Biomolecules: Amino Acids, Proteins & Nucleic Acids | Class 12 Chemistry | JEE/NEET/CUET Preparation

[00:00:09]foreign welcome to the batch of Excellence at physicswala this is your chemistry teacher Sagar Derby and I welcome you to today's class that is lecture number three of biomolecules so guys I'm sure that we all are aware that we have been learning organic chemistry since quite a long time now and uh we are into a chapter that is biomolecules we have discussed a bit about this chapter earlier which basically includes all the information of carbohydrates so just to describe what we have studied in the first two session is we first started our discussion with what exactly biomolecules are then we started learning carbohydrates we saw the age-old concept of carbohydrate and then the modern way of defining carbohydrates followed by studying the classification of carbohydrates and then we studied some of the methods of preparation of glucose we studied the open tin structure of glucose as well as fructose followed by we studied the D series of carbohydrates the entire D family of carbohydrates and then guys we studied some important reactions of opentine structure of glucose after that in lecture number two we studied why it is essential for us to learn the cyclic structure of glucose so we saw in heaven projection how exactly monosaccharides such as glucose and fructose exist in the same process we also learn a term called as yes muta rotation we came across another term called as anomers in the previous class we had discussed about epimers as well and guys after that we also studied the cyclic structure of some important disaccharides and polysaccharides so what I've exactly going to learn in our today's class let me show you so today lastly we'll be discussing about amino acids proteins and nucleic acids so to begin with we'll first get introduced to amino acids then we'll see some examples of amino acids followed by preparation of amino acids then we'll talk about the dipolar form of amino acid of course we'll talk about sweater Rhymes which means and then we'll discuss about the isoelectric point as well we'll discuss about what is peptide linkage what are polypeptides followed by its hydrolysis we'll also see the structure of proteins that is primary secondary tertiary in Cotton this is going to be entirely an informative part for us so lot of data would be coming across you and I want you guys to revise it time and again so that you can remember it we'll talk about a process called as denaturation of protein of course classification of protein further this classification of protein into fibrous and globular is the same thing that we'll be discussing in tertiary structure of protein and at the end we'll be talking about nucleic acids that is deoxyribose deoxyribonucleic acid and ribose nucleic acid so everyone let us first begin with amino acids well we all are aware that proteins are one of the most important form of bimolecule that is required for the growth and the maintenance of living organism don't you know that yes so guys this protease that we talk about are the compounds of high molecular mass and these are called as biopolymer of alpha amino acids and they're found in all the living cells when you talk about term proteins it is being derived from a term called as Proteus Proteus meaning of prime importance like I said when you talk about a human body majorly or largely we say it is made up of Flesh and Bones right but we can't see our human body without flesh without muscle mass so imagining body without muscle is very difficult so those muscles are basically built by building blocks that is what you call it as proteins which means we can understand how important proteins are for the living system because they are so important we call them as Proteus meaning of prime importance other than that they have many other primary functions like they acts like enzyme which catalyzes many biochemical reactions so all those enzymes which catalyzes biochemical reactions are nothing but protein other than that hormones are again the proteins which controls the metabolic processes and another important function of protein as they act like antibodies well in these days of pandemic we all are aware of the term called as antipodies how important to have antibodies to fight against some viral infection so these are the protein molecules which basically are the antibodies that fights against the poisonous substances if you take such proteins and carry out its partial hydrolysis they first get hydrolyzed to peptides or rather you can call them as polypeptides and if you carry out further complete hydrolysis of those polypeptides they eventually gives you the basic unit that is called as amino acids so guys just like we say the carbohydrates such as starch and cellulose are polysaccharide which upon hydrolysis eventually gives you what monosaccharides so you can say starch is a biopolymer of glucose because eventually starch upon hydrolysis gives you glucose exactly in the similar manner I would say amino acids are the ones which are obtained by complete hydrolysis of protein which means protein is a biopolymer of amino acid that's the first statement from where we started our discussion so this was a basic introduction of proteins which means in order to learn protein molecules we'll have to understand its basic unit which is nothing but amino acids because it is amino acids which collectively forms a compound called as proteins so everyone let's try and understand the amino acids well I wanted to look at this Formula First you'll find we have got a compound containing carboxylic acid as well as nh2 group right further if you talk about this compound having acid as well as Amino because of which we are calling it as amino acids priority function of being carboxylic acid we are going to call this compound as a derivative of carboxylic acid hence nh2 group will be considered as a substituent but if you see the location of this substituent with respect to carboxylic acid the next carbon we refer it as Alpha hence Amino is a substitute which is present at the alpha carbon of carboxylic acid so we collectively call it as Alpha amino acids so as far as our today's discussion is concerned as far as the protein molecules are concerned we discuss about amino acids where position of amino being Alpha we talk about Alpha amino acid but just like Alpha if the position of nh2 changes from alpha to Beta to gamma to Delta you get those kind of amino acid like beta amino acid Delta amino acid gamma amino acid Omega amino acid so on and so forth but as far as our today's interest of this chapter is concerned we will be discussing about Alpha amino acids all right everyone so let us first talk about the classification of amino acids well there are several ways by which we classify amino acids per simple classification is on the basis of the requirement of amino acid look having said earlier proteins are building blocks of muscles whereas proteins we saw are made up of amino acid meaning for building muscles eventually what you required is a balanced diet containing required or essential amino acids because amino acids are the ones which are going to give you protein and the protein is going to help you to build muscle or to repair muscles which means these amino acids are the one which are essential for the maintenance or the growth of the muscles right hence based on the requirement we classify amino acids as essential amino acids and non-essentials amino acids so you can say in general around 20 amino acids exist in nature out of which 10 amino acids are the one which are required by our biological system for the growth and maintenance those amino acids which are required for the growth and maintenance we call them as essential amino acids so in fact our body is capable of forming or producing those amino acids but unfortunately the amino acids produced by our bodies are not the essential ones so we call them as non-essential amino acid because our body cannot produce those required amino acids we have to rely on experimental we have to rely on external supplementary foods which gives you the required amino acids hence probably must have seen bodybuilders and the athletes they highly rely on the external source of protein which contains the required essential amino acids so the first classification is simply on the basis of requirement that is essential amino acid and non-essential amino acid second way of classifying amino acid is on the basis of the number of cooh and nh2 group present that is how many are acidic group and how many are basic groups so if a given amino acid contains equal number of acidic coh and basic nh2 group then we call it as neutral amino acids so generally you'll find all the example that we'll be talking about here would be the one which will be containing one carboxylic acid group and one nh2 amino group we will refer them as neutral amino acid however as we'll proceed further we'll also come across some amino acids where number of acidic groups that is cooh groups will be more than number of nh2 groups such amino acids will be referred as of course acidic amino acids on the other hand if any amino acid will contain more number of nh2 groups than the acidic group we refer them as basic amino acids so guys I'm going to show you some examples here of course we have got many examples here because in case if any name comes in the examination you shouldn't be confused so let me show you some amino acids here well guys have a look at the first one is glycine symbolized as gly that is three letter symbol or sometime also mentioned as G and that's how it structurally looks now when you talk about Alpha amino acid I want you guys to recall let's say we have got function of cooh any carbon next to that we call it as Alpha carbon so that is Alpha since it is Alpha amino acid I took nh2 at Alpha carbon now the remaining two valencies one of which would be satisfied by H let's say and other could be satisfied by any side chain so we don't know what is the value of R so as you keep on changing the value of R you will get various types of amino acids and that's what we have done here just to make it simpler let's say the same structure I'm putting in this way r c h then we have got nh2 I'm putting that here and the priority function of cos I'm putting it here see this is one and the same thing now just by changing the value of r just by changing the value of R will be getting various amino acids so have a look at it imagine if I take the value of r as hydrogen of course H is not the alkalu but if you take the value of r as H so this will become h c h meaning ch2 nh2cos so that's how you get the first simplest amino acid called as glycine another important thing if you place the value of alkyl group anything other than hydrogen like we did here then look at this carbon this curve is going to be a chiral carbon right if you take the value of r as any alkyl other than H then this carbon is going to be a chiral carbon and what stereochemistry has taught us precisely speaking Optical isomerism has taught us is if any compound contains only one chiral carbon it is always going to be optically active so such compound is always going to be optically active so you will see all the amino acids are optically active except when the value of R is H meaning except glycine restore amino acids will be optically active if you take the value of r as ch3 it becomes alanine that is another very commonly used Alpha amino acid instead of ch2 suppose if I take isopropyl you see this is isopropyl group and further CH and nh2ch as it is we call it as valine you will see here we have put asterisk on the name of this Valley in asterisk meaning it will indicate that it is an essential Alpha amino acids so guys it is not expected you to learn it by heart but it would be great if you try to remember it so even if you just write it two or three times each amino acid you will be able to remember it now if I change this isopropyl group into let's say isobutyl then valine would be called as leucine you see we have got isobutyl group here this entire is isobutyl group this is isobutyl instead of isobutyl if you make it segbutus that's a sick butyl group this one so the leucine becomes isoleucine both of these are essential amino acid now we have studied alanine let me show you alanine again if I replace one more edge of this CHT group with phenyl it becomes phenylalanine see one h of alanine substituted by phenyl another essential amino acid now what I want you guys to observe is all the example we studied so far the six example Glycine alanine valine leucine isoleucine and phenylalanine the value of r that we have taken is the non-polar hydrocarbon part see we have got only alkyl carbon and hydrogen now you will find there will be a side chain that is r value in amino acid where there will be some polar groups present like hydroxyl group or the phenolic group for example look at the seventh serine in the screen in alanine you replace One S with the oh so now there is a polar group here but still it is a neutral amino acid because number of nh2 and coh are identical see all this example we have come across number of nh2 and coh are identical so all these examples all these examples belonging to the category of neutral amino acids even fourth fifth and sixth number of cos and number of nh2 are equal so as many are acidic group those mean are Basics you are calling it as neutral amino acids even these all are neutral serine tyrosine and methionine because eventually number of acidic group and nh2 groups are same no matter what is present in the side chain so this tree are also neutral amino acids all right some more example here aspergine and glutamine do not get confused by looking at this nh2s basic this is a mild group not amino group so as long as amino group and Coos groups are equal in number we are still going to call them as neutral amino acid only so both this example are still neutral amino acid even though they contain amide group so remember asparagine and glutamine will still belong to a category of neutral amino acids and now look at this example aspartic acid now you will see we have got all together two coh groups and just one nh2 group so two acidic group one basic group because number of acidic groups are more than the basic one we call this example as acidic amino acid other than aspartic acid even glutamic acid is such example where number of cooh groups are more than number of basic nh2 group so this is again acidic amino acid but if you look at the next one lysine and Arginine look at this nh2 group okay let me use other color code here there are two nh2 groups one cos so number of BC groups are more than acid here as well this is nh2 and this is another basic group so because number of basic groups are more than acidic we call such amino acids as basic amino acids a that is amino acid all right guys so that was basic introduction of alpha amino acid as the name suggests an organic compound containing carboxylic group that is acid and energy group together we call them as amino acids but when that nh2 group is present at the alpha carbon of carboxylic acid we call it as Alpha amino acids such amino acids are naturally occurring amino acids out of which 10 are essential amino acid which are not produced in our body so we have to rely on the external Source or the supplementary source we classify these amino acids into two categories first is essential second is non-essential other than that second classification is on the basis of how many coh and how many initial groups are present in a molecule if number of acidic group and the basic groups are equal we call it as neutral amino acids but if number of acidic groups are more than nh2 we call them as acidic amino acid if number of nh2 groups are more than coh we call them as basic amino acids so guys this is what we have seen so far so now processing further with the preparation or you can say synthesis of alpha amino acid the first process is carrying out hvz reaction and followed by direct amonolysis okay now what does that mean well guys while studying reactions of carboxylic acid we came across one reaction called as hell volat zelensky reaction hell volar zelinski reaction in other words we also referred it as Alpha halogenation of carboxylic acid right so the first part of this methods of preparation is again going to remain the same Alpha halogenation so let us say if we have carboxylic acid r ch2 I'm highlighting one of the edge and cooh which if we allow them to react with br2 Plus phosphorus so we know the fact that this P plus br2 together forms pbr3 that substitutes o h by BR then other than this undergoes to automatization and then further halogenation takes place at the alpha carbon atom then upon reaction with second equivalent of carboxylic acid eventually the bromine which was here gets substituted by the oh group eventually if I talk about the final result as a result of Hell Bullard zelinski we have studied the detail mechanism by the way in carboxylic acids So eventually what happens this hydrogen atom at the alpha carbon gets substituted by bromine let's say so we get the product r c h BR followed by c-o-o-h okay so you can call this as Alpha bromo carboxylic acid so we are done with the first part now second part is followed by direct ammonololysis a monolysis is nothing but breaking of carbon hydrogen bond using ammonia even this reaction we studied in the preparation of amines so amines can be obtained by the ammonolysis of alkyl halide so if we allow this to react with ammonia should will carry your simply nucleophilic substitution reaction with the loss of BR minus as soon as nitrogen will form Bond it will carry positive charge since it is sharing electron pair so this will undergo deprotonation so let's assume h plus from here is lost and BR from here is lost effective loss of hbr meaning you can say the product obtained is r c h and now we have got nh2 here right everyone and followed by cooh look at the product obtained the product obtain is carboxylic acid carrying nh2 group at the alpha carbon so this is Alpha amino acids okay everyone so yes that's how hyz reaction on carboxylic acid followed by ammonolysis will give you Alpha amino acids guys a very simple reaction so we shouldn't be spending more time on that next is using Gabriel thalamide synthesis another important reaction which is very handy in the preparation of primary amines that too making sure that the alkyl which we are using has to be less aesthetically hindered that's what we had studied well as of now let's see how this reaction is helpful for preparation of alpha amino acid well so let's talk about thalamide thalamide is a image of falic acid structurally that's how we represent right everyone we can see that this H is protein since it is connected to more electronegative atom so let's say if I allow this to react with aqueous Koh so being base it will accept h plus I and bond pair will go back on N making it n minus which will be balanced by this K plus so this is simply acid base neutralization to produce a salt so we are going to get a salt of thalamide rather we can call it as potassium salt of thalamide c-o-n minus and K plus so that's a potassium salt of thalamide now say this potassium salt of thalamide we are allowing it to react with Alpha Halo Ester Alpha Halo Ester so I'm representing it like this r CH X and since I am saying Alpha hello meaning this is going to be the alpha carbon Alpha hello Ester c o o R Dash okay now look since this nitrogen is nucleophilic and this is the carbon connected to halogen atom because illusion is more electronegative it will acquire Delta minus and the alpha carbon will be now carrying Delta plus charge that is indicating that it is a deficient carbon atom such diffusion carbon being electrophilic will always be attacked by the nucleophile so this nucleophilic thalamide will attack at this carbon with the departure of X so this x minus will combine with K so KX will be a byproduct I'll write it here minus k x now see what product are we getting n will be bonding to this carbon straight away C double bond oh lone pair and now look at this ch this alkyl Loop I'm putting downward here r and further coor Dash Co o r Dash okay and now everybody imagine if we carry out hydrolysis acidic or alkaline hydrolysis acidic or alkaline hydrolysis what will happen so hydrolysis is breakage using water let's say h plus o h minus down here as well h plus o h minus and Ester itself will also undergo hydrolysis h plus o h minus so see what are we getting nh2 that is amino group have been regenerated CH R bonded to c o o h so the product here is nh2 bonded to CHR bonded to cooh okay so what we have got carboxylic acid carrying amino group at its Alpha carbon atom so that's how we got Alpha amino acid of course if conditions are alkaline we won't be getting acid we'll be getting its conjugate base which can be further acidified using acid hydrolysis and you're eventually going to get this product so guys let's see what we have done we do thalamide with aqueous K which we converted that into potassium salt of thalamide which was straight away treated with Alpha Halo Esters on treating with Alpha Halo Esters we got an intermediate which was further hydrolyzed to give you Alpha amino acids that was the second process just like this we can also prepare amino acids by allowing carbonyl compounds to react with ammonia followed by reaction with scn and hydrolysis the process precisely called as trigger synthesis so let me show you what happened since trigger synthesis look like I said we have got some carbonyl compounds so let's say we have aldehyde RC double bond o h we are treating that with ammonia reaction of ammonia which we studied simply we understood this way for the sake of understanding we can put it this way h plus nh2 minus okay because this is the nucleophilic part and the carbonyl compound undergoes nucleophilic addition so if we carry out addition here nucleophilic part let's say attacking here Pi Bond will break towards o making it o minus which will then undergo protonation so addition of ammonia to carbonyl compound will produce r C H this H I am putting downward now rch up here it will become o h and nh2 has attacked here to n H2 I'm highlighting one of the h now this product which is obtained as a result of addition of ammonia will be further heated so upon heating it will undergo elimination of water producing oil Amine so upon loss of water we'll be getting rch double bond because the sigma Bond will shift back here RC is double bond and NH so C is double bond NS indicates that it is immin obtained from earlier so we call it as early mean now this ultimate which we have got will be further treated with hcn h c n so electron Rich nitrogen will attack at h plus so this will become CH double bond nh2 plus So eventually cyanide will attack at the carbon and Pi Bond will break so I'm writing two steps together when n will attack at Express this will become nh2 plus so Pi 1 has to break towards n so that cyanide will attack here so guys the product which we have got I'm writing it down here rch attacked by CN single Bond nh2 are r c h attacked by C and single Bond nh2 what is it now if you look at this compound we have got two function loop again one is nitrile other is nh2 so nitrile is your priority function so the carbon next to function will be zero Alpha so this is Alpha Amino nitrile or alkane nitrile once you get nitrile if you further allow it to undergo a very important characteristics reaction of carboxylic acid if we carry out acid or alkaline hydrolysis the cyanide function gets converted to carboxylic acid so this will be now converted to what c-o-o-h so we will be getting r c h nh2 and here we have got c o o h now if we look at the position of ns2 functional carboxylic acid next carbon is Alpha carrying nh2 so this is Alpha amino acids this process of obtaining amino acids by addition of ammonia to carbonyl compound upon heating followed by action of hcn is what we call it as trigger synthesis so guys three methods handy for the preparation of amino acid which we have studied so far includes number one where we carried out hvz reactions on carboxylic acid to give you mono-halogenation at Alpha carbon followed by action of ammonia called as a monolysis second reaction we saw where we use Gabriel thalamide synthesis and followed by reaction of uh reaction of salt of thalamide on Alpha haloester followed by hydrolysis gave us corresponding amino acid and finally Striker synthesis that was a method of preparation of amino acids now guys we'll first talk about how the naturally occurring amino acid exist and then the most important part coming up your way which is dipolar form of amino acid well I want you all to read this first come on guys go through that how naturally occurring amino acid exists that's information for you okay I want you all to go through that okay I'm hoping that you guys read it all and understood it well as well okay so like we mentioned earlier in any Alpha amino acid except glycine in glycine the value of R becomes H if the value of R is H this carbon is no more a chiral carbon but otherwise in all the amino acids this carbon is always going to be a chiral carbon atom being chiral it is always an optically active organic compound an optically active compounds when we put them in the fishes projection we can certainly put them in two configuration that is capital D and capital L reminding one last name again capital D and capital L has nothing to do with Optical rotation whether it is Dexter or level dextro and Lebo are represented by small D and small L respectively capital D and capital L talks about in the Fisher's position at the lowest chiral carbon lowest meaning which is the last chiral carbon at that carbon where the nh2 group is present if nh2 group at the lowest chiral carbon is present to the left you will call it as L amino acid if it is present to the right meaning if I write a mirror image of this nh2 will be put to the right hand side in the fishes projection you will call it as capital D amino acids whereas if you recall what we saw in carbohydrates in the previous class capital D and designation is given on the basis of the position of orange group at the lowest chiral carbon in the feasters projection here we talk about position of nh2 in the fisces projection one very important point that we always have to keep in mind while riding the fish's position we have to follow all the guidelines of fishes projection that is you write down the carbon chain in a vertical form and the highest oxidized group must be occupying the top position so making sure that cos is at the top and then vertical carbon chain at the lowest calorial energy is to the left so I'm going to call it as L amino acids so just like naturally occurring sugars naturally occurring sugars exist in the configuration naturally occurring amino acids are always L amino acids okay just do remember that and now guys let's talk about dipolar form of alpha amino acid now what does this exactly means everybody pay attention we are now starting an important part of amino acid if you write about amino acids structurally we can simply put it like this hold on nh2 Alpha carbon carrying R and cooh okay one thing is for sure in this amino acid we can see that this part is acidic part this part is a basic group so there are two function Loops so it's a bi-functional organic compound imagine if you take this amino acid and put it in a water the moment you put it in a water it will exist in equilibrium with its another form what is that form being acid it will donate h plus sign and being based this nh2 will accept that h plus ion to become NH3 plus meaning this amino acid will now exist as NH3 plus single Bond ch R and c o o minus you see amino acid in its aqueous solution exists in the form of NH3 plus c h r c o o minus this clearly indicates now amino acid is existing in the form of dipolar form such dipolar form of alpha amino acid is what we call it as sweet Orion we call it as sweeter iron so amino acid in its aqueous solution will exist in dipolar ionic form called as veteran I want you guys to understand one more important thing in the sweeter ionic form this part is no more acidic in fact it is now conjugate base of an acid any acid even loses h plus ion and gets converted to its corresponding anion we call it as its conjugate base similarly nh2 plus is no more in basic form nh2os base NH3 plus now is conjugate acid okay so imagine if we have amino acid in its aqueous solution so in aqueous solution it is not going to exist like this it will exist like a dipolar form so I am taking that here NH3 Plus CH r giving you co minus that's a dipolar ionic form now look this dipolar ionic form can exist in further equilibrium with two more form one is catanic other is an ionic so in general we can say Alpha amino acid in its Aquos solution exist in equilibrium with three of its form one of which is dipolarion another is in the form of cation and then in the form of anion now which form is going to be predominant out of this depends upon certain conditions like it depends upon the pH of the solution whether acidic or basic or whether intermediate and also depends upon the structure of amino acid whether it is neutral amino acid or whether it is acidic amino acid or whether it is basic amino acid as of now to talk about the basics we have got aqueous solution of dipolar form of neutral amino acid one coh1 and H2 but let's say if I make solution acidic making solution acidic acid we are lowering the pH if you lower the ph it will become acidic acidic meaning let's say in presence of h plus ion concentration of course since we are talking about in aqueous solution it's going to be h plus slash water hold on everyone so what will happen in acidic condition between these two this is the conjugate based form so if conditions are acidic based will accept that h plus and will become coos the moment this becomes coh NH3 being already acidic it will not react with the h plus so it will remain as it is so NH3 Plus will exist as it is CH r and this will become t o o h so this is indicating the dipolar form or dipolar iron form we are going to call it as di okay dipolar Ion in acidic solution exists as a cation right whereas if you mix solution alkaline if we increase the pH increasing the pH we can say okay in presence of o h minus sign in water if conditions are alkaline meaning basic the basic end will not react but the acidic end will react not to forget this is conjugate acid form so this base will accept h plus ion from here and this will become ns2 neutral so the group will now exist as ns2 neutral further connected to CH R and coo minus will still remain like that so that is indicating now it is becoming c o o minus meaning it is now existing in the form of an i so this is what we were talking about if we take a aqueous solution of alpha amino acid it contains three of its form which are coexisting equilibrium with each other a dipolar form of iron cationic form of ion and anionic form of an iron now if you talk about the Practical significance of this imagine if you are taking Alpha amino acid neutral amino acid for that matter for the timing and if you're carrying out process of electrophoresis so we'll take aqueous solution of alpha amino acid will suspend two electrodes and will pass electricity so depending upon what is the pH of solution let us assume the pH is lower if pH is lower then amino acid is going to exist in the form of cation since it is existing in the form of quantine upon passing current the times will be migrating towards meaning cationic form of amino acid will migrate towards the oppositely charged electrode that is cathode whereas if the solution is basic or alkaline because in alkaline solution amino acid will exist in predominant anionic form if we pass electricity the anion will migrate towards its supposedly charged electrode that is anode right everyone which means the migration of the amino acids will depend upon what solution or what is the predominant form of amino acid the predominant form of amino acid will depend upon Q condition one is what is the pH of solution and second what is the nature of alpha amino acid however imagine if I maintain an intermediary pH an intermediary pH such that the alpha amino acid is predominantly existing or the maximum concentration is towards the dipolar ioniform or you can say where the concentration of cation and anion is equal so that pH at which the concentration of cationic form and the ionic form of the alpha amino acid is equal which means at that pH Alpha amino acid won't migrate towards any of the electrode under the influence of electric field that pH is what we call it as isoelectric point so guys I'll just note it down isoelectric point electric point foreign at which you may say concentration of cation is equal to that of concentration of a nine all right everyone so what we have studied so far as a dipolar form of alpha amino acid Alpha amino acid is aqueous solution exists in these three forms in its equilibrium lowering the pH catanic formula predominant increasing the pH making it alkaline ionic font will be predominant as a experimental significance passing electricity depending upon in which form it is predominant it will migrate towards its opposite electrode however if we maintain the pH of solutions such that the concentration of cation and anion form is equal amino acid won't migrate towards any of the electrode that's a the net effect we are talking about we'll call that pH as isoelectric Point symbolized as p i so guys now hold on okay hold on everyone yes so that's what we talked about isoelectric point the predominant form of the amino acid present in the solution depends upon two things of course we first talked about pH of the solution and second on the nature of alpha amino acid whether it is neutral acidic or basic in strongly acidic medium meaning when h plus science exists all the amino acids present primarily as a cation in strongly basic medium they are present as an ant at some intermediate pH called isoelectric point the concentration of dipolar ion is at its maximum that's what we said and the concentration of the anions and curtains are equal so that intermediate pH will vary according to the nature of alpha amino acids no guys in exam you will find several times they'll ask you a question to find out the isoelectric point of the given amino acids so there would be three possibilities one they might give you neutral Alpha amino acid having one nh21 cooh they might give you acidic amino acid like aspartic acid or glutamic acid or they might give you the basic amino acids so how exactly are we supposed to find it out let us pay attention guys this is the important part here let's say they're asking about find out the uh isoelectric Point Pi for the neutral amino acids firstly whenever you talk about any amino acids if neutral will have one situation one nh2 imagine if I lower down the pH if I take strongly acidic medium let's say pH is equal to zero okay so being acidic what we have said in strongly acidic medium all the amino acids primarily exist as what cation meaning it is going to be only imagine you have got dipolar ion you made solution acidic so what will happen in acidic solution this Co minus will accept h plus so this will become coh but NST plus will remain as it is so this is existing in the strongly acidic medium okay now if you look at this two groups Coos and ns3 plus from where we started when the pH of the solution is zero meaning in strongly acidic medium it is existing as NH3 plus if it is existing as NH3 Plus which means we can certainly say that it is existing in the form of cation now suppose from PS 0 you started you started diluting it or you can say you started increasing the concentration to the alkaline towards alkaline meaning from pH 0 you started increasing pH 1 pH 2 pH 3 so on and so forth meaning from strongly acidic you are moving towards neutrality and eventually you're going to make it alkaline so what we are doing is we are making solution alkaline that's what you can say because anything above 0 is going to be alkaline as compared to ps0 so if I try and make solution alkaline then at one pH what will happen is this curve this amino acid which is existing in the form of cation will tend to lose h plus ion depending upon which is more acidic whether sewage or whether NST and second depending upon its pka1 value so what is PK A1 corresponding to is pay attention here we have got carboxylic acid group and NST plus acid so carboxylic acid is anyway the acidic NH3 plus is also conjugate acid form of nh2 however because carboxylic acid is way more acidic than NH3 plus it is coh who will lose h plus ions first I repeat as we'll increase the pH from 0 towards making it alkaline in alkaline solution some acid is going to react with that alkaline solution so whichever is more acidic will lose the proton so question is whether Coos will lose it or whether nht plus will lose it because cooh is more acidic than NST plus it is Coos which is going to lose the h plus first so this pka1 is corresponding to the cooh PK A1 value which is 2.3 so as you will make solution alkaline this coh will lose first of its h plus ion right everyone and now if you make solution further alkaline there will be a pH where the whole molecule of cooh will be converted to coo minus and then once this has launched the all amount of h plus ion now NH3 plus which is conjugate acid which is also acidic in nature will tend to lose h plus ion from NH3 Plus and as you'll make the solution even more basic Beyond this 9.7 you will see that NST will lose all its h plus and N will become nh2 now first one was Catan here we have got dipolar ion yes this is dipolar and here we have got a 9.

[00:52:51]and we have been given two PKA values PK A1 corresponding to coh pka2 corresponding to NST plus now because this amino acid was neutral amino acid having one cos and one nh2 if we have to find out isoelectric Point let me tell you isoelectric point p i is when the concentration of cation and anas is equal which means if I plot this on a pH scale let's say this is zero and this is 14.

[00:53:23]okay now see first we've got cation and then we have got an our interest is when the concentration of or the pH or the p i is when the concentration of cation is equal to one and so we should focus on concentration of cation and Anan so I'm not mentioning dipolar ion so we have got Catan and anion because we still don't have Diana or dicotine so in case of neutral amino acid the pi value is simply going to be pi will be equal to p k A1 Plus p k A2 divided by 2.

[00:54:17]now since we have only two values one corresponding to coh which is 2.3 other corresponding to NST plus which is 9.7 so we'll take average of these two so in this case if you take average the P I will be first is 2.3 more acidic then 9.7 whole divided by 2 9.7 plus 0.3 is 10 and 2 is 12 12 by 2 is 6 so isoelectric point for this molecule which is basically alanine this was alanine so isolate big point for alanine is six now you try and understand in acidic solution amino acid primarily exists as cation in strongly alkaline medium it primarily exists as an end so there has to be some intermediate pH in strongly acidic I'll write it here and strongly actually it was cut and strongly basic it was an N so there has to be some intermediate pair between intermediate pH between the concentration of katana and N where it will exist in a dipolar form so that's why the pH is six which is an intermediate between cation and an intermediate between cationic four and the anionic form fine conclusion when your amino acid is neutral amino acid when your amino acid is neutral amino acid simply take the average of pka1 and PK A2 that is going to give you isoelectric point now there could be some different type of question on this imagine if the question is asked the given amino acid let's say this amino acid is given will migrate towards which electrode at pH four let's say at pH 4 or at ph3 anything lesser than 6.

[00:56:05]so if Pi is the isoelectric point at which concentration of cation and N is equal and dipolar form is in the highest form or the maximum concentration if I decrease the pH if I decrease the pH let us say to 4 so I am making solution more acidic from its Pi I am lowering the pH from 6 to 4 making a making solution acidic in strongly acidic medium what form is predominant cation if it is cation it will migrate towards oppositely charged electrode that is cathode so the answer is at pH four this amino acid will migrate towards cathode that's how the question can be asked well but like I said it's not just about the neutral amino acid we may have a question related to acidic amino acid or basic amino acid as well so directly taking you to the example here everyone let's say we are talking about for acidic Alpha amino acid well example right in front of you you can see here we have got nh2coh okay let's look at the structure for coh and ch2 acid group 1 nh2 this number of acidic groups are more than nh2 will call it as acidic Alpha amino acid now again let's talk about this amino acid we have made aqueous solution and we are making solution strongly acidic if you make it strongly acidic the basic group that is nh2 will accept that expression will become NH3 plus meaning in strongly acidic medium it will exist like this isn't it everyone okay so in a strongly acidic medium it is nht plus coh and cos so let's say yo this is existing in the form of cation okay and let's say they have given us some PKA values now naturally PK A1 PK A2 and P K A3 is given to us now first identifying this cationic form of alpha formulation tell me which is the most acidic one naturally two coh are more acidic than NH3 Plus now between two coh which acidic group is more acidic if you apply logic or if you apply the concept of organic chemistry NH3 Plus shows strong electron withdrawing inductive effect right after nr3 plus the best electron withdrawing group effect is shown by is NH3 Plus so because it shows strong minus I effect the conjugate base of this cooh will be stabilized the most more stable the conjugate base stronger the acid so this is the strongest acid then this coh and then NST plus so let's say the corresponding pkar PK A1 here PK A2 and this is pka3 okay now look as we have been doing we make solution alkaline because this is what you see this form Titanic form is in a strongly acidic medium now we are changing our pH towards alkalinity so we are making it more alkaline so this acid will lose coh H first so if base accept h plus it will exist as minus and s t plus and CU minus what form is this this form is a dipolar form dipolar ion isn't it since we are making solution alkaline since we are making solution alkaline now this o h minus ion will accept h plus from this acidic group so this is going to lose h plus so this will become c o minus now we have got two and ionic form one cationic form so overall number of ionic forms being more I will say this is existing in the form of anion right when we make solution further alkaline now the third strongest acid is this NH3 plus so o h minus will accept h plus from here okay so first it accepted from here second it accepted from here so it is accepting from you it will become nh2 plus now two ionic form another neutral meaning now this is existing in the form of di anion correct everyone now if you look at this Alpha amino acids equilibrium it is more complex than the neutral Alpha amino acid a neutral Alpha amino acid we just had what we just had starting cation then dipolarane and then the Anand so we did not have to even consider dipolar and simply because we had only one curtanic form one and any form so the two PKS were given we just took average now we have got three PK here PK A1 p k a two p k a three so the point of confusion that you can have is what average should we take should we take average of PK A1 Plus PK 2 or should we take average of PK A2 plus p k a three I'll write down both the possibilities questionnaire we have is should we take average off meaning should we consider pi as average of PK A1 Plus pka2 by 2.

[01:02:04]or should we take p i as average of PK A2 Plus pka3 by 2.

[01:02:24]now look if you just try to recall what we studied in p i p i is the pH at which the concentration of katana and ananis equal so you have to look for cations yes cation and anion formation you see that here right first we had cation at the very low PH we had Catan when you increase the pH it became dipolar ion which we don't write dipolar and then got converted to an anion then got converted to Diana now what we want we want pH where katanana and concentration is same so cation and ion concentration Katan and anion concentration is as a result of loss of proton from PKA and loss of proton from pka2 hence the pi will be average of pka1 and pka2 in simple words whenever you talk about acidic Alpha amino acid you simply take those PKS which are corresponding to the stronger acidic end meaning coh and coh so you have to take average of this two similarly when you have got basic Alpha amino acid in that case you will take PKA values of the similar function that is NH3 plus and ns3 plus how let me show you that again now let's say this is your basic Alpha amino acid if you make solution very acidic strongly acidic both of this nh2 will accept h plus and will exist as NH3 plus ions meaning this Alpha amino acid in strongly acidic medium will exist as what NH3 Plus ch2 time ch 3 plus and see this is in strongly acidic medium so in strongly acidic medium what do we see we see that molecule is existing in the form of dicatine okay now what are we going to do we are going to make solution basic so what base does base react with the strongest acidic call at first write it down this will have pka1 because this is most acidic PK A2 here and then pka3 here so base will attack at the most asterisk that is cooh upon loss of that h plus from here it will exist as NH3 Plus c h two four times the edge NH3 plus and now this is becoming Co minus what form is this meaning it is now in the form of monocotan form this cation is neutralized by an N so this two charges are neutralizing but let's say this is still cation or you can consider this two neutralizing this is cation all right now we are making solution alkaline further making it further alkaline the next acidic is which one this is the next acidic one why because after loss of h plus or rather you can say this c o o minus is a withdrawing Group which is closer to this NH3 Plus right so this will lose h plus and the electron pair can be stabilized more on this so base will accept h plus from here we will be getting NH3 Plus ch24 times followed by CH now this will become nh2 because it has lost proton from here so this became neutral and coo minus as it is one cation one anion indicate that it is dipolar Ion d i and finally making solution basic will accept the h plus from the least acidic group NH3 Plus at the terminal of the functional group so let's say this o h minus accepted h plus from here upon accepting h plus from here we'll make it nh2 ch24 time CH and H2 and c o o minus neutral neutral anionic which means the amino acid is now existing in the form of why not right so if you again plot a pH scale here for this pH scale where should we write it we'll write it here 0 and 14 let's say so we first had dicatine here after die cut and we had contained here we don't write dipolar and then we have got anion so this was dicatan which was basically pi equal to pka1 plus p k a 2 average that is by 2.

[01:08:33]after die cut time we got cation and then we don't write dipole around so we have got a nine so here isoelectric Point p i is equal to this you obtain from PK A2 and pka3 so average of p k A2 plus p k A3 by 2. so what are we interested in we are interested in isoelectric point is the pH at which concentration of cation and anion or equal to Cotton and an answer will take this intermediate pH which is pi equal to p k a two plus pk3 which means in this case we will be taking average of average of what pka2 and pka3 meaning we are taking those PK values which are corresponding to NH3 plus that's what I told you right in the beginning that now here p i will be equal to p k A2 Plus p k a 3 by 2 okay everyone conclusion if it is neutral amino acid what your pk1 pk2 is given take average of that if it is acidic amino acid find out PK of this similarly function Loop similar function that is coh and coh meaning basically you will take average of pk1 and pk2 if it is basic Alpha amino acid you will find out the average of pka2 and pk3 meaning PK values of those NH3 plus sign that's how you are supposed to do it so guys that was all about the isoelectric point and how to calculate it for neutral acidic and basic Alpha amino acids the next part we are going to learn is about polypeptides and eventually we'll come down to what is called as proteins guys just give me a second you can still read it for your information okay guys here so we are talking about proteins well in our system protein basically are formed by the polymerization of alphamino acid like we said polysaccharide is a polymer of monosaccharide a few minutes back we said proteins are the polymer of alphamino acids so amino acids are polymerized in the living system by enzyme that forms amide linkages well to understand this in a simplest way let's have a look at this reaction let's say if we have got uh uh first amino acid NH3 Plus NH3 Plus for our convenience I'm writing like this NH3 plus highlighting one of the h c h r c o o minus right that's how in aqueous solution amino acid exists in a dipolar form this is let's say first amino acid so I'm going to write it as R1 just to indicate that this is first amino acid and upon polymerization when it condenses with the second amino acid I am writing the second amino acid now so NH3 Plus ch R2 c o o minus right okay A Small Change here I'll put this as H2 NH plus let's say all right now see these are two alpha amino acids which we are allowing them to undergo condensation process so when we allow them to undergo condensation what will happen this o minus and two h's will be lost from here in the form of water since h plus will be lost from your nitrogen will regain its lone pair back similarly even this okay when this we should have written like that guys hold on I'm just putting it in a right way H2 NH Plus okay so as of now if I'm assuming that we have got only two alpha amino acids then this H2 and O will be lost so this will result in the formation of h3n plus CH R1 bonded to C double Bondo directly connected to NH but now this n is going to be neutral because upon loss of proton the bond pair will go back on H to neutralize this positive charge to bring back the lone pair so we will have C double bone oh NH neutral so must show lone pair here further bonded to ch R2 and C double Bondo since this o is lost okay since we are taking only two amino acids so we'll keep we'll keep this o intact here so we have got a product like this this product is obtained as a result of condensation of two alpha amino acids see condensation of two alpha amino acid has produced a new function over here c o n h this c o n h function look in general in organic chemistry we refer it as amide but in the protein chemistry the same function of amide is here referred as peptide okay so two alpha amino acids upon condensation and how condensation is taking place the acidic group of one alpha amino acids is condensing with basic group of another Alpha amino acids since I am writing in the form of dipolarion this is the conjugate base form and this is the conjugate acid form So eventually it's a condensation between acid and base only resulting in the formation of amyl linkage which you call it as peptide further this peptide which is obtained will be referred as dipeptide yes I want you all to focus on this dipeptide although this peptide obtained contain only one peptide link is still while naming such peptide we call them as dipeptide only because the name of peptide is always kept on the basis of how many Alpha amino acids have undergone condensation to form that peptide so dipeptide does not mean having two peptide no dipeptide indicates it is obtained by condensation of how many Alpha amino acid so let's say if I am having three amino acids undergoing condensation so you'll be getting two peptides just like two amino acids give you one peptide but the name is Diet pep right three amino acids upon condensation will produce a compound which will be named as tripeptide because three amino acids have condensed but that structure will ideally be containing only two peptide linkages likewise when you just have one peptide linkage you call it as dipeptide if the number of peptide increases further and if they are countable like having two peptides in case three peptide four peptide we call them as oligopeptide but imagine if many Alpha amino acids condenses to form a polymeric form of that peptide you call it as polypeptide and further if that polypeptide is found to be having molar mass of 10 000 or more then the same polypeptide is referred as protein molecules hence dear students we say proteins are biopolymer of alpha amino acids or while defining we say proteins are nitrogenous naturally occurring nitrogenous organic polypeptides which upon hydrolysis gives you various Alpha amino acids so guys that's how we get the peptide linkage and proteins are nothing but the polypeptide so all the information just in front of you comparatively shorter peptides are termed as oligopeptides when they have lesser number of peptide leakage whereas longer polymers are called as polypeptides further proteins are those polypeptides having molar mass more than 10 000 hence we say proteins are naturally occurring because they contain nitrogen naturally occurring nitrogenous organic polypeptides which upon hydrolysis gives you various Alpha amino acid for example now suppose if I have to represent polypeptide how are we going to represent polypeptide instead of writing dipolar form if I write them in a neutral form it will look like this right everyone r c o o h uh not cos c o n h this was R1 this is let's say RN and Co look here eoh whereas this will be repeated n number of time nhch hold on everyone okay let me correct it foreign CHR and Coos let's say and if I'm saying that we have taken n number of alpha amino acid and subjected into condensation so you'll see this unit will keep on repeating itself several times meaning this will be repeated n number time so how many peptides are we going to get we are going to have many peptides or polypeptides so if the product is polypeptide having molar mass more than 10 000 we are going to refer it as what protein molecules right now in this protein molecules by convention the left side of the protein polymer is represented by nh2 which we call it as n-terminal all n residual terminal and the right side containing cooh group is called as C residual terminal so just to represent a reaction imagine if I carry out hydrolysis by taking n number of water molecules so wherever you will carry out hydrolysis cooh upon hydrolysis h plus o h minus ions here as well upon hydrolysis h plus and o h minus signs see what are we gonna get R1 CH nh2coh amino acid or the whatever is r c h nh2co amino acid rch nh2 cos and N number of such amino acids you're going to get so if you are going to get n number of amino acids I will say the product of this is giving us various Alpha amino acids that's what we say proteins are naturally occurring nitrogenous organic polypeptides which upon hydrolysis produces various Alpha amino acids so we got various Alpha amino acids so at time you might find a question given like that they'll say there is a protein molecule which is formed or not protein there is a polypeptide or rather oligopeptide is formed by the combination of three Alpha amino acid let's say phenylalanine alanine and glycine then find out how many possible combination of oligopeptide exist well everyone let's see the question here a tripeptide on complete hydrolysis gives Glycine alanine and phenylalanine okay so for glycine I'll use three liter symbol that is gly for alanine three liter symbol is ala and for phenylalanine I'm going to use three letter symbol that is ph3 so what they're saying is there is some tripeptide which upon hydrolysis gave us this three amino acid meaning basically tripeptide was formed by the condensation of these three amino acid then using three letter symbols write down the possible sequence of the tripeptide so what are those tripeptides which are possible as a several combinations so let's say if I talk about first combination the one which you represent to the extreme left will have n terminal right and residual terminal like this let's say the first Alpha amino acid we had a glycine second is okay let's go alphabetically so that easier for us to remember yes so we were here let's start with Alan I was bonded to glycine glycine was flanked between Alaine and penile alanine this is one combination possible now keeping alanine same interchanging the position of glycine and phenylalanine so the second combination of tripeptide is alanine was representing in residual terminal phenylalanine was flanked between the two and glycine is the one which was showing the C terminal okay then after Alliance combination is done as end residual and residual could be glycine now second alphabet glycine alanine and phenylalanine let's say keeping n terminal glycine again I'm interchanging alanine and phenylalanine glycine phenylalanine and alanine and now phenylalanine showing n residual terminal followed by alanine and glycine glycine will have C terminal now interchanging these two phenylalanine Glycine and alanized any other combination anyone so these are the three possible combination of tripeptide so any of this you pick and Carry Out complete hydrolysis you're going to get these three Alpha amino acid but you there is a particular sequence of alpha amino acid in which they are bonded to each other this this kind of polymeric chain of alpha amino acid that correspond to precise sequence of alpha amino acid is what we call it as primary structure of corresponding protein imagine if this is protein having many Alpha amino acids hundreds of alphamino acid so the same sequence of alpha amino acid will correspond to primary structure of protein now keeping Alpha amino acid same just like we did it here and if we just change the sequence of alpha amino acid that forms another protein molecule but still will be called as primary structure of proteins so primary structure of protein corresponds to the particular sequence of alpha amino acids in which they are connected to form that corresponding polymer so guys that was all about polypeptides now the next part is the structure of protein like I said this is the most you can say informative part of this chapter and it's just the basic information that you need to know so what we're going to do is I will just explain but all the data that you need to know I put it on the slide you can refer it later okay so what is structure of protein well the structure of protein exists at four stages primary structure secondary structure tertiary and cotton instruction now these four structures of protein are not different protein it is the same polymeric chain of protein studied at a different levels studied at a different stages where every next level is complex than the previous one so how the overall protein molecule look eventually in a three-dimensional space at a different stages is expressed by the force structure of protein primary secondary tertiary and quaternary structure of protein let us talk about primary structure well I briefly to you just now primary structure of protein refers to the particular sequence of alpha amino acid in which they are connected like if I have got alanine Glycine and phenylalanine example I'm giving for tripeptide then that is called as one of the primary structure of protein now keeping this Alpha amino acid same but if I change the sequence if I make it Glycine alanine and phenylalanine now I've changed the sequence that is another primary structure of protein you'll call it so primary structure of protein refers to the manner and the sequence in which different amino acids are joined to form a polypeptide which is what you call it as primary structure now let's say you have got hundreds of alpha amino acid in a particular sequence so that sequence is corresponding to what primary structure of protein now that linear polymeric chain at a further level how it exists in its particular configuration now we talked about sequence now whatever is the sequence the linear polymeric chain is having what kind of configuration as its structure in a three dimension is what you call it as a secondary structure of protein so primarily depending upon what kind of bonding is existing in that linear polymeric chain of alpha amino acid secondary structure exists in two primary for in two forms I should not say primary you will get confused with this exist in two form so that second is structure which exists in two form are alpha Helix and beta pleated sheet structure let me show you the structure first and not the theory well have a look at this structure imagine you have got linear polymeric chain of alpha amino acid so if there are hundreds of such Alpha amino acids which are connected to each other to form a linear polymeric chain at times you'll find that linear polymeric chain coiled around itself this coiling is because of intramolecular hydrogen bondings shown by the alpha amino acids which are condensed to give you that polymeric chain for example if you look at this coiling of alpha amino acid see we have got NH in between you'll have CHR C double bond o for the C double bond or NHC double bond o likewise the polymeric chain is containing The Continuous c o n h c h r c o n s c c o n h c h r c o n s c h r so on and so forth where you will find this carbonyl oxygen of the first coiled form of the alpha amino acid is forming a hydrogen bond with the adjacent H connected to nitrogen so what is this called as the intramolecular hydrogen bonding because of this intramolecular hydrogen bonding this polymeric chain is coiling around itself to exist a structure like a right-handed Helix which you call it as Alpha helix whereas you will find in one coil form there are around 3.6 Alpha amino acids are involved and that forms around 13 member cyclic structure so sometime this is also referred as 3.6 13 helix whatever information I spoke let me tell you the important point is the linear polymeric chain of alpha amino acid exists in a coil form which looks like a right-handed Helix because of intramolecular hydrogen bond which is sometimes also referred as 3.6 13 Helix 3.6 is because approximately in one coil phone 3.6 of alpha amino acid exists so here is the information the arrangement or the configuration of polypeptide chain same sequence of alpha amino acid we are studying its Arrangement now so primary structures Arrangement is what you call it as secondary structure of protein it mainly exists in two form guys give me a moment it exists in two form Alpha Alex and beta pleated sheet structure this is Alpha Alex and this is the beta pleated sheet structure will first come to Alpha Alex so this structure is formed when the chain of alpha amino acids coils at a right-handed screw collar filex because of the formation of intramolecular hydrogen bonding between what amide groups of the same peptide chain so NH of one unit will form hydrogen bonding with carbonyl oxygen of other this hydrogen bonding between the different units is responsible for holding the Helix in a position and the side chain of this unit's project outward from the coiled backbone like I mentioned this Helix is sometime also known as 3.613 Helix why it is so since each turn of the Helix has approximately 3.6 amino acid and it forms 13 membered ring due to hydrogen bonding now because hydrogen bonding is you can say relatively weaker force of attraction this coil can be stretched because those weaker hydrogen bonding can be broken so such protein are elastic that is they can be stretched on stretching the weak hydrogen bonds breaks up and the peptidine acts like a spring and further if you just let that strain go away you will find that that hydrogen bonding will takes place again and the same helical structure can be reformed that was Alpha Helix Now Beta pleated seed structure let's see this was the one only one linear polymeric chain which was showing internal hydrogen morning imagine now you have got two linear polymeric chain of protein or polypeptide so when two or more polypeptide chains are held side by side to each other then they are associated with each other via intermolecular hydrogen bond between the carbonyl oxygen and NH of the adjacent Alpha amino acid chain because of which those several Alpha amino acids are stretched forming a sheet-like structure so we call it as beta pleated sheet structure now this beta pleated sheet structure you will find several such sheets can slide past over each other so we further say a different types of secondary structure is possible when polypeptide chains are arranged side by side in a zigzag manner with alternate alkaloops on the same side these chains are held together by very large number of hydrogen bonds between the carbonyl oxygen and hydrogen of NH is what we said does the neighboring peptide chains are bonded together by intermolecular hydrogen bonding resulting in the formation of a flat sheet these sheets can slide over each other to form three-dimensional structure called as beta pleated sheet structure so guys that was all about the Alpha and the beta form of the secondary structure just to conclude secondary structure of protein is the same primary structure of protein which acquires its particular arrangement in a three-dimensional space in two form Alpha Alex and B Diaries are beta sheeted beta pleated sheet structure I'm sorry now if you consider the same Alpha helical structure and beta pleated structures further folding or twisting or bending that chain considering in a three dimension I am saying if you take the same secondary structure and consider its further folding or twisting to results in a three-dimensional structural form it either appears as a three like structure it either appears like a three like structure called as fibrous protein or sometime exists as a spheroidal sheep you call it as globular protein meaning the same secondary structure of protein at a further complex level in three dimension based on how it is further twisting or how it is bending exist in two more form called as fibrous protein and globular protein and that is what you call it as tertiary structure of protein so see how we started we started with the sequence of alpha amino acid called as primary structure the same sequence of Alpha amino acid which gives primary structure if you consider its arrangement if you consider its Arrangement or if you consider its configuration it exists as Alpha Alex or beta printed called secondary structure now same Alpha Alex or beta pleated when considered in three dimension that is how it further uh bends or how further it folds gives you three dimensional structure called as globular protein or fibrous protein which you call it as tertiary protein whatever we have discussed was all about one polymeric chain let's say that one polymeric chain is forming one unit likewise if you have got many such subunits which comes together to form one aggregate so that structure is what you then call it as quaternary structure of protein I repeat what have we talked up till tertiary structure was only one polymeric chain in three dimension let's call it one unit if I take many such subunits which collectively form an aggregate of it that aggregate is what you call it as the quaternary structure of protein so many protein exist as a stable and ordered non-covalent non-covalent Aggregates of more than one polypeptide chain yes more than one polypeptide chain the oral structure of protein having multiple subunits together is what we call it as quaternary structure of protein so guys that was all about the protein we have studied the important part of protein and I finally just one simple thing that we will be discussing something called as denaturation of protein and we'll talk about the tertiary structure in detail that is fibrous and globular protein so guys denaturation what do we understand from this term denaturation the naturally existing form of protein what we call it as a native protein if I bring that native protein the naturally occurring form of protein to some physical change like change in PH or like change in temperature then some changes in the structure of protein takes place that changed form of protein is what you call it as denaturated protein or you can call it as denaturation of protein for example egg how the natural form of egg exists if I boil it by of course heating it upon boiling of course the structure of egg changes so the boiled egg is a denaturated form of protein yes so denaturation the protein found in the biological system with a specific configuration and the biological activities known as native protein the native protein imagine egg the negative protein is considered to be denaturated if on being subjected to physical or chemical treatment that might change its structure without changing its primary structure meaning upon heating there might be some biological change that might take space but it will not change the primary structure of protein meaning sequence of amino acids still will remain the same boiling of an egg is the best example to understand the phenomena called as denaturation basically changing the original form of protein that change might bring in change in biological activity without any change in the sequence of alpha amino acids so that was denaturation and now guys in primary second and tertiary structure when we came down from secondary to tertiary structure we said the same secondary structure depending upon how are they folding or how are they bending we get a three-dimensional Arrangement which looks like a thread called fibrous or exists like a spiritual ship called as globular so this fibrous and globular protein is what we are going to study now so we are studying details of tertiary structure that is you can see another type of classification of protein fibrous and globular so what are fibers they are linear or three like molecules meaning if you have got polymeric chain which is Hell adjacent to each other so as to have thread-like structure you call it as fibrous Protein that's what they are saying the polypeptide chains are held by hydrogen bonding or sometime by disulfide linkage disulfide is this and hence have high intermolecular force of attraction because of high intermolecular force of attraction they are insoluble in water and stable to moderate pH and temperature example well I'm sure we all are aware that in our hair there exists protein called as keratin the same thing also exists in skin and nails so yes our hair if you see their thread like right so that's a fibrous protein also Coliseum in tendons and myosin in muscle belongs to category of fibrous protein they are water insoluble but the globular one you'll see is going to be water soluble protein and can be subjected to change by changing the ph and temperature so when the polypeptide chain of protein undergoes folding in such a way that it exhibit spiroidal spherical shape in which the hydrophilic part is pointing outward hydrophilic meaning what water attracting or water living so when the overall polypeptide chain appears like the spheroidal shape you call it as globular protein in such a shape you will find the hydrophilic part will be pointing outward because of which it will attract the water molecule hence the solubility of such protein will increase hence you'll call it as water soluble proteins and like I said they are sensitive to a small change of pH and temperature example albumin egg or hemoglobin or insulin are the example of globular protein so guys that was all about protein and now the last small subtopic which is left that is nucleic acid we'll be seeing it shortly with just two to five seconds to break everyone I wanted to go through this flowchart just to understand what are nucleic acids uh-huh okay everyone so nucleic acid we all are aware of this terms DNA RNA deoxyribonucleic acid and ribonucleic acid okay well let's see from where it all begins so we all are aware that in all living cells there is a presence of nuclear proteins which basically consists of two parts protein and the polymer of nucleic acid so this nucleus stands for nucleotide so polymer of nucleic acids basically are of two types deoxyribonucleic acid and ribonucleic acid so these are collectively basically nucleotides which in association with protein the other one which are present in the living cells so this DNA and RNA that is deoxyribonucleic acid and ribonucleic acid are basically the nucleic acid are nothing but polynucleotides so just like we said uh polysaccharides are polymer of monosaccharide also proteins are polymer of alpha amino acid similarly nucleic acid DNA and RNA are the polymer of nucleotides that's why you call them as polynucleotides so nucleic acid meaning these two are polymer of nucleotides so you call it as polynucleotides so what is nucleotide nucleotide is basically a collection of three units one of which is sugar another is base and then the phosphate group whereas out of this if you just take away phosphate and whatever is left that is sugar and base you call it as nucleoside so in other words in nucleoside if you attach phosphate part it will become nucleotide if you polymerize nucleotide it will form polynucleotide polynucleotides are nucleic acid but nucleic acid are of two types d ribose deoxyribou nucleic acid and ribonucleic acid meaning if the sugar used in this nucleotide is deoxyribose then that nucleic acid called DNA if the sugar used in this nucleic acid nucleotide is ribose then that polynucleotide is called as ribose nucleic acid so basically to understand DNA and RNA meaning to understand the nucleotides nucleic acid we will have to first learn what are the sugars what are the bases and what kind of phosphate answer use and how are they connected to each other okay everyone so let us learn this individual things this individual things together will give you nucleotides if you make a polymer of nucleotides you get polynucleotide meaning only nucleic acid okay so let's talk about sugar first as you see the name the sugar used here is deoxyribose and ribose nucleic acid so first we need to understand ribose nucleic acid and that to beta form well guys in the previous class we discussed in detail how the opening structure of sugars exists in a closed chain form so let me show you again if you talk about ribose it was Aldo pentose problem number two three four and five right and right yes now look what happens so that's carbon number four that's carbon number one one two three four so the lone pair of oxygen of carbon number four attacks at the Delta plus of carbonyl carbon these Bond breaks to give you C single Bond o minus which gets protonated so we'll form C single Bond o h so this molecule will exist in of course two form Alpha and beta anomeric form you have seen But in Sugar we use beta form beta meaning in the feature the OS is to be written to the left so I'm just writing beta form of the cyclic structure we all have studied the details of this so as of now I'm directly writing the beta form second third fourth right right and right all right so you'll see this is the anomeric carbon yes you have got oh and or group so since we are talking about beta let's call this is carbon number one anomary carbon number two number three number four and number five so if I write down this in the Havoc projection form how will we write five member cyclic structure that's five member cyclic structure carbon number one problem number two carbon number three four and five okay so that's first second third fourth and fifth well guys now when you talk about beta number we know the fact in beta and umer the groups present at first and the fourth carbon because oxygen is now flanked between first and force so the two group present at first and fourth meaning ch2h and Os should be on the same side so that's beta and this is what is our anomeric carbon because rest all group are to the right you will simply say right right and right rest of the valencies are just edges so that is your sugar now this sugar is a ribose sugar so I'm calling this as beta since o h is o h and ch2 which is both on the same side D because it is obtained from D sugar at the lowest chiral Oasis to the right so it's a d sugar and ribose now another one is beta d deoxyribose when you talk about this term deoxyribose which means removal of oxygen or no oxygen and at Carbon 2 so you can simply remember like this no oxygen at C2 so if you remove oxygen from C to here if you remove this o it will be called deoxyribose so the second structure can be simply represented this way since it is beta we have got oh now see at Carbon number two we have removed O So this oh we are removing so both are edges and rest of the structure carrying edges so important thing is at Carbon number two now there is no oxygen here because there is no oxy and I'll call it as deoxyribose so the name of sugar will be beta d deoxyribose beta d deoxyribose okay everyone survival sugar and deoxyribose sugar so these are the sugar molecule remember nucleic acid out of two type deoxyribose nucleic acid and ribose nucleic acid so we have studied the first term what is ribose what is deoxyribose now this nucleic acid are polynucleotide so it's a polymer of nucleotide what is nucleotide It's a combination of sugar base and phosphate so we have studied sugar now if you talk about bases well guys there exists two types of bases one is purine so this is the purine structure you'll see some changes made in the purine gives you two purine bases called adenine and guanine remember A and G adenine and guanine so adenine is where at this carbon number six you will find there is one nh2 group present and guanine is where at Carbon number six you made it carbonyl carbon atom and also one nh2 present at Carbon number two so that is your guanine which is derived from purine so these two base is called as purine basis so there are two purine bases adenine and guanine and there are three pyrimidine bases so that's your permittent parent structure so you'll see at Carbon number four you make Ketone and also at Carbon number two so this diceto form of second and fourth is uracil in same pyramidine if you make carbon number two Ketone and carbon number four nh2 so this keto have been made nh2 you get cytosine right and then just like you are still at Carbon number five you add one more ch3 here it becomes thymine so adenine guanine uracil cytosine and thymine are the five bases generally observed in DNN RNA we know DNN RNA are the one which are responsible for carrying the hereditary right hereditary character is carried by DNA and RNA well so two purine and three pyramid in bases that we have got so now we know sugar we know what basis we have and other than that what is left is a phosphat ions well guys so when you talk about phosphate I'll just note it down here phosphate is a conjugate base of phosphoric acid the phosphoric acid is h3po4 if you remove three h plus sign you're gonna get phosphate and that is po43 minus structurally if you represent if I draw precise structure it will exist in tetrahedral form like this minus minus minus okay now we have got sugar containing base and containing phosphate then you call it as nucleotide not to forget this everyone nucleotide contains sugar base and phosphate in Sugar question arises base and phosphate are connected at what position in Sugar so let me show you sugar first in sugar if you look at the carbon one two three four and five carbon number two which you see here will never be available for the attachment of neither sugar and neither phosphate nor base I am saying carbon number two will never be available for the attachment of base or phosphate because this two in case of deoxy is going to lose its oxygen so 2 is going to remain as it is it is not will be it will not be using connection anywhere the oh present at Carbon number one oh from carbon number one at Carbon number one will be used to connect with base the oh from carbon number one will be used to connect with base so we know now how sugar is going to connect to the base it will be o h then what we have got carbon number two we are not going to use it it's only left with 3 and Os at fifth so three and fifth so the oh at fifth oh at C5 will be used to connect with phosphate so everyone when we have got combination of Sugar Plus base Plus fate when we have a combination of sugar Plus base plus phosphate this collectively what we call it as is nucleotide so let me tell you a nucleotide base will be connected to sugar to the oh from base will be connected to Sugar through oh from C1 oh at C1 CrossFit connected to sugar from oh at C5 okay this is going to give you what nucleotide when this nucleotide will form a polynucleotide when this nucleotide upon polymerization forms polynucleotide so many nucleotide attaches themselves to form polynucleotides so that's where they use oh from C3 so see out of one two three and five see at four we don't have o h at Fourth we don't have it so fourth is ruled out anyways oh at first will be used where base will be connected to sugar o h at 2 will not be used because in deoxy will not have o h at all there is going to be only H so fourth and fifth are of no use to us fourth and fifth are of no use to us oh one will be used to combine with base oh from Phi will be used to combine with phosphate and which from 3 will be used to combine many nucleotides with each other to form a polynucleotide change so this is the whole thing so in order to understand nucleotide we studied sugar based phosphate is the combination we know how these three are connected to give you nucleotide now nucleotide will be connected to each other to form polynucleotides through oh at C3 so guys now let's see here let's see if I'm talking about individual nucleoside and nucleotide what is nucleoside Sugar Plus base okay let's say I'm talking about sugar of RNA the sugar of RNA is ribose three four five o h since it is beta this is which then right and right rest all our edges now since we are making nucleoside sugar is to be connected to base so base is connected to Sugar through oh from what C1 carbon now let's say we're talking about base let's take example of cytosine because cytosine is present in both RNA as well as DNA so where is cytosine this is cytosine okay so you can see we have got pyrimidine base so aromatic ring where nitrogen present at first and third foreign here we have nh2 and we have C double bond o oh hold on let me just check again an H2 and C double bond oh okay so this has to be a single Bond yes hold on side to scene let me redraw this everyone this is just a representation not really important to you all NH okay that's how it is okay so to make a nucleoside it's going to be a condensation of oh from C1 and NH so if we remove water from here look if you remove water this end will be connected to carbon number one which you can show like this now this is how the molecule will be connected so we have got sugar connected to base that is nucleoside and now if you want to make it nucleotide there has to be a attachment of Base as well and attachment of phosphate as well and phosphate connected to sugar via oh at C5 base connected to Sugar via oh at C1 correct so how are we going to write on that structure if I draw that again for nucleotides this is just giving you one example okay that's double bond o nh2 and ch2oh p double bond o single Bond o minus and o minus that's carbon number five h o h and o h rest all our edges well guys now I want you to observe at C1 we have got base connector at C5 we have got phosphate connected so sugar we are talking about RNA because this is ribose nucleic acid so o is still intact this is not deoxy so from C1 of the sugar it's base connected from C5 of the sugar it's phosphate connected so what is this this is nucleotide and now when we'll make it polynucleotide what will happen for polynucleotide polymerization takes place from C3 guys you remember this it takes place from C3 where is it yes nuclear converted to polynucleotide when OS connected from C3 meaning imagine now if we connect this o h with the C3 of the phosphate of other unit somewhat of this type okay oh connected to be connected to O minus further o minus this is connected to O carbon number five and for the chain like this here we have got some base Orange Orange h and H and just like this oh will be connected to a further chain you see so this was one nucleotide this is second nucleotide similarly now this nucleotide will be further connected so you'll be getting a polynucleotide chain connecting to each other and this polynucleotide is what you call it as nucleic acid if the sugar use contain oxygen it's a ribose nucleic acid so this is a polymer of rib giving you ribose nucleic acid and if you see a chain containing no oxygen at Carbon number two it's going to be deoxyribonucleic acid and that's how DNA and RNA exist well guys now just one typical type of question that you might see asking the exam if you will remember when you talk about when you see the structure of DNA or RNA you see the structure well I won't be able to draw exactly as such but you see the double strand like this not exactly though but somewhat like this and then you see some dotted lines in between like that well let me tell you these dotted lines are nothing but the hydrogen bonds for example let's say here it is we have got c u and we've got a G then likewise you again connect it to a so on and so forth so sometime they will give you code of the basis of one of the Strand and they will ask you to find out the complementary code of other strand which is associated with the previous one why hydrogen bond for example you may have a question like this one strand of DNA has a sequence of this basis by the way this is adenine time being guanine cytosine thymine thymine cytosine adenine if this is the sequence of one of the strand of DNA what is the sequence of the basis in the complementary stand that is what the question is meaning from whatever you see on the left hand side they'll give you sequence of that you'll have to find out from the right hand side basis sequence how do we do that well before that you have to understand this basic thing what is it remember in RNA the bases which are found in the polynucleotide change of RNA are cytosine uracil adenine and guanine cytosine uracil adenine and guanine if you see them I put them in a shape of you this is the trick I am telling you okay first I wrote C then you then I wrote A and G to remember this you can simply remember a sequence like this see you again guys this is very important and simple to understand see you again see you again see you AJ wrote it in a u form I wrote it in a u form okay c u a g or DNA the base is found in DNA are instead of see you again it is ctag see you again coag and ctag so you'll write down the basis like this C t a G see again I wrote them shape of you okay now here you will find the hydrogen bonding between T and G U and a so what we have to do c u a g bonding between C and G U and a in DNA the bonding will be between C and G and TNA so CG is going to be constant the only difference lies in this uracil is present in RNA thymine is present in DNA otherwise rest 3 bases remains same in DNA and RNA so let's say now what they have mentioned is one of the sequence what they have given is a e G C further whatever TT what are sequence they have given then to find out the complementary sequence so a now here they are talking about DNA still have to think of the sequence c t AG or RNA CU again coog for DNA it is ctag so if the sequence given is I'll write down the sequence again if the sequence given is EtG 80 g c e C and A then what is going to be complementary sequence in DNA a is hydrogen bonded to T So for a I'll write down t obviously for T it is going to be a that's a complementary base or G it is going to be C or C it is going to be G or t it is a again t meaning a or C it is G and for 8 is T so if this is the given sequence then this is the complementary sequence the first one is given the second one is complementary okay let's verify a t t a g c c g e a t a c g and a t so guys that's how we find out the complementary sequence which you may see in the questions dear students that was all about the amino acids proteins and nucleic acid we have covered everything that is required the most important thing probably you may get confused in finding out isoelectric point so make sure you do that well especially when acidic or basic alphamino acid is given so guys let me summarize what we have seen today we started our discussion with the first part that was Alpha amino acids so we first understood what is Alpha amino acids how they polymerizes to form protein molecules we saw classification essential and non-essential we understood the importance of essential amino acids then we saw another classification based on how many acid and basic groups are present so we got neutral acidic and basic amino acid well once that was done then we talked about in aqueous solution how amino acid exists in dipolar form called as veteran and then a term called as isoelectric Point how to find out isoelectric Point meaning which PK values to be considered for neutral acidic and basic Alpha amino acid once that was done we studied something called as peptide we studied oligopeptide polypeptide if molar mass of polypeptide is more than 10 000 we call it as protein so if a particular amino acids have been given and if they ask us to find out how many combination of that amino acids can be formed we saw one question related to that then guys we also saw that proteins are the one which are naturally occurring nitrogenous organic polypeptides which upon hydrolysis gives you various Alpha amino acids so we'll have to understand that what is n terminal what is C terminal and make a use of this while solving questions of finding out the sequence of peptides then we studied the structure of proteins primary secondary tertiary and quaternary proteins further we saw classification of amine which is tertiary structure detail fibrous and globular protein we also study term called as denaturation of protein the best example you can remember is boiling of an egg which is irreversible denaturation then we this we we discussed about nucleic acid we saw how living cells consist of the nucleoproteins so other than protein there exists uh the polymeric chain of nucleic acid exists in the form of DNA or RNA so for understanding DNA and RNA we understood a term called as polynucleotide a term called as nucleotide nucleotide is a combination of sugar base and phosphate we saw what kind of sugar exist and what kind of base is purine and pyrimidine and which bases are found in DNA and which of them are found in RNA and we learn how to get the structures so guys that is it from our today's class hoping that you all are paying attention following the lectures and making sure that you get a hold on that particular subject and the chapter so guys one more question as always as always I say solve more dpps and make sure that you guys are right on track I'll see you soon with the next class but today we'll stop here thank you so much everyone see you soon