Pre-Lecture Questions Flashcards
Diffusion
the tendency of molecules to spread out (move from areas of high concentration to areas of low concentration) until evenly dispersed, as a result of (random) thermal motion.
Entropy (S)
the level of disorder among molecules. The second law of thermodynamics states that everything in the universe tends towards higher entropy.
Gibbs free energy (G)
the amount of energy available to do work in a given system; dependent on temperature, the change in entropy, and the value of enthalpy (G= H-TS).
Boltzmann’s constant (Kb)
The relationship between absolute temperature and the kinetic energy contained in each molecule of a gas.
Briefly describe how the γ-tubulin ring complex affect microtubule organization and/or microtubule-based transport:
The γ-tubulin ring complex is important in regulating formation of centrosomal and acentrosomal microtubules, and they nucleate microtubules at the centrosome.
Briefly describe how +TIPs affect microtubule organization and/or microtubule-based transport:
localizes to the ends of actively growing microtubules and regulates microtubule dynamics. This allows the cell to harness energy of microtubule polymerization to drive forces for positioning the spindle, chromosomes, or organelles.
Briefly describe how tau affect microtubule organization and/or microtubule-based transport:
associate with microtubules, primarily in neurons at the distal ends of axons, and play a role in microtubule stabilization and elongation.
Briefly describe how kinesis 1 affect microtubule organization and/or microtubule-based transport:
motor protein walks towards the plus end of microtubules while carrying membrane-enclosed organelles away from the cell body toward the axon terminal.
Briefly describe how cytoplasmic dynein affect microtubule organization and/or microtubule-based transport:
motor protein that moves along microtubules; homodimer of two heavy chains; tail is attached to cargo such as vesicle, and transports the cargo along the microtubule towards the minus end.
What is Reynolds number?
The ratio of inertial forces to viscous forces that occur in a fluid flow. Lower Reynold numbers predict laminar (sheet-like) fluid flow while higher numbers predict turbulent fluid flow.
What is microtubule dynamic instability, and how does GTP hydrolysis contribute to this dynamic instability?
Microtubule dynamic instability: the random alternating between microtubule growth and shrinkage usually at the plus end.
GTP hydrolysis contributes to this dynamic instability in that the rate in which it occurs determines whether the microtubule is growing or shrinking. Growing microtubules have GTP caps (composed of GTP-containing subunits). However, this cap is lost and the microtubule shrinks when the rate of GTP hydrolysis is faster than the addition of new subunits to the plus end. GTP hydrolysis also influences the conformation of the microtubule. When GTP-containing subunits are present and there is a GTP cap, the microtubule assumes a tighter, linear structure. When the cap is lost, a looser, curved shape takes form.
How fast do microtubules polymerize and depolymerize in vivo?
The in vivo depolymerization rate is roughly 500 nm/second. The rate of polymerization is about 30 nm/s, about an order of magnitude smaller than depolymerization rate.
What are the four stages of the cell cycle, and approximately how long do they take in human cells proliferating in culture?
The cell cycle of human proliferation is said to take 24 hours. This cycle is composed of four phases, Growth 1 (G1), Synthesis (S), Growth 2 (G2), and mitosis. Each phase is well regulated and runs according to the following times:
G1: first stage that last approximately 10 hours (most variability with time), growth/increase in cell size
S: second stage during which DNA replication occurs that last between 6-8 hours
G2: third stage and another growth stage during which chromosomes begin to separate from one another and preparation is made for cell division, approximately 2-3 hours
M: fourth stage when cell division happens, takes about 1 hour
How do microtubules contribute to chromosome segregation during cell division?
Microtubules are critical to chromosome segregation because they form the mitotic spindle, the basis of chromosomal separation. Radiating from the centrosomes, the microtubules of the mitotic spindles grow and attach to the kinetochores on the chromosomes. This first helps them align in the center of the cell in preparation for division, then pulls them apart once the cell is ready to fully divide.
What is the limit of resolution of a conventional light microscope, and what sets this limit?
The limit of resolution is the limiting separation at which two objects appear distinct, and it depends on both the wavelength of the light and the numerical aperture of the lens system used. The light microscope can achieve a limit of resolution of about 0.2 μm, or 200 nm.
Fluorescence
the absorption of light and emission of it at a different, longer wavelength; happens when an orbital electron of a fluorescent molecule comes down back to ground state and emits a photon with a longer wavelength
immunofluorescence
A technique used to visualize cells under a light microscope. Antibodies which bind to a molecule/structure of interest are coupled with a fluorescent dye and the cell is washed with it, allowing the antibodies to localize the dye on the structure of interest. Typically, a primary antibody is used to bind the structure of interest, and then a secondary antibody with the fluorescent dye binds to the primary antibody, resulting in a stronger light signal.
green fluorescent protein (GFP)
A naturally occurring protein that fluoresces green when exposed to specific light wavelengths. It is widely used in cell biology to label any number of cellular components.
Cell biologists routinely use fluorescence microscopy to image protein localization patterns in cells. What’s one advantage of using GFP to image protein localization rather than using immunofluorescence?
One advantage of using GFP is that it can be done in vivo without the use of external antibodies. This allows a scientist to observe various phenomena (such as protein localization) as occurring in live cells.
the critical concentration (for actin polymerization)
The concentration of actin monomers in the cytosol at which the rate of filament assembly will equal the rate of disassembly.
actin treadmilling
An event in which the minus end of an actin filament loses subunits, and the plus end gains subunits. This event becomes possible at intermediate concentrations of actin monomers (Cc(T) < C < Cc(D)), when the addition of new subunits is faster than ATP hydrolysis at the plus end but slower than ATP hydrolysis at the minus end.
Is ATP hydrolysis required for actin polymerization? Why or why not?
No, ATP hydrolysis is not required for actin polymerization, as polymerization will occur spontaneously as long as the concentration of actin monomers in solution is high enough for the reaction to be energetically favorable (negative delta G).
How does the cell membrane affect actin polymerization in migrating cells? Please see Keren et al Nature 2008 (and specifically the model description on pages 477-8: Actin-membrane model explains cells shape).
At the cell’s leading edge, membrane tension applies an opposing force on polymerizing actin filaments that is constant per unit edge length, whereby the force per filament is inversely proportional to the local filament density. The membrane resistance and filament density affect how quickly actin can polymerize. At the leading edge’s center, filament density is high and membrane resistance per filament is small, which allows for filaments to grow rapidly and generate protrusion. Towards the cell sides where filament density gradually decreases, the membrane tension-induced forces per filament increase until polymerization is stalled, which would be at the far sides of the cell, which lead to the sides neither protruding nor retracting. The actin network disassembles at the back of the cell, where membrane tension dismantles the weakened network, adding more actin monomer to the cytoplasm to be polymerized at the leading edge, which retracts the back of the cell.
Chromosome
Each chromosome in a eukaryotic cell is composed of a long strand of linear DNA that is wrapped around proteins to form a compact structure. Chromosomes are vital in housing genetic information that contributes to gene expression.
Histones
Histones are small disc-shaped proteins that make up a histone octamer, where DNA wraps around in order to condense. Each histone has an N-terminal amino acid tail that extends out from the histone core to allow for control of chromatin structure and function.
Nucleosome
Composed of eight smaller histones (H2A, H2B, H3, and H4) that form a core protein that 147 nucleotide pairs can wrap around. The nucleosome is essentially the core particle plus one of the adjacent DNA linkers.
Chromatin
Chromatin is the complex of nuclear DNA bound to histones and nonhistone chromosomal proteins.
What is the difference between euchromatin and heterochromatin?
Heterochromatin is a highly organized and highly condensed form of DNA that can restrict gene expression. Euchromatin is less condensed and usually under transcription. When certain areas of DNA condense into heterochromatin, the genes within that sequence can be turned off, since they are inaccessible and cannot be bound to RNA polymerases, transcription factors, etc.
Gated transport
Most consequential between the nucleus and the cytoplasm, gated transport is the
selective movement of molecules through the nuclear pore complex. The complex acts as a
gate that actively transport specific macromolecules. In addition, the gates allow passive
transport of small molecules.
Transmembrane transport:
the movement of small, soluble, nonpolar molecules across
the lipid bilayer of the plasma membrane (passive)
Vesicular transport
Transport of proteins from one cell compartment to another by means of membrane-bounded intermediaries such as vesicles or organelle fragments.
explain how NADH contributes to ATP synthesis in mitochondria
acts as a reducing agent that gives its electron to complex in the electron transport chain which helps establish a proton gradient for ATP synthesis
explain how O2 contributes to ATP synthesis in mitochondria
used in the ETC as the end electron acceptor. It allows electrons to be transferred through the electron transport chain in order to create an electrochemical gradient of protons.
explain how e- transfer chain contributes to ATP synthesis in mitochondria
series of four protein complexes that couple redox reactions and creates the gradient needed to create ATP during oxidative phosphorylation.
Explain how the proton gradient across the mitochondrial inner membrane contributes to ATP synthesis in mitochondria
protons flow down their gradient into the matrix through and drives the rotation of ATP synthase which in turn catalyzes the synthesis of ATP from ADP.
Proteasome
large proteolytic protein complex in the cytosol that degrades proteins marked for destruction (e.g., proteins marked by ubiquitination).
Lysosome
membrane-bound organelle that contains digestive enzymes that break down cellular components.
Autophagy
describes the cells ability to reuse components, for example by reducing a protein down to its constituent peptides only to use those peptides to synthesize new proteins.
Ubiquitin
protein added to other proteins via ubiquitlyation and can mark said protein for degradation via a proteasome, promote or prevent protein activity, or act as a location guide.
