Agricultural Molecular Biology 555522

1. Agricultural Molecular Biology555522

2. Agricultural Molecular BiologyTeaching Team • ดร. อรรัตน์ มงคลพร เกษตร • ดร. คนึงนิตย์ เหรียญวรากร เกษตร • ดร. เสริมศิริ จันทร์เปรม เกษตร • ผศ. ดร. สนธิชัย จันทร์เปรม เกษตร • ดร. จุรีย์รัตน์ ชำนาญพันธ์ ศวท. • ดร. ธีระพล ศิรินฤมิตร สัตวแพทย์

3. Agricultural Molecular BiologyCourse Structure • Credit 3-0 : 45-hour program • Class schedules : Monday 9.00-10.30 Wednesday 9.00-10.30 CAB Lecture room 3rd floor • Evaluation : • Exam I, II, III 75%, TBA • Presentation 10% • Paper 10% • Class participation 5% • Grading system : Score-dependent

4. Agricultural Molecular BiologyCourse Textbooks • Genes VII, 2000. By Benjamin Lewin. • 5 Reserved books, KPS library • Molecular Biology, International Edition. 1999. By Weaver RE. • Genomes, 1999. By TA Brown

5. What is molecular biology? • A study of gene structure and function at the molecular level • Molecular biology grew out of the disciplines of genetics and biochemistry

6. A brief history • Transmission of genetics • Mendel’s law of inheritance • Chromosome theory of inheritance • Genetic recombination and mapping • Physical evidence for recombination • Molecular genetics • Discovery of DNA • Composition of genes • Relationship between genes and proteins • Activities of genes

7. Transmission of genetics 1856 Gregor Mendel: inheritance of 7 traits in garden pea

8. Mendel’s laws of inheritance>> principle of segregation • Genes exist in different forms called alleles. • One allele can be dominant over the other. • Mendel’s work: yellow seed > green seed parents yellow x green F1yellow selfed F2 3 yellow : 1 green

9. Mendel’s laws of inheritance>> principle of independent assortment • 7 genes operated independently • Combinations of 2 different genes 9:3:3:1

10. Chromosome theory of inheritance • 1900 rediscovery Mendel’s findings • First chromosome theory: • Thomas Hunt Morgan: fruit fly (Drosophilamelanogaster) red-eyed x white-eyed most red-eyed F1

11. red-eyed males x red-eyed females 1/4 white-eyed males + no white-eyed females • Eye color is sex-linked, X chromosome • male has 1 copy, female has 2 copies • Genes are located on chromosome : locus • Diploid organisms have 2 copies of chromosomes • homozygous and heterozygous • genotype • phenotype : wild-type vs mutant

13. Genetic recombination and mapping • Genes on separate chromosome behave independently, same chromosome behave as if they are linked • Genes on same chromosome not perfect linked • Eye color and miniature wing on X chromosome are 65.5% linked, with new combination ‘recombinants’ • Answer is recombination process, a crossing over between homologous chromosomes during meiosis • Sturtevant: mathematical relationship between the distance of genes and the recombination frequency • Barbara McClintock : physical evidence for recombination in maize chromosomes

15. Molecular genetics • DNA discovery : 1869 Friedrich Miescher - nuclein • deoxyribonucleic acid (DNA) • ribonucleic acid (RNA) and protein • Composition of genes • DNA or RNA or protein • Avery proved it was DNA • Bacteria transformation • virulent dead cells + avirulent living cells • Relationship : genes and protein

16. Molecular genetics • Relationship : genes and protein • How do genes work? • Human disease alcaptonuria -- black pigment in urine • Defective enzyme • A gene responsible for enzyme (protein) production • Activities of genes • How do genes work? • Genes replicate faithfully • Genes direct production of RNAs and proteins • Genes accumulate mutations and allow evolution

17. Replication • 1953 Watson and Crick • DNA structure is double helix • 4 bases composition : A, G, T and C • A - T, G- C • semiconservative replication

18. Production of polypeptides • Gene product is either RNA or polypeptides • gene expression • Transcription : a single copy of DNA strand (RNA) • Translation : protein production • mRNA carries genetic code to ribosomes • genetic code = codon consisting of 3 bases • 61 amino acids, 3 stop signals • Accumulate mutations • one base change -- sickle cell disease • deletions or insertions • transposon

19. Gene cloning • Isolate genes and place them in new organisms • Benefits : • raw materials for studies in molecular biology • protein product ie human insulin • Bt cotton

20. Genome structure and organisation>>what is genome? • Genome is the entire DNA content of a cell, including all of the genes and all the intergenic regions • Most genome are made of DNA • 2 types of living organisms • prokaryotes: cells lack extensive internal compartmetns • eukaryotes: cells contain membrane-bound compartments ie. Nucleus, mitochondria, chloroplast • animals, plants, fungi and protozoa are eukaryotes

23. Why are genome projects important

24. Why are genome projects important? • Genome sequences are the key to the continued development --opens the way to a comprehensive description of the molecular activities of living cells and the ways in which these activities are controlled • Gene catalog -- isolation and untilisation of important genes • Additional benefits -- study role of noncoding DNA • Challenge of unknown

25. Genomes of eukaryotes • Eukaryotic genome is split into 3 components • nuclear genome • mitochondrial genome • chloroplast genome

26. Human genome • made up of 2 components: nuclear and mitochondria

27. Human genome • nuclear genome: • 3000 Mb DNA • linear genome divided into 24 (22 autosomes + 2 sex chromosome, X and Y) • shortest 55 Mb and longest 250 Mb • mitochondrial genome: • circular DNA 16,569 bp

28. Human genome • immensity of human genome • analog with normal font size --60 nt = 10 cm • genome sequence stretch for 5,000 km

29. Nuclear genome • Genome size ranges <10 Mb to >100,000 Mb • size broadly coincides with organism complexity • larger genome --high repeats

30. Nuclear genome • Split into a set of linear DNA molecules -chromosomes • chromosome number not related to organism features

33. Where are genes in a genome?>>Human EST map --expressed sequence tags

34. Families of genes • Multigene family --groups of genes of identical or similar sequence • rRNA genes : 5S, 28S, 5.8S and 18S • globin gene families • alpha-globin family, on chr#16 • beta-globin family, on chr#11 • Supergene family • globin supergene family --alpha and beta evolve from a single ancestral globin gene

36. Pseudogenes • Genes which for one reason or another have become nonfunctional • conventional pseudogenes --inactivation by mutation ie. Create termination codon within coding region • processed pseudogenes -- abnormality during gene expression

37. Organelle genomes • Mitochondria and chloroplasts • Extra chromosomal genes --unusual inheritance patterns • Most mitochondrial and chloroplast genomes are circular

40. Genetic content of organelle genomes • Mitochondria display greater variability • number of genes : 12-92 • genes for mitochondrial rRNAs, protein components for respiratory chain • Chloroplasts are less variable • gene number ~ 200 • coding for rRNAs, tRNAs and ribosomal proteins and proteins involved in photosynthesis

42. Prokaryotic genome • Physical structure: size < 5 Mb • Genome is contained in a single circular DNA molecule in nucleoid • Circular E. coli chromosome circumference is 1.6 mm, while cell is 1x2 um

43. Supercoiling

44. Prokaryotic genome • Plasmid: small piece DNA, often circular, coexist with main chromosome in a bacteria cell • plasmids carry genes not present in main chromosome

45. Prokaryotic genome • Controversy: should plasmid be part of genome? • E. coli : main chromosme 4.6 Mb+ few kb of plasmid DNA which are not essential • Borrelia burgdorferi: 910 kb main chromosome carrying 853 genes + 17 linear and circular plasmids of 533 kb with 430 genes, some of which are essential

46. Prokaryotic genome • Genetic organisation: bacterial genomes have compact genetic organisations with little space between genes

48. Genetic organisation • Operons: an operon is a group of genes located adjacent to one another in the genome • All genes in an operon are expressed as a single unit