Amino acids structure and properties

Detailed Amino acid structure, Zwitter ions, acid base properties of Amino acids, Chirality, L and D forms of amino acids,standard and non standard amino acids, Essential and non essential amino acids,Learn all amino acids, their properties in detail,methods to quantify amino acids

1. Amino acids structure and properties Dr. Lakshmi

2. Class Learning Objectives (CLO) At the end of the lecture, students should : Describe the general structure of amino acids. Recognize the importance of genetic code in the formation of Peptide bonds Understand the acid/base properties of AA. Examine the chirality and Stereo chemical representations of AA Differentiate the L and D forms of Amino acids Differential standard and non standard amino acids Classify amino acids based on their property.

3. Amino acids are monomers (single units) and join to form polymers (many units) of proteins Basic concepts

4. Making and Breakdown of Polymers Basic concepts A dehydration or condensation reaction occurs when two monomers (amino acids join) bond together through the loss of a water molecule (Making of a protein) (Making of a polymer) Polymers are disassembled to monomers by hydrolysis, a reaction that is essentially the reverse of the dehydration reaction (Breaking of protein to give Amino acids) (Breaking of polymer)

5. Formation of Peptide Bonds Amino acids are monomers and get joined by the formation of a peptide bond (CONH). Amino group of one molecule reacts with the carboxyl group of other, resulting in elimination of water and formation of dipeptide bond. A condensation reaction (loss of water ) forms a peptide bond between two amino acids A dehydration reaction occurs when two monomers bond together through the loss of a water molecule.

6. Protein synthesis   is the  process  in which cells make  proteins . It occurs in two stages: transcription and translation. Transcription is the transfer of genetic instructions in DNA to mRNA in the nucleus. It includes three  steps : initiation, elongation, and termination. Protein synthesis takes place in ribosomes Instruction and Information on the kind of protein synthesis comes from genes .

7. When joined in a series of peptide bonds AA are called residues t o distinguish it from free form and forms found in proteins. Peptide : short sequence of residues Polypeptide : longer chain of residues of known sequence and length

8. Amino acids GENETIC CODE SPECIFIES 20 AMINO ACIDS: All 20 Amino acids are encoded by nucleotide triplets called codons Codon is a 3 letter genetic code (AUG) Genetic codon is Redundant meaning several AA are specified by multiple codons There  are  22  genetically encoded (proteinogenic)  amino acids ,  20  in the standard genetic code and an additional 2 that can be incorporated by special translation mechanisms. Selenocysteine (Sec) and pyrrolysine ( Pyl ) are rare amino acids that are cotranslationally inserted into proteins and known as the 21st and 22nd amino acids in the genetic code. Sec and Pyl are encoded by UGA and UAG codons, respectively, which normally serve as stop signals

9. Amino acids (AA) are building blocks of proteins All proteins are made of 20 different AA, and form building blocks of proteins. There are only five atoms that will appear in your amino acid variable groups:  H, C, N, O, and S. The term amino acid is short for α- amino [alpha-amino-] carboxylic acid . It is called alpha amino acid because amino group is attached to the alpha carbon, the carbon next to carbonyl group Amino acid is any of a group of organic molecules that consist of a basic amino group (― NH2 ), All AA contain key elements such as carbon, hydrogen, nitrogen and oxygen except the two amino acids with sulfur atoms in their side chains: cysteine and methionine . AA is represented by a skeletal diagram as Zwitterion state at neutral pH.

10. Basic Structure of an Amino Acid All amino acids include five basic parts: A central carbon atom (the alpha carbon or chiral carbon): All amino acids contain a  carbon  atom in the middle of the molecule, the alpha-carbon, The first carbon is the part of the carboxyl group. The second carbon, to which is attached the amino group, is called the α-carbon. One is a basic amine group -NH 2: an amino group - consisting of a nitrogen atom (nitrogen is a proton acceptor so it is basic) and two hydrogen atoms. The second one is acidic carboxyl group – COOH: a carboxyl group - consisting of a carbon atom, two oxygen atoms and one hydrogen atom(H is a proton donor so it is acidic) A hydrogen atom The third group is denoted by R group or side chain. This is the variable radical group and is different for every amino acid. This R group makes the amino acid unique. They can be hydrophobic or hydrophilic, aliphatic or aromatic etc

11. Amino acids  containing an  amino  group bonded directly to the  alpha  carbon are also referred to as alpha amino acids .  All amino acids found in proteins have this basic structure, differing only in the structure of the R-group or the side chain . It is the R-group or side chain that differs between the 20 amino acids. The simplest, and smallest, amino acid found in proteins is glycine for which the R-group is a hydrogen (H) and where the α-carbon is symmetric , because in glycine the R group is just hydrogen There are 1000s of amino acids in nature but only about 20 amino acids form a part of the proteins in the human body. These twenty acids will be our focus here. What difference did you notice between these 2 amino acids R group here is methyl group Important points to note on Amino acids

12. Zwitterions - Amino Acids A zwitterion is a molecule with functional groups, of which at least one has a positive and one has a negative electrical charge. The net charge of the entire molecule is zero. Amino acids are the best-known examples of zwitterions. : They contain an amine group (basic- proton acceptors ) and a carboxylic group (acidic- proton donors ). There is an internal transfer of a hydrogen ion from the -COOH group to the -NH2 group to leave an ion with both a negative charge and a positive charge. This is called a zwitterion. The -NH 2  group is the stronger base, and so it picks up H +  from the -COOH group to leave a zwitterion (i.e. the amine group de-protonates the carboxylic acid) The (neutral) zwitterion is the usual form amino acids exist in solution and as solids. It is electrically neutral and carries no net charge In the physiological pH range (5-8), the α carboxyl and α-amino groups of amino acids are completely ionized

13. Depending on the change in pH , AA can exist in 2 forms Adding an acid to AA solution decrease the pH(low pH – 2,acidic condition) If the pH is lower, than the isoelectric point then the amino acid acts as a base and accepts a proton (H) at the amino group. This gives it a positive change. The -COO -  part of the zwitter ion picks up hydrogen ion. During electrophoresis, AA would move towards the cathode (the negative electrode) as Cations are (positively charged). 1.CATIONS +++ 2.ANIONS (-ve) Adding an alkali to AA solution(high pH-12) increases the pH Increase pH of solution of AA by adding hydroxide ions Hydrogen ion is removed from the -NH 3 +  group. In electrophoresis, these negative ions (anions) of AA negative ion flow toward  the  anode

14. THE ACID BASE PROPERTIES OF AA Amino acids  are  amphiprotic : Meaning they can accept or donate protons. Amino acids are amphoteric:  AA can react with  acids  or bases, The carboxyl group is able to lose a proton and the amine group is able to accept a proton Amino acids are dipole: meaning it is an electrically neutral molecule carrying a positive and a negative charge but no net charge and at this pH the AA will not migrate to anode or cathode in electrophoresis. This pH is called the isoelectric point or p I Amino acids are called zwitterion: For each  amino acid  there is a particular pH, the isoelectric point, at which the  amino acid  exists as the neutral zwitter ion. Depending on the pH, AA exist in 3 forms as cations, anions and as zwitter ions. AA functions as buffers. It is important to study acid base properties of AA as it finally influences the behavior of proteins, helps us in methods of identification of different types of AA and to understand AA reactions

15. Chirality (means hand) and Stereoisomerism Chiral atoms not super imposable on mirror image. Click here to watch the video (ctrl plus click) : https://youtu.be/0cfX72BT2Ww

16. Amino Acids are optically active except glycine. (mirror images of each other and rotate plane polarized light but not super imposable). The α-carbon of most amino acids is joined by covalent bonds to 4 different groups. The four bonds of the central (alpha) carbon (C) of an amino acid are directed towards the four corners of a  tetrahedron . Therefore, this carbon atom is also called a chiral carbon or central of chirality or as a stereocenter . A chiral carbon has 4 unique groups attached to it, so it is asymmetrical carbon. In other words, if you pass plain polarized light at an amino acid, then because the carbon is chiral, it would rotate the light. Chirality is an optical activity. Chirality

17. If a molecule contains one asymmetrical carbon, 2 distinguishable stereoisomers exist; these are non super imposable mirror images of one another or called enantiomers as seen in figure. Stereoisomers are designated  D (dextro-rotatory) or L (levo-rotatory ) according to the direction in which the crystalline forms rotate polarized light, to the right and left, respectively. Naturally-occurring proteins comprise exclusively the L forms of amino acids. The L and D can be distinguished from one another experimentally because their solutions rotate the plane of polarized light in opposite directions, so also called as optical isomers In this example, Alanine has a CH3 as a radical group. If you imagine holding the model with the COOH at the top and the NH2 at the bottom, the CH3 radical group in the D form will be on your right. In the mirror image L form, it will be on the left. Another way to project AA structure is by using Fisher projection, It highlights the 4 groups around chiral carbon. Look at the Amino group if its on Left then it is L amino acid and if Amino is on right side then D AA

18. AA is represented by a stereochemical view showing the arrangement of atoms. It represents the position in space of each atom. The amino, carboxyl, hydrogen and R groups are arranged tetrahedrally around central alpha carbon.

19. Why more of L form? Reason not clearly known. Speculations: Repetitive substructure in proteins (helices, sheets, turns) require all amino acids have the same configuration. Apparently, living systems evolved from L amino acids based upon an initial random choice AA with D configuration can be found in microorganisms (e.g. in the bacterial cell wall and in antibiotic peptides) and in certain animals (e.g. the frog skin peptide ‘ dermorphin ’) BUT NEVER FOUND IN PROTEINS

20. Amino acids are represented using one and three letter abbreviations while representing them in a sequence of peptides or protein

21. Some easy ways of remembering the one letter code for amino acids C= Cys =Cysteine H= His=Histidine I=Ile=Isoleucine M=Met=Methionine S= Ser=Serine V=Val = valine If more than one amino acid begins with a certain letter, that letter is given to most commonly occurring amino acid A= Ala = Alanine G= Gly =Glycine L=Leu=Leucine P=Pro=Proline T= Thr =Threonine In others letters close to the initial is used Amides have a leter in middle of alphabet D= Asp=Aspartic acid (near A) E= Glu=glutamic acid (near G) Q= Gln=Glutamine (Qtamine) N=Asn=Asparagine (contain N) K=Lys=Lysine (near L) Some are phenotypically suggestive F= Phe = Phenylalanine R= Arg = aRginine Y= Tyr= tYrosine W= Trp = Trypotophan (double ring in molecule)

22. Types of Amino acids Standard Amino acids / Proteinogenic or Natural Amino acids Nonstandard amino acid A standard amino acid is an amino acid organisms use in the synthesis of peptides. A nonstandard amino acid is an amino acid that occurs naturally in cells but do not participate i n peptide synthesis. There are 22 amino acids which are naturally occurring and are incorporated into polypeptides. They are called Proteinogenic or Natural Amino acids They are generated by modification of standard amino acids in the peptide molecule ( post-translational modification). Out of the 22 standard amino acids, 20 are alpha amino acids encoded by universal genetic code; remaining 2 are incorporated into proteins by unique synthetic mechanism.  Not encoded in the universal genetic code. Selenocysteine (Sec) and pyrrolysine (Pyl) are rare amino acids that are cotranslationally inserted into proteins and known as the 21st and 22nd amino acids in the genetic code. Sec and Pyl are encoded by UGA and UAG codons, respectively, which normally serve as stop signals Example: Significant proportions of the amino acids in collagen are modified forms of proline and lysine: 4-hydroxyproline and 5-hydroxylysine. GABA and L- DOPA)

23. When isolated from proteins, AA are white crystalline solids. AA have high melting and boiling points (not common for other organic compounds) AA have electrical conductivity AA have high solubility All last 3 properties are because of the presence of charged groups. An positive charged Amino NH3 and carboxyl group COO- attached to alpha carbon PROPERTIES OF AMINO ACIDS

24. Classification of Amino Acids based on nutritional requirements Essential Amino acids or Indispensable AA N on-essential amino acids or dispensable AA  Amino Acids are those that cannot be synthesized by the body on its own AA that your body can produce, specifically by the liver, without any outside help. Must be obtained from diet . Does not store them so required on daily basis Do not have to be taken in diet, body can make it. Most of them are produced from glucose.  Number There are 9 essential amino acids Number There are 11 of them Function: As precursor for neurotransmitter in brain, Build and repair muscle tissue Function: Removal of toxins, anti ageing, wound healing etc Provides 55% of daily energy requirement Source Has to be taken with food, animal proteins such as egg, meat, chicken, plant products such as soy Source Can be manufactured in the body from carbohydrates and other amino acids. Also available in food Deficiencies Can occur if your diet is inadequate; weak immune system due to less antibodies, lack of neurotransmitter Starvation. Rare but can occur with illness

25. Classification of Amino Acids based on nutritional requirements Semi essential Amino Acids They are formed in the body but not in sufficient amount for body requirement; especially in children and sick people. Example: Arginine and Histidine can be formed by adults but not kids

26. All amino acids found in proteins have this basic structure, differing only in the structure of the R-group or the side chain . It is the R-group or side chain that differs between the 20 amino acids and accounts for the physical properties of protein. Basic structure for all 19 AA is same except proline ,which has an unusual cyclic ring formed by the side chain bonding directly to amide nitrogen. The simplest, and smallest, amino acid found in proteins is glycine for which the R-group is a hydrogen (H) and where the α-carbon is symmetric , because in glycine the R group is just hydrogen There are 1000s of amino acids in nature but only about 20 amino acids form a part of the proteins in the human body. These twenty acids will be our focus here. What difference did you notice between these 2 amino acids R group here is methyl group Important points to note on Amino acids

27. Basic amino acid structure NH3 + ---------CH--------COO - R group Letz learn and draw the 20 AA and their chemical and physical properties of Amino acid Only R groups have to be replaced

28. Amino acids with Aliphatic side chains Aliphatic  implies that the protein  side chain  contains only carbon or hydrogen atoms. Aliphatic  amino acids are non-polar and hydrophobic . Hydrophobicity increases as the number of carbon atoms on the hydrocarbon  chain  increases. Most  aliphatic  amino acids are found within protein molecules

29. Lets replace this R with hydrogen, you will get simplest amino acid called Glycine. It is represented as Gly in 3 letter word and as G in one letter word. The R or side chain has hydrogen and so is uncharged Does not have chiral alpha carbon. Not a stereoisomer It is superimposable Smallest amino acid not essential AA H Amino acid 1: Glycine – Gly----G NH2 ---------CH--------COO H

30. Letz replace this R with methyl group It is non polar (cannot form hydrogen bonds) Are hydrophobic (Hate water, does not dissolve in water) Aliphatic means carbon atoms form open chains not aromatic rings. Always look for C or H in side chains, then it is non polar Non essential CH 3 Amino acid 2: Alanine – Ala----A NH2 ---------CH--------COO H

31. Letz replace this R or side is hydrophobic with CH-CH3-CH3 It is non polar (cannot form hydrogen bonds) Are hydrophobic (Hate water, does not dissolve in water) Aliphatic means carbon atoms form open chains not aromatic rings. Always look for C or H in side chains, then it is non polar It is a member of the branched-chain amino acid family, along with leucine and isoleucine . Essential AA Valine differs from threonine by replacement of the hydroxyl group with a methyl substituent,   CH Amino acid 3: Valine– Val----V CH 3 CH 3 NH2 ---------CH--------COO H

32. It has one additional methylene group in its side chain (R) compared with valine. It is non polar (cannot form hydrogen bonds) Are hydrophobic (Hate water, does not dissolve in water) Aliphatic means carbon atoms form open chains not aromatic rings. Always look for C or H in side chains, then it is non polar Leucine is an essential amino acid, which means that humans cannot synthesize it, so it must be ingested CH 2 Amino acid 4: Leucine– Leu----L CH 3 CH 3 CH NH2 ---------CH--------COO H

33. It has one additional methylene group in its side chain (R) compared with valine. It is non polar (cannot form hydrogen bonds) Are hydrophobic (Hate water, does not dissolve in water) Aliphatic means carbon atoms form open chains not aromatic rings. Always look for C or H in side chains, then it is non polar Iso Leucine is an essential amino acid, which means that humans cannot synthesize it, so it must be ingested NH2 ---------CH--------COO H CH Amino acid 5: IsoLeucine– Ile----I CH 3 CH 3 CH2

34. Ans1:Alanine, Valine, Isolecine and leucine Ans2:Glycine Ans 3: Valine, leucine and isoleucine . Revision Questions 1. Give examples of AA with aliphatic side chains? 2. Which amino acid is Not a stereoisomer and is superimposable ? 3. Which AA have branched-chain amino acid?

35. Amino acids with Hydroxyl and Suphur containing group

36. R or side chain has OH group (hydroxyl group) so polar Serine and threonine are the two AA having hydroxyl containing amino acids. Serine and Threonine are Hydrophilic due to the hydrogen bonding capacity of the hydroxyl group. Both Serine and threonine are site of phosphorylation (addition of phosphate) and glycosylation which is important for enzyme regulation and cell signaling. Addition of phosphates to create phosphoserine and phosphothreonine occurs as post translational modification. Non essential AA. OH Amino acid 6: Serine –Ser ----S CH 2 OH NH2 ---------CH--------COO H

37. amino acids with polar side chains. Hydrophilic It differs from serine by having in the R group a methyl substituent in place of one of the hydrogens on the β carbon. R or side chain has OH group (hydroxyl group) so polar Threonine and Serine are site of phosphorylation and glycosylation which is important for enzyme regulation and cell signaling. Threonine is an essential amino acid, NH 2 ---------CH--------COO H OH Amino acid 7: Threonine– Thr ----T CH CH 2 OH

38. Amino acids with polar side chains. Has a thiol group (SH) It is a Sulphur containing AA Because of its high reactivity, the thiol group of cysteine has numerous biological functions. It serves as a potent nucleophile and metal ligand (particularly for iron and zinc) Specialty or best known for its ability to form disulfide bonds , which often make an important contribution to the stability of extracellular proteins. Cysteine is a very important amino acid when it comes to tertiary and quaternary structure. Cysteine is a non-essential amino acid Amino acid 8: Cysteine– Cys----C CH 2 SH

39. Amino acids with polar side chains. Has a thiol group (SH) It is a Sulphur containing AA Methionine is hydrophobic amino acid F ound buried within the interior of a protein. It is an essential amino acid. Amino acid 9: Methionine – Met----M SH- thiol

40. Ans1: Serine and threonine Ans2: Threonine is an essential amino acid Ans 3: Threonine and Serine . Revision Questions 1. Give examples of two AA having hydroxyl (OH). ? 2. Which among the 2 AA Threonine or Serine is an essential amino acid ? 3. Phosphorylation and glycosylation is important for enzyme regulation and cell signaling. Name any one of the AA

41. Acidic amino acids and their amides Aspartic acid and glutamic acid are the only amino acids that carry negative charge (anions) at pH7. hence these amino acids are often referred to as aspartate and glutamate Aspartic acid refers to the protonated acidic form of the amino acid. When deprotonated, you’ll often see the conjugate base salt referred to as aspartate. This is the standard nomenclature for carboxylic acids.

42. Aspartic acid is an electrically charged amino acids with acidic side chains COOH . Generally located on the surface of the protein. Aspartic acid and glutamic acid play important roles as general acids in enzyme active centers, as well as in maintaining the solubility and ionic character of proteins. Aspartic acid (sometimes referred to as asparate depending on pH). is non-essential AA Amino acid 10: Aspartate – Asp ---- D COO charged

43. Glutamic acid is an electrically charged amino acids. It also contain a carboxylic acid group in its side chains. These acids play important roles as general acids in enzyme active centers, as well as in maintaining the solubility and ionic character of proteins. Glutamic acid is commonly referred to as  glutamate , because its carboxylic acid side chain will be deprotonated and thus negatively charged in its anionic form at physiological pH. It is a non-essential amino acid Amino acid 11: Glutamate –Glu ---- E COO charged

44. Ans1: Aspartate and Glutamate/aspartic acid and glutamic acid Ans2: Cysteine and Methionine Ans 3: True. Revision Questions 1. Give examples of two AA having COOH or carboxyl group (OH). ? 2. Which among the 2 AA has a thiol or SH group? 3. True or False Cysteine is a non-essential amino acid

45. Amino acid 12: –Asparagine ---- Asn---- N Has an amide functional group like glutamine Because of the hydrogen bonds in amide groups they are polar. Presence of amide group makes it polar They provide many of the functional groups found in proteins. Asparagine is a common site for attachment of carbohydrates in glycoproteins . Asparagine is amide derivative of aspartic acid. Asparagine is not essential AA for humans. carbonyl  group  bonded to a nitrogen

46. Amino acid 13: –Glutamine ---- Q Has an amide functional group like Asparagine Generally amide groups are unreactive, but polar The polarity causes it to act as hydrogen bond donor and acceptor . Presence of amide group makes it polar so it is amino acids with polar side chains. It is an important carrier of ammonia and contributes it to the formation of urea and purines. Glutamine is not recognized as an essential amino acid but may become conditionally essential in certain situations, including intensive athletic training or certain gastrointestinal disorders.

47. Basic amino acids Histidine Lysine Arginine

48. Amino acid 14: Lysine-----Lys-- K It is a basic amino acid along with Arginine. There are 4 methylene (CH 2 ) groups and amine / amino group (NH 2 ) Lysine is an electrically charged amino acids with basic side chains. Lysine is a base, as are arginine and histidine. The amino group is highly reactive and often participates in reactions at the active centers of enzymes. Lysine plays an important role in coordinating negatively charged ligands. It is an essential amino acid, which means that humans cannot synthesize it, so it must be ingested. amino---4 3 2 1

49. Amino acid 15: Arginine-----Arg------ R ---- Arginine is an electrically charged AA with basic side chains. It is similar to lysine, instead of 4 methylene (CH 2 ) there is only 3 methylene group then to amino group (NH 2 ), then carbon double bonded to (NH 2 ), and (NH 2 ). It has a lot of Nitrogen atoms and so basic As a group the charged amino acids are important for making proteins soluble. These residues are generally located on the surface of the protein. Arginine is well designed to bind the phosphate anion, and is often found in the active centers of proteins that bind phosphorylated substrates. As a cation, arginine, as well as lysine, plays a role in maintaining the overall charge balance of a protein. Although arginine is considered an essential amino acid (it must be obtained through the diet, semi essential), this is true only during the juvenile period in humans. 3 2 1 Only 3 methyl groups

50. Aromatic amino acids amino acids  that have an  aromatic  ring in the side-chain Phenyl alanine tyrosine tryptophan

51. Similar to alanine structure but instead of the CH3 replace the Hydrogen from CH3 to CH2 and add a benzene ring to it. Since the benzene ring (more carbon and hydrogen) is there, it is aromatic and non polar. Phenylalanine is hydrophobic amino acids with aromatic side chain. It is quite hydrophobic and even the free amino acid is not very soluble in water. Phenylalanine is large aromatic residue that is normally found buried in the interior of a protein and is important for protein stability. It is an essential amino acid. Amino acid 16: ---Phenyl alanine---Phe---F

52. Similar to phenylalanine, but here you will find a hydroxyl group attached to the aromatic benzene ring so it has a polar OH group and a benzene ring which is non polar. Tyrosine is hydrophobic amino acids with aromatic side chain. Tyrosine is large aromatic residue that is normally found buried in the interior of a protein and is important for protein stability. Tyrosine has special properties since its hydroxyl side chain may function as a powerful nucleophile in an enzyme active site (when ionized) and is a common site for phosphorylation in cell signaling cascades. Tyrosine absorbs ultraviolet radiation and contributes to the absorbance spectra of proteins. It is not essential AA Amino acid 17: ---- Tyrosine -- Y

53. Proline is different from other AA because there is no freeNH 3 , as here nitrogen becomes a part of a heterocyclic side chain. It is non polar as the R group has more hydrocarbons (C and H). Proline has an aliphatic side chain with a distinctive cyclic structure. The secondary amino (imino) group of proline residues is held in a rigid conformation that reduces the structural flexibility of polypeptide regions containing proline. Proline  is formally NOT an  amino acid , but an imino  acid ( both an amide and a  carboxyl group ), bonded to the alpha carbon molecule. When  proline  is in a peptide bond, it  does  not have a hydrogen on the α  amino  group, so it cannot donate a hydrogen bond to stabilize an α helix or a β sheet. It is not an essential amino acid, Amino acid 18: ---- Proline---Pro--- P--

54. Unlike Proline, it is similar to other AA structure, to the methylene group we find a 5 numbered heterocyclic aromatic ring attached. It is electrically charged and because of the high number of nitrogen is basic in nature. Histidine is an electrically charged amino acids with basic side chains. It is an essential amino acid Amino acid 19: ----Histidine _His--H

55. To the alpha carbon a methylene is attached to which 2 aromatic rings can be found, one is heterocyclic ring and other is a benzene ring. Tryptophan is hydrophobic amino acids with aromatic side chain. It is non polar. important for protein stability. It has spectral properties that make it the best inherent probe for following protein folding and conformational changes associated with biochemical processes . It is an essential amino acid Amino acid 20: ----Trypotophan— Trp --W

56. Ans1: Proline Ans2: Asparagine and glutamine Ans 3: NO they don’t have same structure but have similarities in structure. It is Similar to alanine structure but instead of the CH3 replace the Hydrogen from CH3 to CH2 and add a benzene ring to it. Revision Questions 1. Which amino acid is not technically an amino acid or Give example of imido acid ? 2. Give examples of AA which contains amide residues 3. Does Analine and Phenylanaline have same structure?

57. Methods to quantify proteins depends on amino acids Amino acid side chain reactions Concentration of Amino acid 1. Using Beer lamberts law 2. Using Ellmans reagent tp detect reaction between thiol groups of cysteine 3. UsingNinhydrin, fluroscemine, nitrophenol Using BCA or Bicinchoninic acid-colorimetrically detects colour changes Using Biurette reagent;reaction based on the properties of polypeptide back bone Using Folin lowry method(old) uses cupric sulphae and tartarate in aqueous solution. It forms a blue water soluble product which can be measured at 750nm Using Coomassie brilliant blue (Bradford assay)Negatively charged coomasie blue bind to positively charged proteins. When no proteins present inn sample dye absorbs 465nm and has ted colour.when protein is present it changes to blue at 595nm