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Questions and Answers
What occurs during negative autoregulation (NAR)?
What occurs during negative autoregulation (NAR)?
Positive autoregulation (PAR) speeds up the response time in gene transcription compared to a simple regulation system.
Positive autoregulation (PAR) speeds up the response time in gene transcription compared to a simple regulation system.
False
What are the two prevalent classes of regulatory motifs identified in transcriptional networks?
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?
What is a characteristic of a coherent feed forward loop?
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An incoherent feed forward loop results in pulse-like dynamics regardless of repression strength.
An incoherent feed forward loop results in pulse-like dynamics regardless of repression strength.
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Match the following types of regulatory loops with their characteristics:
Match the following types of regulatory loops with their characteristics:
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What is one way to speed up a transcriptional network response?
What is one way to speed up a transcriptional network response?
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Incoherent feed forward loops can make use of stronger ______ to speed the initial response.
Incoherent feed forward loops can make use of stronger ______ to speed the initial response.
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Match the following characteristics with their corresponding network types:
Match the following characteristics with their corresponding network types:
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What is the primary goal of systems biology?
What is the primary goal of systems biology?
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Emergent properties play no role in morphogenesis.
Emergent properties play no role in morphogenesis.
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What is the law that describes enzyme-catalyzed reactions?
What is the law that describes enzyme-catalyzed reactions?
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The concentration of the enzyme substrate complex, denoted as [___], does not change over time in the quasi steady state assumption.
The concentration of the enzyme substrate complex, denoted as [___], does not change over time in the quasi steady state assumption.
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Which of the following components is NOT a part of the systems biology analysis?
Which of the following components is NOT a part of the systems biology analysis?
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Match the following terms with their definitions:
Match the following terms with their definitions:
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Negative autoregulation can help to speed up the promoter response.
Negative autoregulation can help to speed up the promoter response.
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What determines the response time in a simple transcription model?
What determines the response time in a simple transcription model?
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Which type of regulatory network is responsible for signal transduction in cells?
Which type of regulatory network is responsible for signal transduction in cells?
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In the Michaelis-Menten equation, the total enzyme is represented as [___].
In the Michaelis-Menten equation, the total enzyme is represented as [___].
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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.
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Description
Explore the intricate world of systems biology, where complex regulatory networks in biological systems are analyzed. This quiz delves into biochemical reactions, gene regulatory networks, and the influences of kinetics, providing a quantitative framework to understand these interactions. Suitable for students and enthusiasts of biology.
