1. What is the packaging of DNA in eukaryotes?

2. What is the packaging of DNA in bacteria and archaea?

1. Inside the nucleus

2. Nuclear material is free in the cytoplasm

1. What is the cell wall makeup in bacteria?

2. Cell makeup in archaea:

3. The internal structures in bacteria and archaea:

1. Peptidoglycan

2. Cell wall distinct from bacteria and eukaryotes

3. No membrane-bound organelles

What do all bacteria cells have?

- cell wall (except Mycoplasmas)

- cell membrane
- cytoplasm
- ribosomes
- chromosomes

Some structures found in, but not all, bacteria include:

- Outer membrane

- Intracellular membranes

- S layer
- Glycocalyx: Capsule or slime layer

- Pilus

- Fimbriae
- Flagellum

- Actin cytoskeleton
- Inclusion/granule
- bacterial microcompartments
- Plasmid
- Endospore

What necessary life activities can bacterial cells carry out?

- Reproduction
- Metabolism
- Nutrient processing

What groups can bacteria form? 

Colonies or Biofilms

What is the average size of bacteria? 

0.2-10 micrometers

What are the three general shapes of bacteria?

- Coccus/Cocci (spheres, oval, bean-shaped)

- Bacillus/Bacilli (rod)
- Spirillum/Spirilla (helix)

What is Pleomorphism?

Variations in size and shape among cells of a single species

What are the arrangements and groupings of Cocci?

- Tetrads (group of four cocci cells)

- Staphylococci (Irregular clusters of cocci cells)

- Streptococci (chains of a few to hundreds of cocci cells)

- Sarcina (cubical packet of 8, 16, or more cells)

What are the arrangements and groupings of bacilli?

- Diplobacilli (pairs of cells with their ends attached)

- Streptobacilli (chains of cells)

- Palisades (cells of a chain remain partially attached and fold back, creating a side-by-side row of cells

What is the bacterial arrangement of Spirilla?

Occasionally found in short chains

Spirochetes:

Rarely remain attached after cell division

What are the two major groups of appendages?

- Flagella and axial filaments (provide motility)

- Fimbriae and pili (provide attachment but not locomotion)

What are the three distinct parts of flagella?

- Filament: helical structure composed of proteins, inserted into the curved hook

- The hook (rotates 360 degrees together w its filament)
- Motor

What are the types of flagella arrangements?

- Monotrichous (single flagellum)

- Lophotrichous (small bunches)

- Amphitrichous (flagella at both poles of the cell)

- Peritrichous (flagella are dispersed randomly over the surface of the cell)

Taxis:

the ability to move toward or away from certain signals (stimuli).

What are chemotaxis in flagella?

Movement in response to chemical signals. Positive vs. negative.

What are positive chemotaxis?

Movement of a cell in direction of a favorable chemical stimulus.
Ex. good aroma

What are Negative chemotaxis?

Movement of a cell away from a repellent or potentially harmful compound.
Ex. smoke

What are Phototaxis?

move cell towards the light

What are the types of flagellar motility?

- Run: counterclockwise movement of flagella and cell swims in a smooth, linear direction toward a stimulus; repellents cause numerous tumbles

- Tumble: flagellum reverses direction, causing the cell to stop and change course

What is axial filament?

Internal flagellum enclosed between the cell wall and cell membrane
- ≥2 long coiled threads found in spirochetes
- - impart a twisting or flexing

- Ex. Borrelia burgdorferi (causes Lyme disease) and Treponema pallidum (causes syphilis STD disease)

Name the appendages for mating and adhesion.

- Fimbriae

- Pili (aka sex pili)

Describe Fimbriae.

- Small bristle-like fibers sprouting off the surface of certain species of bacteria
- Composition varies but most contain protein
- Stick to each other and to surfaces

Example usage of fimbriae

- E. coli and gonococcus use these to attach to epithelial cells
- May be responsible for biofilms

Describe Pili (aka sex pili).

- Long, rigid tubular structure made of pilin protein
- Production of pili is controlled genetically

Example usage of Pili

- Only found in gram-negative bacteria
- Used in conjugation, the partial transfer of DNA from one cell to another

What is conjugation?

In bacteria, the contact between donor and recipient cells associated with the transfer of genetic material such as plasmids. Can involve special (sex) pili. Not to be mixed with conjugation in eukaryotic ciliated protozoans where it is a sexual recombination.

How do bacterial cells protect themselves?

With S layer or glycocalix (slime layer and capsule)

Describe S Layer.

- Single layers made of protein
- Only produced in hostile environments

Describe Glycocalyx.

- Develops as a coating of repeating polysaccharide units that may or may not include protein
- Protects the cell and sometimes adhere to surfaces in its environment
- Not found in all bacteria

Two conditions of Glycocalyx: Slime layer and Capsule

Describe Slime Layer.

- Forms loosely around the cell
- Protects the cell from loss of water and nutrients

Describe Capsule.

- Denser and thicker than a slime layer

- Formed by pathogenic bacteria as protection against phagocytic white blood cells

- Need a special staining technique - Negative staining

What are the functions of Glycocalyx biofilms?

- Plaque on teeth protect bacteria
- Infect long-term indwelling artificial devices

What is Biofilm (Biological glue)?

What is Biofilm (Biological glue)?

A community of microbes, live in cooperative associations that include other organisms of the same species, as well as other species. Made in microbial habitats with adequate access to food, water, atmosphere, and other environmental factors

What are the two or three basic layers of the cell envelope?

- Cell wall
- Inner cell membrane
- Outer cell membrane (only in G- bacteria)
- Act as a single protective unit

Who is Hans Christian Gram and what did he develop?

In 1884 he developed the staining technique to distinguish between the two major groups of bacteria (gram-positive and gram-negative).

What differences do the gram stains show in bacteria?

The layers of the cell envelope

Describe Gram Positive cells.

- Purple

- Thick cell wall composed of peptidoglycan
- Inner cytoplasmic membrane
+ Teichoic acid 
+ Lipoteichoic acid
+ Membrane proteins

Function of teichoic and lipoteichoic acid:

- Cell wall maintenance
- Enlargement during cell division
- Provides negative charge on cell surface

Describe Gram negative cells.

- Pink

- Outer membrane
- Thin cell wall (thinness of PG layer gives them greater flexibility but also sensitivity to lysis)
- Inner cytoplasmic membrane
+ Phospholipid bilayers
+ Periplasmic space
+ Membrane protein

- Do not have Teichoic and Lipoteichoic acid

Peptidoglycan

- Glycan chains cross linked with short peptide fragments
- Provides a strong but flexible support framework

Characteristics of the cell wall:

- Helps determine shape
- Provides strong structural support to keep the cell from bursting or collapsing due to osmotic pressure

Non-typical cell walls

Include mycolic acid (lipids) and cord factor (glycolipids)

- Found in Mycobacterium and Nocardia
- Long fatty acid chain (lipids)
- Contributes to pathogenicity
- Acid-fast stain to diagnose tuberculosis and leprosy

Mycoplasmas

- Lack a cell wall
- Membrane is stabilized by sterol
- Resistant to lysis
- Pleomorphic shape

What proteins and polysaccharides are in the gram-negative outer membrane?

- Lipopolysaccharide 
- Lipoproteins
- Porin proteins

Lipopolysaccharide

- Plysaccharide chains function as antigens and receptors
- Endotoxin: stimulates fever and shock reactions

Lipoproteins

Anchor the outer membrane to peptidoglycan

Porin proteins

- Completely span the outer membrane
- Only allow relative small molecules to penetrate
- Size can be altered to block the entrance of harmful chemicals
- Act as defense against certain antibiotics

Cell membrane structure:

- Sheet molded around cytoplasm
- Lipids bilayer embedded with proteins
- Mycoplasmas contain high sterol amounts

Functions of the cell membrane

- Energy reactions
- Nutrient processing
- Synthesis
- Transport
- Selective permeability
- Secretion

Cell membrane transport

- Passage of nutrients into the cell
- Discharge of wastes

Selective permeability

- Water and small uncharged molecules diffuse freely
- Special carrier mechanisms exist for passage of most molecules

Cell membrane secretion

Discharge of metabolic products into the extracellular environment

Difference between the cell envelope structures of gram positive and negative

- Gram negative: more impervious to antimicrobial chemicals, more difficult to kill that gram-positive
- Infections are treated differently between the two

Cell envelope interaction with human tissues and diseases

- Proteins in outer cell wall of gram-positive can be toxic
- Lipids in cell wall of mycobacterium can be harmful
- Macromolecules in the cell wall are seen as foreign and can stimulate antibody production

Cytoplasm

- Gelatinous solution contained by cell membrane
- Site for biochemical and enzymatic activities
- 70-80% water
- Mixure of amino acids, sugars, and salts
- Contain chromatin, ribosomes, granules, and fibers

Bacterial chromosome

- Single circular strand of DNA
- Aggregated in a dense area called the nucleoid
- DNA is tightly coiled around the basic protein molecules to fit into the cell compartment

Plasmids

- Nonessential pieces of DNA
- Separate, double stranded circles of DNA
- Duplicated and passed onto offspring
- Confer protective traits
- Important in genetic engineering

Ribosomes

- Made of rRNA and protein
- Dispersed throughout the cytoplasm, often found in chains
- Svedberg (S) units

Size of bacterial ribosomes: (small 30S) + (large 50S) = total 70S

Size of eukaryotic ribosomes: (large 60S) + (small 40S) = total 80S

Inclusion bodies

- Storage sites for nutrients during periods of abundance
- Vary in size, number, and content

Cytoskeleton

- Long polymers of proteins similar to eukaryotic actin
- Arranged in helical ribbons just under the cell membrane

- Function of Cytoskeleton: Contribute to cell shape

Bacterial endospore

- Help bacteria adjust to adverse habitats.
- Withstand hostile conditions and facilitates survival
- Dormant

What are the two-phase life style of endospores?

- Vegetative cell

- Endospore

Vegetative cell

- Metabolically active and growing entity
- Induced by environmental conditions to undergo spore formation (sporulation)

- Sporulation: Spore formation induced by environmental conditions

Endospore

- Metabolically inactive, dormant, resting condition
- Can resist: heating, drying, freezing, radiation, and chemicals

- Stimulus for endospore formation: depletion of nutrients, especially carbon and nitrogen sources

Sporangium

- Sporulating cell
- Transformation takes 6-8 hours in most species

Endospore Formation Steps

1. Vegetative cell begins to deplete in nutrients
2. Chromosome is duplicated and separated
3. Cell is septated into a sporangium and forespore (smaller of the septated, vegetative cell)
4. Sporangium engulfs forespore
5. Sporangium begis to actively synthesize spore layers around forespore (early spore forms) - Sporulating cell
- Transformation takes 6-8 hours in most species

6. Cortex and outer coat layers are deposited
7. Mature endospore
8. Free spore is released with the loss of the sporangium
9. Germination: spore swells and releases vegetative cell

Overall picture of endospore formation:

Forespore à early spore à mature spore

When does germination occur? 

When favorable conditions arise.

Name germination conditions:

- Exposure to water and germination agent
- Germination agent stimulates the formation of hydrolytic enzymes that break down the cortex
- Core rehydrates and takes up nutrients and bacterium grows out of the endospore coats

Name some diseases related to the persistence of their spores

- Anthrax
- Tetanus
- Psudeomembranous colitis
- Gas gangrene
- Botulism

What is the problem with endospores? 

- Constant intruders where sterility and cleanliness are important.
- Resist ordinary cleaning methods

Is Archaea more closely related to eukarya or eubacteria? 

Eukarya

Why is archaea more closely related to eukarya?

- Share rRNA sequences not found in bacteria
- Ribosomal subunit structures are similar

Why are Archaea different from other cell types?

- Certain genetic sequences are only found in their rRNA
- Unique method of DNA compaction
- Unique and chemically distinct cell walls

- Live in habitats that are similar to extremes found anciently (heat, salt, acid pH, pressure, atmosphere)

Functions and characteristics of archaea:

- Methane producers
- Hyperthermophiles
- extreme halophies
- Sulfur reducers

Methanogens

- Convert CO2 and H2 into CH4
- Common inhabitants of anaerobic swamp mud, lakes oceans, and digestive systems
- Gas in swamps may become a source of fuel
- May contribute to greenhouse gases and global warming

Extreme halophiles

- Require salt to grow
- Can multiply in 36% NaCl 
- Use a red pigment to synthesize ATP in the presence of light

Psychrophiles

Archaea adapted to grow at very low temperatures

Hyperthermophiles

- Archaea flourish at temperatures between 80 and 113 celcius and cannot grow below 50 degrees
- live in volcanic waters and soils and submarine vents
- Often salt, acid, and heat tolerant

What is the purpose of classifying bacteria and archaea?

- Differentiating and identifying unknown species
- Studying the relationships and origins of microbes

In the past how did scientists trace/classify the origins and relationships between bacteria and archaea?

- Shape
- Arrangement
- Growth characteristics
- Habitat

What are the newer methods of classifying evolutionary relationships?

- Biochemistry
- Genetics
- Molecular traits

What is the most viable indicator of evolutionary relatedness?

- Through the comparison of nitrogen bases in rRNA.

- Tend to remain stable in their nucleic acid content over long periods
- Any major differences in the signature sequence indicates distance in ancestry

1. Bacterial Species

2. Strain (subspecies)

3. Serotype

1. A collection of bacterial cells which share an overall pattern of similar traits

2. Bacteria of the same species that have differing characteristics

3. Representatives of a species that stimulate a distinct pattern of antibody responses