AT BIO TEST: CH 6, 7, AND 8

**POTENTIAL TEST QUESTIONS ABOUT MICROSCOPES

1. Question: if you want to see details of the mitochondria in an unstained living cell, what would you use; (answer: would either use the phase contrast or differential interference contrast, because they highlight details in unstained cells)/ 2. or what would be the best type of microscope to see amoeboid movement (answer: light microscope, because this is a living organism); 3.what would be the best microscope to see a relatively thick cell tissue (answer: confocal)

Golgi Apparatus

1. Serves as molecular warehouse and finishing factory for products manufactured by the ER; 2. products travel in transport vesicles from the ER to the Golgi; 3. one side of the Golgi functions as a receiving dock for the product and the other as a shipping dock's products are modified as they go from one side of the Golgi apparatus to the other and travel in vesicles to other sites 4. (functions in modification and sorting of macromolecules, and formation of lysosomes and transport vesicles)

Six Organelles Involved in Manufacturing, Distribution, and Breakdown Within the Cell

1. Smooth ER, 2. Rough ER, 3. Golgi, 4. Lysosomes, 5. Vacuoles, and 6. Peroxisomes

Changing Lipid Composition of Cell Membranes

1. The ability to change the lipid composition of cell membranes in response to changing temperatures has evolved in organisms that live where temperatures vary a lot 2. (ex: certain bacteria and archaea can change the number of saturated phospholipids in their cell membranes, depending on the temperature at which they're growing); natural selection favors organisms whose mix of membrane lipids ensures appropriate level of membrane fluidity for their environment

Fluid Mosaic of Plasma Membrane

1. The currently accepted model of cell membrane structure, 2. which envisions the membrane as a mosaic of protein molecules drifting laterally in a fluid bilayer of phospholipids; 3. groups of proteins are associated in specialized patches, where they carry out common functions

Light Microscope (LM)

1. The most frequently used microscope for viewing living organisms is the light microscope, in which light passes through a specimen, then through glass lenses. And the light is projected into the viewer's eye; 2. light microscope shines light through object and the light is bent with glass lenses to make the object appear larger

How Cholesterol Functions as a Fluidity Buffer

1. The steroid cholesterol has different effects on membrane fluidity at different temperatures; 2. at high temperatures, cholesterol makes the membrane less fluid (by restraining phospholipid movement); 3. however, because cholesterol also hinders close packing to phospholipids, it lowers the temp. Required for the membrane to solidify; 4. thus, cholesterol resists changes in membrane fluidity that can be caused by changes in temperature

Characteristics of Cyanobacteria

1. They are prokaryotic, 2. photosynthetic (autotrophs), but don't contain chloroplasts, 3. they have gelatinous cell walls, and 4. they're mostly single-celled

Four Components That All Cells Possess

1. all cells have a cell membrane made of phospholipid bilayer, proteins, and cholesterol, 2. all cells have a cytoplasm (containing water and various molecules (amino acids, carbohydrates, etc.), 3. ribosomes (composed of rRNA and proteins), and 4. genetic material (DNA or RNA)

Characteristics of Domain Archaea

1. archaea are prokaryotic, single-celled, 2. some have cell walls (NOT made of peptidoglycans); 3. they are extremophiles (get their energy from inorganic compounds, live in hot vents at the bottom of the ocean, or sulfur hot springs, etc.); 4. the ribosomes of archaea are more similar to those of Eukaryotes and those of Eubacteria

Prokaryotic Cells

1. do NOT have membrane-bound organelles (nucleus, Golgi, etc.); 2. DNA, ribosomes, might have a cell wall (many eubacteria); 3. might have a capsule, might have cilia, might have flagella; 4. has to have DNA, ribosomes, building blocks of all the macromolecules, etc;

Fluorescence

1. fluorescent stains are used to locate specific organelles 2. fluorescent substances absorb ultraviolet radiation and emit visible light; 3. the fluorescing molecules may occur naturally in the specimen, but more often are made tagging the molecules of interest with fluorescent dyes or antibodies; 4. All of the early stains were lipid soluble

Euglena

1. has a flagella, which has a propellor., so that's how it moves; 2. it can both eat and do photosynthesis (it has an eyespot which is an organelle that allows it to move towards light)

Rough ER

1. lines the outer surface of membranes; 2. makes additional membrane for itself and proteins destined for secretions; 3. synthesizes membrane lipids and proteins, secretory proteins, and hydrolytic enzymes: formation of transport vesicles; 4. Rough ER is also involved in translation (but only the proteins that need to be inside of the membrane)

Paramecium

1. moves due to its cilia; 2. it has an oral groove in order to eat, and incorporates it into a food vacuole, and that incorporates it into the lysosome; 3. has two nuclei: macronuclei and a micro nuclei; 4. it's big claim to fame is its contractile vacuole (helps to maintain the appropriate osmolarity, so it doesn't explode, because water is constantly coming into the paramecium)

Characteristics of Kingdom Fungi

1. one of four kingdoms within domain eukarya; 2. single-celled (yeast) or multicellular (mushrooms), 3. heterotrophs (they eat organic, usually dead material), 4. cell walls made of chitin; 5. mushrooms and yeast; 6. fungi grow on dead trees

Characteristics of Kingdom Plantae

1. one of four kingdoms within domain eukarya; 2. they are multicellular, photosynthetic (autotrophs), and contain cell walls made of cellulose 3. (difference between plant and animal cells is that plant cells contain cell walls-made of cellulose-one central vacuole-while animal cells have multiple vacuoles-chloroplasts, and plasmodesmata, and animal cells contain centrioles and lysosomes while most plant cells don't

Characteristics of Kingdom Protista

1. one of the four kingdoms within domain eukarya; 2. can either be autotrophic or heterotrophic; 3. vast majority of them are single-celled; 4. they are very diverse, and each species of protists is placed into one of three separate categories: animal-like 5. (ex: amoeba-feed on bacteria and smaller protists), plant-like (ex: euglena-unicellular algae that live in freshwater, autotrophs), and fungus-like (ex: fungi-heterotrophs that use spores to reproduce)

Brightfield (unstained specimen)

1. passes light directly through specimen; 2. unless cell is naturally pigmented or artificially stained, image has little contrast

Characteristics of Domain Bacteria

1. prokaryotic, 2. cell walls made of peptidoglycans, 3. mostly single-celled; 4. under prokaryotic realm, there are two domains: archaea and bacteria, and bacteria is comprised largely of eubacteria, which is split into two phyla: bacteria (heterotrophs) and cyanobacteria (autotrophs-do not have chloroplasts, however)

Amoebas

1. pseudopods; 2. it disassembles and reassembles its cytoskeleton, and 3. uses endocytosis to eat; 4. the food vacuole will eventually fuse with a lysosome to eat food

Organelles Included in the Endomembrane System

1. the endomembrane system includes the nuclear envelope, 2. endoplasmic reticulum (ER)-smooth and rough- 3. Golgi apparatus, 4. lysosomes, 5. vacuoles, and the 6. plasma membrane; stuff buds off of rough ER and goes to golgi, and things bud off golgi and go to the plasma membrane;

How Types of Lipids in Membrane Determine its Fluidity

1. the temperature at which a membrane solidifies depends on the types of lipids it's made of; 2. the membrane remains fluid to a lower temp. if it's rich in phospholipids with unsaturated hydrocarbon tails (because of kinks in their tails, they can't pack together as closely as saturated hydrocarbon tails, making the membrane more fluid)

Two Factors That Affect Membrane Fluidity

1. unsaturated vs. saturated hydrocarbon tails 2. cholesterol (fluidity buffer)

Cytoskeleton

Cells contain a network of protein fibers (composed mainly of microtubules, microfilaments, and intermediate filaments), called the cytoskeleton, which functions in structural support and motility, maintenance of cell shape; anchorage for organelles; movement of organelles within cells (crawling, muscle contraction, bending of cilia and flagella; motility and cell regulation result when cytoskeleton interacts with motor proteins)

Internal Compartments of Chloroplasts

Chloroplasts are partitioned into compartments (between the outer and inner membrane is a thin intermembrane space, and inside the inner membrane is a thick fluid called stroma that contains the chloroplast DNA, ribosomes, and many enzymes and a network of interconnected sacs called thylakoids; in some regions, thylakoids are stacked like poker chips, and each stack is called a granum, where green chlorophyll molecules trap solar energy)

Cholesterol Within the Animal Cell Membrane

Cholesterol reduces membrane fluidity at moderate temperatures by reducing phospholipid movement, but at low temperatures, it hinders solidification by disrupting the regular packing of phospholipids

How Cilia and Flagella Move

Cilia and flagella move by bending motor proteins called dynein feet; these feet attach to and exert a sliding force on an adjacent doublet; the arms then release and reattach a little further along and repeat this time after time; this "walking" causes the microtubules to bend

Differences Between Cilia and Flagella

Cilia are the short ones (mostly made out of microtubules); flagella propels a cell by an undulating, whiplike motion; cilia work more like the oars of a crew boat; flagella are longer (sperm cells have these)

Eukaryotic Cells

DO have membrane-bound organelles (nucleus, Golgi, etc.)

Acronym for General to Specific Classification

Domain, Kingdom, phylum, class, order, family, genus, species (Dumb King Phillip Came Over For Good Sushi)

Endosymbiont Theory

Endosymbiont theory proposes that mitochondria and chloroplasts were formerly small prokaryotes, and they began living within larger cells (prokaryotic cell engulfed a mitochondria) since mitochondria and chloroplasts have DNA, ribosomes, two membranes, make their own proteins, divide out of sync with the rest of the cell, Mitochondria was engulfed first (before) chloroplasts; evidence for this is that both plant and animal cells have mitochondria, but only plant cells have chloroplasts

Phase Contrast

Enhances contrast in unstained cells by amplifying variations in refractive index within specimen; especially useful for examining living, unpigmented cells; if you want to look at an unstained cell, to be able to pick up stuff, there's this thing called phase contrast (as the light is coming through a specimen, the phase contrast will accentuate the different refractive index)

Cell Walls

Exist in plants, fungi, and some protists; a plant cell, but not an animal cell has a rigid cell wall that protects and provides skeletal support that helps keep the plant upright against gravity, and is primarily composed of cellulose; binding of cells in tissues; (there are certain types of plant cells-sclerenchyma-have an additional cell walls made of lignin)

Extracellular Matrix (ECM)

In animals; animal cells synthesize and secrete an elaborate ECM that helps hold cells together in tissues and protects and supports the plasma membrane; involved in regulation of cellular activities; interstitial fluid that bathes cells; there has to be some fibers connecting the cells to one another (ex: collagen, proteoglycan complex, fibronectins)

Components of the Extracellular Matrix

Includes glycoprotein complex with long polysaccharide, collagen fiber, connecting glycoprotein, and integrin attached to the plasma membrane

Vacuoles

Large vesicles that have a variety of functions; some protists have contractile vacuoles that help to eliminate water from the protist; in plants, vacuoles may have digestive functions, containing pigments, or poisons that protect the plant; food vacuoles serve in digestion

Dimensions That Varying Microscopes Can Cover

Light microscope can cover from 1 mm - 100 nm, and electron microscope can cover from about 100 μm to 0.1 nm

Endomembrane System

Many of the membranes within a eukaryotic cell are part of the endomembrane system; some of these membranes are physically connected and some are related by the transfer of membrane segments by tiny vesicles (sacs made of membrane); many of these organelles work together in the synthesis, storage, and export of molecules

Importance of the Fluidity of Membranes

Membranes must be fluid in order to work properly (fluidity of membrane affects both its permeability and the ability of membrane proteins to move to where their function is needed); when a membrane solidifies, its permeability changes, and enzymatic proteins in membrane may become inactive; however, membranes that are too fluid can't support protein function either

Two Organelles Involved in Energy-Processing/Metabolism

Mitochondria and Chloroplasts

Internal Compartment of Mitochondria

Mitochondria have two internal compartments (the membrane space, which is the narrow region between the inner and outer membranes, and the mitochondrial matrix, which contains the mitochondrial DNA, ribosomes, and many enzymes that catalyze some of the reactions of cell respiration)

Peroxisomes

Not part of the endomembrane system; they perform diverse metabolic processes, with breakdown of toxic hydrogen peroxide by-product; specifically for breaking down hydrogen peroxide

Two Organelles Involved in Genetic Control

Nucleus and Ribosomes

Microfilaments

One of the three kinds of fibers that the cytoskeleton is composed of; microfilaments are actin filaments, and they support the cell's shape and are involved in motility; also called actin filaments, are the thinnest components; they are involved most in skeletal muscle contractions

Mitochondria

Organelles that carry out cellular respiration in nearly all eukaryotic cells; cell respiration converts the chemical energy in food to chemical energy in ATP

Membrane Proteins and Their Functions

Phospholipids form the main fabric of the membrane, but proteins determine most of the membrane's functions (different types of cells contain different sets of membrane proteins; the various membranes within a cell have a unique collection of proteins)

Movement of Membrane Proteins

Proteins are much larger than lipids and move more slowly, but some membrane proteins do drift; some membrane proteins move in a directed manner, driven along cytoskeletal fibers in the cells by motor proteins connected to the membrane proteins' cytoplasmic regions; however, other membrane proteins seem to be immobile, held to cytoskeleton or extracellular matrix

Intermediate Filaments

Reinforce cell shape and anchor organelles; fibers with diameters in a middle range; the organelles are tethered in place by intermediate filaments

Example of Components of the Bacterium Bacillus Coagulans

They are a typical rod-shaped bacterium, they contain bacterial chromosomes, ribosomes, a nucleoid, a plasma membrane, and a cell wall

Subcategories Under Prokaryotes

Under the category of prokaryotes, we archaea and we have eubacteria; now, under the category of eubacteria, we have bacteria (which are heterotrophic), and cyanobacteria (which are photosynthetic; do not have chloroplast, but they are autotrophs)

**TEST QUESTION ON APPLICATION OF ORGANELLE FUNCTIONS

cancer cells are in part characterized by a high metabolic rate, so they would have a lot of mitochondria; liver cells have a lot of smooth ER, because they're involved

Centrosomes and Centrioles

centrosomes have centrioles; they assemble on opposite sides of the cell during initial stages of cell division

Characteristics of Organelles of Plant Cells

contain nucleus (including nuclear envelope, chromatin, nucleolus), rough ER, smooth ER, ribosomes, mitochondria, one central vacuole, plasmodesma, chloroplasts, as well as the Golgi apparatus

Role of Lysosomes in Recycling Cellular Material

lysosomes also help remove or recycle damaged parts of a cell; the damaged organelle is first enclosed in a membrane vesicle; then a lysosome fuses with the vesicle, dismantles its content, and breaks down the damaged organelle

Role of Lysosomes in Digestion

lysosomes help digest food particles engulfed by a cell (process: a food vacuole binds with a lysosome, the enzymes in the lysosome digest the food, and the nutrients are then released into the cell)

Microtubules

made of tubulin; give the cell rigidity and act as tracks for organelle movement; big, strong, and they give a fairly rigid structure, they function on railroad tracks upon which motor proteins will walk

Plasmodesmata

plant cells have cell junctions that are called plasmodesmata that serve in communication between cells; channels between adjacent plant cells (they transport substances in the cytoplasm)

Lysosomes

(in animal cells and some protists); a lysosome is a membranous sac containing digestive enzymes (digestion of ingested food); the enzymes and membrane are produced by the ER and transferred to the Golgi apparatus for processing; the membrane serves to safely isolate these potent enzymes from the test of the cell, which also recycle a cell's damaged organelles and macromolecules

Electron Microscope (EM)

1. Passes beam of electrons through the object; 2. so, what you have to do is coat parts of the cell with something that is electron dense (ex: gold); after you coat it with gold, then you bombard it with electrons; 3. has a much higher resolution, and you can see down to minute details (i..e phospholipids in a phospholipid bilayer); 4. Two types of electron microscopes: scanning (which sees the surface of tissues, gives you more of a 3D image) and transmission (more of a slice through);

Amphipathic Molecule

1. A molecule that has both hydrophobic and hydrophilic region; 2. a phospholipid and various other types of membrane lipids are amphipathic; 3. a phospholipid bilayer exists as a boundary between two aqueous compartments, because the molecular arrangement shelters hydrophobic tails of phospholipids from water, while exposing the hydrophilic heads to water

Differential Interference Contrast

1. Also uses optical modifications to exaggerate differences in refractive index beam on a single plane within the specimen; 2. only those regions within a narrow depth of focus are imagined; 3. regions above and below the selected plane of view appear black rather than blurry; 4.kind of the same thing as phase contrast

Characteristics of Domain Animalia

1. Animals are eukaryotic, 2. multicellular, 3. do not contain cell walls, and 4. are heterotrophs 5. (organelles in animal cells: smooth ER, rough ER, nucleus-nuclear envelope, chromatin, nucleolus-ribosomes, Golgi apparatus, mitochondria, plasma membrane, peroxisomes, cytoskeleton; **NOTE: centrioles and lysosomes are present in animal cells not not in most plant cells

Six Types of Light Microscopy

1. Brightfield (unstained specimen) 2. Brightfield (stained specimen) 3. Fluorescence 4. Phase Contrast 5. Differential Interference Contrast 6. Confocal

Cell Size

1. Cell size must be large enough to house DNA, proteins, and structures needed to survive and reproduce, 2. but remain small enough to allow for a surface-to-volume ratio that will allow adequate exchange with the environment

Robert Hooke

1. Cells were first observed by Robert Hooke in 1665 (he looked at dead cork); 2. was thus the first to look at cells under a microscope (they were dead though)

Nucleus

1. Contains most of the cell's DNA, and 2. controls the cell's activities by directing protein synthesis by making messenger RNA (mRNA); DNA is associated with many proteins in structures called chromosomes a. Nuclear Envelope: Double membrane that has pores that allow material to flow in and out of the nucleus; it's also attached to a network of cellular membranes called the endoplasmic reticulum b. Nucleolus: Prominent structure in the nucleus where rRNA is made and joined with proteins that make ribosomes

The Five Components of Cells Involved in Structural Support, Movement, and Communication Between Cells

1. Cytoskeleton, 2. Extracellular Matrix, 3. Cell Junctions, 4. Cell Walls (in plants, fungi, and some protists) 5. Centrosomes and centrioles

Free Ribosomes vs. Bound Ribosomes

1. Free Ribosomes: Suspended in the cytoplasm and typically involved in making proteins that function within the cytoplasm 2. Bound Ribosomes: Attached to the ER associated with the nuclear envelope and associated with proteins packed in certain organelles or exported from the cell

Four Categories of Organelle Functions

1. Genetic Control 2. Manufacturing, distribution, and breakdown 3. Energy processing 4. Structural Support, movement, and communication between cells

Importance of High Surface-Area-to-Volume Ratio of Cell

1. In order to prevent cells from becoming too large, you must have a high surface area to volume ratio; 2. you need surface area to get substances in and out 3. (ex: ostrich eggs don't have much metabolism until they've been fertilized, so they don't start dividing to have more surface area until they increase their metabolism upon fertilization)

Ribosomes

1. Involved in the cell's protein synthesis; 2. ribosomes are synthesized from rRNA produced in the nucleolus; 3. cells must synthesize large amounts of protein have a large number of ribosomes; 4. some ribosomes are free ribosomes, and others are bound ribosomes; 5. Ribosomes involved in translation

Smooth ER

1. Lacks attached ribosomes; 2. involved in a variety of diverse metabolic processes: produces enzymes important in the synthesis of lipids, oils, phospholipids, and steroids; 3. functions in detoxification in liver cells, as it produces enzymes that help process drugs, alcohol, and other harmful substances; 4. some smooth ER helps store calcium ions

Membrane Proteins

1. Like membrane lipids, most membrane proteins are amphipathic 2. (can reside in the phospholipid bilayer, with their hydrophilic regions protruding outwards); 3. this organization maximizes contact of hydrophilic regions of proteins with water in the cytosol and extracellular fluid, while providing hydrophobic parts with a non-aqueous environment

Ingredients of Membranes

1. Lipids and proteins are the "staple" ingredients of membranes 2. (carbohydrates are also important); 3. the most abundant lipids in most membranes are phospholipids

The Fluidity of Membranes

1. Membranes aren't static sheets of molecules locked into place; 2. membrane is held together primarily by hydrophobic interactions (much weaker than covalent bonds); 3. most lipids can shift laterally, and this movement is very rapid

9 + 2 Microtubule Pattern in Cilia and Flagella

A ring of nine microtubule doublets surrounds a central pair of microtubules; this arrangement is called the 9 + 2 pattern and is anchored in a basal body with nine microtubule triplets arranged in a ring

Cell Junctions

Adjacent cells communicate, interact, and adhere through specialized junctions between them

Similarities Between Cilia and Flagella:

Although differences exist, flagella and cilia have a common structure and mechanism of movement; both cilia and flagella are made of microtubules wrapped in an extension of the plasma membrane

Scanning Electron Microscope (SEM)

SEM study the detailed architecture of cell surfaces; you can do types of staining with the electron microscopes

Brightfield (stained specimen)

Staining with various dyes enhances contrast, but most staining procedures require that cells be fixed (preserved)

Cell Theory

States that all living things are composed of cells, and that all cells come from cells

Transmission Electron Microscope (TEM)

TEM study the details of internal cell structure

Integrins

The ECM may attach to a cell through glycoproteins that bind to membrane proteins called integrins; integrins span the plasma membrane and connect to microfilaments of the cytoskeleton

Binomial Classification

The classification system developed by Carolus Linnaeus in the 19th century that uses Latin names; the first part of an organism's scientific name is its genus, and the second part is its species (ex: Tyrannosaurus Rex)

Confocal

Uses lasers and special optics to focus illuminating beam on a single plane within the specimen; only those regions within a narrow depth of focus are imagined; regions above and below the selected plane of view appear black rather than blurry; Confocal is when you have tissue that's relatively thick

Evolution of Differences in Membrane Lipid Composition

Variations in the cell membrane composition of many species appear to be the evolutionary adaptations that maintain the appropriate membrane fluidity under specific environmental conditions (ex: fish that live in extreme cold have membranes with high portion of unsaturated hydrocarbon tails, enabling their membranes to remain fluid)

Cilia

While some protists have flagella and cilia that are important in locomotion, some cells of multicellular organisms have them for different reasons; cells that sweep mucus out of our lungs have cilia; animal sperm are flagellated

Unsaturated vs. Saturated Hydrocarbon Tails

While unsaturated hydrocarbon tails prevent packing (enhancing membrane fluidity), saturated hydrocarbon tails pack together, increasing membrane viscosity (resistance to flow)

Antoni van Leeuwenhoek

Working with more refined lenses, Antoni van Leeuwenhoek later described living cells; Leeuwenhook was the first to look at living cells under a microscope (described blood, sperm, and organisms living in pond water)

Resolution

a measure of the clarity of an image (i.e. it's the ability of an instrument to show two close objects as separate)

Four Kingdoms Under Domain Eukarya

the eukaryotes include the following four kingdoms: protists, plants, fungi, and animals

Magnification

the increase in the apparent size of an object

Compartmentalization Within Eukaryotic Cells

the internal membranes of eukaryotic cells partition it into two compartments; cellular metabolism, the many chemical activities of cells, occurs within organelles; by compartmentalizing different metabolic processes into different organelles. The cell is much more efficient; all of the enzymes and raw materials for a particular process can be located within the organelle, and different organelles can have different environments (ex: different pH)

Chloroplasts: (in plants and some protists)

the photosynthesizing organelles of all photosynthesizing eukaryotes; photosynthesis is the conversion of light energy from the sun to the chemical energy of sugar molecules