micro midterm Flashcards
What is Microbiology?
- Specialized area of biology that studies living things too small to be seen without magnification.
Microbiology
o Microbes
o Microorganisms
o Germs
o Bugs
Branches of Microbiology
- Bacteriology
- Mycology
- Protozoology
- Virology
- Parasitology
- Phycology or Algology
Bacteriology
the study of bacteria, a subdivision of microbiology involving:
- Identification
- Classification
- Characterization of bacterial species
Mycology
the branch of biology concerned with the study of fungi, including their:
- Genetic properties
- Biochemical properties
- Taxonomy (the practice and study of classification of things)
Protozoology
a branch of biology which studies a group of unicellular eukaryotic organisms.
Virology
the study of viruses, their:
- Structure
- Classification
- Evolution
- Ways to infect and exploit host cells for reproduction
- Interaction with host organism physiology and immunity
Parasitology
the study of parasites, their hosts, and the relationship between them.
Phycology or Algology
the study of algae
What Microbiology Studies
- Microbial Morphology
- Microbial Physiology
- Microbial Taxonomy
- Microbial Genetics, Molecular Biology
- Microbial Ecology
Microbial Morphology
refers to the size, shape, and arrangement of bacteria
Microbial Physiology
studies function of bacteria at the cellular and molecular levels
Microbial Taxonomy
- Classification
- Naming
- Identification of microorganism
Microbial Genetics, Molecular Biology
studies the function of genetic material and the biochemical reactions of cells involved in metabolism and growth.
Microbial Ecology
studies interrelationships between microbes and the environment, the roles of microorganisms in the nutrient cycles of soil, water and other natural communities.
Applied Microbiology
- Immunology
- Epidemiology
- Food Microbiology
- Agricultural Microbiology
- Industrial Microbiology
- Genetic Engineering
Immunology
studies of the body’s defense that protect against infection.
Epidemiology
studies how to monitor and control the spread of diseases in communities.
Agricultural Microbiology
studies the relationship between microbes and crops, with an emphasis on improving yield and combating plant diseases. Uses microbes which are NOT harmful to humans to kill pests (insect and plant diseases). This rather than pesticides, is a safer and healthier way to increase crop yield.
Industrial Microbiology
studies the use of microbes to produce or harvest large quantities of useful and necessary materials such as vitamins, amino acids, drugs, enzymes. Also for example, they can create bacteria, which will clean up an oil spill.
Genetic Engineering
studies techniques that deliberately alter the genetic makeup of organisms to induce new compounds, different genetic combinations, and even unique organisms.
Characteristics of Microorganisms
- Eukaryotic cells
- Prokaryotic cells
Eukaryotic Cells
- “eu” means “true” or “good” nucleus
- Nucleus present
- Number of chromosomes – more than one
- True membrane bound nucleus – present
- Organelles (endoplasmic reticulum, lysosomes, mitochondria, Golgi apparatus) – present
- Cytoskeleton – present
- Ribosomes – larger
- Cell size – larger
- Examples: plant, animal, fungal cells
Prokaryotic cells
- “pro” means “before” nucleus
- Nucleus absent
- Number of chromosomes – one, but not true chromosome (plasmids)
- True membrane bound nucleus – absent
- Organelles (endoplasmic reticulum, lysosomes, mitochondria, Golgi apparatus) – absent
- Cytoskeleton – may be absent
- Ribosomes – smaller
- Cell size – smaller
- Examples: bacteria
Microorganisms are specified by:
- small size
- Unicellular
- Simplicity
- High Growth Rate
- High Rate of Adaptability
- High Growth Rate
the growth rate of microorganisms is very high in a short time
- High Rate of Adaptability
it is what allows microbes to cause diseases in the humans. They can do their harm to us, but our bodies cannot harm them because they are more adaptable that we are. Viruses have higher adaptability than bacteria.
Simple Microscope
Contains just a single lens and a few working parts.
Compound Microscope
- 2 magnifying lens
- Visible light
- A condenser (a special lens to converge or focus the rays of light to a single point on the object, it does NOT account for magnification).
A microscope should provide adequate:
Magnification
Resolution
clarity of image
- Magnification
capacity of an optical system to enlarge small objects
o Make object bigger
o Defines as the ability of a microscope to enlarge an object
- Resolution
the capacity of optical system to distinguish or separate to adjacent objects or points from each other
o Distinguishing magnified object clearly
o Defines as the ability of a microscope to distinguish two adjacent points
- Clarity of an image
smallest distance between two dots
Objective Lens
- 4x low dry objective lens
- 10x dry objective lens
- 40x high dry objective lens
- 100x oil immersion objective lens
Ocular Lens:
- 10x – 20x
Total magnification
ocular lens x objective lens
- Light Microscopes
(the highest magnification is 2,000x and the resolution on them is 200 nm) Light Field Dark Field Phase-contrast Differential- Interference
a. Bright-field light microscope
the best scope to see DEAD bacteria fixed on a slide
b. Dark-field microscope
good for looking at the living bacteria
c. Phase-contrast microscope
good for looking at living microbes
d. Differential interference microscope
good for looking at 3D, color, living microbes
- Ultra violet microscopes
use ultraviolet rays as source of illumination
a. Fluorescent microscope has magnification 2,000x and resolution 0.2 micrometers
- Electron Microscope
electron beam forms image of specimen.
- Transmssion
- Scanning Electron
a. Transmission electron microscope
magnification is about 1,000,000x and resolution is 0.5 nm (good for viewing viruses)
b. Scanning electron microscope
magnification is about 100,000x and resolution is 10 nm
- Prokaryotic cells
bacteria
- Eukaryotic cells:
o Fungi o Algae o Protozoans o Helminth worms o Animal cells o Plant cells
Bacteria Prokaryotic Cells
- Eubacteria: (more common bacteria):
2. Archaebacteria (less common):
- Eubacteria
a. Eubacteria (-) with cell wall
b. Eubacteria (+) with cell wall
c. Eubacteria with no cell wall (+ and -)
- Archaebacteria
a. Live in extreme environments (high temperature, high salt, or low pH)
b. Cannot grow in the human body, do not cause human pathology
Prokaryotic Cells (structure)
- Appendages
- Cell Envelopes
- Protoplasm
- Appendages:
a. Flagella
b. Axial filaments/endoflagella
c. Pili
d. Fimbriae
- Cell envelopes:
a. Glycocalyx (capsules, slime layers)
b. Cell wall
c. Cell membrane
- Protoplasm:
a. Cell pool
b. Ribosomes
c. Mesosomes
d. Granules
e. Nucleoid, aka. Chromatin bodies
Appendages
- Those that provide motility: o Flagella o Axial filaments - Those that provide attachments: o Fimbriae o Pilli
Function of Flagella
o The primary role of the flagellum is locomotion (self-propulsion, smooth, forward movement)
o It also often has function as a sensory, being sensitive to chemicals and temperatures outside the cell
o Flagella is found mostly in Gram-negative bacteria, but in Gram-positive bacteria it can be found too.
Structure of Flagella
o Flagella is made of protein
o Flagella is composed of three distinct parts:
The filament (out of the bacteria)
The hook (attached to the bacteria)
The basal body (inside the bacteria)
o The basal body has two (Gram-positive) or four (Gram-negative) rings.
The rings rotate counter-clockwise, and the bacteria rotate clockwise
Types of Flagella
o Monotrichous
o Lophotrichous
o Amphitrichous
o Peritrichous
o Monotrichous
bacteria have a single flagellum, e.g. Vibrio cholerae
o Lophotrichous
bacteria have multiple flagella, located at the same spot on the bacteria surface
o Amphitrichous
bacteria have single flagellum on each of two opposite ends
o Peritrichous
bacteria have flagella projecting in all directions, e.g. E. coli
Axial Filaments
o Axial filament is the central often contractile filament of flagellum (a.k.a. endoflagellum)
o A type of modified flagellum that consists of a long, thin microfibril inserted into a hook
o Axial filaments are similar to flagella, except that they wrap around the cell.
o The microfibrils of the axial filament lies between the cell wall and the cell membrane
o These structures contract causing the slow jerky movements of the microfibrils
o Axial filaments are found mostly in Gram negative rod bacteria (e.g. spirochetes)
Appendages of Attachment
- Pili and Fimbriae are made of protein; involved in attachment of acteria to the host cells.
o Pili
refer to the long appendages, (e.g. E. coli)
- The primary function of pili are to attach a bacterial cell to specific surfaces or to other cells
- Pili can also aid in attachment between bacterial cells. Some bacteria are able to produce conjugation pili that allow for the transfer of DNA from one bacterial cell to another
o Fimbriae
refer to short appendages, (e.g. Streptococci)
- A bacterium that has fimbriae is usually covered with short hair-life fibers
- In contrast, pili are much longer, and a cell usually only has one or two pili.
- Pathogenic bacteria can have adhesions on the fimbriae that allow them to attach to the target tissues of their host.
Glycocalyx
bacterial surface coating, has a delicate :sugar coating:, composed of polysaccharides bound in various ways to proteins
- Not each bacteria has a glycocalyx, because it is not necessary for its survival
- Two types of glycocalyx:
- Slime Layer
2. Capsules
- Slime layer
prevents bacteria from phagocytosis, protects bacteria from loss of water and nutrients. Its loose shield can be washed off.
- Capsules
tightly bounded to cell wall and prevent bacteria from phagocytosis. It has thicker, gummy consistency and cannot be easily washed off.
Cell Wall
the layer underneath the glycocalyx. It:
o Defines the shape of bacteria
o Protects bacteria (e.g. osmotic pressure)
- Cell wall is composed of
peptidoglycan
o Peptidoglycan is
a substance that provides the relatively rigid protective quality of the cell wall
o The amount of peptidoglycan varies among the general groups of bacteria
- Gram positive cell wall:
o Thick sheet composed of numerous sheets of peptidoglycan (100-150 layers) and tightly bound acidic polysaccharides
- Gram negative cell wall:
o Contains an outer membrane lipopolysaccharides (40-50 layers)
o A thin sheet of peptidoglycan (3-5 layers)
o An extensive space between outer membrane and peptidoglycan, and peptidoglycan and cell membrane
Gram Staining
- It is a stain for bacteria with cell wall.
primary stain
Crystal Violet
Mordant (fixing agent)
Iodine
Washing Solution (decolorizer)
Alcohol
Secondary Stain (counterstain)
Safranin
Gram +
PURPLE
Gram –
RED
Acid fast staining
- The acid fast stain is a technique that differentiates Mycobacterium species from other bacteria
- The cell walls of the mycobacteria contain mycolic acids giving the cell walls a high lipid content. These bacteria are difficult to Gram stain.
- Acid fast positive
RED
- Acid fast negative
PURPLE
Cell Membrane
(a. k.a. cytoplasmic membrane, plasma membrane) is very thin flexible sheet molded completely around the cytoplasm
- Made of phospholipids and proteins (fluid mosaic model)
- Responsible for flexibility, permeability and transport (of nutrients, water etc.)
- Site of metabolic activity (biosynthesis and degradation)
- Energy reactions
- Synthesis (macromolecules, lipid, nucleic acid)
Protoplasm
the internal content of the cell, and represents a dense, gelatinous solution inside the bacterial envelope.
- Contents of cell protoplasm
o Cytoplasm (a.k.a. cell “pool”) – is the major component of the cell. Composed of water, sugar, amino acids, salts o Chromatin body (bacteria chromosome) – bacteria do not have a true nucleus and their DNA is not enclosed by a nuclear membrane. DNA is aggregated in a central area of the cell called the NUCLEOID.
- Plasmids
are nonessential pieces of DNA which confers protective traits upon bacteria (extrachromosomal DNA), are capable of replication, and may be transferred to another cell, with confers a resistance to antibiotic treatment.
- Ribosomes
tiny special type of RNA which synthesize proteins
- Mesosomes
are areas of the cell membrane which fold up into the cytoplasm and increase the internal surface for membrane function. Additionally, it functions in DNA replication, cell division, secretion
- Granules
storage of energy rich bodies
Two types of granules:
o Membrane-bound granules
o Non-Membrane-bound granules
o Membrane-bound granules
for storage of organic compounds (such as glycogen or starch)
o Non-Membrane-bound granules
for storage of inorganic compounds (such as iron or other metals, sulfur and iodine)
Bacterial Morphology
o Shape
o Size
o Arrangement
o Specific structure of bacteria
Bacterial Shape
- coccus
- baccilus/rod
- spirillum
- spirochete
- vibrio
- Coccus
any microorganism (usually bacteria) whose overall shape is spherical or nearly spherical
- Baccilus or Rod
o Short rod called Coccobacillus (e.g. Serratia marcesecens)
o Long rod called Spirochete or Spirillum (e.g. Treponema pallidum)
- Spirillum
is a thick, rigid spiral
- Spirochete
is a thin, flexible spiral
- Vibrio
is a curved or comma-shaped rod
Bacterial Size
- Cocci – 0.5 to 3 micrometer
- Bacilli – 0.2 to 2 micrometer in diameter and 0.5 to 20 micrometer in length
o Short bacilli – 0.2 to 2 micrometer
o Long bacilli – 0.5 to 50 micrometer
- Cocci could be:
o Single o Paired (diplococcus) o Tetrad o Cluster o Chain
- Bacillus could be
o Single
o Paired
o Chain
o Palisades
- An endospore
dormant, highly resistant part of cell to preserve the cell’s genetic material in times of extreme stress.
- The endospore consists of the bacterium’s
DNA, ribosomes and large amounts of calcium dipicolinate
- Calcium dipicolinate is
a spore-specific chemical that appears to help in the ability for endospores to maintain dormancy (removes water)
- Endospore is unique cellular structure.
o The outer coat surrounding the spore provides much of the chemical and enzymatic resistance.
o Next layer is cortex, it is a very thick layer of specialized peptidoglycan. It is needed for dehydration of the spore core, which aids in resistance to high temperature.
- A germ cell wall resides under the
cortex (peptidoglycan).
- The inner plasma membrane,
under the germ cell wall, is a major permeability barrier against several potentially damaging chemicals.
- The center of the endospore, the core, exists in a very dehydrated state and houses the cells:
o DNA
o Ribosomes
o Large amounts of calcium dipicolinate
- Endospores can be formed in
Gram positive bacilli only (Bacillus and Clostridium)
- The types of position of endospore are:
o Terminal (e.g. Clostridium tetani) o Central (e.g. Bacillus cereus) o Subterminal (e.g. Bacillus Subtilis)
- Terminal endospores are seen
at the poles of cells
- Central endospores
more or less in the middle
- Subterminal endospores
those between these two extremes, not to be considered either terminal or central
- Lateral endospores are seen
occasionally
- Prokaryotic cells reproduce by:
o Binary fission (a.k.a. transverse fission)
o Budding
- Bacteria are prokaryotic organisms that reproduce
asexually , most commonly by binary fission
- In binary fission
the chromosomes duplicate and the cytoplasm splits into equal halves, i.e. binary fission results in the formation of two bacterial cells that are genetically identical
Budding
– is a process in which a small protuberance develops at one end of the cell
o The protuberance enlarges and eventually develops into a new cell that separates from the parent cell
- Bacterial growth in non-visible size
bacteria are so small that its growth in size cannot be measured
- Bacteria Growth is in the number
bacterial growth is measured by how many there are in the population, not how big each individual is
Generation
is doubling process when the population increases by a factor of 2. o 1 cell – 0 generations o 2 cells – 1st generation o 4 cells – 2nd generation o 8 cells – 3rd generation etc.
- Generation time or Doubling time
is the time required for a complete fission cycle from parent cell to two daughter cells
- Each bacteria has its specific doubling time.
o Staphylococcus – 30 minutes
o Streptococcus – 20 minutes
o E. coli – 17 minutes
- Bacterial growth needs
some nutrients, specific temperature, pH, moisture
- The most common component of the Petri plate
AGAR
- Agar is a
complex polysaccharide, and it cannot be digested by bacteria. In room temperature it is solid.
Growth Curve
- Lag phase
- Exponential (log) growth phase
- The stationary phase
- Death phase
- Lag phase
– duration about 5 hours.
o Cells are not yet multiplying to maximum rate (amount of bacteria is constant)
o Bacteria are increasing their size to get read to divide
o It is also now as latent time
- Exponential (log) growth phase
phase – duration about 5-16 hours.
o Growth phase depends on proper pH, temperature and moisture
o This phase will continue as long as cells have adequate nutrients and environmental favorability
o Cells are dividing rapidly
o Patient begins to feel uncomfortable and the first clinical manifestations occur
- The stationary phase
– duration about 16-33 hours.
o Caused by less optimal conditions, the nutrients are limited
o Due to a decrease of nutrients the half of bacteria will eat and divide, and the other half will starve and die (the population of bacteria relatively constant)
o This is marked by declining of bacterial growth rate and an increase of their death rate
o Patient demonstrates an overt clinical manifestations of infection
- Death phase
o The nutrients are depleted to the point where none of bacteria has food, and they all begin to die
o Rapid death occurs depending on the resistance of species
o This phase is slower than the exponential phase
o Patient starts to feel better
Control of microbial growth”:
inhibits or prevents growth of microorganisms in two basic ways:
o By killing microorganisms (Microbiocidal agents)
o By inhibiting the growth of microorganisms (Microbiostatic agents)
Sterilization
- Is the complete elimination of all microbiological organisms to achieve aseptic, a sterile microbial environment. There are no degrees of sterilization: an object or substance is either sterile or not. o Heat o Radiation o Chemicals o Physical removal of cells
- Heat – is the most important and widely used. It depends on:
The type of heat
Time of application and temperature most importantly, to ensure destruction of microorganisms
o Types of heat:
Incineration
boiling
Incineration
burns organisms and physically destroys them. Used for needles.
Boiling
100°C for 30 minutes. Kills everything except some endospores.
• Killing of endospores requires very long boiling (>6 hours)
- Autoclaving
using steam under pressure as the sterilizing agent
– the most effective and most efficient means of sterilization
o Higher temperatures ensure more rapid killing.
o The usual standard temperature/pressure employed is 121°C/15 psi (pound per square inch) for 15 minutes.
o Moist heat is thought to kill microorganisms by causing denaturation of essential proteins
- Dry heat oven – is basically the cooking oven
o The dry heat is not as effective as moist heat (i.e., higher temperatures are needed for longer periods of time)
For example: 160°C/2 hours or 170°C/1 hour is necessary for sterilization
o The dry heat oven is used for glassware, metal, and objects that won’t melt.
- Irradiation:
usually destroys or distorts nucleic acids.
- UV Light
- x-rays, gamma radiation
- Electron beam radiation
o Ultraviolet light (commonly)
inhibiting DNA replication
o X-rays, gamma radiation highly
highly effective in killing microorganisms, break chemical bonds by interacting with the electrons of atomic constituents
o Electron beam radiation
alters various chemical and molecular bonds on contact
In living cells, these disruptions result in damage to the DNA and other cellular structures at the molecular level, cause the death of the organism or incapable of reproduction.
- Filtration
involves the physical removal of all cells in a liquid or gas
-important for sterilization of solutions which would be denatured by heat (e.g. antibiotics, injectable drugs, amino acids, vitamins, etc.) o Chemical and gas: Ethylene oxide Formaldehyde Ozone Hydrogen peroxide
Control of Microbial Growth by Non Sterilizing Methods
- Heat
- Pasteurization
- low temp
- drying
- irradiation
Non ster.
- Heat:
o Boiling 100° for 30 minutes – kills everything except some endospores, it also inactivates viruses.
For the purposes of purifying drinking water:
• 100°C for five minutes is a “standard”
- Pasteurization
the use of mild heat to reduce the number of microorganisms in a product or food
o For pasteurization of milk two methods are used;
Batch method: 63°C/30 minutes
Flash method: 71°C/15 seconds
- Low temperature:
store perishable foods at low temperatures (4°C or less):
o To slow down the rate of bacterial growth
o To prevent production of toxins by bacteria
- Drying
(removal of H2O): methods involve: o Removal of water from product by heat o Evaporation o Freeze-drying o Addition of salt or sugar
Non-steril.
- Irradiation
(microwave, UV, x-ray): destroys microorganisms as described under “sterilization”
Antimicrobial agents are chemicals that:
- Kill microorganisms (Microbiocidals) or
- Inhibit the growth of microorganisms (Microbiostatics)
- Antiseptics
microbiocidal agents, which are applied to living tissue and help reduce infection.
- They harmless enough to be applied to the skin and mucous membrane
- Disinfectants
antimicrobial agents that are applied to non-living objects to destroy microorganisms that are living on the objects
- Disinfection does not necessarily kill all bacteria, especially resistant bacterial spores, and some viruses. Examples:
o Alcohols
o Aldehydes (e.g. formaldehyde)
o Oxidizing agents (e.g. chlorine)
- Antibiotics
antimicrobial agents produced by microorganisms that kill or inhibit other microorganisms. Examples:
- Penicillin (cell wall)
- Cephalosporin (cell wall)
- Polymyxin (cell membrane)
- Erythromycin (protein synthesis)
- Rifamycins (nucleic acid)
Metabolism
- Anabolism or biosynthesis:
2. Catabolism or biodegradation
- Anabolism or biosynthesis
Any process that results in the synthesis of cells molecules or structures – forming larger molecule from smaller molecules. Usually this process takes energy.
a. DNA
b. RNA
c. proteins
- Catabolism or biodegradation:
breaking down of large molecules and producing energy.
a. For biosynthesis
b. Cell movement
c. transport of nutrients
- Enzyme
large biological molecules responsible for the thousands of metabolic processes that sustain life
Enzymes characterized by
o Facilitate reaction by lowering energy of activation
o Each enzyme acts specifically upon its substrate
o Enzymes speed up the rate of metabolic activity
Three types of metabolism:
- Fermentation
- Respiration
- Photosynthesis
Fermentation
The incomplete oxidation of glucose or other carbohydrates in the absence of oxygen (fermentative organisms are anaerobic)
- For fermentation some bacteria obtain metabolic energy by a
Substrate-level Phosphorylation
- Substrate-level phosphorylation is
a type of metabolic reaction that results in the formation of adenosine triphosphate (ATP) or guanosine triphosphate (GTP)
Respiration
- The set of the metabolic reactions and processes that take place in the cells of organisms to convert biochemical energy from nutrients into adenosine triphosphate (ATP) by oxidative phosphorylation
- Almost all aerobic organisms carry out oxidative phosphorylation for production of energy
Photosynthesis
- A process used by plants and other organisms to convert light energy, normally from the sun, into chemical energy that can be later released to fuel the organisms’ activities
- Photosynthesis: Metabolic energy obtained by Cyclic Phosphorylation (similar to respiration except that photochemical processes uses energy of light)
Genetics
- The study of genes, heredity, and variation in living organisms
o Organism
o Cellular
o Chromosome with genes
o Molecular
- Organismal
genetics observes the transmission and expression of genetic factors in the whole organism or cell
- Chromosomal
genetics examines the characteristics and actions of chromosomes
- Molecular
genetics deals with the biochemistry of gene function
