01/20/16
MCB 104
Cell Biology
What is Cell Biology? Study of structure, function, and
organization of biomolecules that make up the basic unit of life
Premise The cell is the machine that the genome makes to pass
itself on the next generation Connect cell biology and genomics
Goal Get a mental model of how a cell works Respond to signals,
whats going on in each cell, etc. We will consider primarily
eukaryotic cells (mostly yeast and animals) Level of resolution
will be generally proteins and macromolecular machines (not so much
protein structure, nor tissues) We will generally consider the cell
in isolation (vs. as a larger part of the organism) Internal
workings of a cellStrategy Cell Organization Cytoskeleton Cell
Division How cell actually divides Regulation of Cell Cycle How it
controls order of events in specific order Intracellular Transport
Signaling Cancer, DiseaseOutline for Today Cell evolution Cell size
Observing cells: microscopy Observing subcellular organization A
molecular census in cells Membrane: assembly and organization ECB
Chap 1, 11Cell evolution- tree of life based on molecular phylogeny
(genome sequences) All life is cellular Everything we know about
life is compartmentalized in the cell Last common ancestor evolved
3.5 billion years ago 3 Domains Bacteria Archaea Unicellular Like
bacteria Genetic sequence reveals them to be quite different from
bacteria Eukaryotes Genome sequence allows the relationships
between the three domainsCell size cells are small, but vary widely
in size Range much in sizeThe scale of lifeSeeing cells requires
microscopes Magnification: increase in size Resolution r = distance
by which two closely spaced objects can be distinguished r alpha
gamma: wavelength of illumination (wavelength proportional to
illumination) light microscope: r ~200 nm Electron microscope: r ~2
nm (higher resolution) Contrast: difference between object and
surroundings Signal to NoiseLight microscopy Max resolution: ~200
nm Distinguish basic parts of cell: Nucleus, cytoplasm, PM See
differences in refractive index: allows visualization of structure
Fritz Zernike Phase contrast amplifies the difference between
refractive index to bring out that contrast to allow visualization
of structure BasicElectron microscopy: Use higher wavelength of
electron Max resolution: ~2nm Higher energy source TEM =
transmission EM ultrastructure Section cells with diamond knife
Heavy metal staining scatters electrons, creates contrast Have to
kill cells and fix them chemicallyCell organization: prokaryotes
Even simple cells have a high degree of internal cellular
organization No: organelles (nor nucleus) No membrane bound
organelles Yes: compartments, cytoskeleton Plasma membrane, binds
and separates inside from outside Have interesting cytoskeleton Ex.
BacteriaCell organization: eukaryotes Membrane-bound organelles
Compartments For biochemical processes, transport, etc.
CytoskeletonLocalizing specific molecules in cells Fluorescence
microscopy Subset of light microscopy Excitation light (gamma 1)
E.g UV source or laser Emission light (gamma 2) Detect in
microscope with specific filters Filters only let through emission
light Excitation of light is different from emission Gamma 2 >
gamma 1 Fluorescent molecule through antibodyGreen Fluorescent
Protein (GFP) Exists in living cells Comes from a jellyfish,
aequorea Victoria Gene and protein can be expressed in most
organisms Non-toxic. Glows autonomously in the living cell Now many
different colored variants of GFP or similar proteins (blue,
yellow, red, green) Important: can do it non-toxic. Dont have to
kill in order to know where proteins are A picture of complexity:
cellular macromolecules Nucleic acids (DNA, RNA) Proteins (and
complexes) Lipids Cells are extremely crowded Space between
molecules is ~size of molecules Constant random collisions,
interactions Wont be tested on number of molecules in cellAt one
level, biology is just a bunch of chemical equilibria so all life
is driven by concentrations and diffusion ratesAdvantages of
compartmentalization and organization to a cell Provide distinct
microenvironment Create environment that favors reactions for life
Sequester harmful molecules Concentrate specific molecules Enable
regulationA major way that the cell does this is through using
membranes (plasma membrane, organelle membranes) Container for
cellular biochemistry Ex. Mitochondria Oxidative phosphorylation
Electron transport, proton gradient wouldnt be possible if we didnt
isolate Ex. Lysosomes Want to digest only certain things and not
the whole cell Gives structure to cell/organelle Fluidity within
the plane Allow regulated permeability Small hydrophobic molecules
(gases) easily Small polar molecules (water) more slowly Large and
charged molecules: not w/o helpMembranes are composed of
amphipathic lipids Nonpolar and polar parts Polar head group
Hydrophobic tailsCellular lipids spontaneously form bilayer Due to
shape and amphipathic nature Free energy (G) is reduced when fatty
acids interact with each other to exclude waterComposition of
membranes Cholesterol (in animals) Incorporated to make membranes
less fluid Polar hydroxyl Rigid steroid ring Non-polar hydrophobic
tail Increases membrane stiffness, less fluidityMembrane bilayers
are spatially organized
