Sevas Educational Society All Rights Reserved, 2008 Module 1 Introduction to Bioinformatics.

Sevas Educational SocietyAll Rights Reserved, 2008

Module 1

Introduction to Bioinformatics


What is Life made of?


Life begins with Cell

• A cell is a smallest structural unit of an organism that is capable of independent functioning

• All cells have some common features


All Life depends on 3 critical molecules

• DNAs• RNAs• Proteins


DNA: The Code of Life

• Adenine (A), Guanine (G), Thymine (T), and Cytosine (C) which pair A-T and C-G to form DNA and these molecules are called as nucleic acids.

See Next Slide for More about DNA….


DNA: The Basis of Life

• Deoxyribonucleic Acid (DNA)– Double stranded with two strands A-T, C-G

• DNA is a polymer– Sugar-Phosphate-Base– Bases held together by Hydrogen bonding to the

opposite strand


DNA, continued• DNA has a double

helix structure which composed of – sugar molecule– phosphate group– and a base (A,C,G,T)

A - Adenine

C - Cytosine

G - Guanine

T - Thymine


DNA: The basis of Life

DNA is Present in Chromosome

The figure shows how DNA is packed in chromosome….


Central Dogma of BiologyThe information for making proteins is stored in DNA. There is a process (transcription and translation) by which DNA is converted to protein.

DNA

RNA

Protein

Transcription (the process of formation of RNA from DNA)

Translation (the process of formation of protein from RNA)


RNA• RNA is similar to DNA chemically. It is usually only a

single strand. DNA and RNA are similar in structure with one difference. DNA consists of Adenine (A), Guanine (G), Thymine (T), and Cytosine (C) and RNA consists of Uracil (U), adenine (A), Guanine (G) & Cytosine (C).

Only difference is T(hyamine) is replaced by U(racil) and it is single strand & DNA is double strand.


Several types of RNA exists as mRNA, tRNA & rRNA and each has its own significance.

Definition of a GeneThe important part of DNA, which is responsible for “RNA and protein” formation is called “Gene” and Gene consists of two parts

1. Exons:

2. Introns:


Formation of RNA from a gene (gene is always present in DNA)

The process of breaking all introns to form mRNA is called “splicing” & the most important region in mRNA which is reponsible for protein formation is called “Open Reading Frame”.


Protein:

Complex organic molecules made up of amino acid subunits.

Protein is formed from 20 different kinds of amino acids. Each has a 1 and 3 letter abbreviation.

Protein is also called as “polypeptide”


Combination of two or more amino acids can be called as proteins or poly peptides.


RNA Protein: TranslationmRNA (messenger RNA) passes through ribosome (A small organ in a cell) and three nucleic acids present in mRNA will produce one amino acid and those three nucleic acids are called codons. In the figure you can see UUC, GGA etc…. are coding for group of amino acids.

Codon table is provided in the next slide which tells which codon codes for which proteins.


RNA Protein: TranslationProtein is formed from RNA and three molecules in RNA, called as codons, are responsible for producing one amino acid present in a protein. As the codon number increases the formation of bigger proteins takes place.

UUA ----- Leucine

CGA ---- Arginine

UAG --- Stop Codon or

no amino acid

UGG -- Tryptophan.

RNA codon ----- Amino Acid


For more explanation (How protein is formed from mRNA)

mRNA

tRNA enters into ribosome by carriing one amino acid (in this case it is carrying valine)

As the amino acids number increases the formation of protein takes place.

(In the figure you can observe a protein consisting eight amino acids)


Proteins are represented by single letter alphabets... (by using the table present in 14th slide)

Write down the name of corresponding amino acids

AGASPFMKLKKAGAKAHLKMSHFWYVHSIL

Example: A – alanine

G - Glycine


DNA consists of four nucleotides Adenine, guanine, cytosine and thymine (and they are represented by single letter alphabets.

Adenine ------- AGuanine ------- GCytosine ------- CThymine ------- T

Write down the names of nucleotides present in DNA

“AAAGAGACGTACGACGAGCGC”

Like: Adenine-Adenine-Adenine-Guanine-………..


We all know that three Nucleotides codes for single amino acid then for example like "UUU" codon produces "Phenylalanine Amino Acid“.

By using the above table find the protein sequence of the following RNA starting from first "A" only.

AAGAGARGACGUGCGACGACGUCGAGUCAAAAACGUCGA

Clue: AAG ---- See the corresponding amino acid in the above table

it is “Lys” or “K”…. Like wise select three codons and

get amino acids


Bioinformatics is generally defined as the analysis, prediction, and modeling of biological data with the help of computers

Bioinformatics:

What is biological data and how to put protein into computer?

Biological data is nothing but protein and nucleic acid sequences represented by alphabets.

Example: Protein Sequence

(consists twenty amino acids)

AAGHWTILKWGRSH

DNA sequence (Consists four nuclic acids)

AAGAGTCGCGAGAGGACG


What is Computational Biology?

This branch of biology involves the use of techniques including applied mathematics, informatics, statistics, computer science, artificial intelligence, chemistry, and biochemistry to solve biological problems usually at the molecular level.


Bioinformatics is multidisciplinary

Genomics

Molecular evolution

BiophysicsMolecular

biology

Biomedicine

Ethical, legal, and social

implications

Bioinformatics

Mathematics/computer science


CGCCAGCTGGACGGGCACACCATGAGGCTGCTGACCCTCCTGGGCCTTCTGTGTGGCTCGGTGGCCACCCCCTTAGGCCCGAAGTGGCCTGAACCTGTGTTCGGGCGCCTGGCATCCCCCGGCTTTCCAGGGGAGTATGCCAATGACCAGGAGCGGCGCTGGACCCTGACTGCACCCCCCGGCTACCGCCTGCGCCTCTACTTCACCCACTTCGACCTGGAGCTCTCCCACCTCTGCGAGTACGACTTCGTCAAG

From chromosomes to sequence data

Large scale DNA sequencing


Genome: In biology the genome of an organism is its whole hereditary information and is encoded in the DNA (or, for some viruses, RNA). Genomes can be represented as base pairs (AT or CG) of nucleic acids.

Human Genome consists of 3 Billion Base Pairs.

etc…….

Genomics is the study of an organism's entire genome. The field includes intensive efforts to determine the entire DNA sequence of organisms.

Some Terminology……..


Genomics generates a vast amount of DNA sequence data. Sophisticated algorithms are used to predict gene regions. Only ~3% of the vertebrate genome codes for proteins.

Genome sequencing and analysis (genomics)

Genbank hold sequences from over 800 organisms. There are currently 113 complete genomes.

The completion of a "working draft" of the human genome was announced in June 2001.

•Estimates of 38 - 120,000 genes (40, 000)


ORGANISM CHROMOSOMES GENOME SIZE GENES

Homo sapiens (Humans)

23 3,200,000,000 ~ 30,000

Mus musculus(Mouse)

20 2,600,000,000 ~30,000

Drosophila melanogaster

(Fruit Fly)

4 180,000,000 ~18,000

Saccharomyces cerevisiae (Yeast)

16 14,000,000 ~6,000

Zea mays (Corn) 10 2,400,000,000 ???

Genome Size as in base pairs….


1. Draw the figure present in sixth slide?

2. Draw the table giving proteins (14th slide)

3. Search what is tRNA in google.com

4. Literature Collection: Type www.google.com in the web site. Type NCBI home page in the google Go to home page of NCBI Click on pubmed in the search space and type any key word you are

interested in to look for, for eg., lung cancer, human genome project, polymerase, immunoglobins etc.

Window will display your result Click on each of the result to read abstract or full text of your interest.

5. Go to www.answers.com and type transcription and see the explanation.

6. Go to google.com and type “ppt introduction to bioinformatics” and collect more than five powerpoint presentation.

(if you add ppt to any keywork you will get PowerPoint presentations)


Reference:

1. http://en.wikipedia.org/wiki/Bioinformatics

2. PowerPoint Slides from internet

http://www.bioalgorithms.info/presentations.old/Ch03_Molecular_Biology_Primer.ppt

Date post:	16-Jan-2016
Category:	Documents
Upload:	ami-charles
View:	213 times
Download:	0 times

Sevas Educational Society All Rights Reserved, 2008 Module 1 Introduction to Bioinformatics.

Documents