RNA STRUCTURE 1

Types of nucleic acid DNA – Deoxyribonucleic acid RNA – ribonucleic acid 2

O O=P-O OPhosphate Group Group N Nitrogenous base (A, G, C, or U) (A, G, C, or U) CH2 O C1C1 C4C4 C3C3 C2C2 5 Sugar Sugar(deoxyribose) Nucleic acids consist of repeating nucleotide that have phosphate ester, a pentose sugar, and a heterocyclic base. 3

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RNA is single stranded 5

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RNA SYTHESIS 8

HIGHER ORDER DNA STRUCTURE TERTIARY PACKAGING OF DNA INTO CHROMOSOME 9

SIZE OF DNA DNA Molecules are much longer than the cellular packages that contain them Viruses Usually consist of no more than one genome (usually a single RNA or DNA molecule) Almost all have RNA genomes Although viral genomes are small-the contour lengths of their DNA s are much greater than the long dimensions of the viral particles that contain them-efficient DNA packaging! 10

Bacteria E.Coli contain almost 100 times DNA length compare to virus Double stranded circular DNA molecule In addition, many bacteria contain one or more small circular DNA molecules that are free in the cytosol – plasmids (can be few thousand pairs). Eg. Plasmid carry multidrug resistance gene SIZE OF DNA 11

DNA is packed into chromosomes Each chromosome contain a single, very large, duplex DNA molecule Mitochondrial DNA (<20kbp) codes for the mitochondrial tRNA and rrNA and few mitochondrial proteins EUKARYOTES 12

Genomic DNA May be Linear or Circular Most DNA exist as double-helical complexes, except for few bacteriophage that can aquire SS form Depending on the source of DNA, the complexes can be linear or circular Circular DNA - formation of phosphodiester bonds between the 3’-5’ termini of linear polynt by enzyme DNA ligase 13

DNA SUPERCOILING Cellular DNA- extremely compacted – implying high degree of structural organization Important property of DNA structure- supercoling – the coiling of a coil DNA is coiled in the form of double helix – further coiling of double helix produce supercoil No bending of DNA upon itself- relaxed state Tertiary structure of DNA 14

Circular DNA without other manipulations – relaxed state – decrease activity in replication and transcription The biological form- superhelical topology created by either unwinding or overwinding the double helix Underwound DNA/right handed superhelix – negative supercoil Overwound DNA/left handed superhelix-positive supercoil Naturally occuring – negative supercoil Genomic DNA May be Linear or Circular 15

Topoisomerase Enzyme Involve in changing the supercoiled state of DNA 2 Classes – Class I and Class II Class I-cut the phosphodiester backbone of one strand DNA, pass the other end through Class II – Cut both strands of DNA, pass some of the remaining DNA helix between the cut ends, and then reseal –e.g. DNA gyrase These 2 enzymes play important role in replication and transcription 16

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Packaging of Prokaryotic DNA DNA is organized as a single chromosome that contains ds circular supercoil Average bacterium DN, e.g E.Coli – contour length of DNA is 80X larger than the diameter of the cell 1mm chromosome need to be packed in 1µm cell Bacterial chromosomes are organized into compacted structure-nucleoids- interaction with HU protein – forming DNA-HU complex 18

EUKARYOTES 19

Packaging of eukaryotic DNA Majority of DNA in euk cells is packaged into nucleosome Can reduce the length into 10,000 fold Nucleosome- composed of a core of eight histone proteins and the DNA wrapped around them Five types of histones- H1A, H2A,H2B,H3 and H4 20

DNA ORGANIZATION IN EUKARYOTE 1.DNA in the form of double helix 2.DNA is tightly associated with proteins histones producing nucleosomes- 10nm fibrils 3.Nucleosomes are organized into 30nm fibers and the fibers are extensively folded to provide 10,000 fold compaction required to fit a typical eukaryotic chromosome into cell nucleus 4.The higher order folding involves attachment to a nuclear scaffold that contains histone H1, topoisomerase II and SMC proteins 5.Youtube: How DNA is packaged (Advanced) 21

EUKARYOTES Contain centromere-a sequence of DNA that functions during cell division as an attachment point for proteins that link the chromosome to the mitotic spindle Telomeres – sequence at the end of eukaryotic chromosomes that help stabilize chromosome 22

The Importance of DNA Packaging Chromosome is the compact form of DNA that readily fits the cell Protect DNA from damage-allowing information encoded to be transmitted efficiently to daughter cells 23