1. From Mendel to Genomics
Historically
Identify or create mutations, follow inheritance
Determine linkage, create maps
Now: Genomics
Not just a gene, but as many genes as may be involved in a process.

2. Genomics: The study of genes and their function
Genomics: The study of genes and their function. Genomics aims to understand the structure of the genome, including the mapping genes and sequencing the DNA. Genomics examines the molecular mechanisms and the interplay of genetic and environmental factors in disease.
Genomics:
Focus: entire genome, not individual genes
Uses recombinant DNA methods
Methodology in place for sequencing entire genomes

3. Genomics includes:
Functional genomics -- the characterization of genes and their mRNA and protein products.
Structural genomics -- the dissection of the architectural features of genes and chromosomes.
Comparative genomics -- the evolutionary relationships between the genes and proteins of different species.

4. Bioinformatics
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

5. Sequencing 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
Sequence all the clones
Use supercomputer to determine order
Sequencing done multiple times to get it right.

6. Clone-by-clone
Shotgun approach
intermediate/all/

7. Is sequencing a genome the answer?
No, only the beginning of the questions.

8. Annotation: 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

9. Where is the reading frame?
Could start in one of 3 different places.

10. Find the start codon. Do all the codons that follow spell out a protein sequence seen before?

11. Functional 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 that have lecuine zippers bind to DNA

12. Fundamental 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.

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

14. Protein synthesis 90
Protein fate 21
Regulatory functions 5
Cell envelope 29
Cellular processes 6
Other categories
Unknown 12
Hypothetical
Database match
168
No database match
Total number
483

15. Advances 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

16. Understanding-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

17. Proteomics 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

18. Proteomics: study of proteins
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

19. 2D gel electrophoresis of proteins
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.