Chapter 21

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Genomes and Their
Evolution
Chapter 21
Tree of Life
 Genomics- is the study of whole sets of genes and their
interactions
 Bioinformatics-uses computers to store the large
amounts of data created by genomics
 Human Genome Project- sequencing human genome
began in 1990 and completed in 2003
3 Stage
Sequencing
 Cytogenetic maps
started the detailed
mapping
 Linkage maps created
the basic order and
relative distances of
genes
 Physical maps express
distances in number of
base pairs
 The final step is
sequencing by dideoxy
chain termination
Shotgun
Approach
 Venter used
step 3 and
computers to
sequence whole
genes.
 Most widely
used method.
Bioinformatics Analyze Genomes
 Analyzing resources were centralized (NCBI)
http://www.ncbi.nlm.nih.gov/ and houses “Genbank”
 Software is available like Blast that allows genome
comparison.
 NCBI also contains 3-D protein structures
 Expressed Sequence Tags (ESTs)are used to search the
sequence for known genes
 For genes of unknown proteins biochemical and
functional studies must be preformed.
Proteomics
 Proteomics is the study of
the whole proteome and its
interactions.
 A study of 10,000 RNA
transcripts yeieded 4700
proteins and over 4000
interactions.
 Global protein interaction
maps show the interactions
Systems Biology
 Systematic approach has
proved valuable in cancer
research
 Gene Chips can hold
microarrays for most of the
human genes.
Genome Size, Number, & Density
 Prokaryote genomes are much smaller than eukaryotes
ranging from 1-6 Mb (million base pairs)
 Most animals and plants are at least 100 Mb
 In eukaryotes the size of the genome has no affect on
complexity.
 Bacteria and archaea have fewer genes 1,500-1,700
compared to 5,000 to 40,000 for eukaryotes
 Humans have 3,200 Mb and 20,488 genes because of
alternative splicing of genes
 Mammals have the lowest gene densities because of the
inclusion of introns and non-coding regions.
Noncoding DNA & Multigene
Families
 Noncoding regions have yet unknown functions but are
highly conserved among related species.
 1.5% of Human DNA is coding and only 24% has a
regulatory function.
 Pseudogenes have acquired mutations and are
nonfuntional account for 15%
 Repetitive DNA 44% sequences in multiple copies, these
include transposable elements.
Transposable Elements
 Transposable elements
can move from one
location to another in the
genome
 Move by a recombination
process.
 Transposons move cut
and paste mechanisms
 Retrotransposons
(common) move using a
RNA intermediate
 Barbara McClintock proposed
mobile genetic elements
Transposon
Sequences
 Alu elements 10% are
transcribed into RNA
but function is
unknown
 Line 1 (L1) is a
retrotransposon that
may regulate gene
expression
Other Repetitive DNA
 Most repetitive DNA occurred from mistakes in
replication or recombination 15%
 Long duplications 5% are copied from chromosomal
location to chomosome.
 Simple Sequence DNA 3% contains multiple copies of
tandemly repeated short sequences.
 Short Tandem Repeats (STRs) consist of 2-5 nucleotides
 Simple Sequence DNA is located in telomeres and
centromeres suggestion chromosome formation function
Gene Families
 Human coding DNA occurs in identical or nonidentical
gene families
 Identical Families usually make RNAs or histones. Eg.
rRNA gene families. 3 rRNAs are made from one family
 Nonidentical families code for related proteins but have
different locations. See Hemoglobin proteins.
DNA Evolution by Duplication,
Rearrangement, & Mutation
 Polyploidy could facilitate gene evolution by one copy
providing essential function and the other evolving new
functions.
 Chromosome alterations can create new species by
altering the chromosome number
 Duplication or divergence of gene sized DNA is
evidenced in the existence of multigene families
Genes of Related Functions
 Hemoglobin а & β share a common ancestor and have
evolved from duplication and divergence about 450
million years ago.
 Sometime the duplication and divergence leads to genes
with new and different functions
Exon Duplication & Exon Shuffling
Clues to Evolution & Development
 The more similar the genome the more closely related
the two organisms
 Comparison of distantly related species provide
information about highly conserved and the origins of
early life
 Closely related analysis shows the fundamental genes
necessary to belong to a group.
 Comparison of closely related species can provide info
about how organisms genomes are evolving.
Transcription Factor Evolution
 FOXP2 is a transcription factor evolving in humans that
functions in vocalizations
 The changes in FOXP2 are being studied to see if these
are the reasons for human and chimp vocalization
differences.
 The detection of SNPs and other genetic markers can
lead to a trail of human evolution and migration.
Homeotic Genes
 Evo-devo is the study of
evolutionary
developmental biology
 Changes in development
genes can help trace
evolution
 The homeobox is included
in every homeotic gene
Hox Gene Expression
 Homeotic genes in animals are called Hox genes
 Hox genes initiate transcription but require more specific
proteins to turn on specific genes.
 Variations in Hox genes can have profound affect on the
development of the phenotype of organisms
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