C VALUE, C VALUE PARADOX , COT CURVE ANALYSIS.pptx

C-VALUE,
C-VALUE PARADOX,
COT CURVE
PRESENTED BY:
MURUGAVENI B
I MSC BIOCHEMISTRY
GENOME:
• Genome is the some total of all genetic material
of an organism.
• Haploid set of genome present in the cell of an
organism.
• Human beings have 3 billion base pairs in their
haploid cells and 6 billion base pairs in their
diploid cells
• An organisms may have either DNA or RNA as
their genetic material.
C- VALUE:
• C-VALUE is the total amount of DNA present in the genome which is
expressed in terms of base pairs or picogram(bp or Mbp or pg)[106
bp= 1Mbp =10_3 pg DNA.
• Term coined by Hewson swift in 1950.
• Genome is chromosomes present within the haploid cell.
• Few examples of C-value;
• It was said that “ as complexity increases, the c-value ( amount of
DNA) increases from simpler to complex forms.”
• For e.g; human beings are the high complex organisms and
bacteria,viruses,mycoplasma,algae,fungi are lower organisms which
are simpler forms.
• This means that the amount of DNA increases from simpler to
complex forms.
• There is a linear relationship between genome size and organism
complexity.
WHAT IS THE C VALUE PARADOX?
• This term is given by C. A. Thomas in 1971, when repeated sequences
of DNA were discovered, explaining in every case no relationship
between genome size and complexity of organisms.
• The DNA content of an organism’s genome is related to the
morphological complexity of eukaryotes but it is observed that it is
different in higher eukaryotes.
• In higher eukaryotes there is no correlation between complexity and
genomic size; this is called the C value paradox. Genome size is the
total amount of DNA contained within the copy of a single genome.
• It is measured in terms of picograms and base pairs.
• Morphologically similar organisms appear to have different amounts
of DNA in their genome.
• Living organisms are classified into two categories: eukaryotes, which
are complex organisms with organized nuclei, and prokaryotes, which
are simpler organisms without organized nuclei.
• It was commonly believed that the complexity of an organism was
reflected in its DNA content, with eukaryotes having a higher
percentage of DNA than prokaryotes.
• However, recent findings have shown that this is not always the case,
and there are many exceptions to this rule. Therefore, it is incorrect
to assume that the amount of DNA in an organism is always
proportional to its complexity.
• In other words, we can say simpler the organism smaller the genome,
complex the organism larger the genome.
• The complexity of an organism can be predicted by knowing the size
of the genome and the size of the genome can be predicted by the
complexity of an organism.
• The eukaryotic genome consists of two parts, coding DNA and non
Coding DNA. Coding DNA is a protein synthesizing DNA and non-
coding DNA is present in multiple copies.
• The human genome consists of 2% of Coding DNA and 98% non
Coding DNA.
C VALUE, C VALUE PARADOX , COT CURVE ANALYSIS.pptx
EXAMPLE;
• 1. Salamanders have 40 times more DNA in comparison to humans,
whereas humans are more complex organisms compared to
salamanders.
• 2. Housefly and Drosophila both are in the same group but the
housefly C value is higher than Drosophila.
REASON FOR C VALUE PARADOX;
• The reason for this is the presence of repetitive DNA, which means
the sequence of DNA which repeats in the genome many times.
C VALUE ENIGMA:
• C value enigma represents an updated term of the C value paradox, It
was given by Dr. T. Ryan Gregory in 2001.
• C value enigma relates to variation in the amount of non Coding DNA
found within the genomes of different eukaryotes.
• The variation of non-coding DNA varies from species to species.
• C Value enigma explains properly the reason for the C value paradox
and defines what types of non-coding DNA are found in the
eukaryotic genome and its function and what proportions they are
present.
COT CURVE ANALYSIS:
• It is a technique for measuring the complexity (size) of DNA or genome.
• The technique was developed by Roy Britten and Eric Davidson in 1960.
• The technique is based on the principle of DNA renaturation kinetics.
Principle: The rate of renaturation is directly proportional to the number of
times the sequences are present in the genome.
Given enough time all DNA that is denatured will reassociate or reanneal in
a given DNA sample.
The more the repetitive sequence the less will be the time taken for
renaturation.
PROCEDURE:
• The process involves denaturation of DNA
by heating and allowed to reanneal by
cooling.
• The renaturation of DNA is assessed
stereoscopically.
• Large DNA molecules take longer time to
reanneal.
WHAT IS COT VALUE?
• The renaturation depends on the following factors DNA concentration,
reassociation temperature, cation concentration and viscosity.
• Cot=DNA Concentration (moles/L) X renaturation time in seconds X buffer
factor (that accounts for the effects of cations on the speed of
renaturation).
• Cot:Co=Concentration of DNA and t= time taken for renaturation Low cot
value indicates more number of repetitive sequences
• High cot value indicates more number of unique sequences or less number
of repetitive sequences.
• For example: Bacteria- 99.7% Single Copy
• Mouse - 60% Single Copy +25% Middle Repetitive+ 10% Highly Repetitive
HOW TO CALCULATE COT VALUE?
• Cot=DNA Concentration (moles/L) X renaturation time in seconds X
buffer factor (that accounts for the effects of cations on the speed of
renaturation).
• Nucleotide concentration = 0.050 M
• Renaturation time = 344 sec
• Buffer factor, 0.5 M SPB = 5.820
• Cot value = 0.050X 344 X 5.820=100.000
C VALUE, C VALUE PARADOX , COT CURVE ANALYSIS.pptx
APPLICATION OF COT CURVE ANALYSIS:
• Understanding genome size and
complexity.
• Understanding complexity of
sequences.
• Understanding relative proportion of
single copy and repetitive sequences.
REFERENCES:
• 1. 4th edition biochemistry Donald Voet &
Judith G. Voet.
• 2. Lehninger, 4th edition, Principal of
biochemistry, David L. Nelson & Michael.
THANK YOU…
1 sur 18

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C VALUE, C VALUE PARADOX , COT CURVE ANALYSIS.pptx

  • 1. C-VALUE, C-VALUE PARADOX, COT CURVE PRESENTED BY: MURUGAVENI B I MSC BIOCHEMISTRY
  • 2. GENOME: • Genome is the some total of all genetic material of an organism. • Haploid set of genome present in the cell of an organism. • Human beings have 3 billion base pairs in their haploid cells and 6 billion base pairs in their diploid cells • An organisms may have either DNA or RNA as their genetic material.
  • 3. C- VALUE: • C-VALUE is the total amount of DNA present in the genome which is expressed in terms of base pairs or picogram(bp or Mbp or pg)[106 bp= 1Mbp =10_3 pg DNA. • Term coined by Hewson swift in 1950. • Genome is chromosomes present within the haploid cell. • Few examples of C-value;
  • 4. • It was said that “ as complexity increases, the c-value ( amount of DNA) increases from simpler to complex forms.” • For e.g; human beings are the high complex organisms and bacteria,viruses,mycoplasma,algae,fungi are lower organisms which are simpler forms. • This means that the amount of DNA increases from simpler to complex forms. • There is a linear relationship between genome size and organism complexity.
  • 5. WHAT IS THE C VALUE PARADOX? • This term is given by C. A. Thomas in 1971, when repeated sequences of DNA were discovered, explaining in every case no relationship between genome size and complexity of organisms. • The DNA content of an organism’s genome is related to the morphological complexity of eukaryotes but it is observed that it is different in higher eukaryotes. • In higher eukaryotes there is no correlation between complexity and genomic size; this is called the C value paradox. Genome size is the total amount of DNA contained within the copy of a single genome. • It is measured in terms of picograms and base pairs.
  • 6. • Morphologically similar organisms appear to have different amounts of DNA in their genome. • Living organisms are classified into two categories: eukaryotes, which are complex organisms with organized nuclei, and prokaryotes, which are simpler organisms without organized nuclei. • It was commonly believed that the complexity of an organism was reflected in its DNA content, with eukaryotes having a higher percentage of DNA than prokaryotes. • However, recent findings have shown that this is not always the case, and there are many exceptions to this rule. Therefore, it is incorrect to assume that the amount of DNA in an organism is always proportional to its complexity.
  • 7. • In other words, we can say simpler the organism smaller the genome, complex the organism larger the genome. • The complexity of an organism can be predicted by knowing the size of the genome and the size of the genome can be predicted by the complexity of an organism. • The eukaryotic genome consists of two parts, coding DNA and non Coding DNA. Coding DNA is a protein synthesizing DNA and non- coding DNA is present in multiple copies. • The human genome consists of 2% of Coding DNA and 98% non Coding DNA.
  • 9. EXAMPLE; • 1. Salamanders have 40 times more DNA in comparison to humans, whereas humans are more complex organisms compared to salamanders. • 2. Housefly and Drosophila both are in the same group but the housefly C value is higher than Drosophila. REASON FOR C VALUE PARADOX; • The reason for this is the presence of repetitive DNA, which means the sequence of DNA which repeats in the genome many times.
  • 10. C VALUE ENIGMA: • C value enigma represents an updated term of the C value paradox, It was given by Dr. T. Ryan Gregory in 2001. • C value enigma relates to variation in the amount of non Coding DNA found within the genomes of different eukaryotes. • The variation of non-coding DNA varies from species to species. • C Value enigma explains properly the reason for the C value paradox and defines what types of non-coding DNA are found in the eukaryotic genome and its function and what proportions they are present.
  • 11. COT CURVE ANALYSIS: • It is a technique for measuring the complexity (size) of DNA or genome. • The technique was developed by Roy Britten and Eric Davidson in 1960. • The technique is based on the principle of DNA renaturation kinetics. Principle: The rate of renaturation is directly proportional to the number of times the sequences are present in the genome. Given enough time all DNA that is denatured will reassociate or reanneal in a given DNA sample. The more the repetitive sequence the less will be the time taken for renaturation.
  • 12. PROCEDURE: • The process involves denaturation of DNA by heating and allowed to reanneal by cooling. • The renaturation of DNA is assessed stereoscopically. • Large DNA molecules take longer time to reanneal.
  • 13. WHAT IS COT VALUE? • The renaturation depends on the following factors DNA concentration, reassociation temperature, cation concentration and viscosity. • Cot=DNA Concentration (moles/L) X renaturation time in seconds X buffer factor (that accounts for the effects of cations on the speed of renaturation). • Cot:Co=Concentration of DNA and t= time taken for renaturation Low cot value indicates more number of repetitive sequences • High cot value indicates more number of unique sequences or less number of repetitive sequences. • For example: Bacteria- 99.7% Single Copy • Mouse - 60% Single Copy +25% Middle Repetitive+ 10% Highly Repetitive
  • 14. HOW TO CALCULATE COT VALUE? • Cot=DNA Concentration (moles/L) X renaturation time in seconds X buffer factor (that accounts for the effects of cations on the speed of renaturation). • Nucleotide concentration = 0.050 M • Renaturation time = 344 sec • Buffer factor, 0.5 M SPB = 5.820 • Cot value = 0.050X 344 X 5.820=100.000
  • 16. APPLICATION OF COT CURVE ANALYSIS: • Understanding genome size and complexity. • Understanding complexity of sequences. • Understanding relative proportion of single copy and repetitive sequences.
  • 17. REFERENCES: • 1. 4th edition biochemistry Donald Voet & Judith G. Voet. • 2. Lehninger, 4th edition, Principal of biochemistry, David L. Nelson & Michael.