Difference between revisions of "Chapter !11 - Systems Biology Code : KSI0020"

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imported>김상인
 
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<p style="text-align: center;"><span style="font-size:36px">&lt;Index of Chapter 11&gt;</span></p>
+
<p style="text-align:center"><span style="font-size:36px">&lt;Index of Chapter 11&gt;</span></p>
 +
 
 +
<p>&nbsp;</p>
  
 
<p><span style="color:#0000CD"><strong>Introduction to systems biology</strong></span></p>
 
<p><span style="color:#0000CD"><strong>Introduction to systems biology</strong></span></p>
 +
 +
<p>The goal of systems biology is the synthesis of all biological data into a unified picture of the structure, dynamics, logistics and ultimately the logic of living things.&nbsp;</p>
 +
 +
<p>System biology focuses on the integration of gene, RNA, and protein activity</p>
 +
 +
<p>Cells contain both physical and logical networks. Many interactions are common to both.</p>
  
 
<p>-Two parallel networks : physical and logical</p>
 
<p>-Two parallel networks : physical and logical</p>
  
 
<p>-Statics and dynamics of networks</p>
 
<p>-Statics and dynamics of networks</p>
 +
 +
<p>Cell- cell communication in microorgansisms : quorum sensing&nbsp;</p>
 +
 +
<p>Static structure stability.&nbsp;</p>
 +
 +
<p>Stability is an important goal of regulatory dynamics.&nbsp;</p>
 +
 +
<p>Sources of metabolic stability include&nbsp;</p>
 +
 +
<p>1. Constant rate of input</p>
 +
 +
<p>2. Feedback inhibition of enzymes</p>
 +
 +
<p>3. allosteric control of activity of enzymes</p>
 +
 +
<p>4. turning proteins on and off &nbsp;by phosphorylation and dephosphrylation&nbsp;</p>
 +
 +
<p>5. control of amounts of proteins by regulation of expression&nbsp;</p>
 +
 +
<p>&gt; Robustness is another crucial feature of the dynamics of biological networks.&nbsp;</p>
 +
 +
<p>&nbsp;</p>
  
 
<p><span style="color:#0000CD"><strong>Pictures of networks as graphs</strong></span></p>
 
<p><span style="color:#0000CD"><strong>Pictures of networks as graphs</strong></span></p>
  
−
<p>-Trees</p>
+
<p>Graphs are abstract representations of networks. They show the connectivity of the network. labelled graphs can show physical distanes between nodes, or other properties of edges such as throughput capacity.&nbsp;</p>
 +
 
 +
<p>Connevtivity / path / cycle&nbsp;</p>
 +
 
 +
<p>A vitamin is a compound that we must eat because we can&#39;t synthesize it. Therefore, there can be no path in the metabolic network leading to a vitamin&nbsp;</p>
 +
 
 +
<p>&nbsp;</p>
 +
 
 +
<p>-Trees &gt; Density of connections / fully connected /Power laws.&nbsp;</p>
 +
 
 +
<p>&nbsp;</p>
  
 
<p><span style="color:#0000CD"><strong>Sources of ideas for systems biology</strong></span></p>
 
<p><span style="color:#0000CD"><strong>Sources of ideas for systems biology</strong></span></p>
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<p>-Computational complexity</p>
 
<p>-Computational complexity</p>
 +
 +
<p>&nbsp;</p>
  
 
<p><span style="color:#0000CD"><strong>The metabolome</strong></span></p>
 
<p><span style="color:#0000CD"><strong>The metabolome</strong></span></p>
Line 40: Line 82:
  
 
<p>-Reconstruction of metabolic networks</p>
 
<p>-Reconstruction of metabolic networks</p>
 +
 +
<p>The enzyme commision (EC) &nbsp;/ Enzyme structures database&nbsp;</p>
 +
 +
<p>An onthology is a formal set of well-defined terms with well-defined interrelationships that is a dictionary and rules of syntax.&nbsp;</p>
 +
 +
<p>&nbsp;</p>
  
 
<p><span style="color:#0000CD"><strong>Regulatory networks</strong></span></p>
 
<p><span style="color:#0000CD"><strong>Regulatory networks</strong></span></p>
Line 46: Line 94:
  
 
<p>-Structures of regulatory networks</p>
 
<p>-Structures of regulatory networks</p>
 +
 +
<p>Several databases assemble biochemical reactions into metabolic pathways. Individual seops are linked to enzyme commisiion and gene ontology consortium classfications of funtion. and to individual proteins that catalyse the reactions. These databases are useful in organizing the assignment of function to proteins identified in newly sequenced genomes&nbsp;</p>
 +
 +
<p>&nbsp;</p>
  
 
<p><span style="color:#0000FF"><strong>Dynamics , stability , and robustness</strong></span></p>
 
<p><span style="color:#0000FF"><strong>Dynamics , stability , and robustness</strong></span></p>
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<p>-Dynamic modelling</p>
 
<p>-Dynamic modelling</p>
 +
 +
<p>&nbsp;</p>
  
 
<p><span style="color:#0000CD"><strong>Protein interaction networks</strong></span></p>
 
<p><span style="color:#0000CD"><strong>Protein interaction networks</strong></span></p>
  
 
<p>-Structural biology of regulatory networks</p>
 
<p>-Structural biology of regulatory networks</p>
 +
 +
<p>Signal transduction and transcriptional control&nbsp;</p>
 +
 +
<p>&gt; General characteristics of all control pathways include the following&nbsp;</p>
 +
 +
<p>1. A single signal can trigger a single response or many responses</p>
 +
 +
<p>2. A single response can be controlled bt a single signal or infulenced by many signals</p>
 +
 +
<p>3. Each responesse may be stimualatroy- decreaaseing an activity.&nbsp;</p>
 +
 +
<p>4. Transmission of signals may damp out stimuli or amplify them.&nbsp;</p>
 +
 +
<p>&nbsp;</p>
  
 
<p><span style="color:#0000CD"><strong>Protein-DNA interactions</strong></span></p>
 
<p><span style="color:#0000CD"><strong>Protein-DNA interactions</strong></span></p>
Line 62: Line 130:
  
 
<p>-An album of transcription regulators</p>
 
<p>-An album of transcription regulators</p>
 +
 +
<p>&nbsp;</p>
 +
 +
<p>DNA-protein complexes mediate several types of process</p>
 +
 +
<p>1. Replication, including repair and recombination</p>
 +
 +
<p>2. Transcription</p>
 +
 +
<p>3. Regulation of gene expression</p>
 +
 +
<p>4. DNA packaging, including nucleosomes and viral capsids.</p>
 +
 +
<p>&nbsp;</p>
 +
 +
<p>Differnt processes requrie different degrees of DNA sequence specificity</p>
 +
 +
<p>&nbsp;</p>
 +
 +
<p>&lt;Specificities of DNA-binding proteins&gt;</p>
 +
 +
<p>DNA binding proteins are relatively non-specific with respect to nucleotide sequence, including DNA replication enzymes and histones.&nbsp;</p>
 +
 +
<p>Some recognize specific nucleotide sequences.&nbsp;</p>
 +
 +
<p>Some DNA binding proteins recognize consensus sequences</p>
 +
 +
<p>Some recognize nucleotide seuqneces indirectly via modulations of local DNA structure&nbsp;</p>
 +
 +
<p>&nbsp;</p>
  
 
<p><span style="color:#0000CD"><strong>Gene regulation&nbsp;</strong></span></p>
 
<p><span style="color:#0000CD"><strong>Gene regulation&nbsp;</strong></span></p>
Line 68: Line 166:
  
 
<p>-Regulation of the lactose operon in E.Coli.</p>
 
<p>-Regulation of the lactose operon in E.Coli.</p>
 +
 +
<p>Operator / Promoter / Repressor / operon / cis-Regulatory rehion / transcription start site / Coonstituve mutant&nbsp;</p>
 +
 +
<p>Common motifs in biological control networks.&nbsp;</p>
 +
 +
<p>Regulatory networks are directed graphs. Some simple motifs, or common small subgraphs, from the lowest level of network struvture. Networks can reprogram themselves, within an orhanism and evolve between species.&nbsp;</p>
 +
 +
<p>&nbsp;</p>
  
 
<p><span style="color:#0000CD"><strong>The genetic regulatory network od Saccharomyces cerevisiae</strong></span></p>
 
<p><span style="color:#0000CD"><strong>The genetic regulatory network od Saccharomyces cerevisiae</strong></span></p>

Latest revision as of 16:46, 30 November 2016

<Index of Chapter 11>

 

Introduction to systems biology

The goal of systems biology is the synthesis of all biological data into a unified picture of the structure, dynamics, logistics and ultimately the logic of living things. 

System biology focuses on the integration of gene, RNA, and protein activity

Cells contain both physical and logical networks. Many interactions are common to both.

-Two parallel networks : physical and logical

-Statics and dynamics of networks

Cell- cell communication in microorgansisms : quorum sensing 

Static structure stability. 

Stability is an important goal of regulatory dynamics. 

Sources of metabolic stability include 

1. Constant rate of input

2. Feedback inhibition of enzymes

3. allosteric control of activity of enzymes

4. turning proteins on and off  by phosphorylation and dephosphrylation 

5. control of amounts of proteins by regulation of expression 

> Robustness is another crucial feature of the dynamics of biological networks. 

 

Pictures of networks as graphs

Graphs are abstract representations of networks. They show the connectivity of the network. labelled graphs can show physical distanes between nodes, or other properties of edges such as throughput capacity. 

Connevtivity / path / cycle 

A vitamin is a compound that we must eat because we can't synthesize it. Therefore, there can be no path in the metabolic network leading to a vitamin 

 

-Trees > Density of connections / fully connected /Power laws. 

 

Sources of ideas for systems biology

-Complexity of sequences

-Shannon's definition of entropy

-Randomness of sequences

-Static and dynamic complexity

-Computational complexity

 

The metabolome

-Classification and assignment of protein function

-Metabolic networks 

-Databases of metabolic pathways

-Methionine synthesis in Escherichia coli

-The kyoto Encyclopedia of genes and genomes (KEGG)

-Evolution and phylogeny of metabolic pathways

-Carbohydrate metabolism in archaea

-Reconstruction of metabolic networks

The enzyme commision (EC)  / Enzyme structures database 

An onthology is a formal set of well-defined terms with well-defined interrelationships that is a dictionary and rules of syntax. 

 

Regulatory networks

-Signal transduction and transcriptional control

-Structures of regulatory networks

Several databases assemble biochemical reactions into metabolic pathways. Individual seops are linked to enzyme commisiion and gene ontology consortium classfications of funtion. and to individual proteins that catalyse the reactions. These databases are useful in organizing the assignment of function to proteins identified in newly sequenced genomes 

 

Dynamics , stability , and robustness

-Robustness through redundancy

-Dynamic modelling

 

Protein interaction networks

-Structural biology of regulatory networks

Signal transduction and transcriptional control 

> General characteristics of all control pathways include the following 

1. A single signal can trigger a single response or many responses

2. A single response can be controlled bt a single signal or infulenced by many signals

3. Each responesse may be stimualatroy- decreaaseing an activity. 

4. Transmission of signals may damp out stimuli or amplify them. 

 

Protein-DNA interactions

-Structural themes in protein-DNA binding and sequence recognition

-An album of transcription regulators

 

DNA-protein complexes mediate several types of process

1. Replication, including repair and recombination

2. Transcription

3. Regulation of gene expression

4. DNA packaging, including nucleosomes and viral capsids.

 

Differnt processes requrie different degrees of DNA sequence specificity

 

<Specificities of DNA-binding proteins>

DNA binding proteins are relatively non-specific with respect to nucleotide sequence, including DNA replication enzymes and histones. 

Some recognize specific nucleotide sequences. 

Some DNA binding proteins recognize consensus sequences

Some recognize nucleotide seuqneces indirectly via modulations of local DNA structure 

 

Gene regulation 

-The transcriptional regulatory network of Escherichia coli

-Regulation of the lactose operon in E.Coli.

Operator / Promoter / Repressor / operon / cis-Regulatory rehion / transcription start site / Coonstituve mutant 

Common motifs in biological control networks. 

Regulatory networks are directed graphs. Some simple motifs, or common small subgraphs, from the lowest level of network struvture. Networks can reprogram themselves, within an orhanism and evolve between species. 

 

The genetic regulatory network od Saccharomyces cerevisiae

-Adaprability of the yeast regulatory network.

 

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