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Introductory terminologies and basic concepts in analysis of genes and genomes

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Introduction to genes, genomes, transcription, translation, polyploidy.

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Introductory terminologies and basic concepts in analysis of genes and genomes

  1. 1. Introductory terminologies and basic concepts in analysis of genes and genomes Presented by: Sarbesh D. Dangol (Genomics Lecture) 3/2/2016 Sarbesh D. Dangol, PhD Agricultural Genetic Engineering
  2. 2. Genome • The genome is all the DNA in a chromosome of the cell. – Includes genes, intergenic sequences, repeats. • Eukaryotes can have nuclear genome, mitochondrial genome, plastid genome. • If not specified, “genome” usually refers to the nuclear genome. 3/2/2016 Sarbesh D. Dangol, PhD Agricultural Genetic Engineering
  3. 3. Genomics • Genomics is the study of genomes, including large chromosomal segments containing many genes. • Map and sequence an initial set of entire genomes. • Functional genomics aims to deduce information about the function of DNA sequences. 3/2/2016 Sarbesh D. Dangol, PhD Agricultural Genetic Engineering
  4. 4. Central dogma of molecular biology: DNA  RNA  Protein 1. Genetic information is stored in DNA. 2. Segments of DNA that encode proteins or other functional products are called genes. 3. Gene sequences are transcribed into messenger RNA intermediates (mRNA). 4. mRNA intermediates are translated into proteins that perform most life functions. 3/2/2016 Sarbesh D. Dangol, PhD Agricultural Genetic Engineering
  5. 5. DNA • Deoxyribonucleic Acid • 4 Bases – Purines • Adenine • Guanine – Pyrimidines • Cytosine • Thymine • Sugar is Deoxyribose Adenine OH P H CH2O H O NH2 N N N N O O 3/2/2016 Sarbesh D. Dangol, PhD Agricultural Genetic Engineering
  6. 6. RNA • Ribonucleic Acid • 4 Nucleotides – Purine • Adenine • Guanine – Pyrimidines • Cytocine • Uracil* • Sugar is Ribose OHOH P H CH2O H O NH2 N N N N O O Adenine 3/2/2016 Sarbesh D. Dangol, PhD Agricultural Genetic Engineering
  7. 7. Proteins • Polymer made of monomers – Amino Acids • 20 Naturally occurring amino acids • Grouped by Side Chain: – Hydrophobic – Hydrophilic • Acidic • Basic OH O C C H N H H Side Chain Amino Acid 3/2/2016 Sarbesh D. Dangol, PhD Agricultural Genetic Engineering
  8. 8. Genes • Genes are the basic physical and functional units of heredity. • Each gene is located on a particular region of a chromosome and has a specific ordered sequence of nucleotides (the building blocks of DNA). 3/2/2016 Sarbesh D. Dangol, PhD Agricultural Genetic Engineering
  9. 9. The same gene can have many versions called alleles. • An allele is any alternative form of a gene. • It occurs at a specific locus on a chromosome. • Alleles are often represented by letters. 3/2/2016 Sarbesh D. Dangol, PhD Agricultural Genetic Engineering
  10. 10. – Each parent donates one allele for every gene. – Homozygous describes two alleles that are the same at a specific locus. – Heterozygous describes two alleles that are different at a specific locus. – Dominant allele. – Recessive allele. RR Rr 3/2/2016 Sarbesh D. Dangol, PhD Agricultural Genetic Engineering
  11. 11. Exons vs Introns • Eukaryotic genes have introns and exons. • Exons contain nucleotides that are translated into amino acids of proteins. • Exons are separated from one another by intervening segments of junk DNA called introns. • Introns do not code for protein. • They are removed when eukaryotic mRNA is processed. • Intron-free mRNA is used as a template to make proteins. 3/2/2016 Sarbesh D. Dangol, PhD Agricultural Genetic Engineering
  12. 12. Exons and Coding What’s the difference between exons and coding sequence? Portions of exons or even entire exons may contain sequence that is not translated into amino acids. These are the untranslated regions or UTRs. UTRs are found upstream and downstream of the protein-coding sequence. 3/2/2016 Sarbesh D. Dangol, PhD Agricultural Genetic Engineering
  13. 13. Splicing mechanism 3/2/2016 Sarbesh D. Dangol, PhD Agricultural Genetic Engineering
  14. 14. Alternative splicing 3/2/2016 Sarbesh D. Dangol, PhD Agricultural Genetic Engineering
  15. 15. Central dogma Sarbesh D. Dangol, PhD Agricultural Genetic Engineering 3/2/2016
  16. 16. General structure of a gene In Prokaryotes In Eukaryotes 3/2/2016 Sarbesh D. Dangol, PhD Agricultural Genetic Engineering
  17. 17. Translation in prokaryotes and eukaryotes In Eukaryotes In Prokaryotes 3/2/2016 Sarbesh D. Dangol, PhD Agricultural Genetic Engineering
  18. 18. 3/2/2016 Sarbesh D. Dangol, PhD Agricultural Genetic Engineering
  19. 19. Euchromatin: Lightly packed. Heterochromatin: Tightly packed. 3/2/2016 Sarbesh D. Dangol, PhD Agricultural Genetic Engineering
  20. 20. 3/2/2016 Sarbesh D. Dangol, PhD Agricultural Genetic Engineering
  21. 21. 3/2/2016 Sarbesh D. Dangol, PhD Agricultural Genetic Engineering
  22. 22. HATs and HMTs 3/2/2016 Sarbesh D. Dangol, PhD Agricultural Genetic Engineering
  23. 23. Function of promoter • RNA polymerase binding site • Initiation of transcription • control by regulatory sequences => control the expression of genes 3/2/2016 Sarbesh D. Dangol, PhD Agricultural Genetic Engineering
  24. 24. Prokaryotic promoters • - 35 box and – 10 box ( also called Pribnow box) are consensus sequences. 3/2/2016 Sarbesh D. Dangol, PhD Agricultural Genetic Engineering
  25. 25. Prokaryotic promoters • Possible to have variations in the consensus sequences. 3/2/2016 Sarbesh D. Dangol, PhD Agricultural Genetic Engineering
  26. 26. Eukaryotic promoters • There are two parts: - The core promoter or basal promoter - Upstream promoter element ( one or more) • Core promoter is constituted by the TATA box and the transcriptional start site (TSS) • Initation complex bind to the core promoter. • Upstream elements are responsible for the regulation of the transcription. 3/2/2016 Sarbesh D. Dangol, PhD Agricultural Genetic Engineering
  27. 27. Eukaryotic promoters 3/2/2016 Sarbesh D. Dangol, PhD Agricultural Genetic Engineering
  28. 28. • Polyploidy = the addition of one or more complete sets of chromosomes to the original set. • Two copies of each autosome = diploid • Four copies of each autosome = tetraploid • Six copies of each autosome = hexaploid Polyploidy 3/2/2016 Sarbesh D. Dangol, PhD Agricultural Genetic Engineering
  29. 29. Polyploidy • Polyploidy permits greater expression of genetic diversity. • Unreduced gametes. • Triploids/ Pentaploids are generally infertile. • Used to genetically deseed certain plant cultivars (eg-Triploid watermelon, banana). 3/2/2016 Sarbesh D. Dangol, PhD Agricultural Genetic Engineering
  30. 30. • Polyploidy refers to a numerical change in a whole set of chromosomes. • Polyploidy may occur due to abnormal cell division, either during mitosis, or commonly during metaphase I in meiosis. • Use of Colchicine or oryzaline. 3/2/2016 Sarbesh D. Dangol, PhD Agricultural Genetic Engineering
  31. 31. Bridging ploidy levels in interspecific crosses Purpose: For disease resistance, stress resistance, improved traits. (Wild) 3/2/2016 Sarbesh D. Dangol, PhD Agricultural Genetic Engineering
  32. 32. •Thank you.  3/2/2016 Sarbesh D. Dangol, PhD Agricultural Genetic Engineering

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