in the cell. The three types of RNA are:

1. Messenger RNA or mRNA

2. Transfer RNA or tRNA

3. Ribosomal RNA or rRNA

In addition there are RNA molecules found in viruses (viral RNA) that serve as the genomic blue print that normally is encoded in DNA, and ribonucleo-proteins of diverse origin both ribosomal and non-ribosomal in nature.

 

Gene expression

Genes are expressed by being transcribed into RNA, and this transcript may then be translated into protein. Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product. These products are often proteins, but in non-protein coding genes such as ribosomal RNA (rRNA) genes or transfer RNA (tRNA) genes, the product is a functional RNA. The process of gene expression is used by all known life - eukaryotes (including multicellular organisms), prokaryotes (bacteria and archaea) and viruses - to generate the macromolecular machinery for life. Several steps in the gene expression process may be modulated, including the transcription, RNA splicing, translation, and post-translational modification of a protein. Gene regulation gives the cell control over structure and function, and is the basis for cellular differentiation, morphogenesis and the versatility and adaptability of any organism. Gene regulation may also serve as a substrate for evolutionary change, since control of the timing, location, and amount of gene expression can have a profound effect on the functions of the gene in a cell or in a multicellular organism. In genetics, gene expression is the most fundamental level at which genotype gives rise to the phenotype. The genetic code stored in DNA in form of nucleotide sequence is "interpreted" by gene expression, and the properties of the expression products give rise to the organism's phenotype.

The gene itself is typically a long stretch of DNA which carries genetic information encoded by genetic code. Every molecule of DNA consists of two strands, each of them having 5' and 3' ends oriented in anti-parallel direction. The coding strand contains the genetic information while template strand (non-coding strand) serves as a blueprint for the production of RNA. The production of RNA copies of the DNA is called transcription, and is performed by RNA polymerase, which adds one RNA nucleotide at a time to a growing RNA strand. This RNA is complementary to the template 3' → 5' DNA strand which is itself complementary to the coding 5' → 3' DNA strand. Therefore, the resulting 5' → 3' RNA strand is identical to the coding DNA strand with the exception that thymines (T) are replaced with uracils (U) in the RNA. A coding DNA strand reading "ATG" is transcribed as "AUG" in RNA.

RNA processing

Transcription of protein encoding genes creates a primary transcript of RNA at the place where the gene was located. This transcript can be altered before being translated; this is particularly common in eukaryotes. The most common RNA processing is splicing to remove introns. Introns are RNA segments which are not found in the mature RNA, although they can function as precursors. RNA processing, also known as post-transcriptional modification can start during transcription, as is the case for splicing, where the spliceosome removes introns from newly formed RNA. Extensive RNA processing may be an evolutionary advantage made possible by the nucleus of eukaryotes. In prokaryotes transcription and translation happen together whilst in eukaryotes the nuclear membrane separates the two processes giving time for RNA processing to occur.

Non-coding RNA maturation

In most organisms non-coding genes (ncRNA) are transcribed as precursors which undergo further processing. In the case of ribosomal RNAs (rRNA), they are often transcribed as a pre-rRNA which contains one or more rRNAs; the pre-rRNA is cleaved and modified at specific sites by approximately 150 different small nucleolus-restricted RNA species, called snoRNAs, which like snRNAs, snoRNAs associate with proteins, forming snoRNPs. In eukaryotes, in particular a snoRNP, called RNase MRP cleaves the 45S pre-rRNA into the 28S, 5.8S, and 18S rRNAs. The rRNA and RNA processing factors are form large aggregates called the nucleolus.

RNA export

In eukaryotes most mature RNA must be exported to the cytoplasm from the nucleus. While some RNAs function in the nucleus, many RNAs are transported through the nuclear pores and into the cytosol. Notably this includes all RNA types involved in protein synthesis. In some cases RNAs are additionally transported to a specific part of the cytoplasm, such as a synapse; they are then towed by motor proteins that bind through linker proteins to specific sequences on the RNA. During the translation, tRNA charged with amino acid enters the ribosome and aligns with the correct mRNA triplet. Ribosome then adds amino acid to growing protein chain.

For some RNA (non-coding RNA) the mature RNA is the finished gene product. In the case of messenger RNA (mRNA) the RNA is an information carrier coding for the synthesis of one or more proteins. mRNA carrying a single protein sequence is monocistronic whilst mRNA carrying multiple protein sequences is known as polycistronic. Each triplet of nucleotides of the coding regions of a messenger RNA corresponds to a binding site for a transfer RNA. Transfer RNAs carry amino acids, and these are chained together by the ribosome. The ribosome helps transfer RNA to bind to messenger RNA and takes the amino acid from each transfer RNA and makes a structure-less protein out of it. In prokaryotes translation generally occurs at the point of transcription, often using a messenger RNA which is still in the process of being created. In eukaryotes translation can occur in a variety of regions of the cell depending on where the protein being written is supposed to be. Major locations are the cytoplasm for soluble cytoplasmic proteins and the membrane of endoplasmic reticulum for proteins which are for export from the cell or insertion into a cell membrane. Proteins which are supposed to be expressed at the endoplasmic reticulum are recognized part-way through the translation process. This is governed by the signal recognition particle - a protein which binds to the ribosome and directs it to the endoplasmic reticulum when it finds a signal sequence on the growing (nascent) amino acid chain.

Protein transport

Many proteins are destined for other parts of the cell than the cytosol and a wide range of signaling sequences are used to direct proteins to where they are supposed to be. In prokaryotes this is normally a simple process due to limited compartmentalization of the cell. However in eukaryotes there is a great variety of different targeting processes to ensure the protein arrives at the correct organelle. Not all proteins remain within the cell and many are exported, for example digestive enzymes, hormones and extracellular matrix proteins. In eukaryotes the export pathway is well developed and the main mechanism for the export of these proteins is translocation to the endoplasmic reticulum, followed by transport via the Golgi apparatus.

Expression system

An expression system is a system specifically designed for the production of a gene product of choice. This is normally a protein although may also be RNA, such as tRNA or a ribozyme. An expression system consists of a gene, normally encoded by DNA, and the molecular machinery required to transcribe the DNA into mRNA and translate the mRNA into protein using the reagents provided. In the broadest sense this includes every living cell but the term is more normally used to refer to expression as a laboratory tool. An expression system is therefore often artificial in some manner. Expression systems are, however, a fundamentally natural process. Viruses are an excellent example where they replicate by using the host cell as an expression system for the viral proteins and genome.

References

DNA Structure. Retrieved on January 10, 2011 from

The Structures of DNA and RNA Retrieved on January 10, 2011 from

DNA. Retrieved on January 10, 2011 from

Gene Expression. . Retrieved on January 10, 2011 from

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