Re 6:26: Would 8.5 be close enough, Leah? I'm using these as my values (I've already memorized them, but I could memorize more specific values if you think it's necessary): Carboxyl: 2 D = 4 E = 4 H = 6 C = 8 Y = 10 K = 11 R = 12 Amino = 9 Thank you!!
8.5 works here! It would actually give you a final answer closer to the correct value. In terms of the MCAT, I usually say 'close enough is good enough'. That small decimal point difference won't distract you from your final answer on test day.
This is helpful, but I'm a little lost on one point. Why doesn't the OH get protonated? You say that the carboxy is already protonated but....how and why? Is it that case because it already has an H? If so, the amine group already has an H as well, and so does the R group of Lysine, so why would those become positive? Or is it because the OH has an inherent negative charge, so when protonated becomes neutral? I get the idea that at low pH everything is protonated so you add a positive charge to all things, but OH not getting it is throwing me off. Is it the case that OH will never be a +1? From my understanding, protonating the Cysteine makes it neutral because it carries a negative charge. The lysine can carry a positive charge, so that checks out. The amine group can become protonated (positive) or deprotonated (neutral). But the OH can....only deprotonate? I love your stuff! Just a little confused.
These are really good questions. The key is to recognize what is going on with each individual atom. Start by reviewing the periodic table trends to understand formal charge and how many bonds each atom can make. Then, when figuring out what to add/remove, it's simply a question of recognizing when an atom is happy and neutral, vs when it can gain and lose electrons. Here are some links to help you get started: leah4sci.com/orgobasics (the later videos on this page) leah4sci.com/formal-charge then perhaps some acid/base chemistry to really solidify: leah4sci.com/acidbase leah4sci.com/mcatacidbase
Quick question. How come if the first example the amino group is rounded to 10 but in the second example the amino group is rounded to 9? I know it is 9.5 really or something like that, but in the second examply Tyr also has a pka of 10 and so if we went from the first example rounding of the amino group then there would be two 10 pka values to consider but you just decide here that it is rounded to 9 so that it can be differen from eachother? what do we do if they are both 10 and we dont just round it down to 9 the second time? Can we just chose to make the amino group a 9 or a 10 depending if another 10 is present? I hope this makes sense, just trying to figure it out! Thanks and I love your videos!
This is a great question, the first thing is it understand how in depth to go based on how you're being tested. If studying for the MCAT or a similar exam, you only need to know estimated values and so I recommend memorizing a very simple set of numbers. However if you're studying this for biochem and your professor will take off points for being off by 0.5 or so, then you must reference the given table and/or memorize more exact values. back to the MCAT, since you won't be tested at such a nitty gritty level, the key is to recognize that 'Close Enough is Good Enough' Hope this helps
Leah I cannot thank you enough. I test next month and your videos have helped me so much
You are so very welcome! I'm so happy to hear that my videos are helping you and wish you all the best on your exam
@@Leah4sciMCAT leah i love you
Re 6:26: Would 8.5 be close enough, Leah?
I'm using these as my values (I've already memorized them, but I could memorize more specific values if you think it's necessary):
Carboxyl: 2
D = 4
E = 4
H = 6
C = 8
Y = 10
K = 11
R = 12
Amino = 9
Thank you!!
8.5 works here! It would actually give you a final answer closer to the correct value. In terms of the MCAT, I usually say 'close enough is good enough'. That small decimal point difference won't distract you from your final answer on test day.
Thank you so much for this video, ma'am. By what I understand this is a simplification of reality but very useful nonetheless.
Glad it was helpful!
This is helpful, but I'm a little lost on one point. Why doesn't the OH get protonated? You say that the carboxy is already protonated but....how and why? Is it that case because it already has an H? If so, the amine group already has an H as well, and so does the R group of Lysine, so why would those become positive? Or is it because the OH has an inherent negative charge, so when protonated becomes neutral?
I get the idea that at low pH everything is protonated so you add a positive charge to all things, but OH not getting it is throwing me off. Is it the case that OH will never be a +1?
From my understanding, protonating the Cysteine makes it neutral because it carries a negative charge. The lysine can carry a positive charge, so that checks out. The amine group can become protonated (positive) or deprotonated (neutral). But the OH can....only deprotonate?
I love your stuff! Just a little confused.
These are really good questions. The key is to recognize what is going on with each individual atom. Start by reviewing the periodic table trends to understand formal charge and how many bonds each atom can make. Then, when figuring out what to add/remove, it's simply a question of recognizing when an atom is happy and neutral, vs when it can gain and lose electrons. Here are some links to help you get started:
leah4sci.com/orgobasics (the later videos on this page)
leah4sci.com/formal-charge
then perhaps some acid/base chemistry to really solidify:
leah4sci.com/acidbase
leah4sci.com/mcatacidbase
what if an aminoacid is repeated in my peptide? Thank you before hand for answering
You treat it the same way where each additional amino acid is treated on its own as if it was another AA
@@Leah4sciMCATbut they will have same pka value... Should we write it's pka two times in step 1 .. And then how to count to zero??
Thanks for helpful info
My pleasure, so happy to help!
Quick question. How come if the first example the amino group is rounded to 10 but in the second example the amino group is rounded to 9? I know it is 9.5 really or something like that, but in the second examply Tyr also has a pka of 10 and so if we went from the first example rounding of the amino group then there would be two 10 pka values to consider but you just decide here that it is rounded to 9 so that it can be differen from eachother? what do we do if they are both 10 and we dont just round it down to 9 the second time? Can we just chose to make the amino group a 9 or a 10 depending if another 10 is present? I hope this makes sense, just trying to figure it out! Thanks and I love your videos!
This is a great question, the first thing is it understand how in depth to go based on how you're being tested.
If studying for the MCAT or a similar exam, you only need to know estimated values and so I recommend memorizing a very simple set of numbers. However if you're studying this for biochem and your professor will take off points for being off by 0.5 or so, then you must reference the given table and/or memorize more exact values.
back to the MCAT, since you won't be tested at such a nitty gritty level, the key is to recognize that 'Close Enough is Good Enough'
Hope this helps
Solid video. I got a great mnemonic I'll email you a picture of.
Thank you! I love new mnemonics, looking forward to it