Cell Dev Midterm

Lecture 1:
- Develop an analogy for the function of organelles within a eukaryotic cell
o Nucleus: synthesis of DNA/RNA; boss, manager, director, etc.
o Cell membrane: wall, gate, fence, etc.
o Rough endoplasmic reticulum (rough ER): work area with the
workers (the ribosomes); synthesize membrane proteins
o Smooth endoplasmic reticulum (smooth ER): synthesizes lipids,
stores Ca++; produces factory parts, breaks down toxic substances
o Ribosomes: workers, employees, etc.
o Golgi apparatus: dispatches/modifies lipids and proteins from ER;
place for modifying, inspecting, packing, and shipping product
o Mitochondria: energy source
o Vacuole: storage or waste area (for water reserves or trash)
o Protein: what you are making or producing.
o Vesicles: packages/boxes to transport products in, around, and out of
the building.
o Chloroplast: converts sun energy to food
o Cytoskeleton/cytoplasm: provides structure and storage space for
building
o Lysosome: worker who cleans up trash and waste in building
o Nuclear envelope: walls of boss or managers office
o Nuclear pore: door to boss or managers office
- List the general components of a cell membrane
o Lipids: amphiphilic lipids with a polar (hydrophilic) head group
(glycerol or sphingosine) and two nonpolar (hydrophobic)
hydrocarbon tails (one is unsaturated=at least 1 cis double bond)
Most abundant are phospholipids
o Cholesterol: hydroxy group (polar) interact with polar head of lipid,
stiff steroid ring structure keeps distance, lipids dont pack as well
o Proteins: 50%
- Explain how the properties of lipids allow for the assembly of a membrane.
o Two tails, one of which is kinked -> cylindrical shape
o Hydrophilic head want to face out (water), keep hydrophobic tail in
- Explain how lipid composition and cholesterol function to increase or
decrease fluidity within the membrane
o Shorter hydrocarbon chains reduce the tendency of interaction; cis
double bonds make kinds so its harder to pack -> fluid at lower temp
o As temp falls, cells synthesize fatty acids with more double bonds
- Explain why detergent is used to lyse cells and how it does so
o Detergents are small amhiphilic molecules that are soluble in water
o They can solubilize proteins and membranes (hydrophobic ends of
detergents bind to hydrophobic regions of membrane proteins,
displace lipid molecules. Other side of detergent is polar -> bring
proteins into solution
- Predict how a given component is transported across a membrane.
o Non polar, small molecules are fast
o Large, polar, or charged are slow
o Protein-free lipid bilayers are impermeable to ions
o Membrane transport proteins:
Transporters: bind specific solute to be transported and
undergo conformational changes to transfer across membrane
Channels: interact with solute to be transported weakly, form
aqueous pores tat extend the later when open, allow solutes
(inorganic ions) to pass
Passive transport: facilitated diffusion -> concentration
gradient drives passive transport
If solute carries net charge, driven by electrochemical gradient
(favors entry of +, opposes entry of -)
Active transport: pump solutes against electrochemical
gradients; coupled to energy source (ATP hydrolysis)
- Identify major features of a eukaryotic cell in a light or electron micrograph.
o Golgi is usually attached to the nucleus
- Identify the best visualization technique for a given experimental situation.
o Light microscopy used in histology
Hematoxylin and eosin, staining
o Transmission Electron: cut into thin sections
o Scanning electron: reconstructs topography, contours
o Fluorescence: can tag cellular components
Immunofluorescence
Dead (fixed) cells
o Live imaging: tag protein with GFP
o Speckle microscopy: injecting fluorescently labeled protein into live
cells, visualize over time with confocal microscopy
Track motion
o Confocal: utilized to depict 3D images of cell interiors (stack)

Lecture 2:
- Name the three major cytoskeletal filaments, their monomer subunits, and
describe how monomers polymerize into filaments
o Intermediate filaments: mechanical strength
o Microtubules determine positions of organelles and direct
intracellular transport
Make mitotic spindle during division, form cilia and flagella,
aligned bundles as tracks for transport
One end attached to MTOC (centrosome)
o Microfilaments (aka actin filaments) determine shape of cell surface,
needed for motility (lamellipodia)
Contractile ring (actin based) to divide cells in two
o Accessory proteins: motor proteins

- Compare and contrast the structural properties of the three cytoskeletal
filaments and the functions they are particularly suited to perform.
- Diagram the dynamics of actin and MT polymerization, explain the role of
nucleotides in the process and why the two ends have different dynamics.
- Cite specific examples of how cytoskeletal accessory proteins can alter actin
and MT polymerization and/or their organization.
- Predict what cytoskeletal modifications would be necessary produce
hypothetical cytoskeletal structures and the molecules suited perform these
roles.
- Using cytoskeletal inhibiting drugs and imaging tools, design experiments to
test the role of the cytoskeleton in cell biological processes.

Lecture 3:
- Name the three types of motor proteins, the filaments they bind to, and the
direction they generally move upon their respective filaments.
- Compare and contrast the movements of the three types of motor proteins.
- Predict how a mutation in a motor or regulatory protein would affect the
function of a higher order structure.
- Design an experiment to determine if a specific motor protein functions in a
cellular process

Lecture 4:
- Explain the signal hypothesis for protein transport.
- Explain how small GTPases function and how they are regulated by GEFs and
GAPs.
- Describe how Kaps and Ran proteins, along with NLS and NES sequences,
function in nuclear import and export.
- Describe how SRP and Sec61 function in protein translocation in the ER.
- Predict the topology of a given transmembrane protein provided with
sequence information and a hydropathy plot.
- Determine where a protein is localized in the cell based on sequence
information, protein modifications and/or protein glycosylation.
- Design experiments to determine if a factor/protein/sequence is necessary
and/or sufficient for a given process.

Lecture 5:
- List the steps by which protein cargos are packaged into membrane vesicles,
delivered, and fused to their destination.
- Know the transport route(s) of a given molecule during export and import.
- Name the three main types of vesicles coats and the cellular compartment
where they are usually formed.
- Describe the assembly and disassembly of COPII coated pits, including the
role of GTPase activity in the process.
- Describe the targeting and fusion of a vesicle to its destination.
- Trace the life of a plasma membrane receptor from its synthesis, exocytosis,
internalization, and degradation.
- Explain how Golgi or ER resident proteins are retained despite constant
membrane flux through them.
- Interpret the phenotypes of trafficking mutants and predict the protein that
is most likely affected by the mutation.
- Design an experiment using pulse-chase techniques and/or cell-free systems
to investigate the transport route of a given protein.

Lecture 6:
- Recognize and identify different cell and tissue types in a histological tissue
sample.
- Predict the types of cell-cell contacts present within a tissue based on its
morphological or functional description.
- Compare and contrast the structure and function of adherens junctions,
desmosomes, tight junctions and gap junctions.
- Name the cell adhesion molecules that mediate the major types of junctional
complexes and the cytoskeletal components to which they link.
- Explain the functions of the different classes of cell-cell adhesions.
- Predict the phenotypes that result from mutation of cell adhesion
components.
- Design and experiment to determine the function of an adhesion protein in
junction assembly and cellular morphology.
- Describe the components and steps of cell polarization and predict the
phenotypes caused by loss of polarity cues.

Lecture 7:
- Compare and contrast the components, properties, and functions of basal
lamina versus connective tissue.
- List the four components of the basal lamina and describe how they interact
with one another and cells to form a thin sheet like material
- Compare and contrast proteoglycans and fibrillar glycoproteins and list
examples of each
- Describe the properties of gycosaminoglycans and how their structure
relates to the function of proteoglycans in connective tissue
- Describe the structure and functions of fibrillar collagens and how they are
assembled and packaged for secretion
- Predict the phenotypes of mutations in distinct components of cell-matrix
adhesions
- Diagram the structure of integrin heterodimers and how their confirmation
changes when they are activated
- Compare and contrast inside-out vs outside-in signaling and cite an example
of both in the context of integrin activation
- Design/interpret experiments to test the activation and binding of integrins
to their ECM ligands

Lecture 8:
- Describe the steps of cell migration and the processes controlling each
- Predict the effect on cell migration when components of the migration
machinery are altered
- Explain how extracellular signals alter the cytoskeletal through the activation
of RhoGTPases
- Compare and contrast the three Rho-family GTPases and their effectors
o Rho
o Cdc42
o Rac
- Predict the effect of dominant negative or dominant active mutations in Rho
family GTPases in cell migration
- Explain how chemotactic gradients produce directional movement. List the
steps in the pathway from signal-to-cytoskeleton that are polarized from
front to back in a migrating cell
- Predict how mutations in the chemotaxis machinery affect cell migration
- Design an experiment that would allow you to determine whether a molecule
acts as a chemoattractant through binding to a given receptor.

Lecture 9
- Diagram the cell cycle and list key events and checkpoints that take place
within each stage
- Explain the processes by which cells decide to enter and exit M phase
- Describe the three main checkpoints that monitor whether proper sequence
has taken place and halt cycle progression if incomplete/damaged
- Interpret experimental data using yeast mutants and Xenopus oocytes to
study the cell cycle
- Predict how the cell cylcle will be affected given mutation
- Analyze flow cytometry data to make conclusions about cellular growth
- Diagram the structure of mitotic spindle and explain force generating
mechanisms that drive chromosome segregation
- Explain how the decision to enter S-phase is made and how cancer mutations
can affect this process
- Distinguish between an oncogene and a tumor suppressor and make
predications about their effect on the cell cycle