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AMINO ACID HELP PLEASE!!!

Discussion in 'MCAT Discussions' started by defendingsilence, Aug 4, 2015.

  1. defendingsilence

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    I'm one of those people who like understanding concepts and applying them...I suck at detail.
    One of my Kaplan instructors told me it would be beneficial to memorize everything we can about amino acids (structure, PI, side chains, etc.). Does anyone have a good resource or summary of all this that they would be willing to share? I'd appreciate it so much
     
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  3. BerkReviewTeach

    BerkReviewTeach Company Rep & Bad Singer
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    Please forgive me for my rant (semi-rant I suppose) in advance. Every day there are threads about amino acids and questions about what information is necessary. Eventually someone is going to post the phrase "do a search", which is generally not helpful to the original poster who likely did a search and failed to find what they had hope to. It's a cycle that needs to be altered by asking more specific questions. Everyone needs to realize that the community at SDN is different now, in that as of April there were no longer experienced test takers posting, but instead a bunch of people speculating. Truth be told is that some of them were off the mark and this is just now coming to light as a few more people posting have taken the current exam. So in asking what you need to know, you are likely going to get a response from someone who has not actually taken the exam (or tracked the exam).

    I know it's unnerving when people say "know everything", but it's pretty much the consensus. The few people who have taken the MCAT and then posted here afterwards have mentioned that you need to know as much about them as possible. Things like the 3-letter abbreviation, the one-letter abbreviation, the side chains, the rough pKa values, the pI values, the classification, details about key amino acids, and ones that impact tertiary and quaternary structure. If you don't know this material, take the time to learn it. Asking for people to assemble it for you is not going to help in the long run. You can assemble it from pretty much any of the four reputable review books (BR, EK, Kap, TPR) and doing so will help you recall and apply it.

    We are slowly becoming a generation looking for pdf hand-feeding of all information. There is so much utility in doing stuff for yourself, especially if you have a specific learning style like you mentioned. Each book approaches this topic a little differently. If you find the one that matches your style and then make a review sheet as you see it, then you'll have the perfect one for you. I don't want to come across as harsh, but ever since the switch to the new MCAT, there has been a change in the general attitude around SDN. I know that uncertainty-induced anxiety plays a big part, and that is compounded by some misinformation that flies around. Part of this is because the AAMC doesn't necessarily know what they plan to do as well as a couple of posters making bold statements that just aren't right. This exam is new to AAMC too, and like every project, you know it has snags and some missed deadlines. Granted, this is the third major change I've witnessed, so I'm a bit numb to the fact that what they list in their guide and show on their exams may not match what they do for a while. But they know they won't get this work-in-progress to a point they like for a few years.

    For now, just know everything you can and learn to apply everything to weird situations and experiments. This will prepare you well. When you read comments at SDN, check to see if they are from someone who has already taken the new MCAT.
     
  4. Ad2b

    Ad2b SDN Gold Donor
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  5. dushash

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    I think AAs are one of easiest thing to learn during MCAT preparation, simply because you have to just memorize them. There's 20 of them - if you follow the advice of previous poster (Ad2b) and draw them 3 or 4 times so you can do it even when woken up at night. Learn what groups they are organized by: Polar/Non-polar, Neutral/Acidic/Basic and learn how to calculate pI. Learn small perks that some of them have. And basically that's it. It all can be done in 1 day. IMHO AA's are nothing compared to Metabolism chapters at the end of BioChem.
     
  6. defendingsilence

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    I appreciate what you have to say, I really do...but you make me sound like someone looking for a freebie. The reality is that I've gone through the chapters and made my notes, however, they were about general characteristics, concepts, not specific numbers. When I talked to my instructor, I came to know that I needed to know the specifics. We're all here to do well on the MCAT and to support others to do the same. Thus, I turned to this forum because I was wondering if anyone had the resources which could help me...if there wouldn't have been an answer, I obviously would have done it myself. You call this a community and then call someone out for asking for help...forgive me, but I fail to understand that.
     
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  7. defendingsilence

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    thank you for the input! :)
     
  8. defendingsilence

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  9. Ad2b

    Ad2b SDN Gold Donor
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    @defendingsilence - click on that link I posted. That is my blog (I'm not sending people there for traffic, I'm here to help).

    I did very, very well in biochem up until my final (family drama).

    Take what people say with a grain of salt, many are frustrated because we're all asking similar questions and panicking and being neurotic and panicking...

    Go draw what I posted. Send me a PM and I can walk you through it. My biochem professor (honors and accolades follow him every single year) taught me this in less than 3 minutes and by the exam, I could draw in less than 5 (still can - even 3 years later).
     
  10. defendingsilence

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    I promise to look at it soon and PM you. I really appreciate you being so helpful. Thank you again!
     
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  11. Ad2b

    Ad2b SDN Gold Donor
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    Why is methionine so important?!??! (start codon - AUG - are u going)

    What is difference between Phenylalanine and Tyrosine? (OH group at bottom)

    Why did I draw NH3+ and COO- instead of the way every other book does it? (to show where electrons predominantly come off or attach for R-groups in building proteins). :)
     
  12. tturchi51

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    Non-polar, polar, basic, acidic. If you can memorize which 20 AAs goes into which category then you should easily be able to use your conceptual ability to figure out any question asked. Example...

    Which of the following would suck at spanning the lipid bilayer?!?

    A. any nonpolar AA

    B. a different nonpolar AA

    C. a polar, water loving, hydronympho AA

    D. nonpolar AA


    Yes the answer choices may seem stupid, but you can look at every AA that way if you know your concepts! And as far as abrv. go there are only 4-5 that are confusing. But once again mnemonics to help save the day!

    F-Fenylalanine, the professional proline got to choose the P first

    tYrosine-Y, tWyptophan-W-speech impediment

    AsparDic acid-D..... get your mind out the gutter!

    Lysine-K+, lysine is basic and has a + charge just like K+!

    Rgenine

    GlutamEEt you!

    Qtamine-not as cute as me or these mnemonics I just came up with ;)

    I have a very good mnemonic for remembering them but its kinda vulgar so if you want it pm me.
     
  13. Cotterpin

    Cotterpin Gluconeogenesis Evangelion
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    I would also recommend to make yourself some flashcards of the structures, their abbreviations, their pKa's, and which group they're in. Just making the flashcards helps you learn the info. Then run through the flashcards once a day for about a week and you will know them all. I recommend downloading a flashcard app like Anki or Flashcard Machine (which lets you upload pictures to put on the flashcards) and then you can practice them on your cell phone while you're waiting on line at Chipotle or whatever.
     
  14. BerkReviewTeach

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    I apologize, because my comment was a result of a build up over the last few days and was meant as a general statement. The truth of the matter is that I did assume that you were looking for someone's list, as many others have too, but that's because you said "Does anyone have a good resource or summary of all this that they would be willing to share? I'd appreciate it so much." My point is that a list can float around, but it provides a false sense of security. Ad2b is absolutely right that you need to draw them and add details. Just that activity will help you immensely.

    Granted, I'm coming at this from a perspective associated with my experience, but the specifics (numbers, structures, protein interactions, and special information) are part of both our books and our lectures. It's a core item, so if you happen to have our books laying around I'd say you should simply make a sheet in your own writing of all the information in the amino acid section of either the organic II book or the Bio II book. That is exactly what you need to know. I assume the books from the other three companies have similar numbers and details.


    I apologize for my tone, but at the same time a community sometimes is about candor. Sometimes it's about emotional support, sometimes it's about sharing ideas, sometimes it's about helping with questions, and sometimes it's about telling it like it is. I am very sorry that this came across wrong, but I've been doing this a long time and have seen what has made students successful and what has not worked. I am a firm believer that people who write their own notes do very well. I've seen it over the years. I've had students write questions following their notes and then come to ask about them. They have generally done exceptionally well. The MCAT is a thinking exam, and the more time a student spends thinking, the better the test goes for them. I really am sorry and feel terrible if it was deflating. Please accept my apology and know that I meant it with no personal ill will.
     
  15. BerkReviewTeach

    BerkReviewTeach Company Rep & Bad Singer
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    Not every book :happy:
     
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  16. Ad2b

    Ad2b SDN Gold Donor
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    My drawing was free though :)
     
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  17. defendingsilence

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    I understand, I think we both misconstrued the tone. Apology accepted and warm regards.
     
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  18. gannicus89

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    I made flashcards. Full name of the amino acid on one side. Side chain, isoelectric point, pKas, three-letter, and one-letter abbreviations on the other side. You MUST know the three-letter and one-letter abbreviations... Prioritize this as well as which category each side chain falls under, i.e. polar, nonpolar, aromatic, etc. Also, have a good understanding of how buffering works. I highly recommend the Khan videos for this part. As others have mentioned, you have to write it out yourself. Using other people's notes can be convenient, but it won't be as effective as you writing it out yourself. Days before my MCAT, I was drawing side chains all over the place lol.
     
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  19. PomiliaAnthony13

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    I am pretty certain that Isoleucine is drawn incorrectly. I haven't looked at anything else. Be careful...
     
  20. lmladdno84

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    Isoleucine is correct. Be careful.
     
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  21. mikil100

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    I wouldn't bother with memorizing the PI of each amino acids. Just remember your acids, bases, STRUCTURE FOR ALL, naming (all 3 ways).
     
  22. Dobechance

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    Head Honcho at TBR told us about Principles of Biochemistry by Lehninger. This or any similar biochem book have a section dedicated just to AA and everything about them. It has been real helpful for me in my prep so far.
     
  23. UNMedGa

    UNMedGa I’m sorry. I-I get lost in my eyes.
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    Polar:
    Threonine (Thr)(T)
    Serine (Ser)(S)
    Asparagine (Asn)(N)
    Glutamine (Gln)(Q)
    Cysteine (Cys)(C)

    Nonpolar:
    Alanine (Ala)(A)
    Leucine (Leu)(L)
    Isoleucine (Ile)(I)
    Proline (Pro)(P)
    Valine (Val)(V)
    Glycine (Gly)(G)
    Methionine (Met)(M)

    Aromatic:
    Phenylalanine (Phe)(F)
    Tyrosine (Tyr)(Y)
    Tryptophan (Trp)(W)

    Basic:
    Lysine (Lys)(K)
    Arginine (Arg)(R)
    *Histidine (His)(H)
    *(pKa is about 6, so it is only slightly basic and acts as a good proton exchanger under physiologic conditions)

    Acidic:
    Aspartic Acid (Asp)(D)
    Glutamic Acid (Glu)(E)

    Here's a chart:

    [​IMG]

    Don't know the molecular weights, but know the rest (including, generally, where the pKa is, basic side chain = higher pKa, acidic side chain = lower pKa)
     
    #22 UNMedGa, Aug 14, 2015
    Last edited: Aug 19, 2015
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  24. defendingsilence

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    You are a gem. Thank you very much.
     
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  25. UNMedGa

    UNMedGa I’m sorry. I-I get lost in my eyes.
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    No problem. Best of luck - the AAs are definitely a high yield topic so know them well!
     
  26. PomiliaAnthony13

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    Oops, my bad.
     
  27. kanda1o

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    Not sure if this has been posted... But this is a quick way to get practice on recalling AA's! http://www.sporcle.com/games/sproutcm/amino-acids-from-structures

    And you can set it to test for Three-Letter abbreviations, or the one letter ones too!


    Some odd tips my post doc taught me a few years back about memorizing AA's: (for the ones that I used to get mixed up all the time)

    Asparagine, Glutamine, Aspartic Acid, Glutamic Acid: The two ones that start with A - (asparagine, and aspartic acid) have a 2 carbon R group. While the two that start with G - (glutamine and glutamic acid) have a 3 carbon R group

    Also, if the R group of these 4 have a carboxylic acid group, it's the acid. (aspartic Acid and glutamic Acid). If it's the amide group, it ends in "-ine", (So, asparagine, and glutamine).

    Not sure if there are specifics that are tripping OP up.. but I know when I was memorizing them, those 4 always screwed me up.
     
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  28. BerkReviewTeach

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    I love your type of post kanda. It's better than straight memorization, because you are giving people a way to visualize the structures and think their way through remembering. Almost like you're telling us that Glu (E) and Gln (Q) are part of the 3G network.
     
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  29. sweetome1

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    Great stuff. I think it's very frustrating that people who haven't taken the exam are giving out advice (which a lot of the time is flat out wrong!)

    For example in another thread @Ad2b was telling people to memorize fine details of metabolic pathways (literally telling someone to draw it all out and memorize mechanisms and structures) yet hasn't taken the exam and has been posting about how poorly they have been doing on the practice exams.

    I've just learned to take everything with a grain of salt. There are people out there who don't bother to look at SDN or reddit or even take the AAMC fl and still do very well, it's all about balance.
     
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  30. Dr. Adamantium

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    Pardon me if I am wrong, but I thought methionine and glycine are non polar?
     
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  31. LakridsA

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    Thats what I thought too
     
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  32. kanda1o

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    Methionine and glycine have non-polar side chains
     
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  33. Ad2b

    Ad2b SDN Gold Donor
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    Wow, called me out in your 1st post? :) I'm honored. BTW, my poor might just be another person's hallelujah. Also, I like to encourage people not beat them down when they are already struggling. You?
     
  34. sweetome1

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    Not my first post, just lost my password to my other account. I'm not trying to beat you down, I'm was just giving an example that was fresh in my mind as I was reading through the August thread. I was just making an observation.
     
  35. Ad2b

    Ad2b SDN Gold Donor
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    Does this help you? I got a 125% in Biochem - the class, not the MCAT.

    And yes, you did make it a point to call me out, and if you read through the plethora of other threads on what was tested topic wise, you will see exactly what I posted is correct. By adding in that you understood my scores to be poor, and by inference, people should not listen to me, you called me out again.

    When my biochem prof - still a prof, still on the adcom of that school - told me to draw, I questioned him. Probably even gave him a weird look. But he is awesome. He has been doing this for years, so I listened. Bought some really good colored pencils and instead of trying to memorize everything, I drew. A lot. This past weekend, I was screwing up a system because I "memorized it" rather than learned it. So I drew it.

    I am not here - ever - to harm someone's study skills, habits, or anything else. I am here to help. That's it.

    Kaplan
    Diag 495 122/126/123/124
    FL 2 501 124/125/126/126
    FL 3 505 126/126/127/126

    I *AM* trying to get above 516 on the actual exam and a bit freaked out I cannot get that dang CP up.
     
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  36. sweetome1

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    You should focus more on studying for the MCAT, not studying precisely on what your biochem classed asked you to study for.

    (It's also interesting that in the September thread you said you got less than a 503 in fl3 -- made reference to doing worse than someone else -- but now you magically have a 505.) Another reason why you have to take everything you read on SDN with a grain of salt. People are always inflating their scores, to prove what? Who knows?? Lol
     
    #35 sweetome1, Aug 19, 2015
    Last edited: Aug 19, 2015
  37. UNMedGa

    UNMedGa I’m sorry. I-I get lost in my eyes.
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    This is something that I think is a bit confusing. I'm thinking of the 5:1 rule, whereby there should be 5 carbons for every polar/hydrogen-bond capable group in the molecule. Because of that the AA's overall should be polar. However, another poster was correct in saying that the side chains by themselves are nonpolar. I suppose that's the more important distinction (since the C and N groups don't determine the behavior in a polypeptide) so I'll go in and change it
     
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  38. geronimo11

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    Posted this in the September thread, figured I'd post it here too. Feel free to add or edit anything to/on the list.

    Grouping
    Nonpolar, non aromatic
    o Gly (G), Ala (A), Val (V), Leu (L), Ile (I), Met (M), Pro (P)​
    • Aromatic
    o Trp (W), Phe (F), Tyr (Y)​
    • Polar
    o Ser (S), Thr (T), Asn (N), Gln (Q), Cys (C)​
    • Acidic
    o Asp (D), Glu (E)​
    • Basic
    o Arg (R), Lys (K), His (H)​

    Hydrophobic (found in protein interior)
    • Ala (A)
    • Leu (L)
    • Val (V)
    • Ile (I)
    • Phe (F)

    Hydrophilic (found on protein periphery)
    • Asp (D)
    • Glu (E)
    • Arg (R)
    • Lys (K)
    • His (H)

    ~ Side chain pKa
    • Tyr (Y): 10.5
    • His (H): 6.0
    • Cys (C): 8.4
    • Asp (D): 3.9
    • Gly (G): 4.0
    • Lys (K): 10.5
    • Arg (R): 12.5

    Isoelectric point
    • Acidic AA’s (D, E)
    o pI around 3​
    • Basic AA’s (R, K, H)
    o Lys and Arg around 10
    o His around 8​
    • Uncharged AA's
    o pI around 6
    • Cys, Asn, Phe: 5-5.5
    • The rest: 5.5-6
    What has a charge at physiological pH
    • Acidic AA have (–) charge
    o Asp (D), Glu (E)​
    • Basic AA are (+) charged
    o Arg(R), Lys (K)
    • Note: His is uncharged NOT charged at physiological pH due to it's side chain pKa being around 6
    Special characteristics
    • Histidine – Can act as buffer in physiological range
    • Cysteine- Disulfide linkages, prone to oxidation
    • Methionine – Start AA
    • Proline- Can introduce ‘kinks’ into structure
    • Glycine- Achiral
     
  39. ChrisMack390

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    Like others have said, I plan to know the side chains, the 'categories' (polar, aromatic, acid, base, etc.), and any special characteristics. I will also know special characteristics and abbreviations.

    Not memorizing PIs or pKas, that is silly. Just know how to calculate them and generally know that if the side chain is acidic the PI will be low and things like that.
     
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  40. kanda1o

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    Thank you for this!

    Quick (stupid) question though.. Why is it that not all the non-polar AA's hydrophobic? Or the polar ones hydrophilic?
     
  41. BiigNerd

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    Could you possibly make this public again? Getting "This blog is open to invited readers only" when I click on it.
     
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  42. Ad2b

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    I didn't think anyone read it ... was there something you'd like to see? or read? I can repost anything from it - send me a PM and I'll respond publicly with whatever you're looking for <3
     
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  43. OchemOficionado

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    The whole thing, lol.
     
  44. Ad2b

    Ad2b SDN Gold Donor
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    See, it started out to help others and sort of be cathartic as I talked about my journey to med school... it became really personal.

    So... that said, it's public again. :oops:
     
  45. OchemOficionado

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    Thank youuuuuu :)
     
  46. Ad2b

    Ad2b SDN Gold Donor
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    yw ... I hope it helps in some way :)
     
  47. rabbott1971

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