Genomes and Their Evolution AP Biology Ch 18 CVHS

Vast stores of Biological Information Genomics: the study of whole sets of genes and their interactions. Proteomics: Study of proteins and their functions (more useful) Bioinformatics: Computation method of storing and analyzing biological information

Physical vs. Linkage Map Figure 15.8 Mutant phenotypes Short aristae Black body Cinnabar eyes Vestigial wings Brown Long aristae (appendages on head) Gray Red Normal Wild-type phenotypes II Y I X IV III 48.5 57.5 67.0 104.5 Linkage Map Order of genetic markers and distance between them Physical Map Actual base pair distance between 2 genes Uses RFLP’s w/ sticky ends to map the gene Used ddNTP (modified nucleotide w/out an OH at the 3’ end) at the end of the strand to stop chain elongation, gel electrophoresis then sequences DNA

Cytogenetic map Chromosome bands Genes located by FISH Linkage mapping Fig. 21-2-4 Cytogenetic map Chromosome bands Genes located by FISH 1 Linkage mapping Genetic markers 2 Physical mapping Figure 21.2 Three-stage approach to sequencing an entire genome Overlapping fragments 3 DNA sequencing

Shotgun Sequencing Cut DNA from multiple copies of a chromosome Clone the DNA fragments (simply to increase #) Sequence each fragment using ddNTP Computer uses sticky ends and base pairing rules to order the DNA

fragments short enough for sequencing Fig. 21-3-3 1 Cut the DNA into overlapping fragments short enough for sequencing 2 Clone the fragments in plasmid or phage vectors. 3 Sequence each fragment. Figure 21.3 Whole-genome shotgun approach to sequencing 4 Order the sequences into one overall sequence with computer software.

National Data-Bases & Uses National Center for Biotechnology Information.mht NCBI has a program called BLAST that allows anyone to compare DNA sequences. You can go home and do this.  NIH is creating a data-base for comparing normal cells to 3 types of cancer cells Ovarian Glioblastoma of the brain Lung cancer

How do we determine the function of New Genes that are discovered? 1. Match a known gene, therefore functions similarly 2. New sequence may be similar to a known gene whose function is unknown & will help us learn the function of the other 3. Completely unknown: use protein coded for to help determine function

Why do organisms with larger genomes not always have more genes? Alternative RNA splicing in eukaryotic cells. In general Prokaryotes have small genomes relative to eukaryotes

Human DNA types

Transposable Elements (25 to 50%) of mammalian genomes: pieces of DNA that move locations in the genome allow evolutionary changes to occur Tranposons Copied by DNA enzymes and the pasted into a new position Retrotranposons: DNA -> RNA-> reverse transcriptase -> DNA Sequences related to transposable elements: Alu: 10% of human genome, no known function L1 :17% of human genome, may help regulate gene expression

Transposons & Retrotransposons

Simple Sequence DNA & Short Tandem Repeats Simple Sequence DNA: short sequences that are tandemly repeated STR: a repetitive unit of DNA w/ 2 to 5 nucleotides Used in forensic science: the # of STR’s on a particular gene varies greatly between individuals, PCR and Gel Electrophoresis can be used to determine if an individual was present at a crime scene

Multigene Families Identical: Clustered together, have RNA as final product rRNA gene (allows a lot of copies to be made) Nonidentical: Usually on separate chromosomes, make a group of related proteins Globins (hemoglobin)

Genome Evolution Ways that Genomes Change: Chromosome Duplication Chromosome Alteration Duplication & Divergence Gene (regions) Duplication & Divergence Exon Duplication & shuffling Transposable Elements

Exon Shuffling http://upload.wikimedia.org/wikipedia/en/9/9a/Exon_shuffling.png

Evolutionary Relationships and Genes Closely related spp. Look to sequences differences Repeating sequences Alu’s, more present in humans than chimps Distantly related spp. Look to highly conserved proteins and compare gene sequences Evo-Devo, compare developmental processes of different organisms Homeobox (Hox genes): Control anterior (front) & posterior (back) development in fruit flies & mice same genetic sequences

Bacteria Most recent common ancestor of all living things Eukarya Archaea 4 3 2 1 Billions of years ago Chimpanzee Human Mouse 70 60 50 40 30 20 10 Millions of years ago