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Introduction to Bioinformatics

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Title: Introduction to Bioinformatics


1
Introduction to Bioinformatics
2
What is Bioinformatics
  • Easy Answer
  • Using computers to solve molecular biology
    problems Intersection of molecular biology and
    computer science
  • Hard Answer
  • Computational techniques (e.g. algorithms,
    artificial intelligence, databases) for
    management and analysis of biological data and
    knowledge

3
Bioinformatics
  • Bioinformatics Biology Information
  • Biology is becoming an information science
  • Computation methods are necessary to analyze the
    massive amount of information that coming out of
    the genome projects

4
Bioinformatics is Another Revolution in Biology
5
Three concepts, which remain central to
Bioinformatics
  • Data representation

A complex, dynamic, three-dimensional molecule
a simple string of characters
6
Three concepts, which remain central to
Bioinformatics
  • The concept of similarity
  • Evolution has operated on every sequence
  • In biomolecular sequences (DNA, RNA or amino acid
    sequences). High sequence similarity usually
    implies significant functional or structural
    similarity.
  • The opposite is not true
  • Algorithms for comparing sequences and finding
    similar regions are at the heart of bioinformatics

7
Three concepts, which remain central to
Bioinformatics
  • Bioinformatics is not a theoretical science it
    is driven by the data, which in turn is driven by
    the needs of biology.
  • Sequences
  • Microarray technologies

8
GenBank Growth
9
Moores Law
10
What do you need to know?
  • It all depends on your background
  • Are you a ?
  • Biologist with some computer knowledge, or
  • Computer scientist with some biology background
  • Few do both well

11
Background
  • Biology for Computer Scientists
  • Computer Science for Biologists

12
Biological Information Flow
Genome
Introns/Exons
Gene Sequence
Protein Sequence
Bioinformatics attempts to model this pathway
Protein Structure
Protein Functions
Cellular Pathways
13
Living Things
  • Entropy (the tendency to disorder) always
    increase
  • Living organisms have low entropy compared with
    things like soil
  • They are relatively orderly
  • The most critical task is to maintain the
    distinction between inside and outside

14
Living Things
  • In order to maintain low entropy, living
    organisms must expend energy to keep things
    orderly.
  • They figured out how to do this 4 billion years
    ago
  • The functions of life, therefore, are meant to
    facilitate the acquisition and orderly
    expenditure of energy

15
Living Things
  • The compartments with low entropy are separated
    from the world.
  • Cells are the smallest unit of such compartments.
  • Bacteria are single-cell organisms
  • Humans are multi-cell organisms

16
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17
The living things have the following tasks
  • Gather energy from environment
  • Use energy to maintain inside/outside distinction
  • Use extra energy to reproduce
  • Develop strategies for being successful and
    efficient at the above tasks
  • Develop ways to move around
  • Develop signal transduction capabilities (e.g.
    vision)
  • Develop methods for efficient energy capture
    (e.g. digestion)
  • Develop ways to reproduce effectively

18
How to accomplish?
  • Living compartments on earth have developed three
    basic technologies
  • Ability to separate inside from outside (lipids)
  • Ability to build three-dimensional molecules that
    assist in the critical functions of life
    (Protein, RNA)
  • Ability to compress the information about how
    (and when) to build these molecules in linear
    code (DNA)

19
Bioinformatics Schematic of a Cell
20
Lipids
  • Made of hydrophilic (water loving) molecular
    fragment connected to hydrophobic fragments
  • Spontaneously form sheets (lipid membranes) in
    which all the hydrophilic ends align on the
    outside, and hydrophobic ends align on the inside
  • Creates a very stable separation, not easy to
    pass through except for water and a few other
    small atoms/molecules

21
What is Nucleotide?
  • Pentose, base, phosphate group

22
Pentose RNA and DNA
23
Base
  • Adenine (A), Cytosine (C), Guanine (G), Thymine
    (T),
  • Uracil (U).

24
Nucleic Acid Chain
  • Condensation reaction
  • Orientation
  • From 5 to 3
  • In DNA or RNA, a nucleic acid chain is called
    Strand
  • DNA double-stranded
  • RNA a single strand
  • The number of bases
  • Base pair (bp) in DNA

25
DNA Structure
26
DNA Structure
27
DNA Structure
28
RNA Structure and Function
  • The major role of RNA is to participate in
    protein synthesis
  • Messenger RNA (mRNA)
  • Transfer RNA (tRNA)
  • Ribosomal RNA (rRNA)

29
mRNA
30
The Genetic Code
31
What is gene?
  • A gene includes the entire nucleic acid sequence
    necessary for the expression of its product.
  • Such sequence may be divided into
  • Regulatory region
  • Transcriptional region exons and introns
  • Exons encode a peptide or functional RNA
  • Introns will be removed after transcription

32
Gene
33
Genome
  • The total genetic information of an organism.
  • For most organisms, it is the complete DNA
    sequence
  • For RNA viruses, the genome is the complete RNA
    sequence

34
Genes and Control
  • Human genome has 3,000,000,000 bps divided into
    23 liner segments (chromosome)
  • A gene has an average 1340 DNA bps, thus
    specifying a protein of about ? (how many) amino
    acids
  • Humans have about 35,000 genes 40,000,000 DNA
    bps 3 of total DNA in genome
  • Human have another 2,960,000,000 bps for control
    information. (e.g. when, where, how long, etc)

35
Gene Expression
  • An organism may contain many types of cells, each
    with distinct shape and function
  • However, they all have the same genome
  • The genes in a genome do not have any effect on
    cellular functions until they are expressed
  • Different types of cells express different sets
    of genes, thereby exhibiting various shapes and
    functions

36
Gene Expression
  • The production of a protein or a functional RNA
    from its gene
  • Several steps are required
  • Transcription
  • RNA processing
  • Nuclear transport
  • Protein synthesis

37
Gene Expression
38
Central Dogma
DNA
RNA
Protein
Next Protein Structure and Function
39
An Amino Acid
  • An amino acid is defined as the molecule
    containing an amino group (NH2), a carboxyl group
    (COOH) and an R group.
  • R-CH(NH2)-COOH
  • The R group differs among various amino acids.
  • In a protein, the R group is also call a
    sidechain.

40
An Amino Acid
41
The Twenty Amino Acids of Proteins
42
The Twenty Amino Acids of Proteins
43
Protein
  • Peptide ? a chain of amino acids linked together
    by peptide bonds.
  • Polypeptides ? long peptides
  • Oligopeptides ? short peptides (lt 10 amino acids)
  • Protein are made up of one or more polypeptides
    with more than 50 amino acids

44
Protein Structure
  • Primary Structure
  • Refers to its amino acid sequence

45
Secondary structure
  • Regular, repeated patterns of folding of the
    protein backbone.
  • Two most common folding patterns
  • Alpha helix
  • Beta sheet

46
Tertiary Structure
  • The overall folding of the entire polypeptide
    chain into a specific 3D shape

47
Quaternary Structure
  • Many proteins are formed more than one
    polypeptide chain
  • Describe the way in which the different subunits
    are packed together to form the overall structure
    of the protein
  • Hemoglobin molecule

48
Quaternary Structure
49
Evolution
  • Mutation ? rare events, sometimes single base
    changes, sometimes larger events
  • Recombination ? how your genome was constructed
    as a mixture of your two parents
  • Through Natural Selection
  • Homology (similarity) different species are
    assumed to have common ancestors
  • The genetic variation between different people is
    (surprisingly ..)

50
References
  • http//www.biology.arizona.edu/biochemistry/proble
    m_sets/large_molecules/
  • http//helix-web.stanford.edu/bmi214/index2004.htm
    l
  • http//www.web-books.com/MoBio/
  • http//www.cs.sunysb.edu/skiena/549/
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