070105 W1 Intro Bio

Outline: 

Outline What is Life made of? What Molecule Codes For Genes? What carries information between DNA to Proteins? How Are Proteins Made? (Translation) How Do Individuals of a Species Differ? Why Bioinformatics? Most materials revised from http://www.bioalgorithms.info

What is Life made of?: 

What is Life made of?

Cells: 

Cells Chemical composition-by weight 70% water 7% small molecules salts Lipids amino acids nucleotides 23% macromolecules Proteins Polysaccharides lipids biochemical (metabolic) pathways translation of mRNA into proteins

Life begins with Cell: 

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 Cells have common Cycles: 

All Cells have common Cycles Born, eat, replicate, and die

Signaling Pathways: Control Gene Activity : 

Signaling Pathways: Control Gene Activity Instead of having brains, cells make decision through complex networks of chemical reactions, called pathways Synthesize new materials Break other materials down for spare parts Signal to eat or die

Example of cell signaling: 

Example of cell signaling

Cells Information and Machinery: 

Cells Information and Machinery Cells store all information to replicate itself Human genome is around 3 billions base pair long Almost every cell in human body contains same set of genes But not all genes are used or expressed by those cells Machinery: Collect and manufacture components Carry out replication Kick-start its new offspring (A cell is like a car factory)

Overview of organizations of life: 

Overview of organizations of life Nucleus = library Chromosomes = bookshelves Genes = books Almost every cell in an organism contains the same libraries and the same sets of books. Books represent all the information (DNA) that every cell in the body needs so it can grow and carry out its vaious functions.

Some Terminology: 

Some Terminology Genome: an organism’s genetic material Gene: a discrete units of hereditary information located on the chromosomes and consisting of DNA. Genotype: The genetic makeup of an organism Phenotype: the physical expressed traits of an organism Nucleic acid: Biological molecules(RNA and DNA) that allow organisms to reproduce;

More Terminology: 

More Terminology The genome is an organism’s complete set of DNA. a bacteria contains about 600,000 DNA base pairs human and mouse genomes have some 3 billion. human genome has 24 distinct chromosomes. Each chromosome contains many genes. Gene basic physical and functional units of heredity. specific sequences of DNA bases that encode instructions on how to make proteins. Proteins Make up the cellular structure large, complex molecules made up of smaller subunits called amino acids.

All Life depends on 3 critical molecules: 

All Life depends on 3 critical molecules DNAs Hold information on how cell works RNAs Act to transfer short pieces of information to different parts of cell Provide templates to synthesize into protein Proteins Form enzymes that send signals to other cells and regulate gene activity Form body’s major components (e.g. hair, skin, etc.)

DNA: The Code of Life: 

DNA: The Code of Life The structure and the four genomic letters code for all living organisms Adenine, Guanine, Thymine, and Cytosine which pair A-T and C-G on complimentary strands.

DNA, continued: 

DNA, continued DNA has a double helix structure which composed of sugar molecule phosphate group and a base (A,C,G,T) DNA always reads from 5’ end to 3’ end for transcription replication 5’ ATTTAGGCC 3’ 3’ TAAATCCGG 5’

DNA, RNA, and the Flow of Information : 

DNA, RNA, and the Flow of Information Translation Transcription Replication

Overview of DNA to RNA to Protein: 

Overview of DNA to RNA to Protein A gene is expressed in two steps Transcription: RNA synthesis Translation: Protein synthesis

Cell Information: Instruction book of Life: 

Cell Information: Instruction book of Life DNA, RNA, and Proteins are examples of strings written in either the four-letter nucleotide of DNA and RNA (A C G T/U) or the twenty-letter amino acid of proteins. Each amino acid is coded by 3 nucleotides called codon. (Leu, Arg, Met, etc.)

Proteins: Workhorses of the Cell: 

Proteins: Workhorses of the Cell 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. Proteins work together with other proteins or nucleic acids as "molecular machines" structures that fit together and function in highly specific, lock-and-key ways.

What Molecule Codes For Genes?: 

What Molecule Codes For Genes?

Outline:: 

Outline: Discovery of the Structure of DNA Watson and Crick DNA Basics

Discovery of DNA: 

Discovery of DNA DNA Sequences Chargaff and Vischer, 1949 DNA consisting of A, T, G, C Adenine, Guanine, Cytosine, Thymine Chargaff Rule Noticing #A#T and #G#C A “strange but possibly meaningless” phenomenon. Wow!! A Double Helix Watson and Crick, Nature, April 25, 1953 Rich, 1973 Structural biologist at MIT. DNA’s structure in atomic resolution. Crick Watson

Watson & Crick – “…the secret of life”: 

Watson & Crick – “…the secret of life” Watson: a zoologist, Crick: a physicist “In 1947 Crick knew no biology and practically no organic chemistry or crystallography..” – www.nobel.se Applying Chagraff’s rules and the X-ray image from Rosalind Franklin, they constructed a “tinkertoy” model showing the double helix Their 1953 Nature paper: “It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material.”

Slide23: 

WATSON, J. D. & CRICK, F. H. C. (1953) MOLECULAR STRUCTURE OF NUCLEIC ACIDS. Nature 171 1962 Nobel Prize in Physiology or Medicine DNA is a double helix structure Guess how long was the report?

Slide24: 

The original Watson and Crick’s paper 1-page report!!

DNA: The Basis of Life: 

DNA: The Basis of Life Deoxyribonucleic Acid (DNA) Double stranded with complementary strands A-T, C-G DNA is a polymer Sugar-Phosphate-Base Bases held together by H bonding to the opposite strand

Double helix of DNA: 

Double helix of DNA James Watson and Francis Crick proposed a model for the structure of DNA. Utilizing X-ray diffraction data, obtained from crystals of DNA) This model predicted that DNA as a helix of two complementary anti-parallel strands, wound around each other in a rightward direction stabilized by H-bonding between bases in adjacent strands. The bases are in the interior of the helix Purine bases form hydrogen bonds with pyrimidine.

DNA: The Basis of Life: 

DNA: The Basis of Life Humans have about 3 billion base pairs. How do you package it into a cell? How does the cell know where in the highly packed DNA where to start transcription? Special regulatory sequences DNA size does not mean more complex Complexity of DNA Eukaryotic genomes consist of variable amounts of DNA Single Copy or Unique DNA Highly Repetitive DNA

DNA: 

DNA Stores all information of life 4 “letters” base pairs. AGTC (adenine, guanine, thymine, cytosine ) which pair A-T and C-G on complimentary strands. http://www.lbl.gov/Education/HGP-images/dna-medium.gif

DNA, continued: 

DNA, continued Phosphate Base (A,T, C or G) http://www.bio.miami.edu/dana/104/DNA2.jpg Sugar

DNA, continued : 

DNA, continued DNA has a double helix structure. However, it is not symmetric. It has a “forward” and “backward” direction. The ends are labeled 5’ and 3’ after the Carbon atoms in the sugar component. 5’ AATCGCAAT 3’ 3’ TTAGCGTTA 5’ DNA always reads 5’ to 3’ for transcription replication

DNA Components: 

DNA Components Nitrogenous Base: N is important for hydrogen bonding between bases A – adenine with T – thymine (double H-bond) C – cytosine with G – guanine (triple H-bond) Sugar: Ribose (5 carbon) Base covalently bonds with 1’ carbon Phosphate covalently bonds with 5’ carbon Normal ribose (OH on 2’ carbon) – RNA deoxyribose (H on 2’ carbon) – DNA dideoxyribose (H on 2’ & 3’ carbon) – used in DNA sequencing Phosphate: negatively charged

Basic Structure: 

Basic Structure

Basic Structure Implications: 

Basic Structure Implications DNA is (-) charged due to phosphate: gel electrophoresis, DNA sequencing (Sanger method) H-bonds form between specific bases: hybridization – replication, transcription, translation DNA microarrays, hybridization blots, PCR C-G bound tighter than A-T due to triple H-bond DNA-protein interactions (via major & minor grooves): transcriptional regulation DNA polymerization: 5’ to 3’ – phosphodiester bond formed between 5’ phosphate and 3’ OH

Slide34: 

The Purines The Pyrimidines

Double helix of DNA: 

Double helix of DNA The double helix of DNA has these features: Concentration of adenine (A) is equal to thymine (T) Concentration of cytidine (C) is equal to guanine (G). Watson-Crick base-pairing A will only base-pair with T, and C with G base-pairs of G and C contain three H-bonds, Base-pairs of A and T contain two H-bonds. G-C base-pairs are more stable than A-T base-pairs Two polynucleotide strands wound around each other. The backbone of each consists of alternating deoxyribose and phosphate groups

DNA - replication: 

DNA - replication DNA can replicate by splitting, and rebuilding each strand. Note that the rebuilding of each strand uses slightly different mechanisms due to the 5’ 3’ asymmetry, but each daughter strand is an exact replica of the original strand. http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/D/DNAReplication.html

DNA Replication: 

DNA Replication

Superstructure: 

Superstructure Lodish et al. Molecular Biology of the Cell (5th ed.). W.H. Freeman & Co., 2003.

Superstructure Implications: 

Superstructure Implications DNA in a living cell is in a highly compacted and structured state Transcription factors and RNA polymerase need ACCESS to do their work Transcription is dependent on the structural state – SEQUENCE alone does not tell the whole story

Transcriptional Regulation: 

Transcriptional Regulation Lodish et al. Molecular Biology of the Cell (5th ed.). W.H. Freeman & Co., 2003.

The Histone Code : 

The Histone Code State of histone tails govern TF access to DNA State is governed by amino acid sequence and modification (acetylation, phosphorylation, methylation) Lodish et al. Molecular Biology of the Cell (5th ed.). W.H. Freeman & Co., 2003.

What carries information between DNA to Proteins: 

What carries information between DNA to Proteins

Outline: 

Outline Central Dogma Of Biology RNA Transcription Splicing hnRNA-> mRNA

Slide44: 

The central dogma of molecular biology: DNA mRNA (messenger) rRNA (ribosomal) tRNA (transfer) Protein Ribosome transcription transcription transcription translation

RNA: 

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. http://www.cgl.ucsf.edu/home/glasfeld/tutorial/trna/trna.gif tRNA linear and 3D view:

RNA, continued : 

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.

Terminology for Transcription: 

Terminology for Transcription hnRNA (heterogeneous nuclear RNA): Eukaryotic mRNA primary transcipts whose introns have not yet been excised (pre-mRNA). Promoter: A special sequence of nucleotides indicating the starting point for RNA synthesis. RNA (ribonucleotide): Nucleotides A,U,G, and C with ribose RNA Polymerase II: Multisubunit enzyme that catalyzes the synthesis of an RNA molecule on a DNA template from nucleoside triphosphate precursors. Terminator: Signal in DNA that halts transcription.

Definition of a Gene: 

Definition of a Gene 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 and donor sites, junk DNA average 1 kb – 50 kb per intron Gene size: Largest – 2.4 Mb (Dystrophin). Mean – 27 kb.

Transcription: DNA  hnRNA: 

Transcription: DNA  hnRNA RNA polymerase II catalyzes the formation of phosphodiester bond that link nucleotides together to form a linear chain from 5’ to 3’ by unwinding the helix just ahead of the active site for polymerization of complementary base pairs. The hydrolysis of high energy bonds of the substrates (nucleoside triphosphates ATP, CTP, GTP, and UTP) provides energy to drive the reaction. During transcription, the DNA helix reforms as RNA forms. When the terminator sequence is met, polymerase halts and releases both the DNA template and the RNA. Transcription occurs in the nucleus. σ factor from RNA polymerase reads the promoter sequence and opens a small portion of the double helix exposing the DNA bases.

Central Dogma Revisited: 

Central Dogma Revisited Base Pairing Rule: A and T or U is held together by 2 hydrogen bonds and G and C is held together by 3 hydrogen bonds. Note: Some mRNA stays as RNA (ie tRNA,rRNA). DNA hnRNA mRNA protein Splicing Spliceosome Translation Transcription Nucleus Ribosome in Cytoplasm

Terminology for Splicing: 

Terminology for Splicing Exon: A portion of the gene that appears in both the primary and the mature mRNA transcripts. Intron: A portion of the gene that is transcribed but excised prior to translation. Spliceosome: A organelle that carries out the splicing reactions whereby the pre-mRNA is converted to a mature mRNA.

Splicing: 

Splicing

Splicing: hnRNA  mRNA: 

Splicing: hnRNA  mRNA Takes place on spliceosome that brings together a hnRNA, snRNPs, and a variety of pre-mRNA binding proteins. 2 transesterification reactions: 2’,5’ phosphodiester bond forms between an intron adenosine residue and the intron’s 5’-terminal phosphate group and a lariat structure is formed. The free 3’-OH group of the 5’ exon displaces the 3’ end of the intron, forming a phosphodiester bond with the 5’ terminal phosphate of the 3’ exon to yield the spliced product. The lariat formed intron is the degraded.

Splicing and other RNA processing: 

Splicing and other RNA processing In Eukaryotic cells, RNA is processed between transcription and translation. This complicates the relationship between a DNA gene and the protein it codes for. Sometimes alternate RNA processing can lead to an alternate protein as a result. This is true in the immune system.

Splicing (Eukaryotes): 

Splicing (Eukaryotes) Unprocessed RNA is composed of Introns and Extrons. Introns are removed before the rest is expressed and converted to protein. Sometimes alternate splicings can create different valid proteins. A typical Eukaryotic gene has 4-20 introns. Locating them by analytical means is not easy.

Posttranscriptional Processing: Capping and Poly(A) Tail: 

Posttranscriptional Processing: Capping and Poly(A) Tail Capping Prevents 5’ exonucleolytic degradation. 3 reactions to cap: Phosphatase removes 1 phosphate from 5’ end of hnRNA Guanyl transferase adds a GMP in reverse linkage 5’ to 5’. Methyl transferase adds methyl group to guanosine. Poly(A) Tail Due to transcription termination process being imprecise. 2 reactions to append: Transcript cleaved 15-25 past highly conserved AAUAAA sequence and less than 50 nucleotides before less conserved U rich or GU rich sequences. Poly(A) tail generated from ATP by poly(A) polymerase which is activated by cleavage and polyadenylation specificity factor (CPSF) when CPSF recognizes AAUAAA. Once poly(A) tail has grown approximately 10 residues, CPSF disengages from the recognition site.

How Are Proteins Made?(Translation): 

How Are Proteins Made? (Translation)

Outline:: 

Outline: mRNA tRNA Translation Protein Synthesis Protein Folding

Terminology for Ribosome: 

Terminology for Ribosome Codon: The sequence of 3 nucleotides in DNA/RNA that encodes for a specific amino acid. mRNA (messenger RNA): A ribonucleic acid whose sequence is complementary to that of a protein-coding gene in DNA. Ribosome: The organelle that synthesizes polypeptides under the direction of mRNA rRNA (ribosomal RNA):The RNA molecules that constitute the bulk of the ribosome and provides structural scaffolding for the ribosome and catalyzes peptide bond formation. tRNA (transfer RNA): The small L-shaped RNAs that deliver specific amino acids to ribosomes according to the sequence of a bound mRNA.

mRNA  Ribosome: 

mRNA  Ribosome mRNA leaves the nucleus via nuclear pores. Ribosome has 3 binding sites for tRNAs: A-site: position that aminoacyl-tRNA molecule binds to vacant site P-site: site where the new peptide bond is formed. E-site: the exit site Two subunits join together on a mRNA molecule near the 5’ end. The ribosome will read the codons until AUG is reached and then the initiator tRNA binds to the P-site of the ribosome. Stop codons have tRNA that recognize a signal to stop translation. Release factors bind to the ribosome which cause the peptidyl transferase to catalyze the addition of water to free the molecule and releases the polypeptide.

Terminology for tRNA and proteins: 

Terminology for tRNA and proteins Anticodon: The sequence of 3 nucleotides in tRNA that recognizes an mRNA codon through complementary base pairing. C-terminal: The end of the protein with the free COOH. N-terminal: The end of the protein with the free NH3.

Purpose of tRNA: 

Purpose of tRNA The proper tRNA is chosen by having the corresponding anticodon for the mRNA’s codon. The tRNA then transfers its aminoacyl group to the growing peptide chain. For example, the tRNA with the anticodon UAC corresponds with the codon AUG and attaches methionine amino acid onto the peptide chain.

Translation: tRNA: 

Translation: tRNA Carboxyl end of the protein is released from the tRNA at the Psite and joined to the free amino group from the amino acid attached to the tRNA at the A-site; new peptide bond formed catalyzed by peptide transferase. Conformational changes occur which shift the two tRNAs into the E-site and the P-site from the P-site and A-site respectively. The mRNA also shifts 3 nucleotides over to reveal the next codon. The tRNA in the E-site is released GTP hydrolysis provides the energy to drive this reaction. mRNA is translated in 5’ to 3’ direction and the from N-terminal to C-terminus of the polypeptide. Elongation process (assuming polypeptide already began): tRNA with the next amino acid in the chain binds to the A-site by forming base pairs with the codon from mRNA

Terminology for Protein Folding: 

Terminology for Protein Folding Endoplasmic Reticulum: Membraneous organelle in eukaryotic cells where lipid synthesis and some posttranslational modification occurs. Mitochondria: Eukaryotic organelle where citric acid cycle, fatty acid oxidation, and oxidative phosphorylation occur. Molecular chaperone: Protein that binds to unfolded or misfolded proteins to refold the proteins in the quaternary structure.

Uncovering the code: 

Uncovering the code Scientists conjectured that proteins came from DNA; but how did DNA code for proteins? If one nucleotide codes for one amino acid, then there’d be 41 amino acids However, there are 20 amino acids, so at least 3 bases codes for one amino acid, since 42 = 16 and 43 = 64 This triplet of bases is called a “codon” 64 different codons and only 20 amino acids means that the coding is degenerate: more than one codon sequence code for the same amino acid

Revisiting the Central Dogma: 

Revisiting the Central Dogma In going from DNA to proteins, there is an intermediate step where mRNA is made from DNA, which then makes protein This known as The Central Dogma Why the intermediate step? DNA is kept in the nucleus, while protein sythesis happens in the cytoplasm, with the help of ribosomes

The Central Dogma (cont’d): 

The Central Dogma (cont’d)

RNA  Protein: Translation: 

RNA  Protein: Translation Ribosomes and transfer-RNAs (tRNA) run along the length of the newly synthesized mRNA, decoding one codon at a time to build a growing chain of amino acids (“peptide”) The tRNAs have anti-codons, which complimentarily match the codons of mRNA to know what protein gets added next But first, in eukaryotes, a phenomenon called splicing occurs Introns are non-protein coding regions of the mRNA; exons are the coding regions Introns are removed from the mRNA during splicing so that a functional, valid protein can form

Translation: 

Translation The process of going from RNA to polypeptide. Three base pairs of RNA (called a codon) correspond to one amino acid based on a fixed table. Always starts with Methionine and ends with a stop codon

Translation, continued: 

Translation, continued Catalyzed by Ribosome Using two different sites, the Ribosome continually binds tRNA, joins the amino acids together and moves to the next location along the mRNA ~10 codons/second, but multiple translations can occur simultaneously http://wong.scripps.edu/PIX/ribosome.jpg

Protein Synthesis: Summary: 

Protein Synthesis: Summary There are twenty amino acids, each coded by three- base-sequences in DNA, called “codons” This code is degenerate The central dogma describes how proteins derive from DNA DNA  mRNA  (splicing?)  protein The protein adopts a 3D structure specific to it’s amino acid arrangement and function

Proteins: 

Proteins Complex organic molecules made up of amino acid subunits 20* different kinds of amino acids. Each has a 1 and 3 letter abbreviation. http://www.indstate.edu/thcme/mwking/amino-acids.html for complete list of chemical structures and abbreviations. Proteins are often enzymes that catalyze reactions. Also called “poly-peptides” *Some other amino acids exist but not in humans.

Polypeptide v. Protein: 

Polypeptide v. Protein A protein is a polypeptide, however to understand the function of a protein given only the polypeptide sequence is a very difficult problem. Protein folding an open problem. The 3D structure depends on many variables. Current approaches often work by looking at the structure of homologous (similar) proteins. Improper folding of a protein is believed to be the cause of mad cow disease. http://www.sanger.ac.uk/Users/sgj/thesis/node2.html for more information on folding

Protein Folding: 

Protein Folding Proteins tend to fold into the lowest free energy conformation. Proteins begin to fold while the peptide is still being translated. Proteins bury most of its hydrophobic residues in an interior core to form an α helix. Most proteins take the form of secondary structures α helices and β sheets. Molecular chaperones, hsp60 and hsp 70, work with other proteins to help fold newly synthesized proteins. Much of the protein modifications and folding occurs in the endoplasmic reticulum and mitochondria.

Protein Folding: 

Protein Folding Proteins are not linear structures, though they are built that way The amino acids have very different chemical properties; they interact with each other after the protein is built This causes the protein to start fold and adopting it’s functional structure Proteins may fold in reaction to some ions, and several separate chains of peptides may join together through their hydrophobic and hydrophilic amino acids to form a polymer

Protein Folding (cont’d): 

Protein Folding (cont’d) The structure that a protein adopts is vital to it’s chemistry Its structure determines which of its amino acids are exposed carry out the protein’s function Its structure also determines what substrates it can react with

How Do Individuals of a Species Differ?: 

How Do Individuals of a Species Differ?

Outline:: 

Outline: Physical Variation and Diversity Genetic Variation

How Do Individuals of Species Differ?: 

How Do Individuals of Species Differ? Genetic makeup of an individual is manifested in traits, which are caused by variations in genes While 99.9% of the 3 billion nucleotides in the human genome are the same, small variations can have a large range of phenotypic expressions These traits make some more or less susceptible to disease, and the demystification of these mutations will hopefully reveal the truth behind several genetic diseases

The Diversity of Life: 

The Diversity of Life Not only do different species have different genomes, but also different individuals of the same species have different genomes. No two individuals of a species are quite the same – this is clear in humans but is also true in every other sexually reproducing species. Imagine the difficulty of biologists – sequencing and studying only one genome is not enough because every individual is genetically different!

Physical Traits and Variances: 

Physical Traits and Variances Individual variation among a species occurs in populations of all sexually reproducing organisms. Individual variations range from hair and eye color to less subtle traits such as susceptibility to malaria. Physical variation is the reason we can pick out our friends in a crowd, however most physical traits and variation can only be seen at a cellular and molecular level.

Sources of Physical Variation: 

Sources of Physical Variation Physical Variation and the manifestation of traits are caused by variations in the genes and differences in environmental influences. An example is height, which is dependent on genes as well as the nutrition of the individual. Not all variation is inheritable – only genetic variation can be passed to offspring. Biologists usually focus on genetic variation instead of physical variation because it is a better representation of the species.

Genetic Variation: 

Genetic Variation Despite the wide range of physical variation, genetic variation between individuals is quite small. Out of 3 billion nucleotides, only roughly 3 million base pairs (0.1%) are different between individual genomes of humans. Although there is a finite number of possible variations, the number is so high (43,000,000) that we can assume no two individual people have the same genome. What is the cause of this genetic variation?

Sources of Genetic Variation: 

Sources of Genetic Variation Mutations are rare errors in the DNA replication process that occur at random. When mutations occur, they affect the genetic sequence and create genetic variation between individuals. Most mutations do not create beneficial changes and actually kill the individual. Although mutations are the source of all new genes in a population, they are so rare that there must be another process at work to account for the large amount of diversity.

Sources of Genetic Variation: 

Sources of Genetic Variation Recombination is the shuffling of genes that occurs through sexual mating and is the main source of genetic variation. Recombination occurs via a process called crossing over in which genes switch positions with other genes during meiosis. Recombination means that new generations inherit random combinations of genes from both parents. The recombination of genes creates a seemingly endless supply of genetic variation within a species.

Why Bioinformatics?: 

Why Bioinformatics?

Why Bioinformatics?: 

Why Bioinformatics? Bioinformatics is the combination of biology and computing. DNA sequencing technologies have created massive amounts of information that can only be efficiently analyzed with computers. So far 70 species sequenced Human, rat chimpanzee, chicken, and many others. As the information becomes ever so larger and more complex, more computational tools are needed to sort through the data. Bioinformatics to the rescue!!!

What is Bioinformatics?: 

What is Bioinformatics?

Bio-Information: 

Bio-Information Since discovering how DNA acts as the instructional blueprints behind life, biology has become an information science Now that many different organisms have been sequenced, we are able to find meaning in DNA through comparative genomics, not unlike comparative linguistics. Slowly, we are learning the syntax of DNA

Sequence Information: 

Sequence Information Many written languages consist of sequential symbols Just like human text, genomic sequences represent a language written in A, T, C, G Many DNA decoding techniques are not very different than those for decoding an ancient language

Amino Acid Crack: 

Amino Acid Crack Even earlier, an experiment in the early 1900s showed that all proteins are composed of sequences of 20 amino acids This led some to speculate that polypeptides held the blueprints of life

Central Dogma: 

Central Dogma DNA mRNA Proteins DNA in chromosome is transcribed to mRNA, which is exported out of the nucleus to the cytoplasm. There it is translated into protein Later discoveries show that we can also go from mRNA to DNA (retroviruses). Also mRNA can go through alternative splicing that lead to different protein products.

Structure to Function: 

Structure to Function Organic chemistry shows us that the structure of the molecules determines their possible reactions. One approach to study proteins is to infer their function based on their structure, especially for active sites.

BLAST: 

BLAST A computational tool that allows us to compare query sequences with entries in current biological databases. A great tool for predicting functions of a unknown sequence based on alignment similarities to known genes.

BLAST: 

BLAST

Some Early Roles of Bioinformatics: 

Some Early Roles of Bioinformatics Sequence comparison Searches in sequence databases

Biological Sequence Comparison: 

Biological Sequence Comparison Needleman- Wunsch, 1970 Dynamic programming algorithm to align sequences

Early Sequence Matching : 

Early Sequence Matching Finding locations of restriction sites of known restriction enzymes within a DNA sequence (very trivial application) Alignment of protein sequence with scoring motif Generating contiguous sequences from short DNA fragments. This technique was used together with PCR and automated HT sequencing to create the enormous amount of sequence data we have today

Biological Databases: 

Biological Databases Vast biological and sequence data is freely available through online databases Use computational algorithms to efficiently store large amounts of biological data Examples NCBI GeneBank http://ncbi.nih.gov Huge collection of databases, the most prominent being the nucleotide sequence database Protein Data Bank http://www.pdb.org Database of protein tertiary structures SWISSPROT http://www.expasy.org/sprot/ Database of annotated protein sequences PROSITE http://kr.expasy.org/prosite Database of protein active site motifs

Sequence Analysis: 

Sequence Analysis Some algorithms analyze biological sequences for patterns RNA splice sites ORFs Amino acid propensities in a protein Conserved regions in AA sequences [possible active site] DNA/RNA [possible protein binding site] Others make predictions based on sequence Protein/RNA secondary structure folding

It is Sequenced, What’s Next?: 

It is Sequenced, What’s Next? Tracing Phylogeny Finding family relationships between species by tracking similarities between species. Gene Annotation (cooperative genomics) Comparison of similar species. Determining Regulatory Networks The variables that determine how the body reacts to certain stimuli. Proteomics From DNA sequence to a folded protein.

Modeling: 

Modeling Modeling biological processes tells us if we understand a given process Because of the large number of variables that exist in biological problems, powerful computers are needed to analyze certain biological questions

Protein Modeling: 

Protein Modeling Quantum chemistry imaging algorithms of active sites allow us to view possible bonding and reaction mechanisms Homologous protein modeling is a comparative proteomic approach to determining an unknown protein’s tertiary structure Predictive tertiary folding algorithms are a long way off, but we can predict secondary structure with ~80% accuracy. The most accurate online prediction tools: PSIPred PHD

Regulatory Network Modeling : 

Regulatory Network Modeling Micro array experiments allow us to compare differences in expression for two different states Algorithms for clustering groups of gene expression help point out possible regulatory networks Other algorithms perform statistical analysis to improve signal to noise contrast

Systems Biology Modeling: 

Systems Biology Modeling Predictions of whole cell interactions. Organelle processes, expression modeling Currently feasible for specific processes (eg. Metabolism in E. coli, simple cells) Flux Balance Analysis

Topics in Bioinformatics: 

Topics in Bioinformatics Sequence analysis Protein folding, interactions and modelling (structural genomics) Microarray; Mass Spectrometry (functional genomics) Comparative genomics Regulatory network modeling; Systems Biology Database exploration and management

The future…: 

The future… Bioinformatics is still in it’s infancy Much is still to be learned about how proteins can manipulate a sequence of base pairs in such a peculiar way that results in a fully functional organism. How can we then use this information to benefit humanity without abusing it?

Slide108: 

R is a free software environment for statistical computing and graphics (www.r-project.org). Download and install the package. Download tutorial files from course web (http://www.biostat.pitt.edu/biost2055/07) and practice.

Slide109: 

R tutorial

Slide110: 

Review slides of basic molecular biology if you are not familiar with. Download and install R software. Follow the tutorial and practice basic operation in R. (Next Friday we’ll have the first computer lab session and homework using R)