Content : Properties of amino acids.. Separation and Analysis of Amino Acids

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1 قسم الكيمياء الحيوية.دولت على سالمه د استاذ الكيمياء الحيوية ٢٠١٥-٢٠١٤ المحاضرة الثانية

2 Content : Properties of amino acids.. Separation and Analysis of Amino Acids 2

3 -3

4 A. Physical properties 1. Solubility: Most of the amino acids are soluble in water and insoluble in organic solvents. 2. Melting points :Amino acids generally melt at higher temparatures,often above 200ºC. -4

5 3.Taste : Amino acids may be sweet( Gly, Ala, Val ), tasteless ( Leu ) or bitter ( Arg, Ile ). Monosodium glutamate is a salt of glutamic acid. It is employed as a flavoring agent in food industry to increase taste and flavor. 4. Optical properties : All amino acids except glycine gy possess optical isomers due to the presence of asymmetric carbon atom. amino acids exist in two forms, D and L, that are mirror images of each other. All amino acids found in proteins are of the L-configuration. 5

6 5.ACIDIC AND BASIC PROPERTIES OF AMINO ACIDS Amino acids in aqueous solution contain weakly acidic α-carboxyl groups and weakly basic α- amino groups. Each of the acidic and basic amino acids contains an ionizable group in its side chain. Thus, both free and some of the combined amino acids in peptide linkages can act as buffers. The concentration of a weak acid (HA) and its conjugate base(a - ) is described by the Henderson-HasselbalchHasselbalch equation. -6

7 Derivation of the equation For the reaction (HA A - + H + ) [H + ] [A - ] pka : the negative log of the K a = --- (1) dissociation constant (ka), which is a measure of strength of an acid/base [HA] By solving for the [H + ] in the above equation, taking the logarithm of both sides of the equation, multiplying both sides of the equation by -1, and substituting ph = -log [H + ] and pk a = -log [K a ] we obtain: [A - ] ph = pk a +log -- (2) It is the [HA] It is the (Henderson-Hasselbalch Hasselbalch l equation -7

8 Amino Acids, and Isoelectric Points In acidic solution, the carboxylate and amine are in their conjugate acid forms, an overall cation In basic solution, the groups are in their base forms, an overall anion In neutral solution cation and anion forms are present This ph where the overall charge is 0 is the isoelectric point, pi 8

9 acid and amine react with each other internally. Isoelectric Point or or the pi.. : is defined as the ph at which a molecule exists as a zwitterion or dipolar ion and carries no net charge. ٩

10 Q The exact structure of an amino acid in solution varies with the ph of the solution.( discuss in details) R COOH CH COO - COO - -H + +OH - R R CH CH NH 3 «+H + «-OH - NH 3 NH 2 PH<pI PH=pI PH>pI An :If the zwitterion is treated with acid, that is, a solution containing H +,theh + will add to the COO - to form COOH. Similarly, treating the zwitterion with base will result in the loss of the removable proton attached to the NH + 3 group to form NH 2. The ph at which amino acids have no net charge is called the Isoelectric Point or the pi. ١٠

11 Amphoteric properties of Amino acid R O H 3 NCHCO zwitterion In acid solution R O + H + 3 O H 3 NCHCOH + H 2 O protonated R O H 3 NCHCO In base solution R O + OH - H 2 NCHCO + H 2 O zwitterion i deprotonated t d ١١ Copyright 1999, Michael J. Wovkulich. All rights reserved.

12 Draw the condensed structural formula for an amino acid at ph values above or below its isoelectric point. Properties of amino acids in proteins and peptides are determined by the R group (also by the charges of the titratable group ). Will ultimately affect protein structure. 12

13 13

14 14

15 Q. Draw the fully protonated structure of Alanine? An: Q: Which protons come off, when? A:1. Look at pka table for amino acids (32-2) Alanine has 2 pkas: α-cooh (pka = 2.34) comes off first (has lower pka) α-nh NH3+ (pka = ) Others come off SEQUENTIALLY in ascending order of pka. 15

16 16

17 2.Write out structures for sequential deprotonation and place pka values over the equilibrium i arrows. Fully protonated 1st proton removed 2nd proton removed Net charge = +1 Net charge = 0 Net charge = -1 So, from looking at the net charges, at different e ph s, amino acids can have different charges! Very important for protein structure!! 17

18 Titration curve of acetic acid The titration curve represents the reaction of each functional group with the hydroxide ion Remember that the pka = ph when ½ of an available amount of an ionizable group is ionized. 18

19 Titration curve of Alanine : B C Looks very much like what we saw for acetic acid last time except that it has 2 midpoints (pka s) one for each proton α-cooh and α-nh NH3+ -At beginning, all protonated. -Need one equivalent of base for each proton. At each HALF equivalent = pka 50% protonated / 50% deprotonated At end all deprotonated A Flat parts of curve are BUFFERING REGIONS: Acts as buffer in TWO ph ranges. +/- 1 ph unit from pkas 19

20 For our purposes, to determine whether the proton is ON or OFF at a certain ph use the following RULES ph>pka H+ off, Substance deprotonated t d if ph is GREATER than the pka of a particular ionizable group, that group will be predominantly deprotonated t d deprotonated ph = pka Equal amounts of protonated and deprotonated species exist pk a ph< pka H+ on, Substance protonated if ph is LESS than the pka of a particular group, that group will be predominantly protonated protonated 20

21 Effects of PH on Amino Acid R-group Charge The ph value at which the chemical group loses a H + is called its pk a. Acid Base Terminal -carboxyl y group: pka ~ 3.0 R-COOH RCOO - Terminal -amino group: pka ~ 8.0 R-NH 3 + R-NH 2 Polar, uncharged amino acid side chains: Cys (R-S-H) R-S - pka= 8.3 Tyr (R-ph-O-H) R-ph-O - pka= 10.6 The pka values of amino acids with charged side chains (acidic & basic) 21

22 For example: Alanine at different ph s (see pka table) At ph 1.5 ph is less than the pka of both the α-cooh and the α-nh3 +, therefore, both protons are ON At ph 7: ph is greater than the pka of the α-cooh H+ OFF ph is less than the pka of the α-nh3 + H+ ON At ph 10.5 ph is greater than the pka of the α-cooh H+ OFF ph is greater than the pka of the α-cooh H+ OFF 22

23 Apply same rules if there are 3 titratable protons: 1. Determine what the pka s of the titratable protons are by looking at the pka table( ) 2) 2. Draw the structures and the equilibria representing the complete deprotonation of the amino acid a. Start with fully protonated and then remove in order of pka values b. Put pka values above equilibrium 3. Determine at the ph of interest whether the proton is ON or OFF using the above rules 23

24 For example, Aspartate (D, Asp): Asp has 3 titratable protons Amino acids can be separated on the basis of their charges at a certain ph 1. pka s for the three groups (look at Table23.2) 2. Draw the structures from fully protonated to fully deprotonated Note that t all amino acids are at one point, electrically ll neutral at some ph value. This ph = isoelectric point (pi) pkas: 2, 3.9, 10 (from Table 3.2) pi = (2+3.9)/2 =

25 For example Lysine:(Lys, K ) Lysine has three ionizable functional groups with the following pka values: α-amino group = 9.04 α-carboxylic group = 2.17 R group = Write the equilibrium equations for its three ionizations and assign the proper pka for each ionization. 2.Show the net charge on the lysine molecule at each ionization stage

26 Q:Write The charges of the lysine at different ph At ph=1 the lysine possesses two positive, at ph=5.6 two positive and one negative, at ph=9.7 one positive and one negative and at ph=11 one negative The lysine has an amino group on its side chain, its isoelectric point is at ph=

27 Question The exact probability that a molecule will be protonated or deprotonated depends on the pk a of the molecule and the ph of the solution.( discuss in details) 27

28 How do you calculate pi? 1. Draw out the complete ionization of amino acid 2. Determine net charge on each ionized form 3. Find the structure that has no net charge 4. Take the average of the pka s that are around the structure with NO NET CHARGE 4. Calculate the pi using the equation below: ( pk1 value is the pk value to the left of the zero net charge and pk2 value is to the right of the net charge of zero). pi = pk1 + pk2 2 pi = /2 pi = Note do NOT just take the average of all pka s s. Amino acids can be separated on the basis of their charges at a certain ph 28

29 pi Depends on Side Chain The 15 amino acids thiol, hydroxyl groups or pure hydrocarbon side chains have pi = 5.0 to 6.5 (average of the pk a ) s) Glu and Asp have acidic side chains and a lower pi His, Arg, Lys have basic side chains and higher pi 27-29

30 pi = pka x + pka y 2 + pi = pka 1 pka 2 2 pi = 6.0 pka 1 + pka 3 pi = 2 pi = 2.7 pi = pka 2 + pka 3 2 pi =

31 A buffer is a solution that resists change in ph following the addition of an acid or base. A buffer can be created by mixing a weak acid (HA) with its conjugate base (A ). - If an acid such as HCl is then added to such a solution, A can neutralize it, in the process being converted to HA. - If a base is added, HA can neutralize it, in the process being converted to A. a buffer as a solution that consists of a mixture of a weak acid and it conjugate base Amino acids have both a carboxylic acid group (acid) and an amine group (base). Those two functional groups can act as "pseudo" buffer sites. If an acid is added, the amine can pick up the extra protons, and if a base is added, the carboxylic acid group can sort of neutralize it. But amino acids, by themselves, do not fit the definition of a buffer. if a base is added d If an acid is added ٣١

32 Glycine As a Buffer Ampholyte Has both acidic and basic groups As base is added the acidic group group looses protons first Glycine can buffer in two ph ranges 2.3 & 9.6 A Exists in 3 forms B ٣٢

33 Study Check CH 3 CH 3 + H N CH COOH N CH COO 3 COOH H 2 COO (1) (2) Which structure represents امثلة لتوضيح العالقة بين : pi? A. alanine at a ph above its B. alanine at a ph below its pi? ph, pi Chemistry: An Introduction to General, Organic, and Biological Chemistry, Twelfth Edition 2015 Pearson Education, Inc.

34 Solution CH 3 CH 3 + H N CH COOH N CH COO 3 COOH H 2 COO (1) (2) Which structure represents A. alanine at a ph above its pi? (2) B. alanine at a ph below its pi? (1) Chemistry: An Introduction to General, Organic, and Biological Chemistry, Twelfth Edition 2015 Pearson Education, Inc.

35 Study Check Consider the amino acid leucine with a pi of 6.0. A. At a ph of 3.0, how does leucine change? B. At a ph of 9.0, how does leucine change? Chemistry: An Introduction to General, Organic, and Biological Chemistry, Twelfth Edition 2015 Pearson Education, Inc.

36 Solution Consider the amino acid leucine with a pi of 6.0. A. At a ph of 3.0, how does leucine change? Because the ph of 3.0 is more acidic than the pi at 6.0, the COO group gains an H + to give COOH. The remaining NH 3+ gives leucine an overall positive charge (1+). B. At a ph of 9.0, how does leucine change? Because a ph of 9.0 is more basic and above the pi of leucine, the NH + 3 loses H + to give NH 2. The remaining i COO gives leucine an overall negative charge (1 ). Chemistry: An Introduction to General, Organic, and Biological Chemistry, Twelfth Edition 2015 Pearson Education, Inc.

37 Problem Would the following ions of serine exist at a ph above, below, or at pi? O O O H 3 N CH C O H 3 N CH C OH H 2 N CH C O CH 2 CH 2 CH 2 OH OH OH ph = pi ph below its pi ph above its pi

38 Problem ph above its pi O O O H 3 N CH C O H 3 N CH C OH H 2 N CH C O CH 2 CH 2 ph above its pi CH 2 OH OH OH

39 Spectroscopic Properties All amino acids absorb in the infrared (bond vibrations). Only Phe, Tyr, and Trp absorb in the UV (electronic ect c transitions t s between energy levels). Absorbance at 280 nm is a good method for determining protein concentration.. The UV spectra of the aromatic amino acids at ph 6. Beer s Law: A = εcl 39

40 Chemical reactions Due to carboxyl group: 1. amino acids form salts (COONa) with bases & ester (-COOR ) with alcohol. 2. Decarboxylation: form corresponding amine. 1. Histidine 2. Tyrosine 3. Tryptophan 4. Lysine 5. Glutamic acid histamine + CO 2 tyramine + CO 2 tryptamine + CO 2 cadaverine + CO 2 GABA + CO 2 40

41 Color reactions of amino acids & proteins Name of the Test Reagent Used Positive results Remarks Biuret Test NaOH, dilute CuSO4 violet + results with polypeptides and proteins Xanthroproteic Conc. H2SO4 AA with benzene Proteins with trp, tyr, Test ring (yellow) phe Million s Test Sulphur Test Hg(NO3) and Hg(NO2)2 Lead acetate, dissolved with NaOH Tyrosine (red) Gray or black precipitate + phenolic compounts + lead sulphide, formed as the result of the decomposition of the cysteine by the alkali. Hopkins Cole Test Glyoxylic acid, Tryptophan (violet + with any compound sulfuric acid ring) with indole ring Ninhydrin Test ninhydrin Free-NH2 group (blue) + results given by NH3, primary amines, amino acids, peptides, and proteins 27-41

42 Test for Protein: Biuret Test Protein present 42

43 Test for Protein: Biuret Test Cheese is rich in protein. pestle mortar Add an equal amount of NaOH to the solution followed by 1-2 drops of CuSO 4 solution 43

44 When a protein reacts with copper(ii) sulfate (blue), the positive test is the formation of a violet colored complex. Purple / Lilac: Positive test t 27-44

45 Question 1. At ph 7, which of the following amino acids have a net positive charge, which have a net negative charge, and which are neutral? Lysine Phenylalanine Leucine 2.List at least 2 amino acids capable of interacting with water. Explain why? a. Water is polar, so the two amino acids need to be hyrdophillic to interact with water.glutnamine and Serine are polar and mix with water because they are hyrophillic. 3. Explain How : a molecule's charge (amino acids) changes with the ph of its surroundings. (١١) فى رقم االجابة 45

46 Separation and Analysis of Amino Acids 46

47 Separation and Analysis using pi values Differences in isoelectric points (and therefore charges) are used to separate mixtures of amino acids by two common methods: - Many chromatographic methods exist for separation of amino acid mixtures Ion exchange chromatography High-performance liquid chromatography Ion exchange chromatography Polyacrylamide gel electrophoresis (PAGE) These methods will be illustrated with a simple mixture of three amino acids having very different isoelectric points: Mixture of: buffered at ph 6.0 H 3 H O H O H O N C CO + H 3 N C CO + H 3 N C CO CH 2 CO 2 CH 3 CH 2 CH 2 CH 2 CH 2 NH 3 D (pi=2.8) A (pi=6.0) K (pi= 9.7) aspartic acid alanine lysine 47

48 Ion Exchange Chromatography Mixture of: buffered at ph 6.0 H 3 N H O H O H O C CO CH 2 CO 2 D (pi=2.8) + H 3 N C CO CH 3 A (pi=6.0) + H 3 N C CO CH 2 CH 2 CH 2 CH 2 NH 3 K (pi= 9.7) SO 3 K (strongly retained) sulfonated polystyrene SO 3 A (slightly retained, & D (unretained) SO 3 aspartic acid (D ) elutes first, followed by alanine (A); lysine(k + ) elutes last, and only after ph of buffer is increased and K + is deprotonated. 48

49 Ion Exchange Chromatography h Recall that in our simple mixture D - elutes first, followed by A; K elutes last, and only after the ph of buffer is increased and K + is deprotonated. D A K injection Increase ph of buffer Retention ti time 49

50 Cations bind most strongly to cation-exchange resins Anions bind most strongly to anion-exchange resins An amino acid analyzer is an instrument that automates ion-exchange chromatography 50

51 A mixture of amino acids can also be separated on the basis of polarity 27-51

52 Separations of Amino Acids 27-52

53 - Q. Mixture of Val (pi = 6) ; asp ( pi = 2.8,) lys (pi = 9.7) in a buffer at ph = 6. What is the form of each? O + H 3 N C _ O CH CH O C H 3 C CH val CH 3 - O C N H 3 + CH 2 asp O - O N H 3 + H 2 C CH 2 lys N H 3 + CH C O H 2 C CH 2 O - Consider THREE amino acids mixed together in a buffer at ph 6.0 Ninhydrin is used to detect the individual amino acids 53

54 54

55 Q 1:What is the ph of a lysine solution if the side chain amino group is ¾ dissociated? ph [3] 10.5 log 10 [1] ph = (0.477) ph = = 11.0 Note that, when the group is ¾ dissociated, ¾ is dissociated and ¼ is not; thus the ratio in the log term is ¾ over ¼ or 3/1. Q 3. List all amino acids by abbreviation which are considered somewhat polar. Q2: What is the ph of a lysine solution if the side chain amino group is 3/4 dissociated? [3] ph 10.5 log 10 [1] ph = (0.477) ph = = 11.0 Note that, when the group is ¾ dissociated, ¾ is dissociated and ¼ is not; thus the ratio in the log term is ¾ over ¼ or 3/1. 55

56 References: Text book of biochemistry- DM Vasudevan. Lippincott s illustrated biochemistry. Biochemistry U Satyanarayana. 56

57 57

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