Biochemistry Prelims Week-2 PDF

STRUCTURE OF AMINO ACIDS PHARMACEUTICAL BIOCHEMISTRY Alpha Amino Acid LECTURE 2: AMINO ACIDS The exception is Proline Proline has a structural...

STRUCTURE OF AMINO ACIDS PHARMACEUTICAL BIOCHEMISTRY Alpha Amino Acid LECTURE 2: AMINO ACIDS The exception is Proline Proline has a structural feature not found in any other standard amino acid OUTLINE - It is an imino acid 1. Definition of Terms 3 - Its side chain, a propyl group, is bonded to 2. General Characteristics of Amino Acids both the ⍺-carbon atom and the amino -2 3. Structure of Amino Acids nitrogen atom, giving a cyclic side chain a. Alpha Amino Acid b. R-Group R-Group 22 c. Optical Isomerism The side chain 4. Classification of Amino Acids It distinguishes ⍺-amino acids from each other a. Essentiality / Nutritional Requirement Vary in size, shape, charge, acidity, functional groups b. Metabolic Fate present, hydrogen-bonding ability, and chemical 5. Acid-Base Properties of Amino Acids ee reactivity a. Zwitter Ion b. Isoelectric Point Optical Isomerism Based on the absolute placement of the amino group: itt DEFINITION OF TERMS Has chiral properties m Protein: a naturally occuring, unbranched polymer in which the monomer units are amino acids om Amino Acid: the building blocks of proteins ○ their chemical properties determine the biologic property of protein C L: Levorotatory GENERAL CHARACTERISTICS OF AMINO ACIDS ○ Amino acid is located on the left Amino-containing carboxylic acids s Alpha amino acids D: Dextrorotatory ○ Amino acid is located on the right ic Proteinogenic Chiral Amphoteric em 4 groups in every AA CLASSIFICATION OF AMINO ACIDS Amino group (NH2) Carboxyl group (COOH) BY R GROUP ad Acid (H) R Group (Side Chain) Neutral Non-Polar AA Every amino acid contains: amino group, carboxyl group, Ac and acid group Only the R Group (side chain) varies Figure 1: Neutral Non-Polar AA Prepared by: Tarrago 1 4ADM-XWTT-L6XD-VXJU  Glycine (Gly, G) Glutamine (Gln, Q) ○ Only contains H as its side chain ○ Extra carbon groups ○ The non-chiral amino acid, it is not able to ○ 3 more carbon groups rotate polarized light Tyrosine (Tyr, Y) Alanine (Ala, A) ○ Contains benzene group 3 ○ Contains methyl group (CH3) as its side ○ Extra Hydroxyl (OH) chain -2 Alcoholic Amino Acids Serine (Ser, S): Single carbon attached to OH Branched Chain Amino Acids (BCAA) or VLI Threonine (Thr, T): Two Carbons attached to OH 22 Valine (Val, V) Leucine (Leu, L) Isoleucine (Ile, I) Polar Acidic AA ee Imino Acids Proline ○ Its side chain, a propyl group, is bonded to itt both the ⍺-carbon atom and the amino nitrogen atom, giving a cyclic side chain Aromatic Amino Acids (MWF) m om Methionine (Met, M): Has sulfur Tryptophan (Trp, W): Indole Ring Figure 3: Polar Acidic AA Phenylalanine (Phe, F): Has benzene ring Aspartic Acid (Asp, D) C ○ Aspartate (-ate = ic acid) ○ 2 Carbons Polar Neutral AA ○ Occurs the most in the body s Glutamic Acid (Glu, E) ic ○ 3 more carbon groups em Polar Basic AA ad Figure 2: Polar Neutral AA Cysteine (Cys, C) Ac ○ contains Sulfhydryl (-SH) ○ reason for curly hair ○ contains thiol ○ can form a double bond with itself (the bonded sulfur atoms form disulfide bridge) Figure 4: Polar Basic AA Histidine (His, H) Asparagine (Asn, N) Lysine (Lys, K) ○ Extra carbon groups Arginine (Arg, R) ○ 2 more carbon groups Prepared by: Tarrago 2 4ADM-XWTT-L6XD-VXJU BY ESSENTIALITY / NUTRITIONAL REQUIREMENT BY METABOLIC FATE Essential Amino Acids Excess amino acids are catabolized to amphibolic “Essential” not because they are more important to intermediates that serve as sources of energy or for the life than the others, but because the body does not biosynthesis of carbohydrates and lipids synthesize them 3 Therefore, they need to be supplied through the diet otherwise they will not be present in the body -2 Phenylalanine Methionine 22 Valine Histidine Threonine Arginine ee Tryptophan Leucine Isoleucine Lysine Figure 5 itt Table 1: Essential Amino Acids (PVT TIM HALL) (Exclusively) Glucogenic Amino acids Generate precursors of glucose or glycogen, such m as pyruvate or a citric acid cycle intermediate Non-Essential Amino Acids The body can synthesize about 10 amino acids to (Exclusively) Ketogenic Amino acids meet the biological needs, hence they need not be om Leucine and Lysine consumed in the diet Amino acids which can be converted into fat (fat producing) Alanine Glutamine Acetyl CoA or Acetoacetyl CoA is produced in the final step of their metabolism generate ketone bodies C Asparagine Glycine Both glycogenic and ketogenic Amino acids Aspartic acid Proline PITTT: Phenylalanine, Isoleucine, Threonine, s Tyrosine, Tryptophan Cysteine Serine Generate precursors of both glucose and fats ic Glutamic acid Tyrosine em Table 2: Non-essential Amino Acids ACID-BASE PROPERTIES OF AMINO ACIDS ZWITTERION ad All amino acids are zwitter ionic Both an acidic group (-COOH) and a basic group (-NH2) are present on the same carbon in an ⍺-amino Ac acid ○ In neutral solution, carboxyl groups have a tendency to lose protons (H+), producing a negatively charged species - COOH → - COO- + H+ Prepared by: Tarrago 3 4ADM-XWTT-L6XD-VXJU  ○ In neutral solution, amino groups have a tendency to accept protons (H+), producing a positively charged species - NH2 + H+ → - NH3+ Review of Concept 3 Brønsted–Lowry Acid-Base Theory Thus, in solution, three different AA forms can exist (zwitterion, ○ Acid: proton donor negative and positive ion) -2 donates H+ ion to some other substance The 3 species are actually in equilibrium with each other, and ○ Base: proton accept the equilibrium shifts with pH change 22 accepts H+ ion from some other substance Zwitter Ion in Neutral Solution ee From the German term meaning “double ion” A molecule that has a positive charge on one atom and a negative charge on another atom, but which has no net charge Figure 3: In acidic solution, the positively charged species on itt Note that the net charge on a zwitterion is zero even the left predominates; nearly neutral solutions have the middle though parts of the molecule carry charge species (the zwitterion) as the dominant species, in basic m solution, the negatively charged species on the right NOTE: In neutral pH predominates All acid groups are deprotonated (COO-) om All basic groups are protonated (NH3) ISOELECTRIC POINT An isoelectric point is the pH at which an amino acid solution has no net charge because an equal number C of positive and negative charges are present At the isoelectric point, almost all amino acid s Zwitter Ion in Acidic Solution molecules in a solution (more than 99%) are present In an acidic solution, the zwitterion accepts a proton in their zwitterion form ic (H+) to form a positively charged ion em NOTE: In acidic pH All acid groups are protonated (COOH) All basic groups are protonated (NH3) ad Ac Zwitter Ion in Basic Solution In basic solution, the NH3 of the zwitterion loses a proton, and a negatively charged species is formed NOTE: In basic pH All acid groups are deprotonated (COOH-) All basic groups are deprotonated (NH2) Prepared by: Tarrago 4 4ADM-XWTT-L6XD-VXJU Examples SUMMARY POINTS: Protein: a naturally occuring, unbranched polymer 1. For an amino acid such as alanine (neutral) (neutral) in which the monomer units are amino acids that has only two dissociating groups, there is no ambiguity. The first pKa (R’COOH) is 2.35 and the Amino Acid: the building blocks of proteins second pKa (R’NH3+) is 9.69. 4 Groups in AA 3 The isoelectric pH (pI) of alanine thus is: Amino group (NH2) Carboxyl group (COOH) -2 pI = (pKa + pKa) / 2 Acid (H) pI = (2.34 + 9.69) / 2 R Group (Side Chain) – only this group varies pI = 6.015 among amino acids 22 20 Amino Acids Neutral Nonpolar AA 2. For polyprotic acids (acidic), pI is also the pH midway ○ Glycine between the pK values on either side of the isoionic ○ Alanine ee species ○ Valine ○ Leucine NOTE: When an amino acid has 3 pKa values, ○ Isoleucine choose only the two values closest to one another ○ Proline (imino acid) itt ○ Phenylalanine ○ Methionine For example, the pI for aspartic acid is: ○ Tryptophan pI = (pKa + pKa) / 2 pI = (2.09 + 3.86) / 2 m Neutral Polar AA ○ Serine om pI = 2.97 ○ Cysteine ○ Threonine 3. For lysine (basic AA) ○ Asparagine ○ Glutamine ○ Tyrosine pI = (pKa + pKa) / 2 C pI = (10.53 + 8.95) / 2 Polar Acidic pI = 9.74 ○ Aspartic Acid ○ Glutamic Acid s Polar Basic ic Practice Problems ○ Histidine ○ Lysine Compute the isoelectric point of the following ○ Arginine em 1. Histidine Essentiality pI = (6.0 + 9.17) / 2 Essential: body does not synthesize these amino pI = 7.59 acids hence needs to be included in our diet ad 2. Glutamic Acid Non-essential: The body can synthesize about 10 pI = (2.19 + 4.25) / 2 amino acids to meet the biological needs, hence pI = 3.22 they need not be consumed in the diet Ac 3. Serine Metabolic Fate pI = (2.21 + 9.15) / 2 Glucogenic Amino acids: Generate precursors of pI = 5.68 glucose or glycogen, such as pyruvate or a citric acid cycle Ketogenic Amino acids: (Leucine and Lysine) amino acids which can be converted into fat (fat producing) Prepared by: Tarrago 5 4ADM-XWTT-L6XD-VXJU  Both glycogenic and ketogenic Amino acids: PITTT: Phenylalanine, Isoleucine, Threonine, Tyrosine, Tryptophan Zwitterion All amino acids are zwitter ionic Both an acidic group (-COOH) and a basic group 3 (-NH2) are present on the same carbon in an ⍺-amino acid -2 In neutral solution ○ All acid groups are deprotonated (COO-) 22 ○ All basic groups are protonated (NH3) In acidic solution ○ All acid groups are deprotonated (COO-) ee ○ All basic groups are protonated (NH3) In basic solution ○ All acid groups are deprotonated (COOH-) itt ○ All basic groups are deprotonated (NH2) m Isoelectric Point: An isoelectric point is the pH at which an amino acid solution has no net charge because an equal number of positive and negative charges are om present (pKa + pKa) / 2 C General reminder: This will be the final reviewer released for the subject of Pharmacetical Biochemistry this Prelims. s ic em ad Ac Prepared by: Tarrago 6 4ADM-XWTT-L6XD-VXJU