Systems Biology I

Choose a study mode

Play Quiz
Study Flashcards
Spaced Repetition
Chat to Lesson

Podcast

Play an AI-generated podcast conversation about this lesson

Questions and Answers

What occurs during negative autoregulation (NAR)?

  • Gene X inhibits its own transcription (correct)
  • Gene X enhances transcription rate
  • Gene X has no effect on its promoter
  • Gene X activates its own promoter

Positive autoregulation (PAR) speeds up the response time in gene transcription compared to a simple regulation system.

False (B)

What are the two prevalent classes of regulatory motifs identified in transcriptional networks?

Feed forward loops and feedback loops

What is a characteristic of a coherent feed forward loop?

<p>It can filter out small perturbations. (A)</p> Signup and view all the answers

An incoherent feed forward loop results in pulse-like dynamics regardless of repression strength.

<p>False (B)</p> Signup and view all the answers

Match the following types of regulatory loops with their characteristics:

<p>Coherent Feed Forward Loop = Same sign for paths to output Z Incoherent Feed Forward Loop = Opposite sign for the two paths to Z Negative Autoregulation = Represses own transcription Positive Autoregulation = Activates own promoter</p> Signup and view all the answers

What is one way to speed up a transcriptional network response?

<p>Increasing the degradation rate.</p> Signup and view all the answers

Incoherent feed forward loops can make use of stronger ______ to speed the initial response.

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

Match the following characteristics with their corresponding network types:

<p>Coherent Feed Forward Loop = Delays 'on' response Incoherent Feed Forward Loop = Speeds up response time Simple Regulation = Slower response times Negative Feedback = Allows stronger promoters</p> Signup and view all the answers

What is the primary goal of systems biology?

<p>To understand the organization and functioning of biological systems quantitatively (C)</p> Signup and view all the answers

Emergent properties play no role in morphogenesis.

<p>False (B)</p> Signup and view all the answers

What is the law that describes enzyme-catalyzed reactions?

<p>Law of Mass Action</p> Signup and view all the answers

The concentration of the enzyme substrate complex, denoted as [___], does not change over time in the quasi steady state assumption.

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

Which of the following components is NOT a part of the systems biology analysis?

<p>Qualitative analysis of growth (B)</p> Signup and view all the answers

Match the following terms with their definitions:

<p>E = Free enzyme ES = Enzyme-substrate complex Kcat = Rate-limiting reaction rate α = Degradation rate</p> Signup and view all the answers

Negative autoregulation can help to speed up the promoter response.

<p>False (B)</p> Signup and view all the answers

What determines the response time in a simple transcription model?

<p>Degradation rate (α)</p> Signup and view all the answers

Which type of regulatory network is responsible for signal transduction in cells?

<p>Signaling network (B)</p> Signup and view all the answers

In the Michaelis-Menten equation, the total enzyme is represented as [___].

<p>E0</p> Signup and view all the answers

Flashcards

Systems Biology

Quantitative study of biological systems, including their organization and function.

Temporal Reaction Networks

Analysis of networks of biochemical reactions, focusing on time-dependent changes.

Law of Mass Action

Describes how the rate of a chemical reaction depends on the concentration of reactants.

Michaelis-Menten kinetics

A model describing enzyme-catalyzed reactions, focusing on substrate saturation.

Signup and view all the flashcards

Quasi-steady state assumption

Assumes that the concentration of an intermediate in a reaction doesn't significantly change over time.

Signup and view all the flashcards

Enzyme

Biological catalysts, speeding up reactions without being consumed.

Signup and view all the flashcards

Positive Regulation

Activation of a process by a signaling molecule.

Signup and view all the flashcards

Negative Regulation

Inhibition of a process by a signaling molecule.

Signup and view all the flashcards

Gene regulatory networks

Networks of genes and proteins involved in controlling gene expression.

Signup and view all the flashcards

Autoregulation

A feedback loop where the output of a process influences its own input.

Signup and view all the flashcards

Positive Autoregulation (PAR)

A regulatory mechanism where a transcription factor (e.g., X) activates its own gene's promoter, thus increasing the expression level of itself

Signup and view all the flashcards

Negative Autoregulation (NAR)

A regulatory mechanism where a transcription factor (e.g., X) represses its own gene's promoter, thus decreasing the expression level of itself.

Signup and view all the flashcards

Feed-Forward Loop (FFL)

A regulatory motif where a stimulus affects an output not directly but through another intermediate variable (a second transcription factor) in a way that modifies the response time

Signup and view all the flashcards

Coherent Feed-Forward Loop

A feed-forward loop where the direct effect of the first transcription factor on the third and the indirect effect through the second have the same sign.

Signup and view all the flashcards

Incoherent Feed-Forward Loop

A feed-forward loop where the direct effect of the input on the output, and the effect mediated by the intermediate factor are opposite.

Signup and view all the flashcards

Pulse-like Dynamics

A response pattern characterized by a short burst of activity followed by a return to the baseline level. This pattern is often observed in incoherent feed-forward loops.

Signup and view all the flashcards

Repression Strength (F)

A parameter that describes the strength of negative regulation in a network. Higher F indicates stronger repression and a sharper pulse response in an incoherent feed-forward loop.

Signup and view all the flashcards

Speeding Up Response Time

There are three main ways to speed up a transcriptional network's response to a signal: 1. Increase the degradation rate; 2. Utilize stronger promoters with negative feedback; 3. Employ incoherent feed-forward loops.

Signup and view all the flashcards

Study Notes

Introduction to Systems Biology

  • Systems biology studies complex regulatory networks in biological systems, spanning diverse spatial and temporal scales.
  • Biological systems, from molecules to organisms, are interconnected.
  • The study involves quantitative analysis of networks.
  • This includes examining components, individual reactions, and interactions within temporal and spatial networks.

Temporal Reaction Networks

  • Focus is on biochemical reactions, signaling networks, and gene regulatory networks.
  • Analysis considers:
    • Transcription
    • Positive and negative feedback
    • Simple network motifs
    • More complex motives

Enzyme Catalyzed Reactions

  • Reactions are governed by mass action and Michaelis-Menten kinetics.
  • The process involves:
    • Free enzyme (E)
    • Enzyme-substrate complex (ES)
    • Total enzyme (ET)
    • Substrate (S)
    • Product (P)
  • Rate constants (kf, kr, kcat) influence the reaction.
  • Enzymes act as catalysts and remain unchanged during the reaction.

Quasi Steady-State Assumption

  • The concentration of the enzyme-substrate complex (ES) remains relatively constant over time.
  • This simplifies kinetic equations.
  • The Michaelis-Menten equation describes reaction rates.

Systems Biology and Network Analysis

  • Quantifying how systems function, with quantitative understanding of biological systems.
  • Identifying components (genomics, transcriptomics, proteomics, glycomics, lipidomics).
  • Analyzing individual reactions (biochemistry).
  • Analyzing temporal (gene regulation, signal transduction).
  • Analyzing spatial networks (interactions controlling cellular structures).
  • Understanding spatio-temporal networks controlling cells and organisms.
  • Examining emergent properties (organ models, digital organisms).
  • Computation and modeling are key components.

Complex Networks and Biological Functions

  • Complex networks (metabolic pathways, gene regulatory networks) are fundamental to biological functions.
  • Example in E.coli gene regulatory network.

Analysis of Gene Regulatory Networks

  • Simple transcription models illustrate how genes and proteins interact.
  • Transcription networks respond to external signals.
  • Example of positive regulations.
  • Example of negative regulation and negative autoregulation.

Positive and Negative Autoregulation

  • Positive autoregulation enhances promoter response comparing to simple regulation.
  • Negative autoregulation makes use of stronger promoter to speed up initial response.
  • Effects are evident in different time scales.

Network Motifs

  • Small, recurring sub-structures within biological networks.
  • Identifying and classifying specific feed-forward loops (FFLs) in example networks.
  • Understanding coherent and incoherent feed-forward loops, their effects on response, and differences between different loop types.
  • Occurrence is shown in various biological systems (e.g., yeast, E.coli).

Coherent and Incoherent Feed-Forward Loops

  • Coherent FFLs: Input and overall output relationships are positively correlated; examples are shown along with diagrams.
  • Incoherent FFLs: Input and output are inversely correlated; examples are shown along with diagrams and graphs.
  • Understanding of the interactions and their effects.

Multi Node Generalizations of Feedforward Loops

  • Expanding the feedforward loop concept to networks with numerous interacting components.
  • Generalizing feedforward loops to multiple-input and multi-output interactions.

Speeding Up Transcriptional Network Response

  • Three ways to enhance network responses—improving degradation rates, utilizing negative feedback, and employing incoherent FFLs.

Studying That Suits You

Use AI to generate personalized quizzes and flashcards to suit your learning preferences.

Quiz Team

Related Documents

Systems Biology I-Temporal Systems PDF

More Like This

Use Quizgecko on...
Browser
Open
Browser
Browser