Micro ch3

• Type of microscopes which use visible light for observing objects
• Visible light passes through a specimen and then through a series of lenses to produce magnified image
• Can magnify up to 1000x, making it relatively easy to observe cell size, shape and motility
• Relatively ease to use, considerably less expensive than electron & atomic force
• Also called compound microscope

• positioned btwn light source and specimen
• does not affect magnification
• focuses light on specimen

• the min distance btwn 2 points at which those points can still be observed as separate objects
• Max resolving of best light microscope is 0.2 μm, or 200 nm

bending of light rays

a measure of the relative speed of light as it passes through the medium

• used when preparing a live specimen
• a drop of liquid on which a coverslip has been placed

• Bright-field
• Dark-field
• Phase-contrast
• Differential interference contrast
• Fluorescence
• Scanning laser

• most common type of light microscope
• Illuminates the field of view evenly

• Cells stand out as bright objects against dark background
• Light is directed toward the specimen at an angle
• Makes unstained cells easier to see
• *Used to see Treponema pallidum, which causes syphilis; as bright field will not work cause cells are too thin and stain poorly

• Makes cells and other dense material appear darker
• Increases contrast by amplifying differences in refractive index
• Makes unstained cells easier to see

• DIC
• Two light beams pass through the specimen and then recombine
• Image of specimen appears 3D

• Used to observe cells or other materials that are either naturally fluorescent or stained or tagged with fluorescent dyes
• Projects ultraviolet light, causing fluorescent molecules in the specimen to emit longer wavelength light
• Used to observe cells stained or tagged with a fluorescent dye

• SLM
• Used to construct a 3D image of structure
• Provides detailed sectional and interior views of intact cell
• Mirrors scan laser beam across successive regions and planes of a specimen
• With that info, computer constructs image

• Type of scanning laser microscope
• Is like a CAT scan for cells

• Similar to confocal microscope, but lower energy light is used
• This light is less damaging to cells, so time-lapse images of live cells can be obtained. 
• Light also penetrates deeper, making it possible to get interior views of relatively thick structures

• can magnify in excess of 100,000x
• Electron beams are used in place of visible light to produce the magnified image
• Includes:
• Transmission
• Scanning
• Drawback: All lenses and specimen must be in vacuum, otherwise molecules in air would interfer with electrons

• TEM
• used to observe fine details of cell structure
• Transmits beam of electrons through specimen
• Elabroate specimen preparation is required

• cryo-EM
• a newer method of preparing and observing specimens with an electron microscope
• involves rapidly freezing the specimen at very low temps, avoiding some of the simple preparation processes that damage cells

• SEM
• Used to observe surface details of cells
• A beam of electrons scans back and forth over the surface of a specimen coated with thin film of metal
• Produces 3D effect

• Major advancement in 1980's
• Produces images of individual atoms on a surface
• A probe moves in response to even the slightest force btwn in and the sample
• Produces a map showing the bumps and valleys of the atoms on the surface of the sample

• Staining procedures typically use basic dyes, meaning the dyes carry a positive charge
• The dyes stain cells because they are attracted to the many negatively charged cellular components
• Most bacteria is negatively charged

• A basic dye is used to stain cells
• Easy way to increase the contrast btwn otherwise colorless cells and transparent background

• a procedure that colors the background
• uses acidic dyes, which DOES NOT stain cells
• As the cells repel the negatively charged dye, it allows the colorless cell to stand out against the background

• A multistep procedure used to stain cells and distinguish one group of microorganisms from another
• Two most frequently used techniques are gram stain and acid-fast stain

• Used to separate bacteria into two major groups: Gram neg and Gram pos
• The staining characteristics of these groups reflect a fundamental difference in the chemical structure of their cell walls
• By far the most widely used staining procedure

• Crystal violet - primary stain which stains cells purple
• Iodine - mordant, which fixes stain into the cell. Cells remain purple
• Alcohol - Decolorizer, Gram-pos cells remain purple, Gram-neg become colorless
• Safranin - counterstain, Gram-pos stays purple, Gram-neg appear pink

Used to detect organism that do not easily take up stains, such as members of the genus Mycobacterium which cause TB and Hansen's disease (leprosy)

Primary stain is red, counterstain is Methylene blue

• Are often negative stains that take advantage of the fact the viscous capsules do not take up certain stains
• In one common method, India ink is added to a suspension of cells to make a wet mount. The fine particles of ink darken background and allow the capsule to stand out as a clear area surrounding the cell

• Needed for members of certain genera, including Bacillus and Clostridium, as they form endospores which are resistant to stain
• Don't stain with the Gram, but can be seen as clear, smooth objects within stained cells
• Uses Malachite green as primary stain

• Usually, flagella are too thin to be seen with light microscope
• This stain uses a substance that allows staining agent to adhere to and coat thin flagella, making them visible using light microscopy

• Fluorescent dyes and tags absorb ultraviolet light and then emit light of a longer wavelength
• They are used in conjunction with a fluorescence microscope

• Some fluorescent dyes bind to compounds found in all cells
• Others bind to compounds specific to only certain types of cells

Antibodies to which a fluorescent molecule has been attached are used to tag specific molecules

• A technique used to tag specific proteins with a fluorescent compound
• can be used to detect organism

• Coccus - round balls (cocks)
• Rod - Duh
• Bacillus - rod-shaped
• Coccobacillus - rod shaped so short it may be mistaken for coccus
• Vibrio - short, curved rod.., or vibrater
• Spirillum - curved rod long enough to form smooth spirals
• Spirochete - long, crimped, slinky thing

• Pleo means many; morphic refers to shape
• When bacteria characteristically vary in their shape

• cocci that occur in pairs & often stick together
• (binary fission)

Cell adhering to one another following division form characteristic arrangements:

• Chains:Cells divide in one plane. long line 
• Packets : Cells divide in two or more planes perpendicular to one another
• Clusters: Cells divide in several planes at random

• Called the cell envelope:
• cytoplasmic membrane
• cell wall
• if present, the capsule (bacteria have capsules, but archaea rarely do)
• Inside are the contents of the cell - the cytoplasm and nucleoid

• the viscous material enclosed in the envelope
• fluid portion is called cytosol

• The gelatinous region where the genetic material resides
• NOT enclosed by a membrane

• Extracellular structure composed of protein subunits that form a helical chain
• Includes:
• Flagella
• Pili

• Long protein structures
• Provide the most common mechanism of mobility
• Has 3 basic parts:
• Filament-extends into external environment
• Hook- flexible, curved segment connects filament to cell surface
• Basal body - anchors structure to cell wall and cytoplasmic membrane

• an arrangement of flagella in which they are distributed over the entire surface
• Ex: E coli

a single flagellum at one end of the cell

• a phenomenon in which motile bacteria can sense the presence of chemicals or oxygen and respond by moving in a certain direction
• If a nutrient, may serve as attracting and cell move toward it
• If toxic, may act as repellent and cause cell to move away

• Considerably shorter and thinner than flagella
• Different types of pili have different functions
• Common types, often called fimbriae, allow cells to adhere to surfaces
• A few types are used for twitching or gliding motility
• Sex pili join cells in preparation for DNA transfer

• Extracellular layers outside the cell wall
• Usually made of polysaccharide and referred to as glycocalyx
• colonies that form either often appear moist and glistening
• Some allow cells to adhere to specific surfaces, including teeth, rocks... and can then grow as biofilm

• Distinct and gelatinous
• Allows bacteria to adhere to specific surfaces
• Allows some organisms to envade innate defense systems and thus cause disease

• Diffuse and irregular
• Allows bacteria to adhere to specific surfaces

• Peptidoglycan provides rigidity to bacterial cell walls, preventing the cells from lysing
• Gram-pos has thick layer of peptidoglycan that contains teichoic acids and lipoteichoic acids
• Gram-neg has thin layer of peptidoglycan surrounded by an outer membrane. The outer layer of the outer membrane is lipopolysaccharide

• Intracellular - duh
• Includes:
• Chromosomal: Carries genetic info required by cell. Typically single, circular, double-stranded DNA molecule
• Plasmid: Extrachromosomal DNA molecule; generally carries only genetic info that may be advantageous to cell in certain situations

• Type of dormant cell
• Generally extraordinarily resistant to heat, desiccation ,UV light, and toxic chemicals
• Can germinate, or exit dormant stage, and become a typical multiplying cell, called vegetative cell

Ex: Bacillus and Clostridium

• endospore formation
• a complex sequence of changes that begin when spore-forming bacteria experience limiting amts of carbon or nitrogen
• 8 hr process begins with DNA duplication & septum divides cell asymmetrically 
• Larger part engulfs smaller, making forespore within mother cell
• Ultimately, mother cell is degraded & endospore is released

• exiting the endospore stage
• can be triggered by a brief exposure to heat or certain chemicals
• takes on water and swells
• Spore coat & cortex crack open, vegetative cell grows out

Involved in cell division and control of cell shape

• Intracellular structure produced by some aquatic bacteria
• Small rigid structures that provide buoyancy to a cell
• Gases, not water, flow freely into the vesicles, thereby decreasing the density of the cell
• By regulating the number of gas vesicles, a cell can float or sink to it's ideal position in the water column

• Intracellular accumulations of high-molecular-weight polymers
• Synthesized from a nutrient that a cell has in relative excess

• Intracellular structure
• Involved in protein synthesis, serve as structures that facilitate joining of amino acids
• Relative size and density is expressed as distinct unit S (which reflects how fast they settle when spun at very high speeds in ultracentrifuge)
• Two subunits, 30S and 50S, join to form the 70S ribosome, which is important as antibiotics that interfere with function of 70S ribosome have no effect on 80S molecule (which is eukaryotic)

• A thin, delicate structure that surrounds the cytoplasm and defines the boundary of the cell
• It's a phospholipid bilayer embedded with proteins
• Is selectively permeable
• Also transmits info about external environment to inside of cell

Refers to the membrane proteins not being stationary; rather, they constantly drift in the lipid bilayer

• Only certain substances can cross (referring to the cytoplasmic membrane)
• Those that pass freely include gases such as:
• Oxygen
• Carbon dioxide
• Nitrogen
• Small hydrophobic molecules and water

pore forming membrane proteins that specifically allow water molecules to pass through cytoplasmic membranes more easily

• Method by which molecules that can pass through the lipid bilayer move in and out of the cell
• The molecules move from a region of high concentration to a region of low concentration, until equilibrium is reached.
• Speed and direction depends on relative concentration on each side - the greater the difference in concentration the higher the rate of diffusion

• The diffusion of water across a selectively permeable membrane
• Occurs when concentrations of solute (dissolved molecules and ions) on 2 sides of membrane are unequal
• Typical of diffusion, water moves down its concentration gradient from high water concentration (low solute concentration) to low water concentration (high solute concentration)
• *wants everything diluted and equal

Hypotonic: hypo means less; tonic means solute

Hypertonic: hyper means more

Isotonic : iso means the same

• Water flows from the hypotonic solution to the hypertonic one
• No net water movement occurs btwn isotonic solutions

• a series of protein complexes of most prokaryotes which act as part of their energy-transforming processes
• Transfers electrons and moves protons in and out of the cell
• The expulsion of protons creates a proton gradient across cell membrane: + charged protons concentrated outside membrane, whereas neg charged hydroxyl ions remain inside
• Because charged ions attract each other, stay close to membrane

• Analogous to the energy stored in a battery
• Refers to the electrochemical gradient created across the membrane from the separation of protons (+ charge) and hydroxyl ions (- charge) resulting from electron transport chain
• Energy can be harvested when protons are allowed to move back into cell

• mechanisms that allow nutrients and other small molecules to enter the cells
• Also used to expel wastes and compounds such as antibiotics and disinfectants that otherwise damage the cell
• Transported molecules enter/exit through transport proteins

• A form of passive transport, does not require energy
• Uses transport protein to move substance from one side to the other by using concentration gradient to move molecules
• *can only eliminate gradient, not create one, so molecules are transported until their concentration is the same on both sides
• **Cause prokaryotes typically grow in nutrient-poor environment, generally rarely use to take in nutrients

• moves compounds against a concentration gradient and uses energy
• 2 main mechanisms use different forms of energy:
• Proton Motive Force
• ATP

As a proton is allowed into the cell, another substance is simultaneously brought along or expelled

• Transport mechanisms called ABC (ATP Binding-Cassette)
• ATP is used as energy source
• This system uses specific binding proteins that reside immediately outside the membrane to gather & deliver molecules to respective transport complexes

• a transport process that chemically alters a molecule during it's passage through the cytoplasmic membrane
• typically done by adding a phosphate group, a process called phosphorylation

Ex: glucose and several other sugars are phosphorylated during their transport

• a process by which cells actively move certain proteins they synthesize out of the cell
• Some of the molecules must be moved to outside of cell as they will become enzymes that will break down macromolecules into their individual subunits
• The macromolecules are too large to transport into cell, but subunits are not
• Others makes up external structures such as flagella

• a characteristic sequence of amino acids, typically at one end of the molecule, that's destined for secretion
• functions as a tag that directs the secretion machinery to move the preprotein across membrane

• a material found only in bacteria
• gives strength to Gram+ and Gram- bacterial cell walls
• Basic structure is alternating series of 2 major subunits: N-acetylmuramic acid (NAM) and N-acetylglucosamine (NAG)
• NAM-NAG-NAM-NAG-NAM-NAG

• Stains purple
• Has thick layer of Peptidoglycan, which is permeable to sugars, amino acids + others
• Also has teichoic acids, which are neg charged atoms
• Has gel like layer btwn cytoplasmic m & peptidoglycan & teichoic acid 
• No outer membrane
• No lipopolysaccharide (endotoxin)
• No porin proteins (unnecessary as no outer membrane)
• Generally more susceptible to penicillin (with notable exceptions)
• Sensitive to lysozyme

• Bacillus
• Staphylococcus
• Streptococcus

• Stains pink
• Thin Peptidgolycan 
• No Teichoic acid
• Has outer membrane & lipopolysaccharide (endotoxin)
• Has porin proteins, which allow molecules to pass through outer membrane
• Generally less susceptible to penicillin
• Not sensitive to lysozyme

• Escherichia
• Neisseria
• Pseudomonas

• lipopolysaccharide
• Makes up the bilayer structure of outer membrane in gram neg cell walls (instead of phospholipid)
• When injected in animal, sx are like infection by live bacteria
• Considered endotoxin

• Lipopolysaccharide, component of outer membrane of gram-neg cells that can cause sx such as fever and shock
• lipid A is responsible for the effects

Lipid A: anchors LPS in lipid bilayer, portion body recognized as sign of invading gram-neg bacteria

O antigen: portion of LPS directed away from membrane, at opposite lipid A. Is chain of sugar... looks like fingers or shaggy carpet.

• specialized channel forming proteins that span the outer membrane of gram-neg bacteria
• small molecules and ions use to cross membrane
• Some are specific, others allow different molecules to cross

• A gel like substance with fills a region between the cytoplasmic membrane and the outer membrane (that space is called the periplasmic space)
• All exported proteins accumulate here, unless specifically moved across outer membrane
• Thus, filled with proteins

• Interferes with synthesis or alters its structural integrity by weakening the molecule to a point where it can no longer prevent cell from bursting
• No effect on eukaryotic cells as peptidoglycan is unique to bacteria

• most thoroughly studied antibiotic that interferes with pep synthesis
• functions by preventing cross-linking of adjacent glycan chains
• Far more effective on Gram-pos than Gram neg due to gram-neg outer membrane

• an enzyme found in tears, saliva, and many other body fluids
• attacks protective walls of bacteria by breaking the bonds that link the alternating subunits of glycan chain
• destroys structural integrity of peptidoglycan molecule

• It's inside of cell, not wall, that is stained
• Gram+ retains dye cause cell walls prevents crystal violet-iodine complex from being washed out by decolorizing agent
• Gram- cells lose dye quite easily. Decolorizing agent thought to dehydrate thick layer of peptidoglycan, wall then acts as permeability barrier & prevents dye from leaving cell

• Mycoplasma - causes mild form of pneumonia
• has extremely variable shape as they lack rigid cell wall
• Neither penicillin nor lysozyme affects these organisms
• Mycoplasma & related bacteria can survive w/o cell wall cause cytoplasmic membrane has sterols in it, making it stronger than most other bacteria

• Have a variety of cell wall types
• None have peptidoglycan, but some have similar molecule called pseudopeptidoglycan

• Typical eukaryotic cell structure
• Phospholipid bilayer embedded with proteins; however layer that faces cytoplasm differs significantly from side that faces outside
• Permeability barrier, transport, and cell-to-cell communication

• (Eukaryotic)
• Membrane proteins that face the outside 
• A given receptor binds a specific molecule, referred to as its ligand
• Relationship allows cells to communicate with each other

• function as either carriers or channels
• Carriers are analogous to proteins in prokaryotic cells that function in facilitated diffusion and active transport
• Channels form small pores in membrane that allow only specific ions to diffuse through

process by which a eukaryotic cell takes up material from surrounding environment by forming invagination (inward folds) in its membrane

• membrane-bound compartment formed from endocytosis
• fuses to digestive organelles called lysosomes to form endolysosome

• Type of endocytosis
• cell takes in liquids

• Variation of pinocytosis
• Allows cell to take up extracellular ligands that bind to cells surface

• type of endocytosis used by phagocytes and protozoa
• Cell sends out armlike extensions called pseudopods, which surround and enclose extracellular material into the cell in an enclosed compartment called a phagosome
• This fuses with endosomes, and ultimately fuses with lysosomes to form phagolysosome

• reverse of endocytosis
• membrane-bound exocytic vesicles inside the cell fuse with the plasma membrane and release their contents to the outside

• As in prokaryotic, proteins destined for secretion have signal sequence, a characteristic amino acid that functions as tag
• When ribosomes synthesize protein with sequence, they attach to complex on membrane of endoplasmic reticulum
• Once inside ER, can easily be transported by vesicles to outside of cell
• Proteins destined for various organelles also have specific amino acid tags

• Involved in protein synthesis
• is 80S, made up of 60S and 40S

• forms framework of cell
• 3 components: 
• actin filaments
• microtubules
• intermediate filaments

• allow cell cytoplasm to move
• filaments rapidly assemble and subsequently disassemble to cause motion

• the thickest of the cytoskeleton components
• long hollow structures made of protein subunits called tubulin
• Form mitotic spindles
• main structure that make up cilia and flagella
• *antifungal drug griseofulvin interferes with action of microtubules in some fungi

• function like ropes, strengthening the cell mechanically
• by providing mechanical support, they allow cells to resist physical stresses

• shorter than flagella
• often covering a cell and moving in synchrony
• Can either propel cell or move material along a stationary cell

• appear to project out of the cell yet are covered by extensions of the plasma membrane
• composed of long microtubules grouped in 9+2 arrangement = nine pairs or microtubules surrounded by 2 individual ones

• duh-contains genetic info in eukaryotic cell
• boundary is two lipid bilayer membrane
• complex protein structures span envelope, forming nuclear pores, allowing large molecules such as ribosomal subunits and proteins to be transported into and out of nucleus
• *Nucleolus is region where ribosomal RNA is synthesized

• function as ATP-generating powerhouses, are found in nearly all eukaryotic cells
• complex structures bounded by two lipid bilayers- the outer and inner membranes
• Outer is smooth, inner is highly folded, forming invaginations called cristae

• Folds increase membrane's surface area
• *Mitochondrial matrix contains DNA, ribosomes, etc necessary for protein synthesis. However, ribosomes are 70S rather than 80S as ribosome found in cytoplasm of eukaryotic cells

• Mitochondrial matrix contains DNA, ribosomes, etc necessary for protein synthesis. However, ribosomes are 70S rather than 80S as ribosome found in cytoplasm of eukaryotic cells
• This observation and fact that mitochondria divide in similar fashion to bacteria, which lead scientists to hypothesize mitochondria evolved from bacterial cells

• found exclusively in plants and algae
• site of photosynthesis in eukaryotic cells
• harvest energy of sunlight to generate ATP, which is used to convert CO2 to sugar and starch (an organic form)

• complex system of flattened sheets, sacs, and tubes
• Site of synthesis of macromolecules destined for other organelles or the external environment

• has characteristic bumpy appearance due to the many ribosomes adhering to surface
• site where proteins not destined for cytoplasm are synthesized
• include proteins targeted for secretion or transfer to an organelle's lumen

• functions in lipid synthesis and degradation, and calcium storage
• vesicles transfer compounds from smooth ER to Golgi apparatus

• consists of a series of membrane-bound flattened compartments
• Site where macromolecules synthesized in ER are modified before transported in vesicles to other destinations

• digestion of macromolecules
• organelles that contain a number of powerful degradative enzymes that could destroy the cell if not contained within the organelle
• endosomes and phagosomes fuse so material taken up by cell can be degraded

• Site where oxidation of lipids and toxic chemicals occur
• the organelles in which o2 is used to help break down lipids and detox certain chemicals