Scanning Probe Microscopes

Microscopy and Cell Morphology

3.1 Microscopic Techniques: The Instruments (Table 3.1) Principles of Light Microscopy: The Bright-Field Microscope

1. In light microscopy, visible light passes through the specimen. The most common type of microscope is the bright-field microscope. (Figure 3.1)

2. The objective lens and the ocular lens in combination magnify an object by a factor equal to the product of the magnification of each of the individual lenses.

3. The usefulness of a microscope depends on its resolving power. (Figure 3.2)

Light Microscopes that Increase Contrast

1. The phase contrast microscope amplifies differences in refraction. (Figure 3.4)

2. The interference microscope combines two light beams that pass through the specimen separately, causing the specimen to appear as a three-dimensional image. (Figure 3.5)

3. The dark-field microscope directs light toward a specimen at an angle. (Figure 3.6)

4. The fluorescence microscope is used to observe cells that have been stained with fluorescent dyes. (Figure 3.7)

5. The confocal scanning laser microscope is used to construct a three-dimensional image of a thick structure and to provide detailed sectional views of the interior of an intact cell. (Figure 3.8)

Electron Microscopes

1. Electron microscopes use electromagnetic lenses, electrons, and fluorescent screens to produce a magnified image. (Figure 3.9)

2. Transmission electron microscopes (TEMs) transmit electrons through a specimen that has been prepared by thin sectioning, freeze fracturing, or freeze etching. (Figure 3.10)

3. Scanning electron microscopes scan a beam of electrons back and forth over the surface of a specimen, producing a three-dimensional effect. (Figure 3.11)

1. Scanning probe microscopes map the bumps and valleys of a surface on an atomic scale. (Figure 3.12)

3.2 Microscopic Techniques: Dyes and Staining (Table 3.2) Differential Stains

1. The Gram stain is the most widely used procedure for staining bacteria; Gram-positive bacteria stain purple and Gram-negative bacteria stain pink. (Figure 3.14)

2. The acid-fast stain is used to stain organisms such as Mycobacteria, which do not take up stains readily; acid-fast organisms stain pink and all other organisms stain blue. (Figure 3.15)

Special Stains to Observe Cell Structures

1. The capsule stain is an example of a negative stain; it colors the background, allowing the capsule to stand out as a halo around an organism. (Figure 3.16)

2. The spore stain uses heat to facilitate the staining of endospores. (Figure 3.17)

3. The flagella stain employs a mordant that enables the stain to adhere to and coat the otherwise thin flagella. (Figure 3.18)

Fluorescent Dyes and Tags

1. Some fluorescent dyes bind compounds that characterize all cells; others bind to compounds specific to only certain cell types. (Figure 3.19)

2. Immunofluorescence is used to tag a specific protein of interest with a fluorescent compound.

3.3 Morphology of Prokaryotic Cells


1. Most common prokaryotes are either cocci or rods; other shapes include coccobacilli, vibrios, spirilla, and spirochetes. Pleomorphic bacteria have variable shapes. (Figure 3.20)

80 Chapter 3 Microscopy and Cell Structure


1. Cells adhering to one another following division form a characteristic arrangement that depends on the plane in which the bacteria divide. (Figure 3.22)

Multicellular Associations

1. Some types of bacteria, such as myxobacteria, typically live in associations containing multiple cells.

2. Cells within biofilms often alter their activities when a critical number of cells are present.

The Structure of the Prokaryotic Cell

3.4 The Cytoplasmic Membrane

Structure and Chemistry of the Cytoplasmic Membrane (Figure 3.24)

1. The cytoplasmic membrane is a phospholipid bilayer embedded with a variety of different proteins.

2. Some membrane proteins function in transport; others provide a mechanism by which cells can sense and adjust to their surroundings.

Permeability of the Cytoplasmic Membrane

1. The cytoplasmic membrane is selectively permeable; water, gases, and small hydrophobic molecules are among the few compounds that can pass through by simple diffusion.

2. The inflow of water into the cell exerts more osmotic pressure on the cytoplasmic membrane than it can generally withstand; however, the rigid cell wall can withstand the pressure. (Figure 3.25)

The Role of the Cytoplasmic Membrane in Energy Transformation

1. The electron transport chain within the membrane expels protons, generating an electrochemical gradient, which contains a form of energy called proton motive force. (Figure 3.26)

3.5 Directed Movement of Molecules Across the Cytoplasmic Membrane

Transport Systems (Table 3.4)

1. Facilitated diffusion, or passive transport, moves impermeable compounds from one side of the membrane to the other by exploiting the concentration gradient. (Figure 3.27)

2. Active transport mechanisms use energy, either proton motive force or ATP, to accumulate compounds against a concentration gradient.

3. Group translocation chemically modifies a molecule during its passage through the cytoplasmic membrane. (Figure 3.30)


1. The presence of a characteristic signal sequence targets proteins for secretion.

3.6 Cell Wall

Peptidoglycan (Figure 3.32)

1. Peptidoglycan is a macromolecule found only in the Bacteria and provides rigidity to the cell wall.

2. Peptidoglycan is composed of glycan strands, which are alternating subunits of N-acetylmuramic acid (NAM) and N-acetylglucosamine (NAG), interconnected via the tetrapeptide chains on NAM.

The Gram-Positive Cell Wall (Figure 3.33)

1. The Gram-positive cell wall contains a relatively thick layer of peptidoglycan.

2. Teichoic acids stick out of the peptidoglycan layer.

The Gram-Negative Cell Wall (Figure 3.34)

1. The Gram-negative cell wall has a relatively thin layer of peptidoglycan sandwiched between the cytoplasmic membrane and an outer membrane.

2. Periplasm contains a variety of proteins, including those involved in nutrient degradation and transport.

3. The outer membrane contains lipopolysaccharides. The Lipid A portion of the lipopolysaccharide molecule is toxic, which is why LPS is called endotoxin. (Figure 3.35)

4. Porins form small channels that permit small molecules to pass through the outer membrane.

Antibacterial Compounds that Target Peptidoglycan

1. Penicillin prevents the cross-linking of adjacent glycan chains during peptidoglycan synthesis.

2. Lysozyme breaks the bond that links alternating NAG and NAM molecules, destroying the structural integrity of peptidoglycan.

Differences in Cell Wall Composition and the Gram Stain

1. The Gram-positive, but not the Gram-negative, cell wall retains the crystal violet-iodine dye complex even when subjected to the trauma of acetone-alcohol treatment.

Characteristics of Bacteria that Lack a Cell Wall

1. Because Mycoplasma species do not have a cell wall, they are extremely variable in shape and are not affected by lysozyme or penicillin. (Figure 3.36)

Cell Walls of the Domain Archaea

1. Archaea have a greater variety of cell wall types than do the Bacteria.

3.7 Surface Layers External to the Cell Wall


1. A capsule is a distinct and gelatinous layer; a slime layer is diffuse and irregular. (Figure 3.37)

2. Capsules and slime layers enable bacteria to adhere to surfaces. Some capsules allow disease-causing microorganisms to thwart the innate defense system.

3.8 Filamentous Protein Appendages

Flagella (Figure 3.38)

1. The flagellum is a long protein structure that is responsible for most types of bacterial motility. (Figure 3.39)

2. Chemotaxis is the directed movement toward an attractant or away from a repellent (Figure 3.40)

3. Phototaxis, aerotaxis, and magnetotaxis are directed movements toward light, oxygen, and a magnetic field, respectively.

Pili (Figure 3.42)

1. Many types of pili (fimbriae) enable attachment of cells to specific surfaces.

2. Sex pili are involved in conjugation, which enables DNA to be transferred from one cell to another.

3.9 Internal Structures

The Chromosome (Figure 3.43)

1. The chromosome of prokaryotes resides in the nucleoid rather than within a membrane bound nucleus; it is typically a single, circular, double-stranded molecule that contains all the genetic information required by a cell.


1. Plasmids are circular, double-stranded DNA molecules that typically encode genetic information that may be advantageous, but not required by the cell.

Ribosomes (Figure 3.44)

1. Ribosomes facilitate the joining of amino acids. The 70S bacterial ribosome is composed of a 50S and a 30S subunit.

Storage Granules (Figure 3.45)

1. Storage granules are dense accumulations of high molecular weight polymers, which are synthesized from a nutrient that a cell has in relative excess.

Gas Vesicles

1. Gas vesicles are gas-permeable, water-impermeable rigid structures that provide buoyancy to aquatic cells, enabling the cell to float or sink to an ideal position in the water column.


1. Endospores are a dormant stage produced by members of Bacillus and Clostridium; they can germinate to become a vegetative cell. (Figure 3.46)

2. Endospores are extraordinarily resistant to conditions such as heat, desiccation, toxic chemicals, and ultraviolet irradiation.

The Eukaryotic Cell (Figure 3.48) (Table 3.6)

3.10 The Plasma Membrane

1. The plasma membrane is a phospholipid bilayer embedded with proteins.

2. Proteins in the membrane are involved in transport, structural integrity, and signaling.

3.11 Transfer of Molecules Across the Plasma Membrane

Transport Proteins

1. Channels are pores in the membrane that are so small that only specific ions can pass through. These channels are gated.

Summary 81

2. Carriers mediate facilitated diffusion and active transport.

Endocytosis and Exocytosis (Figure 3.50)

1. Receptor-mediated endocytosis is the most common form of endocytosis in animal cells. The endocytic vesicle fuses with an endosome, which then fuses with a lysosome.

2. Protozoa and phagocytes take up bacteria and debris through the process of phagocytosis. The phagosome fuses with the lysosome, where the material is digested.

3. Exocytosis expels products and is the reverse of endocytosis.


1. Proteins that are destined for a non-cytoplasmic region are made by ribosomes bound to the endoplasmic reticulum.

3.12 Protein Structures Within the Cytoplasm

1. The 80S eukaryotic ribosome is composed of 60S and 40S subunits.

Cytoskeleton (Figure 3.51)

1. The cytoskeleton is composed of microtubules, actin filaments, and intermediate fibers.

Flagella and Cilia (Figure 3.52)

1. Flagella propel a cell or pull the cell forward.

2. Cilia often cover the surface of a cell and move in synchrony to either propel a cell or move material along a stationary cell.

3.13 Membrane-Bound Organelles

The Nucleus (Figure 3.53)

1. The nucleus, which contains DNA, is the predominant distinguishing feature of eukaryotes.

Mitochondria and Chloroplasts

1. Mitochondria use the energy released during the degradation of organic compounds to generate ATP. (Figure 3.55)

2. Chloroplasts contain chlorophyll, which captures the energy of sunlight; this is then used to synthesize ATP. (Figure 3.56)

Endoplasmic Reticulum (Figure 3.57)

1. The rough endoplasmic reticulum serves as the site where proteins not located in the cytoplasm are synthesized.

2. Within the smooth endoplasmic reticulum, lipids are synthesized and degraded, and calcium is stored.

The Golgi Apparatus (Figure 3.58)

1. The Golgi apparatus modifies and sorts molecules synthesized in the endoplasmic reticulum.

Lysosomes and Peroxisomes

1. Lysosomes carry digestive enzymes.

2. Peroxisomes are the organelles in which oxygen is used to oxidize certain substances.

Chapter 3 Microscopy and Cell Structure

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