hello everybody my name is Iman welcome back to my YouTube channel today we're starting a new series we're doing MCAT biochemistry and so today we're going to start off with the first chapter and what we're going to do for this series because I feel like this format has been better received is we're going to do a quick review of the chapters content and then we'll jump into all the practice problems related to said chapter and hopefully we can continue this along through all of the chapters in this section in this MCAT study session for biochemistry now this chapter our first chapter is going to be focused on amino acids peptides and proteins so let's go ahead and get started with our review now proteins include a diversity of structures that result in a very wide range of functions proteins actually account for more than 50 percent of the dry mass of most cells and they're really important in almost everything organisms do now there are many different proteins with many different functions some proteins speed up chemical reactions While others play a role in defense against Invaders other harmful Invaders uh some proteins play a role in storage some play a role in transport or cellular communication or movement or structural support in the list goes on life also really wouldn't be possible without enzymes most of which are proteins enzymatic proteins they regulate metabolism by acting as catalysts they reduce the activation energy needed for a reaction and speed up reactions and that's very important considering our regulating our metabolism and making sure that the right products are being produced and that reactions happen fast enough to get said products that our body needs and sustain life now because an enzyme can perform its function over and over again without being used up that's the beauty of enzymes these molecules can be thought of as the workhorses that keep cells running by carrying out the processes of life now a human me you we have tens of thousands of different proteins each again with a specific function and a specific structure and in fact proteins are the most structurally sophisticated molecules known and just you know consistent with their diverse function they're going to vary extensively in structure each type of protein having a unique three-dimensional shape what you see here on this first page this is a protein what protein is this this is a myoglobin this is the first protein to have had its 3D structure known using x-ray crystallography now myoglobin is a protein in our heart and skeletal muscles and when you exercise your muscles use up available oxygen and myoglobin has oxygen attached to it which provides extra oxygen for the muscles to keep it at a high level of activity for a longer period of time therefore helping you complete your exercise now proteins like we said have many purposes all right and they and and they range from enzymatic proteins these will selectively accelerate chemical reactions we have defensive proteins that are going to protect against disease Invaders like viruses all right we have storage proteins they can store amino acids for example and we have transport proteins that will move one molecule to where it needs to go to function probably properly or be used where it needs to all right now as diverse as proteins are all right as diverse as they are they are all constructed from the same set of 20 amino acids and these amino acids are linked in unbranched polymers now the the bond between amino acids is called a peptide bond and so a polymer of amino acids is called a polypeptide all right now a protein is a biologically functional molecule that's made of one or more polypeptides each folded and coiled into a specific 3D dimensional structure now where we want to start when discussing proteins is by first really learning about those building blocks of proteins called amino acids once you understand amino acid as a single thing then it becomes easier to imagine one amino acid forming a peptide bond with another amino acid and forming a long chain and then having another long chain of amino acids and then those interact in unique ways to form proteins it becomes easier if we understand the amino acid as the as the building block and understand its structure so right like we said the building blocks for proteins are amino acids all amino acids they share a common structure all right an amino acid is an organic molecule right we have our Center carbon all right we have a center carbon all right and then we have an amino group this is the nh2 group that's the amino group and we have a carboxyl group this is our cooh group all right so we have an amino group and a carboxyl group both attached to the center carbon and then we have a hydrogen as well attached to the centered carbon those are three groups attached to this this Center carbon now this fourth group that is attached to the center carbon is called our side chain all right the side chain is different for every one of our fundamental 20 amino acids that we need to know for this exam all right so this figure at the right right here shows the general formula for an amino acid all right and at the center of the amino acid we have our chiral carbon it has its four different groups amino group carboxyl group hydrogen and that variable R group that will distinguish one amino acid from another date this R Group differs with each amino acid all right now this R Group determines the chemistry and the function of that amino acid all right the physical and chemical properties of the side chain is what's going to determine the unique characteristics of a particular amino acid and that's going to obviously obviously affect its functional role in a polypeptide where it's connected to other amino acids all right now we can look at these you might be wondering well God damn it Iman what are these 20 amino acids all right here they are here are our 20 fundamental amino acids there's more this is what you worry about right here for your mcap you should know the structure of every single one of these amino acids you should know their name their three letter code and their one letter code and really my best advice for learning these is consistently drawing them all the time whenever you have a free five minutes here or there draw a couple of amino acids from memory see which ones you remember all right that gives you some sort of scope of what you don't know that you should be practicing more often all right make flash cards carry them around look at them once in a while whenever you're doing anything that's mundane or you're waiting or whatever all right when it comes to memorization the more you drill it in the better all right and of course what could help potentially is learning about the different groups that these amino acids can fall under right because you're gonna you know under a category of electrically charged side chains you're going to know that there's going to be some charge somewhere right um when you're looking at on when you're looking at hydrophobic amino acids well most of the time these are going to be like long alkane chains because those are hydrophobic all right so things of this nature might help in memorizing but at the end of the day it is pretty much memorization in regards to being able to recall all 20 of these amino acids now these side chains these R groups which you see here right each one of these amino acids has a different side chain and then therefore having a different name being categorized as a different amino acid these side chains they can be polar or nonpolar they can be aromatic or non-aromatic they can be charged or uncharged they can be hydrophilic or hydrophobic and in this figure there are different classifications shown right so this classification shows you the amino acids that are charged positively versus negatively charged and then here we have these uncharged amino acids polar uncharged side chains we have a couple of special cases here we have amino acids with hydrophobic side chains in this category all right and so they they've been categorized here to some extent all right and we and we can even go you know further and categorize them some more all right we can just do hydrophobic hydrophilic and amphipathic sorry um and here's the categories for those you should also be able to know which ones are hydrophobic hydrophilic and pathetic excuse me cannot pronounce that word all right so for example alanine glycine isoleucine leucine phenylal alanine Proline and valine these are all hydrophobic all right and what you notice for most of these that are hydrophobic is that they have as their side chain usually just an alkane an alkane of some variety all right phenyl aniline right this is just an alkane it's just carbon and hydrogens nothing special there's no Oxygen there's no nitrogen there's no sulfur where there's some sort of separation of charge and therefore maybe a variety of hydrophobic versus hydrophilic these are all these all five of these for example just right off the bat notice their side chains just simple alkanes carbon hydrogens all right so you can remember those as being hydrophobic all right and then we have hydrophilic all right these are Arginine aspartic acid cytosine glutamate acid these are carboxylate containing groups this group has a sulfur um histidine serine 309 where's histidine let's take a look at what histidine looks like right here it has a ring and it has it's not an alkane based ring is it now so this sort of thing can help you remember hydrophobic versus hydrophilic for example all right and so there's diff you know these are categories that you can that that different amino acids are assigned to and it's important that you're able to distinguish hydrophobic amino acids from hydrophilic nonpolar from Polar all right fantastic so a few couple things that I want to make mention of before I jump into um the next topic really quickly some quick facts that I think are important to keep in mind all these amino acids let me erase let me erase a little bit of this all these amino acids except for one archiral all right all of these amino acids but one archiral and the one that is not chiral is glycine so let's go ahead and find glycine right here all right glycine is not chiral why here's here's our Central carbon all right let's write it down we have our amino group we have our carboxyl group and attached to it are two hydrogens therefore that carbon cannot be chiral because the requirement for chirality is that that carbon is attached to four different groups but it has two hydrogens so it cannot be chiral all the other amino acids happily abide by that rule that that Center carbon all right it has four different groups attached to it therefore all of these other 19 amino acids are chiral glycine is not chiral all right make sure you remember that now for all these okay let me erase this now for all these amino acids but one they have an S absolute configuration which one is that that's cysteine notice how these are falling under our special cases all of the other amino acids have app have an S absolute configuration right your RNs configuration all 19 other ones of these amino acids have an S absolute configuration except for cysteine all right that's an important one to know all right so we've covered these two special cases now what about Proline Proline is really interesting because all right when you have proline in an amino acid chain right a polypeptide pretend you have a bunch of amino acids uh and they're forming bonds to each other they form a chain if you have proline in this chain it's going to interact with the backbone twice with that with this ring and what that does to a polypeptide linear chain is it gives this chain a little bit of a kink it's no longer nice and straight it has a bit of a kink to it so that's the important thing about Proline to remember it interacts with the backbone the polypeptide backbone twice because of this ring formation and therefore creating a kink in the polypeptide chain all right so those are three important points about this special case category right here all right that you could get tested on so it's important that you know all right nevertheless we've we've introduced our amino acids now all right we understand their General structure let's transition to discussing acid-base chemistry of amino acids all right amino acids all right can either accept or donate protons and the key to remembering and understanding the behavior of amino acids is to remember two facts one fact is that ionizable groups tend tend to gain protons under acidic conditions and they tend to lose them under basic conditions so in general at low PHS ionizable groups tend to be protonated and at high PHS they tend to be indeed protonated all right so low PH ionizable groups tend to be protonated all right high pH ionizable groups tend to be deprotonated fantastic all right now the second thing the pka of a group all right what we're going to see here soon is that for every amino acid the side chains they have has a PKA value what is that PKA value mean well the pka of that R Group side chain is the pH at which an average half of the molecules of that species are deprotonated if the pH is less than the pka a majority of the species will be protonated and if the pH is higher than the pka a majority of the species will be deprotonated all right so your PKA value all right we'll give you information about how much of an ionizable group is is either proteinated or deprotenate depending on where your pH lies all right now because all amino acids all amino acids have at least two groups that can be deprotonated they all have at least two PKA values guess what those two groups that all amino acids have that are all ionizable it's that amino group and that carboxyl group you guessed it right all right every amino acid obviously has a carboxyl group and an amino group that's the distinguishing factor of amino acids both of these groups can lose or both of these groups are ionizable that means protons can be lost or gained all right so all amino acids have at least two PKA values now there are amino acids with ionizable side chains as well all right not glycine but other amino acids have ionizable side chains and that means that there will be a third PKA value for that I actually have a table I really like this table all right this table shows us the pka values for every amino acid all right so if you have glycine here's the pka for the alpha carboxyl here's the pka for the alpha alpha Amino alright so that's the two pkas for the amino group and the carboxyl group beautiful now you know all right now you know that once you hit 2.3 2.34 PKA all right or higher guess what that amino group loses a hydrogen I'm so sorry that amino acid let me rephrase that okay let's go back down here all right for glycine you have your Alpha carboxyl not your Alpha Amino so sorry so once you hit 2.34 pH guess what this carboxyl group now lost its hydrogen if the pH is higher than 2.34 all right before then before then that carboxyl had a nice hydrogen it was protonated as soon as it hit that PKA it high and went higher that hydrogen in the carboxyl group was lost all right that's what the pka of the alpha carboxyl glycine tells us and this is the pka for the alpha amino group in glycine so if we if we exceed 9.6 pH whenever we exceed a 9.6 pH then our amino group loses a hydrogen all right so that's what our PKA values tell us now if we had this is glycine now if we had a different amino acid for example let's take um uh aspartic acid the the or chain for aspartic acid has a PKA value of 3.86 and so that there's a third ionizable group that when it reaches that PKA that pH or higher that group loses a hydrogen too all right and so this table does a good job of conveying that now those are your you probably like those are that's a lot of numbers and for an exam like an MCAT should we know all these numbers to the exact what I would say is take a good look at this most of these groups all right have a similar number for an alpha carboxyl group deprotonation it's usually between 2.3 to about 2.6 on average maybe even just 2 to 2.6 all right within that kind of PH range you will deprotonate your carboxyl group and then looking at the pkas for your Alpha Amino well it's around 9 to 10 pH that you will then deprotonate your amino group what I would say that might be worthwhile to memorize are for a couple groups the third that have a third PKA because they have an ionizable group maybe it would be worthwhile to memorize the third PKA value for these um amino acids all right now at low ph what we see then usually 2.6 and below I mean around 2.32.6 at low PH the amino acid all right below about two let's just say below two at a low PH the amino acid is fully protonated all right your amino group has an extra hydrogen your carboxyl group is protonated all right then at pH near neutral when you're around neutral your amino group is still protonated it still has that positive charge but around neutral your carboxyl group has long lost its hydrogen all right now you have this positive charge you have this negative charge technically your your molecule as a whole is now neutral and this is called the zooter ion all right then at high pH is of course nine and above usually all right your amino group loses that extra hydrogen all right now you just have a negative charge and now your amino acid is fully deprotonated all right so let's take that same information let's rinse and repeat all right from a chemical point of view the common amino acids are all weak polyprotic acids all right the ionizable groups are not strongly dissociating ones in the degree of dissociation really depends on the pH all amino acids at least contain two hydrogens all right that will protein or deproteinate that's going to be the amino the hydrogen associated with your amino group and the hydrogen associated with your carboxyl group now let's consider the acid base behavior of glycine all right this is what we have right here shown as an example this is glycine all right let's erase this all right here we have glycine the simplest amino acid what you notice is at low ph the amino acid is fully protonated at neutral pH your carboxyl group just got deprotonated now you have a negative and a positive charge fully neutral zwitter ion amino acid now and then at really high PHS what you notice is your amino group got deprotonated and now your molecule has a negative charge all right fantastic now for the first dissociation we can actually write the following dissociation constant this is for this first process where our amino group has lost the hydrogen all right and then we can do the same thing for the second deprotonation all right and you can write these sort of dissociation constants something to note that the dissociation constant on both the alpha Hydro Alpha carboxyl and Alpha Amino they're affected by the presence of other groups that's why they're slightly different on this table all right the presence of other groups slightly shift those numbers around which is why they're not all exactly the same even though all amino acids have an amino group and they have a carboxyl group but this this R side chain actually affects a little bit what exactly the pka for the amino group is and what the pka for the carboxyl group is all right so that's something that's important to note all right the dissociation constants are affected by the presence of other groups the adjacent amino group makes the carboxylate group more acidic and that therefore lowers the pka so it gives a proton more readily than just a simple alkyl carboxyl carboxylic acid and you can see the pka of the amino and carboxyl group again for each amino acid in this table different now this dissociation that we've written here right that we've written a dissociation constant for that we can visualize here as well we can also demonstrate through a titration curve all right you can also demonstrate this through a titration curve where you can extract the pkas for the various dissociations from the midpoints of these drastic changes that happen all right when the when when you see that your curve begins and ends like so you're a midpoint here is your PKA extraction now here you have a titration curve you can extract your PK for the various dissociations on top of that you can also determine your isoelectric point this is the pH where the net charge is zero how do you calculate that easy formula pka1 plus pka2 divided by 2 is going to give you your isoelectric point all right so that's another thing that you can do so you have your titration curve you can easily extract your pkas from this and also calculate your Pi with those two PKA values now on this topic I also want to remind you of an important equation that can be used in solving and figuring out for example the pH of an amazing amino acid solution during certain hydrogen dissociations that is the Henderson Hasselback equation all right this is an equation that's it's an appropriate equation that is going to show the relationship between the pH or the poh of a solution and the pka or pkb and the ratio of the concentrations of the dissociated chemical species all right for you to use this equation the acid dissociation constant must be known and you're usually in a word problem we'll be given um a couple of these variables and asked to find the third or fourth all right now with that being said we've really talked about individual amino acids in a lot of depth now what if we have a linear sequence of amino acids connected to each other all right how do you have binding between amino acids that's the question we want to answer next now all right when two amino acids are positioned so that the carboxyl group of one is adjacent to the amino group of another they can be joined together by a dehydration reaction so with the removal of a water molecule we can form what is called a peptide bond this is a covalent bond between two amino acids and if you repeat this process over and over again you're going to have a couple of amino acids linked together and that's called a polypeptide a polymer of many amino acids linked together by peptide bonds now what you see here all right is the peptide bond all right polypeptides can range in length they can be a few amino acids to a thousand or more and each specific polypeptide is going to have a unique linear sequence of amino acids one thing to note about about a polypeptide chain is that on one end it's going to have a free amino group regardless of how long it is it will have on one end a free amino group and on the other end a free carboxyl group the free amino group end is called the n-terminus and the the side with the free carboxyl group at the end is called the c-terminus all right and again forming a peptide bond remember is a dehydration reaction now amino acids are pretty rigid and stable because of resonance all right so your peptide your polypeptide chains are pretty stable structures okay now finally with all this information we can actually talk about proteins all right how do proteins have so much functional diversity based upon these 20 building blocks and the answer lies in the complexity of the primary secondary tertiary and quaternary structures all right now in the primary structure what is considered a primary structure for proteins the primary structure is only going to consist of amino acid is only going to consist of an amino acid sequence all right when you have one amino acid connected to another amino acid connected to another amino acid and there's just a chain of amino acids connected to each other that is a linear chain a polypeptide this is just a the primary structure of proteins all right this is what's considered the primary structure of proteins now even at this level there is substantial biochemical complexity including the acidity size hydrophobicity and charge that's conferred by the different amino acids all right so even though you might think oh it's just a chain of amino acids there's still a lot of biochemical complexity to this chain all right it's not negligible all right fantastic so the primary structure are just amino acids linked together all right your secondary structure consists of these small scale 3D structures that's caused by the interactions between the amide groups in your chain so you have your polypeptide chain all right when it's a linear chain this is your primary structure what causes it to become a secondary structure is if this chain turns and and if it has some sort of dimensionality to it twists and turns where different parts of the chain interact with other parts of the chain then you form secondary structure and the major classes are going to be your Alpha helic structures all right where you have like this loop-de-loop that forms with your linear chain because now you have interactions between different amino acids at different points in your Lin in your in your amino acid chain or you can form beta pleated sheets as well all right Alpha helixes these are rat right hand coiled structures all right um and you're gonna and the way that it's held together is actually by hydrogen bonding between different amino acids that's that's one way of introducing complexity going from a linear chain to secondary structure is Alpha Helix all right and of course you have beta pleated sheets too all right and the way you can think of it which is why I really like this infograph right you can think of our primary structure as developing an alphabet now you have letters your secondary structure now you can put a few letters together to form words all right now we can move on to tertiary structure tertiary uh structure is this large-scale 3D conformation of the protein and it's caused by numerous interactions between side chains Alpha helices and beta-plated sheets so it describes the manner in which the secondary structural elements are arranged in 3D Dimensions to create like a stable molecular entity all right and the tertiary structure is really primarily due to interactions between the r groups of the amino acids that make up the protein these are group interactions that contribute to tertiary structure include things like ionic bonding hydrogen bonding dipole-dipole interactions and lending dispersion forces and so we went from a linear chain and this chain can sometimes interact with other amino acids through hydrogen bonding to form maybe helical Loops that's a secondary structure now you can have part of a protein that's a helical structure and part of the chain that forms beta-plated sheet and the interactions between this complex polypeptide this is one polypeptide can begin to form a tertiary structure all right and so like our uh um analogy right we have primary structures like where we developed an alphabet we can put some letters together to form words that's our secondary structure and then we can grab a couple of these words and put them together to form a sentence and that's how you want to think about your tertiary structure and then you have lastly your quaternary structure all right which is the arrangement of several protein subunits in a complex your quaternary structure is the interaction of different tertiary structures with each other all right and so your sentences can then turn into paragraphs all right and so that is how that is the four levels of complexity for proteins we have our primary secondary tertiary and quaternary structure fantastic so that's the review part of this first chapter in the next video we'll tackle the problems that are associated with this chapter all right let me know if you have any questions comments concerns down below other than that good luck happy studying and have a beautiful beautiful day