9.5 Genomics and Bioinformatics Updates: Restriction enzymes cut sites practice due Homework: –Read 17.3 –Molecular clocks: cytochrome C due tomorrow Unit 5 quiz 2 Thursday Keystone Biology Exam: 5/15, 5/18

9.5 Genomics and Bioinformatics Keystone Question of the Day (review 3.2): Which of the following organelles performs photosynthesis in (most) eukaryotic producers? –chloroplasts –the endoplasmic reticulum –the Golgi apparatus –mitochondria

9.5 Genomics and Bioinformatics Eastern Massasauga Rattlesnake Sistrurus catenatus Size: inches in length Status: Endangered Species Habitat: western PA swamps, marshes, bogs, peat lands, wet meadows, prairie lands, low lying poorly drained soil, dry open fields with lots of vegetation. The habitat will vary with seasons.

9.5 Genomics and Bioinformatics Why do biologists compare DNA and protein sequences? Activator: Identify the type of mutation and its effect on translation. Original DNA: CAC GTG GAC TGA GGA CTC CTC Mutated DNA: CAC GTG GAC TGA GGA CAG CTC Key terms: gene sequencing, genomics, bioinformatics, proteomics,

9.5 Genomics and Bioinformatics Sequencing genes is now a part of basic research. Gene sequencing determines the order of nucleotides in a gene. Why? –Discover genes of interest for research –Identify mutations of interest to medicine –Compare sequences in populations or between species

9.5 Genomics and Bioinformatics Activity: sequencing clock genes Scientists have discovered the genes that control internal clocks: period (per), clock (clk), cycle (cyc), timeless (tim), frequency (frq), doubletime (dbt) and others. Clock genes have been found in people to mice, fish, fruit flies, plants, molds, and even single-celled cyanobacteria. Larks vs. owls? Can’t sleep? Nocturnal vs. diurnal?

9.5 Genomics and Bioinformatics 89% of the DNA sequence of the Clock gene in a mouse is shared with a human CLOCK gene. –Does that mean we are more similar or different? –Related?

9.5 Genomics and Bioinformatics We can now study and compare genes and genomes. Genomics is the study of genomes, the DNA sequences of entire organisms. Basic research medicine ecology & evolution biotechnology

9.5 Genomics and Bioinformatics Whole genome sequencing:

9.5 Genomics and Bioinformatics Human Genome Project Discussion What were some of the strange and unexpected things that scientists discovered when they analyzed the human genome? Why do scientists compare the DNA of bananas, worms, fruit flies, and humans? How can this information be helpful? Scientists have likened the human genome to a parts list. Explain what they mean. Can you think of another analogy?

9.5 Genomics and Bioinformatics

Gene and protein sequences are studies with computers Bioinformatics is the use of computer databases to organize and analyze biological data. –because DNA is shared (conserved) because of evolution, comparisons of genomes within and across species are possible

9.5 Genomics and Bioinformatics Technology allows the study and comparison of both genes and proteins. Proteomics is the study and comparison of proteins.

9.5 Genomics and Bioinformatics GULO (L-gulonolactone oxidase) is the enzyme that produces vitamin C from glucose. Pigs and cows have a high number of conserved bases in this gene when compared to each other, while the human gene has a very low number of conserved bases when compared to pigs or cows. Which is potentially more alike/closely related? –pigs and cows? –cows and humans? –Humans and pigs? Humans historically have a diet rich in fruit and also no longer produce GULO from this gene. What might have happened?

9.5 Genomics and Bioinformatics Discussion: Personal DNA Testing Explain what SNPs are. How are SNPs used in genetic testing, and what can they reveal? Describe the Personal Genome Project and explain its goals. Discuss whether you would agree to provide your DNA sample to the Personal Genome Project. Explain the reasons for your choice.

9.5 Genomics and Bioinformatics Cytochrome C comparisons: clocks and trees

9.5 Genomics and Bioinformatics

Personal DNA Testing Explain what SNPs are. How are SNPs used in genetic testing, and what can they reveal? Discuss whether you would agree to provide your DNA sample to the Personal Genome Project. Explain the reasons for your choice.

9.5 Genomics and Bioinformatics The Costs and Benefits of Treating Gene Defects List two or three of the “downsides” surrounding the genetic testing of children. Would you want to know if one of your own children were likely to have a debilitating condition or disease, like Alexis? If so, how early in their lives would you wish to know? Explain your answers.

9.5 Genomics and Bioinformatics

Updates: Last call for Unit 5 1 st Marking Period Tonight –Predicting evolutionary relationships due tomorrow –Reading 17.3 –Transciption/translation processes –Unit 5 quiz 2 Friday: 1.5, 8.2, 8.4, 8.5, 8.7, 9.5, –Unit 5 test Wednesday November 5 th, vocab due

9.5 Genomics and Bioinformatics What is a molecular clock? Activator: –What did Pardis Sabeti figure out? Why do you think it was considered a scientific breakthrough? –Why do you think Pardis describes her breakthrough as a "wonderful scavenger hunt"? –What is meant by the term "resistant" in the context of disease-causing organisms? Key terms: mitochondrial DNA (mtDNA), molecular clock

9.5 Genomics and Bioinformatics Mutations Revisited Mutations alter the sequence of a gene: –random “typos” –heritable –natural variation Effects: –neutral –beneficial –harmful (deleterious)

9.5 Genomics and Bioinformatics Scientists attempt to link molecular data and real time. –an event known to separate species –the first appearance of a species in fossil record

9.5 Genomics and Bioinformatics Molecular clocks use mutations to estimate evolutionary time. Mutations add up at a constant rate in related species. –This rate is the “ticking” of the molecular clock. –As more time passes, there will be more mutations. DNA sequence from a hypothetical ancestor The DNA sequences from two descendant species show mutations that have accumulated (black). The mutation rate of this sequence equals one mutation per ten million years. Mutations add up at a fairly constant rate in the DNA of species that evolved from a common ancestor. Ten million years later— one mutation in each lineage Another ten million years later— one more mutation in each lineage

9.5 Genomics and Bioinformatics Discussion: What did lice teach us about human evolution?

9.5 Genomics and Bioinformatics Mitochondrial DNA is used to study closely related organisms. –mutation rate ten times faster than nuclear DNA –passed down unshuffled* from mother to offspring grandparents parents child Nuclear DNA is inherited from both parents, making it more difficult to trace back through generations. Mitochondrial DNA is passed down only from the mother of each generation,so it is not subject to recombination. mitochondrial DNA nuclear DNA

9.5 Genomics and Bioinformatics Ribosomal RNA is used to study distantly related species. –many conserved regions –lower mutation rate (slow ticker)

9.5 Genomics and Bioinformatics Summary: What can studying bird brains and bird genes tell us about the evolution of the nervous system? What can making comparisons between humans and birds tell us about language and speech disorders?