[Music] welcome to the course biochemistry 1 conducted by myself Dr s Das Gupta of the Department of Chemistry IIT kukur in this course we will be studying certain aspects of biochemistry starting from the structures and functions of biomolecules right onto bioenergetics and Metabolism the topics that we will be covering are structures and functions of biological molecules in that we will be considering amino acids and proteins enzymes under enzymes we'll be considering the mechanisms of specific enzymes then we will go on to vitamins and co-enzymes carbohydrates and lipids nucleic acids and their components all of the topics of this course will be covered in their entirety as is relevant to this course we then will be considering the principles of bioenergetics with special reference to carbohydrate metabolism the books that we will be covering are common biochemistry books such as strier leninger Voit and Voit apart from this there are many internet sites and websites that give us a lot of information on biology and biochemistry in general so you could also look up those sites where there are specific course material available and specific tutorials and quiz materials also available for you to access when we consider the central dogma of biology the first thing that comes to mind is DNA DNA is the story medium the central dogma of biology goes like this DNA to RNA to protein we have a text that is comprised of DNA which is the four bases of DNA that are the storage medium this is then transcript red to RNA which is the transmission medium that also is comprised of four bases one of them being a bit different the RNA is then translated to the protein the alphabet of DNA RNA and protein is slightly different what is this alphabet in DNA we have four letters to the alphabet the four letters are as you can see here a g t and c these are the four letters that comprise the alphabet of DNA if you look at the corresponding alphabet of RNA you will see that we have U C A and G when we go on to study the structure and the contents of nucleic acids the structures of each of these bases will be much clearer but for now we have to know that DNA and RNA are comprised of these letters which are actually or which actually represent nitrogenous bases the protein alphabet is a bit different the protein alphabet is sometimes represented as a three-letter code which we will see in a moment or by the onlet code which is another representation of the very same three-letter code the protein alphabet is comprised of 20 unique letters that tell us what the protein sequence is we will understand what an amino acid sequence is once we get into the details of what is the peptide bond and what is an amino acid the first thing that we know or we try to understand here is the carbon atom now if we we consider what these proteins are actually made of the proteins consists of amino acids that are linked by peptide bonds we will understand this also in detail to see how a peptide bond is actually form and how we can link these letters together into forming what would be like a sentence each amino acid consists of a central carbon atom which you can see marked as C Alpha here so we have the central carbon atom that is marked as C Alpha to it we have an amino group all of you recognize an amino group as the nh2 group we then have the carboxilic acid group which is C we also have what is called an R Group now this R Group is what is the side chain of the amino acid and we also have the hydrogen group the hydrogen atom here what is common to all amino acids is this part because it has an amino group it has an acid group this is why it is called an amino acid it also has an h a hydrogen attached to it so we see that this Central carbon is actually a chyal carbon meaning that it is asymmetric which again means that there are four different groups attached to the central carbon atom and since all amino acids have a common set of groups here in the amino group the hydrogen atom and the carboxy group what differs is this side chain which can be different atoms different groups of atoms and this is what actually distinguishes the various amino acids we are now going to consider what types of R groups we can actually have now if we look at the different forms of the amino acids that could be incorporated into proteins as we mentioned in the previous slide we have an amino group we have a carboxy group we have a hydrogen atom and we also have an R Group attached to it now because of its chirality it can have an L form or a d form usually L amino acids are incorporated into proteins now you understand that these side chains the R Group can now differ in its size it can differ in its shape it can differ in its polarity we understand what each of these mean but there are 20 common amino acids which have distinctive R groups with distinct properties of size shape and polarity we will consider the amino acid side chains by group in each case and what you have to remember is the three-letter code of the amino acids along with their one letter code as well and obviously you have to remember what the side chain comprises what we have listed here is Glycine and Proline Glycine and Proline are unique amino acids in ways that we will see in a moment glycine is the simplest amino acid because the R Group is just an hydrogen atom now this hydrogen atom makes the carbon Central carbon at atom of glycine symmetric because now now it does not have four different groups attached to it it has two H atoms attached to it which does not make it chyal anymore and this is the only such amino acid so if we look at the side chain of glycine where the R Group is written here and we now know that this is where the R Group is attached this is our amino group and this is our carboxilic acid group now if you notice the way we have written the amino acid we have written it with an nh3+ and a c o minus this is because at physiological pH this o is lost due to the PE a value of the carboxilic group which we will we will be doing in the subsequent class and this amino group is protonated which means that it has an additional hydrogen atom to it making this nitrogen positively charged this is what is called the zwitterionic form of the amino acid it is written as the zwitter ionic form and it is usually usually represented in this fashion so this is what we would call a zwitter ion it is represented in this fashion because we would like to represent the amino acids as what they would be at physiological pH the next unique amino acid is Proline now if you notice it does not have a distinct R Group attached to it but the R Group is actually linked up to what is called the amino group here so the side chain is actually ch2 ch2 ch2 but linked to the nh+ in this case so we have a c Alpha with the hydrogen with the carboxilic acid here but but instead of being an amino acid Proline is actually what we would call an amino acid because we do not have an amine group here we have an amine so we have an amino acid where the ch2 ch2 ch2 bends on to itself to form Proline so these are the two amino acids that are unique in their features glycine being just because it has the hydrogen atom there and it is ayal and Proline because it is an AM amino acid because the side chain bends back upon itself and as I mentioned when we represent the amino acids we represent them in a zionic form where we write nh3+ and and Co minus because this is how they would remain in or at physiological pH in normal solution if we go to the next group of amino acids we consider now hydrophobic amino acids now what are hydrophobic amino acids hydrophobic amino acids are those amino acids that are comprised mostly of carbon atoms and hydrogen atoms in their side chains so they would tend to be away from the solvent usually the solvent being water or waterbased they would be away from water so they would be hydrophobic not liking to be in water water now what are these specific side chains that we can have the simplest one of these side chains is alanine alanine the threel code is a l a and the oneel code is a the side chain is a methy group so this is what we would say is the r group and you recognize again the zionic representation of the amino acid we then come to valine valine is beta branched we have ch ch3 ch3 we then have leucine ch2 ch ch3 ch3 so it is Branched at the GMA atom and the way these are represented is that if this is the C Alpha the next atom is the C beta connected to the C beta are the C gamma atoms which would be a unique representation of the amino acid Vine if we look at Lucine we would again have a unique representation considering that this is C Alpha the next one is C C beta the next one is C gamma and ATT attached to the C gamma are two c Deltas one is represented as cd1 and the other as cd2 in the alanine side chain we would just have a c beta carbon a c b so these could actually be represented very clearly in a unique manner where each amino acid this part being common the side chains could be represented by the types of atoms that are attached to the C Alpha if we look at isoline we have ch ch3 ch2 ch3 so we have two the beta carbon one methy group and one eile group attached to it this is isoline now if you look at all the side chains that have been circled here they are comprised of carbon and hydrogen only which make them hydrophobic in nature methine can fall into this category as well but it has a sulfur atom and a methy group attached to to the sulfur atom so we have the C Alpha we have a c beta a c gamma and to the C gamma is attached this sulfur atom and then we have a methy group attached to the sulfur methionine along with another amino acid which we will consider in a moment cysteine are the two sulfur containing amino acids and they could be grouped together in in a group of their own or they could be considered in this group as well the next group that we will be considering are the polar amino acids now what we mean by polar amino acids are those that have an oxygen or a nitrogen at a atom in their side chain and by virtue of having this o oxygen and nitrogen in the side chain these heter atoms they can participate in polar interactions not only amongst themselves but also within or with the solvent molecules so they can participate in what we call hydrogen bonding which is extremely important in non-covalent interactions in proteins which is what hold a protein folded together the protein chain the amino acid chain we will see that in subsequent classes but the polar amino acids are ones that are likely to interact with the solvent and in this interaction they can allow the oxygen and nitrogen atoms that they are comprised of to interact with the solvent or within themselves to form a network and remain in solvent in contrast the hydrophobic amino acids are unlikely to be on the surface of the protein so when we have a protein which is actually a globular structure which we will see in subsequent classes we will see that there are certain side chains that prefer to be on the surface of the protein and there are certain side chains that prefer to be away from the solvent which we have seen in the previous slide would be the ones that are hydrophobic in nature now if you go back to look at the side chains that comprise is this polar group of amino acids what we have here is each of these have an oxygen or a nitrogen attached to it we have of course the common part of each amino acid the asparagine site chain in the asparagine side chain and the glutamine side chain this being the common part again we have amide groups amide groups are C double bond o nh2 groups so this comprises the amide of asparagin this comprises the amide of glutamine the difference is that the glutamine chain is one carbon longer than the asparagin chain so what we have here is is we have a ch2 that is the beta carbon attached to the alpha carbon followed by a gamma carbon that has attached to it an oxygen atom and an nh2 so this amide group has a single beta I mean a carbon attached to the C Alpha in glutamine we have two ch2 Moes here we have a c Alpha a c beta a c gamma a c Delta and to it is attached to the cble bond o and the nh2 or the oxygen and the nitrogen so what can actually happen is this oxygen and nitrogen similarly in glutamine can participate in what is hydrogen bonding meaning that if we have a specific donor or an acceptor then this could participate in hydrogen bonding not only with other amino acids but also with the solvent if we look at Serene Serene is a small amino acid but a polar amino acid the group that it has is ch2 O and it is this o that can participate in hydrogen bonding threonine is the next amino acid it has attached to the beta carbon a ch3 and an O so again it differs from Serene you see how each of these are unique in their own way the next amino acid is cysteine cysteine is another the amino acids that has with it a sulfur atom the other one that we saw on the previous side slide was methionine that also had a sulfur atom but to the sulfur was attached a methy group here we have a hydrogen atom making this a thol so we have a ch2 sh this is histadine histadine is a very important amino acid which will be we will come across a lot when we consider the enzymes and the enzyme mechanisms because of its specific polarity or specific properties of this side chain that is an imidazol group so again we have a common amino acid part here in histadine we have two nitrogens in the side chain for that is part of of the imidazol ring so what you can see in this polar group of amino acids is all side chains that belong to this group contain what is called a hetero atom the next group of side chains that we will be considering is acidic amino acids we looked at at aspar gen and glutamine in our previous slide what we found in the asparagine was the couble bond nh2 now we know that an amide comes from an carboxilic acid so the asparagine comes from a specific carboxilic acid similarly glutamine also comes from a carboxylic acid so we group them into what are called acidic amino acids and we call all the specific acids aspartic acid which gives rise to as sparten and glutamic acid which gives rise to glutamine now what we have here is a couble bond o o minus now this is apart from the actual carboxilic acid that comprises the part that is common to all amino acids this is part of the R Group the side chain so the side chain in this case also contains a c bond o o minus similarly the side chain in glutamic acid also has the co minus but again we have an additional ch2 in case of glutamic acid just like we had for glutamine now what we have written here in addition is what is called a PKA value we will learn more about this in our next class but just for a preliminary information if the pka value is less than the pH of your solution then your carboxilic acid is going to lose the proton similarly this has lost its proton but this has not what does this mean it means that the pka value of this amino group is actually higher than physiological pH which is why it has still kept its proton attached to it okay but the PK if we consider the physiological pH to be 7.4 it means that the pka of this group is greater than 7.4 and we will see how it is actually something close to 9 between 9 and 10 so if we have the pka value greater than 7.4 this is going to remain protonated but these carboxilic acid groups cannot remain protonated so these comprise what are known as acidic Amino acids if there are acidic amino acids it means that there are also basic amino acids so what are these basic amino acids these are lysine and Arginine considering lysine and Arginine let us look at the groups now what are the side chains this is the long side chain of Lysine and this is the side chain of asparagin now if you look carefully at the side chains here there are two PKA values written what are these PKA values these PKA values are actually greater than the pH physiological pH which is why they are still protonated so we have protonated nitrogens because the physiological pH is 7.4 and we have not reached the pka value where this is going to lose its proton the BK value is where it's going to lose the proton which as I said we will discuss in our subsequent classes so apart from the common part amino group that we have here we have an additional amino group here because it is a basic amino acid in arginine we have what is called a guanidinium group here that is part of the side chain it has a nitrogen here a nitrogen here and a nitrogen here so this is lysine and this is Arginine and because of their properties especially the acidic and basic amino acids residues these are the residues that prefer to be on the surface of the protein so if we look at the different structures of the amino acids that we considered we have specific groupings the groupings are the polar amino acids so we have in a group by itself glycine and Proline because of the uniqueness in their properties we have also other polar amino acids we have hydrophobic amino acids we have acid amino acids and we have basic amino acids now there is another group of amino acids called the aromatic amino acids now the aromatic amino acids are unique as you can see the name itself suggests their property they are aromatic in nature under these we we have three amino acids Phile alanine tyrosine and tryptophan so let's look at their side chains these are the aromatic amino acids we have Phile alanine if you remember what alanine was it was just a methy group attached to the C Alpha in this case one hydrogen has been replaced by a Phile group so its name is pheny alanine we of course have our common part of the amino acid here the threel code for Phile alanine is pH and the one letter code is f so we have a fenile group replacing one hydrogen of alanine Phile alanine so this is aromatic in nature we have tyrosine which is similarly similar to phenyalanine the only difference being that this hydrogen is replaced by an O so the tyrosine can actually also be involved in hydrogen bonding in the grouping of amino acids this could also therefore be put into a polar group but it is usually grouped under the aromatic amino acids because of the Phile ring here so we have a ch2 and we have a Phile and an O attached to this which is called tyrosine in tryptophan we have an Indo ring attached to the ch2 this is a very bulky amino acid as you can see by the sheer size of it and it is quite rare in proteins in that it is not present to a very large extent in many proteins the unique properties of these aromatic amino acids which make the protein useful in an an analytical way is all the aromatic amino acids that we have considered the aromatic amino acids which are as I wrote previously phenyalanine tyrosine and tryptophan each of these absorb UV light they absorb Ultra violet light so their presence in proteins can actually be utilized in this fashion what do we mean by that they absorb UV light in the range they have different Lambda Max values but usually we look at 280 nanom to ident ify a protein so if we have a solution that has a certain amount of protein in it we can actually determine the amount of protein present in the solution by a consideration of the number of phenyalanine tyrosine and tryptophan that are present in the protein chain so if we monitor or we find out the absorbance at 280 nanometer we know what is called the extinction of our protein and we know the length of the cell we know the extinction coefficient of the protein and we know what the absorbance is at 280 nanometer which is also represented as a280 we can determine the concentration of the protein so what we have is the presence of these aromatic amino acids help us in determining whether our solution actually contains protein or not and we can also find out the content or the concentration of the protein in Solution by virtue of their having phenyalanine tyrosine and tryptophan of these tryptophan has the highest Extinction which means that if you have a large number of tryptophan amino acids in the protein you are going to have a larger absorbance at 289 nanometers but the presence of the aromatic amino acids themselves will give an absorbance at 280 nanometers which is how proteins are monitored in Biochemistry Laboratories the next thing that we are going to look into is a representation when we consider a representation of amino acids as we have already seen we have a carboxy group we have an amino group we have a hydrogen which is common to all amino acids and we have a side chain R now if you look at this side chain you recognize that this is an amide group the two amide groups were asparagine and glutamine the glutamine side chain had two ch2 groups so we have two ch2 groups attached here this is what is called a stick representation which we will also look at in the next class where we have the asymmetric carbon in green the others in Gray nitrogen's in blue Oxygen's in red and the other carbon atoms in Gray if we look at now the linking of these amino acids because we know that when we're going to form proteins these are actually the building blocks of proteins now these building blocks have to be linked together how are they linked together they are linked together by what is called a peptide bond now if you look at the representation here that we have shown on the left here this is not a zwitterionic representation because the proton of the carboxilic group is still attached to it and this is the nh2 group in actual form it would remain as has nh3+ and Co minus but what we have here is we have two R groups now how do we have two R groups in the first amino acid that we have on the left hand side we have what is called an amino terminal so this is what is called a dipeptide because we have two amino acids linked by a peptide bond in this linkage which is our peptide linkage we have a cou bond o and an NH but if we look at our original amino acid we are missing an O from the carboxilic acid side and we are missing an H from the amino side what does that make it makes H2O so when we are linking two amino acids by the elimination of H2O we can form a peptide bond we will look at into the features of peptide bonds once we consider the protein structure in general and the amino acid sequence but what we have to remember here is that when these amino acids are linked together on the left hand side you always have the N Terminus and on the right hand side you always have the C terminus because this is the way the proteins are formed this is the way they are synthesized so we have an amino terminal and we have a carboxilic acid terminal and the first amino acid is the one that always has the nh3+ attached to it and the last amino acid in a protein sequence or in a protein chain is the one that has the co minus attached to it so this is what we have a dipeptide linked by a peptide bond there are certain features of the peptide bond unique to protein structure and peptide bonds that we will study in later classes so what do we essentially have in this case we have say a glycine now what has happened to this glycine in this case we have a representation in the zionic form the glycine is one where we have if you remember from our representation of the amino acids we have an R group that is H here we have an R group that is ch3 in cine we have an R group that is ch2 sh so these are for glycine we can actually we actually cannot distinguish which is the R Group because the hydrogen is present and the hydrogen is also the side chain so we have an nh3+ we have a CO and here we are now forming an or eliminating water into forming a couble bond o NH H so this is what has been formed this should not be there so we have a c couble Bond o NH h a couble bond o n h so in the formation of our tripeptide we have glycine alanine cysteine we can go on to form other peptide linkages so what we can have is if we look at the basic structure of an amino acid we have a c Alpha we have an NH H 3+ we have a c o minus we have an h and we have attached to this and R one group if we Now link another amino acid so we would have another nh3+ that would belong to our second amino acid we have our Co minus and we have our H and we have our R2 so now when we combine these two amino acids to form what is called a dipeptide we would have linked these via a peptide bond and we would have our a couble bond o the NH coming from the second amino acid the C Alpha the R2 the H and the co minus so this is what is our peptide linkage this particular linkage is known as the peptide linkage what do we have we have linked now R1 and R2 now in a representation of a protein it is not very convenient to keep on writing all the atoms together we know that in the protein sequence in the primary amino acid sequence the proteins are or the amino acids the building blocks are linked together by the peptide bonds now since they are just linked by the peptide bonds then it is not necessary to write what is common to all the amino acids because these are certain features that we already know so instead of writing in each case the nh3+ or the co minus we also know that the first amino acid is going to be linked with the nh3+ terminal and we know that the last one is going to be linked with the co minus so it is sufficient to write instead of writing this in an elaborate fashion when we write a protein sequence as we will see later to write what is called a protein sequence all the information we actually need is what is R1 and what is R2 because we know that each amino acid looks the same it is only the difference that we have in the R Group so if we just know what R1 and R2 are when we have our protein sequence we need to know how they are linked together so if this is amino acid 1 this is amino acid 2 I know that this has to have the nh3+ attached to it 3 4 and so on say to 120 I know that this has to have the co minus attached to it and I also know that these linkages are nothing but peptide bonds so if this is the information that I know I just need to know what R1 is what R2 is what R3 is what R4 is and so on and so forth this is why we just write either the three-letter code or the onlet code in the three-letter code if this first one were a glycine I would write gly linked with say ala alanine linked with a acidic amino acid aspartic acid linked with the basic amino acid lysine and so on and so forth because now when I have Glycine and alanine and aspartic acid I know what the rest of the atoms are because I know the side chain of glycine I know the side chain of alanine and so on and so forth if I write this in a one letter code it would be g a d k so if I just wrote g a d k you could write the structure of this tetrapeptide similarly when we consider a whole protein chain in this case say just 120 amino acids we could consider the whole protein chain so the differences that we actually look at are in the properties of the amino acid side chains what is so important first is the size and shape of the amino acid that is extremely important in its accommodation how is it going to be accommodated in the protein we look at the charge on the protein is it acidic is it basic we look at the polarity can it be involved in hydrogen bonding is it a polar amino acid hydrophobicity where is this amino acid likely to be located is it going to be located in the center of the protein because it likes to be away from the solvent or is it going to be likely to be on the surface of the protein but we know that any hydrophobic amino acid would prefer to be in the core of the protein aromaticity this the aromatic amino acids that we considered phenyalanine tyrosine tryptophan these are important in imparting UV properties to amino acids because these are the ones that absorb UV light and because of their the absorption of UV light proteins can be detected in solution due to the presence of the aromatic amino acids and from what is known as the beer Lambert's law we can find out the concentration of the proteins provided we know what the extinction coefficient is the confirmation now the confirmation as we looked at is obviously usually determined by the side chain we will see since most of these side chains are linked by single bonds we will see how rotation about the side chains can actually bring about confirmational changes to the amino acid ID orientations in the proteins and this change in confirmation or the change in what is known as the dihedral angles will allow us to look at different properties of the amino acids in the way they interact with other amino acids we also look at their propensity to adopt a particular confirmation what does it mean it means that if a protein were to have an amino acid that would likely form what is known as a helix or be part of a helix that is what we call the propensity is it likely to be in a helix is it likely to be in a sheet now these terms will be be much more apparent will be much more clearer as we go to to our subsequent classes so what we actually did learn today is the different types of amino acids the different groupings of amino acids and the important properties of the side chains of the amino acids we considered that the central carbon atom the asymmetric carbon atom which is also known as the alpha carbon atom has linked to it four different groups these are a hydrogen atom an amino group a carboxilic group and a side chain that is represented as R now each of the r groups there are 20 such different common amino acids the 20 common amino acids have 20 different R groups that differ largely in their properties the H we have different types of amino acids the amino acids are as I said grouped into the type of R group or the type of side chain that they have attached to them we have unique amino acids Glycine and Proline we have hydrophobic amino acids we have polar amino acids we have acidic and basic amino acids and we have aromatic amino acids some of these contain sulfur two of them methionine and cysteine there are others that have hetero atoms in them oxygen and nitrogens and there are others that have their side chains comprised entirely of carbon and hydrogen making them hydrophobic in nature and lastly we look at the overall properties that we can consider together the size the shape the charge the polarity the hydrophobicity and the aromaticity and all of these will actually determine what the property of the protein is in general because we know that these amino acids are linked by peptide bonds in the linkage of the peptide bonds we are bringing different types of amino acids together to form our protein sequence our amino acid sequence which we will study in classes later on where we will be looking at protein structures in detail we looked at the peptide bond and we saw how the amino acids were linked together by the peptide bond and how we can actually represent the protein sequence by just writing either the three-letter code one after the other or the onlet code one after the other because we know that the first amino acid is going to be the N Terminus and the last amino acid is going to be the C Terminus which means that the first amino acid is going to have the NH3 plus attached to it and the last amino acid is going to have the co minus attached to it making up the protein chain we will learn in later classes how the protein actually folds and how the hydrophobic Amino acids tend to remain in the center of the protein thank you