1. Online Counseling Resource YCMOU ELearning Drive… School of Architecture, Science and Technology Yashwantrao Chavan Maharashtra Open University, Nashik – 422222, India

2. OC-SBT092-CP1-02 Introduction Programmes and Courses  SEP – SBT092 – Unit 01 - 02

3. School of Science and Technology, Online Counseling Resource… Credits  Academic Inputs by Arun Punaji More. M.Sc. (Microbiology) Experience: 11 Years.  arunmesh@hotmail.com 33

4. School of Science and Technology, Online Counseling Resource… © 2009, YCMOU. All Rights Reserved.4 How to Use This Resource  Counselor at each study center should use this presentation to deliver lecture of 40-60 minutes during Face-To-Face counseling.  Discussion about students difficulties or tutorial with assignments should follow the lecture for about 40-60 minutes.  Handouts (with 6 slides on each A4 size page) of this presentation should be provided to each student.  Each student should discuss on the discussion forum all the terms which could not be understood. This will improve his writing skills and enhance knowledge level about topics, which shall be immensely useful for end exam.  Appear several times, for all the Self-Tests, available for this course.  Student can use handouts for last minutes preparation just before end exam. 44

5. School of Science and Technology, Online Counseling Resource… © 2009, YCMOU. All Rights Reserved.5 Learning Objectives  After studying this module, you should be able to: Describe physical properties of eukaryotic chromosome Describe C value and C value paradox Describe Cot analysis of eukaryotic chromosomes 55

6. School of Science and Technology, Online Counseling Resource… © 2009, YCMOU. All Rights Reserved.6 Introduction  Physical properties of chromosomes help in study of organisms’ genetic complexity.  Physical properties of eukaryotic chromosomes help in classification of eukaryotic organisms.  Physical properties help in defining a species of a eukaryotic organisms.  Physical properties of eukaryotic chromosomes include C value, melting temperature of DNA, DNA-DNA hybridization kinetics. 66

7. School of Science and Technology, Online Counseling Resource… © 2009, YCMOU. All Rights Reserved.7 C value-1  C value:- C value is defined as total amount of DNA in a haploid genome of a cell. C value is measured in picogram or in terms of base pairs or daltons. C value reflect the size of genome in terms of base pairs or molecular weight in daltons. Each species has his own characteristic c value which remain constant for his haploid cell. Eukaryotic organisms show remarkable variations in C value from species to species 77

8. School of Science and Technology, Online Counseling Resource… © 2009, YCMOU. All Rights Reserved.8 C value-2  In primitive cells of prokaryotic and eukaryotic cell there is some relationship between the complexity of cells and C value.  For example genome size of eukaryotic cell such as S. cerevisiae is five times than that of prokaryotic cell such E. coli.  However as the genome size increases above 8 x 10 7 bs the relationship between genome size and complexity of organisms vanishes. 88

9. School of Science and Technology, Online Counseling Resource… C Value-3  Cot curve:- cot 1/2 represents the total length of different nucleotide sequences of DNA. 9© 2009, YCMOU. All Rights Reserved.

10. School of Science and Technology, Online Counseling Resource… Cot Value-1  Relationship between genome size and DNA content 10© 2009, YCMOU. All Rights Reserved.

11. School of Science and Technology, Online Counseling Resource… © 2007, YCMOU. All Rights Reserved.11 Cot Value-2 Genes are also quantitated by estimating the Cot value of reassociation of two complementary DNA strands. When two complementary single strands are allowed to hybridize with each another at a particular temperature then product of initial concentration of DNA and time of incubation for reassociation of these DNA strands is characteristics for a fixed number of genes. This product of DNA and incubation time (C0 x t) is simply referred to as Cot value. 11

12. School of Science and Technology, Online Counseling Resource… © 2009, YCMOU. All Rights Reserved.12 Cot value-3 Cot 1/2 value is calculated at half the incubation time in reassociation reaction of two single stranded DNA. Cot value is indicated by following formula: 12

13. School of Science and Technology, Online Counseling Resource… © 2009, YCMOU. All Rights Reserved.13 Cot Value-4  The rate of reassociation of DNA single strands depends upon the concentration of complementary strands or in other words rate of reassociation depends upon the total length of different sequences present in the DNA.  The total length of different nucleotide sequences is referred to as complexity of DNA.  Cot 1/2 value represents the total length different nucleotide sequences in DNA molecule. 13

14. School of Science and Technology, Online Counseling Resource… Cot Value-5  Thus more the length of different nucleotide sequences more will be its Cot 1/2 value; therefore the Cot 1/2 value also reflects the genomic complexity expressed in terms of base pairs.  One can determine the genetic complexity of an unknown DNA by comparing its Cot 1/2 value with that of DNA whose complexity is known. 14 © 2009, YCMOU. All Rights Reserved.

15. School of Science and Technology, Online Counseling Resource… Cot Value-6  Usually genetic complexity of an unknown DNA can be determine by comparing its Cot 1/2 value with that of DNA of E. Coli. Which is 4.2 x 10 6 bp.  Cot curve is prepared by plottng the fraction of reassociated DNA against the log of Cot value; slope of this curve indicates the rate of reassociation of DNA strands. More the slope of the cot curve more is the rate of reassociation. 15 © 2009, YCMOU. All Rights Reserved.

16. School of Science and Technology, Online Counseling Resource… Cot Value-7  Cot curve of eukaryotic genome shows different phases indicating the presence of different segments of DNA with different rate of reassociation.  The first portion of this curve has fast rate of reassociation and is due to repeated sequences in the DNA, whereas the slow portion which represents the slow reassociation is due to unique different non-repeated nucleotide sequences. 16 © 2009, YCMOU. All Rights Reserved.

17. School of Science and Technology, Online Counseling Resource… © 2009, YCMOU. All Rights Reserved.17 C value Paradox-1  C value paradox:- As C value reflect the size of genome, it is obvious that all functions exhibited by a species should be proportional to the C value of the genome of that species; however there is no such relationship between the functions expressed by the species and C value of the genome of that species, this non-co- relationship between the C value and functions expressed is known as C value paradox. For example, in mammals actually there are roughly about 10,000 genes are expressed whereas estimate of gene functions calculated from C value come to be 30,000 to 40,000. 17

18. School of Science and Technology, Online Counseling Resource… © 2009, YCMOU. All Rights Reserved.18 C value paradox-2 C value paradox gives the inferences that there are actually thousands numbers of genes which either remain silence or genes intervening nucleotide sequences. These intervening nucleotide sequences or non-functional genes are known as introns. 18

19. School of Science and Technology, Online Counseling Resource… 19 What We learn…  C value of DNA  C value paradox  Cot analysis of DNA 19© 2009, YCMOU. All Rights Reserved.

20. School of Science and Technology, Online Counseling Resource… 20 Critical Thinking Questions  How complexity of genome is determined? 20© 2009, YCMOU. All Rights Reserved.

21. School of Science and Technology, Online Counseling Resource… 21 Hints for Critical Thinking Question  Cot analysis 21© 2009, YCMOU. All Rights Reserved.

22. School of Science and Technology, Online Counseling Resource… 22 Study Tips  Book Title: Molecular Biology of the Gene Title: Molecular Biology of the Gene Author: Author: Watson, baker et al. Publication: Publication: Pearson Education Ltd. Book Title: Genetics Title: Genetics Author: C. B. Pawar Author: C. B. Pawar Publication: Publication: -- © 2009, YCMOU. All Rights Reserved.

23. End of the Presentation Thank You ! 23 © 2009, YCMOU. All Rights Reserved.