Reactions and amino acids structure & properties
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1 Lecture 2: Reactions and amino acids structure & properties Dr. Sameh Sarray Hlaoui
2 Common Functional Groups
3 Common Biochemical Reactions AH + B A + BH Oxidation-Reduction A-H + B-OH + energy ª A-B + H 2 O Condensation A-B + H 2 O ª A-H + B-OH + energy Hydrolysis
4 Oxidation - Reduction An oxidation-reduction (redox) reaction is a type of chemical reaction that involves a transfer of electrons or hydrogen between two species. 1- Oxidation and reduction in terms of electron transfer: Redox reactions are comprised of two parts a reduced half Reduced half and an oxidized half, that always occur together: - The reduced half gains electrons while - the oxidized half loses electrons Simple ways to remember this include the mnemonic devices OIL RIG, meaning "oxidation is loss" and "reduction is gain. oxidized half In these reactions, The ion or molecule that accepts electrons is called the oxidizing agent. Conversely, the one that donates electrons is called the reducing agent. In other words, what is oxidized is the reducing agent and what is reduced is the oxidizing agent. There is no net change in the number of electrons in a redox reaction. Those given off in the oxidation half reaction are taken up by another species in the reduction half reaction.
5 2- Oxidation and reduction in terms of hydrogen transfer: in terms of hydrogen transfer : - Oxidation is a loss of hydrogen - Reduction is gain of hydrogen
6 Condensation Reaction It s the removal of water between two molecules. This generates a covalent bond between the two molecules. Example: - condensation of 2 amino acids to produce a dipeptide. Requires energy (endergonic reaction) A-H + B-OH + energy ª A-B + H 2 O
7 Hydrolysis Reactions The breaking down of a covalent bond by the addition of water. It releases energy (exergonic reaction). The H and OH of water are added to atoms that were in the bonds broken by the reaction: A-B + H 2 O ª A-H + B-OH + energy
8 Amino Acids vthere are bout 300 different amino acids occur in nature, only 20 of them are commonly found as constituents of mammalian proteins vamino acids: the molecular building blocks of proteins Glycine (G) Alanine (A) Valine (V) Isoleucine (I) Leucine (L) Proline (P) Methionine (M) Phenylalanine (F) Tryptophan (W) Asparagine (N) Glutamine (Q) Serine (S) Threonine (T) Tyrosine (Y) Cysteine (C) Asparatic acid (D) Glutamic acid (E) Lysine (K) Arginine (R) Histidine (H) White: Hydrophobic, Green: Hydrophilic, Red: Acidic, Blue: Basic
9 Amino Acids Structure vall amino acids have: - A common core structure: an α-carbon to which are attached hydrogen, amino group and carboxyl group. -A side chain (R): this is different for each of the 20 amino acids naturally found in proteins. vamino acid are ampholytes because they contain both acidic (-COOH) and basic (NH2) groups: they can donate a proton or accept a proton
10 Amino Acids Stereoisomers If a carbon atom is attached to 4 different groups it is asymmetric and therefore exhibits isomerism The amino acids (except glycine) possess distinct groups (R, H, COO-, NH3+) held by the carbon a and is therefore a optically active (or chiral) The mirror image of one amino acids cannot be superposed onto it) Enantiomer Enantiomer Amino acids exist in 2 forms: D (Dextrogyre) and L (Levogyre) which are mirror images of each other. These 2 forms in each pair (D, L) are called stereoisomers, optical isomers or enantiomers Mirror D and L form of Alanine L isomer: NH 2 group is on the left D isomer: NH 2 group is on the right. Amino acids in humans are in the L-configuration (except glycine which is neither L nor D) whereas bacterial amino acids can be either L or D configuration
11 Zwitterion Zwitterion is a hybrid molecule containing positive and negative ionic neutral amino acid R H 3 N É ¾ C ¾ COO H
12 Isoelectric Point (pi or phi) Iso-electric Point (pi): is defined as the ph at which a molecule exists as zwitterion and carries no net electrical charge At a ph È than the pi: the carboxyl group accepts a proton. At a ph Ç than the pi: the amino group looses a proton Therefore the amino acid becomes positively or negatively charged, respectively
13 Essentials amino acids & Non essentials amino acids Glucogenic and/or ketogenic amino acids van essential amino acid is an amino acid that cannot be synthesized de novo by the organism, and therefore must be supplied in its diet. va glucogenic amino acid is an amino acid that can be converted into glucose or glycogen. Only Leu and Lys are not glucogenic (exclusively ketogenic). va ketogenic amino acid: is an amino acid that can be degraded directly into acetyl CoA which is the precursor of ketone bodies and lipids. Leu and lys are exclusively ketogenic vthe amino acids which are glucogenic and ketogenic are precursors for the synthesis of glucose and fat
14 Amino Acid Classification Classification based: on their R side chain on polarity
15 Amino Acid Classification Based on their (R) side chain, the 20 amino acids may be classified into seven distinct groups: 1. Aliphatic amino acids 2. Hydroxyl group containing amino acids 3. Sulfure containing amino acids 4. Acidic amino acids and their amides 5. Basic amino acids 6. Aromatic amino acids 7. Imino acids
16 1. Aliphatic amino acids -This group consists of most simple amino acids - These are: monoamino, monocarboxylic acids Ø Glycine: Gly- G Non essential amino acid Ø Alanine: ALA- A Non essential amino acid Ø Valine: Val- V Essential amino acid Ø Leucine: Leu- L Essential amino acid Ø Isoleucine: Ile- I Essential amino acid
17 Amino acids R group structure GLYCINE H ALANINE CH 3 VALINE Aliphatic hydrophobic side chain (3 Carbons)
18 Amino acids R group structure LEUCINE Aliphatic hydrophobic side chain (4 Carbons) ISOLEUCINE Aliphatic hydrophobic side chain (4 Carbons)
19 2. Hydroxyl group containing amino acids (-OH) ØSerine - Ser - S Non essential amino acid ØThreonine - Thr - T Essential amino acid ØTyrosine - Tyr - Y Non essential amino acid
20 Amino acids R group structure SERINE Alcohol group: CH 2 OH THREONINE Methyl Alcohol side chain TYROSINE Aromatic aa CH 2 - phenol group phenol
21 3. Sulfur containig amino acids ØCysteine - Cys -C Non essential amino acid ØMethionine - Met -M Essential amino acids Cystine, another important sulfur containing amino acid, is formed by the condensation of two molecules of cysteine
22 Amino acids R group structure CYSTEINE CH 2 -SH (Sulfhydryl) CYSTINE METHIONINE S-CH 3 - (CH2) 2 Thioether
23 4. Acidic amino acids and their amides ØAspartic acid - ASP -D Non essential amino acid ØAsparagine - Asn - N Non essential amino acid ØGlutamic acid - Glu - E Non essential amino acid ØGlutamine - Gln -Q Non essential amino acid
24 Amino acids R group structure ASPARTIC ACID (Able to form ionic bonds and involved in chemical reactions) R-COO - Carboxyl group GLUTAMIC ACID R-COO - Carboxyl group ASPARAGINE Amide group GLUTAMINE Amide group
25 5. Basic amino acids ØLysine - Lys - K Essential amino acid ØArginine - Arg - R Essential amino acid ØHistidine - His - H Essential amino acid
26 Amino acids R group structure LYSINE (CH 2 ) 4 NH 2 ARGININE Guanidino group Histidine Imidazole ring
27 6. Aromatic amino acids ØPhenyl alanine - Phe - F Essential amino acid ØTyrosine - Tyr - Y Non essential amino acid ØTryptophan - Trp - W Essential amino acid
28 Amino acids R group structure PHENYL ALANINE CH2-benzene ring CH2-phenol group TYROSINE CH2- indole ring TRYPTOPHAN
29 7. Imino acids A unique amino acid: Proline (non essential amino acid) Proline contain a pyrrolidine ring and it has an imino group (NH). Therefore proline is an iminoacid
30 Classification of amino acids based on polarity Based on their polarity, the amino acids are classified into 4 groups: 1- Non-polar amino acids 2- Polar amino acids with no charge on R-group 3- Polar amino acids with acidic side chain (negative R-group) 4- Polar amino acids with basic side chain (positive R-group)
31 Non polar amino acids Are also referred to hydrophobic amino acids They have no charge on R-group E.g., glycine, alanine, leucine,isoleucine, valine, methionine, phenylalanine, tryptophan and proline
32 Polar amino acids with no charge on R-group Possess groups such as hydroxyl, sulfhydryl, and amide Can participate in hydrogen bond (exp: disulfide bond between 2 Cys) E.g., serine, threonine, tyrosine, asparagine, glutamine, cysteine
33 Polar amino acids with basic side chain (positive R-group) 3 amino acids: Lysine Arginine histidine R groups are fully ionized and positively charged (NH 3+ )
34 olar amino acids with acidic side chain (negative R-group) The dicarboxylic mono amino acids: Aspartic acid or aspartate Glutamic acid or glutamate side chain fully ionized and negatively charged (COO - )
35 The Peptide Bond When a Carboxyl group of one amino acid (with side chain R1) forms a covalent peptide bond with the amino group of another amino acid (with the side chain R2) by removal of a molecule of water. The result is: Dipeptide (i.e. Two amino acids linked by one peptide bond) with an amino (N) and carboxyl (C) terminal R ï H 2 N¾C¾ COOH É ï H R ï (N-terminal) H 2 N ¾C¾CO ï H R1 ï H 2 N¾C¾COOH ï H H 2 O R1 ï HN¾C¾COOH (C-terminal) ï H
36 Naming of peptides To name this peptide, you start with the name of the amino acid at the N-terminal and add a suffix yl followed by the name of the second amino acid e.g. glycyl-alanine or alanyl-alanine If more amino acids are joined together, each will have a yl suffix except the C-terminal amino acid e.g. glutamyl-cysteinyl-glycine An oligopeptide is a linear chain of less than amino acids, longer chains are polypeptides (proteins) The number of peptide bonds is one less than the number of amino acids in the peptide or proteins
37 THE END!
38 Most aa are a amino acids but there is some exceptions
39 Titration of amino acid The zwitterion is the dominant species in aqueous solutions at physiological ph (ph=7). what would happen if we add a strong acid to a neutral solution of an amino acid in water? Acidic ph In the presence of a strong acid, the COO - end of this molecule picks up an H + ion to form a molecule with a net positive charge. Increase ph (Add NaOH)
40 Dissociation reaction of Alanine
41 Titration of Alanine Pk 1 and pk 2 : dissociation constant of carboxylic acid and amino group
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