jOeCHEMists. If you're reading this, that likely means you are close to or even at the end of your organic career. You've put in countless hours to get to this point, and if it means something, I'm proud of you. Just keep pushing--you're so close to the finish line. And, to be honest, this last section isn't anything crazy. In this series, we're getting biological. Not a ton of reactions and mechanisms to be learned here. This section is more concept driven in my opinion. And considering everything you've overcome thus far, my money is on you all to internalize amino acids, peptides, and nucleic acids without a hitch. You got this.
https://joechem.io/videos/174 for video on jOeCHEM and attached worksheet + solution (below video on jOeCHEM aka the link) This video marks our adventure into the wonderful world of amino acids (I know its a bit on the longer side but bear with me--there's good info in here). We'll start with a brief intro to amino acids, but the focus of this video will be talking about how amino acids, at the C2 position, have an S configuration in nature (most often--C2 can be R as well). We'll draw amino acids in bond line in both S and R configurations. We'll also discuss the concept of L & D amino acids and how to represent them in Fischer Projection form. There's a nice little rule we'll discover that only has ONE exception (thanks a lot cysteine), but watch on to become an amino acid master.
https://joechem.io/videos/175 for video on jOeCHEM and attached worksheet + solution (below video on jOeCHEM aka the link) In this video, we'll take a look at how amino acids react to existing in different pH environments. We'll learn how to take the "pH elevator" (something I made up that's not a real thing) to see how different pH's create or remove charges on amino acids. We'll discuss how to handle an amino acid based on the composition of its R side chain (whether its bland/boring, has an acidic component, or has a basic component). And finally, regardless of what the side chain looks like, we'll establish how to determine pI, the isoelectric pH for any amino acid situation. Helpful videos: Intro to Amino Acids - https://joechem.io/videos/174
https://joechem.io/videos/176 for video on jOeCHEM and attached worksheet + solution (below video on jOeCHEM aka the link) In this video, we'll finally look at how to synthesize Amino Acids. By taking an amide (especially one made via the Gabriel Synthesis) and combining it with a beta diester, we can reliably produce amino acids. This video features examples making alanine and serine, and while there is a lot of steps going on, we already know all the chemistry going on under the hood. Helpful videos: Malonic Ester Synthesis - https://joechem.io/videos/147 Gabriel Synthesis - https://joechem.io/videos/88 Decarboxylation - https://joechem.io/videos/146
https://joechem.io/videos/177 for video on jOeCHEM and attached worksheet + solution (below video on jOeCHEM aka the link) In this video, we tackle the Strecker Synthesis, a reaction designed to produce amino acids. The Strecker Synthesis is nice and simple, and heading into it, you know all the chemistry involved: it's taking an aldehyde, turning it into an imine, tacking on a nitrile by tossing in HCN, and hydrating the new nitrile to a carboxylic acid. Sweet and simple *chef kiss*.
https://joechem.io/videos/180 for video on jOeCHEM and attached worksheet + solution (below video on jOeCHEM aka the link) In this video, we get formally introduced to peptides and their characteristics. We'll talk about peptide bonds and why they exhibit limited rotation, making the peptide backbones rigid & planar. And, to round out the video, we'll see how to draw a given polypeptide in bond line when given the abbreviation for that polypeptide. Helpful videos: Amide Formation - https://joechem.io/videos/73 Peptide Synthesis - https://joechem.io/videos/182
https://joechem.io/videos/181 for video on jOeCHEM and attached worksheet + solution (below video on jOeCHEM aka the link) In this video, we dive into the wonderful worlds of proteins to talk about primary, secondar, tertiary, and quaternary structure. This is an oddball jOeCHEM video because there's NO mechanisms, NO rxns--just concepts. So join in on the fun, while we discuss beta pleated sheets, alpha helixes, and a whole lot more.
https://joechem.io/videos/182 for video on jOeCHEM and attached worksheet + solution (below video on jOeCHEM aka the link) In this video, we finally learn how to string amino acids together in order to synthesize di, tri, and longer polypeptides. We keep it simple in this video and only create a dipeptide, but no matter how long your peptides are, the process remains the: you need to use a protecting group of some sort, you perform the condensation rxn to stick your peptide pieces together, and then you deprotect. In this video, I protect using the popular Boc group, so let's see how it works! Helpful videos: Amide Formation - https://joechem.io/videos/73 Decarboxylation - https://joechem.io/videos/146 Intro to Peptides - https://joechem.io/videos/180
https://joechem.io/videos/183 for video on jOeCHEM and attached worksheet + solution (below video on jOeCHEM aka the link) In this video, jump into the wonderful word of nucleic acids. Specifically, we'll discuss nucleotides and how they serve as the building blocks for DNA and RNA. After getting terminology down, we'll then see how we can link nucleotides together. Helpful videos: Nitrogenous Bases & Their Pairing Pattern - https://joechem.io/videos/184
https://joechem.io/videos/184 for video on jOeCHEM and attached worksheet + solution (below video on jOeCHEM aka the link) To round out our biological journey in organic chemistry, we'll explore why the four nitrogenous bases "pair" the way they do. In DNA, Guanine (G) pairs with Cytosine (C) and Adenine (A) pairs with Thymine (T). In RNA, G still pairs with C but A pairs with U (uracil, which is SUPER close to T in structure). They buddy up the way they do because of H-bonding, and in this video we'll discuss and illustrate why that is the case. Helpful videos: Intro to Nucleic Acids--Building Nucleotides - https://joechem.io/videos/183