1From Mendel to Genomics• Historically

– Identify or create mutations, follow inheritance• Determine linkage, create

maps• Genomics: use of recombinant

DNA methods– Focus: entire genome, not

individual genes– Methodology in place for

sequencing entire genomes

www.bastardidentro.com

2Bioinformatics

• Sequencing creates huge amount of information that must be stored and analyzed

• Bioinformatics is the science of methods for storing and analyzing that information– Melding of computer

science and molecular biology

http://www.swbic.org/products/clipart/images/bioinformatics.jpg

3Proteomics

• Proteome: all the proteins an organism makes• Proteomics: the study of those proteins

– Timing of gene expression– Regulation of gene expression– Modifications made to proteins– Functions of the proteins– Subcellular location of proteins

http://www.emc.maricopa.edu/faculty/farabee/BIOBK/3_14d.jpg

4Sequencing the Human Genome• Publicly funded consortium

– Clone-by-clone method– Create library of clones of entire genome– Order clones using various DNA markers– Then sequence each clone

• Craig Venter and private enterprise– Shotgun method– Create library of clones of entire genome– Sequence all the clones– Use supercomputer to determine order

• Sequencing done multiple times to get it right.

5Clone-by-clone Shotgun approach

www.yourgenome.org/ intermediate/all/

6Annotation: making sense of the sequence

• Looking for regulatory regions, RNA genes, repetitive regions, and protein genes.

• Finding protein genes– Look for ORFs (open reading frames)

• Start codon (ATG), stop codon.• Codons must be “in frame”, distance long enough

– Problems: 3 reading frames x 2 strands, widely spaced genes, introns.

– Help: new software finds TATA box and other elements; codon bias can help• Different codons not used equally in organisms

7Where is the reading frame?

Could start in one of 3 different places.

8Functional Genomics

• OK you have a sequence. What does the gene do? What is the function of the protein?– Search database for similar sequences– How does sequence compare to sequences for

proteins of known function?– Use computer to search for functional motifs.

• Various proteins that do the same thing have similar structural elements.

• Example: transcription factors like lecuine zippers

9Fundamental questions

• Questions can be asked using whole genome information that couldn’t before.– How did genomes evolve?– What is the minimum number of genes necessary

for a free-living organism?• Much can be learned about the ecology of an

organism by genomics and proteomics.– First bacterium sequenced: Mycoplasma genitalium– Lives a parasitic existence, evident from genes.

10Protein function # of genesAmino acid biosynthesis 0Purine, pyrimidine, nucleoside and nucleotide metabolism 19Fatty acid and phospholipid metabolism 8Biosynthesis of co-factors, prosthetic groups and carriers 4Central intermediary metabolism 7Energy metabolism 33Transport and binding proteins 33DNA metabolism 29Transcription 13

11Protein synthesis 90Protein fate 21Regulatory functions 5Cell envelope 29Cellular processes 6Other categories 0Unknown 12HypotheticalDatabase match 168No database match 6

Total number 483

12Advances in understanding genomes

• Prokaryotic- eubacterial• not all genomes are circular• not all genomes are in one piece• when is a plasmid not a plasmid but a

chromosome?• not all genomes are small• very little wasted space, very few with introns

• Significant quantity of genes organized into operons

13Understanding-2

• Archaeal genomes similar to eubacteria but• have histones, sequence similarities to

eukaryotes, and introns in tRNA genes• Eukaryotic genomes -wide variations

• low gene density, that is few genes per amount of DNA

• introns, more in some (humans) than others• repetitive sequences

14Proteomics: study of proteins• Proteomics

– 35,000 genes, 100,000 different proteins• must be lots of post translational modifications

–>100 different ways of modifying proteins–addition of groups, crosslinking, inteins

• many genes code for proteins of unknown function

– methods of study• 2D gel electrophoresis• Peptide fragments generated with trypsin, studied

by MS

152D gel electrophoresis of proteins

http://www.biochem.mpg.de/en/research/rd/oesterhelt/web_page_list/Proteome_Hasal_cytosolic/absatz_3_bild.gif

Blue and green arrows mark proteins of interest.

Proteins of Halobacterium.

Left to right: pH

Vertical: MW

Spots digested w/ trypsin then studied using mass spec.

16Biotechnology

• What is Biotechnology?– Use of organisms, especially microbes, to produce

useful products?• Beer, wine, bread, organic solvents, antibiotics• By this definition, very very old.

– Use of recombinant DNA techniques to harness the power organisms to make use products.• Very new technology• Includes herbicide-resistant plants, human

proteins produced in yeasts, new vaccines.

17Biotechnology has several applications:overview

• Agriculture– Herbicide resistant plants– Improved nutritional qualities

• Pharmaceuticals– Production of human proteins as drugs– Production of vaccines

• Medical, legal, biological– Screening for, treatment of genetic disease– DNA fingerprinting, biological conservation

18Herbicide resistance

• Example: glyphosate resistant plants– More than 2/3 of US soybeans and cotton– Glyphosate inhibits EPSP synthase gene

• Engineered plants have extra copies of gene, make more enzyme, so are more resistant.

• Steps in engineering:– Gene from E. coli. Put next to strong promoter – Cloned into Ti plasmid, plasmid put back into

A. tumefaciens which carries plasmid to plant cell.– Grow whole plant from engineered plant cell

19Why and why not?• Use of herbicide-resistant plants means less

herbicide use, no-till farming. – less erosion and less non-point source pollution.

• Safe to eat? Why not?– Proteins not automatically destroyed during

digestion; allergies possible. Otherwise, what’s the problem?

• Environmental concerns– Toxic pollen? Herbicide resistant weeds?

• Biotech: same only more targeted and quicker.

20Ag-2: improved nutrition

• Not every food product has complete nutrition– Corn very low in the amino acid lysine– Countries relying on rice have low intake of beta-

carotene– Some plants have health-improving chemicals

• Transgenic plants can provide relief– Daffodil gene inserted into rice to make beta-

carotene, precursor to Vitamin A = golden rice• Critics say: not enough to make a difference.

21Pharmaceuticals

• Dwarfism, diabetes, cancer can be treated using human proteins– Obtained with difficulty– Insulin from slaughterhouse animals

• Recombinant insulin first from E. coli– Required combination of cloning, chemical

treatment– Starting point: mRNA, reverse transcriptase, then

insertion into plasmid vector– E. coli or yeast cells used.

22Future directions

• “pharming”: growing of protein drugs in farm plants and animals– Cloning into sheep (etc.) with mammary specific

promoter, only expressed in that tissue.• Released in, collected from milk.

– Using tobacco plants, especially for vaccines• Tobacco easy to grow, easy to engineer, easy to

harvest• Years of agricultural experience

23Vaccines

• Exposing host to antigens found on pathogen– Whole, live, weakened pathogen

• Strong immunity, but risk of live pathogen– Whole, dead pathogen

• Nucleic acid not “dead”; • cancer or toxic reaction

– Subunit vaccine: using a molecule from pathogen• Host reacts, then protects against later exposure

to entire pathogen

24Vaccines-2

• Recombinant vaccines– Clone gene for surface antigen of pathogen– Express gene i.e. get antigenic proteins made

• Collect proteins, process into vaccine– Express proteins in food

• Because there are food allergies, proteins taken orally can result in immune reactions

• Eliminates worries about sterilization, storage, needle-phobia

25Transgenic vaccine

26Medical diagnosis

• Sickle cell anemia– Fetal cell samples– CVS or amniocentesis– Gene obtained from fetal DNA

• Sickle cell anemia caused by a single nucleotide base substitution that removes a MstII site.

– Different banding pattern on gel indicates whether fetus will be a carrier or have disease (homozygous)

27Medical diagnosis -2

• Cystic fibrosis– Most cases causes by a specific deletion of DNA– PCR used to make allele-specific oligonucleotides

• This DNA hybridizes to region in normal gene that is deleted in faulty allele

• Absence of hybridization means deletion is present, person has the Cf allele.

• Huntington disease– Because of variable number of trinucleotide repeats,

probably PCR or VNTR-type test looking for varying lengths of DNA fragments.

28Ethics!

• Genetic engineering, medical tests opens up wide range of issues and questions– Environmental and global economic issues– Stem cell research and cloning– Who owns the data? Can someone else patent your

genes? Privacy issues.• Should your boss, insurance company,

government have access to your data?– We can tell you that you have the disease, but

• We can’t do anything about it!