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ELE4120 Bioinformatics
Tutorial Note 1
Outline
1. What is Bioinformatics?
2. Overview of Molecular Biology
3. Examples and Exercises
What is Bioinformatics? (1)
• Bioinformatics:
a) The collection, storage and analysis of biological information
using computers.
b) The creation of algorithms and computational techniques to
solve biological problems.
• Computational Biology and Bioinformatics are
interchangeable.
What is Bioinformatics? (1)
• Biological experiments
-in vivo : within a living organism
-in vitro : in an artificial environment
• Bioinformatics
In-silicon biology :from the silicon chips on which
microprocessors are built.
Common Terms in Molecular Biology
•Amino acids
•Proteins
•Chromosomes
•Nucleotides
•DNA
•RNA
Protein
3D
structure
Protein
Function
Amino
Acid
DNA
www.biotec.or.th/Genome/what_genome.html
Proteins and Amino Acids (1)
1.Proteins are made of amino acids
2.General form of amino acid:
The R group differs among different amino acid
3. 20 standard amino acids
Proteins and Amino Acids (2)
IUPAC code for Protein Sequence
20 standard amino acids codes
Tips:* The complement letters are: B,J,O,U,X,Z
Protein Sequence – Peptidic Bond
•Amino acids in proteins are linked by Peptidic bond (CO-NH)
which is formed between a NH2 group and a COOH group.
Protein Sequence – N to C (1)
•In a protein sequence, there is an unused NH2 at one
end and an unused COOH at the other end.
•N - terminus – extremity with the unused NH2
•C - terminus – extremity with the unused COOH
The constituent amino acids of a protein sequence are
listed from the N- terminus to the C- terminus.
Protein Sequence – N to C (2)
Examples :
Suppose the above sequence is a protein, its constituent
amino acids are listed as M-A-V-L-D, but not D-L-V-A-M
Protein 3D structure
•A protein sequence is not a
chain-like, but has a 3D structure
like a well-bundled ball of string.
•The 3D structure of a protein
depends on its sequence of
amino acids.
•The function of a protein
depends on its structure.
3D structure of a G-Actin (a protein)
http://en.wikipedia.org/wiki/Actin
Sequence
Structure
Function
Chromosomes
•Chromosomes are inside
nucleuses of cells
•Usually paired
•Human cell: 23 pairs of
chromosomes in a cell
•Numbers of chromosomes
are different for species:
Human(46), tobacco(48),
goldfish(94), chimp(48)
http://ghr.nlm.nih.gov/handbook/illustrations/normalkaryotype.jpg
DNA and Nucleotides
•DNA: Deoxyribonucleic Acid
•Double stranded molecule in the
shape of a double helix
•DNA is a macromolecule formed
by nucleotides
•4 types of nucleotides:
-Adenosine (A)
-Cytosine (C)
-Guanine (G)
-Thymine (T)
DNA in double helix form
http://ghr.nlm.nih.gov/handbook/illustrations/dnastructure
Nucleotides (1)
•A nucleotide consists of :
- A heterocyclic base
- A sugar
- A phosphate group
•Nucleotide bases:
- Purines (A and G)
- Pyrimidines (C and T)
The Nucleotide
http://img.sparknotes.com/figures/7/749a4182b7527e44d
289a612e420f40c/nucleotide.gif
Nucleotides (2)



Nucleotides are linked by
forming bond between the 5’
Phosphoryl and 3’ Hydroxyl.
Nucleotides in a DNA sequence
are listed from the 5’ (unused
PO4) to 3’ (unused OH) end.
Examples:
5’-ATGTTGGCA-3’
Double Stranded DNA
The 2 strands of a DNA molecule are :
- Complementary
- A T
- C G
- In opposite direction
5’ – A T G T C C G A – 3’
3’ – T A C A G G C T – 5’

RNA (1)

RNA: Ribonucleic Acid

Differences between the DNA and RNA:
1. DNA is deoxyribonucleic acid with deoxyribose sugar present
while RNA is ribonucleic acid with ribose sugar present.
2. DNA contains Thymine(T), but not Uracil(U), while RNA
contains Uracil buy not Thymine.
3. DNA has a double helix structure with two strands while RNA is
single- stranded.

Single-stranded RNA molecules are pairing different regions of
their sequence to form stable double-helical structure
RNA (2)
Examples
Question:
-Write the complementary sequence of the following nucleotide
sequence (in conventional order).
5’ – A T C G G T C A G C T G – 3’
Answer:
-Conventional order : 5’ to 3’
5’ – A T C G G T C A G C T G – 3’
5’ – C A G C T G A C C G A T – 3’