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Microbiology-basics for biochem engnrs

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Introduction collected in notes form

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									                                   Introductory Microbiology
COMMON CHARACTERISTICS OF LIVING THINGS (ORGANISMS):

All biological systems [living things] have the following characteristics in common:

1. The ability to ingest or assimilate nutrients (food substances) and metabolize them for

  energy and growth.

2. The ability to excrete waste products.

3. The ability to react to their environment sometimes called irritability.

4. The ability to reproduce its own kind.

5. There is susceptibility to mutation.

Microbiology is a science that deals with the study of living organisms that cannot be
seen by the naked eye. These can be seen with the aid of microscopes, which magnify
objects.
Microbiology: Study of structures and activities of microorganisms.

       Form, Structure, Reproduction, Physiology, Metabolism and Identification.
       Distribution in Nature
       Relationship to each other and to other living things.
       Beneficial and detrimental effects on humans, animals, plants.
       Physical and chemical changes they make in the environment
       Microorganisms are unicellular or consist of same kind of cells held together.
       Higher Organisms have a hierarchy of organization: Cells > Tissues > Organs >
        Organ systems > Organism.

An Overview of microbiological Basics




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Cell is the smallest unit of living things that can maintain its structure and reproduce
itself in its suitable environment. Cell is the true basic unit of life.
Viruses: Viruses are not cellular organisms. Viruses are obligate intracellular parasites
of living host cells. Viruses are particles that represent the border line of life. They can
reproduce themselves by being parasites on cells of living things, destroying the host
cells. There are viruses which use animal, plant or human cells as their hosts being
specific to one kind of host.

                Haeckel’s three kingdom classification of microorganisms:

                           Plants       [Protista]       Animals

Haeckel (1866), a German zoologist suggested a third kingdom Protista to include those
organisms that are not typically plants and animals. Bacteria, cyanobacteria, algae,
fungi and protozoa are cellular organisms placed under protista. Bacteria and
cyanobacteria were lower protists while algae, fungi and protozoa were higher protists.

The cells of living organisms are either procaryotic or eucaryotic in nature and there is
not any intermediate condition. The size, shape, morphology and the internal cellular
organizations are different in these two groups.



Protista:

Procaryotic: Eubacteria, Archaebacteria, Cyanobacteria

Eucaryotic: Fungi (Molds and Yeasts), Algae and Protozoa




Procaryotic cells do not have a membrane enclosing a nucleus, and are smaller in size
and have simpler internal constitution in comparison with the eucaryotes. Procaryotes
are organisms with primitive type of nucleus lacking a well-defined membrane, a less
complex nuclear division than mitosis. The nuclear material is a DNA molecule in
prokaryotes compared to chromosomes of higher organisms. Cell wall is made of
peptidoglycan (murein or mucopeptide), a component that is absent in eucaryotic cell
walls.



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Eukaryotes are organisms with cells having true nuclei enclosed in a nuclear membrane
and are structurally more complex them prokaryotes. A varying degree of localization of
cellular functions in distinct membrane bound intracellular organelles like nuclei,
mitochondria chloroplasts etc. are occurring in eucaryote cells. Eucaryotes have
membrane bound organelles. Their DNA is complex and typically associated with
structural and regulatory proteins and it is contained within a membrane bound nucleus.
The cells are about ten times larger than those of prokaryotes. Some eucaryotes (e.g.
plants) have cell walls but are not made up of peptidoglycan molecules.

Replication in eucaryotes involves mitosis and meiosis. Meiosis occurs in sex cells like
sperm and egg. The eucaryote cell member is a fluid phospholipid bilayer containing
sterols and carbohydrates. The membranes can endocytose, phagocytose, pinocytose
and exocytose.

In Meiosis a diploid parent cell creates four haploid daughter cells. The DNA has usually
undergone some crossing over so the chromosomes are not only halved but are also
changed through rearrangement.

 Mitosis: Cells have two main stages in the life cycle. Interphase: the cells grow and
duplicate their DNA, in the second stage the cell’s nucleus divides. In mitosis nuclear
division starts after the cell has duplicated its DNA. The result is two exact copies of the
DNA.

Whittaker (1969) proposed five kingdoms based on three levels of cellular organization
and three principal modes of nutrition, photosynthesis, absorption and ingestion. The
prokaryotes lacking ingestive mode of nutrition are included in the kingdom. Monera.
 In the kingdom Protista unicellular eukaryotic microorganisms representing all the three
modes of nutrition are included.
The multicellular green plants and higher algae were placed in the kingdom Plantae
while multinucleate higher fungi in the kingdom Fungi and the multicellular animals in
the kingdom Animalea.

(1) Binomial nomenclature
(a) Organisms are named using binomial nomenclature (viruses are exceptions)
(b) Binomial nomenclature employs the names of the two lower level taxa, genus and
species, to name a species
(c) Conventions when using binomial nomenclature include:
(i) Genus comes before species (e.g., Escherichia coli)
(ii) Genus name is always capitalized (e.g., Escherichia)
(iii) Species name is never capitalized (e.g., coli)
(iv) Both names are always either italicized or underlined (e.g., Escherichia coli)


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(v) The genus name may be used alone, but not the species name (i.e., saying or
writing "Escherichia," alone is legitimate while saying or writing "coli" is not)
(vi) The genus name may be abbreviated but
· It must be used first without abbreviation
· If abbreviated it must be used with the species name (no E. all by itself)
· It must be abbreviated unambiguously
· If abbreviating as the first letter of the genus is unambiguous, then abbreviating as the
first letter is what one does (e.g., Escherichia abbreviated as E. but only if no other
genera considered also starts with E)
· Genus abbreviations are only used in conjunction with the species name (i.e., E. coli)




Introduction to Bacteria:
The characteristic compound found in all true bacterial cell walls is peptidoglycan.



                                          Coccus
                                          Chain = Streptoccus
                                          Cluster = Staphylococcus
                                          Bacillus
                                          Chain = Streptobacillus
                                          Coccobacillus
                                          Vibrio = curved
                                          Spirillum
                                          Spirochete
                                          Square
                                          Star




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                         Shape

     Gram                                     Flagella,
                                              Fimbriae,
    staining      Morphological                  pili
                        Traits

            Colonial
           Morphology            Capsule and slime
                                      layers




   Gram-positive cell walls                 Gram-negative cell
    walls

   Thick peptidoglycan                Thin peptidoglycan
   90% peptidoglycan                  5-10% peptidoglycan
   Teichoic acids                     No teichoic acids

   1 layer                            3 layers
                                       Outer membrane has lipids,
   Not many polysaccharides
                                        polysaccharides
   In acid-fast cells,
                                       No acid- fast cells (mycolic
    contains mycolic acid
                                        acid)




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The Gram staining process includes the use of:
      a primary stain (crystal violet)
      a mordant (helper) iodine solution,
      a decolorizer (95% ethanol),
      a counterstain (safranin).




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Classification on the bases of source of carbon, electron and energy
CARBON SOURCES: Autotrophs                CO2 sole or principal biosynthetic carbon
                                          source.
                                          Reduced, preformed, organic molecules
                    Heterotrophs
                                          from other organisms
ENERGY SOURCES: Phototrophs               Light
                                          Oxidation of organic or Inorganic
                     Chemotrophs
                                          compounds
ELECTRON SOURCES: Lithotrophs             Reduced inorganic molecules
                     Organotrophs         Organic molecules



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Archaebacteria have distnictive chemistry. Originally thought to exist only in extreme
environments, archaea are now found to be ubiquitous in soil and water, and even in
the human digestive tract. Included are the thermophilic Crenarchaeota, such as
Sulfolobus and Pyrodictium, as well as mesophilic crenarchaeotes and even sponge
endosymbionts. They cover the salt-loving Haloarchaea, the methanogens, and the
elusive Nanoarchaea, whose tiny size pushes the limits of viability.




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History of development of Microbiology as a science:
Many scientists contributed to the science of microbiology.
Louis Pasteur (1822-1895)




Louis Pasteur was a French chemist and a crystallographer. His contribution to
microbiology is so great that he is considered to be the “Father of Microbiology”.

Contribution to science: As a chemist He was working with tartaric acid crystals. He
could pick up the dextro and levo rotatory crystals by seeing the morphology of
the crystals. Later he was called to solve some of the problems in fermentation industry
and turned his attention to biological process of fermentation.
Contribution to wine industry
1. He discovered that alcohol production from grape juice was due to Yeast.
2. He found out that large amounts of lactic acid production was due to the presence or
    contamination of rod shaped bacteria.
3. He observed that the process of alcohol production i.e. FERMENTATION took place
   in the absence of air(high dissolved oxygen in the medium) .
4. He coined the terms aerobic to describe those organisms requiring air and
   anaerobic to describe those organisms which do not require air for their growth.

Contribution to modern microbiology
Pasteur disproved the theory of spontaneous generation. The theory proposed that
living organisms originated spontaneously, particularly from decaying organic matter.
He disproved it.
Pasteur’s swan neck flask
Pasteur poured meat infusions into flasks and then drew the top of each flask into a
long curved neck that would admit air but not dust. He found that if the infusions were
heated, they remained sterile (free from any growth) until they were exposed to dust. He
opened them on a dusty road and resealed them and demonstrated the growth of
microorganisms in all the flasks. The unopened flasks were sterile. Thus he disproved
the theory of spontaneous generation.
Louis Pasteur defined pasteurization to prevent spoilage of food by bacteria, develop
vaccines and disproved the scientific dogma of “Spontaneous Generation”. He defined
“Germ Theory” and demonstrated that germs were responsible for disease.




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Edward Jenner 1796
It was an ancient observation that persons, who had suffered from a specific disease
such as small pox or mumps, resisted the infection on subsequent exposures. They
rarely contracted it second time. Such acquired resistance is specific. Edward Jenner
a country doctor in England noted a pustular disease on the hooves of horses called the
grease. This was carried by farm workers to the nipples of cows (cow pox). This was
again carried by milk maids. They got inflamed spots on the hands and wrists. The
people who got this cow pox were protected from small pox. He reported that 16 farm
workers who had recovered from cow pox were resistant to small pox infection.
He took the material from the cow pox and inoculated into the cut of an 8 year old boy
on 14 May 1796. Two months later Jenner inoculated the same boy with material taken
from small pox patients. This was a dangerous but accepted procedure of that time and
the procedure was called variolation. The boy was protected against small pox. His
exposure to the mild disease cow pox had made him immune to the disease small pox.
In this manner Jenner began the science of Immunology, the study of the body’s
response to foreign substances.
Robert Koch (1843-1910)
Robert Koch was a German physician.
1. For the first time he showed the evidence that a specific germ (Anthrax bacillus) was
   the cause of a specific disease (splenic fever in sheep)
2. He established that a specific germ can cause a specific disease and introduced
    scientific approach in Microbiology.
3. He discovered Bacillus anthracis (Anthrax bacillus), Mycobacterium tuberculosis, and
    Vibrio cholerae.
4. He modified Ziehl-Neelsen acid fast staining procedure which was introduced by
    Ehrlich.
5. He devised the solid medium to grow the microorganism to get single colonies.
6. He introduced Koch’s thread method to find out the efficacy of disinfectants
7. He established certain rules that must be followed to establish a cause and effect
    relationship between a microorganism and a disease. They are known as Koch’s
    Postulates
8. He also described the Koch’s Phenomenon

The need for Koch’s postulates: In those days there were no perfect techniques to
identify the organisms. Solid media and staining techniques were not available. So the
etiological role of organisms was not known. To prove the etiology there were not strict
criteria. So there was a need to establish criteria.

Koch’s Postulates
1. The organism should be regularly seen in the lesions of the disease.
2. It should be isolated in pure culture on artificial media.
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3. Inoculation of this culture should produce a similar disease in experimental
  animals.
4. The organism must be recovered from the lesions in these animals.


Postulate 1
The organism should be found in lesions of the disease. All the causative agents of the
disease are seen in the particular diseases. If we take pneumococci as example, they
are seen in all the pneumonia cases.
Postulate 2
It should be isolated and grown in solid media. Pneumococci are grown in solid media
and are isolated from the diseases. Some organisms do not grow on solid media or the
solid media are not developed yet.
Example: Mycobacterium leprae and
          Treponema pallidum
Postulate 3
The organisms should produce the exact disease in experimental animals
Almost all the pathogenic organisms produce the same disease in experimental
animals. Usually rats, mice, rabbits or guinea pigs are used as experimental animals.
Pneumococci produce pneumonia in animals. Salmonella species do not produce
typhoid fever in rat, mice or rabbit. So chimpanzee is taken as experimental animal and
it produces fever in chimpanzee.
Postulate 4
It should be isolated from the diseased animal also
Pneumococci are isolated from the experimental animals also.

Modern addition to Koch’s Postulates
Today we recognize additional criteria of causal relation between a microorganism and
a disease.
The important one is the demonstration of abnormally high concentration of specific
circulating antibodies to the organism in the infected host Or, the presence of
abnormally high degree of specific immunity or hypersensitivity to the infecting agent in
a recently recovered host.

Limitations
Some organisms have not yet been grown in artificial culture media
Example: Mycobacterium leprae and Treponema pallidum.

Usefulness of Koch’s Postulates
1. It is useful in determining pathogenic organisms


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2. To differentiate the pathogenic and nonpathogenic microorganism
3. For the classification of organisms
4. To detect the susceptibility, resistance of the laboratory animals.

Conclusions
Koch has done a valuable work in the field of Microbiology and has made postulates,
which have merits, demerits and limitations with modern omission and addition.




Other ‘applied microbiologists’:

      Ignaz Semmelweis was the first to recognize the need for good hygiene during
       medical procedures. The first to identify nosocomial infections.
      1827-1912 Joseph Lister developed antiseptic methods for use in surgery and
       medicine.
      1854-1915 Paul Ehrlich developed chemotherapy to cure infectious diseases and
       discovers antibiotics to treat sleeping sickness and syphilis.
      1881-1951 Alexander Fleming discovered penicillin and lysozyme.
      1864-1920 Dmitri Ivansvski discovered the first virus which is known as the
       tobacco mosaic virus (TMV)




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      EXPLOIT THE USEFUL MICROBES. / COMBAT THE HARMFUL ONES.
                 YOU CAN’T BE TOTALLY FREE OF THEM.


Industrial Microbiology

Medicinals, food supplements, alcoholic beverages, enzymes and organic
acids _ these are some of the substances produced on a commercial basis
by using microorganisms. The beneficial chemical activities of
microorganisms like bacteria, yeasts, molds and algae are exploited to
obtain valuable products from these organisms after they have been grown
in a relatively inexpensive medium.

Industrial Microbiology and Food processing:

     Yeast is used make breads, baked goods, alcohol, yogurt and other
      foods and drink items.
     Today’s yeast are specially engineered to work in large scale
      industrial applications.
     Specialized bacteria and molds are used to make cheeses of
      different types.
     Biofertilizers include bacteria such as Rhizobia that fix nitrogen.
     Food additives increase nutritional value, retard spoilage, change
      consistency and enhance flavor. These may be natural compounds
      such as guar gum and xanthan gum or flavor enhancers and
      vitamins.

Industrial Microbiology and Medicine:

   Biosensors are monitors used in the detection of specific targets in
    the environment, human body or other organisms.
   Antibiotic production is a capacity that many microbes have naturally.
   Microbes have been developed as a drug delivery system.
   Lactic acid bacteria (LAB) has been exploited to make and deliver
    vaccines and other bioactive materials.

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   Microbes have been developed that degrade oil so that they it may be
    more easily extracted.

Industrial Microbiology and Economics:

   In the cosmetic industry the botulism toxin derived from Clostridium
    botulinum is utilized.
   Biopesticides have been developed for the control of insect,
    nematodes and other pathogens that effect plants.
   Synthetic energy fuels such as ethanol, methane, hydrogen and
    hydrocarbons are produced by microbes.
   Gasohol which is a 9:1 blend of gasoline and ethanol is a popular fuel
    alternative. The ethanol is produced as a by product of yeast
    fermentation.
   Microbes have been used in mining. An example of this is the
    recovery of metals is facilitated by bacteria by helping to solubilize it
    making it more easily extracted.
   Microorganisms have been used to clean up the environment in a
    process called bioremediation. In bioremediation a microbe is
    introduced into an environment where its natural metabolism results
    in the detoxification or break down of hazardous chemicals or
    pollutants.




Specialized Microbes:

   Rhizobia are bacteria that fix nitrogen and make it available for plant
    nutrition and growth. They form nodules on the roots of legumes.
   Azolla is a fee floating water plant that fixes nitrogen in association
    with cyanobacteria. It acts as a renewable biofertilizer.
   Azotobacter are nitrogen fixing bacteria that do not form nodules on
    plant roots or associate with legumes. They are free living and in
    addition to fixing nitrogen they can produce antibiotics and beneficial
    growth substances.

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 Azospirillum fix nitrogen inside plant roots. They produce beneficial
  compounds for plant growth and can survive in wetland conditions as
  well as soils.
 Mycorrhiza are fungi that form symbiotic relationships with plant
  roots. Vesicular arbuscular mycorrhiza (VAM) is the most important
  member of this group. VAM colonies take up nutrients and water
  which is available for the plant and they act as root extensions.




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Eukaryotes
Basic structure
The basic eukaryotic cell contains the following:
1. plasma membrane
2. glycocalyx (components external to the plasma membrane)
3. cytoplasm (semi fluid)
4. cytoskeleton - microfilaments and microtubules that suspend organelles, give
   shape, and allow motion
5. presence of characteristic membrane enclosed subcellular organelles

Characteristic biomembranes and organelles

Plasma Membrane

A lipid/protein/carbohydrate complex, providing a barrier and containing transport and

signaling systems.

Nucleus

Double membrane surrounding the chromosomes and the nucleolus. Pores allow
specific communication with the cytoplasm. The nucleolus is a site for synthesis of RNA
making up the ribosome.



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Mitochondria

Surrounded by a double membrane with a series of folds called cristae. Functions in

energy production through metabolism. Contains its own DNA, and is believed to have

originated as a captured bacterium.

Chloroplasts (plastids)

Surrounded by a double membrane, containing stacked thylakoid membranes.

Responsible for photosynthesis, the trapping of light energy for the synthesis of sugars.

Contains DNA, and like mitochondria is believed to have originated as a captured

bacterium.

Rough endoplasmic reticulum (RER)

A network of interconnected membranes forming channels within the cell. Covered with

ribosomes (causing the "rough" appearance) which are in the process of synthesizing

proteins for secretion or localization in membranes.

Ribosomes

Protein and RNA complex responsible for protein synthesis

Smooth endoplasmic reticulum (SER)

A network of interconnected membranes forming channels within the cell. A site for

synthesis and metabolism of lipids. Also contains enzymes for detoxifying chemicals

including drugs and pesticides.

Golgi apparatus

A series of stacked membranes. Vesicles (small membrane surrounded bags) carry

materials from the RER to the Golgi apparatus. Vesicles move between the stacks while

the proteins are "processed" to a mature form. Vesicles then carry newly formed

membrane and secreted proteins to their final destinations including secretion or

membrane localization.

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Lysosymes

A membrane bound organelle that is responsible for degrading proteins and
membranes

in the cell, and also helps degrade materials ingested by the cell.

Vacuoles

Membrane surrounded "bags" that contain water and storage materials in plants.

Peroxisomes or Microbodies

Produce and degrade hydrogen peroxide, a toxic compound that can be produced
during metabolism

Cell wall

Plants have a rigid cell wall in addition to their cell membranes.

1. Yeasts

· Unicellular fungi, nonfilamentous, typically oval or spherical cells.

Reproduce by mitosis:

· Fission yeasts: Divide evenly to produce two new cells

(Schizosaccharomyces).

· Budding yeasts: Divide unevenly by budding (Saccharomyces).

Budding yeasts can form pseudohypha, a short chain of undetached cells.

Candida albicans invade tissues through pseudohyphae.

· Yeasts are facultative anaerobes, which allow them to grow in a variety of

environments.

o When oxygen is available, they carry out aerobic respiration.

o When oxygen is not available, they ferment carbohydrates to produce

ethanol and carbon dioxide.

CHARACTERISTICS OF FUNGI

Molds and Fleshy Fungi

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      Multicellular, filamentous fungi.
      Identified by physical appearance, colony characteristics, and reproductive
       spores.
      Thallus: Body of a mold or fleshy fungus. Consists of many hyphae.
      Hyphae (Sing: Hypha): Long filaments of cells joined together.
      Septate hyphae: Cells are divided by cross-walls (septa).
      Coenocytic (Aseptate) hyphae: Long, continuous cells that are not divided by
       septa.

Hyphae grow by elongating at the tips.

Each part of a hypha is capable of growth.

      Vegetative Hypha: Portion that obtains nutrients.
      Reproductive or Aerial Hypha: Portion connected with reproduction.
      Mycelium: Large, visible, filamentous mass made up of many hyphae.




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