DNA Structure PDF

# What is a Nucleotide? ## Definition - Structural unit "Building Block" of DNA and RNA - Composed of pentose sugar, nitrogenous base & phosphate (P) ## Structure - **Pentose sugar** (5 C): - Ribose in RNA. - Deoxyribose in DNA. (Ribose from which oxygen *removed from C2*). - **Phosph...

# What is a Nucleotide? ## Definition - Structural unit "Building Block" of DNA and RNA - Composed of pentose sugar, nitrogenous base & phosphate (P) ## Structure - **Pentose sugar** (5 C): - Ribose in RNA. - Deoxyribose in DNA. (Ribose from which oxygen *removed from C2*). - **Phosphate group** = Phosphoric acid: - Attached to C5 of sugar by *phosphoester bond*. - Removal of phosphate group converts *nucleotide* to *nucleoside*. - **Nitrogenous base:** - **Purine bases:** Guanine & Adenine. - **Pyrimidine bases:** Uracil (in RNA), Thymine(In DNA) & Cytosine. - Purine form *N-glycosidic bond* with C1 by N9. - Pyrimidine form *N-glycosidic bond* with C1 by N1. ## Adenine, Guanine, Cytosine, Thymine & Uracil - **Adenine** has *amino group* at C6. - **Guanine** has *oxygen* at C6 & *Amino group* at C2. - **Cytosine** has *amino group* at C4. - *If deaminated* "remove NH2" → Uracil. - **Uracil** if *methylated* “add CH3" at C5 → Thymine. ## Phosphodiester Bonds - It is the bond that connects nucleotide to form nucleic acid (one strand of DNA or RNA). ### **Characters:** - **3',5' phosphodiester bond** "Covalent": - There is *phosphate group* attached by *two ester bonds* to carbon 3' and 5' of two successive nucleotides. - **Formation of the bond:** - The *triphosphate forms of the building block nucleotide* are broken apart to give off energy required to drive the enzyme catalyzed reaction, remove pyrophosphate. - *One hydroxyl group* of the *phosphate of the added nucleotides* (C5) react with *hydroxyl group* of the *sugar of the nucleotides* in the growing chains(C3). ### **Nucleases:** - *hydrolyze* phosphodiester bonds. - **Endonuclease**: hydrolyze internal phosphodiester bonds. - Can't release free nucleotide, give two short strands. - **Exonuclease**: hydrolyze external phosphodiester bonds. - Release free nucleotide - **Excinuclease**: cause dual "TWO" cut of internal bonds. ## Importance of Nucleotide - DNA and RNA synthesis. - High energy sources e.g. ATP. - Coenzymes: FAD, NAD, NADP & CoA. - Regulatory function :- 2ry messenger cAMP, cGMP ## DNA Structure ### Primary Structure - **Polydeoxynucleotides:** - Deoxyribose - Nitrogenous base (Adenine, Guanine, Cytosine & Thymine) - Phosphate - **3'-5' phosphodiester bonds** between two nucleotides. ### Notes - DNA is polar due to it has phosphate at 5'end & (OH) 3' end. - The nitrogenous bases are written from 5' to 3' end. e.g 5'pApCpT3' = ACT. ### Secondary Structure - **Double strand linear** (in eukaryotic nuclear chromosome). - **Double strand circular** (in mitochondria, Prokaryotes, plasmid, virus & chloroplast). - **Single strand circular** (small viruses). ### Tertiary Structure - Each human cell contains 23 pairs of chromosomes. - Chromosomes (8000 folds less than DNA). - Human genome: Total DNA of these chromosomes. "2 meters". - Total DNA content inside cell, contains 30,000 genes. - Gene: Segment of DNA that code for polypeptide chains or RNA. - Prokaryotes has a single chromosome and non-chromosomal chromatid "Plasmid". - Extranuclear DNA in Eukaryotes = Mitochondrial DNA. ## Chargaff’s Rule & Complementary Bases - Amount of Adenine = amount of Thymine. - Adenine & thymine have 2 electronegative atoms (bind by *hydrogen bonds*). - Amount of Guanine = amount of Cytosine. - Guanine & Cytosine have 3 electronegative atoms (bind by *hydrogen bonds*). - Total amount of purine = total amount of pyrimidine. ## Watson Crick Double Helix Model (B-form) - **Right-handed** double helix (clockwise). - **Spiral** shape (hydrophilic deoxyribose-P outside while base inside). - The *hydrophobic bases* are *stacked* inside perpendicular to axis of helix. ### Features - **Antiparallel:** 5' end of one strand is paired to 3' end of other strand. - Each turn of DNA helix contains 10 base pairs. (3.4nm length, 1.9nm width). - Deep grooves: Minor & major groove. (Binding site for regulatory proteins). - Resendeep grooves between the ribose-phosphate chains ## Denaturation of DNA Double Strand (melting):- - Separation of two strands of DNA by disruption H. bonds. - *Change pH* → Ionization of bases - *Heating*. - A-T base pairs is less stable "cleaved by lower temperature" than G-C. - **Renaturation** :- reform double helix by cooling. ## Factors Stabilize DNA Helix: - Stacking interaction - Hydrophobic interaction between bases - H. Bond. ### Z-form: - Lt handed helix, zigzag, 12 bp/turn. - (May found in region with alternating purine & pyrimidine e.g. Poly GC.) ### A-form: - Rt handed helix, 11 bp/turn. present in DNA-RNA Hybrids. ## Eukaryotes Chromatin Structure - **Chromatin:** - Means the 3ry structure of DNA in cells = DNA + (Nucleoproteins. - It is stabilized by 2 types of binding proteins :- - **Histones** - Different types (H2A,H2B, H3,H4). - Rich in basic amino acids arginine & lysine (facilitate binding to P in DNA). - **Nucleosome** - Nucleosome core: octamer 8" protein (2 H2A,H2B„H3 ,H4) - + 150 bp DNA 2 DNA turns “Wraps”. - Appear as bead in linear DNA. - **H1 present in** between nucleosome (linker histone). (20-200 bp DNA). - About nucleosomes are supercoiled to form chromatin "30nm in diameter" - Chromatins are also supercoiled to form chromosomes. (8000 folds less than DNA). - **Non-histones:** - Protein-DNA structure of chromatin is stabilized by attachment to non-Histone protein scaffold called the nuclear matrix. - Also, there are diverse group of proteins "more than 1000 different types": Enzymes, hormones, transcription factors.