Hi! I'm a medical college student in Korea and I'm currently studying biochemistry. I've been struggling with my studies and just happened to click this video. It was extremely helpful -better than my lectures actually :) and thank you sooo much for your wonderful work!!
Spring 2019, final quarter in the enduring Ochem series. You have enlightened my knowledge and your tutorials are a great supplement to my lecture notes. Thank you so much Leah it's been a great year following your channel. BIOCHEM here I come!
Thank u so much Leah.....I am planning to start my post doc career in protein chemistry and thought of brushing up the things I read long back...came across your videos and i wish if i could get back my college days again..u r a damn gud teacher..i must say...all the very best..keep going and uploading such wonderful tutorials..
This has truly helped with my molecular cell biology class. You make something that is complicated in class and simplify it and make it easy to understand. I really appreciate it!
By far the best videos for biochem! Your explanations are the best, they always flow perfectly with the content, and the visuals are on point. Thank you so much for creating this content, it truly is very valuable
Thank you so much for this!!! You are a life-saver and amazing. I also used your videos for my o-chem class last year and now for biochem! Thanks Leah!
So just an update! Idk if someone else has mentioned this: the MCAT now provides you with either pI or the needed side-chain pKas. You don't need to memorize them.
@@essencie5753 Kaplan MCAT biochemistry book states that you will "not be expected to know exact values for isoelectric points or side chain pKa values. The MCAT will either provide you with numerical data to use in answering questions or test clear cut distinctions that can be made without additional information."-6th edition, 2019. Kaplan is credited to be a reliable source for MCAT prep (rivaled only by Princeton). Obviously, you will need to know what the properties of the AA are (acid/base/NP/polar), and from that, you can estimate where pKas and pIs are (Generally, acid pIs are less than 7 while basic group pIs are above 7). I hope this helps! If you feel you don't want to take any chances then ofc go ahead and memorize but it should be intuitive :)
Kaplan has caused quite a few of my students to miss questions because of this statement. You do, in fact, need to know approximate values as I teach here: leah4sci.com/amino-acid-charge-in-zwitterions-and-isoelectric-point-mcat-tutorial/
thank you so much for these videos i’ve been struggling with this exact concept and simply watching your video on the bus has cleared it up. thank you so much !!
Formal charge is the charge on each individual atom, net charge is the total. For example glycine at pH = 7 has a net charge of zero, but a formal charge of +1 on the amino N and -1 on the carboxy C
I rarely comment on these videos but I had to. I've been struggling with this topic in my biochem class and this one video just solved it! Glad to know you're so clear because I'm starting to study for the MCAT. Thanks soooo much :) Wish you the best!
How is it that (Glu) and the Alpha-Carboxyl group is neutral (0) at 16:55 but (ASP) and the Alpha-Carboxyl Group are (-1) at 3:03? Can you explain why is it like this in this case?
The charge of the carboxyl group changes, depending on the pH of the solution it is in. If pH > pKa of the carboxy, the group is deprotonated with a -1 charge. (As is the case with Asp at 3:03.) If the pH < pKa of the carboxy, the group is protonated with a neutral charge. In the case of Glu at 16:55, pH = pKa, so the charge is in between -1 and 0. You'll see the charge of Glu is -1/2 at this point in the video.
can someone pls explain me why when it's positive it represents a basic amino acid and when it's negative it represents an acidic amino acid and in louis defenition of acids and bases it's totally the opposite i mean the acid should be positive and able to have electrons and the base should be negative and able to donate electrons ?
This is a tricky concept. the charge comes from how you see the side chain at physiological pH, however if you look at each R group in it's neutral state you'll see how they clearly follow the rules for acids and bases. For example: Gluatamic Acid has an acidic H+ when neutral, but a pH = 7 it has acted as an acid does and donated the H+ giving you a negative conjugate base. This is the deprotonated form OF the acid
Hello, thank you for another very helpful video. You did saythat we have to memorize the pKa for every amino acid side chain, but you made a comment on your website that we do not. Which one is it? Here is the comment for reference: "I would not. I’d know a general amino side chain, general carboxyl side-chain, acid/base and Histidine since it’s so close to physiological pH and therefor exists as a 10:1 ratio in many cases".
Yes and no, the key is to memorize a few key values as I explain in detail here: leah4sci.com/amino-acid-charge-in-zwitterions-and-isoelectric-point-mcat-tutorial/
Since the pH of 4 is equal to the pKa of the Glutamic acid side chain, we find that about half of them are protonated in solution and half of them are deprotonated. Remember that a protonated carboxy group carries a neutral charge of zero, while a deprotonated carboxy group carries a -1 charge. Halfway between 0 and -1 is -1/2.
I'll be happy to! When protonated, the carboxyl group is neutral and appears with its hydrogen as -COOH. When deprotonated, it has a charge of -1 and appears without its hydrogen as -COO. As there is only one proton to remove on the carboxyl group, it would not be able to hold a -2 charge.
It is this exact question that the video strives to answer. The short answer is that you must compare the pKa of each ionizable group to the pH of the solution to determine its individual charge, and eventually sum these charges for an overall charge of the peptide. Is there a specific point in the video you have a question about?
Thank you so much for making this video! Very good tips to memorize and easy to understand biochemistry. Please make more videos like this. I really appreciated your hard work.
3:58 I don't understand, I thought if the Pka >pH, it will win a hydrogen for the molecule. So why did Leah write 0? because the 3 and 4 were close to each other? How do you determine when pH and Pka are close to each other?
It's because the carboxyl group in aspartate's side chain is type 1 ionization, making it neutral in its acidic form. So when pH > pKa, and it is deprotonated it has a charge of -1. When pKa > pH (4 > 3), it is protonated and has a charge of 0. It does win a Hydrogen (proton) but because it is originally -1 it becomes 0, not +1. This is opposite to type 2 ionization, for example in the amino group in the side chain of lysine where it is positive in acidic form (protonated from 0 to +1).
Yes, when pKa > pH, it does win a hydrogen for the molecule. In this case, the pKa was about 4 which is greater than the pH of 3. Therefore, the hydrogen was added to the group. It so happens that the acidic, protonated form of a carboxyl group is neutral in charge. That’s why a 0 is written. (If it were deprotonated, the carboxyl group would hold a -1 charge.)
Why does the Carboxy Group on Asp and the R-Group on Asp become (-1) when Deprotonated, but Neutral when they are Protonated? I'm very confused by this. Shouldn't the Carboxy Group on the C-Terminus have a -1 charge to begin with????
The thiol in the side chain of cysteine is considered protonated when neutral (-SH). When deprotonated at pH values greater than 8, it exists as a thiol anion. Similarly, if histidine has a positive charge in its protonated state (pH
Since the pH of the solution is equal to the pKa of the Glutamic acid side chain, we find about half of them protonated in solution and half of them deprotonated. Remember that a protonated carboxy group carries a neutral charge of zero, while a deprotonated carboxy group carries a -1 charge. Halfway between 0 and -1 is -1/2.
I cover this in detail in the Amino Acid pI video and here on my website: leah4sci.com/amino-acid-charge-in-zwitterions-and-isoelectric-point-mcat-tutorial/
Hi Leah , thanks for the Video ❤️ ..its really helpful .. i have a question ... If we have Gln , Ser, Thr, Asn in the peptid .. Why didnˋt you write the Pka for their side Chains ?
You're very welcome, glad you like it! I'm sorry, but I don't offer tutoring through CZcams comments. For help with questions like this and more, I recommend joining the MCAT Study Hall. For more details visit join.mcatstudyhall.com/ or contact me through my website leah4sci.com/contact/
Charge has nothing to do with protonating status. Instead, do a quick formal charge calculation as I teach here leah4sci.com/formal-charge-formula-and-shortcut/
Okay so the way I learned this was that you take the average of the pKas where the amino acid (or peptide) has a net charge of +1/2 and -1/2 to determine the pI. Would this not make it more accurate than taking the avg of pKas at a net charge of +1 and -1?
The approach is very similar, however you can't always count on having a pKa value AT the pH (for the + and - 1/2) additionally, how do you know which is the second pKa value to use with this approach?
Hi! I'm a medical college student in Korea and I'm currently studying biochemistry. I've been struggling with my studies and just happened to click this video. It was extremely helpful -better than my lectures actually :) and thank you sooo much for your wonderful work!!
You're so welcome, I'm glad it helped!
Can't believe how clear and understandable you can explain something. You make it all so much easier. Thank you!
You're very welcome! Glad to help
@@Leah4sciMCATwhere’s the fent pack?
Spring 2019, final quarter in the enduring Ochem series. You have enlightened my knowledge and your tutorials are a great supplement to my lecture notes. Thank you so much Leah it's been a great year following your channel. BIOCHEM here I come!
AWESOME! Glad that the videos have been helpful
Thank u so much Leah.....I am planning to start my post doc career in protein chemistry and thought of brushing up the things I read long back...came across your videos and i wish if i could get back my college days again..u r a damn gud teacher..i must say...all the very best..keep going and uploading such wonderful tutorials..
Aww thanks for your kind words! Happy to help!
This has truly helped with my molecular cell biology class. You make something that is complicated in class and simplify it and make it easy to understand. I really appreciate it!
I'm so glad to help! Thanks for the compliments. :)
I was really stressing bc I wasn't understanding much in my biochemistry course, goshhh did this helppp so so much! thank you lots !
You're so welcome, glad it helped you understand!
Incredibly clear teaching style, makes learning this a breeze.
Glad it was helpful!
This is extremely helpful! Also your voice is very soothing and relaxing.
Thank you and happy to help!
You carried me through organic chemistry, and now you are carrying me through biochem. Thank you, you're the best!
Thank you for your wonderful feedback! You're very much welcome.! :)
By far the best videos for biochem! Your explanations are the best, they always flow perfectly with the content, and the visuals are on point. Thank you so much for creating this content, it truly is very valuable
Wow, thank you! I'm so glad to here how much my resources are helping you!
Thank you so much for this!!! You are a life-saver and amazing. I also used your videos for my o-chem class last year and now for biochem! Thanks Leah!
You're very welcome! I'm glad I have been able to help you!
ABSOLUTELY AMAZING! THE BEST TEACHER EVER!!!
Thanks for your kind words :)
Thank you so much , i was really struggling with this. May god bless you and your channel ❤❤. Subscribing rn😇
You're so welcome! Thank you for watching. :)
Thank you! I was struggling with this concept and this video helped me so much! highly appreciated
You're so welcome! I'm glad to hear that it helped you understand!
You make everything so easy! The shortcut is amazing thank you Leah
You're so welcome!
wow, it's amazing what a skill you are having in teaching.
Aww thanks so much!
So just an update! Idk if someone else has mentioned this: the MCAT now provides you with either pI or the needed side-chain pKas. You don't need to memorize them.
Hey! Can you link the source that says this/ where you heard it from?
@@essencie5753 Kaplan MCAT biochemistry book states that you will "not be expected to know exact values for isoelectric points or side chain pKa values. The MCAT will either provide you with numerical data to use in answering questions or test clear cut distinctions that can be made without additional information."-6th edition, 2019. Kaplan is credited to be a reliable source for MCAT prep (rivaled only by Princeton).
Obviously, you will need to know what the properties of the AA are (acid/base/NP/polar), and from that, you can estimate where pKas and pIs are (Generally, acid pIs are less than 7 while basic group pIs are above 7).
I hope this helps! If you feel you don't want to take any chances then ofc go ahead and memorize but it should be intuitive :)
Kaplan has caused quite a few of my students to miss questions because of this statement. You do, in fact, need to know approximate values as I teach here: leah4sci.com/amino-acid-charge-in-zwitterions-and-isoelectric-point-mcat-tutorial/
Thank you so much!!! Tomorrow I have a test about PI and I didn't understand it but now I do!!!! Thank you so much!❤
You're very welcome!
u r a DIVA! u just rock it... thank u for all the help u r giving me thru ur lectures...
Oh wow, thanks so much!
I really learned more from this video the day of my exam than I have all semester
I'm glad it helped!
thank you so much for these videos i’ve been struggling with this exact concept and simply watching your video on the bus has cleared it up. thank you so much !!
Glad it helped clear things up for you, you're welcome!
Thanks a lot. You helped me save my grades.
That's awesome to hear!
Thank you ! This helped me with JEE
your way of teaching is very clear!
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This is so extremely helpful. Thank you so much!
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I've been struggling to understand this for a while, but you explained it in a very clear and didactic way...Thank you so much!!! :)
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@@Leah4sciMCAT whats the difference between the formal and net charge?
Formal charge is the charge on each individual atom, net charge is the total. For example glycine at pH = 7 has a net charge of zero, but a formal charge of +1 on the amino N and -1 on the carboxy C
Thank you for the thorough explanation!
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Thank you so much for these videos they're super helpful!
Totally worth the sub :)
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Oh my gosh Leah you're such an angel. Thank you so much. I give you my salute. I hope you can help me in my future struggles.
Aww, thank you for your kind words!
Omg this was the best explanation ever. It saved my ass on the exam. Thank you so much
You're welcome. Glad the video helped :)
THIS WAS SO HELPFUL.THANK YOU SO MUCH!
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This is so helpful. Thank you so much!
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Thankyou Ms. Leah bc of u i survived our org chem and got a high grade
You're welcome and CONGRATULATIONS! That's awesome :)
This woman may have just saved my biochem midterm grade
Fantastic!!! So happy to help!
THANK YOU SO MUCH LEAH THIS WAS REALLY HELPFUL
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Thank you!! I've been searching for hours!!!!
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You saved my biochemistry exam 😍❤️
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This is sooooo helpful! best video in this field. Thank you!
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Thank you so much 🙏🏻 really very helpful video for me. Much needed. 🤗
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Thank yo so much, this makes sense to me and I actually feel comfortable doing this now! Here's to hoping I do well on the exam
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I rarely comment on these videos but I had to. I've been struggling with this topic in my biochem class and this one video just solved it! Glad to know you're so clear because I'm starting to study for the MCAT. Thanks soooo much :) Wish you the best!
Thanks to your video I can do it in my head! (I use my fingers and it's very helpful actually)
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thank you! you explained really well!!!
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Thanks for this helpful video! Your explanations are great
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This video is very helpful. More explanation than what I learned from my lecture. Thank you so much.
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Great explanations, you're a lifesaver!
Glad to help!
in all its essence your voice is angelic.
Wow, thanks!
This is the best video ever. Thank you thank you.
Wow, thank you, and you're very welcome!
How is it that (Glu) and the Alpha-Carboxyl group is neutral (0) at 16:55 but (ASP) and the Alpha-Carboxyl Group are (-1) at 3:03? Can you explain why is it like this in this case?
The charge of the carboxyl group changes, depending on the pH of the solution it is in. If pH > pKa of the carboxy, the group is deprotonated with a -1 charge. (As is the case with Asp at 3:03.) If the pH < pKa of the carboxy, the group is protonated with a neutral charge. In the case of Glu at 16:55, pH = pKa, so the charge is in between -1 and 0. You'll see the charge of Glu is -1/2 at this point in the video.
Great job👍👍🔥🔥
Thanks!
Your videos are amazing. Thank you so much for these tips.
You're welcome!
This video is so helpful! thank u!
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Thank you lots, your teaching is best .thank you so much
You are welcome!
can someone pls explain me why when it's positive it represents a basic amino acid and when it's negative it represents an acidic amino acid and in louis defenition of acids and bases it's totally the opposite i mean the acid should be positive and able to have electrons and the base should be negative and able to donate electrons ?
This is a tricky concept. the charge comes from how you see the side chain at physiological pH, however if you look at each R group in it's neutral state you'll see how they clearly follow the rules for acids and bases.
For example: Gluatamic Acid has an acidic H+ when neutral, but a pH = 7 it has acted as an acid does and donated the H+ giving you a negative conjugate base. This is the deprotonated form OF the acid
Hello, thank you for another very helpful video. You did saythat we have to memorize the pKa for every amino acid side chain, but you made a comment on your website that we do not. Which one is it? Here is the comment for reference: "I would not. I’d know a general amino side chain, general carboxyl side-chain, acid/base and Histidine since it’s so close to physiological pH and therefor exists as a 10:1 ratio in many cases".
Yes and no, the key is to memorize a few key values as I explain in detail here: leah4sci.com/amino-acid-charge-in-zwitterions-and-isoelectric-point-mcat-tutorial/
Very helpful! Thank you so much.
Glad to help!
Thanks for great explanation.
You are welcome!
Gdi you're an actual genius. Bless.
Thank you for your kind words :)
great! Thank you so much for the trick!!!
Glad I could help :)
We owe you money for this video thank you🙌
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out-fucking-standing video.. thank you
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I love you, thanks a lot!
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Omg thank you so so much!
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Can't thank you enough!! you are so awesome
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Thanks for putting this into English! My prof doesn't seem to know how to teach this well
LOL! I'm sorry you're having trouble with your professor, but I'm glad I could help!
I wish you the best! Thank you!
Thank you!
you are a GOD
Not a god, but thanks for the compliment. :)
Thank you Leah! You're the best. :)
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Awesome! So helpful!
Glad I could help!
Hey leah thank you so much..... You make learning so easy 😘
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thank you!!! i finally get it!!
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Brilliant!
Glad you liked it!
THANK YOUUUU
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I am thinking how lucky are those students whom you are teaching
You're the students I'm teaching! for more of my resources, check out Leah4sci.com
thanks verry much
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Thank you
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Thank you!
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You teach it like it’s learning addition. My prof made this so confusing.
I'm glad you liked the video! Thanks for watching. :)
You are awesome!
Thank you! You are too!
Beautiful!
thanks
So helpful.
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Thanks alot🥰🥰
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amazing!!
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At timestamp 17:20, why is the R side chain of glu -1/2 and not +1/2 at PH=4?
Since the pH of 4 is equal to the pKa of the Glutamic acid side chain, we find that about half of them are protonated in solution and half of them are deprotonated. Remember that a protonated carboxy group carries a neutral charge of zero, while a deprotonated carboxy group carries a -1 charge. Halfway between 0 and -1 is -1/2.
Thank you so so much ♥️🙏🌹
You're very welcome!
Could you please explain why the deprotonated carboxyl group of Glu is -1 and not -2? Doesn't COO have a -1 charge initially?
I'll be happy to! When protonated, the carboxyl group is neutral and appears with its hydrogen as -COOH. When deprotonated, it has a charge of -1 and appears without its hydrogen as -COO. As there is only one proton to remove on the carboxyl group, it would not be able to hold a -2 charge.
Thank you so much :)
You're welcome!
THANK YOU :D
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How can I know what is the predominant form of the peptide at certain pH?
It is this exact question that the video strives to answer. The short answer is that you must compare the pKa of each ionizable group to the pH of the solution to determine its individual charge, and eventually sum these charges for an overall charge of the peptide. Is there a specific point in the video you have a question about?
Wow this is the best fucking way to find the pI of a peptide. My book says to draw out this big ass table! Thanks so much!
You're very welcome! I'm glad I could help you save some time :)
Thank you so much for making this video! Very good tips to memorize and easy to understand
biochemistry. Please make more videos like this. I really appreciated your hard work.
You're very welcome, I'm so glad my resources have helped!
Thank you Mam
You're welcome :)
3:58 I don't understand, I thought if the Pka >pH, it will win a hydrogen for the molecule. So why did Leah write 0? because the 3 and 4 were close to each other? How do you determine when pH and Pka are close to each other?
It's because the carboxyl group in aspartate's side chain is type 1 ionization, making it neutral in its acidic form. So when pH > pKa, and it is deprotonated it has a charge of -1. When pKa > pH (4 > 3), it is protonated and has a charge of 0. It does win a Hydrogen (proton) but because it is originally -1 it becomes 0, not +1. This is opposite to type 2 ionization, for example in the amino group in the side chain of lysine where it is positive in acidic form (protonated from 0 to +1).
Yes, when pKa > pH, it does win a hydrogen for the molecule. In this case, the pKa was about 4 which is greater than the pH of 3. Therefore, the hydrogen was added to the group. It so happens that the acidic, protonated form of a carboxyl group is neutral in charge. That’s why a 0 is written. (If it were deprotonated, the carboxyl group would hold a -1 charge.)
please explain that why coo are neutral in cases you explained :)
Because COO- and H+
-1 + 1 = 0
bcz it takes proton.
At which point in the video? COO is a carboxylate and will have a negative charge
Why does the Carboxy Group on Asp and the R-Group on Asp become (-1) when Deprotonated, but Neutral when they are Protonated? I'm very confused by this. Shouldn't the Carboxy Group on the C-Terminus have a -1 charge to begin with????
See my formal charge video to understand what's happening here
I am trying to understand why cysteine at ph 1 didn't protonate while others protonated?
And the histidine at ph 10, too. I expected it should be negative, but instead to be neutral?
The thiol in the side chain of cysteine is considered protonated when neutral (-SH). When deprotonated at pH values greater than 8, it exists as a thiol anion. Similarly, if histidine has a positive charge in its protonated state (pH
why we choose -1/2 over +1/2 at 17:15 min? I am not clear on how to choose one over other. Could anyone help clarify. thanks.
Since the pH of the solution is equal to the pKa of the Glutamic acid side chain, we find about half of them protonated in solution and half of them deprotonated. Remember that a protonated carboxy group carries a neutral charge of zero, while a deprotonated carboxy group carries a -1 charge. Halfway between 0 and -1 is -1/2.
how do you know if it's a neutral charge?
I cover this in detail in the Amino Acid pI video and here on my website: leah4sci.com/amino-acid-charge-in-zwitterions-and-isoelectric-point-mcat-tutorial/
Hi Leah , thanks for the Video ❤️ ..its really helpful ..
i have a question ... If we have Gln , Ser, Thr, Asn in the peptid .. Why didnˋt you write the Pka for their side Chains ?
You're very welcome, glad you like it!
I'm sorry, but I don't offer tutoring through CZcams comments. For help with questions like this and more, I recommend joining the MCAT Study Hall. For more details visit join.mcatstudyhall.com/ or contact me through my website leah4sci.com/contact/
Why is the sulfur neutral when protonated?
Charge has nothing to do with protonating status. Instead, do a quick formal charge calculation as I teach here leah4sci.com/formal-charge-formula-and-shortcut/
Great!
Thank you
Okay so the way I learned this was that you take the average of the pKas where the amino acid (or peptide) has a net charge of +1/2 and -1/2 to determine the pI. Would this not make it more accurate than taking the avg of pKas at a net charge of +1 and -1?
The approach is very similar, however you can't always count on having a pKa value AT the pH (for the + and - 1/2) additionally, how do you know which is the second pKa value to use with this approach?