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8/2/2019 Myers Lecture 4 Eukaryotes Fall06
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8/2/2019 Myers Lecture 4 Eukaryotes Fall06
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4HumanBiology2AMyersLecture4: TheEukaryoticGenomeand itsExpression
What use are the genome sequences?
Can deduce most of the biochemical capabilities of a bacterial
species (which genes are present and which are absent are both
important for understanding the biology of each species)
Development of antibacterial drugs and vaccines is greatly
accelerated because coat proteins and other targets are known
DNA tests can be done to determine whether a strain carries
pathogenic versions of particular genes
Strains (especially of Streptomyces species) that produce
antibiotics and other valuable proteins or chemicals can be
identified much more quickly
Many environmental applications
5HumanBiology2AMyersLecture4: TheEukaryoticGenomeand itsExpression
Environmental DNA sequencing
Take uncultured, unseparated biological material from an
interesting site
Soil, water, polluted area
Human site (gums, gut, throat, etc.)
Filter out all organisms that are not bacterial species
Sequence the bacterial DNA as a pool (i.e., dont separate outdifferent bacterial species before sequencing)
Analyze the sequences to determine which species and/or
which types of genes are present in the pool
> 99% of bacterial species are not culturable
6HumanBiology2AMyersLecture4: TheEukaryoticGenomeand itsExpression
Sequenced genomic DNA from biofilm at toxic waste site
Collected about 76 Mb of sequence
Acid mine studyIron Mountain, CA (waste from iron mining)
Nature 438, 37-43 (March 2004)
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7HumanBiology2AMyersLecture4: TheEukaryoticGenomeand itsExpression
Superfund site
Discharging >1 ton of toxic metals/day
(pH
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10HumanBiology2AMyersLecture4: TheEukaryoticGenomeand itsExpression
Eukaryotes vs. prokaryotes
Life: The Science of Biology.
8th Edition. Sinauer Press.
Note: these numbers are not correct:
The smallest (free-living) prokaryotic genome is about 10 6 bp in length
The smallest eukaryotic genomes are about 10 7 bp in length (e,g Saccharomyces cerevisiae [Bakers yeast]genome is 12 Mb)
11HumanBiology2AMyersLecture4: TheEukaryoticGenomeand itsExpression
We now know the complete genome sequences of more
than 100 eukaryotic organisms
A product of The Human Genome Project (begun in 1990)
12HumanBiology2AMyersLecture4: TheEukaryoticGenomeand itsExpression
Uses of genome sequences
Key concept
Functions of many genes can be deduced by comparing the
DNA sequences in different organisms
Why?
Genes that encode proteins with the same or similar functions
in different organisms have similar DNA sequences(this is because all organisms are evolutionarily related, i.e., they all
share a common ancestry)
So: if you know the function of a gene in one organism(based
on experiments), you can guess the function of a gene of similarsequence in another organism
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13HumanBiology2AMyersLecture4: TheEukaryoticGenomeand itsExpression
Life: The Science of Biology.
8th Edition. Sinauer Press.
Complete genome sequences:
This is for the fruit fly, but the proportions are similar for humans
1. identify all the genes in an organism
2. allow classification of most genes into functional categories
14HumanBiology2AMyersLecture4: TheEukaryoticGenomeand itsExpression
50% of the human genome is composed of repetitive sequences
Much of the genome of higher animals is repetitive. Over time, it has become clear that much of this DNAconsists of mobile DNA elements (transposons) or their fossils.
--------- 45% (!!)
1. Small repeats
MicrosatellitesMinisatellites
(simple sequencerepeats)
2. Larger repeats
Gene family membersSegmental duplications (5% of the human genome)Range from several kb to many thousands of kb
15HumanBiology2AMyersLecture4: TheEukaryoticGenomeand itsExpression
Eukaryotic genes vary tremendously in size
Molecular Biology of the Cell.
4th Edition. Garland Science.
Some genes are even larger. The dystrophin gene (which is mutated in
boys with Duchenne muscular dystrophy) is more than 2 million base pairs inlength.
26 exons, 9,000 nucleotide-long
mature mRNA, 2,351 amino acids
in the protein3 exons, 600 nucleotide-longmature mRNA, 146 amino acids in
the protein
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16HumanBiology2AMyersLecture4: TheEukaryoticGenomeand itsExpression
Prokaryotes Eukaryotes
Molecular Biology of the Cell.
4th Edition. Garland Science.
17HumanBiology2AMyersLecture4: TheEukaryoticGenomeand itsExpression
Potential points for regulating gene expression in eukaryotes
Life: The Science of Biology.
7th Edition. Sinauer Press.
18HumanBiology2AMyersLecture4: TheEukaryoticGenomeand itsExpression
How eukaryotes control the expression oftheir genes
1. Transcription
2. Splicing
3. RNA stability (we wont discuss)
4. RNA editing
5. Translational and post-translational
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19HumanBiology2AMyersLecture4: TheEukaryoticGenomeand itsExpression
1. Eukaryotic transcription
Many similarities to prokaryotic transcription
Same directionality, precursors, etc.
RNA polymerase(s) = transcribing enzyme
But very important differences
Many sequence-specific transcription factors
RNA polymerase and promoters are more complex
Many different long-distance transcriptional elements
Enhancers, silencers
Can be >500,000 bp away from promoter
DNA is covered with histone (and other) proteins
Provides a global regulation mechanism
Chromatin = histone/DNA complex
Chromatin is modified +/- transcription
20HumanBiology2AMyersLecture4: TheEukaryoticGenomeand itsExpression
Eukaryotic promoters have RNA polymerase and regulatory protein binding
sites
Long-distance elements can be upstream, downstream and within a gene
Control regions for eukaryotic genes
Molecular Biology of the Cell.
4th Edition. Garland Science.
21HumanBiology2AMyersLecture4: TheEukaryoticGenomeand itsExpression
Life: The Science of Biology.
8th Edition. Sinauer Press.
looping
DNA binding proteins regulate transcription of genes
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22HumanBiology2AMyersLecture4: TheEukaryoticGenomeand itsExpression
Molecular Biology of the Cell.
4th Edition. Garland Science.
(another version)
23HumanBiology2AMyersLecture4: TheEukaryoticGenomeand itsExpression
Genes that need to be expressed at the same time
often share a common regulatory protein
Life: The Science of Biology.
7th Edition. Sinauer Press.
Example:
Genes needed by cells
to respond to stress
24HumanBiology2AMyersLecture4: TheEukaryoticGenomeand itsExpression
The globin gene familyIts genes are differentially expressed at different times during development
There are many gene families in higher eukaryotes
Humans: About half our genes are members of families
Multiple proteins related in sequence and function
Arose during evolution from common ancestral genesLife: The Science of Biology.
7th Edition. Sinauer Press.
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25HumanBiology2AMyersLecture4: TheEukaryoticGenomeand itsExpression
Slightly different proteins are made from each gene
Why?
Fetal -globin genes (G and A)bind O2 more strongly than doesadult -globin
This allows O2 from mothershemoglobin in the placenta to bepicked up by the fetushemoglobin
Life: The Science of Biology.
8th Edition. Sinauer Press.
26HumanBiology2AMyersLecture4: TheEukaryoticGenomeand itsExpression
Eukaryotic DNA in the nucleus is complexed
with histones to form chromatin
Open chromatin
Genes transcribed
Closed chromatin
Genes turned off
Histone
octamers
Life: The Science of Biology.
7th Edition. Sinauer Press.
Molecular Biology of the Cell.
4th Edition. Garland Science.
27HumanBiology2AMyersLecture4: TheEukaryoticGenomeand itsExpression
2. Splicing
Life: The Science of Biology.
7th Edition. Sinauer Press.
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28HumanBiology2AMyersLecture4: TheEukaryoticGenomeand itsExpression
How do enzymes know where to cut and splice?
Molecular Biology of the Cell.
4th Edition. Garland Science.
29HumanBiology2AMyersLecture4: TheEukaryoticGenomeand itsExpression
Splicing in more detail
Life: The Science of Biology.
8th Edition. Sinauer Press.
30HumanBiology2AMyersLecture4: TheEukaryoticGenomeand itsExpression
Alternative splicingAllows a tremendous increase in diversity of proteins from a smaller number of genes
Molecular Biology of the Cell.
4th Edition. Garland Science.
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31HumanBiology2AMyersLecture4: TheEukaryoticGenomeand itsExpression
4. RNA editing
For some genes, the RNA sequence can be changed after transcription (= RNA editing)
Life: The Science of Biology.
8th Edition. Sinauer Press.
32HumanBiology2AMyersLecture4: TheEukaryoticGenomeand itsExpression
5. Translational and post-translational regulation
Rate of translation is highly regulated -- many mRNAs dont gettranslated non-stop, but are held until protein is needed
Example: Regulation of ferritin, an iron storage protein
When iron is low, a translational repressor proteinbinds to ferritin mRNA and prevents translation
When iron levels rise, excess iron binds to therepressor and alters its structure, causing it to detachfrom the mRNA, allowing translation
33HumanBiology2AMyersLecture4: TheEukaryoticGenomeand itsExpression
Low iron
Dont need ferritin
High iron
Need ferritin
Molecular Biology of the Cell.
4th Edition. Garland Science.
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34HumanBiology2AMyersLecture4: TheEukaryoticGenomeand itsExpression
The lifetime of proteins is controlled by the proteasome
Regulating the lifetime of a protein is a way to control its actions