MICB 3301 Exam 1

What is Spontaneous Generation?

The ability for living material to arise from non-living material

What did Spallanzani discover?

Microbes will grow in flask of meat broth UNLESS it is sealed and boiled

What did Pasteur discover about spontaneous generation?

Microbes won't grow in boiled broth until introduced to outside particles -- air carries germs/particles

-Using a swan neck flask, dust/microbes in air could not pass into broth so no growth occurred

-After breaking off the s-curve of the flask, the broth was exposed to air/particles and growth occurred

What is Koch known for?

First to provide evidence that bacteria can cause disease

Discovered this via his work with BACILLUS ANTHRACIS (pathogen that causes anthrax)

What are Koch's Postulates?

1. Microbe must be found in all cases of disease

2. Microbe must be grown and isolated in pure culture

3. Same disease must occur when isolated microbe is re-inoculated into healthy host

4. Same microbe must be isolated again from the newly diseased host

What is Jenner known for?

First vaccine

Took material from cowpox lesions and used it to protect from smallpox

What is Metchnikoff known for?

Macrophages (bacteria-engulfing cells which consume pathogens during immune response)

*Note: TB bacteria figured out how to live in macrophages (bad)

What is Winogradsky known for?

Ecology

Isolated bacteria that oxidizes inorganic compounds (Fe, S) to generate energy -- CHEMOLITHOTROPHY

What is Beijerinck known for?

Ecology

Isolated nitrogen-fixing bacteria (reduces atmospheric nitrogen/N2 to ammonia/NH3 as a source of nitrogen for microbes)

What are the 3 domains of life?

Archaea, Bacteria, & Eukarya

Which domains are sequenced based on 16S rRNA?

Archaea & Bacteria

Which domains are sequenced based on 18S rRNA?

Eukarya

What are the five major groups of microbes?

Archaea, Bacteria, Fungi, Protists, & Viruses

Which groups of microbes are PROKARYOTIC?

(No membrane-bound nucleus)

Archaea & Bacteria

Which groups of microbes are EUKARYOTIC?

(Membrane-bound nucleus)

Fungi (yeasts and molds) & Protists (algae and Protozoa)

Are viruses living?

No, acellular/non-cellular. Do not have rRNA for classification.

What is Robert Hooke known for?

First to discover microbes (larger eukaryotic fungus)

What is Antony Van Leeuwenhoek known for?

First to discover smaller, prokaryotic bacteria

What did Redi's experiments reveal?

3 jars of meat: 1 uncovered, 1 covered and sealed (no air in), 1 covered with mesh (air could pass)

Discovered that flies do not spontaneously generate from meat

What is Lister known for?

Surgeon, known for sterilization

Discovered that wound infection was minimized by disinfecting the area prior to surgery (paved the way for immunology)

How does bacteria reproduce?

Asexually via binary fission

What is the size range for bacteria?

0.3 - 100 micrometers

-Escherichia coli - 4 micrometers

-Thiomargarita - >100 micrometers (Sulfur pearl chemolithotrope)

What are the advantages of bacteria's small size?

Higher surface area to volume ration allows for faster nutrient exchange and growth

Bacteria: Coccus shape

Sphere

-diplococcus: pair of cocci

-streptococcus: chain of cocci

-staphylococcus: grape-like clusters of cocci

-tetrads: four cocci in a square

*Note: Mozart died from strain of streptococcus

What genus is an example of the tetrad shape?

Deinococcus

Known for its ability to survive radiation

Bacteria: Other Shapes

-bacillus: rod shaped

-vibrio: curved rod

-spirillum: rigid helix

-spirochete: flexible helix

-pleamorphic: variable shape

*Note: E. Coli is bacillus

What bacteria has a pleamorphic shape?

Mycoplasma

Has a plasma membrane but no cell wall

What are hyphae and mycelium?

Hyphae: long filaments

Mycelium: branching networks of the long filaments (often found in fungi)

What can be included in the cytoplasm of a cell?

-Inclusions, chromosomes, and ribosomes

-Mostly water

-Highly concentrated

Cytoplasm: What are the three storage inclusions discussed?

Carbon

-Glycogen (storage of carbon)

-Poly-beta-hydroxybutyrate

Phosphate & Sulfur

-Polyphosphate granules

-Sulfur globules

Carbon & Nitrogen

-Cyanophycin granules

Cytoplasm: What are gas vacuoles?

Located in some bacteria (ex: Cyanobacteria), control buoyancy

*Note: Genus-Anabaena

Cytoplasm: What are magnetosomes?

Iron in the form of magnetite (Fe3O4), orient cells in earth's magnetic fields

*Note: Aquaspirillum

Does bacteria contain mitochondria or chloroplasts?

No, bacteria does not contain these complex membranous organelles

What is an example of an internal membranous structure found in some bacteria?

Cyanobacteria have THYLAKOIDS (photosynthetic membranes with chlorophyll)

Cytoplasm/Microcompartments: What are carboxysomes?

Polyhedral-shaped protein shell which houses enzymes for CO2 fixation

Example of enzymes:

-carbonic anhydrase: converts carbonic acid to CO2

-RubisCo: fixes CO2 into sugar (requires energy)

*Note: Cyanobacteria has carboxysomes (and other CO2 fixing bacteria)

What processes take place in the cytoplasm?

Transcription and translation

RNA polymerase transcribes DNA to mRNA

Ribosomes translate mRNA to protein

(DNA -- mRNA -- Protein)

*Note: In archaea & bacteria these processes occur simultaneously

Cytoplasm: What are nucleoids?

Regions containing chromosomes (genetic material)

Typically each nucleoid has only one chromosome but some have more than one

*Note: NOT surrounded by a nuclear membrane the way the nuclei of eukaryotic cells are

Are nucleoids surrounded by a nuclear membrane?

NO

Cytoplasm: What are plasmids?

Small DNA molecule within a cell that is physically separated from a chromosomal DNA and can replicate independently

Can be transferred from one bacteria to another

*Note: may carry genes that confer advantage (Ex: conjugation plasmids and R plasmids), may be inherited, may code for antibiotic resistance

What are R plasmids?

Plasmids which contain genes for resistance of antibiotics

What are the functions of bacterial plasma membranes?

-Separates cell from environment

-Main site of energy generation

-Selectively permeable barrier

-Transport systems

What are some of the main characteristics of bacterial plasma membranes?

Made of lipid bilayer and protein

Organized, asymmetrical, flexible, and dynamic

What are the three components of membrane lipid, phosphatidylethanolamine?

Ethanolamine head + phosphate bond

Glycerol + fatty acid tail (ester bond linked)

Plasma membrane: What are hopanoids?

Sterol compounds that insert into the plasma membrane and help to stabilize it

Bacterial Cell Wall: What are its functions?

-Defines the shape of the cell

-Protects the cell from toxic substances and osmotic lysis

-Aids in osmosis (bacteria are usually in hypertonic solutions where there is more solute inside the cells than outside, making them susceptible to intake of water)

What color do Gram + bacteria stain?

Purple

What color do Gram - bacteria stain?

Pink

Why do cells stain a certain way?

Depends on the compositional differences in their cell walls

Characteristics of Gram + cell walls

Cell wall is comprised of multiple, thick layers of Peptidoglycan

Thick cell wall - periplasmic space - plasma membrane

Characteristics of Gram - cell walls

Cell wall is made of an outer membrane (lipid membrane like plasma membrane) and a thin layer of Peptidoglycan

Cell wall (outer membrane + periplasmic space + peptidoglycan) - periplasmic space - plasma membrane

What is peptidoglycan?

-A component of Gram + and Gram - cells

-A polysaccharide made of two alternating sugars (NAM and NAG) which are connected by a beta 1,4 glycosidic bond

What can cleave the beta 1,4 glycosidic bond between NAM and NAG?

Lysozyme

This disrupts the cell wall and causes it to release genetic material within the cell

What does "NAG" stand for?

N-acetylglucosamine

What does "NAM" stand for?

N-acetylmuramic acid

Why is it beneficial for the NAM sugars to have both L and D amino acids?

Having both makes it harder for foreign substances/organisms to degrade the peptidoglycan cell wall

What kind of bond do NAM sugars have between D-Ala and DAP?

Transpeptidation bond

There can also be peptide interbridges between amino acids

*Note: Some antibiotics can inhibit this reaction

What are Teichoic Acids?

-Polymers of glycerol or ribotol

-Property of Gram + cell walls

-Embedded in peptidoglycan (help to stabilize it and connect it to the plasma membrane)

What kind of microbes are Lipopolysaccharides (LPS) located in?

Gram - microbes

What are the three parts of Lipopolysaccharides (LPS)?

1. Lipid A (embedded in outer membrane)

2. Core polysaccharide (made of different types of sugars)

3. O/antigen side chain (outermost portion)

What is the function of Lipopolysaccharides (LPS)?

-Protects the cell from host defenses

-Attaches a bacterial cell to a surface

-Stabilizes the outer membrane of the cell

-Lipid A portion acts as a toxin

*Note: Example of Lipid A toxin is ENDOTOXINS (causes fever and septic shock)

*Note: There are many types of O antigens that can make up the O side chain of the LPS. For example, E. Coli has O157 and H7

What are Porins?

Proteins which form channels in the outer membrane of GRAM - cells which allow small molecules to diffuse into the cell

What are capsules?

-Polysaccharides which form around cell wall

-Organized, not easily removed

*Note: Bacillus anthrasis protects itself with a capsule

What are slime layers?

-Polysaccharides which form around cell wall

-Diffuse, unorganized, easily removed

What are s-layers?

-Proteins which form around cell wall

-Organized (provides protection to cell)

In what type of microbes are capsules and s-layers common?

-Archaea & Bacteria

-Gram + & Gram -

What is the functions of the layers outside of the cell wall? (Capsules, Slime layers, S-layers)

-Help to attach microbes to a surface

-Protect the cell from chemicals, drying out (desiccation), bacterial viruses (bacteriophages)

-Host immune response

*Note: when you get a vaccine, you are getting a protective capsule

*Note: the bacteriophages are unable to find receptors on the cell to connect with because they are covered with a capsule

Teichoic Acid: Gram + or Gram -?

Gram +

Periplasmic space: Gram + or Gram -?

Both

Plasma membrane: Gram + or Gram -?

Both

Outer membrane: Gram + or Gram -?

Gram -

Lipopolysaccharides (LPS): Gram + or Gram -?

Gram -

Peptidoglycan: Gram + or Gram -?

Both

Capsule: Gram + or Gram -?

Both

External structures: Pili

Thin protein appendages which aid in attachment of a bacterial cell to another cell

External structures: Sex Pili

Used for conjugation (horizontal gene transfer)

Mechanism: holds two cells together so genetic information can be transferred from one cell to the other

External structures: Type IV Pili

Used for movement/twitching motility of a cell

Mechanism: can undergo cycles of extension, attachment, and retraction so that cells can attach to each other and move in groups

External structures: Flagella

Motility organelles found in all domains of life

External structures: Flagella (structure)

Filament - hook - basal body (embedded in membrane)

Filament: made up of protein (FLAGELLIN)

-Proteins move through channel at base of basal body

and are assembled near the filament

Basal body: made up of rod and series of rings

-Stabilizes flagella and acts as the motor

-MS ring can spin

What causes the flagella to move?

A proton gradient

Inward flow of protons causes MS ring to rotate so cell can move

**DOES NOT DIRECTLY USE ATP

Flagella: Counterclockwise movement

Flagella bundles into a ponytail and moves at a forward run

Flagella: Clockwise

Flagella flies apart and tumbles

What is chemotaxis?

The ability to respond to environmental changes and switch movements (flagella can do this)

*Note: uses chemoreceptors which are sensory proteins embedded in the plasma membrane

What is the term used for flagella moving towards an attractant?

Biased random walk

What is the term used for flagella both running and tumbling?

Random walk

What kind of microbe is described with the genus "Haloquadratum"?

Archaea, four square cells with some gas vacuoles

What is special about archaea membranes?

They provide enhanced stability for survival and growth at high temperature

What is an example of an archaea microbe that can withstand high temperatures?

Pyrococcus furiosus

-Thermophile

-Isolated in deep sea hydrothermal vents

-Source of PFU polymerase for PCR

-Can have 30-50 flagella on one end

Why aren't there many antiviral drugs?

It is hard to make something that targets viruses because they don't have a cell wall

What are viruses made of?

Protein and nucleic acid (very simple)

What unit are most viruses measured in?

Nanometers

*Note: Parvovirus (made of only 3 genes)

*Note: Mimivirus (made of 900+ genes)

What is a virion?

Complete virus particle

What is a capsid?

Protein shell/coat around a genome (genetic material)

What is a nucleocapsid?

Nucleic acid + capsid (protein shell)

What is a protomer?

Protein subunit of capsid

What does a naked virus consist of?

Capsid + nucleic acid on inside

What does an enveloped virus consist of?

Envelope + spike proteins + capsid + nucleic acid on inside

What is an example of an icosahedral shaped virus?

Polyomavirus

What is an example of an enveloped virus? (2)

Herpevirus, influenza

What is an example of a helical shaped virus?

Tubulovirus

*Note: the genetic material is inside the tube

What is an example of a binal shaped virus?

T-even coliphage