# BIOL398-01/S11:Class Journal Week 4

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===Reflection=== | ===Reflection=== | ||

+ | # What was the purpose of this assignment? | ||

+ | # What aspect of this assignment came most easily to you? | ||

+ | # What aspect of this assignment was the most challenging for you? | ||

+ | # What (yet) do you not understand? | ||

== Class Responses == | == Class Responses == | ||

Line 15: | Line 19: | ||

=== [[User:Sarah Carratt|Sarah Carratt's]] Journal Entry === | === [[User:Sarah Carratt|Sarah Carratt's]] Journal Entry === | ||

- | # | + | # The purpose of this assignment was to practice using the Michaelis Menten model and Matlab. |

- | # | + | # Finding V<sub>max</sub> and K was easiest for me. |

- | # | + | # Matlab remains the hardest part of the assignment for me |

- | # | + | # I keep getting error messages in Matlab that I have trouble correcting. It can be really frustrating and I feel like I won't ever understand it on the first try. |

- | + | ||

+ | [[User:Sarah Carratt|Sarah Carratt]] 17:22, 6 February 2011 (EST) | ||

=== [[User:Carmen E. Castaneda|Carmen E. Castaneda's]] Journal Entry === | === [[User:Carmen E. Castaneda|Carmen E. Castaneda's]] Journal Entry === | ||

- | # | + | #The purpose for this assignment was to put more of the MATLAB applications that we covered in class into use as well as to keep trying to understand the model of Michealis-Menten, especially when the Lineweaver-Burk approach was used. |

- | # | + | #The easiest part of the assignment was Estimating Michaelis-Menten Parameters. |

- | # | + | #The most challenging aspect was trying tofigure out how to plot the four different values of K<sub>2</sub> on the same graph. So I had a hard time working with MATLAB again. |

- | # | + | #I still do not understand what exactly is happening in the MATLAB programs. I don't think I quite grasp what we produce or what we are doing exactly. Also I still do not understand the programs themselves that well, like what each command does. What I mean by this is if I had to write my own program in MATLAB I do not think I would be able to. As I started to define the terms I also noticed I quite do not understand what Michealis-Menten is and how the Lineweaver-Burk technique improved it. I just have general understanding of what they are. |

- | + | --[[User:Carmen E. Castaneda|Carmen E. Castaneda]] 23:49, 6 February 2011 (EST) | |

+ | |||

=== [[User:James C. Clements|James C. Clements']] Journal Entry === | === [[User:James C. Clements|James C. Clements']] Journal Entry === | ||

- | # | + | # The purpose of this assignment was to learn more about the effect of reaction rates on enzyme kinetics using the Michaelis Menten model. The value for the reaction from the enzyme-substrate complex going back into enzyme and substrate was adjusted, as was the constant for the reaction going from enzyme-substrate complex into product. |

- | # | + | # The Matlab programming came most easily to me. |

- | # | + | # The terminology section was the most difficult for me to understand. I got a little hung up on how to define a chemostat reactor and how to define the Lineweaver-Burk experiment. |

- | # | + | # I don't understand why we're using the Lineweaver-Burk plotting method for measuring enzyme kinetics. The [http://en.wikipedia.org/wiki/Hanes-Woolf_plot Hanes-Woolf plot] seems to be regarded as a superior method. Furthermore, the use of such plots has been made obsolete by nonlinear regression techniques; I'm sure that MatLab is capable of doing a nonlinear regression and giving us the parameters that we're looking for. |

- | + | [[User:James C. Clements|James C. Clements]] 16:56, 6 February 2011 (EST) | |

=== [[User:Nicholas A. Rohacz|Nicholas A. Rohacz's]] Journal Entry === | === [[User:Nicholas A. Rohacz|Nicholas A. Rohacz's]] Journal Entry === | ||

- | # | + | # The purpose of this assignment was to show the relationship of the rate factors, specifically the k<sub>-1</sub> constant, and what happened to the product and substrate when this changed. |

- | # | + | # Describing the terminology in my own words came easiest to me, not only cause matlab is the bane of my existence, but describing the terms in my own words helps me to better understand them. |

- | # | + | # Matlab was the most difficult aspect of this assignment, in particular trying to sort out the for loop. I went through several engineers trying to figure out exactly where this goes in the function. |

- | # | + | # I still don't understand matlab as a whole, I get bits and pieces but I still have trouble joining everything together to make a whole function. |

- | + | ||

+ | [[User:Nicholas A. Rohacz|Nicholas A. Rohacz]] 02:12, 7 February 2011 (EST) | ||

=== [[User:Alondra Vega|Alondra Vega's]] Journal Entry === | === [[User:Alondra Vega|Alondra Vega's]] Journal Entry === | ||

- | # | + | #The purpose of this assignment wasn to see the different effects that the paramters can have in a function. Also, to give us practice with matlab and finish the introductuion of the Lineweaver-burke model. |

- | # | + | #The part of the assignment that came most easily to me was defining the terms. I feel that they are more mathematically based than biology based, so even if I did not know what they meant, it cool to learn about them. This section of the homework did not take me too long. |

- | # | + | #The most challenging part of this assignment was working with matlab and trying to figure out how to put all the plots in the same graph. I had never really worked in matlab and writing a code, so it was not very easy to navigate through the help menu. Once I figured that out, running the code was simple. |

- | # | + | #I still do not understand how the application comes in. If it were not for the legends in the graphs, I would not have been able to figure out what the figures represented. I feel that we are modeling concentrations, but I have a very strong feeling that i am wrong. I do not understand what we are running and why it is important to us. I also don't understand the difference between the catalysis driver and the Michaelis-Menten product driver; I feel that they give the same product. |

- | + | [[User:Alondra Vega|Alondra Vega]] 17:44, 6 February 2011 (EST) | |

[[Category:BIOL398-01/S11]] | [[Category:BIOL398-01/S11]] | ||

[[Category: Biomathematical Modeling]] | [[Category: Biomathematical Modeling]] |

## Current revision

## Contents |

## Instructions

### Formatting

- Link to your journal entry from your user page.
- Link back from the journal entry to your user page.
- Sign your portion of the journal with the standard wiki signature shortcut (
`~~~~`

). - Add the "BIOL398-01/S11" category to the end of the wiki page (if someone has not already done so).

### Reflection

- What was the purpose of this assignment?
- What aspect of this assignment came most easily to you?
- What aspect of this assignment was the most challenging for you?
- What (yet) do you not understand?

## Class Responses

### Sarah Carratt's Journal Entry

- The purpose of this assignment was to practice using the Michaelis Menten model and Matlab.
- Finding V
_{max}and K was easiest for me. - Matlab remains the hardest part of the assignment for me
- I keep getting error messages in Matlab that I have trouble correcting. It can be really frustrating and I feel like I won't ever understand it on the first try.

Sarah Carratt 17:22, 6 February 2011 (EST)

### Carmen E. Castaneda's Journal Entry

- The purpose for this assignment was to put more of the MATLAB applications that we covered in class into use as well as to keep trying to understand the model of Michealis-Menten, especially when the Lineweaver-Burk approach was used.
- The easiest part of the assignment was Estimating Michaelis-Menten Parameters.
- The most challenging aspect was trying tofigure out how to plot the four different values of K
_{2}on the same graph. So I had a hard time working with MATLAB again. - I still do not understand what exactly is happening in the MATLAB programs. I don't think I quite grasp what we produce or what we are doing exactly. Also I still do not understand the programs themselves that well, like what each command does. What I mean by this is if I had to write my own program in MATLAB I do not think I would be able to. As I started to define the terms I also noticed I quite do not understand what Michealis-Menten is and how the Lineweaver-Burk technique improved it. I just have general understanding of what they are.

--Carmen E. Castaneda 23:49, 6 February 2011 (EST)

### James C. Clements' Journal Entry

- The purpose of this assignment was to learn more about the effect of reaction rates on enzyme kinetics using the Michaelis Menten model. The value for the reaction from the enzyme-substrate complex going back into enzyme and substrate was adjusted, as was the constant for the reaction going from enzyme-substrate complex into product.
- The Matlab programming came most easily to me.
- The terminology section was the most difficult for me to understand. I got a little hung up on how to define a chemostat reactor and how to define the Lineweaver-Burk experiment.
- I don't understand why we're using the Lineweaver-Burk plotting method for measuring enzyme kinetics. The Hanes-Woolf plot seems to be regarded as a superior method. Furthermore, the use of such plots has been made obsolete by nonlinear regression techniques; I'm sure that MatLab is capable of doing a nonlinear regression and giving us the parameters that we're looking for.

James C. Clements 16:56, 6 February 2011 (EST)

### Nicholas A. Rohacz's Journal Entry

- The purpose of this assignment was to show the relationship of the rate factors, specifically the k
_{-1}constant, and what happened to the product and substrate when this changed. - Describing the terminology in my own words came easiest to me, not only cause matlab is the bane of my existence, but describing the terms in my own words helps me to better understand them.
- Matlab was the most difficult aspect of this assignment, in particular trying to sort out the for loop. I went through several engineers trying to figure out exactly where this goes in the function.
- I still don't understand matlab as a whole, I get bits and pieces but I still have trouble joining everything together to make a whole function.

Nicholas A. Rohacz 02:12, 7 February 2011 (EST)

### Alondra Vega's Journal Entry

- The purpose of this assignment wasn to see the different effects that the paramters can have in a function. Also, to give us practice with matlab and finish the introductuion of the Lineweaver-burke model.
- The part of the assignment that came most easily to me was defining the terms. I feel that they are more mathematically based than biology based, so even if I did not know what they meant, it cool to learn about them. This section of the homework did not take me too long.
- The most challenging part of this assignment was working with matlab and trying to figure out how to put all the plots in the same graph. I had never really worked in matlab and writing a code, so it was not very easy to navigate through the help menu. Once I figured that out, running the code was simple.
- I still do not understand how the application comes in. If it were not for the legends in the graphs, I would not have been able to figure out what the figures represented. I feel that we are modeling concentrations, but I have a very strong feeling that i am wrong. I do not understand what we are running and why it is important to us. I also don't understand the difference between the catalysis driver and the Michaelis-Menten product driver; I feel that they give the same product.

Alondra Vega 17:44, 6 February 2011 (EST)