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Micro Chap 4: Prokaryotic Profiles- Bacteria & Archae

How are prokaryotes different from eukaryote?`(3)

1. DNA (still double stranded)
a. Not in a nucleus
b. Circular DNA and accessory plasmids (extra genetic information - not needed to survive)
c. Not wrapped (condensed) around (1)_histones (proteins)_
2. Makeup of their cell wall
a. Bacteria- peptidoglycan (sugar protein wall)
b. Archae- tough and made of other chemicals, distinct to them
c. We will be focusing on bacteria
3. Their internal structures
a. No complex, membrane-bound organelles (with some modifications)

prokaryote cell

1. appendages
a. flagella
b. pili
c. fimbriae
2. glycocalyx [majority of bacterial cells]
a. capsule, slime layer

prokaryote cell
cell envelope (3)

1. (outer membrane)
2. cell wall [majority of bacterial cells]
3. cell membrane (all bacterial cells)

prokaryote cell
internal (6)

1. cytoplasm (all bacterial cells)
2. ribosomes (all bacterial cells)
3. inclusions
4. nucleoid/chromosome (all bacterial cells)
5. actin cytoskeleton
6. endospore

Structures common to all bacterial cells (4)

1. Cell membrane largely composed of (2) _phospholipids (polar, semipermeable)_____
2. Cytoplasm (aka cytosol, aqueous components)
3. Ribosomes - size (3) __70S_
4. One (or a few) chromosomes (can have plasmids)

Structures found in MOST bacterial cells (2)

1. Cell wall (might be modified, positive & negative)
2. Surface coating or glycocalyx (capsules, slime layers)

External structures

1. Appendages: Cell extensions
a. Common but not present on all species
b. Can provide motility (flagella and axial (interior) filaments)
c. Can be used for attachment and mating (pili and fimbriae)


Flagella (2)

Appendage for motility

1. Three parts: Filament (made of proteins called FLAGELLIN) , hook (sheath), and basal body. Amount of rings holding in depends on whether gram neg. or positive.
Hook anchored to cell by the Basal body which includes: outer membrane, cell wall & cell membrane.
2. Vary in both number and arrangement
a. Polar arrangement: flagella attached at one or both ends of the cell
i. Monotrichous- (5)__single/one__ flagellum
ii. Lophotrichous- tufts of flagella emerging from the same site
iii. Peritrichous- dispersed randomly over the structure of the cell
iv. Amphitrichous = having at both ends

Flagellar Function (3)

1. Chemotaxis- movement in response to chemical signals. positive and negative
2. Phototaxis - movement in response to light
3. Move by runs [(6) _counterclockwise__] and tumbles [(7) _clockwise___]

Axial Filaments (4)

Internal, imbedded in periplasmic space
1. AKA periplasmic (8) _flagella or axial filaments____
2. In spirochetes - corkscrew shaped bacteria that show interesting movement (it's thought to be the precursor to eukaryote flagellum)
3. A type of internal flagellum that is enclosed in the space between the cell wall and the cell membrane (periplasmic space)
4. Causes movement much like we saw in the vinegar eel helminthes
Note 1: can burrow into agar
Note 2: its thought endoflagellum became microtubules

Other external appendages: 1/2

Used for (9)_attachment/adhesion___ not locomotion
1. Pili
a. Elongate, rigid tubular (hollow) structures - materials pass thru (ex. plasmids) only way to get new genetic info.
b. Made of the protein (10)_PILIN______
c. Found on gram-NEGATIVE bacteria
d. Used in conjugation (bacterial "sex")

Other external appendages: 2/2

Used for (9)_adhesion/attachment__ not locomotion
1. Fimbriae
a. Small, bristle-like fibers
b. Most contain protein
c. Tend to stick to each other and to surfaces

The Glycocalyx (4)

1. Develops as a coating of repeating polysaccharide units, protein, or both
2. Protects the cell
3. Sometimes helps the cell adhere to the environment & other bacteria
4. Differ among bacteria in thickness, organization, and chemical composition
a. Slime layer- a loose shield that protects some bacteria from loss of water and nutrients (protection, loss of water & nutrients) easily washes off
b. Capsule- when the glycocalyx is bound more tightly to the cell and is denser and thicker. Can't be rinsed, hard to phagocytize)

Capsules of Glycocalyx

are seen in some pathogenic bacteria
Helps in evading phagocytosis by immune system WBCs
can be bigger than the bacteria

Bacteria with capsules (3)

1. Streptococcus pneumoniae
2. Haemophilus influenzae
3. Bacillus anthracis

Differences in cell envelope structure (3)

1. The differences between gram-positive and gram-negative bacteria lie in the cell envelope
2. Gram-positive (smaller cell envelope)
a. Two layers
b. Cell wall (PG) and cytoplasmic membrane
c. 'open-faced sandwich' (meat is PG)
3. Gram-negative
a. Three layers
b. Outer membrane, cell wall, and cytoplasmic membrane (phospholipids)
c. 'complete sandwich'

Structure of the cell wall (4)

1. Helps determine the shape of a bacterium
2. Provides strong structural support
3. Helps to prevent (11) _osmosis____
4. Most are rigid because of peptidoglycan (PG)content

***the amount of PG varies between gram positive and gram negative
**PG is unique & essential to bacteria
- if you want to kill bacteria, then target PG

Structure of the typical cell wall (4)

1. Keeps cells from rupturing because of changes in pressure due to osmosis
2. Target of many antibiotics - disrupt the cell wall, and cells have little protection from (12) _lysis (physical rupture or deterioration of a cell)_____
3. Gram-positive cell wall
a. A thick (20 to 80 nm), homogeneous sheath of peptidoglycan
b. Contains tightly bound acidic polysaccharides
4. Gram-Negative Cell Wall
a. Single, thin (1 to 3 nm) sheet of peptidoglycan
b. Periplasmic space surrounds the peptidoglycan (btw 2 layers of phospholipids)

Mycoplasmas & other cell-wall-deficient bacteria (6)

1. Mycoplasma (don't have a cell wall) cell membrane is stabilized by sterols and is resistant to lysis
a. Very small bacteria (0.1 to 0.5 µm) b/c no cell wall
b. Range in shape from filamentous to coccus
c. Not obligate parasites
d. Can be grown on artificial media
e. Found in many habitats
f. Important medical species: Mycoplasma pneumonia

Some bacteria lose their cell wall during part of their life cycle`(3)

1. L-forms
2. Arise naturally from a mutation in the wall-forming genes
3. Can be induced artificially by treatment with a chemical (lysozyme-which is in sweat, tears & saliva, killing gram positive bacteria or penicillin) that disrupts the cell wall

a. When this occurs with gram-positive cells, the cell becomes a protoplast. Gram + more susceptible to lysis (b/c they lost cell wall & don't have an outer membrane, like gram neg. does)
b. With gram-negative cells, the cell becomes a spheroplast

The gram-negative outer membrane (4)

1. Similar to the cell membrane, except it contains specialized polysaccharides and proteins
2. Uppermost layer- contains lipopolysaccharide (maybe pathogenic)
3. Innermost layer- phospholipid layer anchored by lipoproteins to the peptidoglycan layer below
4. Outer membrane serves as a partial chemical sieve
a. Only relatively small molecules can penetrate
b. Access provided by special membrane channels formed by (14) __PORIN___ proteins. Only let certain things thru.

Cell membrane structure (5)

1. Also known as the cytoplasmic membrane
2. Very thin (5-10 nm)
3. Contain primarily phospholipids and proteins
4. The exceptions: mycoplasmas and archae
5. Functions
a. Provides a site for functions such as energy reactions, nutrient processing, and synthesis
b. Regulates transport (selectively permeable membrane)
c. Secretion


accessories. extra genetic info in prokaryotes
not needed to survive

bacteria cell wall

peptidogylcan (sugar-protein)

Appendages - Two main types

1. Motility = flagella & axial filaments
2. Attachment or channels = fimbriae & pili


polar arrangement of flagella

Single flagellum


polar arrangement of flagella

tufts of flagella emerging from same site


polar arrangement of flagella

dispersed randomly over the structure of the cell

polar arrangement of flagella

flagella are attached at one or both ends


flagella at both ends of the cell

what makes up filament in flagella

made out of flagellin (protein)


1. Chemotaxis- movement in response to chemical signals.
a. positive = move toward chemical stimulus (usually nutrient)
b. negative = move away from repellent compound
2. Move by runs = counterclockwise
3. Move by tumbles = clockwise

Flagella movement - general rules chemotaxis

1. receptors in the cell membrane on the outside of bacteria will recognize stimulus & get flagellum moving
2. cell membrane based
3. bacteria move when they receive or don't receive messages.

Runs, tumbles & concentration gradient

Tumble = no attraction or repellent
Increase in chemical gradient (attractant) = increase runs
No chemical gradient = tumbles

periplasmic space

is between the cell wall and the cell membrane

slime layer of Glycocalyx

a loose shield that protects some bacteria from loss of water and nutrients (protection, loss of water & nutrients)
easily washes off

functions of glycocalyx- biofilms

glycocalyx can create biofilms (ex. plaque on teeth)
attach to organic matter, absorb cells to organic matter, more permanent slime layer or capsule, then colonize

PG biosynthesis

1. UDP = energy source
2. phosphate supplies the energy
3. UDP-NAM - 5 AA attached to each other are added to form a pentapeptide side chain
4. NAG gets added to NAM (no AA attached to NAG) then..
5. peptidoglycan - NAM - NAG

PG biosynthesis - transpeptidation

1. transpeptidation reactions = peptide chains linked together to form peptide bonds thru cross bridges
2. ** cross bridge btw pentapeptides via transpeptidation is what links it together to make a solid peptidoglycan
3. peptide cross bridges (aka interbridges)

Gram-positive cell wall

a. A thick (20 to 80 nm), homogeneous sheath of peptidoglycan
b. Contains tightly bound acidic polysaccharides

Gram-negative cell wall

a. Single, thin (1 to 3 nm) sheet of peptidoglycan
b. Periplasmic space surrounds the peptidoglycan (btw 2 layers of phospholipids)


access provided by special membranes channels formed by protein porins. this is in the gram-negative outer-membrane.

cell membrane (4)

1. Also known as the cytoplasmic membrane
2. Very thin (5-10 nm)
3. Contain primarily phospholipids and proteins
4. The exceptions: mycoplasmas (no PG, sterols hold it together) and archae

cell membrane functions (4)

1. Provides a site for functions such as energy reactions, nutrient processing, and synthesis
2. Regulates transport (selectively permeable membrane)
3. Secretion
4. Genetic material can be attached here

practical considerations of differences in cell envelope structure (2)

1. Outer membrane- an extra barrier in gram-negative bacteria
a. Makes them impervious to some antimicrobial chemicals
b. Generally more difficult to inhibit or kill than gram-positive bacteria
2. Cell envelope can interact with human tissues and cause disease
a. Corynebacterium diphtheriae
b. Streptococcus pyogenes

Bacterial internal structure
Contents of the cell Cytoplasm/Cytosol (4)

1. Gelatinous solution. b/c of proteins, a lot of water
2. Site for many biochemical and synthetic activities
70%-80% (15) __water______
3. Also contains larger, discrete cell masses (chromatin body, ribosomes-proteins, granules, and actin strands-give structure)
4. a lot of enzymes

Bacterial chromosome (2)

1. Single circular strand of DNA/double stranded
2. Aggregated in a dense area of the cell- the (16) nucleoid/can be in cell membrane___

Plasmids (6)

1. extra pieces of genetic material
2. Nonessential pieces of DNA (don't break down glucose)
3. Double-stranded circles of DNA
4. Often confer protective traits such as drug resistance or the production of toxins and enzymes (use a new food source)
5. The process that transfers these is called (17) _conjugation (bacterial sex?_____
6. Transferred via (18) _pili (hollow tube - made up of pilin)
how they pick up resistances

Ribosomes (3)

1. Made of RNA and protein
2. Special type of RNA- ribosomal RNA (rRNA)
3. Characterized by S units- the prokaryotic ribosome is 70S

Inclusions (4)

bacteria saving material.
aka - inclusion bodies (single membrane)
1. Some bacteria lay down organic nutrients in these inclusions during periods of nutrient abundance.
Why? (19) when environmental nutrients are gone bacteria use these stored nutrients.
2. Within single layer membranes
3. Some aquatic bacterial inclusions include gas vesicles to provide
(20) _buoyancy______or _flotation_____
especially in cynobacteria b/c they need light

Granules (6)

1. A type of inclusion body
2. Contain crystals of inorganic compounds
3. Are not enclosed by membranes
4. Example- sulfur granules of photosynthetic bacteria
5. Polyphosphate granules of Corynebacterium and Mycobacterium are called metachromatic granules because they stain a contrasting color in methylene blue
[Use? (21) _Phosphates=energy (ATP), bilayer, DNA, RNA. have a lot - store it up_______]
6. Magnetotactic bacteria contain granules with iron oxide- give magnetic properties to the cell

The Actin Cytoskeleton (3)

1. Long polymers of a (22) __protein______ called actin
2. Arranged in helical ribbons around the cell just under the cell membrane
3. Contribute to cell shape

Bacterial Endospores: An extremely resistant stage

1. Dormant state
2. Medical Significance
a. Several bacterial pathogens
i. Bacillus anthracis (nature, animal hides)
ii. Clostridium tetani = tetanus, spores tend to be on outside anaerobic
iii. Clostridium perfringens, Clostridium botulinum (bulging cans)
b. Resist ordinary cleaning methods (can withstand boiling temps)

Endospore-forming bacteria

1. Hardiest of all life forms
a. Withstand extremes in heat, drying, freezing, radiation, and chemicals
b. Heat resistance- high content of calcium and dipicolinic acid
c. Some (23) viable (able to germinate)_ endospores have been found that were more than 250 million years old
These bacteria have a two-phase life cycle

Endospore-forming bacteria Phase One-Vegetative

Phase One- Vegetative cell
(24) _Normal metabolically___ active and growing
Can be induced by the environment to undergo spore formation (sporulation - process of making spores)

Endospore-forming bacteria Phase Two Endospore

1. Stimulus for sporulation- the depletion of nutrients (heat/cold)
2. Vegetative cell undergoes a conversion to a sporangium
3. Sporangium transforms in to an endospore, if released then spore
4. Germination (put in correct environment)
a. Breaking of dormancy
b. In the presence of water and a specific germination agent
c. Quite rapid (1 ½ hours)
d. The agent stimulates the formation of hydrolytic enzymes, digest the cortex and expose the core to water

Bacterial shapes, arrangements & sizes

1. Three general shapes
a. Coccus- roughly (25) _spherical/berry (not circular b/c three dimensional)__________
b. Bacillus- (26) _____rod-shaped
i. Coccobacillus- short and plump
ii. Vibrio- gently curved
c. Spirillum- curviform or spiral-shaped (in 3 dimension)
d. Pleomorphism- when cells of a single species vary to some extent in shape and size (mycoplasmas & archae)

Arrangement or grouping (3)

1. Cocci- greatest variety in arrangement
a. Single (usually broke apart)
b. Pairs (diplococcic)
c. Tetrads (packs of four)
d. Irregular clusters (staphylococci and micrococci)
e. Chains (streptococci)
f. (27) _cubical____ packet of 8, 16, or 32 (sarcina) b/c of tetrads doubling
2. Bacilli- less varied
a. Single
b. (28)_double/pair___ (diplobacilli)
c. (29) _chains of rods__ (streptobacilli)
d. Row of cells oriented side by side (palisades)
3. Spirilla
a. Occasionally found in short chains

arrangement of grouping - cocci

greatest variety in arrangement
a. Single (usually broke apart)
b. Pairs (diplococcic)
c. Tetrads (packs of four)
d. Irregular clusters (staphylococci and micrococci)
e. Chains (streptococci)
f. (27) _cubical____ packet of 8, 16, or 32 (sarcina) b/c of tetrads doubling

arrangement of grouping - bacilli

2. Bacilli- less varied
a. Single
b. (28)_double/pair___ (diplobacilli)
c. (29) _chains of rods__ (streptobacilli)
d. Row of cells oriented side by side (palisades)

arrangement of grouping - spirilla

a. Occasionally found in short chains

Classification systems in the Prokaryotae

1. One of the original classification systems- shape, variations in arrangement (chains, pairs, clusters), growth characteristics (ex. lactose, sucrose), and habitat
2. Now compare sequence of nitrogen bases in (30) __rRNA_____________
3. Definitive published source for bacterial classification
a. Bergey's Manual
b. Since 1923
c. Early classification- the phenotypic (what you see, physical appearance) traits of bacteria
d. Current version- combines phenotypic information with rRNA sequencing
--all organisms have ribosomes b/c they need ribosomes

diagnositc scheme

--used in medicine
1. Many medical microbiologists prefer informal working system (want to know what is wrong with someone)
2. Allows for (31) __assessible____ morphological and physiological tests rather than phylogenetic relationships (quick tests)
See Table 4.2
--what nutrients does it require to treat properly

Species & subspecies (4)

1. Common definition of species used for animals (can produce viable offspring only when it mates with others of its own kind) does not work for bacteria
2. Bacteria do not exhibit a typical mode of sexual reproduction
3. For bacteria- a species is a collection of bacterial cells, all of which share an overall similar pattern of traits (Ex. same shape, size, nutrient source)
4. Individual members of a bacterial species can show variations
a. Subspecies, strain, or type- bacteria of the same species that have differing characteristics (ex. flagella differences)
b. Serotype- representatives of a species that stimulate a distinct pattern of antibody responses in their hosts (looking at the serum)

Free-living nonpathogenic bacteria

1. Photosynthetic Bacteria (nonpathogenic b/c we don't produce sunlight)
a. Produce (32)_oxygen___ during photosynthesis
b. Some produce other substances during photosynthesis, such as sulfur granules or sulfates

cynobacteria: blue-green bacteria (7)

1. For many years, called Blue-Green Algae
2. Gram-negative cell wall (pink)
3. General prokaryotic structure (unicellular, no nucleus, 70S ribosomes)
4. Can be unicellular or can occur in colonial or filamentous groupings (oooOooo gases, so it floats to the surface, needs sunlight)
5. Specialized adaptation- thylakoids (membranes hold in types of pigments)
a. Chlorophyll a
b. Other photosynthetic pigments
c. Extensive internal (33) _membrane that pigments are put in__
6. Gas inclusions (allow to be buoyant)
7. Widely distributed in nature (basis of food webs)

green & purple sulfur bacteria (5)

1. Photosynthetic
2. Contain pigments
3. Contain bacteriochlorophyll (specific to bacteria , precursor to rodoxin - in eyes)
4. Do not give off oxygen - oxygen could be toxic
5. Live in areas deep enough for anaerobic conditions but yet where their pigments can absorb light
a. Sulfur springs
b. Freshwater lakes
c. Swamps

Archae: the other prokaryote (6)

1. Domain Archaea
2. The most primitive of all life forms
3. Most closely related to the first cells that originated on earth
4. Prokaryotic in general structure
5. Share many bacterial characteristics (unicelllular, no nucleus, 70S ribosomes)
6. Evidence may be pointing to them being more closely related to Domain Eukarya than to bacteria

Archae: the other prokaryote

1. Differences from other cell types
a. Certain genetic sequences are found only in their rRNA
****similar to some eukaryotes
b. Unique membrane lipids and cell wall construction (all different types of shapes)

2. Modern archae live in habitats that share conditions as the ancient earth
a. Methane producers (deep sea vents)
b. Hyperthermophiles (high & low temps - have to have proteins that won't be denatured)
c. Extreme halophiles - High salt
d. Sulfur reducers - using for energy

Cocci arrangement - irregular clusters

staphylococci & micrococci

Cocci arrangement - cubical

8,16, or 32 = sarcina

Cocci arrangement - chains


Bacilli arrangement - chains of rods


Bacilli arrangement - rows of cells side by side

palisades, snap back on each other


representative of a species that stimulate a distinct pattern of antibody responses in their host. serum

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