Tuesday, December 1, 2009
Protein Synthesis Article
We are currently learning about protein synthesis in class. I found an interesting article that I want all of you to read and write a response to. The website for the article is: http://tr1.harunyahya.com/Detail/T/EDCRFV/productId/17333/THE_FIVE_ESSENTIAL_CONDITIONS_FOR_PROTEIN_FORMATION. Read the article carefully, and in between the lines in order to figure out what the author is trying to tell us. You may post your responses as comments on this blog. Remember that the point of a blog is to get a discussion going, so read your classmates' responses and respond to them as well. This will be part of your grade.
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The article consists of guidelines that must be met in order for proteins to be made. The 1st requirement is that in order for proteins to be form one of 20 specific amino acids must be present. The 2nd requirement is the amino acids must be in sequence for successful protein making. The 3rd detail of protein formation is the differences between the amino acids in hands. There is no 1 amino acid that can be labeled as right-handed. The 4th piece of information given that is a main point is the peptide bonds. Amino acids are joined together through only peptide bonds. The final information given talks about the linear sequences and that it is important for the ability of the amino acid to do its job of forming proteins.
ReplyDeleteIn the end, the author tries to convey the importance of these 5 conditions when it comes to making proteins.
Hey guys, can someone elaborate more on the linear sequences. Thanks.
In this article the author is trying to say that there are twenty specific amino acids that have to be in a specific area and location in order for a protein to form; if only one different (out of the twenty) amino acid comes in and if one of the amino acids are not in it's designated location, then the entire protein will not form. Then, only left handed amino acids can be used and again if only one right handed amino acid was used, then the protein will be unable to function. Amino acids are bonded through peptide bonds, different from all other bonds which are mostly covalent (in nature). Also, they cannot dissolve unless exposed to high temp. or strong acids. This type of (peptide) bond makes proteins strong and tough. Last of all, amino acids have to have a "linear" structure or else they are just pieces of strings connected together that do not matter at all(cannot have any chains). Thus, the author is trying to say that all these conditions have to be met and if there is a problem in just one, then the protein will not form.
ReplyDeleteRESPONSE QUESTION: What was the point of the Experiment that Sydney Fox conducted?
hie
ReplyDeleteThroughout this article, the author is introducing to his readers the five most essential conditions in protein synthesis. As I read the article, I saw how something so small in size required specific instructions, for instance out of the 200+ amino acids found in nature, only 20 of them can be selected to produce a protein. For awhile, constructing an amino acid-to me- sounded like building a large monument, everything must be in proportion ,or the final result will be a failure. The first condition can be summarized as the importance of withholding the 20 specific amino acids in the equation-if any other amino acids (from the 200+) are selected to be placed into the equation, the protein will not be created. These conditions function as a car-like assembly line, going from one station to the next. For example, if the car in the process did not have the engine put in before the windows, then the car would not be able to function, like this if even one part of the amino acids was not placed into the specific sequence then the protein will not be created. The interesting fact when creating a protein is that all of the amino acids involved in the process have to be left-handed. (Sorry to all of you who are right-handed you will not qualify to be an amino acid…lol) Even if the left-handed amino acids and the right-handed amino acids withhold the same characteristics, the right-handed amino acids will be rejected from the equation. (This shows that even simple items like amino acids discriminate). Moving on to the fourth condition, which requires amino acids to be bounded by polypeptides, the amino acids that make up the protein were found to be bound to each other in different ways than that of how they are found in nature. Peptide bonds can be thought of in a way as a steroid, they help the molecule to be “strong and resistant” – and they only are destroyed in very hot temperatures and by prevailing acids. Finally, in the fifth condition the amino acids are met with even more restrictions like the amino acid sequence must be linear, meaning that it must be a straight chain and cannot branch out into other chains. Curious to find how proteins are produced, Sydney Fox constructed an experiment by utilizing amino acids to create proteins. He found that the amino acids were not linear, but branched out. These amino acids were classified as proteinoids. All in all, this experiment was considered invalid. The author stressed on the importance of all of these conditions to be met before a protein could be made, and these conditions are usually met by a chance of 1 in 10^950.
ReplyDeleteDiscussion Question: If you were an amino acid, what do you believe the hardest condition to follow would be? Why?
As the first to comment, I can't really respond to my classmates, but I'll try to start a discussion of my own. Through this short, intriguing article, I learned a well amount of information. For instance, I never knew that an amino acid must meet five requirements in order to make one protein, and the chances of making one protein is so little!The first condition was pretty easy to understand. The amino acids are monomers, combining to form a polymer (protein). The chain of amino acids is called a polymer. The author clearly stresses that all 20 amino acids MUST be present in order for a protein to form. However, the 20 amino acids will form a polypeptide, then more polypeptides can come together to form an actual protein.The second condition states that the 20 amino acids must be in a specific sequence.In my opinion, the sequences of amino acids is vital to the production of a protein because each sequence represents a specific protein. So each protein has its own specific conformation. Thus, other molecules will identify each protein individually. If one amino acid is changed, then the protein may not function. As mentioned in class before, sickle cell anemia occurs because one nucleotide in DNA is changed. Due to this, the red blood cell changes shape and is unable to carry oxygen properly. The third condition is that ONLY left-handed amino acids are used in the synthesis of proteins. No right-handed amino acids are used in living matter, even though both of them have the same characteristics. This may be a result of a selection process, since it is impossible that ALL living things have left-handed amino acids. The fourth condition is that all amino acids are linked by peptide bonds (this is why they are called polypeptides). Since peptide bonds can only be dissolved when exposed to high temperature, this causes the proteins to be strong, able to handle hard conditions. Since peptide bonds are a form of covalent bonds, then they are bound to be strong themselves. The fifth condition is that the structure of the amino acids is straight. This means that it excludes any branches. Yet, in an experiment done by Sydney Fox, proteiniods where discovered. These are amino acids are not bound by peptide bonds,nor where they linear in structure. Thes where of no importance to proteins, yet these would cause amino acids to not function. Proteinoids, also called thermal proteins, where caused by the heating of amino acids. Since they are caused by high heat, then the regular amino acids may dissolve, therefore, not functioning. This article, overall, was surprisingly interesting.
ReplyDeleteGreat to see all of your comments. The author is trying to make an argument about something, and he is using these requirement for protein synthesis as evidence for his argument. What do you think the argument is for/against?
ReplyDeleteThe author uses the examples of peptide bonds and amino acid combination to argue that molecular composition and the basis of life in general is not random. This article and its evidence is used to disprove Darwanism, as well as the theories established by his followers. It is important to note the intricacies of protein formation, if one amino acid is misplaced, or the chain is arranged in a linear fashion, the entire protein will be malformed, or not formed at all. This is used to assert the reality of creationism, a scientific rule like this is not random.
ReplyDeleteHis argument is showing the many differences that can occur which can upset the formation of proteins. The overall theme also focuses on the chances of all the 5 things being set and the protein being formed. the finale statement given in the article sums most of the above writing. There is such a small chance (10^950) for proteins to be made, yet proteins are made continuously.
ReplyDeleteHyatt= I like how you brought something relatable ans amusing into the article by saying since the proteins are so restrictive they are basically discriminative.
Reama= i like how you stated that each molecule codes for a specific protein.
Badia= Good explanation on how the peptide binds are so strong and durable.
I looked up the school you guys are from...Aqsa School and found out its an Islamic School.I'm from Austrailia and also attend a private islamic school, Bait-Allah...I just wanted to say that I am soo proud that Muslim people have such a productive website! Keep up the great work.
ReplyDeleteI believe that the author is for the fact that every condition spoken about has to be met in order for a protein to form. He mainly means that if only one of those conditions were altered or some small change occurs in them, then a protein will not form and will be considered invalid. Additionally, he argues how miraculous everything is created and how unique they are. Also, even though they are so amazing and Allah made the process of making proteins complex, it is still possible and happens on a regular basis (proteins are always forming). The author shows how great and powerful Allah is by saying that even though there is a 10 to the 950 chance of a protein being formed with all the conditions, it still happens and the proteins still form.
ReplyDeleteTo comment on Taiser's question, I just want to say that when Sydney Fox conducted is experiment, he found out that if the amino acids are not in a line (linear) and not following behind one another, then the protein will not form and will basically be garbage because they are not relative to humans and does not help anything.
To comment on Hyatt's question I would say that the hardest condition would be that all of the amino acids have to be left handed. The reason why is because the right and left handed amino acids both have the exact same characteristics, and they are both mirror like images. Also, if just one of the right handed amino acids were to come into the left handed sequence, it would mess everything up and not create a protein, even though the left and right handed amino acids have the exact same make up.
To comment on Reama's response, I felt that is was nicely done and I really liked how she organized every detail and how she elaborated on all five conditions.
I really enjoyed reading your comments guys! Taiser's was simply said, yet, it was well explained. Badia also included useful information, restating each condition in simpler terms. Hyatt's comment was amusing, and I liked her examples of the left and right handed amino acids. I'm sure Hanna and Reham's comments where pretty useful, too. In this article, I think the author is trying to stress the importance of order and structure in biology and the chance of making a protein. Every single detail has been made with a purpose, some of course, unknown. Subhanallah, this article reflected how Allah (swt) created this small molecules and cause the human body to function in an orderly fashion. The article somewhat implies that life without proteins is impossible.However, the argument here may be that the production of a protein is made by chance, since producing the protein is a small chance and it must meet five conditions, NOT MISSING ANY!
ReplyDeleteThe author is arguing the fact that although many people dwell on the slim chance of a protein formation, this is not as significant as the intricate detail required to produce a protein. In a way he's saying yes, there may be a slim chance, but we must look beyond that and see how detailed science truly is. Also, he implicitly applies that God is the Most Knowledgeable, and before Sydney Fox or other scientists, He knew that poly peptides are the bonds that hold amino acids together and that amino acids must follow five conditions to create a protein.
ReplyDeleteComments: Hello, Taiser I would love to (attempt to ) explain linear. The idea of linear is that the amino acids must be straight and cannot branch out; otherwise these amino acids cannot be used in the equation to create a protein. The amino acids that were classified as not linear, but branched out, where found in Sydney Fox's experiment; however, his work was later considered invalid. Think of linear as a line...usually lines are straight otherwise there would be many curves and twists and it would be harder to travel across. Like this, the amino acids must be uniform in equation and have a straight line...hope this helps :)
Overall, everyone had wonderful comments, and I enjoyed reading them all!!
This is my response to the first article.
ReplyDeleteThe article talks about how in order for proteins to be synthesized, they have to meet these five essential conditions:
The first one is that out of the more than 200 amino acids in nature, only a specific 20 of them need to be selected; any other amino acid will result in no protein.
The second one is that in order for a protein to be made, the amino acid has to follow a certain sequence so that it can form.
The third one is that all amino acids have to be left-handed. The probability of a left handed amino acid to form a protein is 1 in 10210. Right handed amino acids result in no protein being formed.
***Can someone explain what they mean by left and right handed amino acids?***
The fourth one is that amino acids must be bound by peptide bonds. Since peptide bonds are hard to dissolve, they are strong, resistant, and perfect for the job.
The fifth one is that the chains of amino acids have to be in a straigth sequence (a linear sequence) in order to form a protein. If they are branched out then the bonds between the amino acids are not peptide and thus not as strong.
***And I know it was explained in class yesterday but can someone explain the last statment about the 1 in 10^950? Thanks!***
This is a continuation, sorry. =)
ReplyDeleteThe main idea that the author is trying to convey to the reader is that all of these five conditions have to be met in order for a protein to be formed. Even the slightest change in any of them (like the right and left handed amino acids even though they mirror each other) will alter the formation and the protein will not be made.
This is the response to the second question.
The author is trying to argue that - like he mentioned in the first few lines - that he wishes to demolish the foundations of Darwinists (im guessing he hates him or some thing) and show that proteins have to follow certain rules and restrictions in order to be made. He shows that even the slightest change in any of the conditions will stop the protein from forming. Also, based on his probabilities, we are shown that there is an extremely small possibility that a slight alteration will have no effect on the protien forming, but don't get your hoppes up! =)
I just want to say that I read all your comments and they actually helped me out a little in the things I didn't understand, so thanks guys!
A frequently referenced idea in this blog is Sydney Fox's experiment, in which an attempt to synthesize a protein was made. This was also a central idea in the Harun Yahya's attempt to make an argument for Creationism. Sydney Fox's experiment (which was mentioned in the comments as "invalid") is essential to this argument because it showed the futility of human attempts to create life, Creationists recognize and accept that man is incapable of generating life. This experiment failed, and this helps Yahya's argument progress. Another essential idea that was mentioned on several occasions in the user comments is the basis of amino acid formation and arrangement. To explain this, first, it must be noted that the author wrote this article, not necessarily to educate the reader on protein formation alone, but to use these facts as the basis for a "big picture" argument. Although these facts are important, they are used to provide the reader with a visual, solid example to prove that there is a Creator. These facts regarding protein formation are used to assert that protein formation does not occur spontaneously and without reason, but instead there is reason behind this-a Creator. The author asserts that, unlike Darwinian principles, these scientific bases are not random, as a Creator makes way for this to occur.
ReplyDelete