BIOL112

• Prokaryotic cells developed over 3.5 billion years ago
• Prokaryotic cells


  • No membrane bound organelles
  • Most abundant types of cells on earth
• Eukaryotic cells developed from prokaryotic cells around 2 billion years ago
• Types of prokaryotes


  • Bacteria
  • Archaea
• Archaea


  Often live in very extreme environments
• Bacteria


  Have enormous medical and economic importance
• Prokaryotic cell


  • Nucleoid region: contains circular DNA, no nuclear envelope
  • Plasma membrane has the same basic structure of all biological membranes
  • Some prokaryotes have infoldings of the plasma membrane which contain specialized enzymes
  • The cytoplasm contains ribosomes and little else
  • Many prokaryotes have a cell wall
  • Some prokaryotes have flagella composed of the protein flagellin
  • Pili are composed of the protein pilin and help bacteria stick to their substrate or to each other
  • Many bacteria also secret a capsule usually of polysaccharides
  • Bacteria have a diverse range of shapes, the most common being Cocci (spherical), bacilli (rod shaped), and spirochetes (helical)

  
• Prokaryotic cell wall


  • Protects against mechanical and osmotic shocks
  • Composed of the molecule peptidoglycan
  • Can be divided into gram positive and gram negative
• Gram positive bacteria


  • Have a thick layer of peptidoglycan
• Gram negative bacteria


  • Have a much more complex cell wall structure
  • Most dangerous to humans and harder to kill
• Pathogenic Bacteria


  • Gram negative: Chlamydia trachomatis, Vibrio cholerae, Yersinia pestis
  • Gram positive: Clostridium tetani, Clostridium botulinum, Streptococcus pneumoniae
• Modes of nutrition


  • Photoautotrophs
  • Chemoautotrophs
  • Photoheterotrophs
  • Chemoheterotrophs
• Photoautotrophs


  Photosynthetic organisms which use light to synthesize organic compounds from CO2
• Chemoautotrophs


  Use CO2 as a C source and obtain their energy by oxidising inorganic substances. Unique to certain types of prokaryotes
• Photoheterotrophs


  Use light to generate ATP but must obtain C in organic forms
• Chemoheterotrophs


  Use organic molecules to supply both carbon and energy
• Viruses


  • Cannot be considered alive, cannot self-repair, don't have energy transduction system
  • Only visible with an electron microscope
  • Each viral particle is called a Viron, the protein coat is called the capsid, which is made from proteins called capsomers
  • Filamentous viruses – nucleic acid arranged in a helix with protein sub-units surrounding and stabilising it
  • Spheroid viruses – nucleic acid id condensed inside a protein envelope which is usually in a geometric shape
  • Tailed spheroid virus – spheroid virus with a tail
  • Enveloped virus – have lipid envelopes
• Magnification

  The ratio of an object's image size to its actual size
• Resolution


  The measure of the minimum distance of two distinguishing points
• Contrast


  Visible differences in brightness or colour between part of the sample
• Light microscopes


  • Commonest type of microscopy
  • Sample must be at least partially transparent as the light must pass through
  • Can image living cells
  • Includes: fluorescent, phase/differential contrast, and confocal microscopes
  • Limited resolution, approx. 0.2microns

  
• Advanced light microscopy


  • Light phase shifts induced by the specimen are used to generate contrast
  • Phase contrast (refracted and unrefracted light)
  • Differential interference contrast (two light beams)
• Light microscope sample preparation

  1. Whole mounts

  2. Tissue sections

  3. Fixation

  4. Dehydration and clearing

  5. Embedding

  6. Sectioning

  7. Staining

  
• Confocal scanning light microscope

  • 3D image of living cells
  • Removes out of focus image – optical sectioning
• Deconvolution microscopy


  Algorithms remove out of focus light this sharpens the image and improves resolution, super resolution gathers light from individual fluorescent molecules and records their position, combining information from these individual molecules breaks the resolution limit
• Electron microscopes


  • Very short wavelength, 1000x better resolution than light microscopes
  • Electrons have poor penetrating power so it must be kept in a vacuum, focused using magnetic fields
  • Similar arrangement of lenses
• Transmission electron microscope


  • Electron gun: usually heated tungsten filament which produces electron by thermionic emission
  • Electron bean passes through specimen
  • Image focused and magnified by magnetic objective and projector lenses
  • Electron image converted to a visible image by a fluorescent screen, which is viewed through a glass window
  • Inside kept at high vacuum during operation
• TEM sample preparation


  1. Whole mounts

  2. Fixation

  3. Dehydration

  4. Embedding

  5. Sectioning

  6. Staining
• Scanning electron microscope


  • Electron beam scanned across the specimen, and reflect, they are collected by an electron detector and converted to an electronic signal which is displayed on a screen
  • Looks at the surface of the specimen
• SEM sample preparation


  1. Fixation

  2. Dehydration

  3. Critical point drying

  4. Coating
• Cell fractionation


  • Allows the major organelles to be individually separated out
  • Cells are first homogenised to release organelles
  • Differential centrifugation isolated cell components by size and density by using increasing durations and g forces
• Eukaryotic cells


  • Able to be larger than prokaryotic cells because of their internal membrane
  • Genetic material is organised into chromosomes and enclosed in the nuclear envelope
  • Contained within a plasma membrane
  • Endomembrane system – numerous internal membranes
  • Complex cytoskeleton
• Plant cells


  • Contain several types of plasmids, including chloroplasts, which are the site of photosynthesis
  • Chloroplasts capture light and convert it into chemical energy, this occurs in the stacks of thylakoid sacs called grana
  • Contain vacuoles, which store various chemicals and play a role in cell growth
  • Cell wall maintains cell shape and prevents mechanical damage. It is composed of cellulose fibres embedded in a protein/polysaccharide matrix consisting mainly of hemicellulose and pectin
• Nucleus


  • Contains most of the genes that control the cell (some genes are present in the mitochondria and chloroplasts)
  • Nuclear membrane separates it from the cytoplasm
  • Nuclear membrane is a double membrane and contains nuclear pores about 100nm in diameter
  • DNA, along with histones, are organised into chromatin, the nucleolus is where components of ribosomes are manufactured
  • During cell division the chromatin condenses into chromosomes
  • mRNA is synthesized inside the nucleus from a DNA template and released into the cytoplasm via the nuclear pores where it controls protein synthesis

  
• Plasma membrane


  • All membranes have a common structure
  • Defines and contains the cell, separating the cell from its external environment
  • Controls the entry of nutrients and the exit of waste products, maintains electrolyte balance, acts as sensor to external signals
  • Assemblies of lipids and protein molecules held together mainly by non-covalent interactions
  • Lipid bilayer provides the basic structure of the membrane and serves as an impermeable barrier to most water-soluble molecules
  • Protein molecules are dissolved in the lipid bilayer and carry out most of the specialised functions of the membrane
• Lipid bilayer of the PM

  • Membrane lipids are Amphipathic molecules which will spontaneously form bilayers in an aqueous environment
  • In an aqueous environment the lipid molecules either form micelles or bilayers
  • If damaged the lipid bilayer can repair itself
  • Lipids constitute about half of the mass of biological membranes
  • The 3 major types of lipids in cell membranes are phospholipids, cholesterol, and glycoproteins
  • Phospholipids are the most common and typically have a polar hydrophilic head and 2 hydrophobic carbon tails
  • Individual lipid molecules can freely diffuse within lipid bilayers
  • Lipid molecules only rarely move from one side of the bilayer to the other
  • Lipid molecules often exchange places with adjacent lipid molecules over 100,000 times a second, they also rotate rapidly about their axis
  • The fluidity of a particular membrane depends upon its lipid composition
  • The high level of cholesterol increases the membrane stability
• Lipid bilayer


  Membrane lipids are amphipathic molecules which will spontaneously form bilayers in an aqueous environment
• Lipid bilayer


  • If damaged, it can repair itself
  • Lipids constitute about half of the mass of biological membranes
• Major types of lipids in cell membranes

  • Phospholipids
  • Cholesterol
  • Glycoproteins
• Phospholipids


  The most common, typically have a polar hydrophilic head and 2 hydrophobic carbon tails