BIS 1A Handout 6 - The Cell

The Importance of Cells

All organisms are made of cells.

The cell is the simplest collection of matter that can live.

All cells are related by their descent from earlier cells.

Biologists use microscopes and the tools of biochemistry to study cells

The discovery and early study of cells progressed with the invention of microscopes in 1590 and their improvement in the 17th century.

In a light microscope (LM), visible light passes through the specimen and then through glass lenses.

Microscopes vary in magnification and resolving power.

Magnification is the ratio of an object's image to its real size.

Resolving power is a measure of image clarity.

It is the minimum distance two points can be separated and still be distinguished as two separate points.

Resolution is limited by the shortest wavelength of the radiation used for imaging.

The minimum resolution of a light microscope is about 200 nanometers (nm), the size of a small bacterium.

Light microscopes can magnify effectively to about 1,000 times the size of the actual specimen.

While a light microscope can resolve individual cells, it cannot resolve much of the internal anatomy, especially the organelles.

To resolve smaller structures, we use an electron microscope (EM), which focuses a beam of electrons through the specimen or onto its surface.

Because electron beams have shorter wavelengths than visible light, electron microscopes have finer resolution.

Theoretically, the resolution of a modern EM could reach 0.002 nanometer (nm), but the practical limit is closer to about 2 nm.

Transmission electron microscopes (TEMs) are used mainly to study the internal ultrastructure of cells.

A TEM aims an electron beam through a thin section of the specimen.

Scanning electron microscopes (SEMs) are useful for studying surface structures.

The SEM has great depth of field, resulting in an image that seems three-dimensional.

Light microscopes do not have as high a resolution, but they can be used to study live cells.

Microscopes are major tools in cytology, the study of cell structures.

Cell biologists can isolate organelles to study their functions.

The goal of cell fractionation is to separate the major organelles of the cells so their individual functions can be studied.

This process is driven by an ultracentrifuge, a machine that can spin at up to 130,000 revolutions per minute and apply forces of more than 1 million times gravity (1,000,000 g).

Fractionation begins with homogenization, gently disrupting the cell.

The homogenate is spun in a centrifuge to separate heavier pieces into the pellet while lighter particles remain in the supernatant.

As the process is repeated at higher speeds and for longer durations, smaller and smaller organelles can be collected in subsequent pellets.

This enables the functions of these organelles to be determined, especially by the reactions or processes catalyzed by their proteins.

Cytology and biochemistry complement each other in correlating cellular structure and function.

Eukaryotic cells have internal membranes that compartmentalize their functions

Prokaryotic and eukaryotic cells differ in size and complexity.

All cells are surrounded by a plasma membrane.

The semifluid substance surrounded by the membrane is the cytosol, containing the organelles.

All cells contain chromosomes that have genes in the form of DNA.

All cells also have ribosomes, tiny organelles that make proteins using the instructions contained in genes.

A major difference between prokaryotic and eukaryotic cells is the location of chromosomes.

In a eukaryotic cell, chromosomes are contained in a membrane-enclosed organelle, the nucleus.

In a prokaryotic cell, the DNA is concentrated in the nucleoid without a membrane separating it from the rest of the cell.

The region between the nucleus and the plasma membrane is the cytoplasm.

All the material within the plasma membrane of a prokaryotic cell is cytoplasm.

Within the cytoplasm of a eukaryotic cell are a variety of membrane-bound organelles of specialized form and function.

These membrane-bound organelles are absent in prokaryotes.

Eukaryotic cells are generally much bigger than prokaryotic cells.

At the lower limit, the smallest bacteria, mycoplasmas, are between 0.1 to 1.0 micron.

Most bacteria are 1-10 microns in diameter.

Eukaryotic cells are typically 10-100 microns in diameter.

Rates of chemical exchange across the plasma membrane may be inadequate to maintain a cell with a very large cytoplasm.

Larger organisms do not generally have larger cells than smaller organisms-simply more cells. A human is made up of 200 trillion cells.

Internal membranes compartmentalize the functions of a eukaryotic cell.

A eukaryotic cell has extensive and elaborate internal membranes, which partition the cell into compartments.

These membranes also participate directly in metabolism, as many enzymes are built into membranes.

The compartments created by membranes provide different local environments that facilitate specific metabolic functions, allowing several incompatible processes to go on simultaneously in a cell.

The eukaryotic cell's instructions are in the nucleus and carried out by the ribosomes

The nucleus contains most of the genes in a eukaryotic cell.

Additional genes are located in mitochondria and chloroplasts.

The nucleus averages about 5 microns in diameter.

The nucleus is separated from the cytoplasm by a double membrane called the nuclear envelope.

The two membranes of the nuclear envelope are separated by 20-40 nm.

The envelope is perforated by pores that are about 100 nm in diameter.

At the lip of each pore, the inner and outer membranes of the nuclear envelope are fused to form a continuous membrane.

A protein structure called a pore complex lines each pore, regulating the passage of certain large macromolecules and particles.

The nuclear side of the envelope is lined by the nuclear lamina, a network of protein filaments that maintains the shape of the nucleus.

There is evidence that a framework of fibers called the nuclear matrix extends through the nuclear interior.

Within the nucleus, the DNA and associated proteins are organized into discrete units called chromosomes, structures that carry the genetic information.

Each chromosome is made up of fibrous material called chromatin, a complex of proteins and DNA.

Stained chromatin appears through light microscopes and electron microscopes as a diffuse mass.

As the cell prepares to divide, the chromatin fibers coil up and condense, becoming thick enough to be recognized as the familiar chromosomes.

Each eukaryotic species has a characteristic number of chromosomes.

A typical human cell has 46 chromosomes.

A human sex cell (egg or sperm) has only 23 chromosomes.

A nucleolus is a region of densely stained fibers and granules adjoining chromatin, the.

In the nucleolus, ribosomal RNA (rRNA) is synthesized and assembled with proteins from the cytoplasm to form ribosomal subunits.

The subunits pass through the nuclear pores to the cytoplasm, where they combine to form ribosomes.

The nucleus directs protein synthesis by synthesizing messenger RNA (mRNA).

The mRNA travels to the cytoplasm through the nuclear pores and combines with ribosomes to translate its genetic message into the primary structure of a specific polypeptide.

Ribosomes build a cell's proteins.

Ribosomes, containing rRNA and protein, are the organelles that carry out protein synthesis.

Some ribosomes, free ribosomes, are suspended in the cytosol and synthesize proteins that function within the cytosol.

Other ribosomes, bound ribosomes, are attached to the outside of the endoplasmic reticulum or nuclear envelope.

These synthesize proteins that are either included in membranes or exported from the cell.

The endomembrane system regulates protein traffic and performs metabolic functions in the cell

Many of the internal membranes in a eukaryotic cell are part of the endomembrane system.

These membranes are either directly continuous or connected via transfer of vesicles, sacs of membrane.

The endomembrane system includes the nuclear envelope, endoplasmic reticulum, Golgi apparatus, lysosomes, vacuoles, and the plasma membrane.

The endoplasmic reticulum manufactures membranes and performs many other biosynthetic functions.

The endoplasmic reticulum (ER) accounts for half the membranes in a eukaryotic cell.

The ER includes membranous tubules and internal, fluid-filled spaces called cisternae.

The ER membrane is continuous with the nuclear envelope, and the cisternal space of the ER is continuous with the space between the two membranes of the nuclear envelope.

There are two connected regions of ER that differ in structure and function.

Smooth ER looks smooth because it lacks ribosomes.

Rough ER looks rough because ribosomes (bound ribosomes) are attached to the outside, including the outside of the nuclear envelope.

The smooth ER is rich in enzymes and plays a role in a variety of metabolic processes.

Enzymes of smooth ER synthesize lipids, including oils, phospholipids, and steroids.

Smooth ER stores calcium ions needed for muscle contraction

Rough ER is especially abundant in cells that secrete proteins.

As a polypeptide is synthesized on a ribosome attached to rough ER, it is threaded into the cisternal space through a pore formed by a protein complex in the ER membrane.

Secretory proteins are packaged in transport vesicles that carry them to their next stage.

Rough ER is also a membrane factory.

Membrane-bound proteins are synthesized directly into the membrane.

As the ER membrane expands, membrane can be transferred as transport vesicles to other components of the endomembrane system.

The Golgi apparatus is the shipping and receiving center for cell products.

Many transport vesicles from the ER travel to the Golgi apparatus for modification of their contents.

The Golgi apparatus consists of flattened membranous sacs-cisternae

One side of the Golgi, the cis side, is located near the ER. The cis face receives material by fusing with transport vesicles from the ER.

The other side, the trans side, buds off vesicles that travel to other sites.

During their transit from the cis to the trans side, products from the ER are usually modified.

Finally, the Golgi sorts and packages materials into transport vesicles.

Lysosomes are digestive compartments.

A lysosome is a membrane-bound sac of hydrolytic enzymes that an animal cell uses to digest macromolecules - proteins, fats, polysaccharides, and nucleic acids.

These enzymes work best at pH 5.

Rupture of one or a few lysosomes has little impact on a cell because the lysosomal enzymes are not very active at the neutral pH of the cytosol.

Amoebas eat by engulfing smaller organisms by phagocytosis.

The food vacuole formed by phagocytosis fuses with a lysosome, whose enzymes digest the food.

Lysosomes play a role in recycling, or autophagy, of the cell's organelles and macromolecules.

A damaged organelle or region of cytosol becomes surrounded by membrane.

A lysosome fuses with the resulting vesicle, digesting the macromolecules and returning the organic monomers to the cytosol for reuse.

Lysosomes play a critical role in programmed cell death, or apoptosis in multicellular organisms.

The hands of human embryos are webbed until lysosomes digest the cells in the tissue between the fingers.

Vacuoles have diverse functions in cell maintenance.

Vesicles and vacuoles (larger versions) are membrane-bound sacs with varied functions.

Food vacuoles are formed by phagocytosis and fuse with lysosomes.

Contractile vacuoles, found in freshwater protists, pump excess water out of the cell to maintain the appropriate concentration of salts.

A large central vacuole is found in many mature plant cells.

The functions of the central vacuole include stockpiling proteins or inorganic ions, disposing of metabolic byproducts, holding pigments, and storing defensive compounds that defend the plant against herbivores.

Mitochondria and chloroplasts change energy from one form to another

Mitochondria are the sites of cellular respiration, generating ATP from the catabolism of sugars, fats, and other fuels in the presence of oxygen.

Chloroplasts, found in plants and algae, are the sites of photosynthesis converting solar energy to chemical energy.

Both organelles have small quantities of DNA that direct the synthesis of the polypeptides produced by these internal ribosomes.

Mitochondria and chloroplasts grow and reproduce as semiautonomous organelles.

Almost all eukaryotic cells have mitochondria.

A typical mitochondrion is 1-10 microns long.

Mitochondria are quite dynamic: moving, changing shape, and dividing.

Mitochondria have a smooth outer membrane and a convoluted inner membrane with infoldings called cristae.

The intermembrane space is a narrow region between the inner and outer membranes.

The inner membrane encloses the mitochondrial matrix, a fluid-filled space with DNA, ribosomes, and enzymes.

The chloroplast is one of several members of a generalized class of plant structures called plastids.

Amyloplasts are colorless plastids that store starch in roots and tubers.

Chromoplasts store pigments for fruits and flowers.

Chloroplasts contain the green pigment chlorophyll as well as enzymes and other molecules that function in the photosynthetic production of sugar.

Chloroplasts measure about 2 microns × 5 microns and are found in leaves and other green organs of plants and algae.

The contents of the chloroplast are separated from the cytosol by an envelope consisting of two membranes separated by a narrow intermembrane space.

Inside the innermost membrane is a fluid-filled space, the stroma, in which float membranous sacs, the thylakoids.

The stroma contains DNA, ribosomes, and enzymes.

The thylakoids are flattened sacs that play a critical role in converting light to chemical energy. In some regions, thylakoids are stacked like poker chips into grana.

Their shape is plastic, and they can reproduce themselves by pinching in two.

Peroxisomes generate and degrade H2O2 in performing various metabolic functions.

Peroxisomes contain enzymes that transfer hydrogen from various substrates to oxygen.

Some peroxisomes break fatty acids down to smaller molecules that are transported to mitochondria as fuel for cellular respiration.

Peroxisomes in the liver detoxify alcohol and other harmful compounds.

Specialized peroxisomes, glyoxysomes, convert the fatty acids in seeds to sugars, which the seedling can use as a source of energy and carbon until it is capable of photosynthesis.

They split in two when they reach a certain size.

The cytoskeleton is a network of fibers that organizes structures and activities in the cell

The cytoskeleton provides support, motility, and regulation.

The cytoskeleton provides mechanical support and maintains cell shape.

The cytoskeleton provides anchorage for many organelles and cytosolic enzymes.

The cytoskeleton is dynamic and can be dismantled in one part and reassembled in another to change the shape of the cell.

The cytoskeleton also plays a major role in cell motility, including changes in cell location and limited movements of parts of the cell.

The cytoskeleton interacts with motor proteins to produce motility.

The cytoskeleton manipulates the plasma membrane to form food vacuoles during phagocytosis.

Cytoplasmic streaming in plant cells is caused by the cytoskeleton.

There are three main types of fibers making up the cytoskeleton: microtubules, microfilaments, and intermediate filaments.

Microtubules, the thickest fibers, are hollow rods about 25 microns in diameter and 200 nm to 25 microns in length. Microtubule fibers are constructed of the globular protein tubulin.

Microtubules shape and support the cell and serve as tracks to guide motor proteins carrying organelles to their destination.

Microtubules are also responsible for the separation of chromosomes during cell division.

Microtubules growing out from a centrosome resist compression to the cell.

A specialized arrangement of microtubules is responsible for the beating of cilia and flagella.

Cilia usually occur in large numbers on the cell surface.

They are about 0.25 microns in diameter and 2-20 microns long.

There are usually just one or a few flagella per cell.

Flagella are the same width as cilia, but 10-200 microns long.

In spite of their differences, both cilia and flagella have the same ultrastructure.

Both have a core of microtubules sheathed by the plasma membrane.

Nine doublets of microtubules are arranged in a ring around a pair at the center. This "9 + 2" pattern is found in nearly all eukaryotic cilia and flagella.

Flexible "wheels" of proteins connect outer doublets to each other and to the two central microtubules.

The cilium or flagellum is anchored in the cell by a basal body, whose structure is identical to a centriole.

The bending of cilia and flagella is driven by the arms of a motor protein, dynein.

Microfilaments are solid rods about 7 nm in diameter.

Each microfilament is built as a twisted double chain of actin subunits.

The structural role of microfilaments in the cytoskeleton is to bear tension, resisting pulling forces within the cell.

They form a three-dimensional network just inside the plasma membrane to help support the cell's shape, giving the cell cortex the semisolid consistency of a gel.

Microfilaments are important in cell motility, especially as part of the contractile apparatus of muscle cells.

Myosin molecules act as motor proteins, walking along the actin filaments to shorten the cell.

In other cells, actin-myosin aggregates are less organized but still cause localized contraction.

These contractions divide animal cells, drives amoeboid movement and drive cytoplasmic streaming in plant cells.

Intermediate filaments range in diameter from 8-12 nanometers, larger than microfilaments but smaller than microtubules. They reinforce cell shape and fix organelle location.

Intermediate filaments are built from a family of proteins called keratins.

Extracellular components help coordinate cellular activities

Plant and fungal cells are encased by cell walls.

The cell wall, found in prokaryotes, fungi, and some protists, has multiple functions.

In plants, the cell wall protects the cell, maintains its shape, and prevents excessive water uptake.

The basic design consists of microfibrils of cellulose embedded in a matrix of proteins and other polysaccharides. This is the basic design of steel-reinforced concrete or fiberglass.

The extracellular matrix (ECM) of animal cells functions in support, adhesion, movement, and regulation.

Though lacking cell walls, animal cells do have an elaborate extracellular matrix (ECM).

The primary constituents of the extracellular matrix are glycoproteins, especially collagen fibers, embedded in a network of glycoprotein proteoglycans.

In many cells, fibronectins in the ECM connect to integrins, intrinsic membrane proteins that span the membrane and bind on their cytoplasmic side to proteins attached to microfilaments of the cytoskeleton.

Intercellular junctions help integrate cells into higher levels of structure and function.

Neighboring cells in tissues, organs, or organ systems often adhere, interact, and communicate through direct physical contact.

Plant cells are perforated with plasmodesmata, channels allowing cytosol to pass between cells.

Animals have 3 main types of intercellular links: tight junctions, desmosomes, and gap junctions.

In tight junctions, membranes of adjacent cells are fused, forming continuous belts around cells.

This prevents leakage of extracellular fluid.

Desmosomes (or anchoring junctions) fasten cells together into strong sheets, much like rivets.

Gap junctions provide cytoplasmic channels between adjacent cells.

In embryos, gap junctions facilitate chemical communication during development.

A cell is a living unit greater than the sum of its parts.

While the cell has many structures with specific functions, all these structures must work together.

Food vacuoles are digested by lysosomes, a product of the endomembrane system of ER and Golgi.

The enzymes of the lysosomes and proteins of the cytoskeleton are synthesized on the ribosomes.

The information for the proteins comes from genetic messages sent by DNA in the nucleus.

All of these processes require energy in the form of ATP, most of which is supplied by the mitochondria.