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Exam 1: Ch.3 Basic Concepts of Microbiology Ch.4 Bacterial Structure Ch.5 Bacterial Growth and Nutrition

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What are some of the similarities between eukaryotes and prokaryotes?

-Biochemical Reactions- used for growth and energy conversions
-Response to Stimuli
-Reproduce to produce offspring
-Adapt from one generation to the next
-Interact w/ other organisms in environment


Why is homeostasis important?

It maintains a stable internal environment.


What are biofilms?

They interact through a multicellular association.


_____ is a chemical communication and cooperation between cells.

Quorum sensing


What organizational patterns do eukaryotic and bacterial cells share?

Genetic organization with DNA in chromosomes, compartmentation with cell membranes, metabolic organization in the cytoplasm, protein synthesis at ribosomes


Similar organizational patterns: Cell Theory

The cell is the fundamental unit of life.


Similar organizational patterns: Hereditary

Information is organized in chromosomes.


Similar organizational patterns: Cytoplasm

Cytoplasm is surrounded by a cell membrane which selectively allows substances in or out of the cell.


Similar organizational patterns: Metabolism

The chemical reactions that occur in the cell.


Similar organizational patterns: Protein synthesis

Occurs at the ribosome.


Structural Differences: Membrane bound organelles Eukaryotes have membrane-enclosed organelles

Eukaryotes have membrane-enclosed organelles. Some bacteria have micro compartments surrounded by protein.


Structural Differences: Protein/Lipid Transport

Eukaryotes: Endoplasmic reticulum and Golgi apparatus
Prokaryotes: Cytoplasm


Structural Difference: Mitochondria

Eukaryotes: mitochondria perform cellular respiration in eukaryotes, while prokaryotes use the cytoplasm and cell membrane.
*ETS* is performed in the cell membrane (in proks) and everything else is in the cytoplasm.


Structural Difference: Photosynthesis

Both eukaryotes and prokaryotes can perform photosynthesis.


Structural Difference: Cytoskeleton

The eukaryotic cytoskeleton gives the cell structure and transports materials within the cell. **What happens in the prokaryotic?**


Structural Similarity: Flagella

Both eukaryotes and prokaryotes use flagella for motility, though the flagella differ structurally and functionally in the two groups.
Proks=Bacterial flagella
Euks=Eukaryotic flagella or cilia


Structural Similarity: Cell wall

Many prokaryotes and eukaryotes have a cell wall to help maintain water balance by osmosis.


Comparing: Genetic Organization

Prokaryotic: Circular DNA chromosomes
Eukaryotic: Linear DNA chromosomes


Comparing: Cell Compartmentation

Prok's and Euk's= cell membrane


Comparing: Metabolic organization

Prok's and Euk's= Cytoplasm


Comparing: Protein Synthesis

Prok's and Euk's= Ribosomes


Comparing: Protein/Lipid Transport

Prok's= Cytoplasm
Euk's=Endomembrane System


Comparing: Energy Metabolism

Prok's= Cell membrane
Euk's= Mitochondria and chloroplasts


Comparing: Cell structure and transport

Prok's= Thin protein filaments in cytoplasm
Euk's=Protein tubules and filaments in cytoplasm


Comparing: Water Balance

Prok's and Euk's= cell wall


_______ us the science of classification, arranging related organisms into categories.



Classification uses a hierarchal system. What is it?

Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species
Dr. King Philip Can Order Family Good Stuff


_____ gives scientific names to organisms.



In the mid-1700's, who published Systema Naturae, establishing a uniform system for naming organisms?

Carolus Linnaeus


Each scientific name includes two words, the ____ and the ____ ____ that together make up the _____ name.

genus (capital); specific epithet (lower case); species (italics, or underlined)


Trying to make sense of taxonomic relationships

Kingdoms and domains


In 1886, who coined the term "protists" for all microorganisms.

Ernst H. Haeckel


In 1959, who developed the five kingdom system, giving bacteria their own kingdom? Name the five kingdoms.

Robert H. Whittaker: Plantae, Animalia, Protista, Fungi, Bacteria


The three domain system was proposed by ____ ____, based on data from ____ ____ ___. What are the three domains?

Carl Woese; ribosomal RNA sequences.
Three domains include: bacteria, eukarya, and archaea

The three-domain system places the prokaryotes in separate lineages.


Most microbial agents are in the micrometer size range. What is the length of most bacterial and archaeal cells?

1-5 micrometers (um)


Light Microscopy-what is it used for, how many lenses does it have, and what are they?

is used to observe most microorganisms.
-Visible light passes through multiple lenses and through the specimen.
-Light microscopes usually have at least 3 lenses: low power, high power, and oil-immersion
-The lens system must have high resolving power to see the specimen clearly.
*only under oil can you see bacteria clearly but you have to stain them as well.


What is the simple stain technique?

It involves flooding a prepared specimen with basic dye to provide contrast.


Describe the Gram stain technique. (Differential Stain)

Cells are stained with crystal violet and Gram's iodine solution and washed with a decolorizer.
-Safranin is applied as a counter stain.
-Gram-positive bacteria retain the crystal violet, whereas gram-negative bacteria do not (turn orange-red).


Describe Acid-fast technique. (Differential Stain)

Mycobacteria can be stained with carbol-fuchsin in acid-fast technique. The cells turn red. Example: TB.


What are the 3 criteria used to classify organisms into 5 kingdoms?

1. The type of cell: (only 2 types Prokaryotic and Eukaryotic cell)
2. Number of cells: (unicellular- kingdom protista- unicellular eukaryotes) and multicellular-everything else.
3. Type of nutrition: Autotrophic nutrition (photosynthesis=kingdom Plantae) everything else is a heterotroph (other feeders) these fall into two categories: ingestive (kingdom Animalia) and absorptive (kingdom Fungi)


Describe Endospore Stain.

used to confirm: Clostridium bacillus if it's present then it turns aqua/green color if it's absent then it turns pink (all vegetative cells).


Describe morphology, arrangement, and gram: Staphylococcus aureus

Gram +, coccus, staphylococcus (grape like), yellow


Describe morphology, arrangement, and gram: Bacillus subtilis

Gram +, bacillus, streptobacillus


Describe morphology, arrangement, and gram: Clostridium sporogenes

Gram +, bacillus, single, *forms endospores


Describe morphology, arrangement, and gram: Rhodospirillum rubrum

Gram -, spirillum, single, red


Describe morphology, arrangement, and gram: Neisseria sicca

Gram -, coccus, diplococcus


Describe morphology, arrangement, and gram: Streptococcus faecalis

Gram +, coccus, streptococcus


Describe morphology, arrangement, and gram: Corynebacterium xerosis

Gram +, bacillus, palisade arrangement


Describe morphology, arrangement, and gram: Serratia mars

Gram -, bacillus, single


Describe morphology, arrangement, and gram: Enterobacter aerogenes

Gram -, bacillus, single


Describe morphology, arrangement, and gram: Proteus vulgaris

Gram -, bacillus, single


Describe morphology, arrangement, and gram: Mycobacterium smegmatis

Gram +, bacillus, (irregular rod, acid-fast, single)


Describe morphology, arrangement, and gram: Micrococcus luteus

Gram +, coccus, tetrad & sercanae


Describe morphology, arrangement, and gram: Escherichia coli

Gram -, bacillus, single


Phylum-Kingdom Fungi
(The study of Fungi is called mycology)

classified by how they sexually reproduce (produce spores)
1. Zygomycota-sexually reproduce using zygospores
2. Ascomycota- sexually reproduce using ascospores
3. Basidiomycota-sexually reproduce using basidiospores
4. Deuteromycote-mitosporic (no known spores)


Phylum-Kingdom Protista (Protozoans)
(Animal like protists are called Protozoans)

classified by how they move (locomotions) to get their food
1. Mastigophorans-use flagella (whip like motions)
2. Sarcodinia-Pseudopods-false feet, ameba,
3. Ciliphorans- use cilia
4. Apicomplexans- Vectors, use an insect to move


Phylum-Kingdom Animalia (worms=helminths)

classified by morphology
1. Nematoda-roundworms
2. Platyhelminth-flatworms
-Class cestoda-tape worms
-Class trematoda-flukes
3. Annelida- leeches and earth worms, segmented


Kingdom Fungi Molds

Zygomycota-zygospores-Rhizopus nigrocans-not a pathogen, has fibers, black bread cotton white mold.

Basidiomycota-basidiospores-mushrooms-not a pathogen

Ascomycota-ascospores-Penicillium notatum (blue-green mold), Aspergillus niger (black mold *pathogen)

Candida albicans-mold in humans, yeast infection if too much

Saccharyces cervisine-brewer's yeast


Kingdom Protista Sickness Examples

1. Mastigophorans- Trypanosoma- African sleeping sickness, American tryponosomiasis
2. Ciliophorans- Balantidium coli- dysentery (excessive diarrhea)
3. Sarcodinia-Entamoeba histolytica- Amebic dysentery
4. Apicomplexa- Plasmodium vivax- Malaria


***Chapter 4 Starts Here***
The domain _____ contains some of the most studied prokaryotes.



Define Spirochaetes

live in the mouth and some are STD's like Treponema pallidum that causes syphylis


The domain Archaea contains organisms with diverse physiologies. Name them.

Euryarchaeota contain:
-Methanogens-live in anoxic environments
-Extreme halophiles-salt-lovers
-Thermoacidophiles-grow at high temperatures with low pH


Prokaryotes can be distinguished by their cell _____ and ______.

Morphology (shape) and arrangement


A rod shape is called _____. What arrangements does it come in?

Bacillus: single, diplobacillus, streptobacillus


A spherical shape is called _____. What arrangements does it come in?

Coccus; single, diplococcus, streptococcus, staphylococcus


Spiral-shaped bacteria can appear as ______, ____, or _____

Vibrios (comma-shaped), spirilla (helical), or spirochete


Cell structure organizes cell function. Name some functions.

-sensing/responding to the surrounding environment.
-compartmentation of metabolism
-growth and reproduction


External structure: Pili, Conjugation Pili

Pili are protein fibers extending from the surface of many bacteria that are used for attachment.
-Adhesins attach cells to surfaces
-Form biofilms and microcolonies
Some bacterial species have conjugation pili, used to transfer genetic material between cells. (f-plasmid; sex pili)


Prokaryotic ____ are long appendages extending from the cell surface.

Flagella; can be used for motility


Bacteria exhibit chemotaxis. What does this mean?

When bacteria move up the concentration gradient of a chemical attractant.
-Some prokaryotes move without flagella by gliding across a solid surface.


Spirochetes contain _____, which move the cell through torsion exerted on the cell by endoflagellar rotation.

example: Treponema pallidum (causes syphilis)


All bacteria have an outer mucus layer external to the cell wall called ______. If this layer is thin it is called a ____. If it is thick it is called a _____.

Glycocalyx- adhering layer of polysaccharides (and sometimes small proteins) - It protects the cells from the environment and allows them to attach to surfaces
Thin layer- Slime layer
Thick layer- Capsule - Extreme velent; can cause extreme illness (hard for wbc phagocytosis to occur; too slimy and thick) Causes disease like Klebsiella pneumoniae (#1 cause nosocomial hospital death for elderly; acquired pneumonia)


Most bacterial and archaeal cells have a cell envelope. Give some characteristics of the cell wall.

-counter rigidity, not flexible, tough and protective external shell
-maintains cell shape and water balance


Gram + have what kind of cell wall?

Thick peptidoglycan cell walls containing teichoic acid. (amino acid and glucose derivatives) only polysaccharide back bone, NAG NAM-long rod of sugars, Amino acids are the chains attached to the polysaccharide.

*Plants & Algae- cellulose-complex


Gram - have what kind of cell wall?

Have 2D peptidoglycan layer and no teichoic acid. Has an outer membrane, separated from the cell membrane by the periplasmic space.
-The outer membrane contains proteins called porins that selectively allow small molecules into the periplasmic space.
-Lipid A-Endotoxin?
-Much more difficult to deal with medically.


The archaeal cell wall also provides mechanical strength. What kind of cell wall does it have?

No archae have peptidoglycan in the cell wall, but some have pseudopeptidoglycan. Others have polysaccharides, proteins, or both.

-The s-layer is the most common archaeal cell wall, consisting of protein or glycoprotein in a crystal lattice.


The __ _____ represents the interfere between the cell environment and the cell cytoplasm.

Primary function of cell membrane is transport. **
-fluid thin layer of phospholipid and protein (the fluid mosaic model)
-The phospholipid molecules are arranged in a bilayer
-Hydrophobic fatty acid chains in the phospholipids form a permeability barrier.


What may disrupt or dissolve the bilayer?

Antimicrobial substances


What kind of functions can membrane proteins perform or aid in?

cell wall synthesis
energy metabolism
dna replication
sensation of stimuli
molecule transport- passive (facilitated diffusion) active (active transport) using ATP

*Prokaryotes have a lot more function (than Euks) because they have no intercellular membrane.


The archaeal cell membrane differs from bacterial and eukaryal membranes. How?

-Hydrophobic lipid tails are attached to glycerol differently in Archaea.
-Fatty acids are usually absent
-Adjacent lipid tails are bound together forming a lipid monolayer, instead of a bilayer.
-None of them are medically important.


What is a nucleiod?

It represents a subcompartment containing the chromosomes.
-This is the region that gets stained.


Describe a bacterial chromosome.

The chromosome is usually a closed loop of DNA and protein.
The DNA contains the genes.


What is a compete set of genes called?



Most cells have only one copy of each gene (one chromosome). What are they called?



Plasmids are found in many bacterial and archaeal cells. What are they?

Small circular molecules of DNA (smaller than the chromosome)
-Each plasmid is a closed loop, containing 5-10 genes
-extrachromosomal DNA


What can plasmids be used for?

They can be transferred between cells and be used as vectors in genetic engineering.

Plasmids provide genetic flexibility, for example, R plasmids carry genes for resistance to antibiotics.


What are the two types of plasmids?

R plasmids-antibiotic resistance
F plasmids- fertility (conjugation pilli)


What are the only type of bacteria that don't have a cell wall?



What are three spirochete examples? and What do they cause?

Treponema pallidum- syphilis
Borrelia burgdarfeni- lyme disease
Borrelia recurimentas- relapsing fever


Other sub compartments exist in the cell cytoplasm such as ribosomes, what are they used for?

Protein synthesis, same function just different structure than Eukaryotic cells, not membrane bound in proks but are membrane bound in euks


What do inclusion bodies do?

Store nutrients or build blocks for cellular structures.


Some aquatic bacteria use __ _____ to float on the water's surface.

gas vesicles


What do magnetosomes contain?

Contain crystals of magnetite or greigite, allowing cells to respond to magnetic fields.


What do cytoskeletal proteins regulate?

cell division and help determine cell shape.
-Prokaryotes contain a homolog of eukaryotic tubulin--it forms filaments similar to those found in microtubules


**Chapter 5 Starts Here**
What is binary fission?

It is part of the cell cycle.
-Very quick cell division, shorter doubling time quicker incubation period.
-Acid fast micro bacterium grows very slowly symptoms appear 3,6,9 months.


What happens during the B period?

Cell increases in mass and size


What happens during the C period?

DNA replicates and the two strands separate


What happens during the D period?

Synthesis of a septum forms two identical cells.


Bacterial and archaeal cells reproduce ______.



What is the generation (or doubling) time?

The interval of time between successive binary fission.


In pathogens, a ___ doubling time means a _____ incubation period of disease.

shorter, shorter


Microbial Growth Progress: Lag Phase

No cell division occurs while bacteria adapt to their new environment


Microbial Growth Progress: Logarithmic (log) phase

When exponential growth of the population occurs, human disease symptoms usually develop.


Microbial Growth Progress: Stationary phase

When reproductive and death rates equalize


Microbial Growth Progress: Decline (exponential death) Phase

When the accumulation of waste products and scarcity of resources causes the population to die.


What is dormancy?

A response to potential or actual environmental change. Non dividing state.


What are the two dormancy strategies?

Persister Cell Formation
Endospore Formation


Persister Cells

They stop dividing but maintain a low rate of metabolism under stress.


What do Endospores respond to?

Nutrient limitation *** important
-Endospores are a highly resistant structure formed by species of Bacillus and Clostridium when nutrient supplies are low.
-Endospores are resistant to desiccation and heat.


What happens to endospores when environmental conditions are favorable again?

The protective layers break down and the spore germinates into a vegetative cell. (veg cells stain pink in endospore staining, but the spores will stain aqua/green)


What are some physical factors that optimal prokaryotic growth is dependent on?

Temperature, Oxygen, pH level, Hydrostatic and Osmotic Pressure


Temperature: Psychrophiles

Grow optimally at 0-20*C and make up the largest portion of all prokaryotes on Earth.


Temperature: Mesophiles

Live at medium temp. range 20-40*C; includes pathogens in humans.


Temperature: Thermophiles

Live best around 40-80*C; in compost heaps and hot springs.


Temperature: Hyperthermophiles

Are archaea that grow optimally above 80*C, found in seafloor hot-water vents


Oxygen: obligate aerobes

Many prokaryotes are obligate aerobes, which require oxygen to grow.


Oxygen: Microaerophiles

Live in low oxygen environments.


What is thioglycollate broth used for?

Used to test an organism's oxygen sensitivity.
-In lab we use it to grow Clostridium


Oxygen: Anaerobes

Do not or cannot use oxygen; aerotolerant species are insensitive to oxygen, but obligate anaerobes are inhibited or killed by oxygen.
Ex- clostridium


Oxygen: Facultative Anaerobes

Grow either with oxygen or in reduced oxygen environments.


What do Capnophilic bacteria (microaerophils) require?

They require an atmosphere low in oxygen and rich in carbon dioxide.


pH: The majority of species grow optimally at neutral (~7pH) and are called ___.



pH: Acidophiles

Acid tolerant prokaryotes
Ex: those used to turn milk into buttermilk, sour cream, and yogurt


Pressure: Basophiles

Can withstand incredibly high hydrostatic pressure
-Ex: Psychrophiles living at the bottom of the ocean.


Pressure: Halophiles

Salt-tolerant prokaryotes
-They can maintain optimal osmotic pressure
-Ex: Vibrio cholera that causes cholera


Culture media are used to grow microbes and measure their growth. What are the two basic types?

Complex medium and Synthetic medium


What is a complex medium?

A chemical unidentified medium or complex medium such as a nutrient broth (liquid media) or nutrient agar (solidifying agent for solid media).


What is a synthetic medium?

The chemical composition of the medium is known.


What is a selective medium?

It contains ingredients to inhibit growth of certain species and allow the growth of others.


What are two examples of selective medium?

1. Crystal Violet Agar-plates (absorbed well by Gram +) selective not differential, to select gram- bacteria

2. Eosin Methylene blue agar plates (totally inhibit Gram +) both selective and differential. Selects gram - bacteria. White and clear colonies all gram -. Metallic green colonies is also gram - but this confirms the presence of E.coli. EMB Agar used only to confirm presence of E. coli.


What is a differential medium?

Contains specific chemicals to indicate species that possess or lack a biochemical process.
-distinguished groups
-based on colors


What are two examples of differential medium?

1. EMB agar- all the colors are gram -, on exam * EMB is an example of differential & selective media; used to confirm presence of E. coli.

2. Sheep's Blood Agar; selective & differential
-No hemolysis=gamma (V) hemolysis
-Partial hemolysis=alpha (looks like fish) hemolysis
-Complete hemolysis=beta (B) hemolysis



What happens if you have Beta (complete) hemolysis?

You have Streptococcus pyogens that causes strep throat.


When do we use Chocolate Agar?

Cooked sheeps blood. In our lab we use it to grow Neiserria. "Enriched medium" Enriched with iron.
-Some "fastidious" organisms require an enriched medium containing specific nutrients.


Many microbes are viable but can/cannot be cultured in lab.



Population measurements are made using ___ ______.

pure cultures.


What is a pure culture?

A population consisting of only one species of prokaryote.


Define pour-plate isolation method.

Allows separation of species through dilution of a sample. Is this the same as streak plate?** listen to recording 27min. *


What is the streak-plate isolation method?

It is used to spread out individual cells to form discrete colonies of species.


Population can be measured in several ways. What are they?

Turbidity, Microscopic count, Estimate-through most probable # test, and
Standard plate count procedure


What is turbidity?

Cloudiness of a sample can be measured with a spectrophotometer.


How is the microscopic count used?

Using counting chamber, placed under light microscope.


What is the standard plate count procedure?

Colonies grow on a plate containing a sample of diluted broth. The number of colonies indicates the original number of viable (living) cells in the broth.

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