1. INTRODUCTION TO BIOLOGY AND BIOINFORMATICS BIOINFORMATICS COURSE MTAT

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1 1. INTRODUCTION TO BIOLOGY AND BIOINFORMATICS BIOINFORMATICS COURSE MTAT

2 LIFE Is a characteristic that distinguishes objects that have signaling and self-sustaining processes (i.e. living organism) to those that do not have it Is a state of living characterized by capacity for metabolism, growth, reaction to stimuli, and reproduction A diversity of life forms are found on Earth, eg. plants, animals, fungi, protists, archaea and bacteria 2

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4 WHAT IS BIOLOGY? 4

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6 BIOLOGY Is a study of life and living organisms It brings together the structure, function, growth, origin, distribution, adaptation, interactions, taxonomy and evolution of living organism AEROBIOLOGY, AGRICULTURE, ANATOMY, ASTROBIOLOGY, BIOCHEMISTRY, BIOENGINEERING, BIOINFORMATICS, BIOMATHEMATICSOR, MATHEMATICAL BIOLOGY, BIOMECHANICS, BIOMEDICAL RESEARCH, BIOPHYSICS, BIOTECHNOLOGY, BUILDING BIOLOGY, BOTANY, CELLBIOLOGY, CONSERVATION BIOLOGY, CRYOBIOLOGY, DEVELOPMENTAL BIOLOGY, ECOLOGY, EMBRYOLOGY, ENTOMOLOGY, ENVIRONMENTAL BIOLOGY, EPIDEMIOLOGY, ETHOLOGY, EVOLUTIONARY BIOLOGY, GENETICS, HERPETOLOGY, HISTOLOGY, ICHTHYOLOGY, INTEGRATIVE BIOLOGY, LIMNOLOGY, MAMMALOGY, MARINE BIOLOGY, MICROBIOLOGY, MOLECULAR BIOLOGY, MYCOLOGY, NEUROBIOLOGY, OCEANOGRAPHY, ONCOLOGY, ORNITHOLOGY, POPULATION BIOLOGY, POPULATION ECOLOGY, POPULATION GENETICS, PALEONTOLOGY, PATHOBIOLOGY OR PATHOLOGY, PARASITOLOGY, PHARMACOLOGY, PHYSIOLOGY, PHYTOPATHOLOGY, PSYCHOBIOLOGY, SOCIOBIOLOGY, STRUCTURAL BIOLOGY, VIROLOGY 6

7 BIOLOGY Is a study of life and living organisms It brings together the structure, function, growth, origin, distribution, adaptation, interactions, taxonomy and evolution of living organism BIOLOGY COMPRISES AREAS OF STUDY THAT FOCUS ON LIFE AT A VARIETY OF LEVELS AND FROM A DIVERSITY OF PERSPECTIVES AEROBIOLOGY, AGRICULTURE, ANATOMY, ASTROBIOLOGY, BIOCHEMISTRY, BIOENGINEERING, BIOINFORMATICS, BIOMATHEMATICSOR, MATHEMATICAL BIOLOGY, BIOMECHANICS, BIOMEDICAL RESEARCH, BIOPHYSICS, BIOTECHNOLOGY, BUILDING BIOLOGY, BOTANY, CELLBIOLOGY, CONSERVATION BIOLOGY, CRYOBIOLOGY, DEVELOPMENTAL BIOLOGY, ECOLOGY, EMBRYOLOGY, ENTOMOLOGY, ENVIRONMENTAL BIOLOGY, EPIDEMIOLOGY, ETHOLOGY, EVOLUTIONARY BIOLOGY, GENETICS, HERPETOLOGY, HISTOLOGY, ICHTHYOLOGY, INTEGRATIVE BIOLOGY, LIMNOLOGY, MAMMALOGY, MARINE BIOLOGY, MICROBIOLOGY, MOLECULAR BIOLOGY, MYCOLOGY, NEUROBIOLOGY, OCEANOGRAPHY, ONCOLOGY, ORNITHOLOGY, POPULATION BIOLOGY, POPULATION ECOLOGY, POPULATION GENETICS, PALEONTOLOGY, PATHOBIOLOGY OR PATHOLOGY, PARASITOLOGY, PHARMACOLOGY, PHYSIOLOGY, PHYTOPATHOLOGY, PSYCHOBIOLOGY, SOCIOBIOLOGY, STRUCTURAL BIOLOGY, VIROLOGY 7

8 LIVING SYSTEMS Domain - Eukaryota Kingdom - Animalia Phylum - Chordata Vertebrata (Subphylum) Class - Mammalia Order - Primates Anthropoidea (Suborder) Hominoidea (Superfamily) Family - Hominidae Genus - Homo Species - sapiens 8

HUMANS http://www.ncbi.nlm.nih.gov/taxonomy/browser/wwwtax.cgi?

9 HUMANS Lineage (full): root; cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Coelomata; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Euarchontoglires; Primates; Haplorrhini; Simiiformes; Catarrhini; Hominoidea; Hominidae; Homininae; Homo; Homo sapiens 9

10 SPECIES Defined as a group of living organisms consisting of similar individuals capable of exchanging genes or interbreeding 10

12 NO. OF SPECIES 13

13 LEVELS OF ORGANISATION 14

14 LEVELS OF ORGANISATION 15

15 BIOINFORMATICS? 16

16 COMPUTER SCIENCE [CS] STUDIES COMPUTABLE PROCESSES AND STRUCTURES ( WITH THE AID OF COMPUTERS ) 17

17 BIOINFORMATICS AND COMPUTATIONAL BIOLOGY The boundaries between the two diciplines are not well defined and can be distinguished by the problems they solve BIOINFORMATICS is the application of statistics and computer science to the field of molecular biology COMPUTATIONAL BIOLOGY actual process of analyzing and interpreting data 18

18 DEFINITION OF BIOINFORMATICS The term bioinformatics was coined in 1978 Bioinformatics is the application of information technology and computer science to the field of molecular biology The science of using / developing computer software and algorithms to record, analyze and merge biologically related data Using computer technology to manage large amounts of biological data Bioinformatics involves the use of techniques including applied mathematics, informatics, statistics, computer science, artificial intelligence, chemistry, and biochemistry to solve biological problems usually on the molecular level 19

19 DEFINITION OF BIOINFORMATICS The collection, organization, storage, analysis, and integration of large amounts of biological data using networks of computers and databases Bioinformatics involves the integration of computers, software tools, and databases in an effort to address biological questions In summary, the use of computer science to solve biological problems 20

20 BIOINFORMATIC FOCUS MOLECULES CELL TISSUE ORGAN ORGANISM 21

SEQUENCES, PROTEIN DOMAINS, AND PROTEIN STRUCTURES. ORGANISM http://www.nature.

21 BIOINFORMATIC FOCUS MOLECULES CELL ORGAN TISSUE ANALYSIS AND INTERPRETATION OF VARIOUS TYPES OF BIOLOGICAL DATA INCLUDING: NUCLEOTIDE AND AMINO ACID SEQUENCES, PROTEIN DOMAINS, AND PROTEIN STRUCTURES. ORGANISM 22

22 BIOINFORMATIC FOCUS Development of new algorithms and statistics with which to assess biological information, such as relationships among members of large data sets. 23

BIOINFORMATIC FOCUS Development and implementation of tools that enable efficient access and management of different types of information, such as various

23 BIOINFORMATIC FOCUS Development and implementation of tools that enable efficient access and management of different types of information, such as various databases, integrated mapping information

24 UNITS OF INFORMATION IN BIOINFORMATICS DNA Sequence Pathways RNA Structure Interactions Protein Evolution Mutations 25

25 UNITS OF INFORMATION IN COMPUTER SCIENCE File Storage capacity by Bits and Bytes Bit Byte Kilobyte Megabyte Gigabyte bit *8= 8,192 byte *8192= 8,388, *1024= 1,048, * = 8,589,934, * = 1,073,741,824 Kilobyte 8, KB ,048,576 Megabyte 8,388,608 1,048, MB 1024 Gigabyte 8,589,934,592 1,073,741,824 1,048, GB Terabyte Petabyte 8,796,093,022,208 1TB 9,007,199,254,740,9 90 1,099,511,627,776 1,073,741,824 1,048, ,125,899,906,842, TB 1 PB 1,099,511,627,77 6 1,073,741,824 1,048,576 26

26 UNITS OF INFORMATION IN COMPUTER SCIENCE File Storage capacity by Bits and Bytes Bit Byte Kilobyte Megabyte Gigabyte Petabyte 9,007,199,254,740,99 0 1,125,899,906,84 2, TB 1 BO 1,099,511,627,77 6 1,073,741,824 1,048,576 Exabyte 9,223,372,036,854,78 0,000 1,152,921,504,60 6,850,000 1,125,899,906,84 2,620 1,048,576 TB 1024 PB 1 EB 1,099,511,627,7 76 1,073,741,824 Zettabyte 9,444,732,965,739,29 0,000,000 1,180,591,620,71 7,410,000,000 1,152,921,504,60 6,850,000 1,125,899,906,8 42,620 1,073,741,824 TB 1,048,576 PB 1024 EB 1 ZB 1,099,511,627,776 Yottabyte 9,671,406,556,917,030, 000,000,000 1,208,925,819,61 4,630,000,000,00 0 1,180,591,620,71 7,410,000,000 KB 1,152,921,504,6 06,850,000 MB 1,125,899,906,842,62 0 GB 1,099,511,627,776 TB 1,073,741,824 PB 1,048,576 EB 1024 ZB 1 YB 27

27 CELL SIZES 28

HUMAN CELL http://bhavanajagat.files.wordpress.

28 HUMAN CELL 29

29 EXAMPLES OF BIOLOGICAL DATA GENOME DNA TRANSCRIPTOME RNA PROTEOME Proteins The biological information contained in a genome is encoded in deoxyribonucleic acid (DNA) or, for many types of virus, in ribonucleic acid (RNA) 30

30 NAME THE NUMBERS NUCLEUS DNA GENES CHROMOSOME CELL

31 EXAMPLES OF BIOLOGICAL DATA 32

32 CENTRAL DOGMA OF MOLECULAR BIOLOGY DNA is transcribed into RNA and RNA is translated into proteins 33

33 EXAMPLES OF BIOLOGICAL DATA GENOME DNA TRANSCRIPTOME RNA PROTEOME Proteins The biological information contained in a genome is encoded in deoxyribonucleic acid (DNA) or, for many types of virus, in ribonucleic acid (RNA) 34

GENOME Is the entirety of an organism s hereditary information The genome includes both the genes and non-coding sequences of DNA/RNA In 1995, Haemophilus influenzae or was the first genome of a

34 GENOME Is the entirety of an organism s hereditary information The genome includes both the genes and non-coding sequences of DNA/RNA In 1995, Haemophilus influenzae or was the first genome of a living organism to be sequenced in July base pairs of DNA in single circular chromosome that contains 1740 protein-coding gene, 58 transfer RNA genes and 18 other RNA genes 35

35 WHOLE GENOMES 36

36 GENOME SIZES Escherichia coli 4,600,000 bp (1997) Saccharomyces cerevisiae 12,100,000 (1996) Arabidopsis thaliana 157,000,000 (2000) Homo sapiens 3,200,000,000 (2000) 37

37 GENOME SIZES Japanese flower Paris japonica 130 billion base pairs 50 times the human genome 38

38 COMPLETELY SEQUENCED GENOMES 39

39 HUMAN GENOME One cell 23 pairs of chromosomes DNA 3 billion pairs of DNA bases RNA Human body cells (100 trillion) Protein different proteins 21,000 to 23,000 genes 40

40 Relative proportions (%) of bases in DNA CURRENT SCIENCE, VOL. 85, NO. 11, 10 DECEMBER

41 DNA DNA with high GC-content is more stable than DNA with low GC-content, 3 hydrogen bonds 42

DNA vs RNA DNA deoxyribonucleic acid Sugar is deoxyribose DNA is a polymer of deoxyribonucleotides Bases are adenine (A), guanine (G), cytosine (C) and thymine (T) RNA ribonucleic acid

42 DNA vs RNA DNA deoxyribonucleic acid Sugar is deoxyribose DNA is a polymer of deoxyribonucleotides Bases are adenine (A), guanine (G), cytosine (C) and thymine (T) RNA ribonucleic acid Sugar is ribose RNA is a polymer of ribonucleotides Bases are adenine (A), guanine (G), cytosine (C) and uracil (U) 43

43 DNA SEQUENCE Raw DNA sequence Coding or non-coding Parses into genes 4 nucleotide bases ATGC >ENST cdna:known chromosome:grch37:15: : :1 gene:ensg gene_biotype:protein_coding transcript_biotype:protein_coding ATGTGGCCACTGCTCACCATGCACATAACCCAGCTCAACCGGGAGTGCCTGCTGCACCTCTTCTCCTTCCTA GACAAGGACAGCAGGAAGAGCCTTGCCAGGACCTGCTCCCAGCTCCACGACGTGTTTGAGGACCCCGCA CTCTGGTCCCTGCTGCACTTCCGTTCCCTCACTGAACTCCAGAAGGACAACTTCCTCCTGGGCCCGGCACTC CGCAGCCTCTCCATCTGCTGGCACTCCAGCCGCGTGCAGGTGTGCAGCATTGAGGACTGGCTCAAGAGTG CCTTCCAGAGAAGCATCTGCAGCCGGCACGAGAGCCTGGTCAATGATTTCCTCCTCCGGGTGTGCGACAG GCTTTCTGCTGTGCGCTCCCCACGGAGGCGGGAGGCGCCTGCACCGTCCTCGGGGACTCCGATCGCCGTT GGACCGAAATCACCTCGGTGGGGAGGACCTGACCACTCGGAGTTCGCCGACTTGCGCTCGGGGGTGACG GGGGCCAGGGCTGCCGCGCGCAGGGGTCTGGGGAGCCTCCGGGCGGAGCGACCCAGCGAGACCCCGC CGGCTCCCGGAGTGTCCTGGGGACCGCCACCTCCAGGAGCCCCGGTGGTGATCTCGGTGAAGCAGGAGG AGGGGAAGCAGGGGCGCACGGGCAGAAGGAGCCACCGAGCCGCTCCTCCTTGCGGTTTTGCCCGCACG CGCGTCTGCCCGCCCACCTTTCCTGGGGCGGATGCGTTCCCGCAGTGA 44

44 A GENE 45

GENE EXPRESSION REGULATORS http://www.nature.

45 GENE EXPRESSION REGULATORS 46

46 GENE EXPRESSION REGULATORS - EPIGENETICS 47

47 EXAMPLES OF BIOLOGICAL DATA GENOME DNA TRANSCRIPTOME RNA PROTEOME Proteins Transcriptome is a set of all RNA molecules including mrna, rrna, trna, and noncoding RNA produced in one or a population of cells 48

48 TRANSCRIPTION 49

49 TRANSCRIPTION 50

50 ALTERNATIVE SPLICING 51

TYPES OF RNA mrna messenger RNA: encodes amino acid sequences of a polypeptide trna transfer RNA: brings amino acids to ribosomes during translation rrna ribosomal RNA: with ribosome proteins makes

51 TYPES OF RNA mrna messenger RNA: encodes amino acid sequences of a polypeptide trna transfer RNA: brings amino acids to ribosomes during translation rrna ribosomal RNA: with ribosome proteins makes up the ribosomes, the organelles that translate the mrna snrna small nuclear RNA: forms complexes with proteins that are used in RNA processing in eukaryotes 52

52 TYPES OF RNA 53

53 EXAMPLES OF BIOLOGICAL DATA GENOME DNA TRANSCRIPTOME RNA PROTEOME Proteins The proteome is the entire set of proteins expressed by a genome, cell, tissue or organism. 54

FROM TRANSCRIPTION TO TRANSLATION http://www1.cs.

54 FROM TRANSCRIPTION TO TRANSLATION 55

55 TRANSLATION 56

56 TRANSLATION INITIATION 57

57 TRANSLATION TERMINATION 58

58 UNIVERSAL GENETIC CODE 59

59 AMINO ACIDS 60

60 PROTEIN Proteins consists of long chains of amino acid sequences 20 letter alphabet (IUPAC nomenclature) IUPAC amino Three letter acid code code Amino acid A Ala Alanine C Cys Cysteine D Asp Aspartic Acid E Glu Glutamic Acid F Phe Phenylalanine G Gly Glycine H His Histidine I Ile Isoleucine K Lys Lysine L Leu Leucine IUPAC amino Three letter acid code code Amino acid M Met Methionine N Asn Asparagine P Pro Proline Q Gln Glutamine R Arg Arginine S Ser Serine T Thr Threonine V Val Valine W Trp Tryptophan Y Tyr Tyrosine 61

61 PROTEIN SEQUENCE >sp P48431 SOX2_HUMAN Transcription factor SOX-2 OS=Homo sapiens GN=SOX2 PE=1 SV=1 MYNMMETELKPPGPQQTSGGGGGNSTAAAAGGNQKNSPDRVKRPMNAFMVWSRGQRRKMA QENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYKYRPRRKTKTLM KKDKYTLPGGLLAPGGNSMASGVGVGAGLGAGVNQRMDSYAHMNGWSNGSYSMMQDQLGY PQHPGLNAHGAAQMQPMHRYDVSALQYNSMTSSQTYMNGSPTYSMSYSQQGTPGMALGSM GSVVKSEASSSPPVVTSSSHSRAPCQAGDLRDMISMYLPGAEVPEPAAPSRLHMSQHYQS GPVPGTAINGTLPLSHM 62

62 PROTEIN SIZE

63 PROTEIN STRUCTURE 64

64 PROTEIN DOMAINS 65

65 PROTEIN SEQUENCE Proteins are divided into domains >sp P48431 SOX2_HUMAN Transcription factor SOX-2 OS=Homo sapiens GN=SOX2 PE=1 SV=1 MYNMMETELKPPGPQQTSGGGGGNSTAAAAGGNQKNSPDRVKRPMNAFMVWSRGQRRKMA QENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYKYRPRRKTKTLM KKDKYTLPGGLLAPGGNSMASGVGVGAGLGAGVNQRMDSYAHMNGWSNGSYSMMQDQLGY PQHPGLNAHGAAQMQPMHRYDVSALQYNSMTSSQTYMNGSPTYSMSYSQQGTPGMALGSM GSVVKSEASSSPPVVTSSSHSRAPCQAGDLRDMISMYLPGAEVPEPAAPSRLHMSQHYQS GPVPGTAINGTLPLSHM DNA BINDING DOMAIN 66

66 GENE TRANSCRIPTION, TRANSLATION AND PROTEIN SYNTHESIS 67

67 CENTRAL DOGMA 68

68 BIOINFORMATIC APPLICATIONS The integrative approaches are useful and applied in Agricultural Higher yield in crops or fruits Disease or drought resistance crops Medical To understand processes in healthy and disease individuals Genetic diseases Pharmaceutical To find or develop new and better drugs Gene based drugs Structure based drug designing 69

69 BIOINFORMATIC QUESTIONS 1 To identify an unknown gene of interest Sequence matching Is there a match to known sequence in the database Which protein family does it match to How to identify more family members I have an similar structure, how to identify its potential ligands How to identify if my gene/protein is found present also in other species How can I identify genes that are inherited together in a specific region 70

70 BIOINFORMATIC QUESTIONS 2 I have to constructed a artificial gene, how do I design the primers, how to check if I have the right sequence? To know structure of an poorly expressed RNA sequence To identify the structure and function of a protein sequence To cluster protein sequences into families of related sequences and develop models To generate phylogenetic trees to identify the evolutionary relationships using similar proteins/dna To identify which other proteins interacts with sequence of interest. 71

71 BIOINFORMATIC QUESTIONS 3 Find genes that have similar expression in specific conditions Find transcription factors that regulate specific genes Vizualise different gene and protein networks Describe the regulation of genes 72

Proteins: Characteristics and Properties of Amino Acids

Proteins: Characteristics and Properties of Amino Acids SBI4U:Biochemistry Macromolecules Eachaminoacidhasatleastoneamineandoneacidfunctionalgroupasthe nameimplies.thedifferentpropertiesresultfromvariationsinthestructuresof differentrgroups.thergroupisoftenreferredtoastheaminoacidsidechain.