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4: Cells: structure and function (mostly Bacterial)

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  • Bio 440: Prokaryotic/bacterial cell structure: Ch 4 Tortora

    See lecture handout diagrams

    I. Characteristics of cells

    • -growth and division
    • -metabolism
    • -DNA and RNA
    • -ribosomes for protein synthesis
    • -synthesis of cytoplasmic membranes
    • -more…

    II. Viruses are NOT cells

    • Viruses are “acellular”: Viruses lack the characteristics of cells (violate all the characteristicslisted above) and are therefore not considered cellular. Viruses are considered acellular microbial agents.
    • Viruses are obligate intracellular parasites: Viruses are obligate intracellular parasites as they canonly replicate within a host cell. (note some cellular bacteria are also obligate intracellular parasites for example Rickettsia and Chlamydia)

    III. Prokaryotic cell structure: see diagrams from lecture

    • -“pro” – before karyon; nut/kernel ~nucleus
    • -prokaryotes lack a membrane-bound nucleus and other membrane bound organelles
    • -unicellular
    • -first cells to evolve ~3.8 bya ( bya= billion years ago)
    • -size: “Unusual Giants”
    • E. coli ~ 1.0μm x 2.0 μm
    • 1985: Eupulopiscium fishelsoni ~600 μm
    • 1997: Thiomargarita namibiensis ~750μm
    • -prokaryotes are found in Domain Bacteria and Domain Archaea
    • -our discussion will focus on Domain Bacteria


    see handout diagram, textbook.

    A. structure: phospholipid bilayer and proteins based on fluid mosaic model. Hydrophobic core
    made of HC tails of fatty acid residues of phospholipids (review). Hydrophilic heads associate
    with water molecules fig.

    B. functions: semi- or selectively permeable membrane, controls movement of substances into
    and out of cell. Site for electron transport chain and photosystems in some
    bacteria and of flagellar base in flagellated bacteria and more
    -location of membrane transport proteins essential for moving large polar or
    charged substances across membrane

    C. More on transport later…

    D. Damage to cytoplasmic membrane may kill bacteria

    E. Cytoplasmic membranes are relatively weak and are vulnerable to osmotic lysis
    Vulnerability of cytoplasmic membranes: osmosis and osmotic lysis
    -osmosis: diffusion of water from area of high water concentration to area of low water
    concentration through selectively permeable membrane (e.g. cytoplasmic membrane)
    -effects of isotonic, hypertonic and hypotonic solutions on cells (aka isoosmotic, hyperosmotic, hypoosmotic):
    -Osmotic lysis:
    -most bacteria live in hypotonic environments

    -concentration of solutes inside cell is higher than concentration of solutes
    outside cell, consequently concentration of water outside cell is greater than
    concentration of water inside cell, consequently…
    -net flow of water will be from outside cell into cell across cytoplasmic
    membrane consequently

    > water pressure inside cell continues to increase
    until cytoplasmic membrane bursts, cell undergoes “lysis”. This process is called
    “osmotic lysis” and will kill bacterium.

    F. How do bacteria prevent osmotic lysis? Most common solution is formation of “cell wall” (see
    next section)

    V. Cell walls of Domain Bacteria

    A. components of bacterial cell wall: peptidoglycan (“pg”)

    1. only members of Domain Bacteria synthesize peptidoglycan

    2. function: prevention of osmotic lysis; shape of bacterium

    3. Peptidoglycan structure: alternating covalently linked
    -N-acetylglucosamine (NAG or G) and
    -N-acetylmuramic acid (NAM or M; only found in Domain Bacteria!) with
    -tetrapeptide “tails”

    4. peptide cross-links essential for strength of pg; crosslinks formed by bacterial enzymes, “transpeptidases” (aka bacterial PBP Penicillin Binding Proteins)

    a. beta-lactam antibiotics (ex penicillin, ampicillin, amoxicillin) irreversibly bind the bacterial transpeptidases so they cannot form peptide crosslinks in pg, thus weakening pg and leading to osmotic lysis
    of growing bacteria. Beta-lactams are not effective at killing bacteria in “stationary stage’ ie bacteria which are not actively growing, nor are they active against bacteria lacking cell walls ex Mycoplasma.

    b. Penicillin was discovered by Sir Alexander Fleming

    c. Vancomycin also interferes with crosslinking of pg, leading to osmotic lysis of bacteria (different mechanism than beta-lactam antibiotics however)

    5. Lysozyme (also discovered by Alexander Fleming) is an enzyme found in tears, saliva, sweat. Lysozyme cleaves the covalent glycosidic bonds between NAM and NAG, weakening cell wall, leading to osmotic lysis of some bacteria.

    B. Different types of Bacterial cell walls

    1. Gram- positive cell walls: thick layer of peptidoglycan; teichoic and lipoteichoic acids; some have additional carbohydrates; some have cell wall proteins (ex M protein of Streptococcus pyogenes)

    2. Gram-negative cell walls: thin layer of peptidoglycan connected by lipoproteins to outer membrane. Space between cell membrane and outer membrane is called the “periplasmic space”

    a. outer membrane components:
    i. lipopolysaccharide aka “LPS”, “endotoxin”; when released from dying gram- negative bacteria, triggers massive cytokine release leading to vasodilation and increased capillary permeability and “DIC” disseminated intravascular coagulation (blood clots form). Hypotension, decreased tissue perfusion, multiple organ system failure, shock (endotoxic shock) and death may result as a consequence (“endotoxemia). LPS bind to host cell leukocyte Tolllike receptors to trigger cytokine flood (more later).LPS is also used in “serotyping” gram-negative bacteria ( “O” somatic antigens; more later). LPS found only in gram-negative bacteria.
    ii. phospholipids
    iii. porins: protein channels through which hydrophilic substances can
    cross outer membrane

    b. outer membrane functions: prevents diffusion of secreted enzymes; protects
    bacterium against toxic substances (ex some antibiotics such as penicillin,
    lysozyme, bile)

    3. Acid fast cell wall: e.g.,Mycobacterium tuberculosis, leprae: peptidoglycan covered by
    mycolic acid-lipid bilayer. Creates hydrophobic barrier against antibiotics , chemicals, stains,
    drying. Nutrients slow to pass barrier therefore these bacteria are very slow growing (difficult to
    culture and perform antibiotic sensitivity testing). Patients infected with Mycobacterium are often
    on long term antimicrobial therapy (months, years!) Protein porins in mycolic acid-lipid layer
    permit passage of some hydrophilic substances. Described as a ‘waxy or lipid-rich” cell wall.
    Requires special staining procedure (acid-fast stain see p109 in textbook).

    4. Some Bacteria lack cell walls, e.g., Mycoplasm, Chlamydia and “L-forms”. If a patient suffers
    from infection with such bacteria, treatment with beta-lactam antibiotics would have no effect as
    these bacteria lack the target of the antibiotics. (recall Mycoplasma “steal” cholesterol from their
    animal hosts to incorporate into their cell membranes to strengthen membranes in absence of cell

    5. Domain Archaea: Archaea do not synthesize true peptidoglycan-
    External Structures of Prokaryotic cells

    VI. Glycocalyx= “sugar cup”, a “sticky” covering found on some prokaryotes

    Two types of glycocalyces: capsules (tightly attached) and slime layers (loosely attached).
    Capsule/Slime layers: outermost layer, covers cell wall, produced by many but not all bacteria.
    Structure: Usually polysaccharides, some exceptions (Bacillus anthracis produces
    capsule of poly-D-glutamic acid)
    -weakly antigenic, the “K” antigens of Enterobacteriaceae

    • prevents desiccation/drying out
    • adherence to surfaces (oral streptococci make sticky capsule/slime
    layer which permits adherence to tooth surfaces),
    • antiphagocytic : inhibits phagocytosis by leukocytes , essential for
    pathogenicity of many bacteria

    VII. Flagella (plural; singular=flagellum) Read as homework

    • function: motility.
    • structure= flagellin protein subunits make up 20nm diameter filament, attached to hook and basal
    • body . Basal body consists of protein rings and shaft embedded in cell wall/cell membrane (more
    • in lab). Flagellar proteins act as antigens (trigger antibody production). “H” or “Hauch” antigens
    • of Enterobacteriaceae are the flagellar antigens used in serotyping (eg. E . coli O157:H7).
    • Flagellar arrangements: monotrichous( single polar flagellum), amphitrichous (both ends),
    • lophotrichous (tuft), peritrichous (flagella all over) - Flagella rotates similar to boat propeller
    • Chemoreceptors located in cell membrane permit bacteria to detect concentration gradients of
    • chemicals in environment. Chemotaxis is movement in response to chemical gradients. Positive
    • chemotaxis: movement in direction of increasing concentration gradient ex nutrient molecules.
    • Negative chemotaxis: movement down concentration gradient ex toxin molecules
    • Axial filaments or endoflagella : spirochetes are spiral shaped bacteria. Examples are Treponema
    • pallidum (causes syphilis) and Borrelia burgdorferi (causes Lyme Disease). These bacteria have
    • bundles of endoflagella attached at both ends of their cells covered by an outer sheath forming an
    • axial filament . Rotation of the endoflagella causes axial filament to rotate around spirochete,
    • permitting the bacteria to “corkscrew” through their environment, often thick mucous blankets,
    • perhaps even through tissues.

    VIII. Pili and fimbriae

    • function: attachment.
    • structure= pilin protein subunits form hollow tubes projecting from surface of cell.
    • adhesins: Specific proteins in pili called adhesins permit attachment to surfaces in environment, including host cells. Adhesins often bind to specific receptors on host cell surfaces
    • fimbriae: usually numerous, relatively short, used to attach to surfaces in environment, including
    • other cells ex Neisseria gonorrhoeae uses fimbriae to attach to cells of host mucous membranes.
    • Reports have suggested Neisseria can change the types of adhesins expressed on its fimbriae so it
    • can first attach to mucosal cells of genital tract, then to cells of oral region, then cells of eye. What would happen if a mutation inhibited production of fimbriae by Neisseria?
    • Role of fimbriae in Biofilms
    • sex pilus (gram -negative bacteria aka conjugation pilus, “F” pilus): attaches one
    • bacteria to another, facilitates exchange of genetic information/DNA. example.
    • Involved in transfer of antibiotic resistance genes between bacteria.
    • Inside the bacterial cell

    IX. Cytoplasm and internal structures: 90% water. Contains chromosome, plasmids, ribosomes, enzymes, nutrients, waste products, inclusion bodies

    X. Chromosome

    most bacteria have single, circular double stranded DNA chromosome ( a few have linear chromosomes). DNA carries genetic information. DNA base sequence determines amino acid sequence of proteins. (more later -antibiotics fluoroquinolones such as ciprofloxacin used to treat anthrax victims are bacterial DNA gyrase inhibitors; these antibiotics prevent “relaxation” of supercoiled bacterial DNA required for DNA replication and transcription (other DNA gyrase inhibitors include nalidixic acid and novobiocin)

    XI. Plasmids

    extrachromosomal, circular, self-replicating DNA. Frequently carry “extra” genetic
    information example antibiotic resistance genes (“R” or resistance plasmids). May be passed
    from one bacterium to another resulting in spread of antibiotic resistance. Conjugative plasmids
    carry genes for synthesis of sex pili and proteins involved in transfer of bacterial DNA from
    donor to recipient (more later in genetics)

    XII. Ribosomes

    70S ribosomes (compared to larger 80s cytoplasmic ribosomes of eukaryotes)

    • -structure: 2 subunits, 50S and 30S; made of ribosomal RNA/rRNA and ribosomal proteins
    • -site of protein synthesis
    • -S-Svedberg unit, used to express sedimentation rates using ultracentrifuges.
    • -70S bacterial ribosomes are the target of many antibiotics examples tetracycline,
    • chloramphenicol, macrolides (erythromycin, azithromycin) aminoglycosides ex gentamicin,
    • kanamycin. These antibiotics inhibit protein synthesis by bacteria

    XIII. Endospores

    resistant, dormant /resting structures, protect bacterium’s DNA, under harsh
    conditions. Layers of protein, peptidoglycan, high calcium ion contenet and dipicolinic acid, low water
    contenet. .Bacillus and Clostridium are endospore formers. Endospores can germinate to produce new
    metabolically active, replicating vegetative cells. If inhaled, endospores of Bacillus anthracis will
    germinate in lungs causing pneumonia and may spread throughout body (usually lethal). Unfavorable conditions trigger vegetative cells to sporulate and produce endospores. Contain very little water and dipicolinic acid (heat resistance)
    See: anthrax and clostridial diseases

    XIV. Inclusions (not on exam 1)

    XV. Cytoskeleton read (not on exam 1)

    Addition: Homework transport of substances across membranes and eukaryotic cells-read sections in
    Transport of substances across cell membranes is presented following discussion of eukaryotic cells in the
    lecture PowerPoint, however a few notes regarding specialized transport in bacteria follow:
    Reference: Protein Secretion Systems in Gram-negative bacteria Source p63-65 Prescott, Harley and
    Klein’s Microbiology Wiley et al ed 2008 McGraw Hill Publ
    Type III protein secretion systems of some gram-negative bacterial pathogens: these systems
    permit injection of virulence factors (ex toxins) into host target cells. Structurally complex,
    similar to hypodermic syringe/needle; mutation in genes for Type III secretion may have permitted
    evolution of bacterial flagella.
    Type IV secretion systems: used to transport proteins AND to transfer DNA during conjugation;
    components form syringe-like structure similar to Type III system

    Bio 440 Eukaryotic Cells: Ch 4 Tortora

    I. Eukaryotic microorganisms: organisms with membrane bound nucleus.
    Domain Eukarya
    Kingdoms: ( out-of-date" Protista" "algae", "protozoa"), Fungi, Plantae, Animalia

    II. Evolution of endomembrane system
    Primitive prokaryotic cell: in-folding of cell membrane--> nuclear membrane, endoplasmic reticulum, Golgi body, vesicles, lysosomes. Compartmentalization of functions.

    III. Nucleus

    A. Nuclear membrane with pores
    B. Chromosomes and reproduction: multiple, linear chromosomes of double-stranded DNA split into
    coding exons and non-coding introns. DNA associated with histone proteins.
    Eukaryotes which reproduce sexually normally are “diploid”, ie cells contain 2 copies of each
    chromosome, (one copy of each chromosome donated by each parent). Therefore there are usually 2 copies
    of each gene, and the genes may not be identical. Haploid gametes are formed during sexual reproduction,
    containing one copy of each chromosome. 2 haploid gametes fuse to form a diploid zygote (fusion of
    gamete nuclei form zygote nucleus). Some eukaryotic microbes can reproduce asexually and have haploid
    cells. Some organisms can reproduce sexually or asexually (ex fungi) and therefore may have either
    diploid or haploid cells. HOMEWORK read mitosis and meiosis in textbook

    IV. Endoplasmic reticulum

    A. Continuous w/ nuclear membrane
    B. 2 types

    1. RER=Rough Endoplasmic Reticulum: “studded” with ribosomes -synthesis of proteins destined for export, incorporation into membranes or delivery to other organelles
    2. SER= Smooth endoplasmic reticulum -lipid synthesis, detoxification

    V. Golgi Body

    receive proteins/lipids from ER via transport vesicle; processing and shipping to final
    destination (secretion, membranes, other organelles)

    VI. Lysosomes and Peroxisomes

    Lysosomes (animal cells): vesicles filled with hydrolytic enzymes. May fuse with phagosomes to hydrolyze nutrient molecules or destroy invading microorganisms (phagocytosis). Peroxisomes :vesicles containing peroxidase/catalase and other enzymes. Plants: oxidize fats. Animals: oxidize amino acids.

    VII. Ribosomes

    80S cytoplasmic ribosomes ; sites of protein synthesis. Free in cytoplasm or fixed to RER. In mitochondria and chloroplasts, 70S-like ribosomes.

    VIII. Mitochondria

    all aerobic respiring eukaryotes (exception: Giardia lacks mitochondria)
    A. “Powerhouse” of cell, site of ATP generation via aerobic respiration
    C6H12O6 + 6O2--> 6CO2 + 6 H2O + Energy (heat + ATP)
    B. Evolved from primitive prokaryotic cell? see Theory of Endosymbiosis/Endosymbiotic Theory

    IX. Chloroplast: photosynthetic plants and algae

    A. Sites of oxygenic photosynthesis: 6CO2 + 6H2O--light energy--> C6H12O6 + 6O2
    B. Evolved from primitive cyanobacteria? Theory of Endosymbiosis/Endosymbiotic Theory

    X. Theory of Endosymbiosis/Endosymbiotic

    primitive nucleated cell phagocytizes (“eats”)
    primitive aerobic respiring bacterium. Bacterium becomes an endosymbiont, living within host cell,
    generates ATP for host, host provides protection for bacterium. Bacterium eventually evolves into
    mitochondrion. Similar story for chloroplast evolution. Primitive nucleated cell with mitochondria
    phagocytize primitive photosynthetic cyanobacterium. Bacterium becomes endosymbiont, evolves into

    Evidence to support Theory of Endosymbiosis:
    1. mitochondria (mito.) and chloroplast (chloro) are self replicating-divide independently of host
    2. mito. and chloro. have own self-replicating, circular chromosomes similar to prokaryotic
    3. mito/chlor. size similar to bacteria
    4. membrane arrangement of mito./chlor. fit theory of bacterium engulfed in phagosome
    5. mito./chlor. have ribosomes similar to prokaryotic 70S ribosomes and are inhibited by
    antibiotics targeting 70S ribosomes
    6. mito/chloro. ribosomal RNA sequences similar to Bacteria rRNA sequences.

    XI. Cytoskeleton

    A. Microtubules of tubulin subunits: mitotic spindles, flagella and cilia (protein dynein associated w/fl & cilia).
    B. Microfilaments of actin subunits: cytoplasmic streaming; pseudopodia formation f amoeba and slime molds
    C. Intermediate fibers: variety ex keratin: rigidity

    XII. Appendages

    A. Flagella: motility. Structurally very different from bacterial flagella. Microtubules (9 doublets + 2
    central) covered with cell membrane, flex/beat (do not rotate/turn like bacterial flagella). ex Protozoa
    B. Cilia: very similar to flagella except shorter, more numerous. Protozoa ciliates
    Ciliated epithelium of respiratory tract important part of mucociliary escalator; destroyed by viruses,
    smoking, predisposes to bacterial respiratory infections. Ciliated epithelium of oviduct important for
    moving egg to uterus. Pathogens such as Chlamydia and Neiserria gonorrhoeae cause destruction of cilia,
    results in ectopic pregnancy, sterility.

    XIII. Cell wall: provides shape, resists turgor pressure/prevents osmotic lysis

    A. Animals lack cell wall; some protozoa have protein layer called pellicle
    B. Fungi and algae have cell wall
    1. fungi cell wall: may contain chitin, polymer of N-acetylglucosamine (NAG) nitrogencontaining
    2. some algal cell walls and some fungal walls contain cellulose

    XIV. Cell membrane phospholipid bilayer with proteins based on fluid mosaic model. Proteins may move
    laterally. Consistency of membrane is like thin layer of oil. Primary function is to control movement of
    substances into and out of cell

    A. Homework: Movement of substances across membranes text

    1. nonpolar substances may cross: diffusion, passive process
    -Oxygen, carbon dioxide, ethanol and medium-length fatty acids may diffuse across
    membrane. (A small amount of water may also diffuse through phospholipid bilayer )
    2. water may cross rapidly via water-transmitting pores (aquaporins”)
    -osmosis, passive. Know lysis, plasmolysis and when each happens
    - “osmosis” and “tonicity” (know)
    3. Hydrophilic substances ie charged or polar substances, may not cross membrane unless assisted
    by transport proteins ex protein pores/carrier proteins/”permeases”
    4. Note: whenever substances are moved against their concentration gradient( that is from an area
    of low concentration to an area of high concentration), energy must be expended.

    passive transport: substance moved from area / Transport requiring energy/active transport
    of high concentration to low. No NRG req’d. / (energy=ATP, proton/chemical gradient)
    1. Simple diffusion / 4. Active transport: Substance moved from low to
    2. Osmosis / high concentration. Specific protein carriers. sugars,
    amino acids, vitamins
    3. Facilitated diffusion: /
    - protein mediates diffusion. / 5. group translocation: (primarily in bacteria;) --
    Specific channels/pores or / -substance to be transported is modified
    carrier proteins. / as it crosses membrane. ex glucose

    B. Specialized transport: Animal cells/ protozoa lacking cell walls: endocytosis (pinocytosis and
    phagocytosis) and exocytosis; require cytoskeleton rearrangements and energy expenditure
    endocytosis :taking in material in membrane in-folding ->vesicles

    -: engulf cell/solid= phagocytosis engulf liquid =pinocytosis
    ex phagocytic cells of immune system: monocytes-macrophages and
    neutrophils: recognize “foreign” bacterial invaders, attach, phagocytize
    and destroy via phagosomes and lysosomes
    -also receptor mediated endocytosis
    -exocytosis: expel/secrete substances from cell via vesicles