Thursday, February 23, 2017
In today’s lab, we made a 3D semi-permeable phospholipid bilayer cell membrane organized with polar proteins and carbohydrate chains. At the beginning, we were unsure on how to plan our model, but after researching and discussing on the structure of cell membranes, we decided to build a box-like membrane attached with zoomer tools. The building process demonstrated a pattern of measurement as we all had to agree on the size and shape of the model. Building a cell membrane based on observation was not a simple task. Many zoomer tools began to separate from each other, not to mention that we attempted to build large proteins that stick out from the membrane to show polarity between the phosphate region and the protein. Our model is selectively permeable and “semipermeable” in the phosphate region, (as we studied in class), because cellular membranes allow substances to move across with the help of embedded proteins. When we built our model, we realized how easy it is to distinguish permeability in a cell.
Connecting is an intuitive way of learning. In using zoom-tools, we were able to work almost effortlessly to create a very complex membrane. Of course, we had an underlying strategy--to build a boxlike figure that had both lipids and proteins and that was about two feet wide. But after splitting up, we were able to connect the tools to mimic different pieces of a semi permeable bilayer phospholipid membrane. In this mindless work of connecting tools, there is also a layer of imagination that takes place. In mimicking the real world, we have learned that we should not make straight lines, but vary them. This takes some imagination, but this imagination comes naturally--sometimes being imaginative is literally thinking outside the box and not making perfectly straight lines. In this lab we learned that connection and imagination are in fact connected, but both are part of our makeup.
Planning was difficult because most of the times you see a phospholipid bilayer it will be a 2d picture rather than a 3d picture. Transforming the bilayer into a three dimensional form was a real frustrating struggle but through cooperation we were able to manipulate the zometools into something that resembles a phospholipid bilayer membrane. We originally decided to design each phosphate group individually but as your suggestion stated that is not a valid strategy. Instead, we designed the exterior support structure en masse and added the core components of the bilayer later. Instead of looking at each small piece we looked at the structure in a holistic view.
As we built the proteins, we tried to form a structure that adequately represented the relationship between the phospholipid bilayer of the cell membrane and the proteins with which this barrier interacts. Throughout the process, we examined how this interaction relates to concepts of permeability, and how permeability can be applied to making the invisible visible. The form of the phospholipids and the way in which they interact with proteins are usually, literally invisible. While this lab did make the concept of a phospholipid bilayer tangible, it more importantly brought the concept of permeability to the surface. In what ways can permeability bring to the foreground things that are usually overlooked or unnoticed? Can social permeability in the form of exploration and new experiences benefit collaboration and the development of common ground? Can unexpected connections be drawn between one another, similar to the unexpected connections drawn between polar bonds and the way they shape a biological process? During this lab, trial and error were employed to explore newer and more effective ways to show phospholipid bonds. We had to structure our phospholipid bilayer multiple times, trying to create an uneven planar surface that still was representative of all aspects: polarity, fatty acid tails, protein, and the phospholipid.
This lab explored how permeability can be applied to biological process, but it also helped us to understand more about permeability, on a broader scale. With this new understanding, the concept of permeability can be used in other aspects of life (not limited to scientific application). For instance, permeability can help us to understand more about art and music. Just like permeability can help shape biological processes, it is also key in shaping how art is created, or how an audience responds to a musical performance.
Permeability can be present on both a biological level and on a societal level.
The Chinese rock referenced in today’s lab is a prime example of the intersectionality between physical permeability and social permeability. The rock exhibits physical characteristics of permeability through its porous structure, yet retains cultural and aesthetic permeability through its inclusion as a work of art.
To conclude, scientific terms are not just limited to science, and by accepting this, we are able to understand how all facets of society relate to one another.
By using the different colors, we are depicting the concept of polarity. The blue is the fatty acid tail, the red represents the polar bond, the white balls represent the phospholipid, and the large green structure represents the protein.
As a group, our most common words to describe our process are Sorting, Trying, Building, Attaching, and Creating. Building, Attaching and Creating are the most relevant to today’s lab.
When building the model of the phospholipid membrane and the protein, we obviously spent a large timebuilding the model. By trying out and fitting different pieces together, we saw the membrane and protein start to take place. But, before we could build, we had to imagine what our model would look like. By using our knowledge of phospholipids gained in class, we had a rough idea, but some google searches and sketches helped iron out our plan. We began the process by building our own sections individually, while collaborating on how the final product would look like. Eventually, we contributed to each other’s pieces, arranging and combining our separate parts into a homogenous membrane. Then, we had to build our protein, which had to go through the membrane. We thankfully had left a gap in our membrane for the protein to exist, but it took couple tries for us to figure out to how to best represent the protein. Our first attempt did not go very well, but by thinking, along with some teacher input, we found a way to represent the protein existing through the membrane, and making it defined on both sides.
We went to great lengths to make our membrane permeable. By representing it as not a box, but as a 3D, imperfect, biological structure, we hopefully came as close as we could to representing a membrane as it exists in nature. Permeability was executed by assuring that the “walls” were not solid, and that the protein stuck through the membrane, showing how phospholipids can move out of the way for the protein, then move back into envelope the protein. It is this co-existence between the membrane and the protein that assures that they can both exist and perform their requisite functions.
Learning styles differ from person to person, but everyone has a path to successful learning and an approach to the way in which they learn effectively. The past few weeks in lab--whether in the classroom or at the MFA-- we have employed our way of learning in many ways. The list of words and how we learn differed from person to person, but there was also an overlap on key words. These key words identify how though learning can be individual and different there are also similarities and patterns.
The main words found throughout our group were: building, creating, laughing, observing, and planning. Each of these five things have followed us throughout the weeks and we have built not only structures with Zometools, but friendships amongst one another. Building requires a number of pre-requisites such as observing and planning, which are two of our other five main words. At the same time, building requires nothing! There is permeability and change within everything, therefore in the process of creating we need to laugh, imagine, and pretend.
Annie and Liam began their building process laughing and creating. They decided to use the primary colors for the sticks and connected them to the white balls. They worked together to find a way to best represent a "working protein" for their model. They also understood that it required consideration and contemplation. Saed and Melissa worked first with yellow and blue sticks, but found that the lines were straight, they had to reassess the approach they were taking, but that is ok! They are on the path to learning and understanding. Pat and I worked together to make a graph and create a blogpost. We analyzed the way in which our group members worked together to represent proteins and membranes.
Through the lab in week five, our team recognized that we have different learning styles and approaches. By providing us a list of words to describe our learning, our similarities and differences were presented in front of us. Rather than impeding our learning, our differences helped us expand on our knowledge and our similarities create even more strength throughout our team. Our final product was spectacular and even more importantly, we left with a more diverse understanding of how things work.
We may not have realized it at first, but after doing all these labs, all of us used “thinking” as a way to describe our learning progress. We think all the time! We’re thinking right now. Thinking is easy, but focusing our thoughts to formulate the deliverables in all these labs requires much more. That’s where these other adjectives come in: Deciding, Organizing, Connecting, and Talking.
Talking is a way to express out thoughts. Some of us speak our minds and others keep their thoughts to themselves. The more extroverted students in the lab will speak, while more introverted students confirm or contradict their statements in their minds. Each kind of person nevertheless contributes since we all have to tweets to express our thoughts. In the end, talking is a form of verbal thought. Talking helps the entire group come to a consensus, especially in decision making.
After all the talking, we must make some decisions. In the decision making process, after all the talking has taken place, it is usually one student that decides verbally for the entire group, but verbal and expressional approval is almost always made. For example in this lab, two people decided how the structure was going to be made, but towards the end they were stuck. The rest of the group decided together that the protein should be much bigger than the two students originally thought. Decision making is still collaborative, but it wasn’t until one student in the lab made the protein with the zometools that we agreed with her.
For the first aspect of this lab it was especially important for us to organize who does what. Since there was a time limit for this lab period, it was incredibly important for us to divvy up our positions in order to maximize effectiveness. We use organizational skills every single day, from deciding how to balance our schedules to simply selecting our diet at the dining hall. While participating in lab, it is especially important that we maintain an organized group to ensure that we can complete each aspect of the lab to maximize our grades.
Connecting is a way in which we apply what we are learning in lecture to the hands-on activities of lab. Whether it was physically connecting the zometools together to create the selectively permeable membrane, or mentally drawing upon information from lecture to connect how to build the structure for images on the powerpoint in lecture. We establish connections in our daily lives outside of the classroom as well. From connecting our schedules to ensure that we get to the bus stop or T stop on time; to connecting on a mental, or emotional level with peers and friends. We as humans embrace connectivity in the classroom as well as in our daily lives.
The lab today was made up of two parts. The first part of the lab consisted of reading blog posts to get a more complete understanding of permeability. Through the writings Dr. Rita Levi-Montalcini, we were able to connect the ideas of permeability beyond the the natural world and into the way that thought and ideas can permeate in a group of people.
In the second part, we designed and built a phospholipid bilayer out of Zometools. It was difficult because we weren’t allowed to have straight lines, but through experimenting and trial and error, we were able to use the straight tools while creating a model that was more like real life. Textbook phospholipids are straight, flat and rigid whereas the ones in real life are not straight at all. The best part was fitting in the permeating proteins because one of them we actually attached to the structure but some we realized could just be placed in because they fit so nicely.
While building our membrane and protein out of Zometools, we found ourselves incorporating many of the words we later chose on the list. When building, we experimented and tried various different shapes for our creation. We comprehensively connected this building to the study of membranes, proteins, and permeability from class.
In this lab we went out to create a phospholipid bilayer the main difficulty was to try and create a symmetrical yet functional piece that formed the correct shape. Connecting the individual structures we created with the Zometools allowed us to expand our structure. In the end, our structure was a big collaboration of different sizes phospholipids with a couple of large proteins extending through it. We demonstrated the permeability of our structure with another structure by passing one through the other.
However through sheer force of will we were able to create something new and amazing. We were able to create a structure that was both functional and also able to support the proteins within it. Another particular obstacle was making it permeable and structurally sound.
Today, we had to read articles that enhanced our understanding of permeability from the perspective of art, not just biology. We chose the words laughing, building, connecting, observing, and experimenting because that is what we did during this experiment. We worked together to connect the zometools to build proteins and a phospholipid bilayer. We experimented with different shapes and forms and observed each other, accepting constructive criticism from one another so that we could improve on our work and move forward as a group. We were laughing all the while; maintaining a positive attitude is the key to the power of play, it stimulates curiosity and enhances understanding.
The focus of today’s lab was to create a permeable structure using sticks and balls. But before we started creating the structure we read several articles that expanded our definition of the word permeability. While reading the first article we realized that human beings can also be described as permeable. For example, someone that is open and has an inviting personality can be seen as permeable just as a tablecloth can be seen as permeable. After thinking about the meaning behind the second article we saw that there is a connection between the rocks holes and the permeability of our thought processes. A permeable brain is a brain that allows different ideas to flow in it and this allows us to grow as people.
Once we finished reading these articles we spent a lot of time planning out how we wanted to build the structure. Three different structures were built during the process. Two membrane structures and one protein was created using a series of patterned stick and ball formations. Once each was individually constructed, our group then proceeded to connect all of the structures into one working system. At first our group was a little confused when deciding how to begin. Should we all start arranging one cohesive structure together? Or would it be better to work individually and then connect them? We found that the best way was to split the process. We had two membrane teams and a protein team. We knew that proteins were imbedded into membranes so that was why we bonded those two together. One membrane was placed at the top of the structure and the other at the bottom. The protein stood between the two. In the end the molecule resembled one unit. The three parts were not distinguishable.
Today, what we did in lab was mostly based on the materials we learned last week and this week, semi-permeable phospholipid bilayer membrane. Therefore, we used zometool kit to build a version of semi-permeable phospholipid bilayer membrane.
Throughout the process, our group examined how this interaction between materials relates to concepts of permeability, and how permeability can be applied to our main focus this semester: making the invisible become visible. A visible form would be the phospholipids and their interactions with the proteins. We started off doing everything in pieces, eventually putting together the individual parts into one whole membrane. The protein was the hardest part to make, and because of that, we left it last.
Permeability is the exact state of a given material that allows the absorption of liquids, gases and other chemicals through the object’s membranes. Permeability and porosity, although similar as both allow for the passing of liquids, are slightly different. Porosity, is the measure of the amount of space in the object in which the liquids or gases can pass through. Examples of this would be cracks, holes or small cavities in the object. Permeability is how easily the liquid or gas passes through said cavities. High permeability allows the fluids to move more efficiently and quickly through the rocks. An example of a rock that is permeable would be sandstone because that particular rock has grains in which fluids can pass through more easily than other types of rock.
In relating to our topic on shapes and patterns. The phospholipid bilayer is a recurring pattern in nature. This is helped as it is made with hydrophobic and hydrophilic ends. These two ends form the pattern of the bilayer and it is one of nature’s own patterns. The bilayer needs to have a specific pattern and shape to allow materials through. These proteins give the bilayer the ability for it to actively and passively transport.
Overall, in this lab, by making a mini model of the phospholipid bilayer visually, it helped us provide a better understanding of how the model comes together and interacts with all of the pieces.
This lab offered an interesting perspective on semipermeable membranes as it provided us with a visual example of the bonds between the phosphate groups along with a visual example of the protein that is embedded in multiple phosphate groups. The first step in the production of the semipermeable membrane was the idea of creating a few different phosphate groups which were visually represented by the different colored zometool sticks. Each phosphate group was assigned a certain color and that color stayed consistent throughout the entirety of that particular phosphate. The next step was the connection of the different phosphate groups through the glycerol fatty acids. Once the different phosphate groups were connected the protein was embedded and connected into the membrane.
In terms of using the description words and how they applied to today's activity, the idea of connecting and organizing the phosphate groups was certainly a characteristic of today's exercise. Along with connecting and organizing, imagination was also a very key characteristic of today's exercise as it took us a good fifteen minutes or so to be able to conceptually visualize what the semipermeable membrane would look like upon creation. Once we were able to visualize what it would look like, it certainly took a fair amount of planning, talking and reasoning to physically connect the phosphate groups together. Lastly, the words that were most commonly used in today’s lab were certainly the words, organizing, communicating and connecting. These words all relate back to the idea of what a semipermeable membrane is in the first place; through the bonds and connections and organization of the phosphate groups, which make up the membrane, the proteins embed themselves into this membrane in seemingly random pattern however, at the base of it there is a highly complex level of organization.
There were many constraints that came along with this lab. One of the first things that we encountered had to do with the size of our team. Communication and planning, especially with drafting up a sketch of our model, became more difficult. It was harder to stay connected with some of us working on different aspects of the project. Some of us would be working on individual amino acids while others put together more complex proteins or constructed the membrane. We had to also work with the constraints of the zometools. There are only certain ways in which we can connect them to one another. After our initial sketch, we had to attempt to build it before redrafting to create something that worked with our zometools rather than against them. We had to choose the right sizes and arrange them in a way that they could actually attach to one another. We innovated by sticking to our jobs and cooperating with one another to create the plan we imagined. We made sure that we talked throughout the process to ensure that we were all on the same page while our phospholipid bilayer membrane and permeating protein were constantly evolving. Another difficulty that we encountered was carefully making the protein permeate the phospholipid bilayer. The pieces are delicate and prone to falling apart. When we were connecting the membrane around and through the protein, we had to be sure to be extremely delicate.
Overall, this lab was fun in the way that we had to be organized in our approach and work through the problem thoughtfully as a team. Because one of our constraints was that we were not allowed to have straight lines, Kerry and I made sure that we put the lines into the balls at certain angles. We utilized lines of all sizes to make sure everything was connected. This required some approximate measurement on our part. Overall, though, we didn’t have many constraints except for the size of the materials and restrictions of what qualifies as a phospholipid bilayer membrane. Our innovations came from making sure that our membrane was able to hold the protein we initially built.