Chapter 3 Microscopy and Cell structure

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Chapter 3Microscopy and Cell structure

• Biology 261
• Prof. Santos

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• Microscope- tool used to see objects too small to
  be seen by the naked eye. Types of microscopes
  used in the study of microorganisms include the
  light microscope, dark field microscope, phase
  contrast microscope, confocal microscope,
  interference microscope, fluorescence microscope,
  electron microscope, and atomic force microscope.

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Terms to know

• Bright field microscopy- lights rays are used to
  evenly illuminate the field of view.
• Dark field microscopy- light is directed towards
  the specimen at an angle. This makes it possible
  for the unstained specimen to appear more visible
  against a dark background.

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• Contrast- basically it is the number of visible
  shades in a specimen.
• Microscopes that increase contrast include, phase
  contrast microscope, interference microscope,
  dark field microscope, fluorescence, and confocal
  microscope.

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Light Microscope

• 1-Light microscope- uses a beam of light to
  create an enlarged image of the specimen. The
  light microscope can either use a mirror or a
  light bulb to pass light through the specimen.
  You can magnify a specimen up to 1000x with a
  good light microscope

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Electron Microscope

• Electron microscope- uses a beam of electrons
  to create an enlarged image of the specimen. An
  electron microscope can magnify a specimen up to
  250,000x closer. The wavelength used is less than
  the wavelength of light, thus the resolution is
  greater.

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2 types

• TEM- transmission electron microscope allows one
  to see fine detail structures inside the cell.
• SEM- scanning electron microscope allows one to
  see the surface details of cells like the
  membrane proteins.

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• 3-Phase contrast microscope- allows you to see
  unstained cells by altering the background of the
  cell. This microscope has a device that allows it
  to amplifies differences in refractive index to
  create a contrast.

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• 4-fluorescence microscope
• Projects ultra violet light causing
  fluorescent molecules in the specimen to emit a
  longer wavelength.
• 5- Confocal microscope
• Mirrors are used to scan a laser beam
  across successive regions and planes of a
  specimen. A computer program constructs a 3D
  image.

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• 6- Interference microscope causes the specimen to
  appear as a 3D image. The most common one is the
  Nomaski differential interference microscope.
  This microscope has a special device that
  separates light going through a specimen into 2
  beams and then recombines them. The light rays
  are out of phase when they recombine, yielding a
  3D image.

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• 7- Dark field microscope
• this type of light microscope has a special
  device that directs light at an angle so that
  only light scattered by the specimen enters the
  objective so one sees the specimen against a dark
  background.

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• 8- Atomic force microscope
• This very powerful microscope produces a
  very detailed image of the surface of an specimen
  by using a very sharp probe (stylus) to move
  across the surface and feel the bumps and
  valleys of the atoms of the surface.

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Prokaryotic cell

• Morphology
• Three basic shapes spherical called coccus,
  cylindrical called bacillus and spiral. There are
  variations!
• coccobacillus- short rod
• vibrio- a short curve rod
• spirochete- a long helical cell with a flexible
  cell wall and unique mode of motiliy

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• Pleomorphic- bacteria that vary their shape

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Multicellular association

• 1- fruiting body- a complex structure of cells
  congregated together. They tend to be brightly
  colored consisting of a mass of cells held by a
  stalk. This structure is highly resistant to
  heat, drying, and radiation. Ex, Myxobacteria

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• 2- Biofilm
• a thin layer of microorganisms adhering to
  the surface of a structure, which may be organic
  or inorganic, together with the polymers that
  they secrete.

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Structure of prokaryote cell

• 1-Flagella provides motility. The flagella is
  made up of three basic parts, filament, hook and
  basal body.

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• Chemotaxis- movement towards a chemical
• Phototaxis- movement towards light
• Aerotaxis- movement towards oxygen
• Magnetotaxis- reaction towards the magnetic field
• Thermotaxis- movement towards a specific
  temperature

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• 2-Pili proteins that enable the bacterium to
  adhere to surfaces. Fimbriae allow bacteria to
  adhere to surfaces and sex pili allow DNA
  transfer between bacteria.

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• 3-The capsule a viscous and gelatinous layer that
  surrounds bacteria. It enables bacteria to adhere
  to certain surfaces and allows organisms to avoid
  innate defense systems and cause diseases. Ex,
  Streptococcus pneumoniae.

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• 4- slime layer- gel like layer that is diffuse
  and irregular. This layer is composed of
  polysaccharides and enables the bacteria to
  adhere to surfaces and grow as biofilm.
• Ex Streptococcus mutans grows as biofilm on your
  teeth to form dental plaque.

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• 5- The cell wall a rigid covering consisting of
  peptidoglycan that gives the bacterium its shape
  and protection.
• The type of cell wall distinguishes between 2
  types of bacteria gram negative and gram
  positive.
• Peptidoglycan is a macromolecule found only in
  bacteria.

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• The basic structure of peptidoglycan is an
  alternating series of 2 major subunits,
  N-acetylmuramic acid (NAM) and N-
  acetylglucosamine (NAG). These subunits are
  covalently bonded to each other to form a glycan
  chain.

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• Attached to each NAM molecule is a string of 4
  amino acids, a tetrapeptide chain. Cross linkages
  can form between adjacent chains thus joining
  adjacent glycan chains.

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• In gram negative bacteria these tetrapeptides are
  joined directly.
• In gram positive bacteria they are usually joined
  indirectly by a peptide interbridge.
• In gram positive bacteria the peptidoglycan layer
  is thick.
• In gram negative bacteria the peptidoglycan layer
  is thinner.

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Teichoic acid

• In gram positive bacteria there are polymers of
  teichoic acid present. These teichoic acid
  polymers are covalently linked to the NAM
  molecules of the glycan chain. Some are linked to
  the cytoplasmic membrane and are called
  lipoteichoic acids.
• These polymers consists of ribitol-phosphates and
  glycerol phosphates molecules joined together.
  Sugars and D- alanine may be attached to these
  polymers providing antigenic determination.

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• Teichoic acid provides rigidity to the cell wall
  and give the cell negative polarity due to the
  fact that they stick out above the peptidoglycan.

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Outer membrane

• In gram negative bacteria there is an outer
  membrane outside the peptidoglycan. It is a
  unique lipid bilayer.
• The outer membrane is unlike any other membrane.
  The outside leaflet consists of
  Lipopolysaccharides instead of phospholipids.

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• The outer membrane is sometimes called the LPS or
  lipopolysaccharide layer.
• The outer membrane is joined to peptidogylcan by
  means of lipoproteins
• Two parts are importance for medical reasons
• a- Lipid A is the portion that anchors the LPS in
  the lipid bilayer. It plays a role in the immune
  system.
• b- O specific polysaccharide is a chain of sugar
  molecules opposite the Lipid A. Allows for
  identification.

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Gram positive
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periplasm

• In gram negative bacteria, it is the space
  between the inner and outer membrane.

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Intracellular parts

• 6- Bacterial chromosome is usually circular
  double stranded molecule located in a region
  called the nucleoid
• 7- Plasmids are small, supercoiled, circular
  double stranded pieces of DNA that contain few
  genes.
• 8- Endospore is a type of dormant cell that
  resists harsh conditions.

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• 9- Cytoskeleton proteins that provide support.
• 10- Gas vesicles provide buoyancy

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• 11- granules are accumulations of substances
  produced in excess.
• Examples are glycogen, poly beta hydroxybutyrate,
  and volutin.
• Volutin- a storage form of phosphate. They stain
  red with methylene blue, sometimes called
  metachromatic granules. Role is unclear. Thought
  to be involved in energy storage and pH balance
  inside the cell.
• 12- ribosomes involved in protein production

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Eukaryotic cell

• 1- Plasma membrane consisting of asymmetrical
  lipid bilayer.
• The cell membrane consists of proteins and
  lipids.

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Internal protein parts

• 2- Cilia/flagella are protein structures that
  consists of microtubules in a 9 2 arrangement.
  Cilia and flagella function in motility.
• 3- cytoskeleton consists of proteins such as
  microtubules, actin filaments and intermediate
  filaments that function in cell structure/support
  and act as a molecular monorail.

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• 4- ribosomes are involved in protein production.
• 5- Chloroplast- double membrane bound organelle
  involved in photosynthesis
• 6- Endoplasmic reticulum is a system of canals
  involved in the production of macromolecules
  destined to be secreted to other organelles or
  outside. Two types, smooth and rough.

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• 7- Golgi Apparatus is a system of flat membranes
  involved in the modification of material made in
  the ER. The vesicles are coated with special
  carbohydrates and phosphate groups that signal
  the vesicles to their specific location.

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• 9- Nucleus is the control center of the cell.
  Contains the genetic material and is surrounded
  by a nuclear envelope.
• 10- Mitochondrium is the site of cellular
  respiration
• 11- Lysosomes
• 12- peroxisomes are organelles us to oxidize
  substances, breaking down lipids, and detoxifying
  certain chemicals.