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Bioinformatics Programming

Bioinformatics Programming. EE, NCKU Tien-Hao Chang (Darby Chang). Molecular biology. Nucleic acid DNA RNA Central dogma Transcription Translation Protein Amino acid Primary structure Secondary structure Tertiary structure. Nucleic acid.

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Bioinformatics Programming

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  1. Bioinformatics Programming EE, NCKU Tien-Hao Chang (Darby Chang)

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

  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)

  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

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

  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

  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 • The two types of base pairs form different numbers of hydrogen bonds, AT forming two hydrogen bonds, and GC forming three hydrogen bonds • Chargaff rule • A=T and G=C • DNA sequence • 5’CpGpCpApApTpT3’TpTpApApCpGpC • CGCGAATT

  11. http://openlearn.open.ac.uk/file.php/2645/S377_1_005i.jpg

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

  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

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

  15. http://courses.biology.utah.edu/horvath/biol.3525/1_DNA/Fig2/marty_1.jpghttp://courses.biology.utah.edu/horvath/biol.3525/1_DNA/Fig2/marty_1.jpg Major and minor grooves

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

  17. About DNA

  18. Central dogma

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

  20. 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 livingthings on Earth and is describedby the grandly named centraldogma of molecular biology • Information in cells passesfrom DNA to RNA to proteins http://upload.wikimedia.org/wikipedia/commons/3/3a/Crick's_1958_central_dogma.svg

  21. 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

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

  23. 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, from one molecule to the other • DNA sequence is enzymatically copied by RNA polymerase to produce a complementary nucleotide RNA strand, called messenger RNA (mRNA)

  24. DNA transcription http://www.youtube.com/watch?v=vJSmZ3DsntU

  25. Transcription detail http://www-class.unl.edu/biochem/gp2/m_biology/animation/m_animations/gene2.swf

  26. 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 • many RNAs do not code for protein • these non-coding RNA can be encoded by their own genes (RNA genes), but can also derive from mRNA introns • the most prominent examples of non-coding RNAs are transfer RNA (tRNA) and ribosomal RNA (rRNA), both of which are involved in the process of translation • there are also non-coding RNAs involved in gene regulation, RNA processing and other roles

  27. 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 • Many types of transcribed RNA, such as transfer RNA, ribosomal RNA, and small nuclear RNA are not necessarily translated into an amino acid sequence

  28. From RNA to protein synthesis http://www.youtube.com/watch?v=NJxobgkPEAo

  29. Protein translation http://www.youtube.com/watch?v=nl8pSlonmA0

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

  31. About central dogma

  32. Protein

  33. 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

  34. 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 • In the alpha amino acids, the amino and carboxylate groups are attached to the same carbon, which is called the α–carbon

  35. 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

  36. 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

  37. 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

  38. http://juang.bst.ntu.edu.tw/BC2008/images/Amino(1)%202007/A1-7.JPGhttp://juang.bst.ntu.edu.tw/BC2008/images/Amino(1)%202007/A1-7.JPG

  39. http://juang.bst.ntu.edu.tw/BC2008/images/Amino(1)%202007/A1-9.JPGhttp://juang.bst.ntu.edu.tw/BC2008/images/Amino(1)%202007/A1-9.JPG

  40. http://www.russell.embl-heidelberg.de/aas/other_images/lb3.gifhttp://www.russell.embl-heidelberg.de/aas/other_images/lb3.gif

  41. Amino acidThe building blocks of proteins • Amino acids combine in a condensation reaction that releases water and the new “amino acid residue” that is held together by a peptide bond • Proteins are defined by their unique sequence of amino acid residues; this sequence is the primary structure of the protein • Just as the letters of the alphabet can be combined to form an almost endless variety of words, amino acids can be linked in varying sequences to form a vast variety of proteins

  42. 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 Peptide bond

  43. 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

  44. 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

  45. 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 is known as translation, which is part of protein biosynthesis • Twenty amino acids are encoded by the standard genetic code and are called proteinogenic or standard amino acids

  46. Protein structure hierarchy

  47. 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

  48. 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

  49. 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

  50. http://juang.bst.ntu.edu.tw/BC2008/images/Protein(1)%202007/P1-9.JPGhttp://juang.bst.ntu.edu.tw/BC2008/images/Protein(1)%202007/P1-9.JPG

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