Microscopy Fundamentals

Scientists use microscopes to visualize cells too small to see with the naked eye.
Light microscopes (LMs) pass visible light through a specimen and then through glass lenses, magnifying the image by bending the light.
Key parameters of microscopy include magnification, resolution, and contrast.
- Magnification is the ratio of an object's image size to its real size.
- Resolution measures image clarity and is the minimum distance between two distinguishable points.
- Contrast refers to visible differences in parts of the sample.
LMs can magnify objects effectively up to 1,000 times their actual size.
- Techniques like staining and labeling enhance contrast and reveal cell components.
- Most subcellular structures, including organelles, are too small to be resolved by LMs.
Advanced light microscopy techniques, like confocal microscopy and deconvolution microscopy, provide sharper images of 3-D tissues and cells.
- New cell labeling techniques improve resolution.

Two types of electron microscopes (EMs), scanning electron microscopes (SEMs) and transmission electron microscopes (TEMs), are used to study subcellular structures.
SEMs focus a beam of electrons onto the surface of a specimen, creating 3-D-like images.
TEMs focus a beam of electrons through a specimen.
Cryo-electron microscopy (cryo-EM) uses a beam of electrons to visualize molecules.
TEMs are primarily used to study the internal structure of cells.

Cell fractionation separates major organelles from each other by breaking cells apart.
Centrifuges are used to fractionate cells into their component parts.
Cell fractionation helps scientists determine the functions of organelles.
Biochemistry and cytology correlate cell function with structure.

The basic structural and functional unit of every organism is either a prokaryotic or eukaryotic cell.
Organisms in the domains Bacteria and Archaea consist of prokaryotic cells.
Protists, fungi, animals, and plants all consist of eukaryotic cells.
All cells share basic features:
- Plasma membrane
- Semifluid substance called cytosol
- Chromosomes (carry genes)
- Ribosomes (make proteins)
Prokaryotic cells are characterized by:
- Absence of a nucleus
- DNA located in an unbound region called the nucleoid
- Lack of membrane-bound organelles
- Cytoplasm bound by the plasma membrane.

Eukaryotic cells have internal membranes that compartmentalize their functions.
These components either directly connect or communicate through vesicles for transfer.

The endoplasmic reticulum (ER) accounts for more than half of the total membrane in many eukaryotic cells.
The ER membrane is continuous with the nuclear envelope.
There are two distinct regions of the ER:
- Smooth ER, lacking ribosomes.
- Rough ER, studded with ribosomes on its surface.

Has bound ribosomes, which secrete glycoproteins (proteins bound to carbohydrates).
Distributes transport vesicles (membrane-bound proteins).
Serves as a membrane factory for the cell.

Consists of flattened membranous sacs called cisternae.
It modifies ER products, manufactures certain macromolecules, and sorts and packages materials into transport vesicles.

Lysosomes are membrane-bound sacs containing hydrolytic enzymes that digest macromolecules.
Lysosomal enzymes can hydrolyze proteins, fats, polysaccharides, and nucleic acids.
These enzymes work best in the acidic environment inside lysosomes.

Some cells engulf other cells by phagocytosis, forming food vacuoles.
A lysosome fuses with the food vacuole and digests the molecules.
Lysosomes also use enzymes to recycle the cell’s own organelles and macromolecules, a process called autophagy.

Plant and fungal cells may have one or several vacuoles, derived from the ER and Golgi apparatus.
Food vacuoles are formed by phagocytosis.
Contractile vacuoles, found in many freshwater protists, pump excess water out of cells.
Central vacuoles, found in many mature plant cells, hold organic compounds and water.

Contains a large central vacuole, often taking up the majority of the cell's volume.

Convert chemical energy stored in food into a form that cells can use for work, via cellular respiration.
Have two membranes: an outer membrane and an inner membrane folded into cristae.
The inner membrane encloses the mitochondrial matrix.
Contain their own DNA.

Contain the green pigment chlorophyll, as well as enzymes and other molecules involved in photosynthesis.
Found in the leaves and other green organs of plants and algae.
Have a structure that includes:
- Thylakoids, membranous sacs, stacked to form a granum.
- Stroma, the internal fluid.
They are one of a group of plant organelles called plastids.

Extends throughout the cytoplasm, organizing the cell’s structures and activities.
Anchors many organelles.
Composed of three types of molecular structures:
- Microtubules
- Microfilaments
- Intermediate filaments