UNIT 1

Biotechnology and Microbiology

Definition 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.

BiotechnologyThe Biotechnology Revolution - NOVA http://www.youtube.com/watch?v=bukTqy

WgaM8

Lesson 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.

History of Biotechnology What is the difference between classical biotechnology

and modern biotechnology?

Classical 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.

Fermentation Do you remember this? http://people.cst.cmich.edu/schul1te/animations/f

ermentation.swf

Fermentation 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.

Fermentation 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.

Fermentation 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 14th

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.

Selective 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.

Selective 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.

Selective 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.

Modern 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

Modern 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.

Modern 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.

Discussion 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.

Biotechnology – A science of many disciplines

What disciplines contribute to the science of biotechnology?

Biotechnology – 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

Biotechnology- 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.

Biotechnology – 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.

Ethics in Biotechnology What are the ethical concerns in

biotechnology?

Ethics 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?

Ethics 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.

Discussion 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?

Create 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 AnimalApplications Beverage makingBiochemistry BioinformaticsBiotechnology Bread makingClassical biotechnology Computer ScienceDNA recombinant technology Drug developmentEnvironmental biotechnology EthicalFermentation ForensicsGene cloning Genetic engineeringImmunology Interdisciplinary scienceIssues in biotechnology Lactic/acetic acid fermentationLegal Medical biotechnologyMicrobiology Molecular biologyPlant Root sciencesSelective breeding Social

Lesson 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.

Lesson 2 – Work Groups Term 1

A 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?

A 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?

A 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)

A 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?

A 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?

Lesson 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.

Microbial Biotechnology Microbes have been used in

many ways that affect society.1. Manipulating microbial DNA has

created organisms that manufacture food.

2. Manipulated microbes are used to make

- enzymes - vaccines - antibiotics - insulin and growth hormones - detectors for bioterrorism - decontamination processes for

industrial waste.

Agricultural 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.

Animal 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.

Forensic 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.

Bioremediation 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.

Marine 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.

Medical 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.

Lesson 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.

Microbial evolution http://www.youtube.com/watch?v=XawzI

jX72U0 http://www.youtube.com/watch?v=YPgx

El9jzRU&feature=relmfu http://www.youtube.com/watch?v=aF5sL

LLalm8&feature=relmfu http://www.youtube.com/watch?v=vghls

a7oD_8&feature=relmfu

4 parts of video

Lesson 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……..

Species 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.

Species 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.

Species 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.

Species 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.

Evolutionary Tree - Microbiology

Phylogenetic Tree of Life - rRNA

Three 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.

Three 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.

Three 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.

Phenotypic 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

Phenotypic 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

Phenotypic Classification- Bacteria

Cocci Round shape Examples -Staphlococcus (in clusters) -Streptococcus (in chains)

Phenotypic Classification - Bacteria

Bacilli Rod shaped Examples - Bacillus anthracis (agent in anthrax)

- Escherichia coli (used in

biotechnology)

Phenotypic Classification- Bacteria

Spirillum Cork screw shape Example - Treponema

pallidum (agent of syphilis)

Phenotypic Classification-Bacteria

Filamentous Jelly beans in straw

Example -Leptothris

discophora (aquatic bacteria uses

iron the way we use oxygen).

Phenotypic 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

Phenotypic Classification-Bacteria

Gram + cocci

Gram – rods

Phenotypic classification

All bacteria have a cell membrane and a cell wall composed of peptidoglycan.

Phenotypic 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.

Phenotypic 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.

Phenotypic 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.

Phenotypic 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.

Phenotypic 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.

Phenotypic Classification Form - Shape of the colony

Phenotypic Classification- Bacteria

• Elevation – Cross sectional shape

Phenotypic Classification-Bacteria

Margin - Shape of the colony edge.

Phenotypic Classification-Bacteria

Opacity – Clear, Opaque, Iridescent

Iridescent

Phenotypic Classification Chromogensis - Pigmentation

Lesson 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.

Prokaryotic 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..

Prokaryotic 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.

Prokaryotic 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.

Prokaryotic 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.

Lesson 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=relatedPouring agar plates. http://www.youtube.com/watch?v=zZ1NQau1wtwDilutions and spread platinghttp://www.youtube.com/watch?v=AaG3Pt3nwLQ&feature=relmfuStreaking plateshttp://www.youtube.com/watch?v=tBmNitxvqycAseptic transferhttp://www.youtube.com/watch?v=SLkipIg4WRgMaking smearshttp://www.youtube.com/watch?v=-j97pZo5t4g&feature=relatedGram stains

Lab 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

Lesson 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 Review Case Study “Microbial Pie” Track the Epidemic

E.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.

E. 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.

E.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

E.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.

E.coli The following proteins

are manufactured via this technique:

InsulinFor diabetesHuman Growth Hormone

For growth hormone deficiency

Factor VIIIFor hemophiliaErythropoietinFor stimulation RBC growth

E. 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.

E. 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.

E. 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.

Lesson 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.

Gene 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:

1. Transformation2. Transduction3. Conjugation These 3 process are collectively referred to as lateral

or horizontal gene transfer.

Gene Transfer and Recombination

Transformation Is a process by which free DNA is

incorporated into a recipient cell and brings about genetic change.

Gene Transfer and Recombination

Do you remember the Griffith experiment?

http://science.jburroughs.org/mbahe/BioA/starranimations/chapter8/videos_animations/griffith.html

Gene 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

Gene 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.

Gene 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.

Gene 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

Gene Transfer and Recombination

Transduction

Gene 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.

Gene 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.

Gene 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.

Gene 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.

Gene 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.

Gene 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..

Gene 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

Think-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.

Gene Transfer and Recombination

Create 6 groups We will create

pantomimes of horizontal gene transfer.

2 groups – Transformation

2 groups- Transduction 2 groups - Conjugation

Lesson 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.

Products 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

Products 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

Products 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

Products 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

Products 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

Lesson 10 Lecture and discussion: Eukaryotic

microbes and biotechnology products.

Lesson 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.

Microbial Eukaryotic Cells

http://www.biologyjunction.com/cell_functions.htm Review of basic eukaryotic cell

Microbial 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/

Microbial Eukaryotic Cells There are 3 basic types

of fungia. Unicellular fungi -

Yeastb. Filamentous fungi –

Mold and fungic. Macroscopic fungi –

Mushrooms

We will limit our discussion to the first two types.

Microbial 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.

Microbial Eukaryotic Cells

Yeast with pseudohyphae

Pseudohyphae help yeast invade tissues.

Microbial Eukaryotic Cells Yeast

colonies growing on agar.

Microbial 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.

Microbial Eukaryotic Cells Reproduction Yeasts

generally reproduce asexually by budding.

http://www.youtube.com/watch?v=iOvrq6ssy2Y

Microbial 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.

Microbial Eukaryotic Cells

Yeast containing ascospores.

Review 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

Microbial Eukaryotic Cells Filamentous

Fungi Widespread

in nature, usually seen on stale bread, cheese, or fruit.

Called molds.

Microbial 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.

Microbial 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

Microbial 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.

Microbial 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.

Review 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.

Biology of Fungi http://www.youtube.com/watch?v=4NO2

99do_l4 http://www.youtube.com/watch?v=Luxjo

0AsbTY&feature=relmfu

Microbial 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.

Microbial 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.

Lesson 11 MINI -Laboratory :Fungi Read instructions for making a tease

prep. Sketch a diagram of fungal structures

and label. Please refer to your handout.

Lesson 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).

Viruses 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,

Viruses - 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.

a. Double stranded DNAb. Single stranded DNAc. Double stranded RNAd. Single stranded RNAe. Single stranded RNA that

replicates with a DNA intermediate.

Viral genomes can be linear or circular.

Viruses - Structure Virus Structure Structures of viruses vary widely

in size, shape, and chemical composition.

Commonalities of structurea. Nucleic acid (DNA or RNA)b. Capsid- made of one to several

proteins which surrounds nucleic acid.

c. Envelope –most animal viruses have an envelope.

d. The envelope is composed of a phopholipid bilayer from the host and proteins which the virus makes.

e. Viruses without an envelope are called naked viruses.

Viruses - 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.

Viruses - Replication Viral Replication The phases of the

replication process are

a. Attachmentb. Penetrationc. Synthesis of

nucleic acid and proteins

d. Assemblye. Release

Viruses - 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.

Viruses - Replication Penetration Three ways a virus can penetrate a

cell membrane:a. Membrane Fusion or

Hemifusion State: The cell membrane is punctured and made to further connect with the unfolding viral envelope.

b. Entry Pore formation: An opening is established through which viral particles can then enter.

c. 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).

Viruses http://highered.mcgraw-hill.com/sites/00

72556781/student_view0/chapter18/animation_quiz_1.html

Attachment and penetration

Viruses - 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.

Viruses - 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.

Viruses - Replication Synthesis of nucleic acids and proteins- RNA virus Single stranded RNA virus – There are 2 types of single

stranded RNA viruses. a. 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.

b. 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.

Viruses - 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/c

hapter24/animation__hiv_replication.html

Viruses – 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.

Viruses - 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

Viruses 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

Viruses - 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.

Viruses - Vector Viral vectors can be delivery system for

gene therapy. http://www.edu365.cat/aulanet/comsoc/Lab_b

io/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.