systems biology Flashcards
What does the law of mass action state?
the rate of a chemical reaction is proportional to the product of the concentrations of the reactants.
Why are kinetic equations important in Systems Biology?
to quantify dynamics of biological reactions
What is the steady-state assumption in the Michaelis-Menten equation?
rate of formation of enzyme substrate complex equals the rate of its breakdown
What does the enzyme saturation assumption imply in the Michaelis-Menten model?
at high substrate concentrations, the enzyme becomes saturated with substrate, meaning that increasing substrate concentration further will not significantly increase the reaction rate.
What is the initial velocity assumption in the Michaelis-Menten derivation?
reaction rate is measured early enough so that the product concentration is low, minimizing any reverse reactions and ensuring that product formation reflects the forward reaction rate only
What is a feedforward loop in biochemical networks?
where an upstream signal regulates a downstream process directly and indirectly through an intermediate step
What are the advantages of feedforward loops in biochemical systems?
allow faster response to changes in stimuli, can filter out noise
What is a coherent feedforward loop?
a regulatory circuit where the direct and indirect pathways from an input to the output both exert the same type of effect
What is an incoherent feedforward loop?
a regulatory circuit where the direct and indirect pathways from an input to the output have opposite effects.
Can you give an example of a coherent feedforward loop?
transcription factor (TF) may directly activate a gene and simultaneously activate a second TF, which also activates the same gene
Can you give an example of an incoherent feedforward loop?
a transcription factor might activate a gene directly while also activating another factor that inhibits the same gene
What are the temporal dynamics of a coherent feedforward loop?
delayed but sustained response
What are the temporal dynamics of an incoherent feedforward loop?
pulse-like, transient response
How does the response time of coherent feedforward loops compare to incoherent loops?
coherent is usually slower
What is a random walk in the context of diffusion?
where each particle moves randomly due to thermal energy
How is diffusion mathematically described?
described by Fick’s laws of diffusion, where the rate of particle flow (flux) is proportional to the gradient of concentration
What is the mean squared displacement (MSD) in a random walk, and how is it related to diffusion?
The mean squared displacement (MSD) is the average of the squared distances a particle travels over time in a random walk
what is the formula for MSD
MSD=2Dt
What is bacterial chemotaxis?
the movement of bacteria toward chemical attractants (such as nutrients) or away from harmful substances
How do bacteria move during chemotaxis?
Bacteria use flagella to move
chemotaxis modulate frequency of the movement
What role do chemoreceptors play in bacterial chemotaxis?
initiate the intracellular signaling that regulates flagellar motion
What is the role of CheA and CheY in bacterial chemotaxis?
CheA is activated by chemoreceptors and phosphorylates CheY.
Phosphorylated CheY binds to the flagellar motor, causing a switch in rotation from counterclockwise (smooth swimming) to clockwise (tumbling), allowing bacteria to change direction.
What types of chemotaxis occur in eukaryotic cells?
positive chemotaxis that move towards attractants
negative chemotaxis used to move away from repellents
What role do receptors play in eukaryotic chemotaxis?
usually GPCR used to detects attractants or repellents and drive cell movement
How is signal transduction initiated in eukaryotic chemotaxis?
initiated when chemoattractants bind to GPCRs, activating G proteins
What is the role of PI3K in eukaryotic chemotaxis?
generates PIP3
What roles do Rac and Rho GTPases play in eukaryotic chemotaxis?
Rac promotes actin polymerization at the leading edge, driving forward movement, while Rho controls actin-myosin contraction at the trailing edge. Together, they coordinate cell movement by balancing protrusion and retraction
Can you give an example of eukaryotic chemotaxis in a biological process?
movement of neutrophils towards site of infection
What role does myosin play in eukaryotic chemotaxis?
Myosin II mediates contraction at the trailing edge of the cell, helping retract the rear as the cell moves forward.
What types of receptors are involved in bacterial and eukaryotic chemotaxis?
MCPs in bacteria
GPCRs in eukaryotic
What are reaction-diffusion models?
describe how chemical substances distributed in space undergo reactions and diffuse over time
What are Turing patterns?
interaction of two chemicals (one that activates and one that inhibits) that diffuse at different rates.
turning patterns can explain ?
animal coat patterns
what is morphogenesis
organisms develop their shape, relies on the diffusion of signaling molecules that activate or inhibit cell behaviors
