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Structure of biomolecules

  1. Feb 18, 2011 #1
    The question might be a little stupid but I think that since I am very new to the biological world, I must ask

    So, I am a biomedical engineering student with probably very little biology background as I entirely change my filed.

    I have biochemistry as one of my courses and the problem is that I am having problems in memorizing some Weird structures of several biomolecules.

    I remember some of the easy ones but still, those which are a little complex, they all are a little difficult to remember.

    So, any idea or easy way of getting through all those structures ?

    I was thinking about writing all those several times.
  2. jcsd
  3. Feb 18, 2011 #2


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    You don't say what chemical background you have. Nor examples causing difficulties.

    I will try and give you a brief run down when I can, but do not just learn structures separately from what they do - the metabolism and transformations. Only one thing happens at a time and most often only one part of the molecules is ever doing things. E.g. in most of the reactions of adenosine mono, di- and tri-phosphate it really doesn't matter what adenosine is! So you will be able to write the very important phosphate transfers without worrying overmuch about that part. Try and study the essential reactions and keep track of full molecular formula on the side and not all of it. I'll try and do more detail later.
    Last edited: Feb 19, 2011
  4. Feb 18, 2011 #3


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    Imagine the following experiment. Someone shows you a chess board with various chess pieces on different squares of the board for a short amount of time (say 15 sec to a minute). They then take the board away, give you an empty chess board and a set of chess pieces then tell you to arrange the pieces in the same way. How do you think you would do?

    As it turns out, expert chess players are very much better at this task than novice chess players. However, if you show the expert a chess board where the pieces are arranged in such a way that would never be encountered in a chess game, the experts do just as badly as the novices in recalling the positions of the chess pieces.

    What does this tell us about memory and recall? Obviously, the expert chess players are finding some meaning in the positions of the chess pieces that help them remember the positions better (e.g. they might see certain features like pins and forks or certain sittuations like a check or checkmate).

    Similarly, when chemists look at molecular structures, we see more meaning than just simple lines connecting letters. We see functional groups, imagine the possible reactivities of the molecules, relate how the various parts of the molecule influence its properties and may even think about the steps needed to synthesize the molecule. So, appreciating these aspects of the chemistry of the molecules can help one better recognize and memorize the molecules.
  5. Feb 18, 2011 #4
    Have you taken any Organic Chemistry?

    From what I've heard (from Professors I've spoken to who taught or attended colleges other than mine) is that Biochemistry can be taught more from a Biological perspective or a Chemistry perspective. In my school, the Biochemistry lecturer is a Physical Chemist and absolutely teaches it from a Chemistry perspective. That is also why 1 year of Organic Chemistry is a prerequisite for Biochemistry in my school.

    Being in the middle of my second semester of Organic Chemistry I can absolutely understand why this is so. Once you become familiar with the fundamental concepts of Organic Chemistry learning Biochemistry becomes a lot more systematic. Esters, amides, acids, rearrangements, equilibria and driving forces of reactions, energetics/relative stabilities etc are all things you learn about in Organic Chemistry and have to apply constantly when learning the material. After that its a simple matter of applying those concepts to biological systems (not saying there is nothing new in Biochem but it becomes a lot easier to cope with the new information if you have the solid foundation of Organic Chemistry).

    My own education went from the top down. I learned a lot of Biology and some Biochemistry then went back to do an undergrad in Chemistry. You don't realize how much stuff you don't need to memorize if you learn from the bottom up. In some ways I'm lucky because I can immediately connect a concept I learn about in Organic Chemistry to a concept I've memorized from my years of learning (really just memorizing) Biology/Biochemistry. On the other hand I know where you are coming from in that I've had to do the same thing when learning these things. Just memorize a bunch of seemingly random facts.

    So my advice is. Take a year of Organic Chemistry and then go learn Biochem. Unfortunately you may have some problems in Organic Chemistry if you haven't ever taken a General Chemistry course but I think much of General Chem which is applicable to O Chem or Bio Chem can be learned on one's own if the desire/drive is there.
  6. Feb 26, 2011 #5
    Ah well yes ! I have taken Organic Chemistry previously, I did pass it but unfortunately I was weak in it.

    One of the reasons that might be behind it is that we were given too many chemical reactions or chain structures in a very short time. I thought that I could do it all slowly but in the end I had to cram it all up because of very short time. But still, I did perfectly a very detailed and a very nasty study of Benzene with all its reactions and structures, I was able to memorize it.

    Right now in Biochemistry, we have just finished the first chapter of our course, by the name of CARBOHYDRATE. So, it involves the main structure of Glucose and then many other structure like Fructose, Sucrose etc etc.

    So I sometimes mix up things, especially when I come across some sort of isomers or epimers etc.

    But still I would try to pick some of the basic points out of what you guys have just said.
  7. Apr 13, 2013 #6
    You can look at the SCOP database or CATH database because they show you how to describe structure. It may be a little more detailed than you need though. Search TOPS protein topology as well. It has to do with splitting the protein in domains, layers, betas, alphas, facing up, down, order of the beta sheet, etc.

    bioinfo.rpi.edu click on teaching: molec modeling

    edit: sorry, this was only for proteins. ignore this.
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