Cell Biology Notes

The Cell Theory

  • Cells are generated only from pre-existing cells and inherit their characteristics.
  • Cells are the building blocks of all living tissues.
  • Eduard Strasburger in 1880.

Cell Shapes and Sizes

  • Cells come in many shapes and sizes.
  • Nerve cell (cerebellum): branching processes to communicate with 100,000 other neurons.
  • Paramecium ("pond scum", a protozoan): moves using cilia.
  • Plant stem: red (cellulose), orange (pectin).
  • Bacteriovorus: small carnivorous bacteria, propelled using a single flagellum.
  • Human white blood cell engulfing red blood cells.

Common Features of Cells

  • Central dogma of molecular biology: the flow of genetic material.
    • Information storage: the "hard drive".
    • Temporary message: the "cache".
    • Functional units: the "programs".

Viruses

  • Viruses: chemical zombies, exceptions to the central dogma.
    • Some are DNA, some are RNA.
    • Some are double-stranded, some are single-stranded.
    • Cannot replicate without a host cell.
    • Examples:
      • T4 bacteriophage (DNA).
      • Potato virus (RNA).
      • Adenovirus (dsDNA).
      • Influenza (dsRNA).
    • Referred to as "molecular parasites".

Gene Expression

  • Genes hold the code, but their expression determines function.
  • Example: Lemato, a tomato variety produced by Israeli researchers; over half of test tasters preferred it.

Cell Size

  • Nerve/muscle cells can be nearly 1 meter long.
  • Perspective on size:
    • Refer to the provided link for a visual representation of cell sizes.

Microscopes

Light Microscope

  • Magnifies cells up to 1000 times.
  • Resolves details as small as 0.2 μm (limitation due to the wavelike nature of light).
  • Requirements:
    • Bright light focused onto the specimen by lenses in the condenser.
    • Specimen prepared to allow light to pass through.
    • Appropriate set of lenses (objective and eyepiece) to focus an image of the specimen in the eye.
  • Light Path in a Light Microscope
  • Fixed Samples
    • Tissues are chemically fixed and cut into thin slices (sections).
    • Mounted on a glass microscope slide and stained to reveal different components.
  • Looking at Living Cells
    • Unstained, living animal cells (fibroblast) in culture.
    • Viewed with:
      • Straightforward (bright-field) optics.
      • Phase-contrast optics.
      • Interference-contrast optics.
    • Different optical systems exploit differences in how light travels through regions of the cell with differing refractive indexes.
    • The images can be obtained on the same microscope by interchanging optical components.

Confocal Microscopy

  • Specialized type of fluorescence microscope.
  • Builds up an image by scanning the specimen with a laser beam.
  • The beam is focused onto a single point at a specific depth in the specimen.
  • A pinhole aperture in the detector allows only fluorescence emitted from this same point to be included in the image.
  • Scanning the beam across the specimen generates a sharp image of the plane of focus (optical section).
  • A series of optical sections at different depths allows a three-dimensional image to be constructed.
  • Example
    • Intact insect embryo stained with a fluorescent probe for actin.
    • Conventional fluorescence microscopy gives a blurry image.
    • Confocal microscopy provides an optical section showing the individual cells clearly.

Transmission Electron Microscopy (TEM)

  • Uses a beam of electrons instead of light.
  • Magnetic coils focus the beam instead of glass lenses.
  • The specimen is placed in a vacuum and must be very thin.
  • Contrast is introduced by staining the specimen with electron-dense heavy metals.
  • Metals locally absorb or scatter electrons, removing them from the beam as it passes through the specimen.
  • Magnification: Up to a million-fold.
  • Resolution: Can resolve details as small as about 2 nm with biological specimens.
  • Example
    • A small region of a cell in a piece of testis.
    • The tissue is chemically fixed, embedded in plastic, cut into very thin sections, and stained with salts of uranium and lead.

Subcellular Structures

  • Human skin cell (resembles a fried egg).
  • Frog pigment cell: blue (nucleus), red (pigment granules), green (microtubules filaments).

Prokaryote vs. Eukaryote

  • Eukaryote
    • Nucleus
    • Nucleolus
    • Mitochondria
  • Prokaryote
    • Nucleoid
    • Capsule
    • Flagellum
    • Cell Wall
    • Ribosomes
    • Cell Membrane

Prokaryotes

  • Small single-cellular organisms.
  • Most diverse of all cells.
  • Can adapt to extreme environments.
  • Two domains: Bacteria or Archaea.
  • Many different sources of “food” (e.g., oxygen, hydrogen, sulfur); some are even photosynthetic.

Eukaryotes

  • Bigger, more elaborate organisms.
  • Can be:
    • Single-cell organisms (yeast, amoebae).
    • Multi-Cellular (plants, animals, fungi).
  • Always have a nucleus, organized, compartmentalized (membrane-bound).
  • Organelles conserved in most Eukaryotes.

Inside the Cell

  • Tightly packed fluid environment that is constantly moving, changing, refreshing.
  • Membrane-bound organelles: Why the separation?

The Plasma Membrane

  • The fence
    • Components: glycolipid, phospholipid, globular protein, hydrophobic segment of alpha-helix protein, alpha-helix protein, oligosaccharide side chain, cholesterol.

Nucleus

  • The government
    • Nuclear Envelope
    • Condensed Chromosomes
  • Why a nuclear membrane?

Ribosomes

  • The factories
  • Smallest structure you can clearly see here.
  • Comprised of 80-90 molecules that catalyze translation; they make all the new proteins needed to keep the city working!

Mitochondria

  • The power plant
  • Most abundant organelle.
  • Oxidize food molecules to generate ATP: ‘cellular respiration’.
  • Contain their own DNA and reproduce themselves (like bacteria!).

Evolution of Mitochondria

  • Mitochondria evolved from bacteria.
    • The process involved an anaerobic pre-eukaryotic cell engulfing an aerobic bacterium.
    • The bacterium established a symbiotic relationship within the pre-eukaryotic cell.
    • Over time, the bacterium evolved into mitochondria with a double membrane.
    • Some membranes derived from the pre-eukaryotic cell were lost.

Predator Evolution

  • Eukaryotes likely evolved as a predator.
  • Large flexible membrane & cytoskeleton for movement: to allow ‘eating’!?
  • Nuclear compartment may have evolved to protect valuable genetic material from chaos of the cytoplasm.

Chloroplasts

  • The solar power plant.
  • Green organelles found in plants and algae.
  • Photosynthesis: converts sunlight into chemical energy (sugar).

Evolution of Chloroplasts

  • Chloroplasts also evolved from photosynthetic bacteria

Endoplasmic Reticulum (ER)

  • Highway of the cell.
  • RER: Ribosome-coated ER, which makes proteins to be secreted.
  • SER: Smooth ER is involved in lipid synthesis.

Golgi Body

  • Post office.
    • Membrane-enclosed vesicles.

Lysosomes and Peroxisomes

Lysosomes

  • Waste disposal system
  • Small irregular shaped
  • Membrane-bound
  • House intracellular degradation
    • Break down food and release it back to cell.
    • Break down waste for recycling or excretion

Peroxisomes

  • Chemical Plant
  • Small, membrane-enclosed vesicles
  • Contained environment for H<em>2O</em>2H<em>2O</em>2 reactions
  • H<em>2O</em>2H<em>2O</em>2 generated and degraded inside

Cytoskeleton

  • The Cell Scaffolding
    • Chromosomes during cell division
    • Bundle of microtubules

Cytoskeleton

  • Allows directed movement

Continually Exchanging Environment

  • IMPORT BY ENDOCYTOSIS
    • Cytoskeleton helps with this too!
    • Filopodium, plasma membrane movement
  • EXPORT BY EXOCYTOSIS
    • Plasma membrane movement
    • Intracellular
    • F-actin, Arp2/3 complex, capping, vesicle coat

Model Organisms

  • Where do the cells we study come from?

Escherichia Coli

  • We understand E. Coli more thoroughly than any other organism!
  • Single, circular double strand of DNA, ~4.6 million nucleotide pairs long.
  • Produces 4300 different kinds of proteins.

Saccharomyces cerevisiae

  • Minimal model eukaryote

Arabidopsis thaliana

  • Common wall cress
  • Produces thousands of offspring in 8-10 weeks
  • Easy to grow indoors
  • Complete DNA sequence is known

Drosophila melanogaster

  • More than any other organism, has shown us how to trace cause and effect from DNA instruction to the structure of an adult multicellular organism.
  • DNA genome well known, lots of lab supplies available.

Caenorhabditis elegans

  • Develops like clockwork: 959 body cells
  • Neurons of the brain completely mapped!
  • Led to the understanding of programmed cell death.
  • Used in alcohol studies at VCU

Danio rerio

  • Zebrafish
  • Transparent for the first two weeks of life
  • Excellent for developmental studies

Homo sapiens Mus musculus

  • Defect in kit gene, required for development and maintenance of pigment cells

Cell Culture

  • Cells grown in plates in the laboratory

Primary cell culture

  • Isolated directly from a live organism
  • Limited lifespan (Hayflick Limit)

Immortalized cell line

  • ‘Transformed’ cells can grow indefinitely; like cancer!
  • Unlimited uses: study cell behavior, response to drugs & environment, industrial product (proteins, antibodies), ETC.