Tutorial Note 1

1. What is Bioinformatics?
2. Overview of Molecular Biology
3. Examples and Exercises

• 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.

• 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.

•Amino acids
•Proteins
• Chromosomes
• Nucleotides
• DNA
• RNA
Amino
Acid
DNA
Protein
3D structure
Protein
Function 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 NH
2 group and a COOH group.

Protein Sequence – N to C (1)
•In a protein sequence, there is an unused NH
2 at one end and an unused COOH at the other end.
•N - terminus – extremity with the unused NH
2
•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 are linked by forming bond between the 5’
Phosphoryl and 3’ Hydroxyl.

Nucleotides in a DNA sequence are listed from the 5’ (unused
PO
4
) to 3’ (unused OH) end.

Examples:
5’-ATGTTGGCA-3’


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: 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

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’