what practical uses has our knowledge of genetics provided?

WHAT PRACTICAL USES HAS OUR KNOWLEDGE OF GENETICS PROVIDED?

VIDEO(S)Genetics, longevity, and computer science

04/19/23 3

AP Ch 20

Biotechnology and genetic engineering

04/19/23 4

• 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

04/19/23 5

General Applications of DNA technology

04/19/23 6

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# (long vid)

http://www.howstuffworks.com/dna-evidence.htm

http://www.pbs.org/wgbh/nova/genome/program.html

04/19/23 7

Key tools of the trade:

04/19/23 8

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

http://www.people.virginia.edu/~rjh9u/restrenz.html

http://www.people.virginia.edu/~rjh9u/restrenz.html

04/19/23 9

Restriction enzymes in use

Microtiter plates with 96, 384 and 1536 wells (often called “96-well plate”). How helpful?

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

04/19/23 12

Genomic libraries – genetic “library” of an organism’s 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)

http://www.sanger.ac.uk/HGP/


04/19/23 13


(cDNA made in reverse transcription from mRNA)

• What would an advantage of having an entire genome on file have over cDNA?


• What would be next step to make this knowledge useful?



04/19/23 14


(cDNA made in reverse transcription from mRNA)

• What would an advantage of having an entire genome on file have over cDNA?


• What would be next step to make this knowledge useful?

• How would they acquire such knowledge?



04/19/23 15

DNA techniques:

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

04/19/23 16

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”

04/19/23 17

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

http://www.dnalc.org/cloning.html

http://www.dnalc.org/cloning.html

04/19/23 18

Practical uses of cloned genes, including cellular transformation

Use of restriction sites on DNA

segment in gel electrophoresis

04/19/23 19

A technique called Southern blotting combines gel electrophoresis of DNA fragments with nucleic acid hybridizationSpecific DNA fragments can be identified by Southern blotting, using labeled probes that hybridize to the DNA immobilized on a

“blot” of gel

Figure 20.13

cDNA synthesis

PCR amplification

Gel electrophoresis

mRNAs

cDNAs

Primers

-globingene

Embryonic stages1 2 3 4 5 6

2

3

1

RESULTS

TECHNIQUE

Reverse PCR: compares gene expression between samples (such as 6 stages of organismal development)

04/19/23 22

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?

• Real-time PCR – (or quantitative PCR, a.k.a. Q-PCR)

simultaneously amplifies and quantifies segments of DNA

Use of entire genome in biotechnology

• Cloning

• Stem cells

04/19/23 25

Whole–organism cloning:Done by nuclear transfer

How is this useful?

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

Figure 20.21

Culturedstem cells

Differentcultureconditions

Differenttypes ofdifferentiatedcells

Embryonicstem cells

Adultstem cells

Cells generatingall embryoniccell types

Cells generatingsome cell types

Livercells

Nervecells

Bloodcells

Figure 20.22

Remove skin cellsfrom patient. 2

1

3

4

Reprogram skin cellsso the cells becomeinduced pluripotentstem (iPS) cells.

Patient withdamaged hearttissue or otherdisease

Return cells topatient, wherethey can repairdamaged tissue.

Treat iPS cells sothat they differentiateinto a specificcell type.

Figure 20.23Cloned gene

2

1

3

4

Retroviruscapsid

Bonemarrowcell frompatient

Viral RNA

Bonemarrow

Insert RNA version of normal alleleinto retrovirus.

Let retrovirus infect bone marrow cellsthat have been removed from thepatient and cultured.

Viral DNA carrying the normalallele inserts into chromosome.

Inject engineeredcells into patient.

Gene Therapy

• 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)

Protein Production by “Pharm” Animals

© 2011 Pearson Education, Inc.

Figure 20.24

Do you consume

genetically modified

foods?

Food

Properties of the genetically modified variety

Modification

Percent Modified

in US

Percent Modified in world

SoybeansResistant 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 cottonBt crystal protein gene

added/transferred into plant genome

93% 49%

AlfalfaResistant to

herbicidesNew 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 quantiti

es grown

in China

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

ZucchiniResistance to yellow

mosaic virusesContains coat protein genes

of viruses.13%

More examples

Is genetically modified food (GM) safe?

Why or why not?

04/19/23 36

AP Ch 21

Genomes and Their Evolution

• 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


What genomic information distinguishes a human from a chimpanzee?

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© 2011 Pearson Education, Inc.

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


Three-stage approach to sequencing an entire genome.

Cytogenetic map

Genes locatedby FISH

Chromosomebands

Linkage mapping

Geneticmarkers

1

Physical mapping2

Overlappingfragments

DNA sequencing3

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


Cut the DNA intooverlapping frag-ments short enoughfor sequencing.

1

Clone the fragmentsin plasmid or phagevectors.

2

Figure 21.3-1


1


2

Sequence eachfragment.

3

Figure 21.3-2


1


2

Sequence eachfragment.

3

Order thesequences intoone overallsequencewith computersoftware.

4

Figure 21.3-3

• 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


• Technological advances have also facilitated metagenomics, in which DNA from a group of species (a metagenome) is collected from an environmental sample and sequenced


Concept 21.2 Scientists use bioinformatics to analyze genomes and their functions

• The Human Genome Project established databases to make data available on the Internet

• Bioinformatics resources are provided by:– 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


NCBI database – can compare DNA, RNA, or even proteins

Understanding Genes and Gene Expression at the Systems Level

• Proteomics is the systematic study of all proteins encoded by a genome


Translation andribosomal functions

Nuclear-cytoplasmic

transport

RNA processing

Transcriptionand chromatin-

related functions

Mitochondrialfunctions

Nuclear migrationand proteindegradation

Mitosis

DNA replicationand repair

Cell polarity andmorphogenesis

Protein folding,glycosylation, and

cell wall biosynthesis

Secretionand vesicletransport

Metabolismand amino acid

biosynthesis

Peroxisomalfunctions

Glutamatebiosynthesis

Serine-related

biosynthesis

Amino acidpermease pathway

Vesiclefusion

The systems biology approach to protein interactions

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

The expression of all/most genes at the same time.What are the pros/cons of evaluating someone’s entire genome?

Table 21.1

What stands out to you from these data?

Types of DNA sequences in the human genome

Exons (1.5%) Introns (5%)

Regulatorysequences(20%)

UniquenoncodingDNA (15%)

RepetitiveDNA unrelated totransposableelements(14%)

Large-segmentduplications (56%)

Simple sequenceDNA (3%)

Alu elements(10%)

L1sequences(17%)

RepetitiveDNA thatincludestransposableelementsand relatedsequences(44%)

Intergenic DNA is noncoding and 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 (a.k.a. jumping genes) and sequences related to them


Figure 21.8

Barbara McClintock and transposable DNA

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


Figure 21.9

Transposon

Transposonis copied

DNA ofgenome

Mobile transposon

Insertion

New copy oftransposon

Figure 21.10

RetrotransposonNew copy of

retrotransposon

Insertion

Reversetranscriptase

RNA

Formation of asingle-stranded

RNA intermediate

Gene Families

DNARNA transcripts

Nontranscribedspacer Transcription unit

DNA

18S 5.8S 28S

28S5.8S

18S

(a) Part of the ribosomal RNA gene family

-Globin

-Globin gene family

Chromosome 16

-Globin gene family

Chromosome 11

-Globin

Heme

2 1

21

G A

(b) The human -globin and -globin gene families

EmbryoFetus

and adult Fetus Adult

rRNA

Embryo

Humanchromosome 2

Telomeresequences

Centromeresequences

Chimpanzeechromosomes

12Telomere-likesequences

Centromere-likesequences

Humanchromosome 16

13

(a) Human and chimpanzee chromosomes (b) Human and mouse chromosomes

7 8 16 17

Mousechromosomes

Alterations of Chromosome Structure: Humans have 23 pairs of chromosomes, while chimpanzees have 24 pairs……How?

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

–WHY?


• 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– We still have recombination “hot

spots” now. What types of traits are being selected for now intensively?


Nonsisterchromatids

Gene Transposableelement

Crossoverpoint

and

Incorrect pairingof two homologsduring meiosis

Transposable elements can provide sites for crossover

between nonsister chromatids

How do Transposable Elements Contribute to Genome Evolution?


How Transposable Elements Contribute to Genome Evolution

1. may facilitate crossing over between different chromosomes

2. Insertion of transposable elements within a protein-coding sequence may block protein production

3. 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


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


Most recentcommonancestorof all livingthings

Bacteria

Eukarya

Archaea

Chimpanzee

Human

Mouse

Millions of years ago

Billions of years ago4 3 2

010203040506070

01

Figure 21.16

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


• Human and chimpanzee genomes differ by 1.2% at single base-pairs– Several genes are evolving faster in humans

than chimpanzees– Which do you think these would control?


• Human and chimpanzee genomes differ by 1.2% at single base-pairs– 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


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


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


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

– Homeotic genes in animals are called Hox genes


review Adultfruit fly

Fruit fly embryo(10 hours)

Fly chromosome

Mousechromosomes

Mouse embryo(12 days)

Adult mouse

Differences in Hox genes influences

body plan.

Artemia has coexpression in

the thorax region.

Thorax AbdomenGenitalsegments

Thorax Abdomen

Archaea

Most are 16 Mb

Eukarya

Genomesize

Number ofgenes

Genedensity

Introns

OthernoncodingDNA Very little

None inprotein-codinggenes

Present insome genes

Higher than in eukaryotes

1,5007,500 5,00040,000

Most are 104,000 Mb, but a few are much larger

Lower than in prokaryotes(Within eukaryotes, lowerdensity is correlated with largergenomes.)

Unicellular eukaryotes:present, but prevalent only insome speciesMulticellular eukaryotes:present in most genes

Can be large amounts;generally more repetitivenoncoding DNA inmulticellular eukaryotes

Bacteria

Summary: Genomes vary in size, number of genes, and density

what practical uses has our knowledge of genetics provided?

Documents

organisms dna

dna techniques

dna segments

dna copies

dna manipulation

stranded dna

foreign dna

complementary dna cdna