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RNA STRUCTURE
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Types of nucleic acid
• DNA – Deoxyribonucleic acid
• RNA – ribonucleic acid
O OHCH2
OHOH
HO HO O OHCH2
OH
ribose deoxyribose
(no O)
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O O=P-O O
Phosphate Group
N Nitrogenous base (A, G, C, or U)
CH2
O
C1 C4
C3 C2
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Sugar (deoxyribose)
Nucleic acids consist of repeating nucleotide that have phosphate ester, a pentose sugar, and a heterocyclic base.
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RNA is single stranded
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RNA SYTHESIS
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HIGHER ORDER DNA STRUCTURE
TERTIARY PACKAGING OF DNA INTO CHROMOSOME
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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!
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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
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• 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
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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
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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
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• 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
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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
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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
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EUKARYOTES
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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
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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)
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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
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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
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