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Information about THE CHEMISTRY OF GENES

Published on January 31, 2009

Author: e_opena


THE CHEMISTRY OF GENES (STRUCTURES AND ACTIVITIES) : THE CHEMISTRY OF GENES (STRUCTURES AND ACTIVITIES) Edward Laurence L. Opena MS Biology 1 Bio 253 – Molecular Genetics Mindanao State University – Iligan Institute of Technology Slide 3: The path to transcription Slide 4: For a molecule to serve the role of the genetic material, it must possess four major characteristics: Replication Storage of information Expression of information Variation by mutation Nucleic Acid Chemistry : Nucleic Acid Chemistry Nucleotide – the building block of all nucleic acid molecules > 3 components: 1. a nitrogenous base 2. a pentose sugar (5-carbon sugar) 3. a phosphate group A NucleotideAdenosine Mono Phosphate (AMP) : A NucleotideAdenosine Mono Phosphate (AMP) Nucleotide Nucleoside Slide 7: Pyrimidines Purines Forms of Nucleotides : Forms of Nucleotides Nucleoside monophosphate (NMP) – 1 phosphate group attached Nucleoside diphosphate (NDP) – 2 phosphate groups attached Nucleoside triphosphate (NTP) – 3 phosphate groups attached Note: All phosphate attachment in a nucleotide is located at the 5’ end of the sugar group Slide 9: Nucleotides are covalently linked with each other to form a linear polymer/strand, with alternating phosphate-sugar-phosphate groups joined by 3’-5’ phosphodiester bonds 2 ends: 3’-end and the 5’ end which makes it polar 3.4 nm: distance between 1 nucleotide to another Erwin Chargaff (Columbia University) disproved the ‘tetranucleotide’ theory by observing variabilities between organisms (he developed base composition) The Watson-Crick Proposal of DNA Structure : The Watson-Crick Proposal of DNA Structure There are 12 summarized proposal by Watson and Crick of the DNA structure as what the X-ray diffraction data of R. Franklin and M. Wilkins: The molecule is composed of two chains of nucleotides The two chains spiral around each other to form a right-handed helices The two chains comprising one double helix run in opposite direction; that is, they are antiparallel. Slide 11: 4. The-sugar-phosphate-sugar-phosphate-backbone of each strand is located on the outside of the molecule with the two sets of bases projecting towards the center 5. The bases occupy planes that are approximately perpendicular to the long axis of the molecule and are, therefore, stacked one on top of the another like a pile of plates 6. The two strands are held together by hydrogen bonds between each base of one strand and an associated base on the other strand. 7. The distance from the phosphorus atom of the backbone to the center of the axis is 1 nm (thus the width of the double helix is 2nm) Slide 12: 8. A pyramidine in one chain is always paired with a purine in the other chain 9. The nitrogen atoms linked to carbon 4 of cytosine and carbon 6 of adenine are predominantly in the amino (NH2) configuration rather than the imino (NH) form 10. The spaces between adjacent turns of the helix form two grooves of different width – a wider major groove and a more narrow minor groove – that spiral around the outer surface of the double helix 11. The double helix makes one complete turn every 10 residues (3.4 nm), or 150 million daltons of molecular mass 12. Because an A on one strand is always bonded to a T on the other strand, and G is always bonded to a C, the nucleotide sequences of the two strands are always fixed relative to one another. (Complementary) Base PairingGuanine And Cytosine : - + + + - - Base PairingGuanine And Cytosine Base PairingAdenine And Thymine : Base PairingAdenine And Thymine Base PairingAdenine And Cytosine : Base PairingAdenine And Cytosine Base PairingGuanine And Thymine : Base PairingGuanine And Thymine DNA : DNA 3 Forms of DNA Helices : 3 Forms of DNA Helices Hydrophobic Interactions : Hydrophobic Interactions Though the H-bonds between the 2 strands are strongly emphasized by geneticists, these are not the only forces influencing the structure of the DNA. The bases themselves are hydrophobic, and will tend to form structures in which they are removed from the aqueous environment. The hydrogen bonding not only holds the two strands together but also allows the corresponding bases to approach sufficiently closely for the hydrophobic interactions to operate, and much more it gives rise to the specificity of the base pairing between the two chains. DNA Supercoiling : DNA Supercoiling In 1963 Jerome Vinogard of California Institute of Technology observed 2 close, circular DNA molecules of identical mass is coiled more compact than its relaxed counterpart. The DNA is said to be supercoiled. Role of Topoisomerases : Role of Topoisomerases Topoisomerases are enzymes that changes the supercoiled state of the DNA complex. 2 types of topoisomerase: Type 1 – create a transient break in one strand of the duplex; cleaves one strand of the DNA, and allows the intact, complementary strand to undergo a controlled rotation, which relaxes the supercoiled molecules - essential for DNA replication and duplication; prevents excessive supercoiling from building up as the complementary strands of a DNA duplex separate and unwind Type 2 – make a transient break in both strands of DNA Denaturation and Hybridization : Denaturation and Hybridization Denaturation – separation of the two DNA strands Hybridization – the formation of hydrogen bonds between similar DNA sequences 3 Broad Classes of Reanneled DNA Sequences : 3 Broad Classes of Reanneled DNA Sequences Highly Repeated Fraction – constitutes about 10% of the total DNA; sequence repeats itself over and over again without interruption > Satellite DNAs >Minisattelite DNAs >Microsattelite DNAs (the shortest) Moderately Repeated DNA Sequences – 20-80% of the total DNA depending on the organism >Repeated DNA Sequences with coding functions >Repeated DNA Sequences that lack coding functions 3. Nonrepeated DNA Sequences – present in a single copy of the genome (initially predicted by Mendel)/each gene was present in one copy per single (haploid) set of chromosomes 1. DNA ReplicationExtension - The Replication Fork : 1. DNA ReplicationExtension - The Replication Fork Okazaki fragment 2. Transcription – involves RNA : 2. Transcription – involves RNA Eukaryotic Transcription : Eukaryotic Transcription Slide 38: The Bacterial Replication Slide 41: Mismatch Repair – the methylation of DNA that identifies the old and new strands; it recognizes the mismatched bases, removes a short region of the non-methylated strand and fills the gap. Excision Repair – a mechanism which in particular is triggered by UV irradiation Recombination (post-replication) Repair – a repair system involving general recombination of sequences SOS Repair – the modification or abandonment of DNA polymerase in an erroneous replication DNA Repair Major Differences of Gene Organization Between the Prokaryotes and the Eukaryotes : Major Differences of Gene Organization Between the Prokaryotes and the Eukaryotes Prokaryotes Transcription and translation occurs in the same compartment; translated while being transcribed Don’t contain introns (except for some phages) Not consistently polyadenylated Eukaryotes mRNAs act as true messenger and longer life Codes for a single polypeptide only The initial product of transcription is a precursor of the mRNA Contains additional sequences (introns) mRNA is polyadenylated Thanks for attentively listening! : Thanks for attentively listening! Ps 139:14 I will praise thee; for I am fearfully and wonderfully made: marvellous are thy works; and that my soul knoweth right well. KJV

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