Cells: The Fundamental Units of Life

I. Unity and Diversity of Cells

• Cells vary greatly in size, shape, and function. Examples include neurons, paramecium, snapdragon petal cells, macrophages, and yeast.
• All living cells share a similar basic chemistry, as described by the central dogma.
• Living cells can self-replicate through organization, utilizing a blueprint and materials, consuming energy, catalyzing chemical reactions, and employing feedback loops.
• Cell Theory:
  • All living cells arise from the growth and division of existing cells.
  • Scientific theory is an understanding based on facts collected through repeated observation and tests.
  • All living cells are believed to have evolved from the same ancestral cell approximately 3.5 to 3.8 billion years ago.
  • The genome is the entire sequence of DNA nucleotides in an organism.
  • Mutations during replication can be positive, negative, or silent.
  • Mutations drive evolution, which is the process of species modification to adapt to their environment.
• Different cells in the same organism have the same genome.
• Differentiation is the process where a cell undergoes progressive coordinated changes to become a more specialized cell type.
• Cells carry out different subsets of the master plan (genome) by turning on or off different genes.

II. Microscopy of Cells

• Magnification up to 1000X.
• Resolution to 0.2 mm.

A. Conventional Light Microscopy

• Limitation by light.

B. Fluorescence Light Microscopy

• Fluorescent dyes are used for staining cells and are detected with the aid of a fluorescence microscope.
• The illuminating light is passed through two sets of filters:
  • The first filter selects wavelengths that excite the fluorescent dye.
  • The second filter blocks out the excitation light and passes only the wavelengths emitted when the dye fluoresces.
• Dyed objects show up in bright color on a dark background.
• Confocal Fluorescence Microscopy:
  • A specialized type of fluorescence microscope that builds up an image by scanning the specimen with a laser beam.
  • The beam is focused onto a single point at a specific depth, and a pinhole aperture in the detector allows only fluorescence from that point to be included in the image.
  • Scanning the beam across the specimen generates a sharp image of the plane of focus—an optical section.
  • A series of optical sections at different depths allows a three-dimensional image to be constructed.

C. Transmission Electron Microscopy (TEM)

• Specimen is stained with heavy metals.
• A beam of electrons is used instead of light.
• Magnetic coils are used to focus the beam.
• Magnification is about 1x10$^6$ X; resolution is about 1 nm.

D. Scanning Electron Microscopy (SEM)

• Specimen is stained with heavy metals.
• The beam of electrons is scattered off the surface of the specimen.
• Magnetic coils are used to focus the beam.
• Good depth of focus; resolution 3 nm – 20 nm; good for surface details.

E. How Big are Cells and Cell Components?

• Each frame represents a 10X magnification from the previous.
• Cells are visible with the unaided eye at 0.2 mm (200 $μ$m).
• Light microscope: 20 $μ$m.
• Super-resolution fluorescence microscope: 20 nm.
• Electron microscope: 0.2 nm.
• $1 m = 10^3 mm = 10^6 μm = 10^9 nm$

F. Nanoscopy

• Used to study the precise position of atoms within the 3-D structure of biomolecules such as proteins.
• X-ray crystallography can achieve resolution to ~1.5Å (0.15 nm).

III. Prokaryotic Cells

• Most diverse and numerous cells on Earth (approximately $10^{30}$).
• Represent some of the earliest life forms.
• Most are very small (few $μ$m); few can be giant (almost mm).
• Many have only the most essential components for living.
• No nucleus to house the genome.

A. Simple, Yet Numerous and Enduring

B. Prokaryotes Divided into Two Domains: Bacteria and Archaea

• Look similar but have great differences in DNA sequence.
• E. coli bacterium.
• Archaea are found everywhere bacteria can be, plus also found in harsh environments (e.g., acidic volcanic springs).

IV. Eukaryotic Cells

A. Nucleus Stores the Genetic Information

• Nuclear envelope (= double membrane) with pores.

B. Mitochondria Generate Usable Energy from Food Molecules

• Organelle structure.
• Organelle function:
  • Outer membrane.
  • Inner membrane.
  • Intermembrane space.
  • Matrix.
• Consume $O<em>2$, produce $CO</em>2$, make ATP.
• Self-replicating.
• Contains own circular DNA and ribosomes.
• Size.

3) Mitochondria Thought to have Evolved from Engulfed Bacteria

• Early anaerobic eukaryotic cell engulfed aerobic bacteria.
• Symbiotic relationship à shelter and nourishment for power generation.

C. Chloroplasts Capture Energy from Sunlight

1) Structure and Function

• Chlorophyll pigments.
• Produce $O_2$.
• Carbon fixation à sugars.
• Have own DNA.
• Self-replicating.

2) Chloroplasts Believed to Evolve from Engulfed Photosynthetic Bacteria

D. Internal Membranes Create Intracellular Compartments with Different Functions

1) Endoplasmic Reticulum (ER)

• Interconnected membranous sacs.
• Continuous with the nuclear envelope.
• Synthesis of most membrane components.
• Synthesis of materials for export or for incorporation in other organelles.
• Rough and smooth types.

2) Golgi Apparatus

• Interconnected flattened membranous sacs.
• Modifies and distributes molecules.

3) Lysosomes

• Vesicles with acids and digestive enzymes.
• Breakdown of endocytosed material or unwanted molecules.

4) Peroxisomes

• Vesicles containing enzymes that utilize $O<em>2$ and $H</em>2O_2$ to inactivate toxic substances.
• No DNA, but are self-replicating.

E. Endosomes and Secretory Vesicles

• Import by endocytosis.
• Export by exocytosis.

F. Cytosol - a Concentrated Aqueous Gel

G. Cytoskeleton

• Structure, shape, support.
• Dynamic.
• Transport with motor proteins.

V. Cellular Architecture

• Representative structures of animal, plant, and bacterial cells, emphasizing organelles and key components.

VI. Origin of Life/Cells?

• Timeline illustrating the evolution of cells from ancestral prokaryotes to single-celled eukaryotes and the origin of mitochondria and chloroplasts.

VII. Model Organisms

• Focused study on a few species to learn most in-depth about biological processes.

1) Escherichia coli (E. coli)

• Easy-to-grow prokaryotes.
• Reproduce rapidly.
• Represent simpler/earlier life forms.
• Many fundamental processes similar to our cells.
• DNA à RNA à Protein.

2) Saccharomyces cerevisiae (S. cerevisiae)

• Easy-to-grow eukaryotes.
• Reproduce rapidly.
• Represent simpler/earlier life form.
• Many fundamental processes similar to our cells.
• DNA à RNA à Protein.
• Study internal compartments.

3) Arabidopsis thaliana

• Model plant.
• Multicellular.
• Thousands of offspring in 8-10 weeks.
• Genes also found in agricultural species à crop studies.

4) Drosophila melanogaster

• Tremendous molecular genetic studies, mutation analyses.
• Genes for development à very similar to those in humans.

5) Caenorhabditis elegans (C. elegans)

• First multicellular organism to have its genome sequenced.
• Smaller and simpler than Drosophila.
• Developmental studies à fertilized egg to adult of 959 body cells.
• Understanding how developing cells divide, move, become specialized.
• About 70% of human genes have a counterpart in the worm.

6) Zebrafish

• Vertebrates.
• Transparent during the first 2 weeks of life allowing direct vision of development in a living animal.

7) Mice

• Mammals.
• Small, easy to manage, maturation not over decades.
• Many similar genes.
• Genetic studies with engineered mutations.

8) Human Cells

• Different cells in the same multicellular organism… all have the same DNA, all from the same zygote.
• Differentiation.

VIII. Genomes

• Vary in size but can code for similar genes across some species.
• Examples include E. coli (bacteria), Halobacterium sp. (archaea), malarial parasite (protozoans), yeast (S. cerevisiae) (fungi), Arabidopsis (plants), Caenorhabditis (nematode worms), Drosophila (crustaceans, insects), zebrafish (amphibians, fishes), and human (mammals, birds, reptiles).
• Table comparing genome sizes and approximate number of protein-coding genes for various model organisms:
  • Homo sapiens (human): Genome Size = 3200
  • 10^6, Genes = 19,000
  • Mus musculus (mouse): Genome Size = 2800
  • 10^6, Genes = 22,000
  • Drosophila melanogaster (fruit fly): Genome Size = 180
  • 10^6, Genes = 14,000
  • Arabidopsis thaliana (plant): Genome Size = 103
  • 10^6, Genes = 28,000
  • Caenorhabditis elegans (roundworm): Genome Size = 100
  • 10^6, Genes = 22,000
  • Saccharomyces cerevisiae (yeast): Genome Size = 12.5
  • 10^6, Genes = 6600
  • Escherichia coli (bacterium): Genome Size = 4.6
  • 10^6, Genes = 4300
    *Genome size includes an estimate for the amount of highly repeated, noncoding DNA sequence, which does not appear in genome databases.