MOLECULAR CELL BIOLOGY and BiodiversityMANOJKUMAR.K

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DNA

Deoxyribonucleic acid (DNA) is a molecule that encodes the genetic instructions used in the development and functioning of all known living organisms and many viruses

DNA is about 1.7µm (virus)

Uncoiled the DNA of a human would stretch 2m

The average diameter of a nucleus is 10µm

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DNA supercoiling refers to the over- or under-winding of a DNA strand, and is an expression of the strain on that strand

Supercoiling is important in a number of biological processes, such as compacting DNA

Additionally, certain enzymes such as topoisomerases are able to change DNA topology to facilitate functions such as DNA replication or transcription

Mathematical expressions are used to describe supercoiling by comparing different coiled states to relaxed B-form DNA

DNA super coiling

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DNA super coiling

DNA double helix

Nucleosome beads on a string

30-nm chromatin fibre

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DNA super coiling

30-nm chromatin fibre

Chromosome in extended form

Condensed section of chromosome in mitosis

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DNA super coiling

Condensed section of chromosome in mitosis

Condensed chromosome

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Role of supercoil

In a "relaxed" double-helical segment of B-DNA, the two strands twist around the helical axis once every 10.4–10.5 base pairs of sequence

 If a DNA segment under twist strain were closed into a circle by joining its two ends and then allowed to move freely, the circular DNA would contort into a new shape. This is called as super-coil

Extra helical twists are positive and lead to positive supercoiling, while subtractive twisting causes negative supercoiling

Many topoisomerase enzymes sense supercoiling and either generate or dissipate it as they change DNA topology

DNA of most organisms is negatively supercoiled.

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Role of supercoil

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Occurrence of DNA supercoiling

DNA supercoiling is important for DNA packaging within all cells. Because the length of DNA can be thousands of times that of a cell, packaging this genetic material into the cell or nucleus (in eukaryotes) is a difficult feat. Supercoiling of DNA reduces the space and allows for much more DNA to be packaged.

DNA packaging is greatly increased during nuclear division events such as mitosis or meiosis, where DNA must be compacted and segregated to daughter cells

Structural Maintenance of Chromosome proteins that aid in the condensation of sister chromatids and the linkage of the centromere in sister chromatids. These SMC proteins induce positive supercoils.

Supercoiling is also required for DNA/RNA synthesis. Because DNA must be unwound for DNA/RNA polymerase action, supercoils will result.

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Mathematical description

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Linking number

Any two closed curves in space, if allowed to pass through themselves but not each other, can be moved into exactly one of the following standard positions. This determines the linking number

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Satellite DNA

Satellite DNA consists of very large arrays of tandemly repeating, non-coding DNA.

Satellite DNA is the main component of functional centromeres, and form the main structural constituent of heterochromatin.

The name "satellite DNA" refers to how repetitions of a short DNA sequence tend to produce a different frequency of the nucleotides adenine, cytosine, guanine and thymine, and thus have a different density from bulk DNA - such that they form a second or 'satellite' band when genomic DNA is separated on a density gradient

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The C value paradox

The C value:

total amount of DNA in the genome

We would expect that the more complex the organism, the more DNA is needed to “run it”

Therefore, we would expect a linear relationship between genome size and organism complexity.

This idea appears to make sense:

the more complex the organism is, the more genetic information it needs (larger C value)

In smaller organisms (viruses, bacteria) there is no room for excess DNA (smaller C value)

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The C value paradox

► At the lower range of complexity, this holds:

Bacteria have smaller genomes than eukaryotes, and viruses have smaller genomes than bacteria.

In larger organisms, relationship breaks down

Organisms have DNA apparently in excess of what is needed; repetitive sequences, “junk DNA”

This is the C value Paradox, that in the most complex organisms, there doesn’t appear to be the expected relationship between complexity and genome size.

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cot curve

Cot curve is concerned with the measurement of the degree of reannealing of DNA strands

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Reference

Robert H.Tamarin, Principle of Genetics, The McGraw Hill companies, Inc., 1999.

Karp, G. (2005) “Cell and Molecular Biology: Concepts and Experiments”; Fourth Edition,Wiley Publishing Co. USA

Vologodskii AV, Lukashin AV, Anshelevich VV et al. (1979). "Fluctuations in superhelical DNA". Nucleic Acids Res 6 (3): 967–682. doi:10.1093/nar/6.3.967. PMC 327745. PMID 155809

A.V. Chernavskii (2001), "Linking coefficient", in Hazewinkel, Michiel, Encyclopedia of Mathematics, Springer, ISBN 978-1-55608-010-4

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THANK YOU !!!

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