Download Chapter 21 - HCC Learning Web

Chapter 21
GENOMES AND THEIR
EVOLUTION
• Genomics is the study of whole sets of genes
and their interactions
• http://www.youtube.com/watch?v=mmgIClg0Y1k
• Bioinformatics is the application of
computational methods to the storage and
analysis of biological data
• http://www.youtube.com/watch?v=xODTm4a6nsM
&feature=related
Figure 21.2-4
Chromosome
bands
Cytogenetic map
Genes located
by FISH
1 Linkage mapping
Genetic
markers
2 Physical mapping
Overlapping
fragments
3 DNA sequencing
Whole-Genome Shotgun Approach to
Genome Sequencing
• The whole-genome shotgun approach was
developed by J. Craig Venter in 1992
• http://www.wiley.com/legacy/wileychi/reecegenes/
chapter9_ani.html
• This approach skips genetic and physical mapping
and sequences random DNA fragments directly
• Powerful computer programs are used to order
fragments into a continuous sequence
Figure 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.
4 Order the
sequences into
one overall
sequence
with computer
software.
Identifying Protein-Coding Genes and
Understanding Their Functions
• Using available DNA sequences, geneticists can
study genes directly in an approach called reverse
genetics
• The identification of protein coding genes within
DNA sequences in a database is called gene
annotation
• Gene annotation is largely an automated process
• Comparison of sequences of previously unknown
genes with those of known genes in other species
may help provide clues about their function
Understanding Gene and Gene
Expression at the Systems Level
• Proteomics is the systematic study of all proteins
encoded by a genome
• Proteins, not genes, carry out most of the
activities of the cell
Figure 21.5
Glutamate
biosynthesis
Translation and
ribosomal functions
Mitochondrial
functions
Vesicle
fusion
RNA processing
Peroxisomal
functions
Transcription
and chromatinrelated functions
Metabolism
and amino acid
biosynthesis
Nuclearcytoplasmic
transport
Secretion
and vesicle
transport
Nuclear migration
and protein
degradation
Mitosis
DNA replication
and repair
Cell polarity and
morphogenesis
Protein folding,
glycosylation, and
cell wall biosynthesis
Serinerelated
biosynthesis
Amino acid
permease pathway
Table 21.1
• About 25% of the human genome codes for
introns and gene-related regulatory sequences
(5%)
• Intergenic DNA is noncoding DNA found between
genes
– Pseudogenes are former genes that have
accumulated mutations and are nonfunctional
– Repetitive DNA is present in multiple copies in
the genome
• About three-fourths of repetitive DNA is made up
of transposable elements and sequences related
to them
Figure 21.7
Exons (1.5%)
Regulatory
sequences
(20%)
Repetitive
DNA that
includes
transposable
elements
and related
sequences
(44%)
L1
sequences
(17%)
Alu elements
(10%)
Introns (5%)
Unique
noncoding
DNA (15%)
Repetitive
DNA
unrelated to
transposable
elements
(14%)
Simple sequence
DNA (3%)
Large-segment
duplications (56%)
Transposable Elements and Related
Sequences
• The first evidence for mobile DNA segments
came from geneticist Barbara McClintock’s
breeding experiments with Indian corn
• McClintock identified changes in the color of corn
kernels that made sense only by postulating that
some genetic elements move from other genome
locations into the genes for kernel color
• These transposable elements move from one
site to another in a cell’s DNA; they are present in
both prokaryotes and eukaryotes
• http://www.youtube.com/watch?v=_Ol492CLk
dY
Figure 21.9
Transposon
DNA of
genome
Transposon
is copied
Mobile transposon
New copy of
transposon
Insertion
Figure 21.10
Retrotransposon
New copy of
retrotransposon
Formation of a
single-stranded
RNA intermediate
RNA
Insertion
Reverse
transcriptase
Genes and Multigene Families
• Many eukaryotic genes are present in one copy per
haploid set of chromosomes
• The rest of the genome occurs in multigene families,
collections of identical or very similar genes
• Some multigene families consist of identical DNA
sequences, usually clustered tandemly, such as those
that code for rRNA products
• The classic examples of multigene families of nonidentical
genes are two related families of genes that encode
globins
• α-globins and β-globins are polypeptides of hemoglobin
and are coded by genes on different human
chromosomes and are expressed at different times in
development
Figure 21.11
DNA
RNA transcripts
Nontranscribed
Transcription unit
spacer
-Globin
-Globin
Heme
DNA
18S
5.8S
28S
rRNA
28S
5.8S
18S
(a) Part of the ribosomal RNA gene family
-Globin gene family
Chromosome 16

Embryo
   2 1 
2
1
-Globin gene family
Chromosome 11

G
A
Fetus
and adult Embryo Fetus



Adult
(b) The human -globin and -globin gene families
Duplication, rearrangement, and mutation
of DNA contribute to genome evolution
• The basis of change at the genomic level is
mutation, which underlies much of genome
evolution
• The earliest forms of life likely had a minimal
number of genes, including only those necessary
for survival and reproduction
• The size of genomes has increased over
evolutionary time, with the extra genetic material
providing raw material for gene diversification
Figure 21.14
Ancestral globin gene
Evolutionary time
Duplication of
ancestral gene
Mutation in
both copies

Transposition to
different chromosomes
Further duplications
and mutations






   2 1 
2
1
-Globin gene family
on chromosome 16



G

A


-Globin gene family
on chromosome 11

Figure 21.15
EGF
EGF
EGF
EGF
Epidermal growth
factor gene with multiple
EGF exons
F
F
F
Exon
shuffling
Exon
duplication
F
Fibronectin gene with multiple
“finger” exons
F
EGF
K
K
K
Plasminogen gene with a
“kringle” exon
Portions of ancestral genes
Exon
shuffling
TPA gene as it exists today
Figure 21.UN01
Bacteria
Genome
size
Number of
genes
Gene
density
Introns
Other
noncoding
DNA
Archaea
Most are 16 Mb
1,5007,500
Higher than in eukaryotes
None in
protein-coding
genes
Present in
some genes
Very little
Eukarya
Most are 104,000 Mb, but a
few are much larger
5,00040,000
Lower than in prokaryotes
(Within eukaryotes, lower
density is correlated with larger
genomes.)
Unicellular eukaryotes:
present, but prevalent only in
some species
Multicellular eukaryotes:
present in most genes
Can be large amounts;
generally more repetitive
noncoding DNA in
multicellular eukaryotes