Chapter 7: Inside the Cell 7.1 Bacterial and Archael Cell Structures and Their Functions - Eukaryotic cells have a membrane-bound compartment called a nucleus, while prokaryotic cells do not. - Morphology ( form science ) o Prokaryotic o Eukaryotic - Phylogeny ( Tribe Source ) o Bacteria Prokarytoic o Archaea Prokaryotic o Eukarya (algae, fungi, plants, and animals) Eukaryotic The Chromosome is Organized in a Nucleoid - Most bacterial species have a single, circular chromosome that consists of a large DNA molecule associated with a small number of proteins. The DNA molecule contains information, while the proteins provide structural support for the DNA. - The information in DNA is encoded in its sequence of nitrogenous bases, and a segment of DNA that contains the information for building an RNA molecule or a polypeptide is called a gene. Thus, chromosomes contain DNA, which contains genes. - To fit into the cell, the DNA double helix coils on itself with the aid of enzymes to form the highly compact, super-coiled structure. - Bacterial chromosomes are found in the nucleoid. - Plasmids contain genes but are physically independent of the main, cellular chromosome. Plasmids can be considered auxiliary genetic elements in which they help cells adapt to unusual circumstances, such as the sudden presence of a poison in the environment. Ribosomes Manufacture Proteins - Found throughout the cell interior - Complex structures consisting of RNA molecules and proteins. Internal Membrane Complexes in Photosynthetic Species - Photosynthesis is the suite of chemical reactions responsible for converting the energy in sunlight into chemical energy stored for sugars. Organelles Perform Specialized Functions - An organelle is a membrane-bound compartment inside the cell that contains enzymes or structures specialized for a particular function. Bacterial organelles:
o Storing calcium ions or other key molecules o Holding crystals of the mineral magnetite, which function like a compass needle to help cells sense a magnetic field and swim in a direct way o Organizing enzymes responsible for synthesizing complex carbon compounds from carbon dioxide o Sequestering enzymes that generate chemical energy from ammonium ions. The Cytoskeleton Structures The Cell interior - The cytoskeleton consists of long, thin fibers made of long polymers of globular proteins. - Responsible for the cell s shape, cell division, the transportation of plasmids, and the organization of the cell interior into distinctive regions. The Plasma Membrane Separates Life from Nonlife - The cell, or plasma, membrane consists of a phospholipid bilayer and protein that either span the bilayer or attach to one side. - The plasma membrane creates an internal environment that is distinct from the outside, nonliving environment. Membrane proteins allow the passage of compounds required for life, and prohibit the entry of materials dangerous to life. Flagella enable some species to swim - Their rotation allows aquatic cells to swim through the water (60 cell lengths/second) - Few in number and are located on the surface of the cell The Cell Wall Forms a Protective Exoskeleton - Bacterial and archael cell walls are a tough, fibrous layer that surrounds the plasma membrane. - Protects the organism and gives it shape and rigidity. - Lipids that contain carbohydrate groups are termed glycolipids. 7.2 Eukaryotic Cell Structures and Their Functions - Prokaryotic: 1 to 10 micrometers in diameter - Eukaryotic: 5 to 100 micrometers in diameter - Eukaryotic chromosomes are found inside a membrane-bound compartment called the nucleus - Eukaryotic cells are often much larger - Eukaryotic cells contain extensive amounts of internal membrane - Eukaryotic cells feature a particularly diverse and dynamic cytoskeleton 1. The Nucleus:
Contains the chromosomes and functions as an information storage and processing centre. Enclosed by a complex double membrane called the nuclear envelope. The nuclear envelope is studded with pore-like openings, and its surface is linked to fibrous proteins that form a lattice-like sheet called the nuclear lamina. The nuclear lamina stiffens the structure and maintains its shape. The nuclear envelope is continuous with an extensive series of membrane-bound sacs called the endoplasmic reticulum. The nucleolus is where the RNA molecules found in ribosomes are manufactured and the large and small ribosomal subunits are assembled. 2. Rough Endoplasmic Reticulum (protein-manufacturing centre): Knobby-looking ribosomes that attach to the membrane Synthesis of proteins that will be inserted into the plasma membrane, secreted to the cell exterior, or shipped to an organelle. The interior of the rough ER is called the lumen newly manufactured proteins undergo folding and other types of processing. 3. Smooth Endoplasmic Reticulum (lipid-processing centre): Without ribosomes The membrane contains enzymes that catalyze reactions involving lipids Manufacturing site for phospholipids used in plasma membrane Functions as a reservoir for calcium ions (Ca 2+ ) that act as a signal, triggering a wide array of activities inside the cell. 4. Golgi Apparatus: Protein processing Consists of flattened, membranous sacs called cisternae. Distinct polarity. The cis surface is closest to the rough ER and nucleus, and the trans surface is oriented toward the plasma membrane. 5. Peroxisomes: Globular organelles Single membrane, and originate as buds from the ER Are centres for oxidation reactions; oxidation removes electrons from atoms and hydrogen. In plant leaves, glyoxysomes are packed with enzymes that oxidize fats to form a compound that can be used to store energy for the cell. 6. Lysosomes: Function as digestive centres Lumen is acidic and must be maintained at a ph of 5.0 Digestive enzymes are collectively called acid hydrolases because they catalyze hydrolysis reactions that break monomers from macromolecules most efficiently at a ph of 5.0. In the cytosol, where the ph is about 7.2, these enzymes are less active. Three methods of delivery to lysosome: i. Autophagy ( same eating ) 1. A damaged organelle is surrounded by a membrane
2. The membrane-bound organelle is delivered to a lysosome, which takes it in and begins digesting it. 3. Small molecules from the digested organelle are recycled into the cytosol. ii. Phagocytosis ( eat cell act ) 1. The plasma membrane detects a smaller cell or food particle and begins to engulf it 2. The resulting membrane-bound particle is a phagosome 3. The phagosome is delivered to a lysosome, which takes it in and begins digesting it. 4. Small molecules from the digested food particles are released into the cytosol. iii. Receptor-mediated endocytosis: 1. Macromolecules outside the cell bind to membrane proteins that act as receptors. 2. The plasma membrane folds in and pinches off to form an early endosome. 3. The early endosome undergoes a series of processing steps, including activation of proton pumps that lower its ph. 4. The early endosome matures into a late endosome that receives digestive enzymes from the Golgi apparatus. 5. The late endosome matures into a functional lysosome. Endocytosis ( inside cell act ) refers to any pinching off of the plasma membrane that results in the uptake of material from outside the cell. Pinocytosis ( drink cell act ) brings fluid into the cytoplasm via tiny vesicles that form from infoldings of the plasma membrane. Lysosomes, the Golgi apparatus, and the rough and smooth reticulum jointly form a key functional grouping called the endomembrane system, which is the primary centre for protein and lipid synthesis and processing in eukaryotic cells. 7. Vacuoles: The vacuole is the substitute for a lysosome in a plant cell Occupies 80% of the plant and acts as a storage depot Storage such as digestive enzymes, water, ions, seeds, colored pigments, or compounds that protect the leaves and stem from being eaten by predators Serve as recycling centre 8. Mitochondria: Double membrane Outer membrane defines the organelle s surface, while the inner membrane is connected to a series of sac-like cristae. The solution inside the inner membrane is called the mitochondrial matrix. ATP production Human chromosome is 16500 bp long 9. Chloroplasts: Algae and plant cells possess organelles called plastids
In photosynthetic cells, the proplastids mature into chloroplast, which convert solar energy into chemical energy during photosynthesis Proplastids may become storage plastids or chromoplasts The chloroplast has a double membrane and has thylakoids, which are stacked into grana. Many of the pigments, enzymes, and molecular machines responsible for converting light energy into carbohydrates are embedded in the thylakoid membranes. Certain critical enzymes and substrates, however, are found outside the thylakoids in the region called the stroma. Chloroplasts are similar to mitochondria in that they generate useful forms of energy for the cell, but because chloroplasts are larger than mitochondria, cells do not have as many. In addition, they both have their own small chromosomes and ribosomes. 10. The cell wall: Located outside of the plasma membrane, and furnishes a stiff, outer layer that provides structural support for the cell. Rods or fibres composed of a carbohydrate run through a stiff matrix made of other polysaccharides and proteins. Some plants form a secondary cell wall known as lignin. Lignin forms a branching, cage-like network that is almost impossible for enzymes to attack. Wood: cellulose and lignin. 11. Cytoskeleton: An extensive system of protein fibres Cytoskeletal proteins are involved in moving the cell itself and moving materials within the cell Organizes all of the organelles and other cellular structures into a cohesive whole 7.3 Putting the Parts into a Whole - Within a cell, the structure of each organelle and component correlates with its function. In the same way, the overall size, shape, and composition of a cell correlates within its function. The Dynamic Cell: - Differential centrifugation is a technique that allowed researchers to isolate particular cell components and analyze their chemical composition. - Animal pancreatic cell: exports digestive enzymes; animal testis cell: exports lipidsoluble signals; plant lead cell: manufactures ATP and sugar; and plant root cell: stores starch. - Differential centrifugation splits cells into parts that are analyzed independently, and electron microscopy gives a fixed snapshot of the cell or organisms being observed. Neither technique allows investigators to directly explore how things move from place to place in the cell or how parts interact.
- At a scare of a ribosome or an organelle or a cell, gravity is inconsequential. Instead, the dominant forces are the charge or polarity based electrostatic attractions between molecules and the kinetic energy of motion. - Events take nanoseconds, and speeds are measured in micrometers per second this is life. 7.4 Cell Systems I: Nuclear Transport - The nucleus is the information centre of eukaryotic cells. The organelle s overall shape and structure are defined by the mesh-like nuclear lamina. The nuclear lamina provides an attachment point for chromosomes, each of which occupies a welldefined region in the nucleus - The nuclear envelope separates the nucleus from the rest of the cell. The structure is supported by the fibrous nuclear lamina and bounded by two membranes, each consisting of a lipid bilayer. - The envelope is broken with openings called nuclear pores. They connect the inside of the nucleus with the cytosol. Each pore consists of over 50 different proteins, which form an elaborate structure called the nuclear pore complex. Passage through a nuclear pore is selective. - Information coded in DNA is used to synthesize RNA inside the nucleus. - Most ribosomal RNAs (rrna) are manufactured in the nucleolus, where they bind to proteins to form ribosomes, which are then exported to the cytoplasm. - Molecules called messenger RNAs (mrna) carry the information required to manufacture proteins out to the cytoplasm, where protein synthesis takes place. - Nucleoside triphosphates that act as building blocks for DNA and RNA enter the nucleus, as do the proteins responsible for copying DNA, synthesizing RNAs, extending the nuclear lamina, assembling ribosomes, or building chromosomes. - Viruses are parasites that use the cell s machinery to make copies of themselves.