introtobioinfo

1. Introduction to Bioinformatics
Yana Kortsarts
References: An Introduction to Bioinformatics
Algorithms
bioalgorithms.info

2. 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.

3. 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

4. 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

5. 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

6. 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

7. 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 body’s major components (e.g. hair, skin,
etc.)

8. 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)

9. DNA – Double Helix Structure

10. 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.
 DNA’s structure in atomic resolution. Crick Watson
1 Biologist
1 Physics Ph.D. Student
900 words
Nobel Prize

11. 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 Chagraff’s 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.”
Watson & Crick with DNA model
Rosalind Franklin with X-ray image of DNA

12. 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

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

14. 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

15. Double helix of DNA

16. 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)
DNA RNA Protein
transcription translation

17. DNA, RNA, and the Flow of Information
Translation
Transcription
Replication

18.  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.

19. 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/trna/trna.gif
tRNA linear and 3D view:

20. 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

21. 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

22. 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 = 4*4*4 different codons
 Some codons are redundant and some have
special function – to terminate the translation
process

23. 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

24. 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.)

25. 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 it’s amino
acid arrangement and
function

26. 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/MLACours
e/Modules/MolBioReview/iupac_aa_abbreviat
ions.html
Proteins are often enzymes that catalyze reactions.
 Also called “poly-peptides”
*Some other amino acids exist but not in humans.