1. 1

2. Definition The nucleic acids are the building blocks of living organisms they include DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) nucleic acids are the most important biological macromolecules; each is found in abundance in all living things, where they function in encoding, transmitting and expressing genetic information Nucleic acids were discovered by Friedrich Miescher in 1869. Experimental studies of nucleic acids constitute a major part of modern biological and medical research, and form a foundation for genome and forensic science, as well as the biotechnology and pharmaceutical industries.

3. Why study of nucleic acid is important? Experimental studies of nucleic acids constitute a major part of modern biological and medical research form a foundation for genome and forensic science, as well as the biotechnology and pharmaceutical industries

4. Types of Nucleic acid There are mainly 2 types of nucleic acids. 1. Deoxy Ribo nucleic acid( DNA) 2. Ribo nucleic acid (RNA)

5. Deoxy Ribo nucleic acid( DNA) Deoxyribonucleic acid ( DNA) is a nucleic acid containing the genetic instructions used in the development and functioning of all known living organisms. The DNA segments carrying this genetic information are called genes. Likewise, other DNA sequences have structural purposes, or are involved in regulating the use of this genetic information. Along with RNA and proteins, DNA is one of the three major macromolecules that are essential for all known forms of life.

7. Ribo nucleic acid (RNA) Ribonucleic acid or RNA, is part of a group of molecules known as the nucleic acids. Like DNA, RNA is made up of a long chain of components called nucleotides. Each nucleotide consists of a nucleobase, a ribose sugar, and a phosphate group. The sequence of nucleotides allows RNA to encode genetic information. All cellular organisms use messenger RNA (mRNA) to carry the genetic information that directs the synthesis of proteins. In addition, many viruses use RNA instead of DNA as their genetic material. There are 3 types of RNA- mRNA, tRNA, rRNA

8. Chemistry of nucleic acid There are mainly 3 component of nucleic acids. 1. nitrogenous base 2. Sugar 3. Phosphoric acid

9. Sugar

10. Nitrogen-Containing Bases There are mainly 2 types of base 1. purine base- Adenine, guanine 2. pirimidine base- cytosine, thymine, uracil

11. Nitrogen-Containing Bases

12. Flow chart of formation of DNA/RNA Sugar + Nitrogenous Base Nucleoside+ Phosphoric acid Nucleotide Polynucleotide Double helix of DNA

13. Nucleoside Nitrogenous base + sugar = Nuleoside

14. Nucleosides in DNA BaseSugar Nucleoside Adenine (A) Deoxyribose DeoxyAdenosine Guanine (G) Deoxyribose DeoxyGuanosine Cytosine (C) Deoxyribose DeoxyCytidine Thymine (T) Deoxyribose DeoxyThymidine

15. Nucleosides in RNA BaseSugar Nucleoside Adenine (A)riboseAdenosine Guanine (G)riboseGuanosine Cytosine (C)riboseCytidine Uracil (U)riboseUridine

16. Nucleotide Nucleoside + Phosphoric acid = Nucleotide

17. Nucleotides in DNA and RNA DNA dAMPDeoxyadenosine monophosphate dGMPDeoxyguanosine monophosphate dCMPDeoxycytidine monophosphate dTMPDeoxythymidine monophosphate RNA AMPadenosine monophosphate GMPguanosine monophosphate CMPcytidine monophosphate UMPuridine monophosphate

18. Structure of Dinucleotide

19. A molecule of DNA is formed by millions of nucleotides joined together in a long chain PO 4 sugar-phosphate backbone + bases

20. Synthesis of Nucleic Acids DNA and RNA are synthesized in cells by DNA polymerases and RNA polymerases. In all cases, the process involves forming phosphodiester bonds between the 3' carbon of one nucleotide and the 5' carbon of another nucleotide. This leads to formation of the so-called "sugar-phosphate backbone", from which the bases project.

22. A key feature of all nucleic acids is that they have two distinctive ends: the 5' (5- prime) and 3' (3-prime) ends. This terminology refers to the 5' and 3' carbons on the sugar. For both DNA and RNA, the 5' end bears a phosphate, and the 3' end a hydroxyl group. Synthesis of Nucleic Acids

23. Base Pairing and Double Stranded Nucleic Acids Most DNA exists in the famous form of a double helix, in which two linear strands of DNA are wound around one another. The major force promoting formation of this helix is complementary base pairing: A's form hydrogen bonds with T's (or U's in RNA), and G's form hydrogen bonds with C's.

24. Complementary Base Pairs –Two H bonds for A-T –Three H bonds for G-C

25. Hydrogen Bonding

26. The two strands of DNA are arranged antiparallel to one another: viewed from left to right the "top" strand is aligned 5' to 3', while the "bottom" strand is aligned 3' to 5'. This is always the case for duplex nucleic acids. G-C base pairs have 3 hydrogen bonds, whereas A-T base pairs have 2 hydrogen bonds: one consequence of this disparity is that it takes more energy (e.g. a higher temperature) to disrupt GC-rich DNA than AT-rich DNA. Synthesis of Nucleic Acids

27. PO 4 2-stranded DNA 9

28. Features of Watson–Crick Model Two helical polynucleotide chains are coiled around common axis. The chains run in opposite directions. The sugar – phosphate backbones are on the outside and the purine and pyrimidine bases lies on the inside of the helix The bases are nearly perpendicular to the helix axis, and adjacent bases are separated by 3.4 Å. The helical structure repeats every 34 Å, so there are 10 bases (= 34 Å per repeat/3.4 Å per base) per turn of helix. There is a rotation of 36 degrees per base (360 degrees per full turn/10 bases per turn) The diameter of the helix is 20 Å

29. Double Helix of DNA The paired strands are coiled into a spiral called A DOUBLE HELIX

30. Assignment What is the difference between DNA & RNA ?

31. Some definitions Gene- Gene are specific segment of DNA which are responsible for the synthesis of specific protein. One specific gene can synthesis one specific protein. Genome- Combination of all chromosome or DNA are combindly called genome Codon- An amino acid is coded by 3 bases These group of bases are called codon, which are present in mRNA Anticodon- The template recognition site or tRNA is a sequence of 3 bases. These bases are called anticodons

32. Some definitions Template- The term template strand refers to the single strand of DNA that is copied during the synthesis of mRNA Primers- A primer is a strand of nucleic acid that serves as a starting point for DNA synthesis. They are required for DNA replication because the enzymes that catalyze this process, DNA polymerases, can only add new nucleotides to an existing strand of DNA. The polymerase starts replication at the 3'-end of the primer, and copies the opposite strand.

33. Before a cell divides, the DNA strands unwind and separate Each strand makes a new partner by adding the appropriate nucleotides with the help of DNA polymerase and primer The result is that there are now two double-stranded DNA molecules in the nucleus So that when the cell divides, each nucleus contains identical DNA This process is called replication Replication of DNA

34. DNA replication or DNA synthesis is the process of copying a double-stranded DNA strand, prior to cell divisionDNAcell division The two resulting double strands are identical, and each of them consists of one original and one newly synthesized strand. This is called semiconservative replication.semiconservative replication The process of replication consists of three steps, initiation, replication and termination

35. After the helicase unwinds the DNA, single-strand binding protein is used to hold the DNAsingle-strand binding protein RNA primase is then bound to the starting DNA site. Begin of replication, an enzyme called DNA polymerase binds to the RNA primase, which indicates the starting point for the replication.DNA polymerase DNA polymerase can only synthesize new DNA The DNA polymerase can only travel on one side of the original strand without any interruption. Since the DNA replication on the lagging strand is not continuous, a new DNA polymerase has to be added each time as the helicase unwinds more DNA. The replicated DNA is fragmented.

36. PO 4 The strands separate

37. PO 4 Each strand builds up its partner by adding the appropriate nucleotides 18

39. Central dogma of molecular biology

40. Transcription of DNA Transcription is the process of creating a complementary RNA copy of a sequence of DNA The enzyme used in transcription is “RNA polymerase”. There are several forms of RNA polymerase. In eukaryotes, most genes are transcribed by RNA polymerase 2. Unlike replication, transcription does not need to build on a primer. Instead, transcription starts at a region of DNA called a “promoter”. For protein-coding genes, the promoter is located a few bases 5’ to (upstream from) the first base that is transcribed into RNA. 3 steps of transcription- Initiation, Elongation, termination

41. Process of Transcription Transcription starts with RNA polymerase binding to the promoter. This binding only occurs under some conditions: when the gene is “on”. Various other proteins (transcription factors) help RNA polymerase bind to the promoter. Other DNA sequences further upstream from the promoter are also involved. Once it is bound to the promoter, RNA polymerase unwinds a small section of the DNA and uses it as a template to synthesize an exact RNA copy of the DNA strand. The DNA strand used as a template is the “coding strand”; the other strand is the “non-coding strand”. Notice that the RNA is made from 5’ end to 3’ end, so the coding strand is actually read from 3’ to 5’. RNA polymerase proceeds down the DNA, synthesizing the RNA copy. In prokaryotes, each RNA ends at a specific terminator sequence. In eukaryotes transcription doesn’t have a definite end point; the RNA is given a definitive termination point during RNA processing.

43. After Transcription In prokaryotes, the RNA copy of a gene is messenger RNA, ready to be translated into protein. In fact, translation starts even before transcription is finished. In eukaryotes, the primary RNA transcript of a gene needs further processing before it can be translated. This step is called “RNA processing”. Also, it needs to be transported out of the nucleus into the cytoplasm. Steps in RNA processing: –1. Add a cap to the 5’ end –2. Add a poly-A tail to the 3’ end –3. splice out introns.

44. RNA processing

45. Translation In molecular biology and genetics, translation is the third stage of protein biosynthesis Translation of mRNA into protein is accomplished by the ribosome, an RNA/protein hybrid. Ribosomes are composed of 2 subunits, large and small. Ribosomes bind to the translation initiation sequence on the mRNA, then move down the RNA in a 5’ to 3’ direction, creating a new polypeptide. The first amino acid on the polypeptide has a free amino group, so it is called the “N- terminal”. The last amino acid in a polypeptide has a free acid group, so it is called the “C-terminal”. Each group of 3 nucleotides in the mRNA is a “codon”, which codes for 1 amino acids. Transfer RNA is the adapter between the 3 bases of the codon and the corresponding amino acid.

46. Initiation of Translation In prokaryotes, ribosomes bind to specific translation initiation sites. There can be several different initiation sites on a messenger RNA: a prokaryotic mRNA can code for several different proteins. Translation begins at an AUG codon, or sometimes a GUG. The modified amino acid N- formyl methionine is always the first amino acid of the new polypeptide. In eukaryotes, ribosomes bind to the 5’ cap, then move down the mRNA until they reach the first AUG, the codon for methionine. Translation starts from this point. Eukaryotic mRNAs code for only a single gene. (Although there are a few exceptions, mainly among the eukaryotic viruses). Note that translation does not start at the first base of the mRNA. There is an untranslated region at the beginning of the mRNA, the 5’ untranslated region (5’ UTR).

47. More Initiation The initiation process involves first joining the mRNA, the initiator methionine-tRNA, and the small ribosomal subunit. Several “initiation factors”--additional proteins--are also involved. The large ribosomal subunit then joins the complex.

48. Elongation The ribosome has 2 sites for tRNAs, called P and A. The initial tRNA with attached amino acid is in the P site. A new tRNA, corresponding to the next codon on the mRNA, binds to the A site. The ribosome catalyzes a transfer of the amino acid from the P site onto the amino acid at the A site, forming a new peptide bond. The ribosome then moves down one codon. The now empty tRNA at the P site is displaced off the ribosome, and the tRNA that has the growing peptide chain on it is moved from the A site to the P site. The process is then repeated: –the tRNA at the P site holds the peptide chain, and a new tRNA binds to the A site. –the peptide chain is transferred onto the amino acid attached to the A site tRNA. –the ribosome moves down one codon, displacing the empty P site tRNA and moving the tRNA with the peptide chain from the A site to the P site.

49. Elongation

50. Termination Three codons are called “stop codons”. They code for no amino acid, and all protein- coding regions end in a stop codon. When the ribosome reaches a stop codon, there is no tRNA that binds to it. Instead, proteins called “release factors” bind, and cause the ribosome, the mRNA, and the new polypeptide to separate. The new polypeptide is completed. Note that the mRNA continues on past the stop codon. The remaining portion is not translated: it is the 3’ untranslated region (3’ UTR).

52. Genetic Code A group of three bases (a triple) controls the production of a particular amino acid in the cytoplasm of the cell The different amino acids and the order in which they are joined up determines the sort of protein being produced

53. This is known as the triplet code Each triplet codes for a specific amino acid CGA - CAA - CCA - CCA - GCT - GGG - GAG - CCA - AlaValGly ArgProLeuGly AlaValGly ArgProLeuGly The amino acids are joined together in the correct sequence to make part of a protein

54. Genetic Engineering Genetic engineering, also called genetic modification, is the direct human manipulation of an organism's genome using modern DNA technology. Genetic engineering alters the genetic makeup of an organism using techniques that introduce heritable material prepared outside the organism either directly into the host or into a cell that is then fused or hybridized with the host. This involves using recombinant nucleic acid (DNA or RNA) techniques to form new combinations of heritable genetic material followed by the incorporation of that material either indirectly through a vector system or directly through micro-injection, macro-injection and micro-encapsulation techniques

55. Recombinant DNA technology/ Gene Cloning Recombinant DNA (rDNA) molecules are DNA sequences that result from the use of laboratory methods (molecular cloning) to bring together genetic material from multiple sources, creating sequences that would not otherwise be found in biological organisms. Consequently, when DNA from a foreign source is linked to host sequences that can drive DNA replication and then introduced into a host organism, the foreign DNA is replicated along with the host DNA.

56. Gene cloning Gene cloning is the replication of DNA fragments by the use of a self-replicating genetic material. Gene cloning duplicates only individual genes of an organism's DNA.

57. Steps of Gene cloning 1.Isolation of plasma DNA & DNA containing gene of interest 2.Insertion of this gene into the vector DNA such as plasmid to produce a hybrid DNA 3.Introduction of the hybrid DNA into the host cell. The cell with hybrid DNA is called as Recombinant 4.Integration of hybrid DNA with the host genome and expression of the characters of cloned gene by the transformed host

59. Application of Genetic Engineering In medicine genetic engineering has been used to mass-produce insulin, human growth hormones, follistim (for treating infertility), human albumin, monoclonal antibodies, vaccines and many other drugs. Gene therapy is the genetic engineering of humans by replacing defective human genes with functional copies. This can occur in somatic tissue or germline tissue. Gene therapy has been used to treat patients suffering from immune deficiencies (notably Severe combined immunodeficiency) and trials have been carried out on other genetic disorders. Genetic engineering is an important tool for natural scientists. Genes and other genetic information from a wide range of organisms are transformed into bacteria for storage and modification, creating genetically modified bacteria in the process Genetic Engineering are used for diagnosis of genetic disease One of the best-known and controversial applications of genetic engineering is the creation of genetically modified food. There are three generations of genetically modified crops.

60. In genetics, a mutation is a change of the nucleotide sequence of the genome of an organism, virus, or extrachromosomal genetic element. Mutations result from unrepaired damage to DNA or to RNA genomes (typically caused by radiation or chemical mutagens), errors in the process of replication, or from the insertion or deletion of segments of DNA by mobile genetic elements. Mutations may or may not produce discernible changes in the observable characteristics (phenotype) of an organism. Mutations play a part in both normal and abnormal biological processes including: evolution, cancer, and the development of the immune system.

61. naturally environmental 1)Mutations can occur naturally or through environmental factors. mutagens chemicals radiations Environmental mutagens include some chemicals (food additives, pesticides, plastics) and radiations (X-rays to UV light).

62. gene mutation nucleotides 2) A gene mutation is a change of one or more nucleotides in a single gene. There are 3 types. a) Addition b) Deletion c) Substitution

63. GENE MUTATIONS Deletion Deletion: one nucleotide base is left out. All of the amino acids after a deletion will be wrong, so SHAPE and FUNCTION of protein are altered. Serious. Addition Addition: one extra nucleotide base is added. This will also change the entire amino acid sequence of the protein, so SHAPE and FUNCTION of protein are altered. Serious.

66. Substitution Substitution: when single bases or short pieces are replaced with one another. Example: Sickle-Cell Anemia, only one nucleotide base is switched. This causes only 1 amino acid to change, but it is an important one. not as serious This type of mutation is usually not as serious as the 1 st two. It just depends on which amino acid is affected (does it have an ‘R’ group with a +,-, or S group?)

69. Genetic disorder A genetic disorder is an illness caused by abnormalities in genes or chromosomes, especially a condition that is present from before birth. A genetic disorder may or may not be a heritable disorder. Some genetic disorders are passed down from the parents' genes, but others are always or almost always caused by new mutations or changes to the DNA. In other cases, the same disease, such as some forms of cancer, may be caused by an inherited genetic condition in some people, by new mutations in other people, and by nongenetic causes in still other people.

70. Single gene disorder A single gene disorder is the result of a single mutated gene.Over 4000 human diseases are caused by single gene defects. Genomic imprinting and uniparental disomy, however, may affect inheritance patterns. Single gene disorder are mainly 6 types – Autosomal dominant – Autosomal recessive – X-linked dominant – X-linked recessive – Y-linked –Mitochondrial

71. Hemophilia color blindness Muscular dystrophy rickets Sickle cell anemia Cystic Firbosis Phenylketonuria muscular dystrophy Single gene disorder

72. Multifactorial and polygenic (complex) disorders Genetic disorders may also be complex, multifactorial, or polygenic, meaning they are likely associated with the effects of multiple genes in combination with lifestyles and environmental factors. Multifactorial disorders include heart disease and diabetes. Although complex disorders often cluster in families, they do not have a clear-cut pattern of inheritance. This makes it difficult to determine a person’s risk of inheriting or passing on these disorders. Complex disorders are also difficult to study and treat because the specific factors that cause most of these disorders have not yet been identified.

73. Multifactorial and polygenic (complex) disorders asthma autoimmune diseases such as multiple sclerosis cancers cleft palate diabetes heart disease hypertension inflammatory bowel disease mental retardation mood disorder obesity refractive error infertility