BNFO 615 Data Analysis in Bioinformatics

BNFO 615 Data Analysis in Bioinformatics Instructor Zhi Wei

Outline • Cell • Genome • Gene • mRNA • Proteins • Systems biology

Cells • Fundamental working units of every living system. • Every organism is composed of one of two radically different types of cells: prokaryoticcells or eukaryotic cells. • Prokaryotesand Eukaryotesare descended from the same primitive cell. • All extant prokaryotic and eukaryotic cells are the result of a total of 3.5 billion years of evolution.

Prokaryotes v.s. Eukaryotes Different Structures Different Components Different biological processes

Prokaryotes vs Eukaryotes

Prokaryotes bacteria, archaea Ecoli cell 5X106 base pairs > 90% of DNA encode protein 5400 genes Lacks a membrane-bound nucleus. Circular DNA Histones are unknown Prokaryotes v.s. Eukaryotes Eukaryotes • plants, animals, protista, and fungi • Yeast cell • 12.4x106 base pairs • A small fraction of the total DNA encodes protein. Many repeats of non-coding sequences • 5800 genes • All chromosomes are contained in a membrane bound nucleus • DNA is divided between 16 chromosomes • A set of five histones: DNA packaging and gene expression regulation

Cells chemical composition • Chemical composition-by weight • 70% water • 7% small molecules • salts • Lipids • amino acids • nucleotides • 23% macromolecules • Proteins • Polysaccharides • lipids

We have different cells • Cells differ in size, shape and weights • Q: what is the biggest cell in the human body?

Cell Cycle • Born, eat, replicate, and die Lodish et al. Molecular Biology of the Cell (5th ed.). W.H. Freeman & Co., 2003.

Sexual Reproduction v.s. Cell Division • Cell Division: Cells reproduce by duplicating their contents and dividing in two. • Sexual Reproduction • Formation of new individual by a combination of two haploid sex cells (gametes). • Gametes for fertilization usually come from separate parents • Both gametes are haploid, with a single set of chromosomes. The new individual is called a zygote, with two sets of chromosomes (diploid). • Meiosis is a process to convert a diploid cell to a haploid gamete, and cause a change in the genetic information to increase diversity in the offspring.

Meiosisv.s.Mitotic cell division

Genome • A genome is an organism’s complete set of DNA (including its genes). • However, in humans less than 3% of the genome actually encodes for genes. • A part of the rest of the genome serves as a control regions (though that’s also a small part) • The function of the rest of the genome is unknown (junk DNA? An open question).

Comparison of Different Organisms

Promoter Protein coding sequence Terminator Genomic DNA DNA: Deoxyribo Nucleic Acid What is a gene?

Example of a Gene: Gal4 DNA ATGAAGCTACTGTCTTCTATCGAACAAGCATGCGATATTTGCCGACTTAAAAAGCTCAAG TGCTCCAAAGAAAAACCGAAGTGCGCCAAGTGTCTGAAGAACAACTGGGAGTGTCGCTAC TCTCCCAAAACCAAAAGGTCTCCGCTGACTAGGGCACATCTGACAGAAGTGGAATCAAGG CTAGAAAGACTGGAACAGCTATTTCTACTGATTTTTCCTCGAGAAGACCTTGACATGATT TTGAAAATGGATTCTTTACAGGATATAAAAGCATTGTTAACAGGATTATTTGTACAAGAT AATGTGAATAAAGATGCCGTCACAGATAGATTGGCTTCAGTGGAGACTGATATGCCTCTA ACATTGAGACAGCATAGAATAAGTGCGACATCATCATCGGAAGAGAGTAGTAACAAAGGT CAAAGACAGTTGACTGTATCGATTGACTCGGCAGCTCATCATGATAACTCCACAATTCCG TTGGATTTTATGCCCAGGGATGCTCTTCATGGATTTGATTGGTCTGAAGAGGATGACATG TCGGATGGCTTGCCCTTCCTGAAAACGGACCCCAACAATAATGGGTTCTTTGGCGACGGT TCTCTCTTATGTATTCTTCGATCTATTGGCTTTAAACCGGAAAATTACACGAACTCTAAC GTTAACAGGCTCCCGACCATGATTACGGATAGATACACGTTGGCTTCTAGATCCACAACA TCCCGTTTACTTCAAAGTTATCTCAATAATTTTCACCCCTACTGCCCTATCGTGCACTCA CCGACGCTAATGATGTTGTATAATAACCAGATTGAAATCGCGTCGAAGGATCAATGGCAA ATCCTTTTTAACTGCATATTAGCCATTGGAGCCTGGTGTATAGAGGGGGAATCTACTGAT ATAGATGTTTTTTACTATCAAAATGCTAAATCTCATTTGACGAGCAAGGTCTTCGAGTCA A sequence of A,C,G,T

Example of a Gene: Gal4 AA MKLLSSIEQACDICRLKKLKCSKEKPKCAKCLKNNWECRYSPKTKRSPLTRAHLTEVESR LERLEQLFLLIFPREDLDMILKMDSLQDIKALLTGLFVQDNVNKDAVTDRLASVETDMPL TLRQHRISATSSSEESSNKGQRQLTVSIDSAAHHDNSTIPLDFMPRDALHGFDWSEEDDM SDGLPFLKTDPNNNGFFGDGSLLCILRSIGFKPENYTNSNVNRLPTMITDRYTLASRSTT SRLLQSYLNNFHPYCPIVHSPTLMMLYNNQIEIASKDQWQILFNCILAIGAWCIEGESTD IDVFYYQNAKSHLTSKVFESGSIILVTALHLLSRYTQWRQKTNTSYNFHSFSIRMAISLG LNRDLPSSFSDSSILEQRRRIWWSVYSWEIQLSLLYGRSIQLSQNTISFPSSVDDVQRTT TGPTIYHGIIETARLLQVFTKIYELDKTVTAEKSPICAKKCLMICNEIEEVSRQAPKFLQ MDISTTALTNLLKEHPWLSFTRFELKWKQLSLIIYVLRDFFTNFTQKKSQLEQDQNDHQS YEVKRCSIMLSDAAQRTVMSVSSYMDNHNVTPYFAWNCSYYLFNAVLVPIKTLLSNSKSN AENNETAQLLQQINTVLMLLKKLATFKIQTCEKYIQVLEEVCAPFLLSQCAIPLPHISYN NSNGSAIKNIVGSATIAQYPTLPEENVNNISVKYVSPGSVGPSPVPLKSGASFSDLVKLL SNRPPSRNSPVTIPRSTPSHRSVTPFLGQQQQLQSLVPLTPSALFGGANFNQSGNIADSS A sequence of 20 amino acids {A,R,N,D,C,E,Q,G,H,I,L,K,M,F,P,S,T,W,Y,V}

The Central Dogma

DNA  RNA:Gene Transcription promoter G A T T A C A . . . 5’ 3’ 3’ 5’ C T A A T G T . . .

Gene Transcription transcription factor, binding site, RNA polymerase G A T T A C A . . . 5’ 3’ 3’ 5’ C T A A T G T . . . Transcription factors recognize transcription factor binding sites and bind to them, forming a complex. RNA polymerase binds the complex.

Gene Transcription G A T T A C A . . . 5’ 3’ 3’ 5’ C T A A T G T . . . The two strands are separated

Gene Transcription G A T T A C A . . . 5’ 3’ 3’ G A U U A C A 5’ C T A A T G T . . . An RNA copy of the 5’→3’ sequence is created from the 3’→5’ template

Gene Transcription G A T T A C A . . . 5’ 3’ 3’ 5’ C T A A T G T . . . G A U U A C A . . . pre-mRNA 5’ 3’

RNA Processing (Eukaryotes) 5’ cap, polyadenylation, exon, intron, splicing, UTR 5’ cap poly(A) tail exon intron mRNA 5’ UTR 3’ UTR

introns 5’ 3’ promoter exons 3’ UTR 5’ UTR coding non-coding Mammalian Gene Structure • Regulatory regions: up to 50 kb upstream of +1 site • Exons: protein coding and untranslated regions (UTR) 1 to 178 exons per gene (mean 8.8) 8 bp to 17 kb per exon (mean 145 bp) • Introns: splice acceptor (GU) and donor (AG) sites, junk DNA average 1 kb – 50 kb per intron • Gene size: Largest – 2.4 Mb (Dystrophin). Mean – 27 kb. Only 1.5% DNA for coding in Human!

Identifying Genes in Sequence Data • Predicting the start and end of genes as well as the introns and exons in each gene is one of the basic problems in computational biology. • Gene prediction methods look for ORFs (Open Reading Frame). • These are (relatively long) DNA segments that start with the start codon, end with one of the end codons, and do not contain any other end codon in between. • Splice site prediction has received a lot of attention in the literature. • Comparative genomics

RNA • RNA is similar to DNA chemically. It is usually only a single strand. T(hyamine) is replaced by U(racil) • Some forms of RNA can form secondary structures by “pairing up” with itself. This can have change its properties dramatically. DNA and RNA can pair with each other. tRNA linear and 3D view: http://www.cgl.ucsf.edu/home/glasfeld/tutorial/trna/trna.gif

RNA, continued • Several types exist, classified by function • mRNA – this is what is usually being referred to when a Bioinformatician says “RNA”. This is used to carry a gene’s message out of the nucleus. • tRNA –transfers genetic information from mRNA to an amino acid sequence • rRNA –ribosomal RNA. Part of the ribosome which is involved in translation.

Messenger RNA • Basically, an intermediate product • Transcribed from the genome and translated into protein • Number of copies correlates well with number of proteins for the gene. • Unlike DNA, the amount of messenger RNA (as well as the number of proteins) differs between different cell types and under different conditions.

Complementary base-pairing • mRNA is transcribed from the DNA • mRNA (like DNA, but unlike proteins) binds to its complement

Quantify mRNA levels

Proteins: Workhorses of the Cell • Proteins are polypeptide chains of amino acids. • 20 different amino acids • different chemical properties cause the protein chains to fold up into specific three-dimensional structures that define their particular functions in the cell. • Proteins do all essential work for the cell • build cellular structures • digest nutrients • execute metabolic functions • Mediate information flow within a cell and among cellular communities.

Genes Make Proteins • genome-> genes ->protein(forms cellular structural & life functional)->pathways & physiology

Genes Encode for Proteins Second letter First letter Third letter Triplet  one Amino Acid 4^3 combinations mapped to 20 Amino Acids

Open Reading Frames G C U U G U U U A C G A A U U A G G C U U G U U U A C G A A U U A G G C U U G U U U A C G A A U U A G G C U U G U U U A C G A A U U A G

Synonymous Mutation G G C U U G U U U A C G A A U U A G G C U U G U U U A C G A A U U A G Ala Cys Leu Arg Ile G C U U G U U U G C G A A U U A G Ala Cys Leu Arg Ile

Missense Mutation G G C U U G U U U A C G A A U U A G G C U U G U U U A C G A A U U A G Ala Cys Leu Arg Ile G C U U G G U U A C G A A U U A G Ala Trp Leu Arg Ile

Nonsense Mutation A G C U U G U U U A C G A A U U A G G C U U G U U U A C G A A U U A G Ala Cys Leu Arg Ile G C U U G A U U A C G A A U U A G Ala STOP

Frameshift G C U U G U U U A C G A A U U A G G C U U G U U U A C G A A U U A G Ala Cys Leu Arg Ile G C U U G U U A C G A A U U A G Ala Cys Tyr Glu Leu

Protein Structure • Proteins work together with other proteins or nucleic acids as "molecular machines" • structures fit together and function in highly specific, lock-and-key ways. • Four levels of structure: • Primary Structure: The sequence of the protein • Secondary structure: Local structure in regions of the chain. (alpha helix, beta sheet) • Tertiary Structure: Three dimensional structure • Quaternary Structure: multiple subunits

Assigning Function to Proteins • While 25000 genes have been identified in the human genome, relatively few have known functional annotation. • Determining the function of the protein can be done in several ways. • Sequence similarity to other (known) proteins • Using domain information • Using three dimensional structure • Based on high throughput experiments (when does it functions and who it interacts with)

Summary: DNA(Gene) RNA  Protein Replication Transcription Translation

Biological pathway/gene networks • Instead of having brains, cells make decision through complex networks of interactions, called pathways • Synthesize new materials • Break other materials down for spare parts • Signal to eat or die • In order to fulfill their function, proteins interact with other proteins in a number of ways including: • Regulation • Signaling Pathways, for example A -> B -> C • Post translational modifications • Forming protein complexes

An Example

Systems Biology • We now have many sources of data, each providing a different view on the activity in the cell • Sequence (genes) • DNA motifs • Gene expression • Protein interactions • Protein-DNA interaction • Etc. • Putting it all together: Systems Biology

BNFO 615 Data Analysis in Bioinformatics