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WIDGET Meeting Minutes 3/18/2007
Funding from Chancellor John Wiley and College of Engineering (CoE)
- CoE 2010 proposal due Tuesday (3/20)
- More detailed proposal needed by end of semester
Plans for April
- one lecture on bacteria and gene regulation
- have students present on existing iGEM projects (2-3 meetings)
- brainstorm some project ideas at very high level by end of April
- tour of wetlab and introduce lab techniques
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WIDGET Study Group #1: Intro to Cellular Biology
and Signal Transduction (Andrew Clark)
All images are from wikipedia and MIT openwetware
http://en.wikipedia.org/wiki/Main_Page
http://openwetware.org/wiki/BE.180:Bio
Cell Types
Bacterial
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Animal
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Plant
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Macromolecules
Concept of hydrophobic/nonpolar and hydrophilic/polar regions
Lipids
1. Bilipid layer
2. Micelle
3. Liposome – like micelle, except another hydrophilic region inside
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Proteins
Polymer of amino acids
Conformation (shape) is important to function
Nucleic acids
Polymer of nucleotides
Store information
Central Dogma
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Cell Components (focus on animal cells)
Plasma membrane
Fluid mosaic model
“Fluid” part
Lipid bilayer, amphipathic (molecule with both hydrophobic and hydrophilic parts)
Regulate transport of molecules and ions
“Mosaic” part
Proteins embedded in membrane, used for signaling and others…
Vesicles
Liposome structure
Lysosomes/peroxisomes are like special vesicles containing enzymes that perform certain
function (such as degrading molecules)
Cytoskeleton
Highly organized proteins that provides structure and transport
Very dynamic, can change shape and move on order of seconds
Microfilaments (MF) - actin fibers, mechanical support
Microtubule (MT) – important for transport and signaling
Intermediate filaments (Ifs) - provide a structural scaffolding network for rigidity of the
cell
Motor proteins
Myosin – head and tail. Can bind to actin filaments
Branch/dendritic network – actin can be used to push membrane in certain direction
Kinesin/Dynein – like walking, bind to MTs and move, directional
Ribosomes
Protein factory
Mitochondria
Produce ATP, the universal energy currency
Oxidative phosphorylation – proton gradient travel down ATP synthase
All processes use ATP to perform function
Endoplasmic Reticulum (ER)
Large membrane connected to nuclear membrane and has many invagination
Rough ER has embedded ribosomes that produce proteins
Store calcium ion (Ca2+) in lumen
Nucleus
contains DNA
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What does a cell need to do?
Acquire energy
Get rid of waste
Grow
Respond to environment
Homeostasis (maintain certain state)
Adenosine triphosphate (ATP)
Adenosine + 3 phosphate groups
breaking bonds between phosphate groups releases energy/increases reactivity required to
catalyze cellular reactions
numerous negative charges from the oxygen in a confined area create a great deal of
strain, which is relieved when the final phosphate is cleaved, releasing a great deal of
energy
Cell Growth
Not physical growth, but proliferation (multiplying)
Cell sizes are fairly constant
Mitosis (Eukaryotic – Animal and plant)
DNA replicates, then divide into two cells
Cytokinesis
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Signal Transduction
Signals/messages are carried by proteins and ions
Can analyze signaling pathways with biochemistry techniques such as looking at
antibodies that attach to certain activated forms of proteins
Growth stimulation (EGFR pathway)
epidermal growth factor (EGF) tell cell to
divide
• EGF binds to EGF receptors on cell
membrane
• EGF receptor dimerize (recruit receptors
to form pairs) and add phosphate groups
Path 1
• Adapter proteins recognize receptor
proteins that are activated (w/ phosphate
groups)
• Then adapter proteins activates Ras
(which is an embedded protein)
• MAP kinase cascade
• P90 Rsk -> regulate gene
Path 2
• Activate PLC gamma instead of adapter
protein
• PLC gamma -> cleave lipids in certain
spots
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Bind to ER channel and let Ca2+ diffuse
out
• Ca2+ will activate PKC, turn on MAP
kinase cascade, and regulate gene
expression
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Locomotion
Muscle cells arranged in compact structure
Tear muscle, gap between cells, how to tell cells to move/grow and fill in gap?
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GF diffuse mutually across tear interface
GF bind to receptor
Don’t need to dimerize
Activate DOCK180 RacArp 2/3
Arp 2/3 – tell actin to form branch, not linear segments
Cells divide only ~25% of time
Apoptosis
Tell cell to kill itself
• If cell is infected with virus, T-cells (immune system) can tell if cell is infected and
release a number of proteins (such as Fas)
• Fas will be recognized by receptor on infected cell and elicit change in mitochondria
• Mitochondria will release a small molecule called Cytochrome C
• CytC will initiate cascade of events called the “caspase” to kill itself
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Blebbing  break cell into vesicles
(with infected cells parts trapped inside)
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