Principles of genetics

This PPT file includes the outline of the principles of genetics suitable for higher secondary and university level students.

1. Principles of Genetics Mohammad Rashed Lecturer Department of Fisheries Biology and Genetics

2. Lecture 1 Objective of the Course Genetics Gene Branches of Genetics Three great milestones of genetics Scope and significance of genetics

3. Objective To know the importance of studying genetics To know background of genetics To understand basic principles of genetics Applications of genetics To know gene expression Mutation and so on

4. Genetics The word genetics derived from the Greek root gen means to become or to grow into . it was first coined by William Bateson in 1906 for the study of physiology of heredity and variations. The biological science which deals with the phenomena of heredity , (i.e. transmission of traits from one generation to another) and variation (the study of the laws governing similarities and differences between individuals related by descents) is called genetics.

5. Gene A gene is the basic physical and functional unit of heredity Genes are made up of DNA Some genes act as instructions to make molecules called proteins However, many genes do not code for proteins

6. Microbial Genetics Branches of Genetics Mycogenetics Plant Genetics Animal Genetics Human Genetics Population Genetics Cytogenetics Biochemical Genetics Molecular Genetics Clinical Genetics Developmental Genetics Radiation Genetics Quantitative or biometric Genetics Ecological Genetics

7. Three great milestones of genetics Mendel: Genes and the rules of inheritance (1866) Watson and Crick: The structure of DNA (1953) The Human Genome Project: Sequencing DNA and Cataloguing Genes (1990)

8. Scope and significance of genetics

9. Lecture 2

10. DNA (Deoxyribonucleic Acid) Adenine (A) Guanine (G) Thymine (T) Cytosine (C)

11. Nucleoside vs Nucleotide Nucleoside = Sugar + Base Nucleotide = Sugar + Base + Phosphate

12. Antiparallel orientation

13. Complementary base pairs

14. The important features of Watson – Crick Model or double helix model of DNA are as follows- 1. The DNA molecule consists of two polynucleotide chains or strands that spirally twisted around each other and coiled around a common axis to form a right-handed double-helix. 2. The two strands are antiparallel i.e. they ran in opposite directions so that the 3′ end of one chain facing the 5′ end of the other. 3. The sugar-phosphate backbones remain on the outside, while the core of the helix contains the purine and pyrimidine bases.

15. 4. The two strands are held together by hydrogen bonds between the purine and pyrimidine bases of the opposite strands. 5. Adenine (A) always pairs with thymine (T) by two hydrogen bonds and guanine (G) always pairs with cytosine (C) by three hydrogen bonds. This complimentarily is known as the base pairing rule. Thus, the two stands are complementary to one another. 6. The base sequence along a polynucleotide chain is variable and a specific sequence of bases carries the genetic information. Continued

16. Continued 7. The base compositions of DNA obey Chargaff s rules (E.E. Chargaff, 1950) according to which A=T and G=C; as a corollary ∑ purines (A+G) = 2 pyrimidines (C+T); also (A+C) = (G+T). It also states that ratio of (A+T) and (G+C) is constant for a species (range 0.4 to 1.9)

17. 8. The diameter of DNA is 2.0 nm or 20 A. Adjacent bases are separated 0.34 nm or by 3.4 A along the axis. The length of a complete turn of helix is 3.4 nm or 34 A i.e. there are 10bp per turn. (B- DNA-Watson rick DNA) 9. The DNA helix has a shallow groove called minor groove (1.2nm) and a deep groove called major groove (2.2nm) across. Continued

18. DNA replication Molecular mechanism of DNA replication (Roles of DNA polymerases and other replication enzymes. Leading and lagging strands and Okazaki fragments)

19. Key points: DNA replication is semiconservative . Each strand in the double helix acts as a template for synthesis of a new, complementary strand. New DNA is made by enzymes called DNA polymerases , which require a template and a primer (starter) and synthesize DNA in the 5' to 3' direction.

20. Key points (Continued): During DNA replication, one new strand (the leading strand ) is made as a continuous piece. The other (the lagging strand ) is made in small pieces. DNA replication requires other enzymes in addition to DNA polymerase, including DNA primase, DNA helicase, DNA ligase, and topoisomerase .

21. DNA polymerase

22. Key features of DNA polymerases They always need a template They can only add nucleotides to the 3' end of a DNA strand They can't start making a DNA chain from scratch, but require a pre-existing chain or short stretch of nucleotides called a primer They proofread , or check their work, removing the vast majority of "wrong" nucleotides that are accidentally added to the chain

23. *The addition of nucleotides requires energy In prokaryotes such as E. coli , there are two main DNA polymerases involved in DNA replication: DNA pol III (the major DNA-maker), and DNA pol I , which plays a crucial supporting role

24. Starting DNA replication Origins of replication replication forks replication bubble

25. Helicase single-strand binding proteins Primers and primase RNA primer

26. Leading and lagging strands

27. The maintenance and cleanup crew Sliding clamp Topoisomerase

28. DNA polymerase I DNA ligase

29. Helicase opens up the DNA at the replication fork. Single-strand binding proteins coat the DNA around the replication fork to prevent rewinding of the DNA. Topoisomerase works at the region ahead of the replication fork to prevent supercoiling. Primase synthesizes RNA primers complementary to the DNA strand. DNA polymerase III extends the primers, adding on to the 3' end, to make the bulk of the new DNA. RNA primers are removed and replaced with DNA by DNA polymerase I. The gaps between DNA fragments are sealed by DNA ligase.

30. DNA Repair Mechanism

31. Proofreading DNA polymerases  are the enzymes that build DNA in cells During DNA replication (copying), most DNA polymerases can “check their work” with each base that they add. This process is called  proofreading If the polymerase detects that a wrong (incorrectly paired) nucleotide has been added, it will remove and replace the nucleotide right away, before continuing with DNA synthesis

32. Direct reversal Single-strand damage Base excision repair (BER) Nucleotide excision repair (NER) Mismatch repair Double-strand breaks Non-homologous end joining (NHEJ) Microhomology-mediated end joining (MMEJ) Homologous recombination (HR)

33. Direct reversal The formation of pyrimidine dimers upon irradiation with UV light results in an abnormal covalent bond between adjacent pyrimidine bases. Such direct reversal mechanisms are specific to the type of damage incurred and do not involve breakage of the phosphodiester backbone

34. Photolyase, an old enzyme present in bacteria , fungi , and most animals no longer functions in humans , who instead use nucleotide excision repair to repair damage from UV irradiation. The photoreactivation process directly reverses this damage by the action of the enzyme photolyase , whose activation is obligately dependent on energy absorbed from blue/UV light (300–500 nm wavelength) to promote catalysis. Direct reversal

35. Another type of damage, methylation of guanine bases , is directly reversed by the protein methyl guanine methyl transferase (MGMT) , the bacterial equivalent of which is called ogt . This is an expensive process because each MGMT molecule can be used only once; that is, the reaction is stoichiometric rather than catalytic . Direct reversal

36. Single-strand damage When only one of the two strands of a double helix has a defect, the other strand can be used as a template to guide the correction of the damaged strand. excision repair mechanisms

37. Base excision repair (BER) Base excision repair (BER) repairs damage to a single nitrogenous base by deploying enzymes called glycosylases . These enzymes remove a single nitrogenous base to create an apurinic or apyrimidinic site (AP site) . Enzymes called AP endonucleases nick the damaged DNA backbone at the AP site. DNA polymerase then removes the damaged region using its 5’ to 3’ exonuclease activity and correctly synthesizes the new strand using the complementary strand as a template.

38. Nucleotide excision repair (NER) Nucleotide excision repair (NER) repairs damaged DNA which commonly consists of bulky, helix-distorting damage, such as pyrimidine dimerization caused by UV light . Damaged regions are removed in 12–24 nucleotide-long strands in a three-step process which consists of recognition of damage , excision of damaged DNA both upstream and downstream of damage by endonucleases , and resynthesis of removed DNA region .

39. NER is a highly evolutionarily conserved repair mechanism and is used in nearly all eukaryotic and prokaryotic cells. In prokaryotes , NER is mediated by Uvr proteins . In eukaryotes , many more proteins are involved, although the general strategy is the same. Nucleotide excision repair (NER) (continued)

40. Mismatch repair These systems consist of at least two proteins . One detects the mismatch , and the other recruits an endonuclease that cleaves the newly synthesized DNA strand close to the region of damage. In E. coli , the proteins involved are the MUT class proteins . This is followed by removal of damaged region by an exonuclease , resynthesis by DNA polymerase, and nick sealing by DNA ligase.

41. Double-strand breaks Three mechanisms exist to repair double-strand breaks (DSBs) : Non-homologous end joining (NHEJ), Microhomology-mediated end joining (MMEJ), and Homologous recombination (HR)

42. Non-homologous end joining (NHEJ) In NHEJ , DNA Ligase IV , a specialized DNA ligase that forms a complex with the cofactor XRCC4 , directly joins the two ends . To guide accurate repair, NHEJ relies on short homologous sequences called microhomologies present on the single-stranded tails of the DNA ends to be joined.

43. Homologous recombination (HR) Homologous recombination requires the presence of an identical or nearly identical sequence to be used as a template for repair of the break. The enzymatic machinery responsible for this repair process is nearly identical to the machinery responsible for chromosomal crossover during meiosis. This pathway allows a damaged chromosome to be repaired using a sister chromatid (available in G2 after DNA replication) or a homologous chromosome as a template.

44. Unlike double-stranded DNA, RNA is a single-stranded molecule in many of its biological roles and consists of much shorter chains of nucleotides. However, a single RNA molecule can, by complementary base pairing, form intrastrand double helixes, as in tRNA . While the sugar-phosphate "backbone" of DNA contains deoxyribose, RNA contains ribose instead. Ribose has a hydroxyl group attached to the pentose ring in the 2' position, whereas deoxyribose does not. The hydroxyl groups in the ribose backbone make RNA more chemically labile than DNA by lowering the activation energy of hydrolysis. The complementary base to adenine in DNA is thymine, whereas in RNA, it is uracil, which is an unmethylated form of thymine. RNA

45. Thank You