ISC 11>Content>Unit-4>Biomolecules :Nucleic acid

Structure and functions of DNA, types of RNA. Differences between DNA and RNA 
NUCLEOTIDES: (BUILDING BLOCKS OF NUCLEIC ACID)
COMPOSITION: 
  • Nucleotides contain carbon, hydrogen, oxygen, nitrogen and phosphorus. 
  • Each nucleotide is made up of following components.
  1. Ribose sugar
  2. Phosphoric acid
  3. Nitrogenous bases
1. Ribose sugar
The sugar molecule in the nucleotide is a 5-carbon pentose sugar.
 It is represented by either ribose sugar (C5H10O5) or deoxyribose sugar (C5H10O4). 
2. Phosphoric acid
It is a made up of three acid groups.
These acid group react with OH group of ribose or deoxyribose to form pentose monophosphate esters.
3. Nitrogenous bases: 
  • Nitrogenous bases are in the form of heterocyclic aromatic rings, formed of carbon and nitrogen.
  • Two types of nitrogen bases occur, namely
  1. Purines, which have a double ring structure.(Adenine and Guanine)
  2. Pyrimidines, which have a single ring structure. (Cytosine, Thymine and Uracil)
Online activity
FORMATION OF NUCLEOSIDES & NUCLEOTIDES
NUCLEOSIDE: 
  • Combination of the nitrogenous base with the pentose sugar is known as nucleoside.
  • N- base is joined to the sugar molecule by a glycosidic bond.
  • The bond develops between the first carbon of sugar and the nitrogen at position 1 in the case of pyrimidine base and at 9 in the case of purine base.
NUCLEOTIDE:
  • Nucleotide is formed by the combination of nucleoside with phosphate group at 5' position (sugar) by an ester bond.
  • Nucleotide with ribose sugar is called ribonucleotide and a nucleotide with deoxyribose sugar is termed deoxyribonucleotide.
Picture
FUNCTIONS OF NUCLEOTIDES
  1. Building blocks of nucleic acid.(RNA, DNA)
  2. Regulatory chemicals (cAMP)
  3. Formation of energy carriers (ADP and ATP)
  4. Formation of coenzymes (NAD, NADP, FMN, FAD)
HIGHER NUCLEOTIDES : (The energy carriers)
  • Nucleotides with more than one phosphate molecule is termed higher nucleotides.
  • Examples: ADP, ATP, GDP, GTP, CDP, CTP, TDP, TTP, UDP and UTP.
  1. ADP - Adenosine diphosphate
  2. ATP – Adenosine triphosphate
  3. CDP -Cytidine diphosphate
  4. CTP – Cytidine triphosphate
  5. TDP - Thymidine diphosphate
  6. TTP – Thymidine triphosphate
  7. GDP- Guanosine diphosphate
  8. GTP – Guanosine triphosphate
  9. UDP -Uridine diphosphate
  10. UTP –Uridine triphosphate
High energy or energy rich bond
  • Linkage of additional phosphate groups involves large amount of energy.
  • This is provided by the oxidation of food.
  • Separation of phosphate groups release large amount of energy.
  • Thus these bonds joining the additional phosphate groups to the nucleotides are called high energy or energy rich bonds. 

COENZYMES
  • Organic carrier molecule cooperating with an enzyme in promoting a chemical reaction in a cell.
  • Composition: Formed from nucleotides by replacing nitrogenous base with an vitamin.
  • Mode of action: In many reaction, removal of group of atoms and addition to other. This is done with enzyme and coenzyme helps in its transfer to another acceptor compound.
  • Examples:
  1. NAD: Nicotinamide adenine dinucleotide
  2. NADP : Nicotinamide adenine dinucleotide phosphate
  3. FMN : Flavin mononucleotide
  4. FAD : Flavin adenine dinucleotide
  5. Coenzyme A
NAD :
The compound is a dinucleotide, since it consists of  two  nucleotides  joined through their phosphate groups, with one nucleotide containing an adenine base and the other containing nicotinamide.
FAD
This compound is made up of one nucleotide containing ribose and adenine and one with an unusual structure  involving a linear molecule RIBITOL instead of ribose. 

NUCLEIC ACID

HISTORY OF NUCLEIC ACID
1. Friedrich Miescher (1844-1895)
In 1869, Friedrich Miescher isolated "nuclein," DNA with associated proteins, from cell nuclei. He was the first to identify DNA as a distinct molecule.
2. Albrecht Kossel  (1853 – 1927)
Kossel isolated and described the five organic compounds that are present in nucleic acid adenine, cytosine, guanine, thymine, and uracil. These compounds were later shown to be nucleobases.
3. Oscar Hertwig (1849– 1922)
He discovered fertilization of sea urchins, he recognized the role of the cell nucleus during inheritance and chromosome reduction during meiosis
_4. Richard Altman ( (1852 – 1900)) :Altmann is credited for coining the term "nucleic acid", in exchange for Friedrich Miescher's (1844-1895) nuclein, when it was demonstrated that nuclein had acidic properties.
FORMATION OF DINUCLEOTIDE AND POLYNUCLEOTIDE
NUCLEIC ACID
  • Nucleic acids are a polynucleotides consisting of repeated units of mononucleotides.
  • Classification : Nucleic acids are classified into 
  1. DNA : DEOXYRIBONUCLEIC ACID 
  2. RNA : RIBONUCLEIC ACID
DNA: HISTORY
Animation: DNA- TIMELINE 
  1. Article _1 (Envisioning DNA)
  2. Article_2 (Collaboration and Competition- Rosalind Franklin's story)
1. PHOEBUS  LEVENE: Phoebus Levene (1869-1940) had discovered that the cell nucleus contains two types of nucleic acids - DNA and RNA. He also found that DNA contained the four bases, deoxyribose, and a phosphate group. 
2. ERWIN CHARGAFF
 In 1950, Erwin Chargaff published a paper stating that in DNA of any given species, the ratio of adenine to thymine is equal, as is the ratio of cytosine to guanine. This is known as Chargaff's ratios and it was a crucial clue that helped solve the structure of DNA. Chargaff's ratios are universal: all forms of life obey this rule. Only the balance of A-T pairs and C-G pairs varies between species. 
3. ROSALIND FRANKLIN
Rosalind Franklin and Raymond Gosling obtained this X-ray diffraction pattern, which triggered the idea that DNA was a helix.  
She produced the X-ray crystallography pictures of DNA which Watson and Crick used to determine the structure of double-stranded DNA. 
Biography : Rosalind Elsie Franklin (1920-1958)
4. WATSON AND CRICK 
James D. Watson and Francis Crick were the two co-discoverers of the structure of DNA in 1953. They used x-ray diffraction data collected by Rosalind Franklin and proposed the double helix or spiral staircase structure of the DNA molecule. 
WATSON AND CRICK MODEL OF DNA
The six feet tall metal DNA model made by Watson and Crick in 1953. 
Discovering the double helix structure of DNA, James Watson, video with 3D animation and narration
ACTIVITY
dna_temp_coloured.pdf ((take colour print))
File Size: 71 kb
File Type: pdf
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instruction_a4.pdf
File Size: 223 kb
File Type: pdf
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In 1953, J.D. Watson and F.H.C. Crick proposed a precise three dimensional model of DNA structure based on model building studies,
base composition and X-ray diffraction studies. This model is popularly known as the DNA double helix.
DNA DOUBLE HELIX 
SCHEMATIC REPRESENTATION OF DNA DOUBLE HELIX
  1. Two polynuleotide chains are coiled around a central axis in the form of a right handed double helix.
  2. The backbone of each strand consists of alternating sugar and phosphate. The bases project inwards and they are perpendicular to the central axis.
  3. The 2 strands run in opposite direction (ie.) they are antiparallel. Each polynucleotide chain has 5’ phosphorylated and 3’ hydroxyl ends
  4. The strands are complementary to each other due to specific base pairing of the opposite strands.  Base pairing occurs through hydrogen bonding and it is specific. Adenine pairs with thymine through two hydrogen bonds. Guanine pairs with cytosine with three hydrogen bonds. 
  5. Major and minor grooves are present on the double helix.
  6. One turn of helix measures 34 angstrom  and has 10 nucleotides.
  7. Distance between adjacent nucleotides is 3.4  angstrom.
  8. The diameter of the helix is 20 angstrom. 
Online activity: DNA 
FUNCTIONS OF DNA
  1. Carries hereditary information.
  2. Controls the metabolic activity of the cell.
  3. Enables cell to maintain, grow and divide.
  4. Contributes to variation by undergoing mutation.
  5. Brings about differentiation of cells
RNA : RIBONUCLEIC ACID
  • RNAs are present in the nucleus, ribosomes and cytoplasm of eukaryotic cells.
  • RNA also function as genetic material for  some plant virus, animal viruses and bacteriophage.
  • RNAs are also polynucleotides. In RNA polymer, purine and pyrimidine nucleotides are linked together through phosphodiester linkages. The sugar present is ribose. The nitrogenous bases present in RNA are adenine and guanine (purine bases), uracil and cytosine (pyrimidine bases).
TYPES OF RNA
  • There are mainly three types of RNAs in all prokaryotic and eukaryotic cells. 
  • They are
  1. Messenger RNA (mRNA) 
  2. Transfer RNA (tRNA) 
  3. Ribosomal RNA (rRNA). 
  • They differ from each other by size, formation and stability.
  1. Messenger RNA (m RNA)
  • It accounts for 1-5% of cellular RNA. 
  • They are single standed linear molecules consist of 1000-10,000 nucleotides. They have a free or phosphorylated 3’ and 5’ end. 
  • mRNA is a direct carrier of genetic information from the nucleus to the cytoplasm. 
  • It contain information required for the synthesis of protein molecules.
2.   Ribosomal RNA (r RNA) 
  • This accounts for 80% of the total cellular RNA. 
  • In ribosomes, r-RNA is found in combination with protein.
  • It is known as ribonucleoprotein. 
  • The length of rRNA ranges from 100-600 nucleotides.
  • They are required for the formation of risosomes.
  • They are involved in the initiation of protein synthesis.
3.   Transfer RNA (t RNA) 
  • It accounts for 10-15% of total cell RNA. 
  • They are the smallest of all the RNAs. Usually they consist of 50-100 nucleotides. 
  • Secondary structure of t-RNA is in the form of a clover leaf.
  • It is the carrier of amino acids to the site of protein synthesis.
  • There is at least one t-RNA molecule to each of 20 amino acids required for protein synthesis.
FUNCTIONS OF RNA
  1. Protein synthesis.
  2. Genetic material.
  3. Component of ribosomes.
  4. Associated with DNA replication.
  5. Some RNA have enzymatic activity (ribonuclease)
DIFFERENCES BETWEEN DNA & RNA

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CARBOHYDRATES

LIPIDS

PROTEINS
Why is DNA  called an acid, especially since it contains a ‘base’ and doesn’t appear to have any dissociating hydrogen?