Chapter 7- Inside the Cell

7.1 Bacterial and Archaeal Cell Structures and Their Functions

• Transmission electron microscope, which passes a beam of electrons through extremely thin sections of cells to visualize their internal structure
• The most prominent structure inside a prokaryotic cell is the chromosome
  • Segments of DNA that contain information for building functional RNAs, some of which may be used to make polypeptides, which are called genes.
• The region of the cell where the circular chromosome is located is called the nucleoid
• Plasmids contain genes but are physically independent of the cellular chromosome.
• Ribosomes are observed in all prokaryotic cells and are found throughout the cell interior.
• Protein filaments such as these form the basis of the cytoskeleton
• An organelle is a compartment inside the cell-often bounded by a membrane- that contains enzymes or structures specialized for a particular function.
• Bacterial organelles perform specialized tasks, including:
  • storing calcium ions
  • holdingcrγstals of the mineral magnetite, which function like compass needles to help cells swim in a directed way
  • concentrating enzymes responsible for synthesizing complex carbon compounds from carbon dioxide.
• In most bacteria and archaea, this pressure is resisted by a stiff cell wall.
• A prokaryotic flagellum (plural: flagella) is assembled from many different proteins at the cell surface of certain species.
• A fimbria (plural: fimbriae) is a needle-like projection that extends from the plasma membrane of some bacteria and promotes attachment to other cells or surfaces.

7.2 Eukaryotic Cell Structures and Their Functions

• ==As a cell increases in diameter, its volume increases more than its surface area.==
• Because eukaryotic cells are subdivided, the cytosol-the fluid portion between the plasma membrane and 1ese organelles-is only a fraction of the total cell volume.
• While prokaryotic chromosomes are in a loosely defined nucleoid region, eukaryotic chromosomes are enclosed within a membrane bound compartment called the nucleus. 
  • It is enclosed by a unique double-membrane structure called the nuclear envelope.
  • The nuclear envelope is studded with pore-like openings, and the inside surface is linked to fibrous proteins that form a lattice-like sheet called the nuclear lamina.
• One of these regions, called the nucleolus, is responsible for manufacturing and processing the RNA molecules that assemble into large and small ribosomal subunits.
• Portions of the nuclear envelope extend into the cytoplasm to form an extensive membrane enclosed factory called the endoplasmic reticulum (ER)
• The rough endoplasmic reticulum, or more simply rough ER, is named for its appearance in transmission electron micrographs
• The inside compartment of the rough ER, like the interior of any sac-like structure in a cell or body, is called the lumen.
• The smooth endoplasmic reticulum or smooth ER are parts of the ER that are free of ribosomes that appear smooth and even.
• Most of the proteins that leave the rough ER must pass through the Golgi apparatus before reaching their final destination.
• The Golgi apparatus consists of a set of membranous compartments called cisternae.
• Animal cells contain organelles called lysosomes that function as recycling center
• Even though lysosomes are physically separated from the Golgi apparatus and the endoplasmic reticulum, these various organelles jointly form a key functional grouping referred to as the endomembrane system.
• The cells of plants, fungi, and certain other eukaryotes contain a prominent organelle called a vacuole.
• Virtually all eukaryotic cells contain globular organelles called peroxisomes
• In the leaves of plants, specialized peroxisomes called glyoxysomes are packed with enzymes that oxidize fatty acids to form a compound that can be used to store energy for the cell.
• The organelle primarily responsible for supplying ATP in animals, plants, and virtually all other eukaryotic cells is the mitochondrion
  • The solution enclosed within the inner membrane is called the mitochondrial matrix.
  • Each mitochondrion has many copies of a small, circular-in some species,linear-chromosome called mitochondrial DNA (mtDNA) that is independent of the nuclear chromosomes.
• Most algal and plant cells possess an organelle called the chloroplast, in which sunlight is converted to chemical energy during photosynthesis
• A third membrane forms an independent network of hundreds of flattened, sac-like structures called thylakoids throughout the interior.
• Most thylakoids are arranged in interconnected stacks called grana
• The fluid-filled space surrounding grana, called the stroma, contains enzymes that use this chemical energy to produce sugars.
• According to the endosymbiosis theory, these bacteria were engulfed by the ancestors of modern eukaryotes, but were not destroyed-instead, a mutually beneficial relationship evolved.
• The cells of animals lack a cell wall, but are often supported by a more diffuse mixture of secreted proteins and polysaccharides that form the extracellular matrix, orECM.
• Within a cell, the structure of each component correlates with its function.

7.3 Putting the Parts into a Whole

• For several decades,
• A technique called differential centrifugation was particularly important because it allowed researchers to isolate particular cell components and analyze their chemical composition.

7.4 Cell Systems I: Nuclear Transport

• Ribosomal RNAs are manufactured in the nucleolus, where they bind to proteins to form the large and small subunits of ribosomes.
• Molecules called messenger RNAs (mRNA) carry the information required to manufacture proteins.
• Nuclear localization signal (NLS) is where proteins that leave the nucleus have a different signal, required for nuclear export.

7.5 Cell Systems II: The Endomembrane System Manufactures, Ships, and Recycles Cargo

• George Palade and colleagues did pioneering research on the secretory pathway using a pulse chase experiment to track protein movement.
• This strategy is based on two steps
  • The “Pulse”: Expose experimental cells to a high concentration of a modified amino acid for a short time.
  • The “Chase”: End the pulse by washing away the modified amino acid and replacing it with the normal version of the same molecule.
• The cells for the experiment were grown in culture, or in vitro.
• They identified a “send-to-ER” signal, or ER signal sequence, that guides the growing protein and associated ribosome to the rough ER.
• The signal sequence binds to a signal recognition particle (SRP)-a complex of RNA and protein.
• Because carbohydrates are polymers of sugar monomers, the addition of one or more carbohydrate groups is called glycosylation. The resulting molecule is a glycoprotein.
• When exocytosis occurs, the vesicle membrane and plasma membrane make contact.
• Two of these three pathways involve pinching off the plasma membrane to take up material from outside the cell-a process called endocytosis
  • As its name implies, receptor mediated endocytosis is a sequence of events that begins when particles outside the cell bind to receptors on the plasma membrane.
• These vesicles then drop off their cargo in an organelle called the early endosome
• As proton pumps continue to lower the early endosome's pH, it undergoes a series of processing steps that cause it to mature into a late endosome.
• A second pathway that involves recycling material brought in from 1e outside of the cell is called phagocytosis
• Cells are also involved in recycling large structures and organelles that exist within the cytoplasm through a process called autophagy

7.6 Cell Systems III: The Dynamic Cytoskeleton

• ==The cytoskeleton is a dense and complex network of fibers that helps maintain cell shape by providing structural support.==
• Sometimes called microfilaments because they are the cytoskeletal element with the smallest diameter, actin filaments are fibrous structures made of globular protein subunits called actin
• ==Myosin is a motor protein-a protein that converts the chemical energy in ATP into the kinetic energy of mechanical work, just as a car’s motor converts the chemical energy in gasoline into spinning wheels.==
• Cytokinesis (“cell-moving”) is 1e final stage in cell division when the cytoplasm is divided to form two cells.
• Cytoplasmic streaming is the directed flow of cytosol and organelles that is often seen within plant and fungal cells.
• In addition, the movement called cell crawling occurs when groups of actin filaments grow, causing bulges in the plasma membrane that extend and move the cell.
• There are many types of intermediate filament, each consisting of a different-though similar in size and structure-type of protein subunit
• Nuclear lamins, which make up the nuclear lamina layer
• Microtubules have the largest diameter of the three cytoskeletal filaments.
• The eukaryotic flagellum is closely related to a structure called the cilium (plural: cilia), which is a short, hairlike projection that is also found in some eukaryotic cells
• The nine doublets of the axoneme originate from a structure called the basal body.