systems biology

Question 1

What does the law of mass action state?

Answer 1

the rate of a chemical reaction is proportional to the product of the concentrations of the reactants.

Question 2

Why are kinetic equations important in Systems Biology?

Answer 2

to quantify dynamics of biological reactions

Question 3

What is the steady-state assumption in the Michaelis-Menten equation?

Answer 3

rate of formation of enzyme substrate complex equals the rate of its breakdown

Question 4

What does the enzyme saturation assumption imply in the Michaelis-Menten model?

Answer 4

at high substrate concentrations, the enzyme becomes saturated with substrate, meaning that increasing substrate concentration further will not significantly increase the reaction rate.

Question 5

What is the initial velocity assumption in the Michaelis-Menten derivation?

Answer 5

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

Question 6

What is a feedforward loop in biochemical networks?

Answer 6

where an upstream signal regulates a downstream process directly and indirectly through an intermediate step

Question 7

What are the advantages of feedforward loops in biochemical systems?

Answer 7

allow faster response to changes in stimuli, can filter out noise

Question 8

What is a coherent feedforward loop?

Answer 8

a regulatory circuit where the direct and indirect pathways from an input to the output both exert the same type of effect

Question 9

What is an incoherent feedforward loop?

Answer 9

a regulatory circuit where the direct and indirect pathways from an input to the output have opposite effects.

Question 10

Can you give an example of a coherent feedforward loop?

Answer 10

transcription factor (TF) may directly activate a gene and simultaneously activate a second TF, which also activates the same gene

Question 11

Can you give an example of an incoherent feedforward loop?

Answer 11

a transcription factor might activate a gene directly while also activating another factor that inhibits the same gene

Question 12

What are the temporal dynamics of a coherent feedforward loop?

Answer 12

delayed but sustained response

Question 13

What are the temporal dynamics of an incoherent feedforward loop?

Answer 13

pulse-like, transient response

Question 14

How does the response time of coherent feedforward loops compare to incoherent loops?

Answer 14

coherent is usually slower

Question 15

What is a random walk in the context of diffusion?

Answer 15

where each particle moves randomly due to thermal energy

Question 16

How is diffusion mathematically described?

Answer 16

described by Fick’s laws of diffusion, where the rate of particle flow (flux) is proportional to the gradient of concentration

Question 17

What is the mean squared displacement (MSD) in a random walk, and how is it related to diffusion?

Answer 17

The mean squared displacement (MSD) is the average of the squared distances a particle travels over time in a random walk

Question 18

what is the formula for MSD

Answer 18

MSD=2Dt

Question 19

What is bacterial chemotaxis?

Answer 19

the movement of bacteria toward chemical attractants (such as nutrients) or away from harmful substances

Question 20

How do bacteria move during chemotaxis?

Answer 20

Bacteria use flagella to move
chemotaxis modulate frequency of the movement

Question 21

What role do chemoreceptors play in bacterial chemotaxis?

Answer 21

initiate the intracellular signaling that regulates flagellar motion

Question 22

What is the role of CheA and CheY in bacterial chemotaxis?

Answer 22

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.

Question 23

What types of chemotaxis occur in eukaryotic cells?

Answer 23

positive chemotaxis that move towards attractants
negative chemotaxis used to move away from repellents

Question 24

What role do receptors play in eukaryotic chemotaxis?

Answer 24

usually GPCR used to detects attractants or repellents and drive cell movement

Question 25

How is signal transduction initiated in eukaryotic chemotaxis?

Answer 25

initiated when chemoattractants bind to GPCRs, activating G proteins

Question 26

What is the role of PI3K in eukaryotic chemotaxis?

Answer 26

generates PIP3

Question 27

What roles do Rac and Rho GTPases play in eukaryotic chemotaxis?

Answer 27

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

Question 28

Can you give an example of eukaryotic chemotaxis in a biological process?

Answer 28

movement of neutrophils towards site of infection

Question 29

What role does myosin play in eukaryotic chemotaxis?

Answer 29

Myosin II mediates contraction at the trailing edge of the cell, helping retract the rear as the cell moves forward.

Question 30

What types of receptors are involved in bacterial and eukaryotic chemotaxis?

Answer 30

MCPs in bacteria
GPCRs in eukaryotic

Question 31

What are reaction-diffusion models?

Answer 31

describe how chemical substances distributed in space undergo reactions and diffuse over time

Question 32

What are Turing patterns?

Answer 32

interaction of two chemicals (one that activates and one that inhibits) that diffuse at different rates.

Question 33

turning patterns can explain ?

Answer 33

animal coat patterns

Question 34

what is morphogenesis

Answer 34

organisms develop their shape, relies on the diffusion of signaling molecules that activate or inhibit cell behaviors