Introduction to Bioinformatics

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Introduction to Bioinformatics

• Yana Kortsarts
• References An Introduction to Bioinformatics
  Algorithms
• bioalgorithms.info

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What is Bioinformatics?

• Bioinformatics is a relatively new
  interdisciplinary field that integrates computer
  science, mathematics, biology, and information
  technology to manage, analyze, and understand
  biological, biochemical and biophysical
  information.
• Bioinformatics is a computational science and the
  subset of larger field of Computational Biology.

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What is Bioinformatics?

• Bioinformatics is the use of computers to study
  biology
• Bioinformatics is the science of using
  information to understand biology
• Bioinformatics is integration of information
  technology (IT) and biology
• Bioinformatics is the development of
  computational methods for studying structure,
  function and evolution of genes, proteins and
  whole genomes

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Course Curriculum

• Ethics, Computing and Genomics
• Review of Molecular Biology and Biochemistry
  Concepts
• DNA and protein structure
• Gene expression (transcription and translation)
• Molecular Biology Central Dogma
• Biological Research on the Web
• Public Biological Databases and Data Formats
• Searching Biological Databases

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Course Curriculum

• Introduction to Bioinformatics Algorithms
• Sequence alignments, scoring, gaps
• Algorithm Design Techniques Exhaustive Search,
  Dynamic Programming
• The Needleman and Wunsch Algorithm
• The Smith-Waterman Algorithm
• Introduction to BLAST
• Multiple Sequence Alignment
• Phylogenetic Trees
• Introduction to Python and Biopython in UNIX
  environment

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Some Terminology

• Cell is a primary unit of life
• Cell consists of molecules, chemical reactions
  and a copy of the genome for that organism
• All life on this planet depends on three types of
  molecules DNA, RNA and proteins

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Some Terminology

• DNA
• Holds information on how cell works
• RNA
• Acts to transfer short pieces of information to
  different parts of cell
• Provide templates to synthesize into protein
• Proteins
• Form enzymes that send signals to other cells and
  regulate gene activity
• Form bodys major components (e.g. hair, skin,
  etc.)

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DNA - Deoxyribonucleic Acid

• Genetic material
• Consists of two long strands
• Each strand is made of
• Phosphates
• Sugar
• Nucleotides
• A (adenine)
• G (guanine)
• C ( cytosine)
• T (thymine)

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DNA Double Helix Structure
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Discovery of DNA

• DNA Sequences
• Chargaff and Vischer, 1949
• DNA consisting of A, T, G, C
• Adenine, Guanine, Cytosine, Thymine
• Chargaff Rule
• Noticing A?T and G?C
• A strange but possibly meaningless phenomenon.
• Wow!! A Double Helix
• Watson and Crick, Nature, April 25, 1953
• Rich, 1973
• Structural biologist at MIT.
• DNAs structure in atomic resolution.

Crick Watson
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Watson Crick the secret of life

• Watson a zoologist, Crick a physicist
• In 1947 Crick knew no biology and practically no
  organic chemistry or crystallography..
  www.nobel.se
• Applying Chagraffs rules and the X-ray image
  from Rosalind Franklin, they constructed a
  tinkertoy model showing the double helix
• Their 1953 Nature paper It has not escaped our
  notice that the specific pairing we have
  postulated immediately suggests a possible
  copying mechanism for the genetic material.

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DNA The Basis of Life

• Deoxyribonucleic Acid (DNA)
• Double stranded with complementary strands A-T,
  C-G
• DNA is a polymer
• Sugar-Phosphate-Base
• Bases held together by H bonding to the opposite
  strand

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DNA, continued
Sugar
Phosphate
Base (A,T, C or G)
http//www.bio.miami.edu/dana/104/DNA2.jpg
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DNA, continued

• DNA has a double helix structure. However, it is
  not symmetric. It has a forward and backward
  direction. The ends are labeled 5 and 3 after
  the Carbon atoms in the sugar component.
• 5 AATCGCAAT 3
• 3 TTAGCGTTA 5
• DNA always reads 5 to 3 for transcription
  replication

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Double helix of DNA

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The Central Dogma of Molecular Biology

• Information has been transferred from DNA
  (information storage molecule) to RNA
  (information transfer molecule) to a specific
  protein (a functional, non-coding product)

transcription
translation
DNA
RNA
Protein
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DNA, RNA, and the Flow of Information
Replication
Translation
Transcription
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• Central Dogma
• (DNA?RNA?protein) The paradigm that DNA directs
  its transcription to RNA, which is then
  translated into a protein.
• Transcription
• (DNA?RNA) The process which transfers genetic
  information from the DNA to the RNA.
• Translation
• (RNA?protein) The process of transforming RNA to
  protein as specified by the genetic code.

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RNA

• RNA is similar to DNA chemically. It is usually
  only a single strand. T(hyamine) is replaced by
  U(racil)
• Some forms of RNA can form secondary structures
  by pairing up with itself. This can have
  change its properties dramatically.
• DNA and RNA
• can pair with
• each other.

http//www.cgl.ucsf.edu/home/glasfeld/tutorial/trn
a/trna.gif
tRNA linear and 3D view
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More Terminology

• Transcription of DNA
• DNA transcribed into RNA
• RNA exits as a single-strand unit and as a
  double-helix as well
• RNA consist of A, C, G and U (uracil)
• Types of RNA
• Messenger RNA mRNA
• Transfer RNA tRNA
• Ribosomal RNA rRNA

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More Terminology

• Translation of Messenger RNA (mRNA)
• mRNA is translated into protein
• Proteins
• linear polymers built from amino acids
• The transfer of information from DNA to specific
  protein via RNA takes place according to the
  genetic code.
• The RNA sequence is divided into blocks of three
  letters
• This block is called CODON
• Each codon corresponds to the specific amino acid
  

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More Terminology

• Four different nucleotides are used to build DNA
  and RNA molecules A, G, C, T and A, G, C, U
• 20 different amino acids are used in protein
  synthesis
• Four nucleotides can be arranged in 64 different
  combinations of three.
• There are 64 444 different codons
• Some codons are redundant and some have special
  function to terminate the translation process

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Translation

• The process of going from RNA to polypeptide.
• Three base pairs of RNA (called a codon)
  correspond to one amino acid based on a fixed
  table.
• Always starts with Methionine and ends with a
  stop codon

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Cell Information Instruction book of Life

• DNA, RNA, and Proteins are examples of strings
  written in either the four-letter nucleotide of
  DNA and RNA (A C G T/U)
• or the twenty-letter amino acid of proteins. Each
  amino acid is coded by 3 nucleotides called
  codon. (Leu, Arg, Met, etc.)

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Protein Synthesis Summary

• There are twenty amino acids, each coded by
  three- base-sequences in DNA, called codons
• This code is degenerate
• The central dogma describes how proteins derive
  from DNA
• DNA ? mRNA ? (splicing?) ? protein
• The protein adopts a 3D structure specific to
  its amino acid arrangement and function

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Proteins

• Complex organic molecules made up of amino acid
  subunits
• 20 different kinds of amino acids. Each has a 1
  and 3 letter abbreviation.
• http//www.ncbi.nlm.nih.gov/Class/MLACourse/Module
  s/MolBioReview/iupac_aa_abbreviations.html
• Proteins are often enzymes that catalyze
  reactions.
• Also called poly-peptides

Some other amino acids exist but not in humans.