Nucleic Acid_DNA Lecture Notes PDF

Nucleic Acids Nucleic acid serve as repositories and transmitters of genetic information There are two type of nucleic acid - Deoxyribonucleic acid (DNA) - Ribonucleic acid (RNA) DNA encodes the information the cell needs to make proteins RNA comes in different molecular forms t...

Nucleic Acids Nucleic acid serve as repositories and transmitters of genetic information There are two type of nucleic acid - Deoxyribonucleic acid (DNA) - Ribonucleic acid (RNA) DNA encodes the information the cell needs to make proteins RNA comes in different molecular forms that participate in protein synthesis  Central Dogma of Life The flow of information from DNA to RNA to protein is termed the “central dogma” of molecular biology and is descriptive of all organisms, with the exception of some viruses that have RNA as the repository of their genetic information. From DNA to protein - 3D - YouTube Central Dogma of Life From DNA to protein - 3D - YouTube  Brief History History of Molecular Biology 1859 1869 1910 1944 1961 Charles Darwin Friedrich Miescher 1916 Thomas Hunt Oswald Avery, Sydney Brenner, Published On the Discovered DNA Morgan, Calvin Colin McLeod, and Fran çois Jacob, Origin of Species Bridges Maclyn McCarty Matthew Meselson Demonstrated that identified DNA as Discovered genes are on the material genes messenger RNA chromosomes are made of Gregor Mendel James Watson, Advanced the Harriet Creighton, Francis Crick, principles of Walter Sutton, Barbara McClintock Rosalind Franklin, Marshall Nirenberg, segregation and Theodor Boveri Obtained physical Maurice Wilkins Gobind Khorana independent Proposed the evidence for Determined the Finished unraveling assortment chromosome theory recombination structure of DNA the genetic code 1865 1902 1931 1953 1966 1/23/2024 5  BriefBiology History of Molecular History 1970 1977 1997 2005 2008 Hamilton-Smith Frederick Sanger Ian Wilmut and Many Discovered Worked out colleagues Cloned investigators Jian Wang and colleagues restriction methods to a sheep (Dolly) Reported the Used “next-generation” enzymes determine the from an adult rough draft of the sequencing to obtain the sequence of bases sheep udder cell genome of the first sequence of an Asian in DNA genome chimpanzee, our (Han Chinese) human closest relative Many investigators Craig Venter and David Bentley and Determined the colleagues Used colleagues Used Many investigators base sequence of traditional single-molecule Paul Berg Made the Reported a finished the genome of sequencing to sequencing to first recombinant sequence of the Saccharomyces obtain the first obtain the first DNA in vitro human genome cerevisiae sequence of an sequence of an individual human African (Nigerian) 1972 1996 2003 (Craig Venter) human 1/23/2024 2007 2008 6 1/23/2024 7  Brief History Maclyn McCarty Oswald Avery Colin MacLeod Johann Friedrich Miescher (with Watson and Crick Watson and Crick https://www.youtube.com/watch?v=UFChDmR65kE DNA Discoveries Before Watson and Crick DNA as Genetic material: Avery-MacLeod-McCarty experiment (Animation) - YouTube Watson and Crick  Component of Nucleic Acid Nucleic acids are the polymers of nucleotides held by 3’ and 5’ phosphate bridges  Nucleotide Nucleotides are composed of a Functions nitrogenous base, a pentose sugar and a phosphate Building blocks of nucleic acids Structural component of some co-enzymes of B-complex vitamins e.g. FAD, NAD+ Involved in the energy reaction of the cell (ATP) Pentose sugar Nucleoside refer to Nucleoside base + sugar Thus, nucleotide is nucleoside + phosphate Nitrogenous bases The nitrogenous bases found in nucleotides are aromatic heterocyclic Numbered in the Numbered in the compounds clockwise anti-clockwise The bases are of two types-purines and pyrimidines Major nitrogenous bases in nucleic acid DNA and RNA contain the same purines – Adenine and Guanine The pyrimidine cytosine found in both DNA and RNA However, the nucleic acids differ with respect to the second pyrimidine base- DNA contains Thymine whereas RNA contains Uracil (U) Tautomeric form of purines and pyrimidines Tautomerism is a well-known phenomenon occurring in nucleic acid bases in which proton transfer from the heterocyclic ring center to an exocyclic oxo- or imino- group leads to the formation of either an –OH or an –NH groups. These processes are known as keto-enol or imino-amino tautomerism, respectively. Tautomeric form of purines and pyrimidines Other biologically important bases  Sugars of nucleic acids The five carbon monosaccharides (pentoses) are found in the nucleic acid structure. RNA contains D-ribose while DNA contains D- deoxyribose. Ribose and deoxyribose differ in structure at C2. Deoxyribose has one oxygen less at C2 compared to ribose  Nomenclature of nucleotides The addition of a pentose sugar to base produces a nucleoside. If, the sugar is ribose, ribonucleosides are formed. Adenosine, guanosine, cytidine and uridine are the ribonucleosides of A, G, C and U respectively. If the sugar is a deoxyribose, deoxyribonucleosides are produced The term mononucleotide is used when a single phosphate moiety is added to nucleoside. Thus adenosine monophosphate (AMP) contains adenine + ribose + phosphate. Sugars are represented with prime (') for differentiation as nitrogen bases also numbered. Nomenclature of nucleotides Nucleosides and nucleotides  Nucleotide Analogs These are synthetic compounds which resemble nucleosides, but have altered heterocyclic ring or sugar moiety The treatment of viral infectious diseases such as AIDS and Hepatitis C has witnessed spectacular progress with new nucleotide analogs as drugs Ex: Tenoforvir – HIV Penciclovir - HSP  Structure of DNA DNA - Polymer of deoxyribonucleotide It is composed of monomeric units namely deoxyadenylate (dAMP), deoxyguanylate (dGMP), deoxycytidylate (dCMP) and deoxythymidylate (dTMP). The monomeric deoxyribonucleotides in DNA are held together by 3’→ 5’ phosphodiester bridges  Chargaff’s Rule Erwin Chargaff in late 1940s quantitatively analysed the DNA hydrolysates from different species He observed DNA had equal no. of adenine and thymine residues and equal no of guanine and cytosine residues This is known as Chargaff’s rule of molar equivalence between the purine and pyrimidines in DNA structure DNA double helix The double helical structure of DNA was proposed by James Watson and Western Cricks in 1953 Won Nobel prize -1962 Comparable to a twisted ladder DNA Double Helix  DNA Double Helix 1. DNA is a right-handed double helix. 2. It consists two polydeoxyribonucleotide chains, twisted around each other on a common axis 3. The two strands are antiparallel i.e one strand runs 5’→3’ direction while the other runs 3’→5’ direction 4. The width (or diameter) of a double helix is 20 Ao 5. Each turn of the helix is 34 Ao with 10 pairs of nucleotide 6. Each strand has hydrophilic deoxyribose phosphate backbone on outside and hydrophobic bases inside 7. The two polynucleotides are complementary to each other due to base pairing  DNA Double Helix 8. Two strands are held together by hydrogen bonds formed by A-T pairs with two hydrogen bond while G-C pairs with 3 hydrogen bond 9. Hydrogen bonds are formed between a purine and pyrimidine 10. The complementary base pairing in DNA helix proves Chargaff’s Rule 11. One of the two strands known as template/ sense strand and other antisense strand 12. The double helix has wide – major groove and narrow- minor grove along the phosphodiester backbone. Protein binds to this groove without disturbing the DNA Conformation of DNA Double Helix The double helical structure of DNA exists in at least 6 different forms. Among these B, A and Z forms are important. B form described by Watson and Crick A form is also right-handed helix. Contains 11 base pairs per turn Z form is a left-handed helix and contains 12 base pairs per turn Properties of major form of DNA Properties of major form of DNA Other types of DNA Bent DNA Bent DNA is curved over a stretch of several bases resulting in different orientation It was shown that short repeated stretches of poly-TA sequences or repetitive runs of 4–6 adenine base pairs (“A- tracts”) introduce a bent nature to the heliX Other types of DNA Triple- strand DNA Triple-strand DNA formation may occur due to additional H-bonds between the bases A helical structure composed of three strands in which a single DNA strand binds to the major-groove of a Watson–Crick duplex Not stable  Denaturation of DNA The two strands of the DNA helix are held together by hydrogen bonds. Disruption of hydrogen bonds (by the change in pH or increase in temperature) results in the separation of polynucleotide strands. This phenomenon of loss of helical structure of DNA is known as denaturation. The phosphate bonds are not broken by denaturation. Loss of helical structure can be measured by the increase in absorbance at 260 nm Denaturation of DNA