What would be the outcome of not regulating of gene expression?

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(No Transcript)
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What would be the outcome of not regulating of
gene expression?
3
AP Ch 18

• Regulation of Gene Expression

4
Why do cells differentiate if all undergoing
mitosis from the zygote?
5

• How can bacterial cells differentiate/evolve
  without sex or meiosis?

6

• How can bacterial cells differentiate/evolve
  without sex or meiosis?
• mutations occur every 107 cells, E.coli make
  2x1010 a day, ? 2000 mutants a day a lot of
  variation 

7
Related bacteria terms (skip)

• Transformation alter a bacterias genotype by
  the uptake of (plasmid) DNA
• Plasmid small, circular, self-replicating piece
  of DNA
• R plasmids special
• genes inserted
• Transduction transfer of bacterial genes via
  phages
• Conjugation direct transfer of genetic info.
  between 2 joined bacteria (pilus), like sex 
• Transposons jumping genes genes that move or
  get duplicated into other parts of the genome

8
Gene control (in bacteria)

• Operons- group of genes that controls expression,
  Starts with the promoter, RNA polymerase binds
• operator turns transcription on, mRNA gets made
• repressor protein that can stop transcription
  by binding to the operator, there are also
  corepressors that help
• inducer activates by inactivating the repressor
  (binds)
• ex. lac operon ? turns on when lactose is present
  because allolactose binds to the repressor, makes
  genes that digest lactose,

9

• OPERONS
• Repressible (trp) vs inducible (lac) enzymes
• Negative vs positive gene regulation

10
Figure 18.3
trp operon
Promoter
Promoter
Genes of operon
DNA
trpE
trpD
trpC
trpA
trpR
trpB
Operator
Regulatory gene
RNApolymerase
Start codon
Stop codon
3?
mRNA 5?
mRNA
5?
E
D
C
B
A
Protein
Inactive repressor
Polypeptide subunits that make upenzymes for
tryptophan synthesis
(a) Tryptophan absent, repressor inactive, operon
on
DNA
No RNAmade
mRNA
Protein
Activerepressor
Tryptophan (corepressor)
(b) Tryptophan present, repressor active, operon
off
11
Eukaryotic Genomes

• ? most of our DNA is repeated meaningless
  pieces, 15 are tandem repeats
• ? some diseases have more repeats
• Huntingtons CAG repeats, more repeats worse
• ? some genes are broken into pieces through the
  genome (intron), some genes are duplicated,
  creates families of genes and pseudogenes
• ? transposons (jumping genes) can consist of 10
  of humans DNA (McClintock)

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Stages in eukaryotic gene expression
Signal
NUCLEUS
Chromatin
Chromatin modificationDNA unpacking
involvinghistone acetylation andDNA
demethylation
DNA
Gene availablefor transcription
Gene
Transcription
Exon
RNA
Primary transcript
Intron
RNA processing
Tail
mRNA in nucleus
Cap
Transport to cytoplasm
CYTOPLASM
mRNA in cytoplasm
Translation
Degradationof mRNA
Polypeptide
Protein processing, suchas cleavage and
chemical modification
Active protein
Degradationof protein
Transport to cellulardestination
Cellular function (suchas enzymatic
activity,structural support)
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Gene Expression Control

• 20 of genes in humans expressed at a given time
• control occurs at any stage from replication to
  post translation

14
Major Methods of Gene RegulationHow are color
groups related?

• Histone Acetylation promotes transcription b/c
  it opens tightly packed nucleosomes, giving
  transcription proteins easier access (COCH3 )
• DNA methylation add CH3 groups to DNA, often
  shuts genes off
• Control elements before the coded DNA that
  regulate transcription transcription factors
• Splicing of RNA by spliceosomes
• Non-coding RNAs siRNAs, miRNAs degrade
  transcripts or block translation
• Protein degradation

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Figure 18.7
Histone tails
DNA double helix
Amino acidsavailablefor chemicalmodification
Nucleosome(end view)
(a) Histone tails protrude outward from a
nucleosome
Unacetylated histones
Acetylated histones
(b)
Acetylation of histone tails promotes loose
chromatinstructure that permits transcription
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Figure 18.10-1
Promoter
Activators
Gene
DNA
Distal controlelement
TATA box
Enhancer
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Figure 18.10-2
Promoter
Activators
Gene
DNA
Distal controlelement
TATA box
Enhancer
Generaltranscriptionfactors
DNA-bendingprotein
Group of mediator proteins
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Figure 18.10-3
Promoter
Activators
Gene
DNA
Distal controlelement
TATA box
Enhancer
Generaltranscriptionfactors
DNA-bendingprotein
Group of mediator proteins
RNApolymerase II
RNApolymerase II
Transcriptioninitiation complex
RNA synthesis
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Expression of different genes in different cell
types
Enhancer
Promoter
Controlelements
Albumin gene
Crystallingene
LENS CELLNUCLEUS
LIVER CELLNUCLEUS
Availableactivators
Availableactivators
Albumin genenot expressed
Albumin geneexpressed
Crystallin genenot expressed
Crystallin geneexpressed
(a) Liver cell
(b) Lens cell
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Splicing Regulation Method 4
Enhancer(distal controlelements)
Proximalcontrolelements
Poly-Asignalsequence
Transcriptionterminationregion
Transcriptionstart site
Exon
Intron
Exon
Exon
Intron
DNA
Upstream
Downstream
Promoter
Poly-Asignal
Transcription
Exon
Intron
Intron
Exon
Exon
Primary RNAtranscript(pre-mRNA)
Cleaved3? end ofprimarytranscript
5?
RNA processing
Intron RNA
Coding segment
mRNA
3?
P
P
G
P
AAA ??? AAA
Startcodon
Stopcodon
Poly-Atail
5? Cap
5? UTR
3? UTR
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RNA degradation Regulation Method 5
Regulation and gene expression by miRNAs
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RNAi A form of siRNA

• Used to treat various gentically-based disorders
• Recall bio 1

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Cell Differentiation How does a cell know what
job it will do?

• 250 different cell types, all from one stem
  cell, HOW?
• Differentiation cell becomes specialized in
  structure or function
• Morphogenesis organisms shape is established
• mice, C. elegans fruit flies etc.. used to
  study development goal is to find a cells
  lineage

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3 Factors that influence early development

• 1) Influence of the eggs cytoplasm
• cytosol is distributed unevenly, causes
  differences in the new cells
• axis of the developing egg cell
• the eggs RNA
• 2) embryonic induction - chemical signals from
  neighboring cells signal change

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Sources of developmental info for the embryo
26

• 3) Homeotic Genes
• hox genes, turn genes on off
• 180 base segment, called a homeobox that is
  consistent across species, evolution p.370 and
  p.445
• Apoptosis - programmed cell death, all cells are
  destined to die
• -why? Essential for proper development, ex.
  webbed feet, when cells go "bad"

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Why did this occur?
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Cancer from expression of cell cycle genes

• Oncogene- cancer causing, 1 copy is bad cancer
• Tumor suppressor prevent uncontrolled cell
  growth, both copies must be faulty

• p53- fix DNA or shut bad DNA off, 5-7 things must
  happen for cancer to occur

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Figure 18.24
Two different transcription pathways can result
in cancerous formations
MUTATION
Growthfactor
Protein kinases
Hyperactive Ras protein(product of
oncogene)issues signals on itsown.
Ras
MUTATION
G protein
GTP
Defective or missingtranscription factor,such
asp53, cannotactivatetranscription.
Ras
P
P
GTP
Activeformof p53
UVlight
P
P
P
P
Protein kinases(phosphorylation cascade)
Receptor
DNA damagein genome
DNA
NUCLEUS
Transcriptionfactor (activator)
Protein thatinhibitsthe cell cycle
DNA
Gene expression
(b) Cell cycleinhibiting pathway
Protein that stimulatesthe cell cycle
EFFECTS OF MUTATIONS
Proteinoverexpressed
Protein absent
(a) Cell cyclestimulating pathway
Cell cycleoverstimulated
Increased celldivision
Cell cycle notinhibited
(c) Effects of mutations
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Figure 18.23
Turning proto-oncogenes into oncogenes
Proto-oncogene
DNA
Translocation ortransposition genemoved to new
locus,under new controls
Point mutation
Gene amplificationmultiple copies ofthe gene
within a controlelement
withinthe gene
New promoter
Oncogene
Oncogene
Normal growth-stimulatingprotein in excess
Normal growth-stimulatingprotein in excess
Normal growth-stimulatingprotein inexcess
Hyperactive ordegradation-resistantprotein
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SUMMARY
Transcription
Chromatin modification
Genes in highly compactedchromatin are
generally nottranscribed.
Regulation of transcription initiationDNA
control elements in enhancers bindspecific
transcription factors.
Histone acetylation seemsto loosen chromatin
structure,enhancing transcription.
Bending of the DNA enables activators tocontact
proteins at the promoter, initiatingtranscription
.
DNA methylation generallyreduces transcription.
Coordinate regulation
Enhancer forliver-specific genes
Enhancer forlens-specific genes
Chromatin modification
Transcription
RNA processing
Alternative RNA splicing
RNA processing
Primary RNAtranscript
Translation
mRNAdegradation
mRNA
or
Protein processingand degradation
Translation
Initiation of translation can be controlledvia
regulation of initiation factors.
mRNA degradation
Each mRNA has a characteristic life
span,determined in part bysequences in the 5?
and3? UTRs.
Protein processing and degradation
Protein processing anddegradation by
proteasomesare subject to regulation.
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Quick Quiz
34
Quick Quiz

1. Name four ways in which genes can be regulated.

35
Quick Quiz

1. Name four ways in which genes can be regulated.
2. What chemical group would bind up a strand of DNA
   inhibiting transcription?

36
Quick Quiz

1. Name four ways in which genes can be regulated.
2. What chemical group would bind up a strand of DNA
   inhibiting transcription?
3. What would be the effect of reordering hox genes?

37
Quick Quiz

1. Name four ways in which genes can be regulated.
2. What chemical group would bind up a strand of DNA
   inhibiting transcription?
3. What would be the effect of reordering hox genes?
4. Name four structures that participate in
   transcription regulation in eukaryotes.

38
Quick Quiz

1. Name four ways in which genes can be regulated.
2. What chemical group would bind up a strand of DNA
   inhibiting transcription?
3. What would be the effect of reordering hox genes?
4. Name four structures that participate in
   transcription regulation in eukaryotes.
5. What does the operon include?

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AP Ch 19

• Viruses

40

• Virus microscopic particle that can infect the
  cells of biological organisms made of a protein
  coat capsid and enclosed with DNA or RNA
• genetic material is often single stranded,
  circular, RNA
• virus shape varies

41

• - most viruses enter the cell by tricking the
  cell with its envelope
• - most common are bacteriophages

42
Phage reproduction p.385-386

• Lytic cycle - DNA injected, new phages made, cell
  bursts, host dies
• Lysogenic cycle- DNA injected and becomes part of
  host DNA, host doesnt die, new bacteria can make
  phages
• RNA Virus transfers genetic material via RNA
• Retrovirus virus makes their RNA into DNA by
  using reverse transcriptase, DNA is inserted into
  the hosts genome
• HIV, p389 awesome virus

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(No Transcript)
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(No Transcript)
46

• Vaccines mild forms of the virus, causes body
  to build immunity, doesnt work with all viruses
• - recent evidence has shown that some viruses may
  cause cancer, ex. mono Burkitts lymphoma
• Viroid- simpler than viruses, dont make
  proteins, made of 100s of nucleotides, infect
  plants, p.393
• Prions proteins, cause mad cow, CJD, S.
  Prusiner 1997 Nobel, ? passed by altering
  proteins

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48
WHAT PRACTICAL USES HAS OUR KNOWLEDGE OF GENETICS
PROVIDED?
49
VIDEO(S) Genetics, longevity, and computer science
50
AP Ch 20

• Biotechnology and genetic engineering

51

• Biotechnology use of organisms genes and
  current technology to advance society
• Genetic Engineering manipulation of genes for
  practical purpose
• Genomics study of genomes and proteins
  (proteomics)
• Genomics is HOT
• Now lets explore some DNA manipulation and usage
  lab techniques

52
General Applications of DNA technology

• Diagnosis of diseases
• Gene therapy
• Forensics matching crime scene DNA to suspects
  and victims
• Genetic engineering of food/animals
• adding traits of other organisms to hosts
• Removing, modifying, or enhancing pre-existing
  genes
• Inserting designer genes into organism (e.g.
  antibiotic production in corn)
• http//www.pbs.org/wgbh/nova/genome/program.html

53

• Key tools of the trade
• Restriction enzymes protective enzymes from
  bacteria are used to cut other DNA segments at
  specific locations
• often used to make plasmids with genes of
  interest, p 398
• Vectors delivers chosen gene into a host cell
  where it will be replicated (e.g. bacterial
  plasmid, virus)
• Electroporation, microscopic needles, and bullets
  can also introduce foreign DNA into host

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Restriction enzymes in use
55
Microtiter plates with 96, 384 and 1536 wells
(often called 96-well plate). How helpful?
56

• Probes piece of single-stranded DNA or RNA of a
  known gene (p. 400)
• used to find a specific DNA sequence by
  hybridization
• Probe can be traced because it is labeled with a
  glowing isotope

57

• Genomic libraries genetic library of an
  organisms DNA, over 1000 completed
• Can be genomic libraries or complementary DNA
  (cDNA made in reverse transcription from mRNA)
• What would an advantage of having an entire
  genome on file have over cDNA?
• Human Genome Project - (accomplished 2001)

58

• Genomic libraries genetic library of an
  organisms DNA, over 1000 completed
• Can be genomic libraries or complementary DNA
  (cDNA made in reverse transcription from mRNA)
• What would an advantage of having an entire
  genome on file have over cDNA?
• Human Genome Project - (accomplished 2001)
• What would be next step to make this knowledge
  useful?

11/17/2013
58
59

• Genomic libraries genetic library of an
  organisms DNA, over 1000 completed
• Can be genomic libraries or complementary DNA
  (cDNA made in reverse transcription from mRNA)
• What would an advantage of having an entire
  genome on file have over cDNA?
• Human Genome Project - (accomplished 2001)
• What would be next step to make this knowledge
  useful?
• How would they acquire such knowledge?

11/17/2013
59
60

• DNA techniques
• PCR- see diagram to right, make copies of chosen
  of DNA segments

11/17/2013
60
61

• DNA techniques
• PCR- see diagram to right, make copies of chosen
  of DNA segments
• How long until you have 100 DNA copies? 1
  billion?
• Gel electrophoresis see diagram next pg.,
  separates DNA based on size,
• moves by electric charge as DNA is -,
• Used for DNA fingerprinting

62

• Gene Cloning producing copies of chosen gene
• Benefits 1. amplifying a chosen gene 2.
  produce a chosen protein product

Give an example of 2 for practical purpose
11/17/2013
62
63
Practical uses of cloned genes, including
cellular transformation
11/17/2013
63
64
Use of restriction sites on DNA segment in gel
electrophoresis
65
A technique called Southern blotting combines gel
electrophoresis of DNA fragments with nucleic
acid hybridization?Specific DNA fragments can be
identified by Southern blotting, using labeled
probes that hybridize to the DNA immobilized on a
blot of gel
66
Figure 20.13
TECHNIQUE
cDNA synthesis
mRNAs
cDNAs
Primers
PCR amplification
?-globingene
Gel electrophoresis
Embryonic stages
RESULTS
2
1
3
4
5
6
Reverse PCR compares gene expression between
samples (such as 6 stages of organismal
development)
67

• Microarrays tests thousands of genes in tissue
  under different environmental conditions
• Can reveal profiles of genes over a lifetime of
  an organism
• How can this technique be used for medical
  discovery?

68

• Real-time PCR
• (or quantitative PCR, a.k.a. Q-PCR)
  simultaneously amplifies and quantifies segments
  of DNA

69
Use of entire genome in biotechnology

• Cloning
• Stem cells

70
Wholeorganism cloning Done by nuclear transfer
How is this useful?
11/17/2013
70
71
Stem cells

• Unspecialized cells that can reproduce
  indefinitely and under can become other types of
  specialized cells?
• What would determine the type of cell a stem cell
  becomes?
• Can be multipotent, pluripotent, omnipotent stem
  cells

72
Figure 20.21
Embryonicstem cells
Adultstem cells
Cells generatingall embryoniccell types
Cells generatingsome cell types
Culturedstem cells
Differentcultureconditions
Livercells
Bloodcells
Nervecells
Differenttypes ofdifferentiatedcells
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Figure 20.22
Remove skin cellsfrom patient.
Reprogram skin cellsso the cells becomeinduced
pluripotentstem (iPS) cells.
Patient withdamaged hearttissue or otherdisease
Treat iPS cells sothat they differentiateinto a
specificcell type.
Return cells topatient, wherethey can
repairdamaged tissue.
74
Figure 20.23
Gene Therapy
Cloned gene
Insert RNA version of normal alleleinto
retrovirus.
Viral RNA
Let retrovirus infect bone marrow cellsthat have
been removed from thepatient and cultured.
Retroviruscapsid
Viral DNA carrying the normalallele inserts into
chromosome.
Bonemarrowcell frompatient
Bonemarrow
Inject engineeredcells into patient.
75
Protein Production by Pharm Animals

• Transgenic animals are made by introducing genes
  from one species into the genome of another
  animal
• Transgenic animals can be pharmaceutical
  factories, producers of large amounts of
  otherwise rare substances for various uses
  (medical, nourishment)

76
Figure 20.24
77
Do you consume genetically modified foods?
78
Food Properties of the genetically modified variety Modification Percent Modified in US Percent Modified in world
Soybeans Resistant to herbicides Herbicide resistant gene taken from bacteria inserted into soybean 93 77
Corn, Resistant to herbicides and insects. Vitamin-enriched corn New genes, some from the bacterium added/transferred into plant genome. 86 26
Cotton (cottonseed oil) Pest-resistant cotton Bt crystal protein gene added/transferred into plant genome 93 49
Alfalfa Resistant to herbicides New genes added/transferred into plant genome. Planted 2005-07, unbanned 1/2011
Tomatoes enzyme (PG) is suppressed, retarding fruit softening after harvesting. RNAi of PG enzyme added into plant genome Failed commercially in US Small quantities grown in China
79
More examples
Food Properties of the genetically modified variety Modification Percent Modified in US Percent Modified in world
Sugar beet Resistance to herbicides New genes added/transferred into plant genome 95 9
Golden Rice contain beta-carotene (a source of vitamin A) contain gene from daffodils and from a bacterium on the market in 2013
Zucchini Resistance to yellow mosaic viruses Contains coat protein genes of viruses. 13
80
Is genetically modified food (GM) safe? Why or
why not?
81
AP Ch 21

• Genomes and Their Evolution
• Key slides have yellow background

82

• Genomics is the study of whole sets of genes and
  their interactions
• Bioinformatics is the application of
  computational methods to the storage and analysis
  of biological data

83
Figure 21.1
84
Concept 21.1 New approaches have accelerated the
pace of genome sequencing

• The most ambitious mapping project to date has
  been the sequencing of the human genome
• Officially begun as the Human Genome Project in
  1990, the sequencing was largely completed by
  2003
• The project had three stages
• Genetic (or linkage) mapping
• Physical mapping
• DNA sequencing

85
Three-Stage Approach to Genome Sequencing

• Step 1 A linkage map (genetic map) maps the
  location of several thousand genetic markers on
  each chromosome
• Recombination frequencies are used to determine
  the order and relative distances between genetic
  markers

86
Figure 21.2-1
Chromosomebands
Cytogenetic map
Genes locatedby FISH
87
Figure 21.2-2
Chromosomebands
Cytogenetic map
Genes locatedby FISH
Linkage mapping
Geneticmarkers
88
Figure 21.2-3
Chromosomebands
Cytogenetic map
Genes locatedby FISH
Linkage mapping
Geneticmarkers
Physical mapping
Overlappingfragments
89
Three-stage approach to sequencing an entire
genome.
Chromosomebands
Cytogenetic map
Genes locatedby FISH
Linkage mapping
Geneticmarkers
Physical mapping
Overlappingfragments
DNA sequencing
90
Whole-Genome Shotgun Approach to Genome Sequencing

• The whole-genome shotgun approach was developed
  by J. Craig Venter in 1992
• 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

91
Figure 21.3-1
Cut the DNA intooverlapping frag-ments short
enoughfor sequencing.
Clone the fragmentsin plasmid or phagevectors.
92
Figure 21.3-2
Cut the DNA intooverlapping frag-ments short
enoughfor sequencing.
Clone the fragmentsin plasmid or phagevectors.
Sequence eachfragment.
93
Figure 21.3-3
Cut the DNA intooverlapping frag-ments short
enoughfor sequencing.
Clone the fragmentsin plasmid or phagevectors.
Sequence eachfragment.
Order thesequences intoone overallsequencewith
computersoftware.
94

• Both the three-stage process and the whole-genome
  shotgun approach were used for the Human Genome
  Project and for genome sequencing of other
  organisms
• A complete haploid set of human chromosomes
  consists of 3.2 billion base pairs
• The development of newer sequencing techniques
  has resulted in massive increases in speed and
  decreases in cost
• Comparisons of genomes among organisms provide
  information about the evolutionary history of
  genes and taxonomic groups

95

• Technological advances have also facilitated
  metagenomics, in which DNA from a group of
  species (a metagenome) is collected from an
  environmental sample and sequenced
• This technique has been used on microbial
  communities, allowing the sequencing of DNA of
  mixed populations, and eliminating the need to
  culture species in the lab

96
Concept 21.2 Scientists use bioinformatics to
analyze genomes and their functions

• The Human Genome Project established databases
  and refined analytical software to make data
  available on the Internet
• This has accelerated progress in DNA sequence
  analysis

97
Centralized Resources for Analyzing Genome
Sequences

• Bioinformatics resources are provided by a number
  of sources
• National Library of Medicine and the National
  Institutes of Health (NIH) created the National
  Center for Biotechnology Information (NCBI)
• European Molecular Biology Laboratory
• DNA Data Bank of Japan
• BGI in Shenzhen, China

98

• Genbank, the NCBI database of sequences, doubles
  its data approximately every 18 months
• Software is available that allows online visitors
  to search Genbank for matches to
• A specific DNA sequence
• A predicted protein sequence
• Common stretches of amino acids in a protein
• The NCBI website also provides 3-D views of all
  protein structures that have been determined

99
Figure 21.4
100
Understanding Genes 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

101
How Systems Are Studied An Example

• A systems biology approach can be applied to
  define gene circuits and protein interaction
  networks
• Researchers working on the yeast Saccharomyces
  cerevisiae used sophisticated techniques to
  disable pairs of genes one pair at a time,
  creating double mutants
• Computer software then mapped genes to produce a
  network-like functional map of their
  interactions
• The systems biology approach is possible because
  of advances in bioinformatics

102
Figure 21.5
Glutamatebiosynthesis
Serine-relatedbiosynthesis
Mitochondrialfunctions
Translation andribosomal functions
Vesiclefusion
Amino acidpermease pathway
RNA processing
Peroxisomalfunctions
Transcriptionand chromatin-related functions
Metabolismand amino acidbiosynthesis
Nuclear-cytoplasmictransport
Secretionand vesicletransport
Nuclear migrationand proteindegradation
Protein folding,glycosylation, andcell wall
biosynthesis
Mitosis
DNA replicationand repair
Cell polarity andmorphogenesis
103
Application of Systems Biology to Medicine

• A systems biology approach has several medical
  applications
• The Cancer Genome Atlas project is currently
  seeking all the common mutations in 13 types of
  cancer by comparing gene sequences and expression
  in cancer versus normal cells
• Silicon and glass chips have been produced that
  hold a microarray of most known human genes

104
Figure 21.6
105
Concept 21.3 Genomes vary in size, number of
genes, and gene density

• By early 2010, over 1,200 genomes were completely
  sequenced, including 1,000 bacteria, 80 archaea,
  and 124 eukaryotes
• Sequencing of over 5,500 genomes and over 200
  metagenomes is currently in progress

106
Genome Size

• Genomes of most bacteria and archaea range from 1
  to 6 million base pairs (Mb) genomes of
  eukaryotes are usually larger
• Most plants and animals have genomes greater than
  100 Mb humans have 3,000 Mb
• Within each domain there is no systematic
  relationship between genome size and phenotype

107
Table 21.1
What stands out to you from these data?
108
Figure 21.UN02
Human genome
Protein-coding,rRNA, andtRNA genes (1.5)
Introns andregulatorysequences (?26)
Repetitive DNA(green and teal)
109
Figure 21.7
Exons (1.5)
Introns (5)
Regulatorysequences(?20)
RepetitiveDNA thatincludestransposableelements
and relatedsequences(44)
UniquenoncodingDNA (15)
L1sequences(17)
RepetitiveDNA unrelated totransposableelements
(14)
Alu elements(10)
Large-segmentduplications (5?6)
Simple sequenceDNA (3)
110
Concept 21.4 Multicellular eukaryotes have much
noncoding DNA and many multigene families

• The bulk of most eukaryotic genomes neither
  encodes proteins nor functional RNAs
• Much evidence indicates that noncoding DNA
  (previously called junk DNA) plays important
  roles in the cell
• Sequencing of the human genome reveals that 98.5
  does not code for proteins, rRNAs, or tRNAs
• About a quarter of the human genome codes for
  introns and gene-related regulatory sequences

111

• 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

112
Figure 21.8
Barbara McClintock and transposable DNA
113
Transposable Elements and Related Sequences

• The first evidence for mobile DNA segments came
  from geneticist Barbara McClintocks 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 cells DNA they are present in both
  prokaryotes and eukaryotes

114
Types of transposable elements

• Eukaryotic transposable elements are of two types
• Transposons, which move by means of a DNA
  intermediate
• Retrotransposons, which move by means of an RNA
  intermediate

115
Figure 21.9
New copy oftransposon
Transposon
DNA ofgenome
Transposonis copied
Insertion
Mobile transposon
116
Figure 21.10
New copy ofretrotransposon
Retrotransposon
Formation of asingle-strandedRNA intermediate
RNA
Insertion
Reversetranscriptase
117
Sequences Related to Transposable Elements

• Multiple copies of transposable elements and
  related sequences are scattered throughout the
  eukaryotic genome
• In primates, a large portion of transposable
  elementrelated DNA consists of a family of
  similar sequences called Alu elements
• Many Alu elements are transcribed into RNA
  molecules however their function, if any, is
  unknown

118
Other Repetitive DNA, Including Simple Sequence
DNA

• About 15 of the human genome consists of
  duplication of long sequences of DNA from one
  location to another
• In contrast, simple sequence DNA contains many
  copies of tandemly repeated short sequences

119
Genes and Multigene Families

• Many eukaryotic genes are present in one copy per
  haploid set of chromosomes
• The rest of the genes occur 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

120
Gene Families
DNA
RNA transcripts
?-Globin
Nontranscribedspacer
?-Globin
Transcription unit
Heme
DNA
?-Globin gene family
?-Globin gene family
18S
5.8S
28S
Chromosome 16
Chromosome 11
rRNA
5.8S
G?
A?
??
?
??
??
?
?
?
?1
?2
28S
Fetusand adult
18S
Embryo
Fetus
Adult
Embryo
(a) Part of the ribosomal RNA gene family
(b) The human ?-globin and ?-globin gene families
121

• The classic examples of multigene families of
  nonidentical genes are two related families of
  genes that encode globins
• a-globins and ß-globins are polypeptides of
  hemoglobin and are coded by genes on different
  human chromosomes and are expressed at different
  times in development

122
Concept 21.5 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

123
Alterations of Chromosome Structure Humans have
23 pairs of chromosomes, while chimpanzees have
24 pairsHow?
Humanchromosome 2
Chimpanzeechromosomes
Telomeresequences
Centromeresequences

Telomere-likesequences
12
Humanchromosome 16
Mousechromosomes
Centromere-likesequences
13
7
8
16
17
(a) Human and chimpanzee chromosomes
(b) Human and mouse chromosomes
124
Alterations of Chromosome Structure Humans have
23 pairs of chromosomes, while chimpanzees have
24 pairsHow?
Humanchromosome 2
Chimpanzeechromosomes
Telomeresequences
Centromeresequences
Telomere-likesequences
12
Humanchromosome 16
Mousechromosomes
Centromere-likesequences
13
7
8
16
17
(a) Human and chimpanzee chromosomes
(b) Human and mouse chromosomes
125

• The rate of duplications and inversions seems to
  have accelerated about 100 million years ago
• WHY?

126

• The rate of duplications and inversions seems to
  have accelerated about 100 million years ago
• This coincides with when large dinosaurs went
  extinct and mammals diversified
• Chromosomal rearrangements are thought to
  contribute to the generation of new species
• Some of the recombination hot spots associated
  with chromosomal rearrangement are also locations
  that are associated with diseases

127
Duplication and Divergence of Gene-Sized Regions
of DNA

• Transposable elements can provide sites for
  crossover between nonsister chromatids

128
Figure 21.13
Nonsisterchromatids
Transposableelement
Gene
Crossoverpoint
Incorrect pairingof two homologsduring meiosis
and
129
Story of Evolution of Genes with Related
Functions Human Globin Genes

• The genes encoding the various globin proteins
  evolved from one common ancestral globin gene,
  which duplicated and diverged about 450500
  million years ago
• After the duplication events, differences between
  the genes in the globin family arose from the
  accumulation of mutations

130
Figure 21.14
Ancestral globin gene
Duplication ofancestral gene
Mutation inboth copies
?
?
Transposition todifferent chromosomes
Evolutionary time
?
?
Further duplicationsand mutations
?
?
?
?
?
G?
A?
??
??
??
??
??
?1
?
?
?
?
?2
1
2
?-Globin gene familyon chromosome 16
?-Globin gene familyon chromosome 11
131

• Subsequent duplications of these genes and random
  mutations gave rise to the present globin genes,
  which code for oxygen-binding proteins
• The similarity in the amino acid sequences of the
  various globin proteins supports this model of
  gene duplication and mutation

132
Table 21.2
133
Rearrangements of Parts of Genes Exon
Duplication and Exon Shuffling

• The duplication or repositioning of exons has
  contributed to genome evolution
• Errors in meiosis can result in an exon being
  duplicated on one chromosome and deleted from the
  homologous chromosome
• In exon shuffling, errors in meiotic
  recombination lead to some mixing and matching of
  exons, either within a gene or between two
  nonallelic genes

134
Figure 21.15
EGF
EGF
EGF
EGF
Epidermal growthfactor gene with multipleEGF
exons
Exon duplication
Exon shuffling
F
F
F
F
Fibronectin gene with multiplefinger exons
F
EGF
K
K
K
Exon shuffling
Plasminogen gene with akringle exon
Portions of ancestral genes
TPA gene as it exists today
135
How Transposable Elements Contribute to Genome
Evolution

• Multiple copies of similar transposable elements
  may facilitate recombination, or crossing over,
  between different chromosomes
• Insertion of transposable elements within a
  protein-coding sequence may block protein
  production
• Insertion of transposable elements within a
  regulatory sequence may increase or decrease
  protein production
• changes are usually detrimental but may on
  occasion prove advantageous to an organism

136
Concept 21.6 Comparing genome sequences provides
clues to evolution and development

• Help explain how the evolution of development
  leads to morphological diversity

137
Figure 21.16
Bacteria
Most recentcommonancestorof all livingthings
Eukarya
Archaea
4
3
2
0
1
Billions of years ago
Chimpanzee
Human
Mouse
40
0
10
20
30
50
60
70
Millions of years ago
138
Comparing Distantly Related Species

• Highly conserved genes have changed very little
  over time
• These help clarify relationships among species
  that diverged from each other long ago
• Bacteria, archaea, and eukaryotes diverged from
  each other between 2 and 4 billion years ago

139
Comparing Closely Related Species

• Genetic differences between closely related
  species can be correlated with phenotypic
  differences
• For example, genetic comparison of several
  mammals with nonmammals helps identify what it
  takes to make a mammal

140

• Human and chimpanzee genomes differ by 1.2, at
  single base-pairs, and by 2.7 because of
  insertions and deletions
• Several genes are evolving faster in humans than
  chimpanzees
• These include genes involved in defense against
  malaria and tuberculosis and in regulation of
  brain size, and genes that code for transcription
  factors

141

• Humans and chimpanzees differ in the expression
  of the FOXP2 gene, whose product turns on genes
  involved in vocalization
• Differences in the FOXP2 gene may explain why
  humans but not chimpanzees communicate by speech

142
Figure 21.17
EXPERIMENT
Heterozygote onecopy of FOXP2disrupted
Homozygote bothcopies of FOXP2disrupted
Wild type two normal copies of FOXP2
Experiment 1 Researchers cut thin sections of
brain and stainedthem with reagents that allow
visualization of brain anatomy in aUV
fluorescence microscope.
Experiment 2 Researchers separatedeach newborn
pup from its motherand recorded the number
ofultrasonic whistles produced by thepup.
RESULTS
Experiment 1
Experiment 2
400
300
Number of whistles
200
100
(Nowhistles)
Wild type
Heterozygote
Homozygote
0
Wildtype
Hetero-zygote
Homo-zygote
143
Comparing Genomes Within a Species

• As a species, humans have only been around about
  200,000 years and have low within-species genetic
  variation
• Variation within humans is due to single
  nucleotide polymorphisms, inversions, deletions,
  and duplications
• Most surprising is the large number of
  copy-number variants
• These variations are useful for studying human
  evolution and human health

144
Comparing Developmental Processes

• Evolutionary developmental biology, or evo-devo,
  is the study of the evolution of developmental
  processes in multicellular organisms
• Genomic information shows that minor differences
  in gene sequence or regulation can result in
  striking differences in form

145
Widespread Conservation of Developmental Genes
Among Animals

• Molecular analysis of the homeotic genes in
  Drosophila has shown that they all include a
  sequence called a homeobox
• An identical or very similar nucleotide sequence
  has been discovered in the homeotic genes of both
  vertebrates and invertebrates
• Homeobox genes code for a domain that allows a
  protein to bind to DNA and to function as a
  transcription regulator
• Homeotic genes in animals are called Hox genes

146
Figure 21.18
Adultfruit fly
Fruit fly embryo(10 hours)
Fly chromosome
Mousechromosomes
Mouse embryo(12 days)
Adult mouse
147

• Related homeobox sequences have been found in
  regulatory genes of yeasts, plants, and even
  prokaryotes
• In addition to homeotic genes, many other
  developmental genes are highly conserved from
  species to species

148

• Sometimes small changes in regulatory sequences
  of certain genes lead to major changes in body
  form
• For example, variation in Hox gene expression
  controls variation in leg-bearing segments of
  crustaceans and insects
• In other cases, genes with conserved sequences
  play different roles in different species

149
Figure 21.19
Genital segments
Thorax
Abdomen
Thorax
Abdomen
150
Figure 21.UN01
Archaea
Eukarya
Bacteria
Most are 10?4,000 Mb, but a few are much larger
Genome size
Most are 1?6 Mb
Number ofgenes
5,000?40,000
1,500?7,500
Genedensity
Lower than in prokaryotes(Within eukaryotes,
lowerdensity is correlated with largergenomes.)
Higher than in eukaryotes
None inprotein-codinggenes
Present insome genes
Introns
Unicellular eukaryotespresent, but prevalent
only insome speciesMulticellular
eukaryotespresent in most genes
OthernoncodingDNA
Can be large amountsgenerally more
repetitivenoncoding DNA inmulticellular
eukaryotes
Very little