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Slide1
Unit 1
Biotechnology and Microbiology
Slide2Definition Biotechnology
Biotechnology is broadly defined as the science of using living organisms or the products of living organisms for the benefit of humans and their surroundings.
Slide3Biotechnology
The Biotechnology Revolution - NOVA
http://www.youtube.com/watch?v=bukTqyWgaM8
Slide4Lesson 1
Lecture and Discussion: Introduction to classical and modern biotechnology, interdisciplinary nature of biotechnology, and ethics in biology.
Assessment: Create a concept map from lecture.
Slide5History of Biotechnology
What is the difference
between
classical biotechnology
and
modern biotechnology
?
Slide6Classical biotechnology
Our ancient ancestors used two classic biotechnology techniques:
Fermentation
– use of microorganisms to make food and beverages.
Selective Breeding
– breeding of animals and plants with desirable traits.
Slide7Fermentation
Do you remember this?
http://people.cst.cmich.edu/schul1te/animations/fermentation.swf
Slide8Fermentation
Actual existence of micro-organisms and their role in contaminating food are recent discoveries, dating back 200 years ago.
Bread baking
- Earliest breads were unleavened (pita bread).
- Fermented dough probably discovered by accident.
- Egyptians and Romans both used fermented dough to make a lighter, leavened bread.
Slide9Fermentation
Lactic Acid and Acetic Acid Fermentation
5,000 BC, milk curd to make cheese was made in Mesopotamia.
By 4,000 BC, Chinese used fermentation to make yogurt, cheese, and vinegar.
Slide10Fermentation
Beverages
Beer Making
- Egyptians probably began beer making around 6,000 BC.
- Babylonians used barley to make beer.
- Brewing became an art form by the 14
th
century AD.
Wine making
- Originated in valley of the Tigris River, date unknown.
- First made by accident with grapes contaminated by yeast.
- Egyptians, Greeks, and Romans made wine.
Slide11Selective Breeding
About 10,000 years ago, people established agrarian societies.
Origins of biotechnology date back to this time.
People settled and began domesticating both animals and plants.
Both animals and plants, were artificially selected for valuable traits.
Slide12Selective Breeding
Animals
- Babylonians, Egyptians, and Romans selectively bred livestock.
- Romans have left written descriptions of their livestock selective breeding practices.
- British white cattle (on right) can trace its ancestry back to the Roman empire.
Slide13Selective Breeding
Plants
- Superior seeds, cuttings, and tubers have been selected for thousands of years to save for the next planting.
-
Sumarians
, Egyptians, and Romans collected and traded superior seeds and plants.
- (On right) Evolutionary changes in corn from 5,000 BC to 1,500 AD in Mexico.
Slide14Modern Biotechnology
Advances in genetics and molecular biology have led to innovations and new applications in biotechnology.
Classical biotechnology took advantage of natural microbial processes or artificially selected phenotypes. Genetics of these selected organisms proceeded naturally.
Modern biotechnology uses
-
Genetic Engineering
- Gene Cloning
Slide15Modern Biotechnology
Genetic Engineering -
Ability to manipulate DNA of an organism. Manipulation due to
Recombinant DNA Technology.
Recombinant DNA technology combines DNA from different sources.
Gene Cloning –
The ability to identify and reproduce a gene of interest.
Slide16Modern Biotechnology
Recombinant DNA technology has dominated modern biotechnology.
Has led to:
- Production of disease resistant plants.
- Genetically engineered bacteria to degrade environmental pollutants and to produce antibiotics.
Gene cloning and recombinant DNA technology have impacted human health through the Human Genome Project.
Slide17Discussion questions
What are the differences between classical and modern biotechnology? Be sure to discuss the processes involved
Discuss the differences with a partner.
Class discussion will follow.
Slide18Biotechnology – A science of many disciplines
What disciplines contribute to the science of biotechnology?
Slide19Biotechnology – A science of many disciplines.
The roots of biotechnology are formed by
:
- Human, animal, and plant physiology
- Mathematics
- Molecular and cell biology
- Immunology
- Statistics
- Microbiology
- Biochemistry
- Genetics
- Physics
- Chemical Engineering
- Computer Science
Slide20Biotechnology- A science of many disciplines
The “root” subjects pieced together can lead to genetic engineering approached with applications in:
- Drug development
- Environmental and Aquatic Biotechnology
- Agricultural Biotechnology
- Forensics and Detection
- Medical Biotechnology
- Regulatory Approval and Oversight.
Slide21Biotechnology – A science of many disciplines
A typical example of interdisciplinary nature of biotechnology.
- Scientific microbiology research discovers a gene or gene product of interest.
- Biochemical, molecular, and genetic techniques are used to determine the role of the gene.
-
Bioinformatics
(computer data bases) are used to study gene sequence or analyze protein structure.
- Gene then used in a biotechnology application.
Slide22Ethics in Biotechnology
What are the ethical concerns in biotechnology?
Slide23Ethics in Biotechnology
Powerful applications and potential promise of biotechnology raises ethical concerns.
Not everyone is a fan of biotechnology.
The wide range of legal, social, and ethical issues are cause for debate and discussion among scientists, the general public, clergy, politicians, lawyers, and many others.
Some questions of concern:
- Should human cloning be permitted?
- Will genetically modified foods be harmful to the environment?
- Should we permit the development of synthetic genomes?
Slide24Ethics in Biology
We will be looking at and discussing some of the ethical concerns in biotechnology.
Our goal
is not to tell you
what
to think but to empower you with the knowledge you can use to make your own wise decisions.
Slide25Discussion questions
What is a typical example of biotechnology as an interdisciplinary science?
What is bioinformatics?
What is our goal with respect to making ethical decisions about biotechnology?
Slide26Create a Concept Map
Read how to create a concept map.
http://www.libraries.psu.edu/psul/lls/students/research_resources/conceptmap.html
Create a concept map which incorporates the following terms:
Agricultural biotechnology Animal
Applications Beverage making
Biochemistry Bioinformatics
Biotechnology Bread making
Classical biotechnology Computer Science
DNA recombinant technology Drug development
Environmental biotechnology Ethical
Fermentation Forensics
Gene cloning Genetic engineering
Immunology Interdisciplinary science
Issues in biotechnology Lactic/acetic acid fermentation
Legal Medical biotechnology
Microbiology Molecular biology
Plant Root sciences
Selective breeding Social
Slide27Lesson 2
Case Study : A Glimpse into the
Futre
Start by viewing the video:
http://bigthink.com/ideas/16344
Read case study: “ A Glimpse into the Future,” by Lee Silver a molecular biologist at Princeton University.
Work in groups of 4 students and discuss the focus questions: What arguments does Silver give for thinking that human genetic enhancement be regarded as morally permissible? What arguments are used by opponents of genetic enhancement?
Complete: Student self and group evaluation of group participation
Whole class discussion: How we make ethical decisions, as well as any points of clarification needed by students.
Write
an individual
persuasive 5 paragraph essay supporting your opinion on use of genetic enhancement.
Slide28Lesson 2 – Work Groups Term 1
Slide29A Framework for Ethical Decisions
1. Recognize an Ethical Issue
Could this decision or situation be damaging to someone or to some group? Does this decision involve a choice between a good and bad alternative, or perhaps between two "goods" or between two "
bads
"?
Is this issue about more than what is legal or what is most efficient? If so, how?
Slide30A Framework for Ethical Decisions
2. Get the Facts
What are the relevant facts of the case? What facts are not known? Can I learn more about the situation? Do I know enough to make a decision?
What individuals and groups have an important stake in the outcome? Are some concerns more important? Why?
What are the options for acting? Have all the relevant persons and groups been consulted? Have I identified creative options?
Slide31A Framework for Ethical Decisions
3. Evaluate Alternative Actions
Evaluate the options by asking the following questions:
Which option will produce the most good and do the least harm? (The Utilitarian Approach)
Which option best respects the rights of all who have a stake? (The Rights Approach)
Which option treats people equally or proportionately? (The Justice Approach)
Which option best serves the community
as a whole, not just some members?
(The Common Good Approach)
Which option leads me to act as the sort of person I want to be? (The Virtue Approach)
Slide32A Framework for Ethical Decisions
4. Make a Decision and Test It
Considering all these approaches, which option best addresses the situation?
If I told someone I respect-or told a television audience-which option I have chosen, what would they say?
Slide33A Framework for Ethical Decisions
5. Act and Reflect on the Outcome
How can my decision be implemented with the greatest care and attention to the concerns of all stakeholders?
How did my decision turn out and what have I learned from this specific situation?
Slide34Lesson 3
Individually read the
Powerpoint
slides for lesson 3 and respond to the questions.
Create 7 groups.
Each group will be assigned one of the following topics and a corresponding article:
1. Microbial Biotechnology 2. Agricultural Biotechnology
3. Animal Biotechnology 4. Forensic Biotechnology
5. Bioremediation 6. Marine Biotechnology
7. Medical Biotechnology
Read the article and work together to create an accurate summary of the article
One member from each group will then present their assigned section of the
powerpoint
and provide a summary of their article. Write your article title on the whiteboard.
Slide35Microbial Biotechnology
Microbes have been used in many ways that affect society.
Manipulating microbial DNA has created organisms that manufacture food.
Manipulated microbes are used to make
- enzymes
- vaccines
- antibiotics
- insulin and growth hormones
- detectors for bioterrorism
- decontamination processes for industrial waste.
Slide36Agricultural Biotechnology
Plants have been bioengineered for
- Drought resistance
- Cold tolerance
- Pest resistance
- Greater food yield
Plants have been used for
molecular
pharming
.
Plants are bioengineered to produce recombinant proteins.
Downside:
Gene transfer from engineered plants to non- target plants in the environment has produced some super weeds.
Slide37Animal Biotechnology
Goats, cattle, sheep, and chickens are being used to produce antibodies and other medically needed proteins.
Transgenic animals become bioreactors. They contain genes from another sources and produce these proteins in their milk.
Animals are used in “knockout” experiments. Genes are disrupted and much is learned about gene function.
Many animals have been cloned; possible uses for using cloned animals for genetically engineered organs have been explored.
Slide38Forensic Biotechnology
DNA fingerprinting, methods to detect unique DNA patterns are being used in:
- Law enforcement
- Paternity testing
- Poaching of endangered species
- Tracking AIDS, Lyme disease, West Nile virus, TB.
- Testing of food products to see if food substitutes are being used.
Slide39Bioremediation
Microbial processes are used to degrade natural and man made substances.
Bioremediation is used in the clean up of massive oil spills; cleans up shorelines three times faster than traditional clean up methods.
Slide40Marine Biotechnology
Aquaculture
– raising fish or shellfish in controlled conditions to use as food sources.
- Genetically engineered disease resistant oysters
- Vaccine against viruses that infect fish
- Transgenic salmon injected with growth hormone that have extraordinary growth rates.
Bioprospecting
– Identifying marine organisms with novel properties to exploit for commercial purposes. Ex. Snails are a rich source of anti-tumor molecules.
Slide41Medical Biotechnology
New drugs and vaccines have been developed.
Human Genome Project is helping to identify defective genes and in the creation of new genetic tests.
Gene Therapy –
Inserting normal genes into a patient to replace defective ones.
Stem Cell Technology
– Possible use in the development of new tissues to replaced damaged tissues.
Slide42Lesson 4
View the video “Microbial Evolution” and respond to student worksheet
Lecture: Species Concept and Evolutionary Domains. Response to questions.
Lecture: Phenotypic
Classifcation
. Complete
Powerpoint
review of lecture
At the end of the lesson, write for 2 minutes about what you learned in Lesson 4.
Slide43Microbial evolution
http://www.youtube.com/watch?v=XawzIjX72U0
http://www.youtube.com/watch?v=YPgxEl9jzRU&feature=relmfu
http://www.youtube.com/watch?v=aF5sLLLalm8&feature=relmfu
http://www.youtube.com/watch?v=vghlsa7oD_8&feature=relmfu
4 parts of video
Slide44Lesson 4
What is a species?
A species is defined as a population that can naturally interbreed and produce fertile offspring, and that is reproductively isolated from other species.
Right!
Well, maybe not……..
Slide45Species Concept - Microbiology
A bacterial species is a prokaryote whose 16S ribosomal RNA sequence differs by no more that 3%.
http://www.microbeworld.org/careers/tools-of-the-trade/genetic-tools-and-techniques/16s-rrna
That is, at least 97% of the
rRNA
sequence is identical in a bacterial species.
A bacteria whose
rRNA
differs by more than 3% usually turns out to be a different species.
Slide46Species Concept- Microbiology
Prokaryotes do not fit the biological species concept because they are haploid and reproduce asexually.
They cannot produce “fertile offspring” like plants and animals can.
In microbiology,
evolutionary (molecular)chronometers
measure evolutionary change.
In other words, differences in nucleotide or amino acid sequences of functionally similar (homologous) macromolecules are a function of their evolutionary distance.
The greater the number of differences in a sequence the more distantly related the two species are.
Slide47Species Concept - Microbiology
Molecular Chronometers
The chronometer must be present in all groups being classified and it must be functionally homologous (not many sequence differences).
The following genes and proteins are most frequently used to classify bacteria.
- ribosomal RNA
-
ATPase
proteins (synthesize ATP)
-
RecA
(enzyme facilitates genetic recombination)
- Certain translation proteins.
Slide48Species Concept- Microbiology
Ribosomal RNA is the most widely used chronometer for identifying bacterial species :
- It is relatively large.
- Universally distributed
- Has many nucleotide sequences that are conserved.
16S
rRNA
are part of the small subunit (SSU) of the ribosome; used to classify prokaryotes.
Slide49Evolutionary Tree - Microbiology
Phylogenetic
Tree of Life -
rRNA
Slide50Three Domains - Microbiology
Bacteria
At least 40 phyla of bacteria in this domain.
Most of the phyla are related from a
phylogenetic
standpoint but have little in common in terms of phenotype.
Proteobacteria
contain species which are the ancestors of mitochondria.
Slide51Three Domains - Microbiology
Archaea
4 phyla in this domain
Contain
extremophiles
-
Hyperthermophiles
: live in high temperatures.
-
Methanogenic
: produce methane.
- Extreme
halophiles
: live in high salt environments.
Contains
Ignicoccus
,
bacteria with the smallest genome.
Slide52Three Domains - Microbiology
Eukarya
rRNA
phylogeny based on 18S
rRNA
.
Four kingdoms:
Protista
, Fungi, Plant, and Animal.
Range from single cell to complex multi-cell organisms. Rapid diversification of
Eukarya
was tied to changes in oxygen levels on earth.
Slide53Phenotypic Classification-Bacteria
Working microbiologists use phenotypic commonality in identifying bacteria. Most frequently these
phenotypes
are:
Cell shape
Cell wall structure
Cell respiration
Growth factors
Colony morphology
Slide54Phenotypic Classification-Bacteria
Cell Shape
There are 4 bacterial shapes:
-
Cocci
(
coccus
s.) or round
- Bacilli
(bacillus s.) or rod shaped
- Spirillum or cork screw shaped
-
Filamentous
or like jelly beans in straw
Slide55Phenotypic Classification- Bacteria
Cocci
Round shape
Examples
-
Staphlococcus
(
in clusters)
-
Streptococcus
(in chains)
Slide56Phenotypic Classification - Bacteria
Bacilli
Rod shaped
Examples
-
Bacillus
anthracis
(agent in anthrax)
-
Escherichia coli
(used in biotechnology)
Slide57Phenotypic Classification- Bacteria
Spirillum
Cork screw shape
Example
-
Treponema
pallidum
(
agent of syphilis
)
Slide58Phenotypic Classification-Bacteria
Filamentous
Jelly beans in straw
Example
-
Leptothris
discophora
(
aquatic bacteria uses
iron the way we use oxygen).
Slide59Phenotypic Classification -Bacteria
Composition of Cell Walls
Difference in cell wall structure becomes clear when a technique called the
Gram stain
is used.
Bacteria on a glass slide are stained first with a purple dye; the slide is rinsed with ethanol, and then a red counter stain is applied.
If bacteria remain purple =
Gram
positive.
If bacteria turn red =
Gram negative.
http://www.youtube.com/watch?v=Qk2OjqatCqc&feature=related
Slide60Phenotypic Classification-Bacteria
Gram +
cocci
Gram – rods
Slide61Phenotypic classification
All bacteria have a cell membrane and a cell wall composed of
peptidoglycan
.
Slide62Phenotypic Classification-Bacteria
Gram positive bacteria have their cell membrane and a simple but thick cell wall of
peptidoglycan
.
Peptidoglycan
gives shape to the cell.
Gram negative bacteria have their cell membrane and a thinner layer of
peptidoglycan
plus an outside layer of
lipopolysaccharides
.
Lipopolysaccharides
make gram negative organisms more threatening than gram positive organisms.
Slide63Phenotypic Classification-Bacteria
Cell Respiration
There are 3 types of cell respiration( synthesis of ATP):
-
Aerobic
: Use oxygen for cell respiration.
-
Anaerobic
: Cannot tolerate oxygen. Use fermentation
-
Facultative anaerobes: Can use or not use oxygen depending on availability.
Slide64Phenotypic Classification-Bacteria
Growth Factors
Nutrient Source
-
Heterotroph
:
Consume energy from outside source.
-
Autotroph
: Make and consume energy.
Energy Source (
Autotrophs
)
- Chemoautotroph :
Use chemicals as energy source.
-
Phototrophs
:
Use light as energy source.
Slide65Phenotypic Classification-Bacteria
Colony morphology
A single bacteria put onto a solid agar plate, if given sufficient nutrients, optimal temperature and pH, will multiply and form a colony.
All members of the colony are genetically identical.
Bacterial colonies of different species differ from one another.
Slide66Phenotypic Classification-Bacteria
To identify a colony, the following basic elements are noted.
Form
- What is the basic shape of the colony?
Elevation
- What is the cross sectional shape of the colony?
Margin
- What is the magnified shape of the edge of the colony?
Surface
- How does the surface of the colony appear?
Opacity
– Is the colony translucent, transparent, iridescent?
Chromogenesis
– pigmentation.
Slide67Phenotypic Classification
Form - Shape of the colony
Slide68Phenotypic Classification- Bacteria
Elevation – Cross sectional shape
Slide69Phenotypic Classification-Bacteria
Margin - Shape of the colony edge.
Slide70Phenotypic Classification-Bacteria
Opacity – Clear, Opaque, Iridescent
Iridescent
Slide71Phenotypic Classification
Chromogensis
- Pigmentation
Slide72Lesson 5
Visit the 3 websites noted on your handout to learn about prokaryotic structures and function.
Respond to all questions.
Next read the
Powerpoint
slides on prokaryotic structure and respond to all questions.
Slide73Prokaryotic structure
DNA in prokaryotes
DNA is found in the
-
Nucleoid
Region
- Plasmids
A typical prokaryote has one chromosome containing most of the genes in the cell.
A few species of
Bacteria &
Archaea
contain two chromosomes.
The DNA is a double stranded circular molecule.
Bacterial genomes contain from 500,000 base pairs to about 4 million base pairs, depending on the species..
Slide74Prokaryotic Structure
Plasmids
Plasmids are genetic elements (DNA) that exist and replicate separately from the chromosome.
Most are circular, some are linear.
Many prokaryotes contain one or more plasmids.
They range in size from 100 to 1,000 base pairs.
Plasmid DNA can be exchanged among bacteria.
For example, genes for antibiotic resistance are found on plasmids and one bacteria can transfer these genes to another bacteria.
Bacterial plasmids play a role in recombinant DNA technology.
Slide75Prokaryotic Structure
The differences between a bacterial chromosome and a plasmid:
- Chromosomes
carry many more genes than plasmids and the genes are essential to cellular function. Essential genes are called
housekeeping genes
.
-
Plasmids
carry far fewer genes and are expendable because the genes are not necessary for growth under all conditions.
Slide76Prokaryotic Structure
Restriction
Endonucleases
(Enzymes)
Are naturally found in bacteria.
When viruses invade bacteria, restriction
endonucleases
have the ability to cut up the foreign viral DNA. The possibility of viral infection plummets.
Can be thought of as a bacterial immune system because the role of restriction
endonucleases
is to protect the bacteria.
Bacteria can have more than one type restriction enzymes.
Bacterial restriction enzymes play a role in recombinant DNA technology.
Slide77Lesson 6
Lab experiment to demonstrate effectiveness of antimicrobial soap.
Lab:
- Review the following videos for instruction in microbiological techniques.
http://www.youtube.com/watch?v=PiWwnBbCrNs&feature=related
Pouring agar plates
.
http://www.youtube.com/watch?v=zZ1NQau1wtw
Dilutions and spread plating
http://www.youtube.com/watch?v=AaG3Pt3nwLQ&feature=relmfu
Streaking plates
http://www.youtube.com/watch?v=tBmNitxvqyc
Aseptic transfer
http://www.youtube.com/watch?v=SLkipIg4WRg
Making smears
http://www.youtube.com/watch?v=-j97pZo5t4g&feature=related
Gram stains
Slide78Lab
Day 1: Handwashing
and plate
innocculation
Day 2: Review Streaking for isolation video, collect data, and streak plates for isolation
Day 3: Collect data, study colony morphology, and gram stain
Slide79Lesson 7
E.coli
Lecture:
-
E.coli
the organism and its use in biotechnology.
- Pathogenic
E. coli
Read handout on pathogenic
E.coli
. Respond to questions. Class ReviewCase Study “Microbial Pie”
Track the Epidemic
Slide80E.coli
Escherichia coli
Gram negative rod normally found in the intestines of warm blooded animals.
E.coli
can benefit its host by producing vitamin K and by reducing numbers of pathogenic bacteria in the intestine.
Slide81E. coli
E.coli
is a hardy organism that is easy to culture and easy to manipulate in the lab.
It is a
model organism
in biotechnology.
Model organisms are extensively studied to understand biological phenomena and the information can be applied to other organisms.
E.coli
genome was one of the first to be sequenced in 1997.
Slide82E.coli
Most economically robust area in biotechnology is production of human proteins.
E.coli
has played a major role in production of these proteins.
Human genes for proteins can be cloned and inserted into plasmids in
E.coli
through recombinant DNA technology
Slide83E.coli
E.coli
is then grown in large
bioreactors
and it produces the protein of interest.
Purification methods
separate the target protein from the biological molecules in which it was produced.
The proteins can then be used by humans.
Slide84E.coli
The following proteins are manufactured via this technique:
Insulin
For diabetes
Human Growth Hormone
For growth hormone deficiency
Factor VIII
For hemophilia
Erythropoietin
For stimulation RBC growth
Slide85E. coli
Pathogenic vs. Non-pathogenic
E.coli
.
Most
E.coli
strains live commensally in the intestines of warm blooded animals. These strains are
non-pathogenic
.
Non-pathogenic strains of
E.coli
strains are used in biotechnology research.
Some
E.coli
strains are
virulent
and produce gastrointestinal disease. These strains are
pathogenic
.
Slide86E. coli
Causes of virulence
Toxicity
- Ability to cause disease by a preformed toxin. Toxin inhibits host cell function and kills host cell.
Invasiveness
- Ability of organism to grow in host cell tissue in such large numbers that pathogen inhibits host cell activity.
Slide87E. coli
E.coli
virulence
Due to an
enterotoxin
, a type of
exotoxin
.
The
enterotoxin is secreted by the bacteria and affects the cell membrane of intestinal cells. It makes the host cell membrane more permeable to chloride ions. As chloride enters the host cells, sodium and water leave the host cells.
This causes diarrhea and abdominal pain.
Virulent
E.coli
is acquired by eating contaminated food.
Slide88Lesson 8
Lecture: Natural gene transfer and recombination.
Whole class lecture: Gene transfer in prokaryotic organisms.
Pantomime of gene transfer
Case Study: Antibiotic resistance
Read each section of case study. Respond to questions.
In between each section of the case study, the whole class will have a discussion to clarify any of your concerns.
Slide89Gene Transfer and Recombination
Bacteria pass on their genetic material to the next generation asexually through binary fission.
Many bacteria, however, have the capacity to physically exchange genetic material with other bacteria.
There are 3 processes in which genetic material can be exchanged:
Transformation
Transduction
Conjugation
These 3 process are collectively referred to as
lateral
or horizontal gene transfer
.
Slide90Gene Transfer and Recombination
Transformation
Is a process by which free DNA is incorporated into a recipient cell and brings about genetic change.
Slide91Gene Transfer and Recombination
Do you remember the Griffith experiment?
http://science.jburroughs.org/mbahe/BioA/starranimations/chapter8/videos_animations/griffith.html
Slide92Gene Transfer and Recombination
Transformation
If a bacterial cell is
lysed
, the DNA pours out.
The bacterial chromosome then breaks apart into fragments with about 10 genes on them.
Other bacterial cells that are
competent
can take up the DNA from the environment. Competency is genetically determined.
The DNA enters the cell and is escorted through the cytoplasm by competence specific proteins to prevent degradation.
DNA is then recombined (integrated) into the bacterial chromosome.
http://highered.mcgraw-hill.com/sites/0072556781/student_view0/chapter13/animation_quiz_1.html
Slide93Gene Transfer and Recombination
Transformation in Biotechnology
In biotechnology procedures, the term transformation has a slightly different meaning.
E.coli
are poorly transformed under natural conditions.
If you treat the organism with calcium ions and chill it, it becomes easily transformed.
Transformation of this organism generally occurs in the plasmid.
Slide94Gene Transfer and Recombination
Transduction
DNA is transferred from cell to cell by a virus. Virus can transfer host cell DNA along with its own genetic material.
Slide95Gene Transfer and Recombination
In transduction, any gene on a donor bacterial chromosome can be transferred to a recipient.
A phage (virus for bacteria) enters the host cell and during a
lytic
infection enzymes responsible for packaging viral DNA sometimes package the host DNA accidentally.
The resulting virus with a piece of the donor DNA is called a
transducing
particle.
This
transducing
particle cannot go on to cause infection in a new cell. The DNA released is incorporated into a recipient bacterial cell chromosome.
http://highered.mcgraw-hill.com/sites/0072556781/student_view0/chapter13/animation_quiz_2.html
Slide96Gene Transfer and Recombination
Transduction
Slide97Gene Transfer and Recombination
Plasmids revisited
Before we learn conjugation, let’s review plasmids.
Plasmids:
Are genetic elements that replicate independently of the host chromosome.
Are unessential, do not control vital cell functions.
Are double stranded, mostly circular (some linear), structures with fewer genes than the bacterial chromosome.
Of different types may be present in a cell and numbers of these types can vary.
Called
episomes
can integrate into the bacterial chromosome.
Slide98Gene Transfer and Recombination
Types of plasmids
F (fertility) plasmid -
most studied, results in the expression of
sex
pili
.
R (resistance) plasmids
- contain genes that can build a resistance against antibiotics
Col plasmids -
which contain genes that code for
bacteriocins
that can kill other bacteria.
Degradative
plasmids
, which enable the digestion of unusual substances.
Virulence plasmids
- which turn the bacterium into a pathogen.
Slide99Gene Transfer and Recombination
Conjugation
Is a process of genetic transfer that involves cell to cell contact.
A
conjugative plasmid
uses this process to transfer a copy of itself to a new host.
The process involves a donor cell and a recipient cell.
Slide100Gene Transfer and Recombination
Conjugation
(using the F plasmid as an example)
The
F+ cell
has the plasmid and the ability to donate it. (donor)
The
F- cell
is the recipient
.
Slide101Gene Transfer and Recombination
Conjugation
F+ cell synthesizes a
sex
pillus
.
Sex
pillus
makes specific contact with the F- cell; pulling it toward the F+ cell.
Slide102Gene Transfer and Recombination
Conjugation
The DNA (plasmid) is transferred from the F+ to the F- cell through the sex
pillus
.
Depending on the species, sometimes the plasmid is replicated first in the F+ cell and then transmitted to F-. Other times, the 2 DNA strands are separated in F+ and one strand is transferred to F-. Both cells will then make a complimentary strand..
Slide103Gene Transfer and Recombination
The original F- cell turns into an F+ cell and can conjugate with other bacteria.
Conjugative plasmids can spread rapidly through populations much like infectious agents.
If plasmids contain genes that offer a selective advantage (like an antibiotic resistance gene), this can ensure survival of that population.
http://highered.mcgraw-hill.com/sites/0072556781/student_view0/chapter13/animation_quiz_3.html
Slide104Think-Pair-Share
Work with a partner and explain transformation, transduction, and conjugation to your partner.
Exchange places and have your partner explain the same to you.
Slide105Gene Transfer and Recombination
Create 6 groups
We will create pantomimes of horizontal gene transfer.
2 groups – Transformation
2 groups- Transduction
2 groups - Conjugation
Slide106Lesson 9
Products of microbial biotechnology
For homework read and familiarize yourself with the
Powerpoint
.
Read each article on the website at the bottom of each slide and make a copy of it for your notes.
Class Review: You will be assigned one of the articles and you will have to write an abstract of the article on the following day in class.
Genetically modified foods
Work with a partner and read research articles on genetically modified foods. Discuss the pros and cons of the argument with partner.
Work in groups of 4 on assigned topic. Research on computer additional information to support your topic. Develop a 5 minute argument defending your position.
Debate: One person from each group will present pro or con argument.
Instead of rebuttal, each student will have to speak for 1 minutes about their opinion on genetically modified food. Class will vote at end of debate.
Slide107Products Microbial Biotechnology
Food Biotechnology - fermentation
We have discussed fermentation of foods.
Scientists are currently working on ways to improve micro-organisms for food production.
- Developing virus resistant organisms through recombinant DNA technology to prevent economic losses in the dairy industry.
- Developing bacteria to produce chemicals to kill contaminating organisms in food making processes.
- Produced a microbial enzyme used to make cheese.
http://www.gmo-compass.org/eng/grocery_shopping/processed_foods/29.dairy_products_eggs_genetic_engineering.html
Slide108Products Microbial Biotechnology
Enzymes, Antibiotics, and Human Proteins.
Recombinant DNA technology has enabled production of new enzymes, antibiotics, and human proteins from microbial fermentation.
Prourokinase
is an enzyme which helps heal wounds infected with
E.coli
.
New and novel antibiotics with two pathways for treatment are being developed.
Tissue
plasminogen
activator, a protein which dissolves blood clots is being produced.
Read about biotechnology and detergents.
http://www.biotecharticles.com/Biotechnology-products-Article/Biotechnology-in-the-Manufacturing-of-Detergents-159.html
http://www.biotecharticles.com/Biotechnology-products-Article/Biotechnology-in-the-Manufacturing-of-Detergents-159.html
Slide109Products Microbial Biotechnology
Fuels and Biopolymers
Hydrogen power is a fuel of the future. Biotechnologists are looking at
Clostridium species
as generators of hydrogen.
Plastics worldwide are polluters because they are not biodegradable. Several organisms are being studied as producers of
bioplastics
. These biodegradable plastics will have several applications in the industrial and medical fields.
http://news.softpedia.com/news/Bacteria-Converts-Vegetables-to-Bioplastic-167546.shtml
Slide110Products Microbial Biotechnology
Agriculture
A
Pseudomonas
bacteria has been bioengineered with
B.
thuringiensis
toxin . The bacteria colonizes plants and acts as a
biopesticide
to kill insect larvae.
Baculoviruses are used to contaminate plant material. Insects ingest the plant and develop a lethal viral infection Biotechnologists are working on ways to bioengineer the
Baculovirus
to enhance its ability as a
biopesticide
.
http://www.biocontrol.entomology.cornell.edu/pathogens/baculoviruses.html
Slide111Products Microbial Technology
Bioremediation
Microorganisms with hydrocarbon oxidizing enzymes clean oil spills.
Microorganisms are used in waste water treatment facilities to purify water.
Bacteria are being studied which have the capacity to remove heavy metals such as arsenic, copper, tin, and mercury from the environment.
http://freshscience.org.au/2003/aussie-arsenic-eating-bacteria-may-save-lives-and-clean-mines
Slide112Lesson 10
Lecture and discussion: Eukaryotic microbes and biotechnology products.
Slide113Lesson 10 Eukaryotic Cells
Eukaryotic cell review: Review structure & function, sketch a eukaryotic cell, and trace the pathway of lipoprotein assembly.
Lecture: Yeast, Fungi, and Biotechnology products.
Video: The Biology of Fungi (16 min)
Reading and response: Evolutionary ties of fungi.
Slide114Microbial Eukaryotic Cells
http://www.biologyjunction.com/cell_functions.htm
Review of basic eukaryotic cell
Slide115Microbial Eukaryotic Cells
Fungi – General Characteristics
Fungi are composed of eukaryotic cells.
Some are unicellular and some are
multicellular
.
Habitats
: Most are terrestrial and some are aquatic
Energy : Fungi are heterotrophic decomposers. (A few are parasitic)
Cell Walls
: Resemble plants architecturally but are made of
chitin
not cellulose.
Reproduction
: Many reproduce asexually and sexually using spores.
Recent molecular evidence suggests fungi are probably more closely related to animals than to plants or
protists
.
http://www.fungionline.org.uk/
Slide116Microbial Eukaryotic Cells
There are 3 basic types of fungi
Unicellular fungi
- Yeast
Filamentous fungi
– Mold and fungi
Macroscopic fungi
– Mushrooms
We will limit our discussion to the first two types.
Slide117Microbial Eukaryotic Cells
Yeast
There are 1,500 species of yeast and yeast are not part of a single
taxon
.
Cells
- typically spherical, oval, or cylindrical
- usually 3-4 microns in size
- most are unicellular
- some
multicellular
: a string of connected yeast cells connected by
psuedohyphae
.
Slide118Microbial Eukaryotic Cells
Yeast with
pseudohyphae
Pseudohyphae
help yeast invade tissues.
Slide119Microbial Eukaryotic Cells
Yeast colonies growing on agar.
Slide120Microbial Eukaryotic Cells
Energy
Yeast flourish in environments where sugar is present.
They are facultative aerobes; using aerobic cell respiration and fermentation.
In a lab, yeast can be cultured with nutrient agar and grow colonies.
Slide121Microbial Eukaryotic Cells
Reproduction
Yeasts generally reproduce asexually by budding.
http://www.youtube.com/watch?v=iOvrq6ssy2Y
Slide122Microbial Eukaryotic Cells
Reproduction
Yeast can sexually reproduce by
mating.
Two different mating types fuse into a diploid cell.
Diploid cell can bud to make additional diploid cells.
Diploid cell undergoes meiosis and produces haploid cells called
ascospores
.
Ascospores
create new yeast cells.
Slide123Microbial Eukaryotic Cells
Yeast containing
ascospores
.
Slide124Review
What are the general characteristics of fungi?
Name the 3 types of fungi and provide an example.
Describe the following:
1. Structure of yeast
2. Energy use in yeast
3. Asexual and sexual reproduction of yeast
Slide125Microbial Eukaryotic Cells
Filamentous Fungi
Widespread in nature, usually seen on stale bread, cheese, or fruit.
Called
molds
.
Slide126Microbial Eukaryotic Cells
Cell Structure
A filament called a
hypha
(
hyphae
p,) grows from a single terminal cell.
The
hyphae
grow together across a surface and form compact tufts called
mycelium
.
This compact mat represents many intertwined
hyphae
.
Slide127Microbial Eukaryotic Cells
Cell Structure
From the mycelium,
hyphae
grow upward.
At the end of the vertical
hyphae
are spores called
conidia
.
Conidia are asexual spores and are often pigmented.
http://bugs.bio.usyd.edu.au/learning/resources/CAL/Microconcepts/Reproduction/fungiRepro.html
Slide128Microbial Eukaryotic Cells
Reproduction (asexual)
The function of the conidia is the dispersal of the fungus(via spores) to new habitats.
When new conidia form they are white and eventually become pigmented.
Slide129Microbial Eukaryotic Cells
Reproduction (Sexual)
Fungi can reproduce sexually.
An example is bread mold
Rhizopus
.
Hyphae
called
stolons
of opposite mating types (+ & -) fuse to form a structure called
gametangia
Dipoid
zygospore
is formed.
Zygospore
produces
sporandia
which undergo meiosis and release haploid spores.
Slide130Review
Describe the structure of a mold and the functions of each structure. Include the terms fungal cell,
hyphae
, mycelium, and conidia in your description.
Explain fungal asexual and sexual reproduction.
Slide131Biology of Fungi
http://www.youtube.com/watch?v=4NO299do_l4
http://www.youtube.com/watch?v=Luxjo0AsbTY&feature=relmfu
Slide132Microbial Eukaryotic Cells
Products
Several yeasts, in particular
Saccharomyces
cerevisiae
, have been widely used in biotechnology.
S.
cerevisiae
is a simple eukaryotic cell, serving as a
model organism
for all eukaryotes.Fundamental cellular processes such as the cell cycle,, DNA replication, recombination, cell division, and metabolism have been studied.
In 1996,
S.
cerevisiae
was announced to be the first eukaryote to have its genome, consisting of 12 million base pairs, fully sequenced as part of the Genome project.
Slide133Microbial Eukaryotic Cells
Products
S.
cerevisiae
as a model organism has improved our understanding of human disease genes.
Genetically engineered yeast and filamentous fungi have been used in the development of flavors, fragrances, food colorants, enzymes, pharmaceuticals (many human proteins), and solvents.
Slide134Lesson 11
MINI -Laboratory :Fungi
Read instructions for making a tease prep.
Sketch a diagram of fungal structures and label.
Please refer to your handout.
Slide135Lesson 12
Homework: Review and understand
powerpoint
and videos on virus structure, replication, and vectors.
Class: Create 4 work groups and develop review questions on assigned slides
Class: Present your slides and review questions to the class.
Work in groups of 4 to create a rap song involving virus content.
Create and present a rap song about viruses.(
See handout).
Slide136Viruses
General Properties
A minute particle containing nucleic acid, a protein coat, and sometimes other macromolecules.
Can exist in extracellular or intracellular form.
Extracellular
–is metabolically inert.
Intracellular
– viral replication occurs,
Slide137Viruses - Genomes
Genomes
Viral genomes are very small (3 to 100 genes)and encode for those functions that they cannot adapt from their host.
Viral genomes are categorized by the type of nucleic acid present.
Double stranded DNA
Single stranded DNA
Double stranded RNA
Single stranded RNA
Single stranded RNA that replicates with a DNA intermediate.
Viral genomes can be linear or circular.
Slide138Viruses - Structure
Virus Structure
Structures of viruses vary widely in size, shape, and chemical composition.
Commonalities of structure
Nucleic acid
(DNA or RNA)
Capsid
- made of one to several proteins which surrounds nucleic acid.
Envelope
–most animal viruses have an envelope.
The envelope is composed of a
phopholipid
bilayer
from the host and proteins which the virus makes.
Viruses without an envelope are called
naked
viruses.
Slide139Viruses - Structure
Enzymes
Some viruses contain enzymes.
Bacteriophages
have
lysozyme
to make a small hole in bacterial cell wall.
Retroviruses have
reverse transcriptase
that transcribes DNA from their RNA.Viruses have enzymes because the cell would not be able to replicate the viruses with out them.
Slide140Viruses - Replication
Viral Replication
The phases of the replication process are
Attachment
Penetration
Synthesis of nucleic acid and proteins
Assembly
Release
Slide141Viruses - Replication
Attachment
Viruses are specific for the host cells they infect.
Proteins on the outside of naked or enveloped virus interact with specific cell membrane receptors.
If a cell membrane is altered, the virus cannot infect the cell; host resistance.
However, viruses protein mutation enable viruses to interact with changed receptors.
Slide142Viruses - Replication
Penetration
Three ways a virus can penetrate a cell membrane:
Membrane Fusion
or
Hemifusion
State
:
The cell membrane is punctured and made to further connect with the unfolding viral envelope.
Entry Pore
formation: An opening is established through which viral particles can then enter.
Viral Penetration
:
The viral
capsid
or genome is injected into the host cell's cytoplasm. (enveloped viruses can
uncoat
the envelope at the cell membrane, cytoplasm, or nuclear membrane, depending on virus species).
Slide143Viruses
http://highered.mcgraw-hill.com/sites/0072556781/student_view0/chapter18/animation_quiz_1.html
Attachment and penetration
Slide144Viruses - Replication
Synthesis of nucleic acids and proteins - DNA viruses
How viruses synthesize nucleic acids in the cell depends on the type of nucleic acid present in the virus.
Double stranded DNA virus-
Incorporates its DNA into the host genome and protein synthesis can begin.
Single stranded DNA virus –
A complimentary DNA strand must be synthesized in the host because RNA polymerase requires double stranded DNA.
Slide145Viruses - Replication
Synthesis of nucleic acid and protein – RNA viruses
RNA
viruses need an RNA-dependent RNA-polymerase to replicate their RNA.
Cells do not have this enzyme.
RNA viruses need to code for an RNA-dependent RNA polymerase.
No viral proteins can be made until viral messenger RNA is available .
The nature of the RNA in the virus affects its replication strategy.
Slide146Viruses - Replication
Synthesis of nucleic acids and proteins- RNA virus
Single stranded RNA virus
–
There are 2 types of single stranded RNA viruses.
Plus-stranded RNA viruses
-In these
viruses,RNA
is the same sense (direction) as mRNA and it functions as mRNA. This mRNA can be translated immediately upon infection of the host cell.
Negative-stranded RNA viruses
- The virus RNA is negative sense (complementary to mRNA)
and must therefore be copied into the complementary plus-sense mRNA before proteins can be made
. The virus uses its own RNA polymerase to make the plus stranded m RNA.
Double-stranded RNA virus
- The virus RNA is double stranded and can’t function as mRNA; these viruses also need to package an RNA polymerase to make their mRNA after infection of the host cell.
Slide147Viruses - Replication
Synthesis of nucleic acids and proteins – retrovirus.
The single strand of retrovirus RNA serves as a template to make a single strand of DNA with the virus’ enzyme reverse transcriptase.
A complimentary DNA strand is made and the double stranded DNA is then a template for mRNA synthesis.
http://highered.mcgraw-hill.com/sites/0072495855/student_view0/chapter24/animation__hiv_replication.html
Slide148Viruses – Replication
Synthesis of nucleic acids and proteins
Once mRNA is made proteins can by synthesized.
Early proteins
– are made first which are necessary for viral replication.
Late proteins-
are then synthesized such as the viral coat protein.
Slide149Viruses - Replication
Assembly
Viruses self assemble in cells.
Virus self-assembly within host cells has implications for the study of the origin of life, as it lends credence to the hypothesis that life could have started as self-assembling organic molecule
Slide150Viruses
Release
Naked virus release
http://faculty.ccbcmd.edu/courses/bio141/lecguide/unit3/viruses/release_nv_fl.html
Enveloped virus release
h
ttp://highered.mcgraw-hill.com/sites/0072556781/student_view0/chapter18/animation_quiz_2.html
Slide151Viruses - Vector
Viruses as vectors
Vector
(in biotechnology) DNA that can be used to carry and replicate foreign DNA in biotechnology experiments.
Viruses can serve as vectors.
Genes of interest can be inserted into the viral genome and the genes of interest will replicate along with the virus.
Slide152Viruses - Vector
Viral vectors can be delivery system for gene therapy.
http://www.edu365.cat/aulanet/comsoc/Lab_bio/simulacions/GeneTherapy/GeneTherapy.htm
Viruses have potential as delivery systems in gene therapy because
A. They naturally enter cells.
B. They can integrate in the host cell genome.
C. They are cell specific which would allow for targeted gene therapy.