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

2. SEP-SBI074-CP2-01 Introduction Programmes and Courses SEP–SBI074-CP02-U02

3. School of Science and Technology, Online Counseling Resource… Credits  Academic Inputs by Sonali Alkari Faculty YCMOU Nagpur Centre, Faculty LAD college P.G. D of Biotechnology Research officer Ankur Seeds Pvt Ltd sonalisa_alkari@yahoo.co.in Sonalisaal@rediffmail.com

4. School of Science and Technology, Online Counseling Resource… © 2007, 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.

5. School of Science and Technology, Online Counseling Resource… © 2007, YCMOU. All Rights Reserved.5 Learning Objectives  After studying this module, you should be able to: Describe DNA in details Explain physical and chemical propreties of DNA Explain Major and minor grooves? Explain Base pairing Explain Sense and antisense Strand in DNA

6. School of Science and Technology, Online Counseling Resource… Introduction :DNA:1  Deoxyribonucleic acid, or DNA, is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms.  The main role of DNA molecules is the long-term storage of information and DNA is often compared to a set of blueprints, since it contains the instructions needed to construct other components of cells, such as proteins and RNA molecules.  The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in regulating the use of this genetic information.

7. School of Science and Technology, Online Counseling Resource… Introduction :DNA:2  Chemically, DNA is a long polymer of simple units called nucleotides, with a backbone made of sugars and phosphate groups joined by ester bonds.  Attached to each sugar is one of four types of molecules called bases.  It is the sequence of these four bases along the backbone that encodes information.  This information is read using the genetic code, which specifies the sequence of the amino acids within proteins.

8. School of Science and Technology, Online Counseling Resource… Introduction :DNA:3  The code is read by copying stretches of DNA into the related nucleic acid RNA, in a process called transcription.  Most of these RNA molecules are used to synthesize proteins, but others are used directly in structures such as ribosomes and spliceosomes.  Within cells, DNA is organized into structures called chromosomes and the set of chromosomes within a cell make up a genome.  These chromosomes are duplicated before cells divide, in a process called DNA replication.

9. School of Science and Technology, Online Counseling Resource… Physical and Chemical Properties:2  The sugar in DNA is 2-deoxyribose, which is a pentose (five carbon) sugar.  One of the major differences between DNA and RNA is the sugar, with 2-deoxyribose being replaced by the alternative pentose sugar ribose in RNA.

10. School of Science and Technology, Online Counseling Resource… Physical and Chemical Properties:3  The backbone of the DNA strand is made from alternating phosphate and sugar residues.  The sugars are joined together by phosphate groups that form phosphodiester bonds between the third and fifth carbon atoms of adjacent sugar rings.

11. School of Science and Technology, Online Counseling Resource… Physical and Chemical Properties:4  The DNA double helix is stabilized by hydrogen bonds between the bases attached to the two strands.  The four bases found in DNA are adenine (abbreviated A), cytosine (C), guanine (G) and thymine (T). Pyrimidine Bases:Cytosine and thymine

12. School of Science and Technology, Online Counseling Resource… Physical and Chemical Properties:5  These four bases are shown in figure and are attached to the sugar/phosphate to form the complete nucleotide, as shown for adenosine monophosphate.  Purines are the larger of the two types of bases found in DNA Purine Bases:Adenine and guanine are purines.

13. School of Science and Technology, Online Counseling Resource… Physical and Chemical Properties:6

14. School of Science and Technology, Online Counseling Resource… Physical and Chemical Properties:7  These asymmetric bonds mean a strand of DNA has a direction.  In a double helix the direction of the nucleotides in one strand is opposite to their direction in the other strand.  This arrangement of DNA strands is called antiparallel.  The asymmetric ends of DNA strands are referred to as the 5′ (five prime) and 3′ (three prime) ends.

15. School of Science and Technology, Online Counseling Resource… Major and Minor Grooves:2  The narrowness of the minor groove means that the edges of the bases are more accessible in the major groove.  As a result, proteins like transcription factors that can bind to specific sequences in double-stranded DNA usually make contacts to the sides of the bases exposed in the major groove.

16. School of Science and Technology, Online Counseling Resource… Base Pairing:1  Each type of base on one strand forms a bond with just one type of base on the other strand.  This is called complementary base pairing.  Here, purines form hydrogen bonds to pyrimidines, with A bonding only to T, and C bonding only to G.

17. School of Science and Technology, Online Counseling Resource… Base Pairing:2  This arrangement of two nucleotides binding together across the double helix is called a base pair.  In a double helix, the two strands are also held together via forces generated by the hydrophobic effect and pi stacking, which are not influenced by the sequence of the DNA.

18. School of Science and Technology, Online Counseling Resource… Sense and Antisense  A DNA sequence is called "sense" if its sequence is the same as that of a messenger RNA copy that is translated into protein.  The sequence on the opposite strand is complementary to the sense sequence and is therefore called the "antisense" sequence.  Both sense and antisense sequences can exist on different parts of the same strand of DNA (i.e. both strands contain both sense and antisense sequences).

19. School of Science and Technology, Online Counseling Resource… DNA Bending - 1  DNA bending has been found to affect transcription, which is the first step in gene expression.  Several studies have indicated the presence of bends in DNA upon binding of transcriptional proteins to DNA, such as the TATA box binding protein.  Studies have also shown that DNA bends can be created without proteins or created with proteins non-native to the system of interest.  There have been other studies done where it was shown that bends induced in DNA that were in the opposite direction of the naturally occurring bend inhibited transcription.

20. School of Science and Technology, Online Counseling Resource… DNA Bending - 2  This role of DNA bending in transcription leads to the hypothesis that small, man-made molecules could induce a bend in DNA, thus regulating gene expression, and this regulation could be either activating or repressing, depending on the phase (direction) of the bend.  The naturally occurring polyamides distamycin and netropsin bind sequence- specifically to DNA.

21. School of Science and Technology, Online Counseling Resource… DNA Bending - 3  DNA bending is also important for the regulation of gene expression and protein-DNA binding.  It is of fundamental importance therefore to understand the nature of the forces that govern the bending of charged DNA molecules into non-linear structures and quantify the magnitudes of their associated energetic factors.  Bending is important in DNA packaging and in regulating diverse cellular processes.

22. School of Science and Technology, Online Counseling Resource… DNA Bending - 4  DNA bending by proteins appears to be the rule rather than the exception with the topological distortions ranging from tens of degrees to nearly 720° in the nucleosome core.  The Escherichia coli integration host factor (IHF), discovered as a host protein required for lysogeny by bacteriophage, plays both of these roles.  IHF is an excellent model system for analyzing the mechanism by which proteins bend DNA by virtue of its cellular functions, sequence specificity, tight binding, and robust protein-induced DNA bending

23. School of Science and Technology, Online Counseling Resource… Integration Host Factor (IHF)  A depiction of the IHF–DNA crystal structure showing the protein subunits in pink (ß) and white () and the intercalating prolines in yellow.  Two segments of DNA from symmetry-related complexes within the crystal are included at the bottom to accommodate the full IHF footprint.  The attachment positions for the donor and acceptor fluorophores are indicated by arrows.

24. School of Science and Technology, Online Counseling Resource… What You Learn…  You have learnt : DNA, is a nucleic acid that contains the genetic instructions Chemically, DNA is a long polymer of simple units called nucleotides. The DNA double helix is stabilized by hydrogen bonds. The four bases found in DNA are A, C. G,and T. There are two grooves twisting around, i.e the major groove, the other, the minor groove. Both sense and antisense sequences can exist on different parts of the same strand of DNA

25. School of Science and Technology, Online Counseling Resource… Critical Thinking Questions 1.Describe in detail what is DNA? 2.Describe in details the physical and chemical properties of DNA. 3.Describe major groove and minor groove. 4.What is sense and antisense sequences? © 2007, YCMOU. All Rights Reserved.25

26. School of Science and Technology, Online Counseling Resource… Hints For Critical Thinking Question 1.DNA is structure composition organization and role. 2.DNA is a long polymer, sugar backbone, phosphate diester bonds and base pairing. 3.gaps between each set of phosphate backbones reposible for groove formation. 4.“ sense" sequence is the same as that of a messenger RNA copywhere as sequence on the opposite strand is “antisense” © 2007, YCMOU. All Rights Reserved.26

27. School of Science and Technology, Online Counseling Resource… Study Tips:1  Book1 Title: Molecular Cell Biology Author: Harvey Lodish, David Baltimore Publisher:Publishers: W. H. Freeman and Company  Book2 Title: Principles of Biochemistry Author: AlbertL Lehninger Publisher:CBS Publishers & Distributors

28. School of Science and Technology, Online Counseling Resource… Study Tips:2  Book3 Title: Biochemistry Author: Lubert stryer Publishers: Freeman International  Book4 Title: Biochemistry Author: Keshav Trehan Publishers: Wiley Eastern

29. School of Science and Technology, Online Counseling Resource… Study Tips www.en.wikipedia.org Microsoft Encarta Encyclopedia http://en.wikipedia.org/wiki/ Wikipedia the free encyclopedia

30. School of Science and Technology, Online Counseling Resource… End of the Presentation Thank You !