1. Ch 12: Genomes

2. Open Reading Frame

3. Transcription Termination Sequence
PROMOTER
(TATA box) A B C
Transcription Termination Sequence
DNA A
Exon B
Intron C
Pre-mRNA
Mature RNA
5’ Cap
Start Codon A C
Stop Codon
Poly-A Tail
Open Reading Frame

4. Human Genome

5. Human Genome Project 1970: (Frederick Sanger)- 13 years, $2.7 billion
2000: (PCR/Flourescent Tagging)- days, $thousands
CHALLENGE: “Reads” or fragments of DNA are so hard to put in order
2.5M fragments in 100bp
Introduced the field of Bioinformatics

6. Bioinformatics

7. Bioinformatics: Genomics
Functional Genomics look at Open Reading Frame:
Recognize the START/STOP of a gene
Where introns are removed
Comparative Genomics- compare genomes of other organisms

8. Bioinformatic Studies
Genomics
Proteonomics
Metabolomics
Determine DNA nucleotide order & genes made from it
PCR amplifies DNA fragments (reads), & Fluorescent tags are added
Determine all possible expressed proteins
Gel Electrophoresis
Mass Spectroscopy
Determine metabolites (enzyme reactions)
Hormones, signal molecules, antibiotics
Spectroscopy gives “chemical snap shots”

9. GENOME PROTEOME METABOLOME PHENOTYPE E E I E E Gene mRNA Protein
Metabolites
*1 gene has many exon combo’s, therefore, many protein possibilities
*different in different environments
Genome

10. Genome Differences

11. Genome Differences Prokaryotic Genome Eukaryotic Genome Large
Small (160,000-12,000,000bp) circular chromosome
Mostly protein-coding DNA (minimal introns)
Tiny Plasmid DNA passes between individuals
Transposons- small movable sequences of DNA that can bounce around
Large
More Protein-Coding DNA
Lots of Regulatory Sequences (Transcription Factors)
Mostly Non-Coding DNA

12. Findings from the Genome

13. Helpful Organisms Functions of the Eukaryotic Genome
Yeast (Saccharomyces cerevisiae)- organelles
Fruit Fly (Drosophila melanogaster)- genetics
Roundworm (Caenorhabditis elgans)- embryonic differentiation
Functions of the Eukaryotic Genome

14. Gene Families (closely related genes)
Gain Functions
1 functional gene/protein, while the other genes mutate *Evolution
Ex. Hemoglobin (ɑ-globin, ß-globin, ϒ-globen)
ADULT: ɑ, ɑ, ß, ß
FETUS: ϒ *holds more oxygen –gets oxygen from mom
BEFORE BIRTH: ɑ, ɑ, ß, ß
Pseudogenes (Ψ)- a protein that lost its function due a mutation

15. Repetitive Sequences Don’t code for proteins
Highly Repetitive (<100bp)- repeat 1,000x
10% of human genome (50% in fruit flies)
Short Tandem Repeats (STR’s) (1-5bp)- repeat 100x
Moderately Repetitive (Transposons) -repeat 10-1,000x
40% human genome
Retrotransposons- RNA copies of themselves that get turned back into DNA
DNA Transposons- stay DNA, just move around

16. Genome Surprises
Splicing (RNA editing) causes way less protein-coding genes than expected
Gene sizes can vary
Genes: 1,000-2,400,000bp
Protein Size: 100-5,000 amino acids
All human genes have introns
A lot of the genome is non-coding, but functional
50% of the Genome is Transposons & Repetitive Sequences
Genome is 97% identical in humans

17. Benefits Identify Genetic Disorders with Halotype Maps
Halotype- piece of chromosome with a set of SNP’s
Use Single Nucleotide Polymorphism (SNP’s)- point mutations, passed down in groups
DNA Fingerprinting- Easily display Short Tandem Repeats (STR’s)
FBI stores 13 STR loci in its database
Pharmacogenomics- how people’s genetics would react to a drug
Proteomics- compare proteins to find out evolutionary relatives
Metabolomics- relate metabolites to diseases (diabetes)