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 • 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)

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

Nucleic acid componentsSugar http://www.mun.ca/biology/scarr/Fg10_09b_revised.gif

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

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

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

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

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

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

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

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

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

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

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

About DNA

Central dogma

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

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

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

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

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)

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

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

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

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

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

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

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

About central dogma

Protein

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

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

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

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

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

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

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

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

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

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

Protein structure hierarchy

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

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

Bioinformatics Programming