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Questions and Answers

In negative autoregulation (NAR), X is a transcription factor that represses its own ______.

promoter

In positive autoregulation (PAR), X activates its own ______.

promoter

NAR speeds the response time relative to a simple-regulation system that reaches the same steady-state ______.

expression

The eight types of feedforward loops (FFLs) are classified into coherent and ______ FFLs.

<p>incoherent</p> Signup and view all the answers

In a type 1 Coherent Feed Forward Loop, the promoter displays ______ logic, requiring binding of both X and Y to be active.

<p>AND</p> Signup and view all the answers

Coherent feed forward loop results in delay of 'on' response and has no effect on 'off' response, while incoherent feed forward loop can speed up response time compared to simple ______.

<p>regulation</p> Signup and view all the answers

A coherent feed forward network can act as a ______ filter, helping to filter out small perturbations.

<p>noise</p> Signup and view all the answers

The pulse response of an incoherent feed-forward loop can be sharp depending on the strength of ______.

<p>repression</p> Signup and view all the answers

Incoherent feed forward loops can use stronger promoters to speed the ______ response.

<p>initial</p> Signup and view all the answers

There are 199 possible four node connected ______ within network motifs.

<p>graphs</p> Signup and view all the answers

Biological Systems are controlled by complex ______ networks.

<p>regulatory</p> Signup and view all the answers

Quantitative understanding of organisation and functioning of biological systems includes ______ analysis.

<p>network</p> Signup and view all the answers

The law of ______ action describes the rates of chemical reactions.

<p>mass</p> Signup and view all the answers

In enzyme catalysed reactions, the enzyme is represented as ______.

<p>E</p> Signup and view all the answers

The concentration of the intermediate enzyme substrate complex does not change with ______.

<p>time</p> Signup and view all the answers

Negative and positive auto regulation can speed up or slow down the ______ response.

<p>promoter</p> Signup and view all the answers

The degradation rate, represented as ______, determines the response time in transcription networks.

<p>α</p> Signup and view all the answers

Analysis of ______ regulatory networks is essential for understanding gene expression.

<p>gene</p> Signup and view all the answers

Systems biology utilizes various omics approaches including genomics and ______.

<p>proteomics</p> Signup and view all the answers

Transcription networks respond to external ______.

<p>signals</p> Signup and view all the answers

What is one effect of an incoherent feed-forward loop compared to simple regulation?

<p>It speeds up response time. (C)</p> Signup and view all the answers

How can a transcriptional network increase its response speed?

<p>By using incoherent feed forward loops. (A), By utilizing negative feedback. (D)</p> Signup and view all the answers

What characterizes the pulse response of an incoherent feed-forward network?

<p>It can be sharp depending on repression strength. (B)</p> Signup and view all the answers

What is the role of coherent feed forward loops in relation to noise in a network?

<p>They act as a filter to reduce noise. (D)</p> Signup and view all the answers

In a transcriptional network with four nodes, how many possible connected graphs exist?

<p>199 (A)</p> Signup and view all the answers

What is the key characteristic of a negative autoregulation (NAR) system?

<p>It represses its own promoter through a feedback mechanism. (A)</p> Signup and view all the answers

How does positive autoregulation (PAR) affect the response time of transcription?

<p>It prolongs the response time. (B)</p> Signup and view all the answers

In feedforward loops, what defines a coherent feedforward loop?

<p>The direct and indirect paths produce the same overall output sign. (C)</p> Signup and view all the answers

Which type of logic does the promoter utilize in a type 1 coherent feedforward loop?

<p>AND logic, requiring both X and Y to bind for activation. (D)</p> Signup and view all the answers

What is one of the eight types of feedforward loops (FFLs) classified based on input characteristics?

<p>Coherent FFL where inputs maintain the same sign. (C)</p> Signup and view all the answers

Which of the following is a key component necessary for the quantitative analysis in systems biology?

<p>Computation and modelling for network analysis (C)</p> Signup and view all the answers

What does the quasi-steady state assumption imply in enzyme catalyzed reactions?

<p>The concentration of intermediate complex does not change with time (D)</p> Signup and view all the answers

How does negative autoregulation influence transcription factor response times?

<p>It speeds up response times relative to simple regulation (D)</p> Signup and view all the answers

Which of the following analyses is NOT part of understanding temporal networks in systems biology?

<p>Analysis of cellular interactions (B)</p> Signup and view all the answers

Which of the following accurately describes positive regulation in transcription networks?

<p>A signal activates transcription factor Y (C)</p> Signup and view all the answers

What is a primary focus of spatial networks in systems biology?

<p>Controlling the formation of structures at various biological levels (C)</p> Signup and view all the answers

Which statement about enzyme catalyzed reactions is true?

<p>Enzymes maintain their form and participate in multiple cycles (B)</p> Signup and view all the answers

Which of the following best explains the role of feedback in biological networks?

<p>Feedback mechanisms determine the overall response time of the system (A)</p> Signup and view all the answers

Which concept is critical for understanding gene regulatory networks?

<p>Both negative and positive regulation compete to modulate transcription factors (C)</p> Signup and view all the answers

What does the Law of Mass Action describe in the context of biochemical reactions?

<p>The effect of substrate concentration on reaction velocity (A)</p> Signup and view all the answers

Flashcards

Systems Biology

Quantitative study of biological systems, examining components, reactions, and their spatial/temporal networks to understand emergent properties and functions.

Temporal Analysis

Study of how biological processes change over time, including reaction kinetics and dynamics.

Reaction Networks

Sets of interconnected biochemical reactions, encompassing signalling, gene regulation, and metabolism.

Enzyme Kinetics

The study of how rates of enzyme-catalyzed reactions change, typically based on substrate concentration (Michaelis-Menten).

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Michaelis-Menten Kinetics

A mathematical model describing the relation between reaction rate and substrate concentration for enzyme-catalyzed reactions.

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Quasi-steady-state assumption

The concentration of intermediate enzyme-substrate complexes stays roughly constant during an enzymatic reaction.

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Gene Regulatory Networks

Networks of interacting molecules controlling gene transcription through various regulatory mechanisms.

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Positive Regulation

A mechanism where a signal (activator) increases the rate of gene expression.

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Negative Regulation

A regulatory mechanism where a signal (repressor) decreases the rate of gene expression.

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Autoregulation

A regulatory mechanism where a protein or molecule controls its own synthesis or degradation.

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Positive Autoregulation (PAR)

A regulatory mechanism where a transcription factor activates its own gene's promoter, increasing its expression.

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Negative Autoregulation (NAR)

A regulatory mechanism where a transcription factor represses its own gene's promoter, decreasing its expression.

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Coherent Feed-Forward Loop

A regulatory pathway where the direct and indirect paths from a transcription factor to an output have the same sign (both stimulating or both inhibiting).

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Incoherent Feed-Forward Loop

A regulatory pathway where the direct and indirect paths from a transcription factor to an output have opposite signs (one stimulating, one inhibiting).

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AND Logic in 3-node FFL

A 3-node FF loop that needs binding of two different factors (X and Y) to activate the output.

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Coherent Feed-Forward Loop (CFFL)

A regulatory network where the direct and indirect paths from an input to an output have the same sign (both activate or both repress the output).

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Incoherent Feed-Forward Loop (IFFL)

A regulatory network where the direct and indirect paths from an input to an output have opposite signs. One path activates the output, while the other inhibits it.

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Pulse-like dynamics in IFFL

A three-node IFFL often exhibits a pulse-like response to an input, where the output quickly rises and then quickly falls back to its initial state.

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Repression strength in IFFL

The strength of repression in an IFFL affects the sharpness of its pulse response. Stronger repression results in a sharper and faster pulse.

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Speeding up response time

IFFLs can enhance the speed of response compared to simple regulation, reaching the same steady-state level faster.

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Temporal Network Analysis

The study of how biological processes change over time, examining the dynamics of reactions, signaling pathways, and gene regulation.

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Simple Transcription Model

A basic model describing how a gene is activated or repressed to produce RNA.

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What does PAR do to response time?

Positive autoregulation (PAR) slows the response time of a system, meaning it takes longer to reach a steady-state level compared to a simple regulatory system.

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What is a coherent feed-forward loop?

A coherent feed-forward loop (CFFL) is a regulatory network where the direct and indirect paths from a transcription factor to an output have the same sign (both activate or both repress the output).

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What does a type 1 CFFL require?

A type 1 coherent feed-forward loop requires the binding of both transcription factors X and Y to activate the output.

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How is response time affected with IFFL?

An incoherent feed-forward loop (IFFL) can speed up the response time compared to simple regulation, allowing the system to reach a steady-state level faster.

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What does a 3-node feed-forward loop consist of?

A 3-node feed-forward loop consists of three nodes: X, Y, and Z, where X directly regulates Y and Y directly regulates Z. X may also indirectly regulate Z through Y.

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Study Notes

Introduction to Systems Biology

  • Biological systems are controlled by complex regulatory networks
  • These networks span a wide range of space and time scales

Temporal Reaction Networks

  • Biochemical reactions
  • Signaling networks
  • Gene regulatory networks

Analysis

  • Transcription
  • Positive and negative feedback
  • Simple network motifs
  • More complex motifs

Enzyme Catalysed Reactions

  • Law of Mass Action/Michaelis Menten kinetics
  • Formulas for enzyme-catalysed reactions are shown
  • Enzyme acts as a catalyst and is conserved in the reaction: [E] + [ES] = [E]o
  • Defining variables (E, ES, E, S, P, Kfwd, Krev, Kcat)

Quasi Steady State Assumption

  • Assumed that the concentration of the enzyme-substrate complex does not change with time
  • This assumption simplifies the equations

Michaelis-Menten Equation

  • A derived equation that describes the rate of an enzyme-catalysed reaction
    • v = (Vmax*[S])/(Km + [S])

Complex Networks

  • Underlying critical biological functions
  • Examples of complex networks are: metabolic pathways, E. coli gene regulatory network
  • Quantitative understanding of organisation and functioning of biological systems is a goal of Systems Biology

Systems Biology ≈ Network Biology

  • Goal: Develop a quantitative understanding of the function of genetic and biochemical networks
  • Need to consider the function of individual interactions (feedbacks and feedforwards) within the context of the whole network
  • Function of gene products A-F
  • System approach

Analysis of Gene Regulatory Networks

  • Simple transcription models
    • DNA, Promoter, Gene, mRNA, RNA polymerase, Protein, Translation, Transcription are involved.

Transcription Networks

  • Respond to external signals
  • Shows signals and transcription factors
  • Shows how genes are involved

Simple Positive Regulation

  • Shows the activator and how it affects the binding site of the gene
  • Equations for steady state and half time are included

Kinetics of Y Accumulation

  • Shows accumulation of Y over time and its decay
  • Graph of Y(t) = Yst (1 - e-at)

Negative and Positive Autoregulation

  • Speed up/slow down the promoter response

3 Node Feed Forward Loops

  • Coherent and incoherent types
  • Shows the different possible types
  • Coherent feed forward loops results in delay of "on" response, and incoherent feed forward loop speeds up the response time

Coherent Feed Forward Network

  • Can filter out small perturbations (noise filter)

Three Node Incoherent Network

  • Results in pulse-like dynamics
  • Can be sharp pulse if repression strength is high

Generalisation of Feed Forward Loop

  • Double input, double Y, double output

Multi Node Generalisations of Feed Forward Loop

  • Multi input, Multi Y, Multi output

4 Node Networks

  • 199 possible four node connected graphs

Transcription response speed up

  • Three ways to increase response speed
    • Increase degradation rate of a gene to speed up the simple response
    • Use negative feedback promoters, thereby speeding up the initial response
    • Use incoherent feed-forward loops to speed up the initial response

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Systems Biology I-Temporal Systems PDF

Description

This quiz covers the fundamentals of systems biology, including biochemical reactions, signaling networks, and gene regulatory networks. Explore the principles of enzyme-catalysed reactions and the Michaelis-Menten equation, as well as the analysis of complex regulatory networks. Test your understanding of how these concepts interconnect within biological systems.

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