DNA Rep and RNA structure well explained

DNA is a molecule that contains the genetic instructions used in the development and functioning of all living organisms.It consists of two long strands that coil around each other to form a double helix structure.The four nucleotides that make up DNA are adenine (A), thymine (T), guanine (G), and cytosine (C).Adenine pairs with thymine, and guanine pairs with cytosine in DNA.RNA (Ribonucleic Acid):

1. DNA Structure Watson and Crick proposed that DNA is made up of two strands that are twisted around each other to form a right-handed helix. The two DNA strands are antiparallel , such that the 3ʹ end of one strand faces the 5ʹ end of the other. Eg. 5’ CAGCAGCAG 3 ’ / 5’ CTGCTGCTG 3 ’. The 3ʹ end of each strand has a free hydroxyl group, while the 5ʹ end of each strand has a free phosphate group.

2. DNA Structure The sugar and phosphate of the polymerized nucleotides form the backbone of the structure, whereas the nitrogenous bases are stacked inside. These nitrogenous bases on the interior of the molecule interact with each other, base pairing . The asymmetrical spacing of the sugar-phosphate backbones generates major grooves (where the backbone is far apart) and minor grooves (where the backbone is close together ).

3. DNA Structure These grooves are locations where proteins can bind to DNA. The binding of these proteins can alter the structure of DNA, regulate replication , or regulate transcription of DNA into RNA.

4. ( a) The sugar-phosphate backbones are on the outside of the double helix and purines and pyrimidines form the “rungs” of the DNA helix ladder. (b) The two DNA strands are antiparallel to each other . (c) The direction of each strand is identified by numbering the carbons (1 through 5) in each sugar molecule . The 5ʹ end is the one where carbon #5 is not bound to another nucleotide; the 3ʹ end is the one where carbon #3 is not bound to another nucleotide.

5. BASE PARING Base pairing takes place between a purine and pyrimidine . In DNA, adenine (A) and thymine (T) are complementary base pairs , and cytosine (C) and guanine (G) are also complementary base pairs, explaining Chargaff’s rules (Figure 7). The base pairs are stabilized by hydrogen bonds; adenine and thymine form two hydrogen bonds between them, whereas cytosine and guanine form three hydrogen bonds between them.

6. Hydrogen bonds form between complementary nitrogenous bases on the interior of DNA.

7. LABOURATORY SEPARATION In the laboratory, exposing the two DNA strands of the double helix to high temperatures or to certain chemicals can break the hydrogen bonds between complementary bases, thus separating the strands into two separate single strands of DNA (single-stranded DNA [ ssDNA ]). This process is called DNA denaturation and is analogous to protein denaturation .

8. LABOURATORY SEPARATION The ssDNA strands can also be put back together as double-stranded DNA ( dsDNA ), through reannealing or renaturing by cooling or removing the chemical denaturants, allowing these hydrogen bonds to reform . The ability to artificially manipulate DNA in this way is the basis for several important techniques in biotechnology (Figure 8 ). Because of the additional hydrogen bonding between the C = G base pair, DNA with a high GC content is more difficult to denature than DNA with a lower GC content.

9. In the lab, the double helix can be denatured to single-stranded DNA through exposure to heat or chemicals, and then renatured through cooling or removal of chemical denaturants to allow the DNA strands to reanneal .

10. DNA Nucleotides The building blocks of nucleic acids are nucleotides. Nucleotides that compose DNA are called deoxyribonucleotides . The three components of a deoxyribonucleotide are a five-carbon sugar called deoxyribose , a phosphate group, and a nitrogenous base , a nitrogen-containing ring structure that is responsible for complementary base pairing between nucleic acid strands (Figure 1 ). The carbon atoms of the five-carbon deoxyribose are numbered 1ʹ, 2ʹ, 3ʹ, 4ʹ, and 5ʹ (1ʹ is read as “one prime”). A nucleoside comprises the five-carbon sugar and nitrogenous base.

11. DNA Nucleotides Nitrogenous bases within DNA are categorized into the two-ringed purines adenine and guanine and the single-ringed pyrimidines cytosine and thymine. Individual nucleoside triphosphates combine with each other by covalent bonds known as 5ʹ-3ʹ phosphodiester bonds , or linkages whereby the phosphate group attached to the 5ʹ carbon of the sugar of one nucleotide bonds to the hydroxyl group of the 3ʹ carbon of the sugar of the next nucleotide . Phosphodiester bonding between nucleotides forms the sugar-phosphate backbone

12. . ( a) Each deoxyribonucleotide is made up of a sugar called deoxyribose, a phosphate group, and a nitrogenous base—in this case, adenine. ( b) The five carbons within deoxyribose are designated as 1ʹ, 2ʹ, 3ʹ, 4ʹ, and 5ʹ.

13. Nitrogenous bases within DNA are categorized into the two-ringed purines adenine and guanine and the single-ringed pyrimidines cytosine and thymine. Thymine is unique to DNA.

14. Phosphodiester bonds form between the phosphate group attached to the 5ʹ carbon of one nucleotide and the hydroxyl group of the 3ʹ carbon in the next nucleotide, bringing about polymerization of nucleotides in to nucleic acid strands. Note the 5ʹ and 3ʹ ends of this nucleic acid strand.

15. DNA Function DNA stores the information needed to build and control the cell. The transmission of this information from mother to daughter cells is called vertical gene transfer and it occurs through the process of DNA replication . DNA is replicated when a cell makes a duplicate copy of its DNA, then the cell divides, resulting in the correct distribution of one DNA copy to each resulting cell. DNA can also be enzymatically degraded and used as a source of nucleosides and nucleotides for the cell. Unlike other macromolecules, DNA does not serve a structural role in cells.

16. RNA STRUCTURE RNA or ribonucleic acid is a polymer of nucleotides which is made up of a ribose sugar, a phosphate, and bases such as adenine, guanine, cytosine, and uracil. RNA has a structure very similar to that of DNA . The key difference in RNA structure is that the ribose sugar in RNA has a hydroxyl (-OH) group which is absent in DNA. RNA plays a very crucial role in the gene expression pathway by which genetic information in DNA is coded into proteins that determine cell function.

17. RNA STRUCTURE

18. RNA (Ribonucleic acid ) RNA is a polymer of ribonucleotides linked together by 3’- 5’ phosphodiester linkage

19. Types of RNA In both prokaryotes and eukaryotes, there are three main types of RNA – messenger RNA or mRNA, ribosomal or rRNA, and transfer RNA or tRNA. These 3 types of RNA are discussed below . Other RNA include: small nuclear RNA (SnRNA), micro RNA(miRNA ) and small interfering RNA(Si RNA) and heterogeneous nuclear RNA (hnRNA).

20. Messenger RNA (mRNA) mRNA accounts for just 5% of the total RNA in the cell . mRNA is the most heterogeneous of the 3 types of RNA in terms of both base sequence and size . It carries the genetic code copied from the DNA during transcription in the form of triplets of nucleotides called codons. Each codon specifies a particular amino acid, but one amino acid can be coded by many different codons. Although there are 64 possible codons or triplet bases in the genetic code, only 20 of them represent amino acids; there are also 3 stop codons.

21. Messenger RNA (mRNA) As part of post-transcriptional processing in eukaryotes, the 5’ end of mRNA is capped with a guanosine triphosphate nucleotide, which helps in mRNA recognition during translation or protein synthesis. Similarly , the 3’ end of an mRNA has a poly A tail or multiple adenylate residues added to it, which prevent enzymatic degradation of mRNA. Both 5’ and 3’ end of an mRNA imparts stability to the mRNA.

22. Ribosomal RNA (rRNA) rRNAs are found in the ribosomes and account for 80% of the total RNA present in the cell . Ribosomes are composed of a large subunit called the 50S and a small subunit called the 30S, each of which has its own rRNA molecules. Different rRNAs present in the ribosomes include small rRNAs and large rRNAs, which denote their presence in the small and large subunits of the ribosome.

23. Ribosomal RNA (rRNA) rRNAs combine with proteins in the cytoplasm to form ribosomes, which act as the site of protein synthesis and has the enzymes needed for the process. These complex structures travel along the mRNA molecule during translation and facilitate the assembly of amino acids to form a polypeptide chain. They bind to tRNAs and other molecules that are crucial for protein synthesis. In bacteria, the small and large rRNAs contain about 1500 and 3000 nucleotides, respectively, whereas in humans, they have about 1800 and 5000 nucleotides, respectively. However , the structure and function of ribosomes is largely similar across all species.

24. Transfer RNA (tRNA) tRNA is the smallest of the 3 types of RNA having about 75-95 nucleotides . tRNAs are an essential component of translation, where their main function is the transfer of amino acids during protein synthesis. Therefore they are called transfer RNAs. Each of the 20 amino acids has a specific tRNA that binds with it and transfers it to the growing polypeptide chain. tRNAs also act as adapters in the translation of the genetic sequence of mRNA into proteins . Therefore they are also called adapter molecules.

25. Transfer RNA (tRNA) tRNAs have a clover leaf structure which is stabilized by strong hydrogen bonds between the nucleotides . Apart from the usual 4 bases, they normally contain some unusual bases mostly formed by methylation of the usual bases, for example, methyl guanine and methylcytosine.

26. Small RNA Most of these molecules are complexed with proteins to form ribonucleoproteins and are distributed in the nucleus, in the cytoplasm, or in both. They range in size from 20 to 300 nucleotides and are present in 100,000 – 1,000,000 copies per cell.

27. Small Nuclear RNAs (snRNAs) 1. Small Nuclear RNAs (snRNAs) snRNAs , a subset of the small RNAs, are significantly involved in mRNA processing and gene regulation. 2. Micro RNAs, miRNAs, and Small Interfering RNAs, siRNAs These two classes of RNAs represent a subset of small RNAs; both play important roles in gene regulation. miRNAs and siRNAs cause inhibition of gene expression by decreasing specific protein production albeit apparently via distinct mechanisms

28. Significance of mi RNAs and siRNAs Both miRNAs and siRNAs represent exciting new potential targets for therapeutic drug development in humans. In addition, siRNAs are frequently used to decrease or "knock-down" specific protein levels in experimental procedures in the laboratory , an extremely useful and powerful alternative to gene-knockout technology .

29. Differences between RNA and DNA S.No. RNA DNA 1 Single stranded mainly except when self-complementary sequences are there it forms a double stranded structure (Hair pin structure) Double stranded (Except for certain viral DNA s which are single stranded) 2 Ribose is the main sugar The sugar moiety is deoxyribose 3 Pyrimidine components differ. Thymine is never found(Except tRNA) Thymine is always there but uracil is never found 4 Being single stranded structure- It does not follow Chargaff’s rule It does follow Chargaff's rule. The total purine content in a double stranded DNA is always equal to pyrimidine content. 5 RNA can be easily destroyed by alkalies to cyclic diesters of mono nucleotides. DNA resists alkali action due to the absence of OH group at 2’ position 6 RNA is a relatively a labile molecule, undergoes easy and spontaneous degradation DNA is a stable molecule. The spontaneous degradation is very 2 slow. The genetic information can be stored for years together without any change.

30. Differences between RNA and DNA S.No. RNA DNA 7 Mainly cytoplasmic, but also present in nucleus (primary transcript and small nuclear RNA) Mainly found in nucleus, extra nuclear DNA is found in mitochondria, and plasmids etc 8 The base content varies from 100- 5000. The size is variable. Millions of base pairs are there depending upon the organism 9 There are various types of RNA – mRNA, r RNA, t RNA, Sn RNA, Si RNA, mi RNA and hn RNA. These RNAs perform different and specific functions. DNA is always of one type and performs the function of storage and transfer of genetic information. 10 No variable physiological forms of RNA are found. The different types of RNA do not change their forms There are variable forms of DNA (A to E and Z) 11 RNA is synthesized from DNA, it cannot form DNA (except by the action of reverse transcriptase). It cannot duplicate (except in certain viruses where it is a genomic material) DNA can form DNA by replication, it can also form RNA by transcription. 12 Many copies of RNA are present per cell Single copy of DNA is present per cell.