DNA - Structure and Organization

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DNA - Structure and Organization

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DNA = DEOXYRIBONUCLEIC ACID RNA = RIBONUCLEIC ACID Strong acid hydrolyses DNA & RNA into 3 components: nitrogenous base (4 different ones) sugar phosphoric acid Mild acid hydrolyses DNA & RNA into 2 components: Nucleoside = base—sugar Nucleotide = base-sugar-phosphate

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The NUCLEOTIDE (base—sugar—phosphate ) is the MONOMER unit of the nucleic acids DNA and RNA DNA and RNA are polymers of (mono)nucleotides

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NUCLEOTIDE structure 1. THE BASES Two PURINE bases Three PYRIMIDINE bases

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keto (carbonyl) amino amino NUCLEOTIDE structure PURINE ADENINE — A GUANINE — G

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methyl amino keto (carbonyl) keto (carbonyl) NUCLEOTIDE structure PYRIMIDINE CYTOSINE — C THYMINE — T URACIL— U

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NUCLEOTIDE structure 2. THE SUGARS — pentoses 1 2 4 3 5 D-ribose ( RNA ) 1 2 4 3 5 H D-2-deoxyribose ( DNA )

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NUCLEOTIDE structure 3. PHOSPHORIC ACID (H 3 PO 4 ) Phosphoric acid pH 7 (HPO 4 2- ) Phosphate ion

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NUCLEOSIDE = base—sugar e.g. ADENOSINE = adenine—ribose adenine ribose DEOXYADENOSINE = adenine—deoxyribose deoxy H

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NUCLEOSIDE = base—sugar e.g. CYTIDINE = cytosine—ribose ribose DEOXYCYTIDINE = cytosine—deoxyribose deoxy H

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The 3' and 5' positions are very important for understanding DNA and RNA structure and function NUCLEOSIDE numbering 5 4 3 2 1 6 5 4 3 2 1 ' ' ' ' ' "Prime" mark: '

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NUCLEOTIDE structure Base—sugar—phosphate adenine ribose e.g. ADENOSINE Adenosine 5'-monophosphate (5'-AMP) 5'

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ribose adenine 5' Adenosine 5'-monophosphate (5'-AMP) Adenosine 5'-diphosphate (5'-ADP) Adenosine 5'-triphosphate (5'-ATP)

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How are mononucleotides linked together to form the polymers DNA and RNA? 5' O 3' 3' 5' O 3',5'-phosphodiester bond

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5' O 3' 3' 5' O 5' O 3' A C C Single-stranded polynucleotides have one free 5' end and one free 3' end — they exhibit POLARITY POLARITY

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O 3' O 5' O A C C The LINEAR sequence of bases reading from 5' to 3' is the PRIMARY structure of a polynucleotide, i.e. 5' ACC 3'

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PRIMARY STRUCTURE of DNA and RNA DNA: 5' AGGTCGAGATTCGTGATA 3' RNA: 5' AGGUCGAGAUUCGUGAUA 3' Sometimes : pApGpGpTpCpGpApGpA Usually the 5' end has a phosphate attached, while the 3' end does not (OH)

Functions of Nucleotides:

Functions of Nucleotides Building block of nucleic acids DNA & RNA Linkage of energy yielding reaction: ATP, GTP Intermediates in many biosynthetic process: UDP-Glucose Synthesis of important co-enzymes – NAD, FAD Metabolic regulation: cyclic AMP Medical application: cancer chemotherapy, antifungal agents, antiviral agents,

Salient Features of DNA:

Salient Features of DNA DNA is a right handed double helix,consist of two polyribonucleotide chains (strands) twisted around each other on a common axis. The two strands are antiparallel,one strand runs in 5’ to 3’direction, other 3’ to 5’. The width of a double helix is 20 A ˚(2nm). Each turn (pitch)of the helix 34A˚(3.4nm) with 10 pairs of nucleotides, each pair placed at a distance of about 3.4 A(0.34nm).

Salient Features of DNA:

Salient Features of DNA Each strand of DNA has a hydrophillic deoxyribose phosphate backbone on the outside, hydrophobic bases are stacked inside(core). Two polynucleotide chains are complementary to each other due to base pairing. The two strands are held together by hydrogen bonds formed by complementary base pairs. The A-T pair has 2 hydrogen bonds while the C-G pair has 3 hydrogen bonds.

Salient Features of DNA :

Salient Features of DNA The hydrogen bonds are formed between a purine and pyrimidine only. The only base arrangement possible in DNA structure is A-T, T-A , G-C, C-G. The complementary base pairing in DNA helix proves Chargaff’s rule. The content of adenine equals to that of thymine and guanine equals cytosine. The genetic information resides on one of the two strands known as template strand or sense strand. The opposite strand is antisense strand. The double helix has (wide) major grooves and (narrow) minor grooves along the phosphodiester backbone.

Organization of DNA - eukaryotic :

Organization of DNA - eukaryotic The length of DNA is considerably reduced by formation of 10nm fiber. The continuous string of nucleosome represents – beads on a string form of chromatin. The 10nm fiber further coiled to produce 30nm fiber with 6 nucleosomes in every turns. These 30 nm fibers are further organized into loops by anchoring the fiber at A/T rich regions namely scaflold associated regions(SARS) to a protein scafold

Organization of DNA - eukaryotic :

Organization of DNA - eukaryotic The DNA is associated with various proteins to form chromatin which then gets organized into compact structures, the chromosomes. The DNA double helix is wrapped around the core proteins, histones - basic in nature. The core is composed of two molecules of histones(H2A,H2B,H3& H4) Each core with two turns of DNA wrapped round it into nucleosome-basic unit of chromatic.

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