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Chapter 4 - Functional Anatomy of Prokaryotic Cells
Be able to Compare and Contrast Prokaryotes and Eukaryotes (See Ch 5 )
Genetic Material
Cell Division
 Located in nucleoid region – not
membrane bound
 1 circular chromosome;loosely
attached to plasma membrane
 Enclosed in membrane bound nucleus
 Many linear chromosomes
DNA & histone protein complex =
complexed with basic proteins
Binary fission
Inclusions serve various
functions, e.g. storage
Nucleus, Smooth & Rough ER, Golgi,
Mitochondria, Chloroplasts; Lysosomes,
Vesicles, Peroxisomes
Some actin microfilaments
Microtubules, Microfilaments,
Intermediate filaments
Bacteria all except Mycoplasma
Contains peptidoglycan
Plants – cellulose
Green Algae – cellulose
Fungi – chitin
Animals - NONE
Archaea – cell wall is absent or
lacks peptidoglycan
Phospholipid bilayer
No sterols
Energy production
Phospholipid bilayer
Animal Cells – cholesterol
Fungi - ergosterol
70S found in mitochondria and
Protists ( algae, protozoa, )
Cell Wall
Cell Membrane
II. Bacterial Cells – Size, Shape, Arrangement
A. Size -- 2-8 um long X 0.2 – 2 um wide
B. Shape ( Morphology) & Arrangement
1. Cocci – spherical, round-oval
 Diplococci - pairs
 Tetrads - in fours
 Sarcinae – groups of 8,16,32
 Streptococci - chains
 Staphylococci – clumps or clusters
2. Bacilli – rod shaped –
 Single
 Diplobacilli - pairs
 Streptobacilli - chains
 Pill shaped – regular with blunt ends
 Fusiform - pointed ends
 Coccobacilli - short, rounded like cocci
 Filamentous – long and branching
 Pallisade formation – lined up like the slats in a fence
 Spore formers
3. Spiral – helical or curved bacteria - Table 4.2 for comparison
 Vibrios – very short, curved like a comma
 Spirilla – wavy , coiled and rigid
 Spirochetes - tightly coiled – corkscrew – flexible
C. Monomorphic – maintains 1 shape; Pleomorphic – has multiple shapes
III. Organization of Prokaryotic Cells
A. External Structures - Outside the Cell Wall
1. Flagella
 Function – motility
 Arrangement
o Monotrichous – 1 at one pole
o Amphitrichous – a tuft at each end
o Lopotrichous – 2 or more at one end
o Peritrichous – many covering entire cell
 Structure
o Filament – a helical protein chain with a hollow core ; unique proteins exposed
on the filament can be used to identify bacteria – called “H antigens”
o Hook – attached to the filament
o Basal Body – anchors to the cell wall & plasma membrane
 Motility
o Flagella rotate – propels bacterium
o Pattern – smooth movement in one direction ( runs)  followed by tumbles
which produce abrupt random changes in direction
o Swarming – on solid agar – characteristic of Proteus species.
o Taxis – Directional Movement in response to a stimulus
 Chemotaxis – response to chemical signal
 Phototaxis – response to light
 Attraction – movement toward a (+) signal ( the attractant)
 Repulsion – Movement away from a (-) signal (the repellent)
2. Axial Filaments – Periplasmic Flagella
o Like a flagella, but located beneath the outer sheath
o Spirals around the bacteria, producing a corkscrew motion
o Found in spirochetes – (Spirilla have flagella
3. Fimbriae and Pili
o Both are composed of a protein called pilin
o Shorter, straighter & thinner than flagella – Not Motility Structures
o Fimbriae
 Few – 100’s / cell
 Polar or evenly distributed
 Function -- Adherence ( e.g. to mucous membranes ) ; necessary for
bacteria to colonize a surface
o Pili
 Only 1-2 / cell
Longer than fimbriae
Conjugation pilus – joins cells and facilitates transfer of DNA from a
donor cell to a recipient cell during bacterial conjugation Fig 4.8
4. Glycocalyx ( sugar coat)
 Composition – polysaccharides, proteins or mixture of both
Capsule – organized – attached to cell wall
o Virulence factor – e.g., Streptococcus pneumoniae, Bacillus anthracis encapsulated strains are pathogenic; strains lacking capsules may be nonpathogenic
o Protects bacteria from phagocytosis
o Unique proteins or polysaccharides on the capsule are called “K” antigens –
can be used to identify the bacteria
Slime layer – unorganized – loosely attached to cell wall
 Formation of biofilms – dental plaque, on plastic tubing, etc.
Other Functions of the Glycocalyx
o Serve as a reserve supply of nutrients
o Prevents dehydration
o Prevents loss of nutrients
B. The Cell Envelope ( The Cell Wall, Cell Membrane and Outer Membrane)
1. Function
o Semi-rigid – maintains shape of the cell
o Prevents rupture from osmotic pressure
o Anchors flagella
o Contributes to pathogenicity
o Site of action of some antibiotics
o Differentiates major types of bacteria
2. Gram Positive Cell Walls
o Peptidoglycan
 Carbohydrate (NAG and NAM) backbone with protein side-chains
 strands are cross-linked by peptide bridges between the protein chains
 Some antibiotics (Penicillins) prevent the cross-links from forming; cell
o Thick layer of peptidoglycan – makes gram positives susceptible to antibiotics
in the penicillin family
o Teichoic Acids – negatively charged – regulate movement of (+) ions in/out of
cell; serve as specific identification markers for the type of cell
o Surface Polysaccharides – if they are unique antigens, they can also be used to
ID a cell ( e.g., Streptococcus species)
o Lipids – mycolic acids – found in the Mycobacterium( includes the bacteria
which cause tuberculosis and leprosy) -- make these bacteria Acid-fast
3. Gram Negative Cell Walls
o Fewer, thinner layers of peptidoglycan – located next to the plasma membrane
o Outer membrane – covers the peptidoglycan layer
 Lipoprotein
 Lipopolysaccharide (LPS)
 “O” polysaccharides – antigens – used to ID gram negative
 Lipid A – an endotoxin – causes fever and shock if released into
the bloodstream
Strong negative charge
Helps bacteria evade immune system
Acts as a barrier to antibiotics, digestive enzymes, detergents, heavy
metals, dyes, bile salts
Porins – protein channels which allow nutrients to cross – can also be a
site where bacteria can be invaded
4. Gram Stain Mechanism – based on differences in structure of cell walls of gram positive and
gram negative bacteria
o Primary Stain – Crystal Violet – both types accept the CV
o Mordant – Iodine – forms crystal complexes with the CV – fixes it to the
peptidoglycan layer of the cell wall
o Decolorizer – Acetone/alcohol – washes out the lipid in the outer
membrane of the gram negatives and they lose the CV/Iodine complex –
become decolorized; Gram positives will not decolorize – retain the purple CV
o Counterstain – Safranin – will be accepted by the colorless gram negatives ;
stains them pink
o Gram positives don’t decolorize; remain purple
o Gram negatives decolorize ; accept safranin; appear pink
5. Non-Typical Cell Walls
o Mycobacteria and Nocardia – waxy fatty acids ( mycolic acid) – “acid-fast”
o Mycoplasma – the smallest bacteria; lack cell walls ; cell membrane is
stabilized by sterols
o Archaea – most lack cell walls ; a few have cell walls but lack peptidoglycan
o L-Forms – cell wall deficient variations – bacterial species that normally
produce cell walls, but have lost them ; can be due to chemical exposure or
6. Damage to Cell Walls
o Bacterial cell walls do not resemble those found in eukaryotic cells ( remember,
animal cells NEVER have cell wall at all )
o Make good targets for controlling growth of bacteria ; agents that target the cell
wall will kill bacteria, but not the host cells
o Weaken the cell wall  cells rupture due to osmotic lysis
o Lysozymes – digestive enzymes found in tears, mucus, saliva, breat milk, sweat
; more effective against the gram positive cell wall ; weakly effective against gram
o Antibiotics – Penicillins – prevent peptidoglycan from forming cross bridges and
linking into a stable cell wall ; more effective against gram (+) bacteria
7. Plasma Membrane – Fluid Mosaic Model
 Encloses the cytoplasm
 Phospholipids, Proteins, No sterols
 Phospholipid bilayer
o Phospholipids – hydrophilic head; hydrophobic tail
o Bilayer – hydrophilic exterior; hydrophobic interior
 Proteins
o Peripheral – attached to surface of membrane – enzymes, support,
o Integral – embedded in the membrane – channels & transport proteins
 Membrane fluidity – like olive oil; self-sealing; proteins & phospholipids move freely
within the layer; “flip-flop” from one layer to the other rarely occurs
 Functions
o Selective barrier ; semipermeable
o Location of enzymes that break down nutrients & produce ATP
o Site of photosyntheses
Many antimicrobial agents act by damaging the membrane
C. Bacterial Internal Structure
1. The Cytoplasm
 Area inside the membrane
 About 80% water
 Proteins, carbohydrates, lipids, ions, DNA, ribosomes, inclusions
2. Nucleoid (Nuclear ) Region
 Single circular chromosome (most bacteria)– genetic information is DNA
 Coiled around basic proteins,
 Not enclosed within a nuclear membrane
 Loosely attached to plasma membrane
 Plasmids – small circular pieces of dsDNA found in the cytoplasm
o Independent of chromosomal DNA
o About 5-100 genes
 antibiotic resistance; tolerance for toxic metrals; production of toxins ;
synthesis of enzymes
o Easily gained or lost ; transferred between bacteria during conjugation
o Used to transfer genes in biotechnology applications
3. Ribosomes
 Found in all cells – prokaryotic or eukaryotic
 Site of protein synthesis
 2 subunits – large & small
 composed of proteins and ribosomalRNA ( rRNA )
 Bacterial ribosomes are 70 S; unique target for some antibiotics
 Eukaryotic ribosomes are 80S; eukaryotes have 70S ribosomes in their mitochondria
 Antibiotics which target 70S ribosomes may be toxic to eukaryotic mitochondria
4. Inclusions – reserve deposits in the cytoplasm
o Metachromatic Granules – phosphate reserves;
 stain red with methylene blue
 found in algae, fungi, protozoa, bacteria
o Polysaccharide Granules – store carbohydrates
 Stain with iodine
 Glycogen – stains reddish brown
 Starch – stains blue-purple
o Lipid Inclusions
 Found in Mycobacterium sp., Bacillus sp.
 Stain with the Sudan dyes
o Sulfur Granules – energy reserves of sulfur
 Some bacteria use sulfur for metabolism ( e.g. Thiobacillus)
o Carboxysomes
 Photosynthetic bacteria need these for C02 fixation
 Found in nitrifying bacteria, cyanobacteria, thiobacillus
o Gas Vacuoles – used to maintain buoyancy in aquatic prokaryotes
o Magnetosomes
 Iron oxide deposits – act like magnets; for movement and orientation
 Decompose toxic peroxide
 Used to make magnetite – magnetic coating for recording and data tapes
5. Actin Cytoskeleton – found in rod-shaped and spiral bacteria ; reinforce the cell membrane
and help maintain shape of the cell
6. Endospores
o “resting” cells – unique to bacteria
o for survival in unfavorable environments – resist heat, drying, chemicals, UV
radiation – persist for years in the soil
o formed by gram positive bacteria
o position – terminal, subterminal, central
o sporulation (spore formation) – can be triggered by lack of nutrients – takes
o DNA duplicates, a layer of peptidoglycan and a protein spore coat surround the
o The vegetative cell eventually dies and only the spore remains
o Germination – return to the vegetative state – triggered by damage to spore coat
o NOT A MEANS OF REPRODUCTION – 1 cell  1 spore  1 cell
o Concern for food processing – spores are resistant to heating, freezing, drying
o Some spore producing species ( e.g., Clostridium botulinum, Clostridium tetani,
Bacillus anthracis) produce toxins that can cause food poisoning or disease.
o Special Stain for Spores – Schaefer-Fulton Stain
IV. Classification Systems in the Prokaryotes
Aid in differentiation, identification, organizing, demonstrating origins and relationships
A. Classification by Phenotype
o Shape, arrangement, staining characteristics, growth characteristics, biochemistry and genetics
o Genetic and Molecular analysis is most helpful ( especially rRNA comparison)
o Bergey’s Manual of Determinative Bacteriology - provides identification schemes based on cell
wall composition, morphology, differential staining, oxygen requirements, biochemical testing.
Does NOT classify according to evolutionary relationships.
o Bergey’s Manual of Systematic Bacteriology – for classification – organized according to
evolutionary relationships.
o Only about 10% of the 2600 species listed in the Approved Lists of Bacterial Names are human
B. Taxonomic Scheme – Classification of Bacteria ( according to Bergey’s Manual of
Determinative Bacteriology)
There are 4 divisions; each divided into classes; seven classes total
Division I -- Thin, gram-negative cell walls
1. non-photosynthetic bacteria
2. anaerobic photosynthetic bacteria
3. cyanobacteria
Division II -- Thick, gram positive cell walls
1. rods and cocci
2. filamentous branching cells
Division III -- without cell walls
1. Mycoplasmas
Division IV - Unusual cell walls
1. Archaeobacteria
Classification of Viruses
Not part of any of the kingdoms; obligate intracellular parasites – discussed in Ch 6
C. Diagnostic Scheme -- Medically Important Bacteria An adaptation of the phenotypic scheme – Bacteria are identified by morphology, arrangement,
differential and structural staining, colony characteristics, biochemical analysis, serological typing
and genetic and molecular identification methods.
D. Species and Subspecies in Bacteria
The bacterial species – a population of cells with similar characteristics.
All members of the same species may not be identical. A subspecies or strain is a group of
identical bacteria that all belong to the same species, but may differ from other members of that
same species. A serotype is a group within a species that can be differentiated by having
distinct surface molecules (antigens) which stimulates a distinct pattern of antibody responses in
their host’s serum.
V. Survey of Prokaryotic Groups with Unusual Characteristics
A. Obligate Intracellular Parasites
o Rickettsia – transmitted to mammals by bite of blood sucking arthropods ( fleas, ticks,
lice, etc.) - Pathogenic – Rocky Mountain Spotted Fever; epidemic typhus
o Chlamydias - Sexually transmitted diseases; trachoma; pneumonia
B. Free-Living Non-Pathogenic Bacteria
 Photosynthetic Bacteria
 Cyanobacteria: Blue-Green Bacteria ; contain chlorophyll a; perform oxygenic
photosynthesis; widespread in aquatic environments
 Green and Purple Sulfur Bacteria; do not contain chlorophyll a; do not give off
oxygen as a result of photosynthesis; found in anaerobic environments – sulfur
springs, freshwater lakes, swamps
C. The Archaea
o Form a separate Domain
o Share many characteristics with eukaryotic cells
o Methanogens, Extreme Thermophiles, Acidophiles, Extreme halophiles, sulfur
reducers; Psychrophiles
Chapter 5 – Eukaryotic Cells
Be able to describe the structure and function of the Eukaryotic cell and its organelles
Be able to compare and contrast Eukaryotic cells and Prokaryotic Cells
Be able to explain the Endosymbiont Theory of the Evolution of Eukaryotic Cells – See Insight 5.1
The Evolution of Eukaryotes - Endosymbiont Theory – Lynn Margulis
Explains how eukaryotic cells with cell organelles evolved.
Cell Organelles such as mitochondria and chloroplasts may have evolved from a relationship between
two prokaryotic organisms.
Chloroplasts may have evolved from photosynthetic bacteria that invaded and lived inside larger
heterotrophic cells.
Mitochondria may have evolved from aerobic bacteria that invaded & lived inside larger, anaerobic
cells. Eventually, the smaller cells ( endosymbionts) lost the ability to live on their own, and the larger
cells lost the ability to survive without the smaller endosymbionts.
Evidence : Mitochondria and Chloroplasts
 Contain some of their own DNA – which is circular like that of prokaryotes
 Have their own ribosomes – 70S like those in prokaryotes
 Can make their own proteins independent of nuclear DNA
 Replicate independently of nuclear DNA
 Are motile
 Have double membranes that resemble the plasma membrane