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Chapter 8

Recombinant DNA Technology

*   Intentionally modifying genomes of organisms, by natural and artificial processes, for practical purposes

Three Goals of Recombinant DNA Technology

*   Eliminate undesirable phenotypic traits in humans, animals, plants, and microbes

*   Combine beneficial traits of two or more organisms to create valuable new organisms

*   Create organisms that synthesize products humans need

Tools of Recombinant DNA Technology

*   Mutagens

*   Reverse transcriptase

*   Synthetic nucleic acids

*   Restriction enzymes

*   Vectors

*   Creation of gene libraries

Restriction Enzymes

*   Bacterial enzymes that cut DNA molecules only at specific locations (restriction sites)

Techniques of Recombinant DNA Technology

*   Polymerase Chain Reaction

*   Clone Selection

*   Separation of DNA Molecules

*   Inserting DNA into Cells

Multiplying DNA in vitro: The Polymerase Chain Reaction (PCR)

*   Large number of identical molecules of DNA produced in vitro

*   Repetitive process consisting of three steps

*   Denaturation

*   Priming

*   Extension

Applications:Epidemiologists use to amplify genome of unknown pathogen (West Nile virus)

*           Amplify DNA from Bacillus anthracis spores in 2001 to identify source of spores

 

 

Gel Electrophoresis

*   DNA has negative charge; drawn by electric current toward positive electrode

*   Agarose makes up gel; acts as molecular sieve

*   Smaller fragments migrate faster and further than larger ones

*   Determine size by comparing distance migrated to that of standards and constructing standard curve

Applications of Recombinant DNA Technology

*   Pharmaceutical and Therapeutic Applications

*   Agricultural Applications

 

*   Pharmaceutical and Therapeutic Applications

*   Protein synthesis

*   Vaccines

*   Genetic screening

*   DNA fingerprinting

*   Gene therapy

*   Xenotransplants

Protein Synthesis

*   Creation of synthetic peptides for cloning

Vaccines

*   Production of safer vaccines

*           Subunit vaccines

Genetic Screening

*   Southern blots used to screen patients, prospective parents, and fetuses for inherited disease caused by mutations

*   Can also identify pathogen’s DNA in blood or tissues

Gene Therapy

*   Missing or defective genes replaced with normal copies

                *           Successfully treated patients with severe combined immunodeficiency disease

*           Others that may respond well – cystic fibrosis, sickle cell anemia, some types of hemophilia, some types of diabetes

Xenotransplants

*   Animal cells, tissues, or organs introduced into human body

*           Agricultural Applications

*   Herbicide resistance
              Round-up resistance induced in desirable crop

*  Salt tolerance
              Gene for salt tolerance inserted into tomato and canola plants

*   Freeze resistance
              Crops sprayed with genetically modified bacteria can tolerate mild freezes

*   Pest resistance
              Gene for Bt-toxin inserted into potatoes, cotton, and corn; Bt-toxin naturally occurring, harmful to insects only, and biodegradable

*   Improvements in nutritional value and yield
                        Gene for enzyme that breaks down pectin suppressed; tomatoes allowed to ripen on vine and shelf life increased

Ethics and Safety of Recombinant DNA Technology

*   Long-term effects of transgenic manipulations are unknown

*   Unforeseen problems arise from every new technology and procedure

*   Natural genetic transfer could deliver genes from transgenic plants and animals into other organisms

*   Transgenic organisms could trigger allergies or cause harmless organisms to become pathogenic

*   Studies have not shown any risks to human health or environment

*   Standards imposed on labs involved in recombinant DNA technology

*   Can create biological weapons using same technology

*   Ethical issues

*   Routine screenings?

*   Who should pay?

*   Genetic privacy rights?

*   Profits from genetically altered organisms?

*   Required genetic screening?

*   Forced correction of “genetic abnormalities?”


Chapter 9

Controlling Microbial Growth in the Environment

Terminology of Microbial Control

•Sterilization

The removal or destruction of all microbes in or on an object

Includes viruses and bacterial endospores, but we can’t sterilize prion contaminated material without incinerating it.

Example: autoclaving nutrient agar to make plates.

•Aseptic

Free of microbes, especially pathogens

•Disinfection(disinfectants)

inhibition or killing of microorganisms on inanimate objects by chemicals

Example: Viruses on glass slides are killed by soaking in 10% bleach .

•Antisepsis(antiseptic)

inhibition or killing of microorganisms on skin or tissue by chemicals

Example- a phlebotomist uses alcohol to clean the skin prior to drawing blood.

•Degerming

removal by mechanical means, like scrubbing.

Example: a surgeon washes her hands prior to performance of a procedure.

•Sanitization

an approved procedure known to produce acceptable levels of microbe reduction or removal

Example: restaurants are required to have written sanitization procedures that explain how food preparation surfaces are disinfected

•Pasteurization

use of heat to kill pathogens and reduce numbers of spoilage microbes

•Suffix –stasis/-static-suspend the growth without killing

•Suffix – cide/-cidal – destroys or inactivates a microbe

Types of controls:

     Physical Methods of Microbial Control
     Chemical Methods of Microbial Control

 

Action of Antimicrobial Agents

•Modes of action fall into two basic categories

•Alteration of cell walls or cytoplasmic membranes

•Interference with protein and nucleic acid structure

 

 

Alteration of Cell Walls and Membranes

•Cell wall maintains integrity of cell

•When disrupted, cannot prevent cell from bursting due to osmotic effects

•Cytoplasmic membrane contains cytoplasm and controls passage of chemicals into and out of cell

•When damaged, cellular contents leak out

Damage to Proteins and Nucleic Acids

•Protein function depends on 3-D shape

•Extreme heat or certain chemicals denature proteins

Selection of Microbial Control Methods

•Ideally, agents should be:

•Inexpensive

•Fast-acting        

•Stable during storage

•Control all microbial growth while being harmless to humans, animals, and objects

Factors Affecting the Efficacy of Antimicrobial methods

•Nature of site to be treated

•Harsh chemicals and extreme heat cannot be used on humans, animals, and fragile objects

 

Relative Susceptibility of Microorganisms

Environmental Conditions

Physical Methods of Microbial Control

•Exposure to extremes of heat

•Exposure to extremes of cold

•Desiccation

•Filtration

•Osmotic pressure

•Radiation

Moist Heat

•Used to disinfect, sanitize, and sterilize

•Kills by denaturing proteins and destroying cytoplasmic membranes

•More effective than dry heat; water better conductor of heat than air

•Methods of microbial control using moist heat

•Boiling

•Autoclaving

•Pasteurization

•Ultrahigh-Temperature Sterilization

Dry Heat

•Used for materials that cannot be sterilized with or are damaged by moist heat

•Denatures proteins and oxidizes metabolic and structural chemicals

•Requires higher temperatures for longer time than moist heat

•Incineration – ultimate means of sterilization

Refrigeration and Freezing

•Decrease microbial metabolism, growth, and reproduction

•Chemical reactions occur slower at low temperatures

•Liquid water not available

Desiccation and Lyophilization

•Drying inhibits growth due to removal of water; only microbiostatic

•Lyophilization used for long term preservation of microbial cultures

•Prevents formation of damaging ice crystals

Filtration

          Used for sensitive materials like tissue culture medium.

Osmotic Pressure

•High concentrations of salt or sugar in foods to inhibit growth

Radiation

•Radiation described as ionizing or nonionizing

Ionizing Radiation

•Electron beams – effective at killing but do not penetrate well

•Used to sterilize some sliced meats, microbiological plastic ware, and medical and dental supplies

•Gamma rays – penetrate well but require hours to kill microbes

•Used to sterilize meats, spices, and fresh fruits and vegetables

•X-rays require too much time to be practical for growth control

Nonionizing Radiation

•Wavelengths greater than 1 nm

•Excites electrons and causes them to make new covalent bonds

•Affects 3-D structure of proteins and nucleic acids

•Suitable for disinfecting air, transparent fluids, and surfaces of objects

Chemical Methods of Microbial Control

•Affect microbes’ cell walls, cytoplasmic membranes, proteins, or DNA

•Effect varies with temperature, length of exposure, and amount of organic matter

•Also varies with pH, concentration, and age of chemical

•Tend to be more effective against enveloped viruses and vegetative cells of bacteria, fungi, and protozoa

Chemical Methods of Microbial Control

•Major Categories

•Phenols

•Alcohols

•Halogens

•Oxidizing agents

•Surfactants

•Heavy Metals

•Aldehydes

•Gaseous Agents

•Antimicrobics

Development of Resistant Microbes

          Major emphasis by CDC on preventing the development and spread of resistant organisms


Chapter 10

Controlling Microbial
Growth in the Body:
Antimicrobial Drugs

Drugs

•   •   Chemicals that affect physiology in any manner

•   •   Chemotherapeutic agents – drugs that act against diseases

•   •   Antimicrobial agents – drugs that treat infections

True or False- all antimicrobials are chemotherapeutic agents, but not all chemotherapeutic agents are antimicrobials


True!

Ideal Antimicrobial Agent

·       ·        Readily available

·       ·        Inexpensive

·       ·        Chemically stable

·       ·        Easily administered

·       ·        Nontoxic and nonallergenic

·       ·        Selectively toxic against wide range of pathogens

•   •   Paul Ehrlich

•   •   “Magic Bullets”

•   •   Arsenic compound that killed trypanosomes and another that worked against treponemes

•   •   Alexander Fleming

•   •   Penicillin released from Penicillium

•   •   Antibiotics – antimicrobial agents produced naturally by organisms

Mechanisms of Antimicrobial Action

•   •   Key is selective toxicity

Inhibition of Cell Wall Synthesis

Examples

•   •   Vancomycin and cycloserine interfere with particular alanine-alanine bridges that link NAM subunits in many Gram-positives

•   •   Bacitracin blocks secretion of NAG and NAM from cytoplasm

•   •   Isoniazid and ethambutol disrupt formation of arabinogalactan-mycolic acid in mycobacterial species

Inhibition of Cell Wall Synthesis

•   •   Prevent bacteria from increasing amount of peptidoglycan

•   •   Have no effect on existing peptidoglycan layer

•   •   Effective only for growing cells

•   •   No effect on plant or animal cells; no peptidoglycan

Inhibition of Protein Synthesis

True or false?   Because all cells synthesize protein, few drugs selectively inhibit this process.


 

False- prokaryotic ribosomes are 70S, eukaryotic are 80S


 

Disruption of Cytoplasmic Membranes

True or false- many antimicrobials that affect the cell membrane are only used externally because they are toxic to humans.


 

True!


 

Inhibition of Metabolic Pathways

Inhibition of Nucleic Acid Synthesis

Prevention of Virus Attachment

Evaluation of Antimicrobial

•   •   Spectrum of action

•   •   Efficacy

•   •   Dosages required to be effective

•   •   Routes of administration

True or false- spinal cord infections are difficult to treat because most drugs cannot diffuse out of the blood into the spinal column.


 

True!

•   •   Overall safety

•   •   Side effects

Disruption of Normal Microbiota

•   •   May result in secondary infections

•   •   Overgrowth of normal flora – superinfections

The Development of Resistant Organisms in Populations

•   •   Some are naturally partially or completely resistant

•   •   Resistance by bacteria acquired in 2 ways

•   •   New mutations of chromosomal genes

•   •   Acquisition of R-plasmids via transformation, transduction, and conjugation

Multiple Resistance and Cross Resistance

Retarding Resistance

•   •   High concentrations of drug maintained in patient for long enough time to kill all sensitive cells and inhibit others long enough for immune system to destroy

•   •   Use antimicrobial agents in combination; synergism vs. antagonism

•   •   Limit use of antimicrobials to necessary cases

•   •   Development of new variations of existing drugs (novel side chains added to original molecule)


Chapter 11

Characterizing and Classifying Prokaryotes

Prokaryotes

"  "  Most diverse group of organisms

"  "  Habitats

"   "   From Antarctic glaciers to thermal hot springs

"   "   From colons of animals to cytoplasm of other prokaryotes

"   "   From distilled water to supersaturated brine

"   "   From disinfectant solutions to basalt rocks

"  "  Only a few capable of colonizing humans and causing disease

Reproduction of Prokaryotic Cells

"  "  All reproduce asexually

"  "  Three methods

"   "   Binary fission (most common)

"   "   Snapping division

"   "   Reproductive structure formation

Arrangements of Prokaryotic Cells

"  "  Result from two aspects of division during binary fission

"   "   Planes in which cells divide

"   "   Separation of daughter cells

Modern Prokaryotic Classification

"  "  Currently based on genetic relatedness of rRNA sequences

"  "  Three domains

"   "   Archaea

"   "   Bacteria

"   "   Eukarya

Survey of Archaea

   Lack peptidoglycan
No known human pathogens

Extremophiles

"  "  Require extreme conditions of temperature, pH and/or salinity to survive

"  "  Prominent members are thermophiles and halophiles, methanogens

Non-Archaea Prokaryotes:

Deeply Branching Bacteria

"  "  Scientists believe these organisms are similar to earliest bacteria

"  "  Autotrophic

"  "  Aquifex – considered to represent earliest branch of bacteria

"  "  Deinococcus – has outer membrane similar to Gram-negatives, but stains Gram-positive

Phototrophic Bacteria

"  "  Five groups

"   "   Blue-green bacteria (cyanobacteria)

"   "   Green sulfur bacteria

"   "   Green nonsulfur bacteria

"   "   Purple sulfur bacteria

"   "   Purple nonsulfur bacteria

Low G + C Gram-Positive Bacteria

"  "  Clostridia

"  "  Mycoplasma

"  "  Low C + C Gram-positive bacilli and cocci

"   "   Bacillus

"   "   Listeria

"   "   Lactobacillus

"   "   Streptococcus and Enterococcus

"   "   Staphylococcus

Endospores

"  "  Produced by Gram-positive Bacillus and Clostridium

"  "  Each vegetative cell transforms into one endospore

"  "  Each endospore germinates to form one vegetative cell

"  "  Constitute a defensive strategy against hostile or unfavorable conditions

"  "  Extremely resistant to drying, heat, radiation, and lethal chemicals

"  "  Stable resting stages

"  "  Can remain viable for tens to thousands of years

"  "  Serious concern to food processors, health care professionals, and governments

High G + C Gram-Positive Bacteria

"  "  Includes rod-shaped cells and filamentous bacteria

"  "  Corynebacterium

"  "  Mycobacterium

"  "  Actinomycetes

"   "   Actinomyces

"   "   Nocardia

"   "   Streptomyces

Gram-Negative Proteobacteria

"  "  Largest and most diverse group of bacteria

"  "  Five distinct classes

"   "   Alphaproteobacteria

"   "   Betaproteobacteria

"   "   Gammaproteobacteria

"   "   Deltaproteobacteria

"   "   Epsilonproteobacteria

Other Gram-Negative Bacteria

"  "  Chlamydias

"   "   Chlamydia

"  "  Spirochetes

"   "   Treponema

"   "   Borrelia

"  "  Bacteroids

"   "   Bacteroides

"   "   Cytophaga

 


Chapter 12,

Characterizing and Classifying Eukaryotes

Eukaryotes

"  "  Four major groups

"   "   Protozoa

"   "   Fungi

"   "   Algae

"   "   Walter Molds and Slime Molds

"  "  Include both human pathogens and organisms vital for human life

Reproduction in Eukaryotes

"  "  More complicated than that in prokaryotes

"   "   Eukaryotic DNA packaged with histones as chromosomes in the nucleus

"   "   Have variety of methods of asexual reproduction (budding, fragmentation, spore formation, and schizogony)

"   "   Many reproduce sexually by forming gametes and zygotes

"   "   Algae, fungi, and some protozoa reproduce sexually and asexually

Nuclear Division

"  "  Two types

"   "   Mitosis

"   "   Meiosis

Mitosis

"  "  Begins after cell has duplicated its DNA; cell partitions replicated DNA equally between two nuclei

"  "  Maintains ploidy of parent nucleus

Meiosis

"  "  Nuclear division involving partitioning of chromatids into four nuclei

"  "  Diploid nuclei use meiosis to produce haploid daughter nuclei for sexual reproduction

Schizogony

Classification of Eukaryotic Organisms

Protozoa

"  "  Diverse group defined by three characteristics