Time to Finish:
| Date | Duration (Hours) |
|---|---|
| 2/27/2025 | 6h: 38min |
| 3/1/2025 | 4h: 21min |
| 3/2/2025 | 1h: 17min |
| 3/3/2025 | 40min |
Week 4: Protein Design Part I
Picture Source: Bordin, Nicola et al (2023). Novel machine learning approaches revolutionize protein knowledge. Trends in Biochemical Sciences, Volume 48, Issue 4, 345 - 359
<aside> <img src="/icons/slide_green.svg" alt="/icons/slide_green.svg" width="40px" /> Lecture slides: Zhang - Protein Design - 2.25.25
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<aside> <img src="/icons/video-camera_yellow.svg" alt="/icons/video-camera_yellow.svg" width="40px" /> Recording will be updated here after the class!
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<aside> <img src="/icons/slide_green.svg" alt="/icons/slide_green.svg" width="40px" /> Recitation Slides will be updated here after the class!
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<aside> <img src="/icons/video-camera_yellow.svg" alt="/icons/video-camera_yellow.svg" width="40px" /> Recording will be updated here after the class!
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<aside> ⚠️ Please read through the full assignment before you get started. This assignment is mandatory for MIT/Harvard students and Committed Listeners
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<aside> <img src="/icons/push-pin_green.svg" alt="/icons/push-pin_green.svg" width="40px" /> Key Links: http://docs.google.com/spreadsheets/d/1AsYRLlrRLd6I8abxNHfuz1OtFTSqYZ87_kefBMsxhMo/edit?gid=0#gid=0 https://docs.google.com/spreadsheets/d/19_u8Sd8TdseHP6yAVrDSjIKf0vDU9RNH3SEACx8L22Y/edit?gid=0#gid=0
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Answer any of the following questions by Shuguang Zhang:
Okay so first I have to know what a Daltons is:
A dalton (Da) is a unit of mass used to measure very small things like atoms and molecules.
Okay so base on this it is I think pretty easy to find an estimate of what it will be.
I like to search about the percentage of meat that is protein / amino acids. and after that we can divvied by 100 Dalton to find and estimate of number of amino acids.
So, I searched “how much protein is in 100g of meat”
Base on this it seems like there is 26 g of protein in 100 g and since we want to know it for 500 g then we multiple by 5 and it will be 130g of protein.
Now I have to find the conversion rate between gram and Dalton so the question is what is the equivalent of 1 gram in Dalton?
Since we have 130 grams of protein and not 500 grams
it would be 130*6.022 * 10^23:
78.286 * 10 ^ 24 Daltons (Da)
Okey so based on these the answer would be
N = (78.286 * 10 ^ 24) / 100
So N is the number of amino acids in 500 grams of meat!
This question is kind of easy for me! The that makes our Identity as species is roughly our DNA.
When we eat other animals there are several factors that help us to not convert to them!
first our digestive system breaks everything and therefore we only absorb the materials like blocks of bricks.
second our body has a sophisticated mechanism to prevent alien DNA to integrate in our genome! so, the body is actively destroying them and also scanning the DNA to find these things and destroy them!
I would say because it has been sufficient to create life with various shapes! it seems 20 is enough for nature to build different animals! however, I would say there might be other reasons as well! so for example if there was another planet with different number of materials like nitrogen in there the nature might choose different type of amino acids! so, nature is trying to find what works! and in here it seems these 20 works!
Sure! the main difference between amino acids are in the R group and we can for sure create new ones with different R group!
Let’s use an amino acid as a start point and change it to make a new one!
Let's use Phenylalanine!
Let’s add another Ring! (I don't know if it can work or no!)
I don’t Know! this is a hard question! 😂
like any other molecule like water! they are combinations of atoms! and earth in different environment there is always conversion of different molecules to each other and that can certainly create an amino acid!
Ref: https://www.ph.unimelb.edu.au/~dnj/jl/jl99/sld005.htm
I don’t know what exactly alpha- helix is also I don’t know what is D- amino acid so have to search about that as well!
D-Amino acids are amino acids where the stereogenic carbon alpha to the amino group has the D-configuration. For most naturally-occurring amino acids, this carbon has the L-configuration. D-Amino acids are occasionally found in nature as residues in proteins. (Ref: https://en.wikipedia.org/wiki/D-Amino_acid#:~:text=D-Amino acids are amino,nature as residues in proteins.)
If light is rotated clockwise (to the right) it's called dextrorotation. If light is rotated counter-clockwise (to the left) then it's called levorotation. You can remember this because the word 'levorotation' starts with 'l' just like the word 'left' starts with 'l'. (Ref: https://study.com/academy/lesson/rotational-direction-of-plane-polarized-light-dextrorotation-levorotation.html#:~:text=If light is rotated clockwise,' starts with 'l'.)
(Ref: https://www.google.com/url?sa=i&url=https%3A%2F%2Foldsite.pup.ac.in%2Fe-content%2Fscience%2Fzoology%2FMScZoo42.pdf&psig=AOvVaw38FZ9svfFDl-ztOEsdMl8H&ust=1740758073116000&source=images&cd=vfe&opi=89978449&ved=2ahUKEwjkz_ylm-SLAxW_wgIHHWFRGc8Qjhx6BAgAEBo) base on all of these a D amino acid since the nitrogen will be on right the rotation will be like the left hand on the picture!