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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