system biology

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What is the main focus of Systems Biology?

Studying all genes or proteins in a large scale research.

Studying a few genes or proteins in a small scale research.

Studying many genes or proteins in an integrated study. (correct)

Studying individual genes or proteins.

What is the main difference between Genetics and Genomics?

Genetics studies a few genes, while Genomics studies many genes.

Genetics studies individual genes, while Genomics studies all genes. (correct)

Genetics studies all genes, while Genomics studies individual genes.

Genetics studies many genes, while Genomics studies a few genes.

What is the analogy used to describe the replacement of molecules in a cell over time?

Replacing every molecule in a radio over time.

Replacing every molecule in a cell over time.

Replacing every cell in a body over time.

Replacing every plank in a boat over time. (correct)

According to the text, what is the definition of a system?

A collection of interacting parts with emergent behavior Signup and view all the answers

What is the study of systems biology mainly focused on?

Understanding the interactions between components of biological systems Signup and view all the answers

What is emergence in the context of systems biology?

When the whole is greater than the sum of its parts Signup and view all the answers

Why is systems biology important in understanding diseases?

Many diseases are caused by malfunctioning of dynamic bionetworks Signup and view all the answers

Which of the following is a typical timescale for the transcription and translation of a gene in E. coli?

5 min Signup and view all the answers

What is the purpose of mathematical modeling in biology?

All of the above Signup and view all the answers

Which of the following is true about biological networks?

They consist of nodes and edges Signup and view all the answers

What is the purpose of community standard data models in omics data and modeling?

To store and represent data Signup and view all the answers

What is a model in the context of mathematical modeling?

A simplified representation of a real-world entity Signup and view all the answers

Which of the following characteristics are important for model organisms?

Well-studied biology Signup and view all the answers

What is one advantage of computational modeling in biology?

It can assist experimentation Signup and view all the answers

What is the purpose of modeling in systems biology?

To study the interactions of parts Signup and view all the answers

Which type of model describes the components and their relations using a graph representation?

Structural/Qualitative model Signup and view all the answers

Which of the following is a common approach used in mathematical modeling of biochemical systems?

All of the above Signup and view all the answers

What is a system state in a computational model?

A set of variables used to summarize the properties of interest in the study system Signup and view all the answers

What is the purpose of creating a mathematical model of a biological system?

All of the above Signup and view all the answers

What is the purpose of constructing models in such a way that disregarded properties do not compromise the basic results?

To ensure the basic results of the model are not affected Signup and view all the answers

What is the most frequently used approach to model the static and dynamic behaviors of biochemical networks?

Systems of ordinary differential equations (ODE) Signup and view all the answers

What is the difference between a variable and a parameter in a model?

A variable is a quantity with a changeable value, while a parameter is a quantity with a fixed value Signup and view all the answers

What is the purpose of the iterative modeling cycle mentioned in the text?

All of the above Signup and view all the answers

Which state function relates enthalpy (H), entropy (S), and temperature (T)?

Gibbs free energy (G) Signup and view all the answers

Systems Biology is the study of _______ in biological systems.

interactions Signup and view all the answers

Systems Biology focuses on _______ study on many genes/proteins.

integrated Signup and view all the answers

Mathematical modeling is a process of creating and refining a ______.

model Signup and view all the answers

Simulation is the manipulation of a ______ in such a way that it operates on time or space to predict how the system works.

model Signup and view all the answers

A ______ represents specific aspects of reality and is sufficient to answer particular questions.

model Signup and view all the answers

Modeling highlights ______ in knowledge or understanding.

gaps Signup and view all the answers

Models are never 'right,' but can be _______ and helpful.

appropriate Signup and view all the answers

A model contains various kinds of statements and equations describing facts about the model _______.

elements Signup and view all the answers

The quantities in a model can be classified as variables, ________, and constants.

parameters Signup and view all the answers

A biological process can be described with different (mathematical) models. The choice of a mathematical model or an algorithm to describe a biological object depends on the problem, the purpose, and the ________ of the investigator.

intention Signup and view all the answers

Systems biology views biology as dynamic networks of interactions. A system is any collection of interacting parts with ______ behavior.

emergent Signup and view all the answers

The interconnections of biological components of cells are taking center stage in ______.

biology Signup and view all the answers

Systems biology is the study of the interactions between the components of biological systems, and how these interactions give rise to the function and behavior of that ______.

system Signup and view all the answers

Biological processes are the result of complex and dynamic interactions within and between cells, organs, and entire ______.

organisms Signup and view all the answers

Biological networks are best represented by ______ that consist of nodes and edges.

graphs Signup and view all the answers

Common schemes for data storage, data representation, and data transfer in omics data include ______.

XML (extensible markup language)-like language style Signup and view all the answers

Model organisms are organisms that are well-studied, fit for laboratory study, have a short life cycle, are small and easy to maintain, and have rapid and reliable growth in a laboratory. They also have the existence of excellent ______.

genetic tools Signup and view all the answers

Modeling is an abstraction of reality and is not the reality itself. Model organisms can be used to study a simple organism rather than a complex one, as long as the basic biology is ______.

similar Signup and view all the answers

Mathematical modeling is necessary in biology because it is difficult to intuitively figure out how the concentrations of different species behave over time. We need support by mathematical modeling and software tools to ______ that.

do that Signup and view all the answers

One major function of models is to make assumptions about the underlying process explicit and, hence, ______.

testable Signup and view all the answers

Three major types of computational/mathematical models used in biological systems are network-based models, rule-based models, and ______.

statistical models Signup and view all the answers

The most frequently used approach to model the static and dynamic behaviors of biochemical networks is through systems of ordinary differential equations (ODE). This formulation allows us to assign kinetic laws to all reactions and determine the values of the ______.

kinetic parameters Signup and view all the answers

Chemical reactions in a cell are accompanied by changes in ________.

energy Signup and view all the answers

Gibbs free energy (G) is a state function that relates ________, entropy (S), and temperature (T).

enthalpy Signup and view all the answers

Activation energy is the energy required to bring all molecules in a chemical reaction into the ________ state.

reactive Signup and view all the answers

system biology

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Questions and Answers

What is the main focus of Systems Biology?

What is the main difference between Genetics and Genomics?

What is the analogy used to describe the replacement of molecules in a cell over time?

According to the text, what is the definition of a system?

What is the study of systems biology mainly focused on?

What is emergence in the context of systems biology?

Why is systems biology important in understanding diseases?

Which of the following is a typical timescale for the transcription and translation of a gene in E. coli?

What is the purpose of mathematical modeling in biology?

Which of the following is true about biological networks?

What is the purpose of community standard data models in omics data and modeling?

What is a model in the context of mathematical modeling?

Which of the following characteristics are important for model organisms?

What is one advantage of computational modeling in biology?

What is the purpose of modeling in systems biology?

Which type of model describes the components and their relations using a graph representation?

Which of the following is a common approach used in mathematical modeling of biochemical systems?

What is a system state in a computational model?

What is the purpose of creating a mathematical model of a biological system?

What is the purpose of constructing models in such a way that disregarded properties do not compromise the basic results?

What is the most frequently used approach to model the static and dynamic behaviors of biochemical networks?

What is the difference between a variable and a parameter in a model?

What is the purpose of the iterative modeling cycle mentioned in the text?

Which state function relates enthalpy (H), entropy (S), and temperature (T)?

Systems Biology is the study of _______ in biological systems.

Systems Biology focuses on _______ study on many genes/proteins.

Mathematical modeling is a process of creating and refining a ______.

Simulation is the manipulation of a ______ in such a way that it operates on time or space to predict how the system works.

A ______ represents specific aspects of reality and is sufficient to answer particular questions.

Modeling highlights ______ in knowledge or understanding.

Models are never 'right,' but can be _______ and helpful.

A model contains various kinds of statements and equations describing facts about the model _______.

The quantities in a model can be classified as variables, ________, and constants.

A biological process can be described with different (mathematical) models. The choice of a mathematical model or an algorithm to describe a biological object depends on the problem, the purpose, and the ________ of the investigator.

Systems biology views biology as dynamic networks of interactions. A system is any collection of interacting parts with ______ behavior.

The interconnections of biological components of cells are taking center stage in ______.

Systems biology is the study of the interactions between the components of biological systems, and how these interactions give rise to the function and behavior of that ______.

Biological processes are the result of complex and dynamic interactions within and between cells, organs, and entire ______.

Biological networks are best represented by ______ that consist of nodes and edges.

Common schemes for data storage, data representation, and data transfer in omics data include ______.

Model organisms are organisms that are well-studied, fit for laboratory study, have a short life cycle, are small and easy to maintain, and have rapid and reliable growth in a laboratory. They also have the existence of excellent ______.

Modeling is an abstraction of reality and is not the reality itself. Model organisms can be used to study a simple organism rather than a complex one, as long as the basic biology is ______.

Mathematical modeling is necessary in biology because it is difficult to intuitively figure out how the concentrations of different species behave over time. We need support by mathematical modeling and software tools to ______ that.

One major function of models is to make assumptions about the underlying process explicit and, hence, ______.

Three major types of computational/mathematical models used in biological systems are network-based models, rule-based models, and ______.

The most frequently used approach to model the static and dynamic behaviors of biochemical networks is through systems of ordinary differential equations (ODE). This formulation allows us to assign kinetic laws to all reactions and determine the values of the ______.

Chemical reactions in a cell are accompanied by changes in ________.

Gibbs free energy (G) is a state function that relates ________, entropy (S), and temperature (T).

Activation energy is the energy required to bring all molecules in a chemical reaction into the ________ state.

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