Ch. 7 bio - Lecture notes 7 PDF

Preview

Summary

professor Wilson bio 1330 chapter 7 lecture notes...

Description

Chapter 7 Prokaryotic - Bacteria and archea Cells are divided into two fundamental types based on morphology: 1.Eukaryotes have membrane-bound nucleus 2.Prokaryotes lack membrane-bound nucleus Based on phylogeny, or evolutionary history, organisms are divided into three domains: 1.Bacteria—prokaryotic 2.Archaea—prokaryotic 3.Eukarya—eukaryotic All cells have: 1. Proteins—perform most of the cell’s functions 2. Nucleic acids—store, transmit, and process information 3. Carbohydrates—provide chemical energy, carbon, support, and identity 4. Plasma membrane—serves as a selectively permeable membrane barrier Prokaryotic cells: Contain at least one chromosome Protein-synthesizing ribosomes Phospholipid components differ: Bacterial phospholipids consist of fatty acids bound to glycerol Archaeal phospholipids used branched isoprenoid chains bound to glycerol Chromosome: Most prominent structure inside prokaryotic cell Most bacterial and archaeal species have single, circular chromosomes: Consists of large DNA molecules associated with proteins DNA molecules contain genetic information Proteins give DNA structural support Prokaryotic cells may contain circular, supercoiled DNA molecules called plasmids Proteins give DNA structural support and guide supercoiling.

Archaea have histones for wrapping DNA (same as eukaryotes). Bacteria use different DNA-condensing proteins (they do not use histones). Archaea and bacteria do not have a membrane-surrounded nucleus. Defining characteristics of prokaryotes. Eukaryotes do have a nucleus with a nuclear membrane. The nucleoid: No membrane Irregular shaped region that contains the chromosome Plasmids are not associated with chromosome(s). Plasmids replicate independently of the chromosome. Prokaryotes also have ribosomes: Macromolecular machines Have large and small subunit Consist of R N A molecules and protein Used for protein synthesis Ribosomes in bacteria and archaea are similar in size and function: Primary structure of R N A and protein components are different Bacteria and archaea contain long, thin protein filaments in cytoplasm: Protein filaments form the basis of cytoskeleton Serve variety of roles In bacteria, cytoskeleton essential for cell division Maintains the cell’s shape Many prokaryotes have internal photosynthetic membranes: Convert energy in sunlight to chemical energy Multiple membranes passing through internal region of cell observed in photosynthetic bacteria Develop as infoldings of plasma membrane Contain enzymes and pigment molecules required for reactions to occur Cell wall forms protective “exoskeleton”

Most prokaryotes have cell walls: Composed of tough, fibrous layer Surrounds plasma membrane Protects shape and rigidity of cell In bacteria: Primary structural component of cell wall is the polysaccharide peptidoglycan Some have outer membrane made of glycolipids Many prokaryotes interact with their environment via structures that grow from their plasma membrane Flagella and fimbriae: Structures found on bacterial surfaces Flagella—long filaments that rotate to propel cell Fimbriae—needlelike projections that promote attachment to other cells or surfaces

Feature

Bacteria

Archaea

Eukaryotes

Chromosomes

Circular, usually 1 Nucleoid

Circular, usually 1 Nucleoid

Other Proteins

Histones

Linear, usually multiple Nucleus (membrane) Histones

Common

Common

Rare

Fatty acid tails

Isoprenoid tails

Fatty acid tails

Rudimentary and rare organelles Yes

Rudimentary and rare organelles Yes

Many complex organelles

DNA compartment Supercoiling compression Plasmids Membrane Phospholipids Cytoplasm

Ribosomes

Eukaryotic: subcellular structures and functions

•range in size from microscopic algae to 100-meter-tall redwood trees: Protists, fungi, plants, and animals are eukaryotes

Yes

May be multicellular or unicellular Most eukaryotic cells are larger than most prokaryotic cells: Prokaryotic cells measure 1 to 10 µm in diameter Eukaryotic cells measure 5 to 100 µm in diameter Organelle advantages: separation and efficiency Organelles compartmentalize volume inside eukaryotic cells into small bins: Fluid portion of cell, cytosol, has small volume Offsets effects of low cell surface-area-to-volume ratio Compartmentalization offers two advantages: 1.Separation of incompatible chemical reactions 2.Increasing efficiency of chemical reactions The Nucleus—Large, highly organized membrane bound compartment: Surrounded by a double-membrane nuclear envelope: Studded with pore-like openings Inside surface is linked to the nuclear lamina: Lattice-like sheet of fibrous proteins Has a distinct region called nucleolus: Location where ribosomal RNA is synthesized, and ribosome subunits are assembled Ribosomes in cytoplasm or Rough ER Location of the ribosome is the first fork in the path that determines the proteins’ eventual location. Ribosomal subunits are made inside the nucleolus, but they function outside the nucleus. Ribosomes are complex molecular machines that manufacture proteins: Lack membrane—not considered organelles Some ribosomes are free in the cytosol: Manufacture proteins that remain in cytosol or are imported to other organelles (e.g., nucleus) Some are attached to endoplasmic reticulum: Manufacturing proteins with other fates The Endoplasmic Reticulum Is a Site of Synthesis, Processing, and Storage.

Endoplasmic reticulum—extensive membrane-enclosed factory: Continuous with nuclear envelope Two regions, distinct in structure and function: Rough endoplasmic reticulum (rough ER) Smooth endoplasmic reticulum (smooth ER) Rough endoplasmic reticulum (rough ER, RER): Studded with ribosomes: Dark, knobby looking structures Synthesizes proteins that will be: Shipped to another organelle Inserted into plasma membrane Secreted to the cell exterior Smooth endoplasmic reticulum (smooth ER, SER): Lacks ribosomes Contains enzymes that catalyze reactions involving lipids, that may: Synthesize lipids needed by the organism Break down lipids and other molecules that are poisonous Reservoir for Ca2+ ions As proteins are manufactured on Rough Endoplasmic Reticulum (R E R), they move into the lumen: Lumen—inside of any sac-like structure In RER lumen, proteins are folded and processed Proteins made on RER may: Carry messages to other cells Act as membrane transporters or pumps Catalyze reactions Smooth ER synthesizes lipids and stores calcium ions Golgi apparatus: Most proteins that leave R E R must pass through Golgi apparatus

Formed by series of stacked, flat, membranous sacs called cisternae Has distinct polarity, or sidedness: Cis (“on this side”) surface closest to nucleus Trans (“across”) surface oriented toward plasma membrane Function of Golgi apparatus: Processes, sorts, and ships proteins synthesized in rough E R Cis side of Golgi apparatus receives products from rough E R Trans side ships them out to other organelles or cell surface Membranous vesicles carry materials to and from organelle Lysosomes: Are only in animal cells Contain ~40 different hydrolytic enzymes For digesting different macromolecules Enzymes called acid hydrolases work best at pH 5.0 Proton pumps in membrane maintain low internal pH Collectively, lysosomes, Golgi apparatus, and ER make up the endomembrane system: Center for producing, processing, and transporting proteins, carbohydrates and lipids Example: acid hydrolases: Synthesized in the rough endoplasmic reticulum (RER) Processed in the Golgi apparatus Shipped to the lysosomes Digest and recycle macromolecules Storage of water and ions In seeds, they are filled with proteins In flower petals or fruits, they contain pigments May contain noxious compounds to protect leaves and stems from being eaten Globular organelles for digesting fatty acids, detoxifying alcohols and other toxins, producing H2O2, which also gets detoxified. Made by loading empty vesicles from the ER with specific enzymes from cytosol.

Glyoxysomes are specialized plant peroxisomes that oxidize fats into energy-storage compounds. Peroxisomes Are the Site of Oxidation Reactions. Center for reduction-oxidation (redox) reactions, that produce hydrogen peroxide, H2O2, which is “detoxified”. Outer and inner membranes Cristae – folds of inner membrane Matrix – space inside inner membrane Mitochondria Have their own DNA Have their own ribosomes Multiply by binary fission Abundant in high-energy cells Outer and inner membranes Thylakoids – inner membrane disks Grana – stacks of thylakoids Stroma – space inside inner membrane Chloroplasts: Have their own DNA Have their own ribosomes Multiply by binary fission Conduct photosynthesis in plants Like mitochondria, chloroplasts contain their own DNA and make their own ribosomes. Chloroplasts grow and divide independently of cell division. They can only be made from other chloroplasts. Endosymbiosis theory: Proposes that mitochondria and chloroplast were once free-living bacteria Bacteria were engulfed by ancestors of modern eukaryotes but were not destroyed Mutually beneficial relationship evolved Cytoskeleton:

Extensive system of protein fibers Gives cells shape and structural stability Transport materials within cell Organizes all organelles and other cellular structures into a cohesive whole Fungi, algae, and plants have stiff outer cell walls in addition to plasma membrane: Cell wall is located outside of plasma membrane Provides durable outer layer Gives structural support to cell Cells of animals lack a cell wall: Supported by extracellular matrix (E C M) Diffuse mixture of secreted proteins and polysaccharides Three eukaryotic processes: nuclear transport, secretion, & lysosome recycling

Nucleus: Information center of eukaryotic cells Genetic information in D N A is decoded and processed Large suites of enzymes interact to produce R N A messages Messenger R N A (m R N A) carries information to synthesize proteins Nucleolus functions as site of ribosome assembly: Ribosomal R N A binds proteins to form ribosomes Structure of the Nuclear Envelope and Nuclear Pore Complex. Structure and function of nuclear envelope: Separates nucleus from rest of the cell Perforated with openings called nuclear pore complexes Connects inside of nucleus with cytosol Consists of about 30 different proteins Inbound traffic into the nucleus: Nucleoside triphosphates Proteins responsible for copying DNA

Proteins responsible for synthesizing RNA s Proteins needed for assembling ribosomes Typical cell imports over 500 molecules through 2000–5000 nuclear pores every second Inbound traffic into the nucleus: Nucleotide triphosphates Proteins responsible for copying DNA Proteins responsible for synthesizing RNA s Proteins needed for assembling ribosomes Typical cell imports over 500 molecules through 2000–5000 nuclear pores every second Import of large molecules into the nucleus is selective: Nuclear pores serve as dynamic gate to control passage through envelope Nuclear proteins contain a 17-amino-acid-long nuclear localization signal (NLS): Directs nucleoplasmin to nucleus Serves as “zip code” (molecular address): Marks proteins for transport through nuclear pore complex Allows them to enter nucleus Nuclear Localization Signals Direct Cytosolic Proteins into the Nucleus. Addition of the 17 amino acid nuclear localization signal to pyruvate kinase converts it from a cytoplasmic enzyme to a nuclear-localized enzyme. Most proteins found inside organelles are actively imported from cytosol: Many proteins must be transported to compartments inside cell Each protein must have specific zip code and delivery system to get to correct location Example: Acid hydrolases must be shipped to lysosomes The Secretory Pathway Hypothesis: An Overview. Secretory pathway exists and R E R and Golgi function together as parts of integrated endomembrane system Free floating ribosomes make proteins that go to the cytosol, nucleus. Ribosomes attached to the rER make proteins directly into the rER lumen. These proteins are delivered inside organelles or outside of the cell.

The Signal Hypothesis Explains How Proteins Destined for Secretion Enter the Endomembrane System. The “signal hypothesis:” Proteins bound for endomembrane system have molecular zip code Directs growing polypeptide to RER Zip code is 20-amino-acid-long ER signal sequence How Do Proteins Enter the Endomembrane System? Step 1: Ribosome synthesizes E R signal sequence Step 2: E R signal sequence binds to signal recognition particle (S R P) Step 3: Ribosome + signal sequence + S R P move to R E R membrane and bind to S R P receptor Step 4: S R P is released—protein synthesis continues through channel called translocon Step 5: Growing protein is fed into E R lumen—E R signal sequence is removed Eukaryotic processes In R E R lumen, proteins are folded into their three-dimensional shape Glycosylation is the addition of one or more carbohydrate groups onto the protein The resulting molecule is a glycoprotein The resulting changes in structure direct the shipment to next destination, the Golgi apparatus Proteins in E R lumen interact with enzymes that catalyze the addition of carbohydrate side chains Glycosylation starts in the ER and is completed in the Golgi Golgi apparatus is dynamic: New cisternae form at cis face Old cisternae break off from trans face and are replaced by cisternae behind them Different cisternae contain different enzymes: Proteins enter Golgi apparatus at cis face Cargo is modified as it moves within compartments at different stages of maturation Cargo complexes form cargo-filled vesicles: Places proteins in particular types of transport vesicles

Some transport vesicles are bound for plasma membrane to secrete contents outside of the cell— exocytosis Each type of transport vesicle has tags that direct transport to the correct destination Three pathways exist to recycle materials in the lysosome: One pathway is autophagy Two pathways are through endocytosis—materials brought into cell by pinching off plasma membrane Two types of endocytosis: 1.Receptor-mediated endocytosis: Particles bind to receptors on plasma membrane Plasma membrane pinches off to form endocytic vesicle Vesicles drop off their cargo in organelle called early endosome Proton pumps lower p H; receptor releases particle Vesicles mature into late endosome Acid hydrolases are dropped off, making it a lysosome 2.Phagocytosis (“eat-cell-act”): Recycling materials brought in from outside of cell Plasma membrane engulfs smaller cells or food particles: From phagosome Phagosome structure is delivered to lysosome Phagosome and lysosome membranes fuse and contents of phagosome are digested Autophagy (“same-eating”) Cells are also involved in recycling large structures and organelles within cytoplasm: Damaged organelles are marked for destruction Get enclosed within internal membrane and form autophagosome Membrane of autophagosome fuses with lysosome and contents are digested...