exam 1 Flashcards
Microorganisms
are minute living things that are too small to see with the naked eye - Bacteria - Archaea - Fungi - Protozoa - Algae - Viruses - Helminths
Microbiology
is the study of microorganisms.
Eubacteria
“true-bacteria” – Small unicellular organisms. – Its genetic material is not enclosed in a nuclear membrane. – are prokaryotes (“prenucleus”) – Most common shapes of cells are: 1. bacillus (rod) 2. coccus (spherical or ovoid) 3. spiral or corkscrew – Have cell wall composed primarily of peptidoglycan. – Generally reproduce by binary fission
prokaryotes
(“prenucleus”)Its genetic material is not enclosed in a nuclear membrane
bacillus shape
(rod)
coccus shape
(spherical or ovoid)
Archaea:
“exteme-ophile” - are prokaryotes - cell walls lack peptidoglycan - are found in extreme environments - There are 3 main groups of Archaea 1. Methanogens: produce methane gas as waste product 2. Extreme halophiles: salt-loving 3. Extreme thermophiles: heat-loving; live in hot sulfurous water such as hot springs in Yellowstone National Park.
Methanogens:
produce methane gas as waste product
Extreme halophiles:
salt-loving
Extreme thermophiles:
heat-loving; live in hot sulfurous water such as hot springs in Yellowstone National Park.
Fungi
- are eukaryotes. - are members of the kingdom Fungi. - are unicellular (yeasts) or multicellular (mushrooms). - True fungi have cell walls composed of chitin. - Yeasts are oval-shaped microorganisms larger than bacteria. - Molds are typical fungi. - reproduce sexually (meiosis) or asexually (mitosis).
meiosis)
reproduce sexually
(mitosis)
asexually
Yeasts
are oval-shaped microorganisms larger than bacteria
Protozoans:
- unicellular eukaryotes - are members of the kingdom Protista - are classified according to their means of locomotion 1. cytoplasmic streaming (amoebas) 2. flagella 3. cilia - shapes vary - can live free or as parasites. - reproduction is sexual or asexual. (Fig. 1.1c)
Algae:
DIVERSITY OF MICROORGANISMS - are photosynthetic eukaryotes. - wide varieties of shapes. - are members of the kingdom Protista. - reproduction is sexual or asexual.
Viruses :
- are so small that they can only be seen with an
electron microscope.
- are not cellular.
- are parasites which require a host cell to replicate itself.
- simple structure:
- Core contains the nucleic acid (DNA or RNA)
- Protein coat surrounds core
- Lipid envelope may surround coat
Multicellular Animal Parasites
2 major groups collectively called helminths
- flatworms
- roundworms
- During some stage of their life
cycle the helminths are microscopic in size.
Robert Hooke
1665 observed and made drawing of “cells” from a cork
M. J. Schleiden & T. Schwann
(1838) established the cell theory
cell theory
- “all living things are composed of cells” -Modern tenets of the cell theory:
1. all known living things are made of cells
2. cell is the basic structural & functional unit of all living things
- all cells come from pre-existing cells by division
- cells contains hereditary information
- all cells are basically the same in chemical composition
- metabolism and biochemistry of life occurs within cells
Anton van Leeuwenhoek
1674
observed microorganisms through magnifying lenses.
Made numerous drawings of bacteria and protozoa and sperms
Spontaneous generation:
life could arise spontaneously from non-living matter.
People thought that toads, snakes, and mice could be born from moist soil and that flies could emerge from manure, and that maggots, the larvae of flies could arise from decaying corpses.
Francesco Redi
Opposition to spontaneous generation: 1668
expirament:
3 jars with decaying meat and sealed them tightly, no maggots
• 3 jars with decaying meat and left them open, maggots • There were doubter still…magical substance in fresh
air was needed for spontaneous generation to occur…
John Needham
Proponent of spontaneous generation 1745
He heated nutrient fluids (chicken broth and corn broth), cooled it, and then poured it into covered flasks, the solutions were teeming with microorganisms.
Needham claimed that the microbes developed spontaneously from the fluids.
Lazzaro Spallanzani
1765
disproved Needham conclusion
- suggested that microorganisms from the air probably entered the solutions from the air after they were boiled.
- showed that nutrient fluids heated after being sealed did not develop microbial growth.
Rudolf Virchow
1858 Theory of biogenesis: living cells can arise only from preexisting living cells
Theory of biogenesis:
living cells can arise only from preexisting living cells
Louis Pasteur
1861 demonstrated that microorganisms are present in the air and that they can contaminate sterile solutions, but air itself does not create microbial life.
During a job on understanding why wine and beer sour, discovered that microorganisms called yeasts convert sugars to alcohol in the absence of air.
This is called FERMENTATION (1857).
Discovered pasteurization (1864)…process of
heating to kill bacteria to reduce/prevent spoilage
This was the first link that microorganisms can cause changes in organic materials.
that microorganisms might cause disease
introduced germ theory of disease
Vaccination
is the process of conferring immunity using a vaccine which is a preparation of killed, inactivated, or attenuated microorganisms or toxoids to induce artificially acquired active immunity
Edward Jenner
1798
developed the first vaccine for smallpox
milkmaid couldn’t get smallpox because she had already been sick with cowpox, a much milder disease
Jenner decided to test this story:
collected scrapings from cowpox blisters and made inoculations with this material by scratching the arm of a healthy volunteer with the cowpox contaminated needle.
The person became mildly sick but recovered and never
contracted either cowpox or smallpox
Simple stain
is an aqueous or alcohol solution of a single basic dye
- is used to highlight the entire microorganism so that cellular shapes and structures are visible.
- A mordant may be added to the simple stain to:
increase the affinity of a stain for the specimen
coat a structure (such as a flagellum) to make it thicker.
- Examples of simple stains: 1. methylene blue (blue) 2. carbolfuchsin (red)
3. crystal violet (purple) 4. safranin (pink)
mordant
may be added to the simple stain to:
increase the affinity of a stain for the specimen
coat a structure (such as a flagellum) to make it thicker.
Differential Stains
react differently with different bacteriacan be used to distinguish them
- 2 types of differential stains 1. Gram Stain
2. Acid-Fast Stain
Gram Stain
was developed in 1884 by the Danish microbiologist
Hans Christian Gram
- differentiates/classify bacteria into 2 large groups
a. gram positive (+) purple
b. gram negative (-) pink
gram stain procedure
- Apply crystal violet which colors all bacteria purple (primary stain)
• Wash off w/ddH O. 2
- Apply iodine, a mordant, all bacteria still purple.
- Wash with ethanol or ethanol- acetone solution, a decolorizing agent
- Gram + bacteria will be purple; Gram - bacteria will be colorless
- wash off w/ddH2O
- stain with safranin, a counterstain.
- Gram (-) will be pink; Gram (+) will be purple - wash off w/ddH2O
- blot dry 19
- examine microscopically
Gram-positive
no membrane covering peptidoglycan wall
Gram (+) bacteria have a thicker cell wall composed of peptidoglycan than gram (-) bacteria
Gram-negative
outer membrane covers peptidoglycan wall
Gram (-) bacteria have a thin layer of peptidoglycan and outside of that, a layer of lipopolysaccharide
- Gram stain: Procedure why it works
rystal violet and iodine can go through the thick cell wall, but once inside form a complex (CV-I) which can not go out of the cell.
- gram (+) bacteria stain purple because of the trapped CV-I complex
- gram (-) bacteria will be colorless because the alcohol wash disrupts the lipopolysaccharide and allow the CV-I complex to be washed out of the cell
- gram (-) bacteria are pink because of the counterstain with safranin
- Gram stain is most consistent when used on young, growing bacteria.
result of gram staining provide information for proper treatment of disease
- Generally, gram (+) bacteria are easily killed by penicillin and sulfonamide drugs.
- Gram (-) bacteria are resistant to these drugs, but are more susceptible to streptomycin, chloramphenicol, and tetracycline.
Acid-Fast Stain
stain binds to bacteria that have a waxy materia(mycolic acid and evades immune system and phagocytosis happens) l in their cell walls
- used to identify all bacteria in the genus Mycobacterium Ex. Mycobacterium tuberculosis causes tuberculosis. Ex. Mycobacterium leprae causes leprosy.
- used to identify the disease-producing strains of the genus Nocardia
Acid-fast stain: Procedure
a. Apply carbolfuchsin to heat-fixed smear and gently heat to enhance penetration and retention of the dye. (All organisms will be red.)
b. Wash
c. Decolorize with acid-alcohol.
- Acid-fast organisms will be red since carbolfuchsin is soluble in the waxy material of the cell wall
- Non-acid-fast organisms will be colorless since these organisms do not have the waxy material in their cell walls to retain the carbolfuchsin
d. Counterstain with methylene blue.
- Acid-fast organisms will be red.
- Non-acid-fast organisms will be blue.
Negative Staining for Capsules
- capsule: a gelatinous covering of some microbes;
confers virulence(polysacharide or polysacharide protine)
- is more difficult than other types of staining procedures because capsules are soluble in water and may be removed during washing.
Negative staining for capsuls: Procedure
a. Mix bacteria with Nigrosine, an acidic dye which provides a
dark purple background.
b. Spread dye as in negative staining.
c. Stain slide with crystal violet, basic dye to stain bacteria (purple)
d. Capsules will appear as colorless halos surrounding purple bacterial cells against a dark purple background.
Endospore (Spore) Staining
Endospores are resistant, dormant structures within a cell which protects the microbe from adverse environmental conditions.
- are formed by 7 genera of bacteria (including Bacillus and Clostridium)
- do not stain with ordinary stains because the dyes do not penetrate the wall of the endospore.
- 2 methods used:
- A. Schaeffer-Fulton endospore stain - B. Dorner endospore stain
Schaeffer-Fulton Endospore Stain
a. Apply malachite green to heat-fix smear on slide and steam heat for 5 minutes. Spores will stain green and cells will be colorless.
b. Wash
c. Counterstain with safranin, which will stain the cells
pink. Spores will be green. d. Wash
Dorner Endospore Stain
a. Put carbolfuchsin, red, in a test tube
b. Add several loopfuls of organism
c. Boil in a beaker of water for 10 minutes
- *Spores will be red, cells colorless.**
d. Add several loopfuls of the carbolfuchsin- bacteria
mixture to a drop of nigrosine on a slide e. Smear mixture
- Bacterial cells will be colorless against dark purple background (Negative Staining).
- Endospores inside the cells will be red.
- Flagella Staining
Flagella are structures of locomotion.
- Staining flagella involves using a mordant and carbolfuchsin to build up the diameters of the flagella until they become visible under the light microscope.
- It is a tedious and delicate staining procedure.
GOLDEN AGE OF MICROBIOLOGY
1857- 1914
A period of explosion of discoveries in
microbiology which led to the establishment of microbiology as a science.
1867 - Joseph Lister
English surgeon
initiates aseptic surgical techniques.
He began soaking surgical dressings in a mild solution of carbolic acid (phenol) which kills bacteria.
This reduced the incidence of infections and deaths in surgical patients.
Founder of aseptic surgery
1876 -83 Robert Koch
proved the germ theory of disease
discovered a rod-shaped bacteria now known as Bacillus anthracis in the blood of cattle that had died of anthrax.
He cultured the bacteria and injected samples of the culture into healthy animals which became sick and died.
Koch isolated the bacteria in the blood and found it to be the same as the original bacteria isolated.
Experimental procedure used to relate specific microbe to a specific disease is known as Koch’s postulate
1881 - developed pure culture and staining techniques.
• 1882 - discovered Mycobacterium tuberculosis, the causative agent of
tuberculosis.
• 1883 - discovered Vibrio cholerae, the
causative agent of cholera.
1879 - Albert Neisser
1880 - Louis Pastuer
developed immunization techniques based on Edward
Jenner’s work with smallpox (vaccination)
• Avirulent form of bacterium causing fowl cholera can induce immunity against subsequent infections by virulent counterpart.
Vaccine: cultures of avirulent microorganism used for preventative inoculations
also discovered Streptococcus pneumoniae (1881), the causative agent of pneumococcal pneumonia.
1884 - Hans Christian Gram
developed a differential staining technique
called the Gram stain which differentiates bacteria into 2 groups, gram (-) and gram (+).
1885 - Theodor Escherich
of Germany discovered Escherichia coli, the
causative agent of urinary tract infections and traveler’s diarrhea.
1887 - Richard Julius Petri
of Germany introduced a covered dish for growing microorganisms on a solid medium. (petri dish)
1890 - Paul Ehrlich
of Germany proposed a theory of immunity in which antibodies are responsible for immunity.
- Discovery of chemotherapy—treatment of disease by use of chemical substances (i.e. synthetic drugs & antibodies)
- Magic bullet — substance that could target and destroy the pathogen without harming the host
- Salvarsan (arsenic derivative; 1910)— chemotherapeutic agent against syphillis
1892 - Dmitri Iwanowski
of Russia discovered a filterable organism (virus) caused tobacco mosaic disease.
1928 - Alexander Fleming
Scottish physician and bacteriologist
discovered the antibiotic, penicillin, by accident
Thus he discovered a mold (fungus), Penicillium chrysogenum which could inhibit the growth
of bacteria.
1735 – Carolus (Carl) Linnaeus
established the system of nomenclature (naming) for organisms which assigns each organism 2 names…
A. Genus is the 1st name and is always Capitalized and underlined or italicized.
B. Specific epithet or species is the 2nd name and is not capitalized, but is underlined or italicized.
Example:
1. Staphylococcus aureus or
- Staphylococcus aureus*
2. Escherichia coli or Escherichia coli
Beneficial Activities of Microorganisms
1. Microorganisms degrade dead plants and animals and recycle chemical elements such as nitrogen, carbon, oxygen, sulfur, and phosphorus.
Example - bacteria and fungi return carbon dioxide to the atmosphere when decomposing organic matter…carbon cycle
Example - Nitrogen fixation - converting nitrogen gas into ammonia (i.e. Rhizobium species)
2. Microorganisms are used to decompose
organic matter in sewage…recycle water and prevent pollution (bioremediation) of rivers and oceans
Bioremediation: use of microorganisms to remove environmental pollutant
(Zoogloea ramigera).
3. Microorganisms (i.e. Bacillus thuringiensis) cause disease in insects and thus can be used as a biological control in insect pests (instead of pesticides which harm the environment).
-
Microorganisms can be used to produce food such as:
a. soy sauce (Aspergillus oryzae (fungi) b. yogurt (Streptococcus thermophilus)
for acid production,
Lactobacillus bulgaricus for flavor and aroma).
- Using biotechnology and recombinant DNA technology, bacteria, can be used to produce human proteins:
a. insulin
b. factor VIII
c. tissue plasminogen activator d. growth hormone
e. use in gene therapy
Microbes and Human Disease
- The body has a normal flora of microorganisms
inside and on its surface that usually are a benefit to the body. - The important factors which determine whether a person will contract a disease include:
a. the disease producing properties of the microorganism
b. the resistance of the body.
- Only a minority of microorganisms are pathogenic (disease producing).
Biofilms: community/aggregate of microorganisms that are usually attached to a surface through secretion of a matrix. Ex. dental plaque
Emerging Infectious Diseases (EID): diseases that are new or changing and are increasing or have potential to increase in the near future
i.e. H1N1 influenza, S. aureus – MRSA, VISA, Ebola virus, Zika virus
Atom
smallest particle of an element that still retains its distinctive chemical properties
Isotopes
Atoms that contain the same number of protons and electrons
but different number of neutronsdifferent atomic mass.
Radioisotopes
sotopes that can decay and emit electromagnetic radiation, which can damage DNA/protein.
– It can be detected by X-ray film or other methods.
– Is widely used in molecular biology studies to label molecules.
– Can be detected by:
- a Geiger counter (monitor)
- exposure to X-ray film (autoradiography)
Molecules
made up of two or more atoms joined together by covalent chemical bonds
Covalent bonds:
– Involves the sharing of electrons between two atoms
– Bond strength is ~12- kcal/mol (the energy needed to break a bond)
– Single bond: 2 atoms sharing 1 pair of electrons
– Double bond: 2 atoms sharing two pairs of electrons
Polar bonds:
electrons are shared unequally by bonded atoms
Non-polar:
Electrons are shared equally by bonded atoms
Electronegativity
the power of an atom to draw electrons to itself
Non-covalent bonds:
– Interaction between atoms that do not involve sharing of electrons
– Weak bonds, but many non-covalent bonds working together can stabilize the 3D structure of a large molecule (intra- molecular interactions)
– Important for biomolecules; help molecules bind to other molecules (intermolecular interactions)
Types of non-covalent bonds:
Ionic interaction
Hydrogen bonds
Van der Waals interaction
Hydrophobic interaction
Hydrophobic
“water-fearing”
Non-polar molecules do not form hydrogen bonds with water.
Hydrophobic interaction is formed because all parties that “hate” water are pushed together.
why are Non-covalent bonds are critical for inter-molecular interactions
Individually, they are weak
Together, they are strong
Confers stability of a molecule
Confers specificity of binding
macromolecules
Small organic molecules combine to form large molecules
macromolecules are usually polymers (made of repetitive monomers)
Condensation
(dehydration synthesis
reaction)
dehydration synthesis reaction)
water producing reaction
Hydrolysis
water obsorbing reaction
disaccharides
Formed by the bonding of 2 monosaccharides in a dehydration synthesis reaction
i.e. glucose + fructosesucrose glucose + galactoselactose
glucose + glucosemaltose
Triglycerides
are formed by the dehydration reaction of one glycerol with 3 fatty acids.
- glycerol have 3 hydroxyl (-OH) groups attached to 3 C atoms
- fatty acids are composed of long hydrocarbon (H-C) chains ending with carboxyl (-COOH) group.
Saturated fatty acids
have no double bonds between the carbon atoms; thus, the carbons have the maximum number of hydrogens attached (saturated with hydrogens).
- Most animal fats are saturated fats.
Unsaturated fatty acids
have at least one double or triple bond between the carbons.
- Most plant fats are unsaturated fats.
Complex lipids:
- contains elements (i.e. phosphorus, nitrogen, sulfur) in addition to C, H, O
- Examples are waxes and glycolipids.
- cell walls of bacteria belonging to the genus
Mycobacterium contain waxes & glycolipids; provides distinguishing staining characteristic
(acid-fast stain)
- example: phospholipids (glycerol, 2 fatty acid, phosphate group)
has polar and non-polar ends
- is major constituent of cell membranes—phospholipid bilayer
There are five different nitrogenous bases:
Which nucleotide is present in DNA?
RNAstructure
Consists of 1 strand of nucleotides
Primary structure: the sequence of nucleotides in RNA
Secondary structure: RNA is usually single stranded; some regions may form double stranded within the molecule.
Tertiary structure: three- dimensional structure of a single RNA molecule
Amino acids (aa)
are the monomeric building blocks of proteins
There are 20 different aa.
All organisms on earth have the same 20 aa.
Each protein being synthesized are made from the different arrangements of the aa.
Each aa monomer has 4 different groups attached to the central carbon atom (C)
The nature of an aa is based on the composition of its side chain.
- 20 different aa20 different side chains
- Each side chain differ in: – Size
Hydrogen
– Shape
– Charge
– Hydrophobicity
Protein chain (polypeptide)
is formed by amino acid monomers joined together by covalent peptide bonds
TransmissionElectronMicroscopy (tem)
- can resolve objects as close as 2.5 nm
- Magnification is from 10,000X to 100,000X.
- Only a very thin section (about 100 nm) of a specimen can be studied effectively
- can’t obtain 3D image
- Specimens must be fixed, dehydrated, and viewed under vacuum; therefore, shrinkage and distortion may occur; may get artifacts
Fluorescence microscopy:
- uses an ultraviolet source of illumination that causes fluorescent compounds to emit light.
- Some organisms fluoresce naturally.
- Other organisms can be stained with fluorescent dyes called fluorochromes.
- Specimens appear as luminescent objects against a dark background
Combine a fluorochrome to a
specific antibody for a specific antigen.
Allow the antibody to combine with the specific antigen
Wash to remove non-specific binding
Thefluorochrome-antibody- antigen fluoresces under UV light
- is useful in diagnosing syphilis and rabies or detecting specific cell types, tissues, or structures
(Fig. 3.6a)
7
Scanning Electron Microscope: (sem)
- Image is 3-dimensional
- It can study surface structures of intact cells & viruses
- resolves objects as close as
20 nm
- Magnification is 1000X to 10,000X
Power of resolution of human eye, light microscope, and electron microscope:
Prokaryotes: Shape
-1. Spherical or coccus (pl. cocci)
- Diplococci = two cocci
- Streptococci = cocci in chains
- Tetrads = cocci that divide in two planes and remain in groups of four
- Sarcinae are cocci that divide in 3 regular planes and produce a cube- like group of 8
- Staphylococci are those that divide at random planes and form grape like clusters or broad sheets
Prokaryotes: Shape
- Rod-shaped, bacillus (bacilli, pl.)
- divide only across their short axis.
- Diplobacilli appear in pairs after division.
- Streptobacilli occur in chains. - Some have tapered ends like
cigars.
- Coccobacilli are oval and may look like cocci.
- Most appear as single rods.
- bacillus means:
a. bacterial shape
b. genus (i.e. Bacillus anthracis)
Flagellum: structure
- Three basic parts:
a. Filament is the long outermost region which is constant in diameter and contains the globular protein flagellin - not covered by membrane or sheath
b. Hook is the structure to which the filament is attached
c. Basal body anchors the flagellum to the cell wall and the plasma membrane.
(Fig. 4.8)
- It is composed of a central rod inserted into a series of rings.
Axial Filaments:aka endoflagellum
- are bundles of fibrils that arise at the ends of the cell
beneath the outer sheath and spiral around the cell.
- used as a form of locomotion by spirochetes such as Treponema pallidum, the causative agent of syphilis.
3. Rotation of filament causes spiral motion that resembles the movement of a corkscrew
Structure of peptidoglycan:
Gram (+) bacteria:
- contain teichoic acids, which consists of an alcohol (glycerol) and phosphate
- Have negative charge due to phosphate
- F(x)s: regulates cation (+) movement in and out of cell
- Preventing extensive wall breakdown and cell lysis - Provide antigenic specificity
- Gram (-) Bacteria Cell Wall:
- consist of an outer membrane, very few layer of
peptidoglycan, and a periplasmic space (gel-like fluid) - peptidoglycan interacts with lipoprotein in the outer
membrane
- does not contain teichoic acids
a. The outer membrane consists of:
- lipoproteins
- lipopolysaccharides (LPS) = lipid + polysaccharide
- polysaccharide: O polysaccharides that function as antigens which can identify species of bacteria - lipid: lipid A (endotoxin) is toxic in host blood, causes fever and shock
3. phospholipids: strong (-) charge help evade phagocytosis
- simple diffusion:
movement of lipid soluble substances such as oxygen, carbon dioxide, and nonpolar organic
molecules from area of high concentration to low concentration
- facilitated diffusion:
require the help of carrier protein to transport molecule across the membrane (i.e. glucose)
osmosis
net movement of water from an
area of high water to low water concentration
• A bacterial cell may be exposed to 3 kinds of osmotic solutions:
a. Isotonic solution: the same solute concentration as the cell
b. Hypotonic solution: less solute and more water than the cell therefore water will move into the cell which is hypertonic
c. Hypertonic solution: more solute and less water than the cell so that water will move out of the cell and the cell will shrink (plasmolysis).
