1. Genomes and Their Evolution
AP Biology Ch 18 CVHS

2. 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

3. 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

4. Cytogenetic map Chromosome bands Genes located by FISH Linkage mapping
Fig
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

5. 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

6. fragments short enough for sequencing
Fig 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.

7. 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

8. 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

9. 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

10. Human DNA types

11. 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

12. Transposons & Retrotransposons

13. 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

14. 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)

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

16. Exon Shuffling

17. 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

18. 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