2.  Definition; A buffer solution is that solution that resists large changes in pH upon the addition of limited amounts of acids or bases.  Chemically buffer solutions are made up of a mixture of two substances, a conjugate base and a conjugate base.  Types of buffers according to their chemical nature;  1-Acidic buffers; Which are made up of a weak acid and its salt of a strong base.  2-Basic buffers; Which are made up of a weak base and its salt of a strong acid. How do buffers resist changes in pH(mechanism of action of buffers); Together the two species, conjugate base and conjugate acid(the buffer components) will resist large changes in pH by partially absorbing the added H + ions and OH - ions as demonstrated in the following buffer example HA/ A -.

3.  a)When an acid is added to the buffer solution the H + ions will react with the conjugate base, H + + A - HA.  b) When a base is added to the buffer solution the OH - ions will react with the conjugate acid, OH - + H A H 2 O + A -, producing water and the conjugate base.  In both cases the limited amount of H + ions and OH - ions added (which if left free in the solution could change the pH of the solution significantly) reacted with the two basic buffer components,producing products that do not have a significant effect on the pH of the solution.  Note; 1- Buffer solutions do show a change in pH upon the addition of acid or base, but the change is insignificant compared to the change if no buffer was present.  2- The amount of change recorded (or resistance) depends on the strength of the buffer and A - /HA ratio.

4. 3-The capacity of the buffer(its resistance) is maximum at pH = pK a, buffering capacity extends ± 1 pH unit on either side of pKa. 4- The capacity of the buffer is directly related to the buffer concentration. Example ; a)Describe the components of an acetate buffer. b)Show the mechanism by which it resists changes in pH. Solution; a) The acetate buffer is composed of a mixture of CH 3 COOH representing the conjugate acid, and CH 3 COO - representing the conjugate base,( a mixture of CH 3 COOH/ CH 3 COO - ). b)when an acid is added, it will react with the conjugate base H + + CH 3 COO - CH 3 COOH. When a base is added, it will react with the conjugate acid OH - + CH 3 COOH H 2 O + CH 3 COO -.

5.  Buffer capacity ; The quantitative measure of the buffers resistance to changes in pH upon the addition of acid or base. Buffer capacity can be defined as the number of moles of H + ions Or OH – ions required to cause a one unit change in pH in one liter of buffer solution.  Importance of buffer solutions;  In biological systems many metabolic reactions are accompanied by the release or uptake of protons, thus most intracellular reactions are buffered to maintain a constant normal pH, example of the biological buffers include, phosphate, bicarbonate, and proteins which accept or release protons to resist a change in pH.  For experiments using tissue extracts or enzymes, a constant pH Should be maintained and this is made possible by the addition of buffers.

7. 1. Calculate the pKa of lactic acid, given when the concentration of lactic acid is 0.010 M and the concentration of lactate is 0.087 M, the pH is 4.80. 2. Calculate the pH of a mixture of 0.10 M acetic acid and 0.20 M sodium acetate. The pKa of acetic acid is 4.76. 3. Calculate the ratio of the concentrations of acetate and acetic acid required in a buffer system of pH 5.30. 4-Calculate the [H + ] of a sample of gastric juice that has a pH of 1.5. 5-Calculate the pOH of a solution that has a [H + ] = 1x10 -3 M.

8. 6- A student was performing an experiment at the following pH values pH 4, 6, 12, which of the following buffer solutions would you choose for each pH? Buffer solutions ; H 2 PO 4 - /HPO 4 -2 pK a = 7.2, H 2 CO 3 /HCO3 - pKa= 6.4, CH 3 COOH /CH 3 COO -, pKa= 4.67. HPO 4 -2 / PO 4 -3 pK a = 12.32.

9. Amino acids are the building blocks of proteins. The general structure of amino acids includes an α-amino group, an α-carboxylate group and a variable side chain (R).

10.  Examples of the Biological significance of amino acids ; Although over 200 different amino acids occur in nature only about one tenth of these occur in proteins, indicating other biological functions performed by these small organic molecules; 1- They are the building blocks of peptides and proteins. 2- As Precursors. Many biologically important molecules are derivates of amino acids. For example Tyrosine is the precursor of the hormone thyroxine and the skin pigment melanin, Tyrosine is also the precursor of a compound abbreviated as DOPA (dihydroxy- phenylalanine). It acts as a neurotransmitter, i.e., trasnmission of impulses in the nervous system, Tryptophan is the precursor of a vitamin named nicotinic acid (B3). 3-As Source of Sulphur. Derived from the sulfur containing amino acids. 4- Amino acids are involved in many metabolic pathways such as in Gluconeogenesis where it is involved in glucose synthesis.

13. 1- Optical activity; All amino acids show optical activity except for glycine, since all amino acids except for glycine contain at least one asymmetrical carbon atom (in all amino acids except glycine the α-carbon atom is asymmetrical). What is an asymmetrical carbon atom ? It is a carbon atom that is attached to four different chemical groups(four different substituted groups). Why does glycine lack optical activity? Since its” R-group” is a Hydrogen atom thus its α-carbon atom is not asymmetrical. What does possessing optical activity mean? It means that the amino acid in solution can be present in two isomers; The (dextrarotatory)(+) isomer which has the ability to rotate the plane of polarized light to the right. The (laevorotatory)(-) isomer which has the ability to rotate the plane of polarized light to the left. So both isomers can rotate the plane of polarized light by the same magnitude but in opposite directions.

14. 2- Acid-Base properties of amino acids; All amino acids contain at least two ionizable groups the α-amino group and the α-carboxyllic group,some contain an additional acidic or basic group in their side chain,which are responsible for the amino acids, acid- base behaviour. As a result of their ionizability the following equilibrium reaction can be written; R-COOH R-COO - + H + (ionization of the carboxylic group) R-NH 3 + R-NH 2 + H + (ionization of the protonated amino group) Since these reactions are reversible this indicates that they can act as acids (as demonstrated by the forward reaction) or as bases (as demonstrated by the reverse reaction) which explains the acid-base behavior and thus the Amphoteric property of amino acids. What is the Zwitterions form ?  All neutral amino acids are present in the Zwitterions form at physiological pH (around 7.4) the carboxyl group will be unprotonated and the amino group will be protonated.

15. As seen in the following figure ; Why are all neutral amino acids present in the Zwitterions form at physiological pH ? The α-amino group has a pK a = 9.8 therefore it will be ionized (+v charged, -NH 3 + )at physiological pH. The α-carboxylic group has a pK a = 2.5 therefore it will be ionized (-ve charged, COO - ) at physiological pH. Thus the Zwitterions form is a dipolar ion form. Amphoteric properties of amino acids; amino acids due to the presence of their ionizable α-amino and α-carboxylic group can act sometimes as acids and sometimes as bases depending on the pH of their media..

16.  In solutions more basic than the pI of the amino acid, the amino group —NH3 + in the amino acid donates a proton.  In solution more acidic than the pI of the amino acid, the carboxylic group COO- in the amino acid accepts a proton.  Thus behaving sometimes as an acid and other times as a base depending on the pH of the solution.

17. a)Polarity of amino acids; Since amino acids are present in the Zwitterions form at physiological pH. Where it carries a +ve charge on the α-amino group and a –ve charge on the α-carboxylic group, thus creating two opposite charges On both sides of the molecule thus showing polar properties. b)Isoelectric point pI ; It is that pH at which the amino acid net electrical charge is equal to zero,and thus cannot move in an electrical field.

18. 3-Ultraviolet Absorption Spectrum of Aromatic amino acids; The aromatic amino acids tryptophan, tyrosine, histidine and phenyl alanine absorb ultraviolet light at 280nm,which explains the absorption of proteins at 280nm.

19.  General properties of αlpha-amino acids.  Amino acids can be present in two Configurations the L-isomer and the D-isomer which are mirror images, which differ in the arrangement of the chemical groups around the α-carbon atom. All amino acids in proteins are in the L-configuration, L-amino acids.

20. 1-Classification according to the structure of the side chain R. a)Aliphatic amino acids ; They are amino acids with aliphatic groups in their side chains. b)Aromatic amino acids; They are amino acids with aromatic groups in their side chains (contain a phenyl group). 2-Classification according to the polarity of the side chain R. a)Polar amino acids ; 1-Polar uncharged amino acids. 2-Polar charged amino acids which can be; Polar acidic or positively charged amino acids. Polar basic or negatively charged amino acids. b)Non-polar amino acids. 3- Classification based on their nutritional value. 4-Classification based on their metabolic fate.

21. Physical properties of amino acids; 1-Amino acids are mainly water soluble which is explained by its polarity and the presence of charged groups. They are soluble thus in polar solvents and not soluble in non-polar solvents. 2-They have a high melting point reflecting the high energy needed to break the ionic forces maintaining the crystal lattice. It is important to note that the general properties of amino acids is shared by all the amino acids and is in many cases contributed by its α-amino and α- carboxyl group. Amino acids can posses other specific properties dictated by they unique side chain.

25. b)Aromatic amino acids;

29. The non-polar side chain cannot ionize and cannot form Hydrogen bonds.These side chains are have a hydrophobic nature thus they are participate in hydrophobic interactions. Non-polar amino acids cluster and are usually buried in the interior of the protein molecule far from the aqueous polar enviroment. The polar side chain can form Hydrogen bonds and charged polar side chains can form ionic bonds. Due to their polar hydrophilic nature they are usually located at the exterior of the protein molecule in contact with aqueous polar enviroment.

30. 1-Essential amino acids ;They are those amino acids that cannot be synthesized in the body thus they are essential in the diet. Essential amino acids include the following amino acids ; 2- Non-essential amino acids; They are those amino acids that can be synthesized in the body thus they are non-essential in the diet.

31. 1-Glucogenic amino acids ;They are amino acids that can be used for glucose synthesis.

32. 2-Ketogenic amino acids ; They are those amino acids that can be used for ketone body synthesis only. Such as Lys and Leuc. 3-Ketogenic and glucogenic amino acids ; They are those amino acids that can be used both for ketone body synthesis,and glucose synthesis.

34.  Dissociation of the α-amino group; When the α-carboxyl group is fully titrated the additional base added will start titrating the α-amino group which is a weaker acidic group pka = 9.1 compared to the α- carboxylic group which which explains it being titrated after the α-carboxylic group, thus dissociating and donating a proton to the enviroment leading to the formation of –NH 2 or form III, which carries a net negative charge.

38. Titration curve of glycine ; a) At point(a) predominant form is the fully protonated form. b) At point (b) 50% of the a.a is in the fully protonated form and 50% in the zwitterions' form. At this point the concentration of the conjugated acid is equal to the concentration of the conjugated base and pH= pKa1 (pKa of α-carboxylic group) Point( b) represents the midpoint Where half of the α-carboxylic group is titrated. At the midpoint buffering behavior is maximum.

39. c) At point (c) the predominating form is zwitterion form which has a net charge of zero. At point (c) the pH = pI isoelectric point of the amino acid. The isoelectric point pI for neutral amino acids Can be calculated from ; pI = pKa 1 + pKa 2 / 2 d) At point(d) 50% of the amino acid is in the zwitterion form and 50% in the anionic form.Point (d) represents the second midpoint where half the α-amino group is titrated, and pH = pKa 2, the pka of the α-amino group, with maximum buffer capacity. e) At point (e) the predominating form is the anionic fully deprotonated form.

40. The titration of acidic and basic amino acids involves three stages of titration one for the titration of the α-carboxylic group, a second for the titration of the α-amino group and the third for the additional acidic or basic group in the side chain. Thus showing three midpoints, three pka”s and three buffering zones. The isoelectric point pI is obtained by calculatingthe average of the two closest pKa values.

43. Ninhydrin Reaction; (2,2-Dihydroxyindane-1,3-dione) is a chemical used to detect ammonia or primary and secondary amines. When reacting with these free amines a deep blue or purple color is produced.

44. The ninhydrin reaction targets the free α-amino group in amino acids, thus all the standard α-amino acids will produce a blue purple complex when reacted with ninhydrin except proline which will produce a yellow color since it does not contain a free α-amino, its α-amino group is involved in a ring structure. This reaction is an important reaction used to detect amino acids.