1 / 67

Machine Learning & Bioinformatics: Nucleic Acid Structure and Central Dogma

Learn about the structure and function of nucleic acids, including DNA and RNA, and understand the central dogma of molecular biology. This topic is essential for machine learning and bioinformatics.

rogertorres
Download Presentation

Machine Learning & Bioinformatics: Nucleic Acid Structure and Central Dogma

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Machine Learning and Bioinformatics機器學習與生物資訊學 Machine Learning & Bioinformatics

  2. Molecular biology • Nucleic acid • DNA • RNA • Central dogma • Transcription • Translation • Protein • Amino acid • Primary structure • Secondary structure • Tertiary structure Machine Learning & Bioinformatics

  3. Nucleic acid • A nucleic acid is a macromolecule composed of chains of monomeric nucleotide • In biochemistry these molecules carry genetic information or form structures within cells • The most common nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) Machine Learning & Bioinformatics

  4. http://juang.bst.ntu.edu.tw/BC2008/images/NA%20Fig1.jpg

  5. Nucleic acid componentsSugar http://www.mun.ca/biology/scarr/Fg10_09b_revised.gif Machine Learning & Bioinformatics

  6. Nucleic acid componentsBase • Purine • Adenine (A) and guanine (G) • Pyrimidine • Thymine (T), cytosine (C) • Uracil (U, only in RNA) Machine Learning & Bioinformatics

  7. http://www.elmhurst.edu/~chm/vchembook/images/580bases.gif

  8. http://fig.cox.miami.edu/~cmallery/150/chemistry/sf3x14a.jpg

  9. DNA • 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 oneof four types of moleculescalled bases • It is the sequence of these fourbases along the backbone thatencodes information http://upload.wikimedia.org/wikipedia/commons/8/87/DNA_orbit_animated_small.gif Machine Learning & Bioinformatics

  10. DNABase pairing • Each type of base on one strand forms a bond with just one type of base on the other strand • Here, purines form hydrogen bonds to pyrimidines, with A bonding only to T, and C bonding only to G • DNA sequence • 5’CpGpCpApApTpT3’TpTpApApCpGpC • CGCGAATT Machine Learning & Bioinformatics

  11. http://www.ucl.ac.uk/~sjjgsca/NucleotidePairing.jpg

  12. Double helix http://www.coe.drexel.edu/ret/personalsites/2005/dayal/curriculum1_files/image001.jpg

  13. Hydrogen bond • A hydrogen bond exists between an electronegative atom and a hydrogen atom bonded to another electronegative atom • This type of force always involves a hydrogen atom and the energy of this attraction is close to that of weak covalent bonds (155 kJ/mol), thus the name – Hydrogen Bonding • Biological functions • DNA/RNA base paring • protein secondary/tertiary structure formation • some properties of water molecule • antibody-antigen (and other protein-protein) binding Machine Learning & Bioinformatics

  14. Hydrogen bond is resulted from electronegativity http://upload.wikimedia.org/wikipedia/commons/4/43/Liquid_water_hydrogen_bond.png

  15. Grooves http://courses.biology.utah.edu/horvath/biol.3525/1_DNA/Fig2/marty_1.jpg

  16. DNA structure http://www.youtube.com/watch?v=qy8dk5iS1f0&NR=1 Machine Learning & Bioinformatics

  17. About DNA Machine Learning & Bioinformatics

  18. Central dogma http://fig.cox.miami.edu/~cmallery/255/255hist/mcb4.1.dogma.jpg

  19. Central dogma • The process by witch information is extracted from the nucleotide sequence of a gene and then used to make a protein is essentially the same for all living things on Earthand is described by the grandlynamed central dogma ofmolecular biology • Information in cells passes fromDNA to RNA to proteins http://upload.wikimedia.org/wikipedia/commons/3/3a/Crick's_1958_central_dogma.svg Machine Learning & Bioinformatics

  20. RNA • Information stored from DNA is used to make a more transient, single-stranded polynucleotide called RNA (Ribonucleic Acid) • RNA is very similar to DNA, but differs in a few important structural details • in the cell RNA is usually single stranded, while DNA is usually double stranded • RNA nucleotides contain ribose while DNA contains deoxyribose (a type of ribose that lacks one oxygen atom) • in RNA the nucleotide uracil substitutes for thymine, which is present in DNA Machine Learning & Bioinformatics

  21. http://www.dadamo.com/wiki/dna-rna.png

  22. Central dogmaTranscription • Transcription is the synthesis of RNA under the direction of DNA • Both nucleic acid sequences use the same language, and the information is simply transcribed, or copied • DNA sequence is copied by RNA polymerase to produce a complementary nucleotide RNA strand, called messenger RNA (mRNA) Machine Learning & Bioinformatics

  23. DNA transcription http://www.youtube.com/watch?v=vJSmZ3DsntU Machine Learning & Bioinformatics

  24. Transcription detail http://www-class.unl.edu/biochem/gp2/m_biology/animation/m_animations/gene2.swf Machine Learning & Bioinformatics

  25. RNAVarious types • mRNA • messenger RNA (mRNA) is the RNA that carries information from DNA to the ribosome • the coding sequence of the mRNA determines the amino acid sequence in the protein that is produced • Non-coding RNA Machine Learning & Bioinformatics

  26. Various RNA typesNon-coding RNA • Many RNAs do not code for protein • These ncRNAs encode in specific genes (RNA genes) or mRNA introns • The most common ncRNAs are transfer RNA (tRNA) and ribosomal RNA (rRNA) • Other ncRNAs such as microRNA (miRNA) involve in post-transcriptional gene regulation Machine Learning & Bioinformatics

  27. http://eurheartj.oxfordjournals.org/content/vol0/issue2010/images/large/ehp57301.jpeghttp://eurheartj.oxfordjournals.org/content/vol0/issue2010/images/large/ehp57301.jpeg

  28. Central dogmaTranslation • Translation is the second stage of protein biosynthesis • Translation occurs in the cytoplasm where the ribosomes are located • In translation, mRNA is decoded to produce a specific polypeptide according to the rules specified by the genetic code Machine Learning & Bioinformatics

  29. From RNA to protein synthesis http://www.youtube.com/watch?v=NJxobgkPEAo Machine Learning & Bioinformatics

  30. Protein translation http://www.youtube.com/watch?v=nl8pSlonmA0 Machine Learning & Bioinformatics

  31. http://biology.kenyon.edu/courses/biol114/Chap05/code.gif

  32. About central dogma Machine Learning & Bioinformatics

  33. Protein Machine Learning & Bioinformatics

  34. Protein • Proteins are large organic compounds made of amino acids arranged in a linear chain and joined together by peptide bonds between the carboxyl and amino groups of adjacent amino acid residues • Proteins can also work together to achieve a particular function, and they often associate to form stable complexes Machine Learning & Bioinformatics

  35. ProteinAmino acid • In chemistry, an amino acid is a molecule that contains both amine and carboxyl functional groups • In biochemistry, this term refers to alpha-amino acids with the general formula H2NCHRCOOH, where R is an organic substituent Machine Learning & Bioinformatics

  36. http://upload.wikimedia.org/wikipedia/commons/thumb/c/ce/AminoAcidball.svg/702px-AminoAcidball.svg.pnghttp://upload.wikimedia.org/wikipedia/commons/thumb/c/ce/AminoAcidball.svg/702px-AminoAcidball.svg.png

  37. Amino acidVarious side chains • The various alpha amino acids differ in which side chain (R group) is attached to their alpha carbon • They can vary in size from just a hydrogen atom in glycine through a methyl group in alanine to a large heterocyclic group in tryptophan Machine Learning & Bioinformatics

  38. http://upload.wikimedia.org/wikipedia/commons/thumb/3/37/Aa.svg/2000px-Aa.svg.pnghttp://upload.wikimedia.org/wikipedia/commons/thumb/3/37/Aa.svg/2000px-Aa.svg.png

  39. http://juang.bst.ntu.edu.tw/BC2008/images/Amino%281%29%202007/A1-7.JPGhttp://juang.bst.ntu.edu.tw/BC2008/images/Amino%281%29%202007/A1-7.JPG

  40. http://juang.bst.ntu.edu.tw/BC2008/images/Amino%281%29%202007/A1-9.JPGhttp://juang.bst.ntu.edu.tw/BC2008/images/Amino%281%29%202007/A1-9.JPG

  41. http://www.russell.embl-heidelberg.de/aas/other_images/lb3.gifhttp://www.russell.embl-heidelberg.de/aas/other_images/lb3.gif Machine Learning & Bioinformatics

  42. Amino acidThe building blocks of proteins • Amino acids combine in a condensation reaction and the new “amino acid residue” are held together by peptide bonds • Proteins are defined by their unique sequence of residues (primary structure) • As the letters form various words, amino acids form a vast variety of sequences/proteins Machine Learning & Bioinformatics

  43. http://upload.wikimedia.org/wikipedia/commons/thumb/6/6d/Peptidformationball.svg/2000px-Peptidformationball.svg.pnghttp://upload.wikimedia.org/wikipedia/commons/thumb/6/6d/Peptidformationball.svg/2000px-Peptidformationball.svg.png

  44. http://juang.bst.ntu.edu.tw/BC2008/images/Amino(1)%202007/A1-11.JPGhttp://juang.bst.ntu.edu.tw/BC2008/images/Amino(1)%202007/A1-11.JPG

  45. http://juang.bst.ntu.edu.tw/BC2008/images/Amino(1)%202007/A1-13.JPGhttp://juang.bst.ntu.edu.tw/BC2008/images/Amino(1)%202007/A1-13.JPG

  46. ProteinAfter knowing amino acids • Amino acids form short polymer chains called peptides or longer chains called either polypeptides or proteins • The process of such formation from an mRNA template (obeying genetic code) is known as translation, which is part of protein biosynthesis Machine Learning & Bioinformatics

  47. Protein structure hierarchy Machine Learning & Bioinformatics

  48. http://cropandsoil.oregonstate.edu/classes/css430/lecture%209-07/figure-09-03.JPGhttp://cropandsoil.oregonstate.edu/classes/css430/lecture%209-07/figure-09-03.JPG

  49. http://juang.bst.ntu.edu.tw/BC2008/images/Protein(1)%202007/P1-4.JPGhttp://juang.bst.ntu.edu.tw/BC2008/images/Protein(1)%202007/P1-4.JPG

  50. http://juang.bst.ntu.edu.tw/BC2008/images/Protein(1)%202007/P1-8.JPGhttp://juang.bst.ntu.edu.tw/BC2008/images/Protein(1)%202007/P1-8.JPG

More Related