Bioinformatics

Lecture 2

Bioinformatics: is the computational branch of molecular

biology

Using the computer software to analyze biological data

The term in silico biology

The course theme

Lecture will emphasize the biological concept

Lab will use hand on experience to manipulate bioinformatic techniques to analyze this

biological concept

Course grading system

Weekly quizzes: 10 pts each Mid term exam: 50 ptsFinal exam: 100 ptsOral presentation : 20 pointsFour internet assignments: 10 pts eachAttendance 5 pts / lecture and lab i.e 2.5 pts each /week

Structure of DNA

Deoxyribonucleic Acid (DNA)Deoxyribonucleic Acid (DNA) Double-stranded Double-stranded

helical molecule helical molecule found in the nucleus found in the nucleus of the cellof the cell

Replicates itself Replicates itself before the cell before the cell divides, ensuring divides, ensuring genetic continuitygenetic continuity

Provides instructions Provides instructions for protein synthesisfor protein synthesis

Chemical structure of DNAChemical structure of DNA

Composed of carbon, oxygen, hydrogen, Composed of carbon, oxygen, hydrogen, nitrogen, and phosphorusnitrogen, and phosphorus

DNA is a polymerDNA is a polymer its structural unit is the its structural unit is the nucleotide nucleotide

composed of nitrogenous base composed of nitrogenous base a pentose sugar, a pentose sugar, a phosphate groupa phosphate group

Chemical structure of DNAChemical structure of DNANitrogenous bases Nitrogenous bases

Chemical structure of DNAChemical structure of DNA

Chemical structure of DNAChemical structure of DNA

Reading the DNA molecule is from the 5` to 3`

Base pairing of DNABase pairing of DNA

Chargaff's rules:Chargaff's rules: • • The amount of adenine equals that of The amount of adenine equals that of

thymine: [A] = [T].thymine: [A] = [T]. • • The amount of guanine equals that of The amount of guanine equals that of

cytosine:[G] = [C]cytosine:[G] = [C] [A] + [G] = [T]+ [C][A] + [G] = [T]+ [C]

The amount of purine base equals that of The amount of purine base equals that of pyrimidine bases:pyrimidine bases:

True or falseTrue or false

The amount of purine base equals that of The amount of purine base equals that of pyrimidine bases in any DNA moleculespyrimidine bases in any DNA molecules

DNA is composed of 2 strandsDNA is composed of 2 strands

Forward ( 5`-3`)Forward ( 5`-3`) Reverse ( 3`-5`)Reverse ( 3`-5`) By knowing the sequence of one strand can By knowing the sequence of one strand can

you deduce the sequence of the other ? you deduce the sequence of the other ?

How DNA is replicated in living How DNA is replicated in living cells?cells?

DNA content and the number of DNA content and the number of genes genes

DNA content is DNA content is constant constant among the same among the same species but it varies among different species but it varies among different speciesspecies

This is Known as C- value This is Known as C- value

C- value paradoxC- value paradox

In prokaryotes the number of genes is In prokaryotes the number of genes is somehow correlated with the DNA content somehow correlated with the DNA content but this case does not apply to eukaryotesbut this case does not apply to eukaryotes

The DNA size is not correlated with The DNA size is not correlated with organism complexityorganism complexity

Solving the C- value paradoxSolving the C- value paradox

Why in Eukaryotes the DNA size is not Why in Eukaryotes the DNA size is not proportional with the number of genes?proportional with the number of genes?

The C- value and organism The C- value and organism complexity complexity

Why in Eukaryotes the DNA size is not Why in Eukaryotes the DNA size is not proportional with the number of genes?proportional with the number of genes?

The non coding DNA in human The non coding DNA in human

Genomic DNA means the coding and non Genomic DNA means the coding and non coding hereditary materialcoding hereditary material

1.5 % 1.5 % of Human DNA codes only for of Human DNA codes only for protein protein

The other 98.5 % are mostly non coding The other 98.5 % are mostly non coding

These includes These includes transposable elementstransposable elements

The terms The terms

GenomeGenome The hereditary material in an organismThe hereditary material in an organism GenomicsGenomics

Comparing the genomes among different Comparing the genomes among different speciesspecies

Genetics Genetics

Looking at the gene regulation and function Looking at the gene regulation and function

Comparative genomics Comparative genomics

Computational analysis of different Computational analysis of different genomes among different organismsgenomes among different organisms

This is to identify This is to identify - Regulatory sequences Regulatory sequences - siRNAsiRNA- Transposable elementsTransposable elements- Conserved regionsConserved regions

Ultra conserved region in DNAUltra conserved region in DNA

Indicates functional similarities Indicates functional similarities Can be used to track down evolutionary Can be used to track down evolutionary

eventsevents E.g. The human brain development E.g. The human brain development

Ultra conserved region in DNAUltra conserved region in DNA

DNA regions coding for DNA regions coding for enzyme binding enzyme binding sitessites and and hormonal receptorshormonal receptors are ultra are ultra conserved among different organisms conserved among different organisms

DNA molecule in DATABASEDNA molecule in DATABASE

Information about DNA is retrieved from Information about DNA is retrieved from extensively studied model organisms extensively studied model organisms

Model organism criteria: Model organism criteria:

has compact DNA has compact DNA

Small genome size with the least amount of Small genome size with the least amount of junkjunk DNA ( non coding DNA that might DNA ( non coding DNA that might include pseudo genes and retro include pseudo genes and retro /transposons) /transposons)

DNA molecule in DATABASEDNA molecule in DATABASE

Model organism in each species Model organism in each species Bacteria ( Bacteria ( E. coliE. coli and and Heamophilus influenzaHeamophilus influenza))Fungi ( yeast)Fungi ( yeast)Virus ( T4 and Lambda bacteriophage)Virus ( T4 and Lambda bacteriophage)Worms( Worms( Coedorhabditis elegansCoedorhabditis elegans))Insects ( Drosophylla)Insects ( Drosophylla)Plants ( Arabidopsis)Plants ( Arabidopsis)Animals ( rat and mice)Animals ( rat and mice)Humans ( there is no model but DNA is collected from Humans ( there is no model but DNA is collected from

donor’s blood samples and surgical operations)donor’s blood samples and surgical operations)

DNA molecule in DATABASEDNA molecule in DATABASE

Identifying the DNA coding regionIdentifying the DNA coding region Open reading frame (ORF)Open reading frame (ORF) Regulatory sequences Regulatory sequences The coding region is divided into motifsThe coding region is divided into motifs

DNA forms DNA forms

Linear double helixLinear double helix CircularCircular

RelaxedRelaxed Coild Coild SupercoiledSupercoiled

The lab session The lab session

Different DNA searching engines over the Different DNA searching engines over the net net

Retrieving DNA information by different Retrieving DNA information by different waysways

DNA Data analysisDNA Data analysis

Thank you Thank you QuestionsQuestions