1
Q
Microbiology
A
Is the study of microorganisms
2
Q
Microorganism
A
A microscopic organism consisting of a single cell or cell cluster, including the viruses
Includes bacteria, fungi, protozoa and microscopic algae
Take up 60% of the earths biomass
3
Q
How to get rid of microorganisms
A
If you really want to get rid of them, think of, what can you deprive them of
4
Q
Bacteriology
A
The study of bacteria
5
Q
Mycology
A
The study of fungi
6
Q
Parasitology
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The study of protozoa and parasitic worms
7
Q
Virology
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The study of viruses
8
Q
Immunology
A
The study of immunity and the immune system
You have to have bacteria to keep your immune system prime
9
Q
Three domain systems
A
Carl Woese created the three domain system in 1978
Bacteria - Cell walls contain peptidoglycan (average bacterial cell 0.2-2.0 um x 2-8 um)
Archaea - Cell walls when present lack peptidoglycan
Eukarya - includes protists, fungi, plants and animals.
10
Q
Prokaryotes
A
- Bacteria and Archaea
- Unicellular microorganisms
- Have a cytoplasmic membrane
- No nucleus to contain their DNA
- Free-floating DNA
- No membrane bound organelles
- They have a nucleoid (pre nucleus ) and it is tightly wound and not enclosed in a membrane.
11
Q
Characteristics of Prokaryotes
A
- DNA is not enclosed in a membrane: one circular chromosome.
- DNA is not associated with histones.
- Lack membrane bound organelles.
- Cell walls are complex; contain peptidoglycan.
- Typically divide by the process of binary fission
12
Q
Pleomorphic
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“shape-shifter”, having many shapes
13
Q
Fixation
A
- Kills the cell
- Solidifies cell
- Avoids creation of artifacts
14
Q
Staining
A
- Increases visibility
- Increases difference in refractive index.
- Emphasizes cell differences through light absorption.
15
Q
Mordant
A
- Creates or increases affinity between dye and cell or cell structure.
- May change cell permeability.
- May hasten reaction between cell substrate and dye.
- May be applied prior to staining or incorporated in fixing or staining solution.
16
Q
Decolorization
A
- Tests degree of attachment of dye to cell substrate
- Differential staining
17
Q
Counter stain
A
- Emphasizes difference between cells that retained primary (original) stain and decolorized cells.
- Must not replace original stain.
18
Q
Simple stain
A
- Aqueous or alcohol solution of a single basic dye.
- Highlights entire microorganism to visualize basic cell structure and shape.
19
Q
Differential stain
A
React differently with different kinds of bacteria.
(gram-stain and acid fact stain)
20
Q
Gram stain
A
- Primary stain applied to heat-fixed smear.
- Rinse primary stain, apply iodine mordant, rinse.
- Decolorize to remove primary stain
- Counterstain with basic red dye
21
Q
Gram-positive cell wall
A
- Typically contain several layers of peptidoglycan; layer
- Contain teichoic acid
- Purple when stained
22
Q
Gram-negative cell wall
A
- Contain few layers of peptidoglycan but include an outer membrane; peptidoglycan insides the outer membrane is situated in the periplasm.
- Periplasm contains high concentrations of degradative enzymes and transport proteins
- Pink when stained
- They contain lipopolysaccharide (LPS)
23
Q
Acid fast stain
A
Binds only to bacteria with a waxy cell wall
24
Q
Negative stain
A
- In negative staining, the results yield a clear cell with a dark background.
- Used for capsule staining
- Colloidal suspension of India ink or nigrosin provides dark background.
25
Endospore stain
- Schaeffer-Fulton endospore stain.
- Primary stain is steam heated for 5 minutes.
- After rinsing, safranin applied as a counterstain.
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Synthetic reactions
A chemical process in which two or more simple elements or compounds combine to form a more complex product
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Decomposition reactions
A complex compound breaks down into two or more simpler compounds
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Exchange reactions
A chemical reaction in which both synthesis and decomposition occur
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Endergonic reaction
A reaction that requires energy to be absorbed in order for it to take place.
Absorbs more energy than it releases.
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Exergonic reaction
Chemical reaction that releases energy in the form of heat
Releases more energy than it absorbs or requires.
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Water
- Best solvent
- Average microbial cell contains 70% water.
- Acts as a good temperature buffer and offers protection to microbial cells against fluctuations in environmental conditions.
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pH
Most microorganisms grow best in pH ranges near neutrality
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Acidophile
Bacterium which grows below pH 4.0
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Alkaliphile
Organism growing best at high pH 7.0
35
Carbs
- Contain carbon, hydrogen, and oxygen and perform major functions in living systems including cell wall structure in bacterial cell
- Monosaccharides, disaccharides, polysaccharides
- Basic building blocks of life
36
Phospholipids
- Consist of glycerol, two fatty acids and a phosphate group.
- Specific building blocks of biological membranes.
- Both polar (hydrophilic) and nonpolar (hydrophobic) ends.
0 Primary barrier between cells and the environment
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Proteins
- Function as enzymes (help speed up reactions)
- Made of amino acids
- Protein denaturation can occur in response to unfavorable conditions of temp, pH, or salt concentrations
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ATP
- Principle energy carrying molecule of all cells
- Consists of an adenosine unit with three phosphate groups attached
- Considered a high energy material
39
All 6 Characteristics of living things
- Metabolism
Uptake of nutrients from the environment, their transformation within the cell, and elimination of wastes into the environment. The cell is thus an open system.
- Reproduction (growth)
Chemicals from the environment are turned into new cells under the direction of preexisting cells.
- Differentiation
Formation of a new cell structure such as a spore, usually as part of a cellular life cycle.
- Communication
Cells communicate of interact primarily by means of chemicals that are released or taken up.
- Movement
Living organisms are often capable of self-propulsion.
- Evolution
Cells contain genes and evolve to display new biological properties. Phylogenetic trees show the evolutionary relationships between cells
Anything that’s living should be capable of all these things.
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How can microorganisms can be classified metabolically
Microorganisms can be classified metabolically according to a nutritional pattern.
Based on energy source
Phototroph = Light is primary source
Chemotroph = Inorganic or organic compounds for energy
Based on carbon source
Autotroph = Use CO2 as their main carbon source (lithotroph)
Heterotroph = Organic carbon source from other organisms (organotroph)
41
Photoautotrophs
- utilizes light energy from sunlight and elements from inorganic (carbon dioxide) compounds
- Photosynthetic bacteria (green and purple bacteria, cyanobacteria), algae, green plants.
- Oxygen is mostly made by them, we wouldn’t have enough oxygen without them.
42
Photoheterotrophs
- Use light for energy and organic C source
- e.g. Green nonsulfur bacteria, purple nonsulfur bacteria
43
Anoxygenic photosynthesis
- The phototrophic process where light energy is captured and converted to ATP, without the production of oxygen
- Use sulfur compounds or hydrogen gas
44
Chemoautotrophs
- Use inorganic compounds as an energy source and carbon dioxide as primary C source.
- e.g. Inorganic energy sources – hydrogen sulfide, elemental sulfur, ammonia, nitrite, iron.
45
Chemoheterotrophs
- Energy and carbon sources often the same organic compound e.g. glucose.
- Can be considered saprophytes (lives off of nonliving tissue) or parasites
46
What is a Cytoplasmic membrane
The cytoplasmic membrane, also called the plasma membrane, is found in all cells and separates the interior of the cell from the outside environment.
The cell membrane consists of a lipid bilayer that is semipermeable.
- Composed primarily of phospholipids and proteins
Phospholipid bilayer (head is hydrophilic, tail is hydrophobic)
Peripheral and integral proteins
47
Cytoplasmic membrane function
- Its the semipermeable membrane that determines what goes in and out of the cell
- Site of energy conservation in the cell charged state: proton negative force.
- Movement of material across the membrane may be passive or active.
48
Passive processes
Energy is NOT required, as the substance moves along with the concentration gradient
From high to low
Doesn’t require energy because its takes advantage of an existing concentration gradient to save energy
49
Active processes
Molecules move against the concentration gradient and require chemical energy to move compounds
From low to high
Spends energy because it goes against a gradient. Some organisms live in environments that lacks nutrients, so it allows goes against the gradient
50
Simple diffusion
Net movement of molecules or ions from an area of high concentration to an area of low concentration until the point of equilibrium
51
Facilitated diffusion
Passive process that moves a substance to be transported by combining it with a transporter
52
Osmosis
Net movement of water from an area of low solute concentration to one of higher solute concentration across a semi-permeable membrane.
53
Osmotic pressure
Pressure required to stop the osmotic flow of water across the membrane
54
Transport protein
- A protein that serves the function of moving other materials within an organism against concentration gradient
- High degree of specificity- may react on with a single molecule or a specific class of molecules
55
Three classes of membrane-transporting systems
Simple transporters
Group translocation
ABC system
56
Simple transporters
Simple transport, also known as uniport, is a passive transport mechanism that allows the movement of molecules across the cell membrane along their concentration gradient.
* This type of transport does not require energy input from the cell and relies solely on the concentration difference of the transported molecule between the extracellular and intracellular environments.
57
Group translocation
- Exclusive to prokaryotic cells, such as bacteria and archaea.
- In this mechanism, a substance is chemically modified as it is transported into the cell.
- The modification occurs through the transfer of a chemical group, usually a phosphate group, from a high-energy molecule to the transported substance, altering the molecule's structure and preventing it from leaving the cell.
58
ABC Transporter
- ABC transport is a type of active transport found in both prokaryotic and eukaryotic cells.
- This mechanism involves ATP hydrolysis to provide the energy needed to transport substances across the cell membrane.
- ABC transporters are integral membrane proteins that utilize the energy from ATP hydrolysis to actively transport various molecules, including ions, sugars, amino acids, lipids, and peptides, across the cell membrane.
59
Uniporter
Protein that only transports one type of solute through the membrane
60
Symporter
Protein that transports two types of solute across the membrane
Because of one solute creating energy by going down its concentration gradient the symporter is able to use that energy to move the other solute against its concentration gradient.
61
Antiporter
Protein that transports one solute in one direction and second solute in the opposite direction
Its pushing both solutes against there concentration gradient
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Morphology
Cell wall determines bacteria shape
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Bacteria cell wall primary function
Prevent cell rupture
(To prevent cell rupture it has to have a little bit of flexibility)
64
What is the bacteria cell wall composed of?
Composed of murein (peptidoglycan): alternating units of N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM)
Bacteria have cell walls made up of polysaccharides that help with its strength and rigidity
65
Periplasm
The space between the inner and outer membrane in Gram-negative bacteria
66
Gram-negative outer membrane
- Composed of lipopolysaccharides (LPS), lipoproteins and phospholipids
- Assists in evading phagocytosis and destruction by complement activation
- Provides a barrier to some antibiotics digestive enzymes, detergents, heavy metals, bile salts and specific dyes
67
Outer membrane porins
- Proteins embedded in the outer membrane which serve as channels to allow passage of essential molecules such as nucleotides, disaccharides, peptides, amino acids, vitamins and Fe
68
Microbial atypical cell wall
Some cells have no walls or a very small amount of wall material
69
Mycoplasma
Smallest known bacteria that can reproduce outside host cells
70
Nucleoid
- DNA is located in the nucleoid
- Not enclosed by a membrane
71
Plasmids
- Small, circular double-stranded DNA molecules
- Often, the genes carried in plasmids provide bacteria with genetic advantages, such as antibiotic resistance
- Can be transferred between bacteria
72
Ribosomes
The site of protein synthesis in the cell
73
Inclusions
- Reserve deposits found in prokaryotic cells that hold nutrients
- Include metachromatic granules, polysaccharide granules, lipid inclusions, sulfur granules, carboxysomes, gas vacuoles, magnetosomes
74
Endospores
- Specialized resting cell produced by certain Gram-positive bacteria
- They form within the vegetative/mother cell (also called sporogenesis)
- Usually initiated by a lack of available nutrients or environmental stress.
- The DNA is replicated and stretched out to the length of the cell
- Which ever polar division has more DNA on it's side becomes the forespore when septation occurs
- The forespore is smaller than the mother cell, they both contain a chromosome
- The mother cell membrane then engulfs the forespore, The forswore is then encircled by two membranes
- The mother cells chromosome is then destroyed and a cortex of peptidoglycan is then placed in-between the two membrane layers
- Protein layers attach to the membrane and form a spore coat
- Once mature, vegetative/mother cell ruptures and dies, releasing the endospore.
- Water content within the endospore is significantly reduced and no metabolic reactions are carried out.
- Only vital cell components are retained – can remain dormant for several thousand years.
- They are environmentally tolerant to heat, low aw, toxic chemicals and radiation
75
Germination
When nutrients are available the cell triggers germination that wake the dormant cell
It dissolves the spore cortex and coat and returns the cell to its vegetative state
76
Characteristics of endospores
1. Not a means of reproduction
2. Resistant to adverse conditions: heating, freezing, desiccation, chemicals, radiation
3. Composition and activity different from vegetative cell
4. Little or no metabolic activity
5. Low water content
6. Large number of Ca++ ions
7. Contain dipicolinic acid
77
Glycocalyx
Coat external to the plasma membrane
Made up of polysaccharides (carbs) and polypeptide
Basically a cover for the membrane and protects the cell by acting as a barrier
Helps the immunity of the cell to infection
Helps with cell adhesion (cells sticking to each other)
Bacteria with glycocalyx can cause disease
78
Capsule
- A form of glycocalyx that is tightly associated with the cell wall
- Organized layer
79
Slime layer
- Type of glycocalyx that is loosely associated with the cell wall
- Unorganized thin layer
- Can be easily washed off
80
EPS – extracellular polysaccharide - exopolysaccharide
Provides support and protection from the harsh environment (its basically just another name for glycocalyx)
81
Microorganisms that are protected by glycocalyx
- Bacillus anthracis
- Streptococcus pneumoniae
- Klebsiella
- Streptococcus mutans
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Archaeal membranes
- Lipids contain ether linkages rather than ester linkages.
- Fatty acid side chains replaced by isoprene.
- Lipid monolayer structure rather than bilayer
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Aquaporin
Aquaporins facilitate water transport across the cytoplasmic membrane
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Extremophiles
An organism that is able to live in extreme environments
They are usually archaea
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Key dates in the history of microbiology
1665 – Robert Hooke: cell theory
1684 - Antoni van Leeuwenhoek: “wee animalcules”
1745 - John Needham: found microbes after heating fluids
1861- Louis Pasteur: downfall of spontaneous generation; microbes present in air; concept of sterility
*Importance of aseptic technique*
1876 - Robert Koch: proof that bacteria caused disease
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Bacillus
Rod like shape
87
Coccus
Spherical shape
88
Spiral
Corkscrew, curved shape
89
Eukaryotes
Fungi – unicellular forms include yeasts and molds.
Protozoa – unicellular, free-living (don’t need a host) or parasitic.
Algae – unicellular forms, photosynthetic eukaryotes.
90
Transmission E.M
Magnifies objects 10,000 to 100,000 times.
Requires sectioning and fixing of specimen
91
Scanning E.M
Scans specimen with electron beam and magnifies 1000 to 10,000X
92
Isotopic solution
Overall concentration of solutes equals that found inside the cell
93
Hypotonic
Solute concentration outside the cell is lower than inside the cell
94
Hypertonic
Molecules outside the cell has a higher solute concentration than compounds found inside the cell
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1665
Robert hooke, he created cell theory
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1684
Antoni van Leeuwenhoek: “wee animalcules”
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1745
John Needham: found microbes after heating fluids
98
1861
Louis Pasteur: downfall of spontaneous generation; microbes present in air; concept of sterility
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1876
Robert Koch: proof that bacteria caused disease
Life on Earth: Microbes - BI276
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