MICROBIOLOGY CLASS NOTES

Final Exam Study Guide for Fall 2004

2004-12-12T13:52:00.000-08:00

Important: Use the Search menu to find the different subject material within this website and on the web. The information may include notes, lab features (on the lab page), and answers to questions from past tests and websites..

Eukaryotes vs. Prokaryotes- Know the various structures, functions and differences.
Taxonomic hierachy- The categories and the phenotipic and genotipic mechanisms of classification. (IE: Domain, Kingdom, Class, Order, Family, Genus, Species).
Chemistry- Know the structure and function of macromolecules, what makes an organic compound organic, pH, functional groups, hydrolysis, and dehyration synthesis -- Anderson Exam I
Importance of the lipid bilayer Anderson Exam I
Gram positive vs. Gram negative- what are the physical differences involved in microbes of medical significance photo gallery
Know the various staining techniques and their targets link
How to determine numbers of organisms in a sample link
Various tests and mechanisms used in identification of microorganisms link
Methods of disinfection, sanitation, etc.
Growth dynamics of microorganisms- their requirements and how they are manipulated
Genetics- DNA, RNA structure, function, and replication mechanisms
Central Dogma of Molecular Biology- what it is and why it is so amazing
Metabolic processes- anaerobic, lithotrophs, and their meanings (Chapter 6 in Bauman book)
Environmental issues facing microorganisms that must be dealt with in order to survive
Mutations, causes and types, PCR, etc..
Know what a virus is, what problems they cause, and other viral issues Link
Eukaryotic members- each group and their impacts on our world
Respiratory tract infections
GI infections Link
Epidemiology of disease
Technology to combat disease

Anderson Exam IV

2004-12-07T16:35:00.000-08:00

1) What type of infection is acquired in a hospital?
[a] subclinical
[b] focal
[c] nosocomial
[d] zoonosis

2) Which of the following is NOT a port of entry?
[a] meninges
[b] placenta
[c] skin
[d] small intestine

3) The time that lapses between encounter with a pathogen and the first symptoms is the
[a] prodromium
[b] period of invasion
[c] period of convalescence
[d] period of incubation

4) A living microbe with reduced virulence that is used for vaccination is considered
[a] a toxoid
[b] attenuated
[c] denatured
[d] an adjuvant

5) A subunit vaccine contains
[a] parts of bacterial cells
[b] parts of viruses
[c] antiserum
[d] both A and B

6) Viruses that exist in cells and cause recurrent disease are considered
[a] oncogenic
[b] cytopathis
[c] latent
[d] resistant

7) A propahge is an early stage in the development of a\an
[a] bacterial virus
[b] poxvirus
[c] lytic virus
[d] enveloped virus

8) The general steps in the viral multiplication cycle are
[a] adsorption, penetration,replication, maturation and release
[b] endocytosis, uncoating, replication, assembly and lysis
[c] adsorption, uncoating, replication, assembly and budding
[d] endocytosis, penetration, replication, maturation and exocytosis

9) A virus is a tiny infectious
[a] cell
[b] living thing
[c] particle
[d] nucleic acid

10) The protozoan trophozoite is the
[a] active feeding stage
[b] inactive dormant stage
[c] infective stage
[d] spore-forming stage

11) Explain why a virus can enter some types of human cells but not others:
Viral specifity is due to the specific affinity of viral surface proteins or glycoproteins for the glycoproteins or the complimentary proteins on the surface of the host cell. HIV, for example, is specific to Helper T cells.
All types of organisms are susceptible to a viral attack, though HIV only attacks humans.

Anderson Exam III w\answers

2004-12-07T14:01:00.000-08:00

1) PCR is used for DNA fingerprinting
2) Ames Test involves the use of an altered microbe for screening of suspected carcinogens
3) Indirect Selection of Mutants involves sterile violet
4) Direct Selection of Mutants example: Incubation of E.Coli in a broth with streptomycin
5) Litmus Test involves the use of primers and cylces of heat

6) A gene synthesized from an RNA template is:
[a] Complimentary DNA
[b] Probe DNA
[c] Reverse transcriptinase
[d] Recombinant DNA

7) Which of the following is true concerning recombinant DNA technology?
[a] It will replace biotechnology in the future
[b] It is a single technique for genetic manipulation
[c] It is useful in manipulating genotypes but not phenotypes
[d] It involves modification of an organism's genome

8) The cell wall is often found in which Eukaryotes?
[a] Fungi
[b] Algae
[c] Protozoa
[d] a and b

9) All algae have some type of
[a] spore
[b] chlorophyll
[c] locomotor organelle
[d] cyst stage

10) All protozoa have
[a] locomotor organelle
[b] a cyst stage
[c] pellicle
[d] feeding structure

11) Helminth parasites reproduce with
[a] spores
[b] eggs and sperm
[c] mitosis
[d] cysts

12) Elephantitis is cause by
[a] blood flukes
[b] liver flukes
[c] filarial roundworms
[d] tapeworms
[e] flatworms

Anderson Exam II w\answers

2004-12-07T09:22:00.000-08:00

1) In order for a colony to be visible to the naked eye, about how many cells must be present?
_a) 1,000,000
_b) 100,000
_c) 10,000
_d) 1,000

2) The simplest technique for isolating bacteria in growth media is referred to as the
_a) pour plate method
_b) streak plate method
_c) serial dilution method
_d) MPN method

3) The solidifying agent used most successfully in bacterial nutrition media is
_a) gelatin
_b) peptone
_c) agar
_d) starch

4) Prokaryotic cells divide by a process known as
_a) conjugation
_b) mitosis
_c) binary fussion
_d) binary fission

5) In the growth curve of a bacterial population, the bacteria are rapidly increasing in number in the
_a) lag phase
_b) exponential log phase
_c) stationary phase
_d) decline phase
_e) boomer phase

6) A hot tub would most likely contain
_a) psychrophiles
_b) partiers
_c) thermophiles
_d) mesophiles

7) The optimal temperature for most human pathogens might be expected to range from
_a) 35 to 40° C
_b) 20 to 45° C
_c) 15 to 25° C
_d) 93 to 98.6° C

8) Bacteria on fish caught in the Arctic Ocean would
_a) be psychrophiles
_b) be mesophiles
_c) continue to grow while the fish is in the refrigerator
_d) not grow very well in the refrigerator
_e) A and C

9) Organisms that are indifferent to the presence of oxygen and do not use it are
_a) aerotolerant anaerobes
_b) facultative anaerobes
_c) obligate aerobes
_d) microaerophiles

10) Mycobacterium lepre is typically found infecting the ears, toes and fingers of its hosts due to its
_a) requirements for well-oxygenated blood
_b) easy access to those parts
_c) need for cooler temperatures
_d) long incubation period

11) High concentrations of salt and sugar in foods
_a) are useful in preserving the food
_b) tend to draw water out of a cell
_c) tends to force water into a cell, causing plasmolysis
_d) have no effect on water availability
_e) A and B

12) The prefix photo- indicates that an organism will make use of
_a) chemicals
_b) organics
_c) light
_d) inorganics

13) Growth factors are
_a) compounds that must be synthesized by the organism
_b) compounds that must be provided to the organism
_c) physical factors such as temperature
_d) inorganic molecules

14) An organism called Bacillus fastidiosus
_a) might be expected to be very flexible as to growth requirements
_b) might be expected to be very strict as to its growth requirements
_c) would probably be grown on a chemically defined media
_d) might be expected to have a rod shape
_e) B, C and D

15) A medium that inhibits the growth of organisms other than the one being sought is termed
_a) synthetic medium
_b) specific culture medium
_c) selective medium
_d) enrichment medium

16) A sterile item is free of
_a) microbes
_b) endospores
_c) viruses
_d) prions
_e) A, B and C

17) Pasteurization
_a) is the use of heat to sterilize food products
_b) is the use of heat to reduce pathogenic spoilage bacteria to a safe level
_c) is a process which uses intense cold to kill microorganisms on foods
_d) is a process which uses short bursts of radiation to kill microorganisms on foods

18) Typical conditions used for sterilization are
_a) 100° C for 10 minutes
_b) 121° C at 15 psi for 15 minutes
_c) 80° C for 15 minutes
_d) 72&#176 C for 15 seconds

19) Which of the following is not a sterilization method
_a) hot air oven
_b) autoclave
_c) pasteurization
_d) filtration

20) Chemical germicides
_a) may react irreversibly with proteins and enzymes
_b) may react with cytoplasmic membranes or viral envelopes
_c) may be disinfecting or sterilizing
_d) are sensitive to dilution factors, time of contact, and temperature of use
_e) all of the above

21) Which of the following is true of hydrogen peroxide
_a) it is a sterilant for inanimate objects and is quickly inactivated on human tissue
_b) it leaves a toxic residue
_c) it is broken down by catalase into water and oxygen
_d) it is even more effective when used in combination with peracectic acid
_e) A, C and D

Matching:
a.) sterilization (b) disinfection (c) pasteurization (d) sanitation (e) antiseptic

22) eliminates most pathogens on a material or surface

23) for use on the skin

24) reduction of microorganisms to meet health standards

25) use of heat to eliminate pathogens and spoilage of organisms

26) removal of all pathogens including endospores but not prions

True\False
27) Organic acids, such as benzoic acid, are often added to foods to prevent microbial growth

28) Boiling is very effective at removing most common waterborne pathogens

29) Pasteurization results in the sterilization of food products

30) The strands of DNA are bonded to one another by
_a) covalent bonds
_b) oxygen bonds
_c) hydrogen bonds
_d) carbon bonds

31) Which pairing is incorrect
_a) A:T
_b) G:C
_c) A:U
_d) A:G

32) RNA is characterized by
_a) deoxyribose
_b) thymine
_c) ribose
_d) double-stranded

33) DNA is characterized by
_a) ribose
_b) single stranded
_c) deoxyribose
_d) thymine
_e) C and D

34) How many nucleotides are in a codon
_a) 1
_b) 2
_c) 3
_d) 4
_e) 5

35) There are _____ possible codons to code for the 20 possible amino acids
_a) 20
_b) 30
_c) 64
_d) 61

36) tRNA functions to
_a) transfer an amino acid to mRNA
_b) transcribe the mRNA
_c) terminate the proteins on the mRNA
_d) transribe the genetic code on rRNA

37) Gene regulation may entail
_a) turning on genes only when needed
_b) turning off genes when not needed
_c) turning on or off entire groups of genes
_d) all of the above

38) The source variation among microorganisms that were once identical is
_a) antibiotic resistance
_b) virulence factors
_c) sigma factors
_d) mutation

39) Irradiation of cells with ultraviolet light may cause
_a) 4 nucleotides covalently bonding together
_b) thymine dimers
_c) adenine complementary base pairing with cytosine
_d) the addition of uracil

40) Which would have the least effect on the amino acid sequence
_a) addition of 1 nucleotide
_b) deletion of 2 consecutive nucleotides
_c) addition of 2 nucleotides
_d) addition/deletion of 3 consecutive nucleotides
_e) A and C

41) The largest group of chemical mutagens consist of
_a) radiation
_b) base analogs
_c) nitrous acid
_d) alkylating agents

42) Chemical mutagens that mimic the naturally occurring bases are called
_a) nitrogen mustards
_b) alkylating agents
_c) base analogs
_d) nitrous oxide

43) Three-ringed planar molecules used as chemical mutagens are called
_a) nitrous oxide
_b) base analogs
_c) alkylating agents
_d) intercalating agents

44) Segments of DNA capable of moving from one area in the DNA to another are called
_a) Base analogs
_b) intercalating agents
_c) transposons
_d) palindromic sequences

45) On which strand would UV radiation have the most effect
_a) AACCGGG
_b) TATATACG
_c) AATTAGTTC
_d) B and C

46) Thymine dimers are dealt with by
_a) no repair mechanisms
_b) dimer repair
_c) SOS repair
_d) endonuclease repair

47) The mechanism by which genes are transferred into bacteria via viruses is called
_a) ellipsis
_b) replica plating
_c) transformation
_d) transduction
_e) conjugation

48) In conjugation, the donor cell is recognized by the presence of
_a) an F plasmid
_b) a Y chromosome
_c) diploid chromosomes
_d) an SOS response
_e) A and C

49) Gene transfer that requires cell to cell contact is
_a) transformation
_b) conmpetency
_c) conjugation
_d) functional genomics

50) Which is true of DNA replication
_a) it is semiconservative
_b) it starts at an origin of replication
_c) it is bi-directional
_d) it requires RNA primers
_e) All are correct

Anderson Exam I

2004-12-06T18:22:00.000-08:00

Fall 2004 Microbiology Lecture Exam I (w/answers)

The hypothesis that organelles such as mitochondria in eukaryotic cells evolved from prokaryotic organisms, which were engulfed by primitive, nucleated cells is know as the ENDOSYMBIOTIC THEORY.

We cannot describe viruses as prokaryotes or eukaryotes because viruses ARE NOT CONSIDERED ALIVE.

Eukaryotic microorganisms include: PARASITES, PROTOZOA, FUNGI AND ALGAE.

The difference between Domain Archaea and Domain Bacteria is ONE HAS PEPTIDOGLYCAN IN ITS CELL WALL.

A eukaryote may be MULTICELLULAR OR UNICELLULAR, HAVE A TRUE NUCLEUS THAT IS MEMBRANE BOUND, ONE THAT HAS CHLOROPLAST AND/OR A MITOCHONDRIAN.

A ph of 2.1 is more acidic than a ph of 9.4 (View Scale)

Which type of lipid is most important in biological membranes? PHOSPHOLIPID BILAYER

A sample from a hot thermal vent contained a single-celled organism that lacked a nucleus. What is the most likely classification? DOMAIN ARCHAEA

What are the two classifications of prokaryotes? DOMAIN BACTERIA AND ARCHAEA

The primary structure of a protein is: NUMBER AND SEQUENCE OF AMINO ACIDS

Pure water does not have the ability to: DISSOLVE LIPIDS

The macromolecules that are composed of carbon, hydrogen and oxygen in a 1:2:1 ratio and are used as a quick energy source for many organisms are the CARBOHYDRATES

Weak bonds that are responsible for holding strands of DNA together are HYDROGEN BONDS

Lipids are THE SMALLEST MACROMOLECULES, COMPOSED OF FATTY ACIDS AND GLYCEROL SUBUNITS, EXTREMELY VERSATILE IN FORM AND FUNCTION, AND INSOLUBLE IN WATER.

The secondary structure of a protein IS CAUSED BY THE R-GROUP INTERACTIONS OF AMINO ACIDS AND CAN BE HELICAL OR PLEATED

DNA differs from RNA in that DNA has TWO STRANDS OF THYMINE AND DEOXYRIBOSE SUGAR

Phospholipids HAVE POLAR AND NONPOLAR ENDS AND ARE FOUND IN CELL MEMBRANES.

The six most commonly occurring elements in living organisms are carbon, hydrogen, nitrogen, phosphorus, sulfur, and OXYGEN.

Microbes are useful FOR NATURAL FLORA TO PROTECT AGAINST INFECTION, TO CLEAN UP HAZARDOUS SPILLS, TO MAKE FOODS, AND TO USE AS A CURE FOR SOME DISEASES.

Proper order of classification: DOMAIN, KINGDOM, PHYLUM, CLASS, ORDER, FAMILY, GENUS, SPECIES.

With regard to prions, THEY ARE WITHOUT DNA AND RNA.

The Gram stain is A DIFFERENTIAL STAIN AND A TEST FOR THE PRESENCE OF AVAILABLE PEPTIDOGLYCAN.

The process of building a macromolecule from smaller molecules involves DEHYDRATION SYNTHESIS.

The equal sharing of electrons by two elements is COVALENT BONDING.

The weakest bond type is the HYDROGEN BOND.

The subatomic unit that dictates the behavior of an element is the ELECTRON

The two subatomic particles that are located inside the nucleus and account for the mass of an element are the PROTON AND NEUTRON.

Peptidoglycan IS A SUGAR COMPLEX FOUND IN THE CYTOPLASMIC MEMBRANE OF BACTERIA.

A disease that has plagued a population during the course of history, disappeared, and then came back again, is said to be A RE-EMERGENT DISEASE.

Trace elements, are necessary TO AID ENZYMATIC ACTIONS

You decide to fry an egg and when it hits the griddle, it turns white and hardens.
What has occurred? DENATURIZATION OF A PROTEIN.

What structural level has been altered? ALL LEVELS. HEAT BREAKS THE PEPTIDE BONDS BETWEEN THE AMINO ACIDS.

The bacteria Clostridium botulina produces an extracellular toxin that can be lethal to humans. With that in mind, you can deduce that THERE IS AN ABUNDANCE OF FREE RIBOSOMES IN THE CELL.

The shape of a microorganism can determine how effective an antibiotic can be IS TRUE.

If we did not have E. Coli in our intestines, we would surely die IS TRUE

The nucleotide bases are the same building blocks in our cells and in bacterial cells IS TRUE.

The warriors of Norway would ingest mushrooms, a fungus, shortly before rampaging a neighboring country. The secretions made them froth at the mouth and become aggressive. In three hours, uncontrollable diarrhea was produced.
What type of cell is a fungi? A EUKARYOTIC PROTOZOA

What organelle would likely be abundant in this organism? CELL WALLS.

Would this be a pathogenic organism? YES

A functional group is responsible for the behavior of an organic compound. TRUE

H.pylori is currently listed as the only known living carcinogen. TRUE

A chloroplast is A PHOTOSYNTHETIC ORGANELLE, WHERE SUGAR IS MADE FROM SOLAR E AND CO2, DOUBLE MEMBRANE BOUND, AND HAS A LOOP OF BACTERIAL DNA.

An endospore IS MOST RESISTANT LIFE FORM, A DORMANT FORM, ALLOWS INFECTION/DISEASE ONLY FROM A FEW BACTERIA, AND IS PRIMARILY FORMED BY CLOSTRIDIUM AND BACILLUS.

Buffering capacity is a life saver. TRUE

Prokaryotic cell:
cell wall- FORMS SHAPE OF THE CELL.
Ribosomes- FORM PROTEINS FOR THE CELL
Flagella- WHIP-LIKE EXTENSION USED FOR MOVEMENT
Nucleoid- CONTAINS ONE CHROMOSOME OF DNA

Eukaryotic cell:
Rough ER- PROTEIN SYNTHESIS
Smooth ER- LIPID SYNTHESIS AND TRANSPORT
Golgi Apparatus- PACKAGES PRODUCTS FOR SHIPMENT OUT OF CELL
Free Ribosomes- FORMS PROTEIN FOR THE CELL
Mitochondria- CELL’S ENERGY SOURCE
Cell membrane- FORMS SHAPE OF CELL AND IS POROUS.

Bacteria- PROKARYOTIC CELLS WITH CELL WALLS AND PEPTIDOGLYCAN.

Virus- INFECTIOUS ACELLULAR AGENTS WITH NUCLEIC ACID SURROUNDED BY A PROTEIN COAT CALLED A CAPSID.

Prions- INFECTIOUS PARTICLE THAT LACKS NUCLEIC ACIDS AND REPLICATES BY CONVERTING SIMILAR NORMAL PROTEINS INTO NEW PRIONS.

Fungi- EUKARYOTIC CELLS LACKING CELL WALLS AND CONTAIN NUCLEUS OF GENETIC MATERIAL SURROUNDED BY A MEMBRANE.

Protozoa- SINGLE-CELLED EUKARYOTES LACKING CELL WALLS AND NUTRITIONAL NEEDS AND STRUCTURE ARE SIMILAR TO ANIMALS.

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Frequency of Disease

2004-12-06T18:01:00.000-08:00

Epidemiology is important concerning causes and frequency of disease. The vocabulary of the frequency of disease is as follows..

INCIDENCE is the number of new cases in a certain population.
PREVALENCE includes both the number of old and the number of new cases combined.
(Both of the previous are expressed as a ratio of the number of cases divided by the number of people at risk)
Incidence = # of new cases/# of people at risk
Prevalence = # of old and new cases/# of people at risk
SPORATIC disease is considered when only a few cases occur within a population .
ENDEMIC diseases occur at a regular frequency within geographical distribution.
EPIDEMIC disease occurs at a greater frequency than usual within a population or area.
PANDEMIC disease is referred to as one that occurs simultaneously on more than one continent. (AIDS is considered pandemic worldwide)

Quizz on Viruses

2004-12-05T13:07:00.000-08:00

Try this quizz on the topic of viruses:
Quizz 1

Classification of Viruses

2004-12-05T10:59:00.000-08:00

Viruses are classified in the following ways:

-- Genome Structure. (This is the main way viruses are classified).
---- DNA viruses (all are double-stranded except Parvoviriridae and Hepadnaviridae)
---- RNA viruses (all are single-stranded except Reoviridea)
-- Shape. Isohedrical, Rod shape, Irregular, or Complex
-- Enveloped or Naked
-- Taxonomy. Informally grouped prior to Family
-- Nomenclature. Uses Family and Genus
-- Species. Includes the common name based on the disease it is associated with and always ends the word "virus". Rabies virus, Polio virus, etc.

Major Characteristics of Bacteriophages
-- Normally complex in shape and are naked viruses
-- Phages can be productive, extruded, or temperate in nature.
-- Has a host of range factors
----attachment protein is needed to bind to a specific receptor site on the bacteria. Normally on the cell wall, but occasionally on the flagella or pilli.
Replication Cycle
Steps of Lytic Replication
-- Replication of animal viruses is the same basic replication pathwa as bacteriophages.
----Differences include:
1) Presence of envelopes around some viruses
2) Eukaryotic nature of animal cells
3) Lack of cell wall in animal cells

-- Assembly and Release of Animal Viruses
----Most RNA viruses develop soley in the cytoplasm
---- Number depends on type of virus and size and initial health of the host cell
---- Enveloped viruses cause persistant infections
---- Naked viruses released by exocytisis may cause lysis and death of the host cell

Characterization of Viruses

2004-12-02T10:58:00.000-08:00

I) Introduction
A virus is a miniscule, acellular, infectious agent having one or several pieces of nucleic acid, either DNA or RNA, but never both.
Pasteur first defined them as a "living thing smaller than bacteria" and termed them virus- Latin for poison.
In 1884 the first vaccine for rabies was developed. Rabies is 100% fatal without this vaccine.
In 1898, viral studies intensified as foot/mouth disease was discovered and was found to be non-cellular.
In the 1950's the study of virology emerged as a science.
_B) Virus Terminology

Non-living agent with either DNA or RNA but never both
Nucleic acid is surrounded by a protein coat called a capsid
The shape is determined by the capsid
They are associated with all life forms- all organisms contain viruses
Usual ranges in size is 1/100 to 1/1,000 of the size of a host cell
Viruses have an extracellular state, called a viroin, consisting of a protein coat called the capsid.
They lack a cytoplasmic membrane and have no cytosol.
An envelope can be on selected virus types and is made of a lipid bilayer over the capsid

_C) Virus Types

Naked-- lacks an envelope and is hardest to control
Enveloped--easier to kill and normally infects humans
There are two states of a virus. (1) Chemically inert being outside of the host, and (2) Viroin state- replicating within a host.

Isohedral shape -- Official page

Helical shape, usually infectious of plants and animals (example from tobacco mosaic virus)

Bacteriophage, infects bacteria Official page

Viral envelope (example from herpesvirus family)

Naked vs. Enveloped

Exam III Material/Chapter 12- Eukaryotes

2004-11-23T06:00:00.000-08:00

The Eukaryotes are comprised of: Algae, Protozoa, Fungi, and Multicellular parasites.
I ALGAE
_a) are classified by their pigment
_b) Photosynthetic
__1)Dinoflagellates - (toxins) Red tide, Parasytic Shellfish poisons from shrimp, oysters and other "bottom-dwellers"
__2) Pfiesteria- sludge bug. When a gene is induced, they grow flagella, swim up to fish and secrete toxins, the scales are affected and fall off of the fish, the sludge bug devours the fish as a blood meal, then swims back down as flagella fall off in association with reproduction of other pfisteria.
II PROTOZOA
_a) are classified by their method of locomotion
Giardia, caused by deer and beaver urine infected stream water is an example of a protozoa.
III FUNGI
_a) are classified according to method of reproduction, it can be sexual or asexual
_b) they can be unicellular or multicellular- the multicellular can produce toxins (mushrooms)
_c) few are mobile, but some are airborne
IV MULTICELLULAR PARASITES
_a) have similar modes of transmission as bacterial helminths
_b) have parasitic behavior
_c) refer to Table 23:2 in the Bauman book.

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Exam III Material/Chapter 11- Prokaryotes

2004-11-23T04:06:00.000-08:00

Please use DNA technology definitions, as a reference for this section.
I) Biotechnology Defined- Intentionally modifying genomes of an organism, by natural and biological modification. It has three goals.
1) Eliminate the undesirable phenotype
2) Combine beneficial traits of two or more organisms, in order to create a valued new organism
3) Create organisms to synthesize products of human need
II) Tools of the Trade
_A) Mutagens- These will change a gene to a desired effect.
_B) cDNA- (complimentary) made by reverse transcriptinase and will produce a product without inserting the gene desired.
_C) Restrictive Enzymes- helps cut DNA at desired area to extract that gene. Sticky= not bluntly cut. Blunt= can be cut and extracted (T A G C T A G)
_D) Vectors- transmit one gene into another
III Idnetifying and Classifying Prokaryotes:
_A)PHENOTIPIC- has existed for 300 years.
__1) Morphology - microscopy
__2)Metabolic differences
___a) colonial/agar color- M. Lutus has yellow colonies

___b) differential/selective agars

___c) fermentation tubes

___d) aerobic and anaerobic differences
__3) Serology- look for proteins of a particular polysaccharide that could indicate the presence of a particular organism.(immunoassays)
__4) Fatty Acid analysis- all organisms will have different fatty acids at different levels, so this test is a last resort due to cost and time consumption.
_B) GENOTIPIC
__1) Nomenclature- suffix is usually Latin and the name reflects a characteristic of the organism.
IV In Ecophysiology, the environment will dictate the function of an organism. Problems and solutions exist in ecophysiology.
_A) Problems:

__ 1) Temperature changes
__ 2) exposure to UV rays, and
__ 3) nutrient and moisture fluctuations.
_B) Solutions:
__1) Endospore formation such as bacillus and clostridium
__ 2) Gists which are temperature sensitive
__ 3) communal populations sense a harsh environment and will differentiate to the conditions.

AQUATIC PROKARYOTES
Nutrients are a problem for these prokaryotes.
A solution to this would be sheathed bacteria, which are the slime layers.
A second solution is to prosthecate. These bacteria can increase their surface are to obtain nutrients.
HOST- is usually resident flora in humans. In plants, rhizobium and legumes make amino acids
Agrobacteriums in plants act like carcinogens in humans.
Quarum Sensing- when a population will sense its density and simultaneously reduce a gene to express. EX: Bioluminescence

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Mitochondrial DNA Knowledge

2004-11-20T22:14:00.003-08:00

This page explains in detail an introduction to understanding mitochondrial DNA. It also includes laboratory methods such as PCR, D-probe preparation, and the Southern Blot assay. A results section shows results of a human placenta sample treated with RNAse Agarose Gel stained with ethidium bromide.
See the entire page at this link>>> Genetics and Molecular Research- mitochondrial DNA from human placenta.

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Top-Pick website on Infectious Diseases

2004-11-20T03:36:00.000-08:00

This site is an A to Z index of infectious diseases as written in the Material Safety Data Sheet of Infectious Diseases by the Public Health Agency. The descriptions include: Cross-references, Health Hazards, Communicability, Laboratory Hazards, Viability, and others.
It is an excellent site for reference information on pathogenic organisms.
MSDS of Infectious Diseases

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Animations of Polymerase Chain Reactions

2004-11-16T03:47:00.000-08:00

POLYMERASE CHAIN REACTION(PCR) is a technique in which a large number of DNA molecules are produced in vitro. It starts with a single molecule, and billions of exact replications can be generated within hours. We can use PCR to amplify genomes and also to determine nucleotide sequences.
There are three steps to the process:
1) Denaturization. Exposure to extreme heat(94 degrees C) breaks weak hyrogen bonds and separates the two strands of the target DNA. The separated strands are not altered.
2) Priming. An excess of primers are added to the target DNA, then cooling to around 65 degrees C enables the double-stranded DNA to re-form. The excess of primers causes the single strands to bind to a primer rather than one another.
3) Extension. Raising the temperature to about 72 degrees C increases DNA polymerase replication, thus each strand produces more DNA.

Confused? Check out these cool animations of Polymerase Chain Reactions at work!
The Polymerase Chain Reaction
The Gene Library- PCR Animation (all cycles)

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More on DNA Technology and Biotechnology

2004-11-11T16:34:00.000-08:00

Mutants are descendants of a cell that does not successfully repair a mutation.
Wild Types are cells normally found in nature
Methods to recognize mutants:
1) Positive or Direct selection- when something is introduced into a bacterial population that should kill them, unless they have a mutation that makes them resistant.
2) Negative or Indirect selection- when a mutation results from requirements that the rest of the population does not need. (This usually has a growth factor requirement)
3) Ames Test- A test of mutagenic effects of a chemical of interest. Salmonella is mutated to metabolize differently than wild type. If the test chemical is a mutagen, these mutated salmonella will "mutate" back to metabolize like the wild type.
However, sensitivity may cause false-positives in the Ames Test.
History and Procedure of the Ames Test
Biotechnology- involves the intentional modification of genomes of an organism, by natural and biological modification. There are three basic goals:
1) To eliminate the undesirable phenotype
2) To combine beneficial traits of two or more organisms to create valuable new organisms
3) To create organisms to synthisize products of human need.
Note: Take time to read Barbara Kingsolver's "A Fist in the Eye of God". It's an essay from her new book "Small Wonders", that talks of biotechnology in several viewpoints. Barbara Kinsolver has a phD in Microbiology and Ecology.
You can read more about Barbara Kinsolver here

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DNA Technology Notes

2004-11-10T15:28:00.000-08:00

DNA nucleotides are linked through their sugars and phosphates to form the two backbones of a helical, double-stranded molecule. The carbon atoms are numbered "1" through "5". The "5" end terminates in a phosphate group attached to a 5' carbon. The opposite 3' end terminates with a hydroxyl goup bound to 3' carbon of deoxyribose.

I Prokayrotic Chromosomes- consists of circular DNA localized in the nucleoid.
_A) They consist of plasmids, which replicate independently of the chromosome and thus
_B) can replicate in half the time of Eukaryotic Chromosomes.

II Eukaryotic Chromosomes- typically have more than one chromosome in their genome. _A) They are linear (rather than the circular prokaryotic type)
_B) are contained within the nucleus.
_C) The number of chromosomes vary with the species that will code for a product (protein).

III Protein Synthesis is using a part of DNA to encode an RNA in turn will have the nucleotide sequences that can be translated into amino acid sequences and make a protein.

IV The Central Dogma is the process of a protein being made from a gene or genes.

Anatomy of DNA/RNA- here is an excellent website on the anatomy and differences of the nucleic acids. A simulation of "the replication of DNA" is included in a re-enaction concept series.
VisionLearning-DNA and RNA (Flash player is required)
Protein Synthesis and Gene Expression
Genotype is an actual set of gene make-up.
Phenotype is reference to physical characteristics, such as hair color.
Constitutive Enzymes are enzymes in constant need by the organism (75%)
Induced Enzymes are ones that are not produced routinely, but can be turned on (pregnancy)
Repressed Enzymes are ones that are normally synthesized but can be turned off.
Refer to this site for more detailed information.
Mutation- the changing in nucleotide base sequence of a genome is rare. This leads to a protein having a novel property that improves the ability of an organism and its descendents to live.
---TYPES:
Point Mutation- one of a few base pairs are affected. (substitutions, deletions, insertioins)
Frameshift Mutation- nucleotides affected after mutation is displaced.(insertions, deletions)
Insertion/Deletion- (worst type)- affects every codon "downstream"
More information on mutation is found at The Microbiology of Mutation

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The Meatrix (flash animation movie)

2004-11-03T13:03:00.000-08:00

Check out this cool flash animation movie from Fight Factory Farms! It's an award-winning animation about the meat we eat.
(Requires Flash Player)

Chapter 7: DNA Technology (Definitions)

2004-10-30T04:05:00.000-07:00

Genes- nucleotide sequences coding for a product.
Codon- sets of 3 nucleotides that will code for one amino acid.
Genome- a cell's entire genetic compliment, including its genes.
Chromosomes- segments of DNA.
Plasmids- small circular molecules of DNA that replicate independently of the chromosome.
Histones- globular proteins
Genotype- actual set of genes in its genome.
Phenotype- physical features and functional traits of an organism, including characteristics.
Transcription- gene information is copied as RNA nucleotide sequences.
Translation- Polypeptides are synthesized by RNA molecules in ribosomes.
Central Dogma- the processes of transcription and translation.
Transduction- a method of horizontal gene transfer.
Promoter- a nucleotide sequence located near the beginning of a gene and initiates transcription.
Mutation- a change in the nucleotide base sequence of a genome, particularly its genes.
Point Mutations- when just one or a few nucleotide base pairs are affected.
Frameshift Mutations- insertions and deletions creating new sequences of codons that result in largely altered polypeptide sequences, usually affecting proteins more than substitutions.
Thymine Dimers- mutation caused by nonionizing radiation in the form of UV light, causing adjacent thymine bases to covalently bond to one another.
Light Repair- prokaryotic DNA photolysase enzyme breaks bond between adjoining thymine nucleotides, restoring the original DNA sequence.
Dark Repair- enzymes cut damaged DNA sections from a molecule, creating a gap that is repaired by DNA polymerase and ligase.
Excision Repair- enzymes exise DNA strand that is in error, and filling the gap with DNA polymerase.
SOS Response- prokaryotic cells with extensive DNA damage use various processes to induce DNA polymerase to copy the damaged DNA.
Bacteriophage- a virus that infects a bacteria
Conjugation- horizontal gene transfer where bacteria containing a fertility plasmid forms a conjugation pilus that attaches and transfers plasmid genes to a recipient.

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Mechanisms and Retardation of Antibiotic Resistance

2004-10-25T13:59:00.000-07:00

I The three main categories of side effects of antimicrobial drugs are:
1.) Toxicity- this means that the body has identified the agent as a poison and can damage normal cells.
2.) Allergies - Some of us are sensitive to certain ingredients in antibiotics, and although rare, anaphylactic shock (shock resulting from ingesting or contacting any agent that triggers the body's allergic immune response) may be immediate and life- threatening.
3.) Disruption of Normal Flora - Normal flora may be affected by some antimicrobials, allowing pathogenic activity to cause a secondary infection.

In nature, we have certain "wild type" populations of organisms. Infection plus antibiotics cause susceptible organisms to die, while resistant organisms still flourish. The resistant organisms are named Mutants. Resistance to antimicrobials was first noticed in the 1940's. This resistance is hastened by three main groups of activity.
1.) Mis-prescribed antibiotics- an increasing problem that has gotten the attention of the CDC.
2.) Medical noncompliance- unmonitored dosage or early cessation of the antimicrobial(s).
3.) The same antibiotics are being used for both livestock and humans.

II) Resistance by Bacteria to Antimicrobial Drugs- there are five mechanisms possible. 1.) Natural Mutation- (vertical gene transfer)
2.) Plasmid Transfer- (horizontal gene transfer)
3.) Conjugation- transfer of plasmids from one organism to another via sex pillus.
4.) Transformation- taking up a plasmid or gene fragment from environment and incorporating it into the genome.
5.) Transduction- A (phage) has a gene from a previous host that it takes into the next host cell.

III) Multiple and Cross Resistance to Antimicrobial Drugs - there are three basic types included.
1.) The pathogen itself can acquire resistance to more that one drug at a time.
2.) Cross-resistance occurs when antimicrobial drugs given are similar in their structure.
3.) Pathogens resistant to most antimicrobial strains are called superbugs.

IV) Retarding Resistance - The development of pathogen resistant populations can possibly be averted in at least six different ways.
1.) Giving high concentrations for a short time.
2.) Using antimicrobial combinations. (synergism)
3.) Limit usage in necessary cases.
4.) Develop new variations of existing drugs.
5.) Second-generation drugs. (adding side chains to the original molecule)
6.) Third-generation drugs. (adding side chains . . . )

V) Notes on Certain Antimicrobial Drugs
_A) The Beta-lactams - inhibit cell wall synthesis and are the penicillins.
__1) They have limited action against most Gram negative bacteria
___a) resistance to Gram negatives is due to the peptinoglycan layer of the bacterial cell.
Chloramphenicol - is an antibacterial that inhibits protein synthesis. It is prescribed for Typhoid Fever and is rarely used due to its dangerous adverse effects, including death.
_B) Antivirals
__1) inhibit viral protein synthesis.
__2) Protease inhibitors are used for HIV.
_C) Antifungals
__1) active against fungi
__2) no resistance is known
__3) are especially effective against Gram positive pathogens. (topical drugs are examples)
_D) Antiprotozoans
__1) include heavy metals
__2) little or no resistance is known
__3) their spectrum of action has a better chance to cause allergic reactions than other antimicrobials.

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Antibiotic Quizzes and Practice Tests

2004-10-24T16:29:00.000-07:00

Before taking and reviewing some of the quizzes below, check out this material on the discovery of antibiotics. It is an oultined format of important information concerning antibiotic targets, resistance, alternatives, consumption, therapy and failed therapy, resistant mechanisms and more..

Table of Antibiotics

Now, here are some practice tests on the topics of antibiotics and some certain diseases. Check them out!
First, information by the CDC about antimicrobial resistance.

Antibiotics

True/False quiz

Antimicrobial Therapy

Quiz for non-science majors

Antibiotic Resistance Quiz for Pre-Med Students The completed test results are given, but the correct answers are not viewable.
(Test provided by the University of Florida College of Medicine)

Conditions and Diseases
E. Coli and E. Coli 0157

Autoimmune Diseases

HIV and AIDS

Shingles

Smallpox

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Chapter 10: Controlling Microbial Growth

2004-10-24T15:57:00.000-07:00

Alexander Fleming reported in 1929 that the antibacterial action of penicillin released from Penicillium. He defined antibiotics as antimicrobial agents that are produced naturally by an organism. Today, antibiotic means "an antibacterial agent", excluding antiviral and antifungal agents.
Penicillin is a natural occurring antibiotic. Additionally, by altering the chemical structure of antibiotics, semisynthetics are produced. These are more effective, last longer, or easier to administer than natural antibiotics. Synthetics are antimicrobials that are completely synthesized in a laboratory.

Mechanisms of Antimicrobial Action
Because there are many differences between the structure and metabolism of pathogenic bacteria and their eukaryotic hosts, antibacterial drugs constitute the greatest number of diversity of antimicrobial agents. Although they can have a variety of effects on pathogens, antimicrobials can be catagorized into 6 different groups according to their mechanisms of action.

1.) Inhibition of cell wall synthesis. (Penicillins) The most common antibacterial agents act by preventing cross-linkage of NAM subunits (a macromolecule of peptinoglycan in bacteria). Thus, cell walls of pathogens are weakened and are less resistant to the effects of osmotic pressure. The underlying cytoplasmic membrane bulges through the weakened portion as water moves into the cell and the cell lyses.
2.) Inhibition of protein synthesis. (Tetracyclines) Understanding this inhibition first requires understanding the process of translation. The tetracyclines can change the shape of certain subunits, making it impossible for the ribosome of the cell to read the codons of RNA properly. Some antimicrobials can prevent movement of the ribosome from one codon to the next altogether. As a result, translation is frozen and protein synthesis is stopped.
3.) Disruption of cytoplasmic membrane.(Polymyxins) Some antimicrobials have the ability to become part of the cytoplasmic membrane and thus, damaging it. The drug amphotericin B binds to molecules of ergosterol, causing them to congregate and form a spore within the membrane.
4.) Inhibition of metabolic pathways. (Sulfonamides) Humans take simple folic acids found in our diets and covert them to into tetrahydrofolic acid (THF). As a result, our human metabolism is unaffected by sulfonomides. Some pathogens desire certain acids to be converted into THF, a reaction required for their DNA and RNA synthesis. Sulfonamides decrease this acid production which slows the production of proteins required for pathogenic synthesis.
5.) Inhibition of nucleic acid synthesis. (analogs) DNA and RNA are built from purine and pyrimidine nucleotides and are critical to cell survival. Because only slight differences exist between nucleic acids of both prokaryotic and eukaryotic cells, drugs that affect replication often acts against both types of cells. Generally these drugs are not used to treat infections, but rather as research in DNA replication and to slow replication of cancer cells. Analogs change the shape of nucleic acid molecules and prevent further replication, trascription, or translation.
Additionally, viral acid synthesis is faster than the synthesis of cells, so viruses are more susceptible to analogs than their hosts.
Here is what we've discussed so far
6.) Prevention of virus attachment.(Arildone) Viruses must attach to their host's cells via chemical interaction. Attachment of viruses can be blocked by peptide and sugar analogs of either attachment or receptor proteins. When these sites are blocked, viruses can neither attach or enter a host cell. Arildone blocks receptor sites of polio viruses and some cold viruses, making them unable to attach to host cells.

Clinical Considerations in Prescribing Antimicrobial Drugs.
The ideal antimicrobial agent to treat infection would probably be one that is:

1.) readily available
2.) inexpensive
3.) chemically stable (for ease of transport and shelf-life considerations)
4.) easily administered
5.) nontoxic and nonallergenic
6.) selective toxicity against a wide range of pathogens

Oral drugs are easy to take and usually low cost, but are not monitored, which holds the capabilitiy of resistance.
Injectable drugs are high cost, quickly effective, the entire dosage is ensured, and are closely monitored.
Topical drops and mists are usually low cost, but are not monitored and can gain resistance without proper use. Underdosage and overdosage is especially dangerous with mists.

The spectrum of action is the number of different kinds of pathogens an antimicrobial agent can act against. Narrow-spectrum drugs act only against a few kinds of pathogens, where broad-spectrum drugs can act against a wide range of organisms. Using a broad-sprecrum antibiotic can also kill normal flora that is necessary to defend against pathogenic organisms in the first place. For example, a woman taking erythromycin for a throat infection, is more susceptible to vaginitis resulting from excessive yeast growth when the agent kills normal bacteria contained in the vagina.

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Links, personal and professional

2004-10-14T06:54:00.000-07:00

Class Notes Home
Northeast State Technical Community College
E.T.S.U.
King College
Milligan College
American Society for Microbiology
Society for General Microbiology
USC School of Medicine An online medical school text with studies in bacteriology, virology, mycology, parasistology and more!
Quillen College of Medicine
AORN Online for surgical Registered Nurses
American Association for Respiratory Care
Frontline Approach to Common Pulmonary Disease Presentations
Lung Health Education for physicians and respiratory therapists.

Logos:
AARC
AORN
John F.Murray, MD
American Association for Respiratory Care
Healthy Lungs

MUSIC SITES
Gretchen (Christian Rock band Official Site)
ChristianRock.net
PureVolume.com
Evanescence (Official Site)

OTHERS
The Charmed Ones
Charmed Two
Law and Order SVU

Test Yourself Here

2004-10-13T14:51:00.000-07:00

You can test your knowledge of Microbiology through the links in this thread. Informational links are also listed here. (Note: this site is still under construction, and more information is added daily.)

>>> Top Pick! An awesome site that lets you make up your own quizz! You can choose what types of questions, which bugs, and even select the number of questions you want to answer. An answer score is also included.

>>> Advanced level Problem sets and tutorials are available at this site. This is an advanced level testing site for Honors Micro students.

>>> Biological Weapons Resource Center A.S.M. site. Discusses policy, detection, treatment, preparedness and homeland security.

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Chapter 9-10 "Controlling Microbial Growth"

2004-10-11T16:14:00.000-07:00

Environmental Control includes physical and chemical processes. Some examples of physical control methods are:
Sterile - Free from all life forms, including viruses.
High Level Disinfectant - Kills all life forms except endospores.
Mid Level Disinfectant- Kills all life forms except endospores, encapsulated mycobacteria, viruses
Low Level Disinfectant -Kills vegetative bacteria, enveloped viruses, and some fungi.
Aseptic -Free of pathogenic organisms and without addition during a procedure.
Sanitized- Mimimized to what is considered safe.
Pasteurize- High heat/short time. Minimizes number of bacteria in food products and juices without harming food.
Degerming Agents:
Antimicrobial
Antibacterial
Antifungal
Antiviral

HOSPITAL SETTINGS
Critical Level Items- are items that penetrate the epithelial layer of tissue, therefore, they must be sterilized.(Needles, scissors, etc.)
Semi-Critial Items -Do not penetrate the epithelial layer but may enter a cavity. Sterilization of these items is not required. (Endoscopes, speculas, etc.)
Non-Critical Items -Do not break the tissue or enter into any cavity. (stethescopes, bp cuffs, etc.)

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Homepage

Beginning with Chapter Six "Microbial Nutrition and Growth"

2004-10-11T15:58:00.000-07:00

Like all organisms, microbes desire nutrients in order to live and grow. Some of these requirements include, but are not limited to: nutrients, oxygen, ph, temperature, moisture and reproduction.
Replication is based on the bacterial requirements being met.
BACTERIA ARE GROUPED BY ENERGY ACQUISITION
Photo-auto- trophs derive their energy from sunlight and CO2, a carbon source.Chemo auto trophs derive their energy from sulfer and hydrogen. CO2 is the carbon source.
Chemo auto trophs derive their energy from sulfer and hydrogen. CO2 is the carbon source.
Photo hetero trophs use sunlight as an energy source and organic material as the carbon source.
Chemo hetero trophs derive energy from chemical compounds, and organic compounds as a carbon source. (Humans are in this category)
BACTERIA ARE GROUPED FURTHER BY THEIR RANGES IN ENVIRONMENTAL CONDITION.
Temperature
Psychophile- Cold Range (0-20 degrees C)
Mesophile- Range from 20-40 degrees C (flora)
Thermophile- Range from 45-80 degrees C
Hyperthermophile- over 80 degress C
ph
Most are between 6.5-7.5
Neutrophils-- 6.5-8.5
Acidophils-- less than 6.0 and varying ranges
Alkalinophiles-- more than 8.0
Salinity (Salt content)
Plasmolysis is an issue for most cells, so they cannot stand an increase in salt content.
Halophils can withstand high salinity.
Hydrostatic Pressure Most cells are sensitive to pressures.

Viable Cell Count-- (Bauman book, page 190) Lab Procedure

MEDIA TYPES
Complex Has a variety of ingredients.
Defined Pure chemicals within the mixture. They also need a buffer added to them.(Good source for anti-microbial requirements, AKA growth factors)
Selective Helps to narrow down organism of interest. EX: Glucose salts
Thayer-Martin Isolates N.Gonorrhea, Antibiotics will inhibit growth of fungi, Gram + and Gram - rods, and will allow growth with little competition.
Differential Created in mind that different organisms metabolize different materials in different ways. A bacteria type can change a substance in a recognizable way. EX: Blood agar- "strep test"

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