Amino Acid Biochemistry PDF

BIOCHEMISTRY I AMINO ACIDS , PEPTIDES DR IBRAHIM FOUAD AND PROTEIN CHEMISTRY BY PROF. DR. IBRAHIM FOUAD 1  AMINO ACIDS, PEPTIDES AND PROTEINS AMINO ACIDS Structure: There are about 300 amino acids o...

BIOCHEMISTRY I AMINO ACIDS , PEPTIDES DR IBRAHIM FOUAD AND PROTEIN CHEMISTRY BY PROF. DR. IBRAHIM FOUAD 1  AMINO ACIDS, PEPTIDES AND PROTEINS AMINO ACIDS Structure: There are about 300 amino acids occurring in nature. Only 20 of them occur in proteins. Structural features of amino acids (shown in their fully protonated form). * Each A.A has the following 4 groups or atoms: attached to (α)carbon: 1. Amino group: (NH2). 2. Carboxyl group: (COOH). 3. Hydrogen atom (H). 4. Side chain or (R). *Characters of amino acids: all are 1. α-Amino acids: i.e. (NH2) attached to next to carboxyl group (COOH) 2. L-Amino acid i.e. (NH2)on left side configuration. One of 20 amino acids (Proline) not amino acid. It is imino acid as it contains imino group (-NH-). *At physiological pH:(pH=7.4) (COOH)dissociated forming a (-ve)carboxylate ion (-COO-) &(NH2)protonated, forming positively charged ion (-NH+3).  D and L forms of alanine are mirror images. Amino acids that have an asymmetric center at the α-carbon can exist in two forms, designated D and L, that are mirror images of each other. The two forms in each pair are termed stereoisomers, optical isomers, or enantiomers. All amino acids found in proteins are of the L-configuration. However, D-amino acids are found in some antibiotics and in plant and bacterial cell walls.  Classification of amino acids ❑ Many methods used to classify amino acids. The most common are chemical, nutritional&metabolic classifications. Chemical Nutritional Metabolic According to: 1-Essential 1-Glucogenic 1-FA derived from 2-Nonessential 2-Ketogenic 2-Polarity of R. 3-Glucogenic 3-Aromatic,heterocyclic,& aliphatic & ketogenic 4-Neutral, acidic & basic 5-Branched and nonbranched 6-Amino and imino acids 7-Sulfer&hydroxyl a.a Classification of Amino acids based on R Polarity Amino acids (at pH : 6.0 - 7.0) are classified into 4 groups: 1. Nonpolar (hydrophobic) amino acids: least soluble AAS(Glycine, alanine, valine, leucine, isoleucine, methionine, phenylalanine, tryptophan & proline) 2. Polar hydrophilic uncharged AAS: more soluble in water than first gr. R contains polar functional gr. which bind with water by H-bond. They include: a) Suffer containing AAs: cysteine. b) OH containing AAs:serine, threonine, tyrosine, hydroxylysine & hydroxyproline. c) Amide containing AAs: glutamine and asparagine. 3.Polar AAs with +ve charged on R: basic aas. lysine, arginine &histidine. 4. Polar AAs with -ve charge on R :Acidic aas. aspartate and glutamate. Nutritional classification 1- Essential amino acids: These amino acids can't be formed in the body and so, it is essential to be taken in diet. Their deficiency affects growth, health and protein synthesis. H LIT TV LAMP H=histidine* L= lysine I= isoleucine. T = tryptophan. T= threonine. V= valine. L=leucine A = arginine* M= methionine. P= phenylalanine *= arginine and histidine are semi essential 2.Semiessential AAs: formed in the body but not in sufficient amount for body requirements especially in children. 3. Non essential AAs:the rest of amino acids that formed in the body in amount enough for adults and children. They are the remaining 10 AAS.  Metabolic classification Amino acids may be classified according to their metabolic fate in the body into pure ketogenic, pure glucogenic and both ketogenic&glucogenic amino acids. A. Ketogenic amino acids: these give ketone bodies. Leucine & Lysine are the only pure ketogenic amino acids. B. Glucogenic and ketogenic amino acids: these give both ketone bodies and glucose. They are: 1. Isoleucine. 2. Phenylalanine. 3. Tyrosine. 4. Tryptophan. C. Glucogenic amino acids: these give glucose. They include the rest of amino acids not included in the 1st and 2nd groups Amino acids that not enter in protein structure: A. Non alpha amino acids: NH2 not attached to α position. These amino acids perform important functions e.g. 1. β-Alanine: enters in structure of pantothenic acid(Vit),Acyl carrier protein and coenzyme A 2. Taurine: It is a neurotransmitter, Occurs in bile salts and bile acids. γ-Aminobutyric acid (GABA) 3. GABA NOT penetrate the blood-brain barrier; it synthesized in the brain. synthesized from glutamate by decarboxylase and vitamin (B6) as cofactor. This process converts glutamate, excitatory neurotransmitter → inhibitory neurotransmitter (GABA). B. Amino acids which participate in urea cycle: These are: 1.Arginine (α amino δ guanido valeric acid). 2. Orinithin (α, δ diamino valeric acid). 3. Citruline (α amino δ urido valeric acid) C. Amino acids in intermediary metabolism: 1. Homoserine 2. Homocysteine D. Amino acids containing iodine: These are precursors of thyroid hormones: 1. Monoiodotyrosine. 2. Diiodotyrosine. 3. Triiodotyrosine (T3). 4. Tetraiodotyrosine (T4). E. Cystine: It is 2 cysteine (dicysteine) united together by removal of hydrogen of -SH groups. It is important for protein structure. IV. Amino acids found in proteins and formed after protein synthesis: Name Structure Source Hydroxyproline Collagen and gelatin Hydroxylysine Collagen and gelatin N-methyl-lysine Fast muscle' myosine MethylHistidine muscle myosine  Name Structure Source γ-Carboxyglutamate Prothtombin& bone protein Desmosine Elastin (four lysine residue) V. Functions (biomedical importance) of amino acids: A. Structural function: enter in the structure of: 1. Body peptides & proteins: e.g. plasma proteins, tissue proteins, enzymes, etc. 2. Hormones: some hormones are amino acid derivatives e.g. thyroxine and catecholamines. 3. Amines: Some amino acids give corresponding amines by decarboxylation e.g. histidine gives histamine which is vasodilator. B. Neurotransmitters: Some amino acids as glycine and glutamate act as neurotransmitters. C. Detoxication: Some amino acids are used in detoxication reactions e.g. glycine. D. Health and growth: Essential amino acids support growth in infants and maintain health in adults. Physical properties A. Solubility: All amino acids are soluble in water, dilute acids, alkalies and ethanol. B. Optical activity: All amino acids except glycine- are optically active because they contain asymmetric carbon atom (=α- carbon).Thus they can rotate plane polarized light.Glycine contains no asymmetric carbon atom, so it is optically inactive. C. Melting point: Amino acids are present in crystals with high ionic forces, stabilizing these crystals. So amino acids have high melting points above 200°C i.e. they are very stable molecules. Amphoteric properties and isoelectric point of amino acids: Amino acids contain both acidic (COOH) group and basic (NH2) group. They react with both acids and alkalies. In acidic medium, the NH2 group reacts with acid e.g. HCl form positively charged cation. When electric direct current passed, this cation will move towards cathode. In alkaline medium, the COOH group will react with the alkali, e.g. NaOH, and negatively charged anion is formed. When electric current is passed, this anion move towards anode. At certain pH which is specific for each amino acid, this amino acid will carry net zero charge (equal negative and positive charges). This pH is called "Isoelectric point", and the amino acid molecule is called in this case "Zwitter ion" or "dipolar ion" or "hybrid ion".Zwitter ion is considered neutral and it does not move in an electric field. d) Isoelectric pH (isoelectric point; PI): the pH at which zwitter ion formed. 1)Each amino acid has certain pH at which zwitter ion is formed. 2)This pH is at midway between the pK values of the carboxyl and amino groups. 3) Example: alanine i- In strongly acidic pH (at pH zero) alanine present mainly in the form +ve charged molecule. Its pK (pKI) = 2.34 ii- By adding NaOH, carboxyl group loses its proton (H +) and alanine carries both positive and negative charges (zwitter ion). iii-By adding more NaOH, the solution Becomes strongly alkaline, and ammonium group (-NH3) will lose its proton and alanine will become negatively charged. Its pK (pK2) = 9.69 (PK=acid dissociated constant) iv- IP for alanine = pK1+ pK2 = 2.34 + 9.69 = 6.105 2 2 Isoelectric point of alanine is 6.105 when alanine carries both positive and negative charges (zwitter ion).  Peptide bond formation 1. covalent bond formed between carboxyl group (COOH) of one amino acid and amino (NH2) of another. 2. formed by removal of water. 3. Peptide formation needs energy, from. ATP. 4. Peptide bond is TRANS and semi-rigid bond i.e. no free rotation can occur around bond axis.  Peptide Definition: Peptides are compounds, formed of less than 50 amino acids linked together by peptide bonds. 1. Dipeptide (2 amino acids and one peptide bond). 2. Tripeptide (3 amino acids and two peptide bonds). 3. Oligopeptide (3-10 amino acids). 4. Polypeptide (10-30 amino acids). II. Primary structure of peptides: ▪ arrangement of AA in peptide chain In a polypeptide chain: N-terminal amino acid (i.e. contains free NH2) at left side. C-terminal amino acid (i.e. contains free COOH)at right side. III. Separation of peptides: A. By electrophoresis. B. By exchange chromatography technique. IV. Biologically active peptides: Peptides include many active compounds as hormones, neurotransmitters, neuromodulators, antibiotics, anti-tumour agents, aspartame and glutathione. A. Hormones: 1. Insulin and glucagon from pancreas. 2. Vasopressin and oxytocin from posterior pituitary gland. 3. ACTH from anterior pituitary gland.  ❖ Insulin From ß cell of pancreas Contains 30 + 21 amino acids Hypoglycemic Hormone ❖ Glucagon From α cell of pancreas Contains 29 amino acids Hyperglycemic Hormone  Oxytocin Hormone of posterior pituitary: 9 amino acids Stimulates contraction of uterus ❑ Function of oxytocin: Action on pregnant uterus Throughout the period of pregnancy, oxytocin secretion is inhibited by estrogen and progesterone. At the end of pregnancy, ↓ secretion of estrogen and progesterone suddenly and↑ the secretion of oxytocin. Oxytocin causes contraction of uterus and helps in the expulsion of fetus. Thus oxytocin initiates and completes parturition. ✓ The structure Of oxytocin is very similar to that Of vasopressin: ✓ Cysteine — tyrosine — phenylalanine — glutamine — asparagine — cysteine — p Ine — arginine — glycine. ✓ Vasopressin is also a nonapeptide with a sulfur bridge, whose sequence differs from oxytocin by 2 amino acids.  Vasopressin Also called antidiuretic hormone(ADH) Hormone secreted by posterior pituitary Contains 9 amino acids Decreases GFR and retains body water ↑Increases Blood pressure Natriuretic factor Peptide ( 28 aa )produced by specialized cells in the heart and nervous tissue. stimulates the production of dilute urine (opposite to vasopressin). ↓ Blood pressure  Corticotropin Hormone of Anterior pituitary Contains 39 amino acids Stimulates adrenal cortex for secretion of steroid hormones TRH(thyrotropin releasing H) Hormone of Anterior pituitary Contains 3 amino acids Stimulates release of thyrotropin from anterior pituitary TRH→TSH →T3&T4  Biologically IMP peptides Glutathione Tripeptide : Glutamic acid, Cysteine and Glycine Reduced form as GSH - Oxidised form as GS-SG Found in all mammalian cells except neurons Characterised by Gama peptide bonds, Not digested by peptidase Found in all cell except nerve cell Biological antioxidant, Amino acid absorption.  Glutathione Functions: 1.Coenzyme in oxidation reduction reaction. 2.Maintains RBCs Membrane integrity:Protect against damage&hemolysis RBCs : It break down (H2O2) which causes cell damage and hemolysis. H2O2+Glutathione )G-SH )→H2O +oxidized glutathione) GS-SG) 3.Protects HB against Oxidation (prevent Ferrous →ferric). 4.Help to scavenging Free radical and peroxide 5. Help in detoxification of xenobiotics :Defence mechanism against certain toxic compounds (T): G-SH combine with toxic to produce non-toxic compounds. T (toxic) + Glutathione → Non-toxic compound 6. Help in amino acids absorption 7.Prevents oxidation of sulfhydryl group of proteins 8. 7. Activation of some enzymes. 8. Inactivation of insulin hormone. Hemolytic anemia due to G6PD deficiency  PLASMA KININS (Bradykinin(9) and Kallidin(10) ❑ Bradykinin →Bradys,= "slow," and kinein, ="to move. ❑ Trypsin and certain snake venoms acted on plasma globulin to produce a substance that lowered blood pressure and caused a slowly developing contraction of the gut. Bradykinin ✓ Contains 9 amino acids, Formed in blood ✓ Vasodilator(lower blood pressure ) ✓ Causes contraction of smooth muscles ✓ Mediators of pain By directly stimulating nerve endings and by ↑ PG production. Kallidin Contains 10 amino acids. -Power full vasodilator ❑ β-Lipotropin: polypeptide produced by anterior pituitary, precursor of β -Endorphins "endogenous morphine" A peptide hormone(31 AAs) released by pituitary (into blood) and hypothalamus (into brain). Beta-endorphin→ the best in pain relief Inhibits pain perception (called Body's natural analgesic or opiate). Produced at the time of physical or emotional stress. affect your mood , emotions and may be responsible for your body feeling pleasure. Acts as neurotransmitter and neuromodulator. Has analgesic effect powerful 18-30 times than morphine.  Enkephalins ✓ Formed in CNS, Binds to certain receptors in brain ✓ Pentapeptide neurotransmitters produced by the brain to reduce pain. ✓ i.e: Inhibit sense of pain. The action of morphine and codeine is based on binding at the same receptor sites. Met-enkephalin: Tyr—Gly—Gly—Phe—Met Leu-enkephalin: Tyr—Gly—Gly—Phe—Leu  Aspartame ✓ Di-peptide.(Discovered in 1965) ✓ sweetening agent, being used in replacement of cane sugar. ✓ 200 times sweeter than sucrose ✓ Made of Phenylalanine and L-Aspartic acid ✓ L aspartyl.L-phenylalaninyl methyl ester. ✓ Low-calorie sweeteners ✓ It is a dipeptide that is completely ✓ digested after consumption Antilbiotics-. e.g. valinomycin. - Antitumor agent: e.g. bleomycin.  Proteins I. Nature of proteins: A. Composition: 1. Proteins are macromolecules formed of amino acids united together by peptide bonds. 2. 20 Amino acids are found in proteins, in different proportions. 3. Some proteins are formed of 2 or more polypeptide chains. B. Size of proteins: 1. Proteins having very high molecular weight, ranging from 5,000 to several millions. 2. The term protein is applied to describe molecules greater than 50 amino acids. 3. Molecules contain less than 50 A.A. are termed: peptides.  Conformation of proteins = (protein structure) Every protein in its native state has 3 dimensional structure (primary, secondary and tertiary) which known as conformation. Conformation is essential for the functions of each protein. Any change in protein conformation may lead to a disease. Proteins which formed of more than one peptide chain have additional quaternary structure. The function of a protein arises from its conformation. ✓ Protein structure can be classified into four levels ✓ The number and sequence of (AAs) in the protein are different in different proteins. 4 Levels of protein organization  Primary structure It is a linear sequence of AAs linked by peptide bond forming a backbone proteins. Peptide bonds: covalent bonds responsible for 1◦ ry str. Peptide bond →linear , planner ,rigid ,partial double bond character. e.g. Glutathione: Tripeptide : Glutamyl-Cystienyl - Glycine. Methionine Enkephalins : pentapeptide: Try- Gly- Gly- Phe –Me. Free amino end (N-terminal AAs/residue) →N+H3 is on left. Free carboxyl end (C-terminal AAs/residue) →COO- is on right.  Primary structure The remaining amino acids in the chains are termed: amino acid residues. AAs sequence is written and read from left to right. The types and arrangement of AAs in each protein determined by genetic information present in DNA.  Secondary Structures of proteins It is spatial relationship of adjacent AAs close to each other. Spatial arrangement of protein formed by twisting or folding polypeptide chain. Results from interaction of adjacent AA residues (1st &4th). Hydrogen bonds are responsible for secondary structure. H-bond between (H) of -NH gr. of one AA and (O) of carbonyl gr. (C=0) of the fourth one. Helical coiling in (Alpha helix) OR zig-zag linear (beta-sheet). If a backbone of polypeptide chain is twisted by equal amounts about each α-carbon , it forms a coil or helix. The α-helix is a rod like structure. ✓ H-Bond have optimal N to O (N-O) distance of 2.8 AO. ✓ The axial distance between adjacent AAs is 1.5 AO and gives 3.6 AA residues per turn of helix.  ß- PLEATED SHEET Almost fully extended and its surface appear pleated. Formed between 1 or more polypeptide chains. also formed between segments of the same polypeptide chain. Stabilized by H-bonds bet. P. bonds. Found in fibrous and globular protein. ✓Types ✓Parallel ß-pleated sheet: formed of 2 or more polypeptide chains running in the same direction (Nterminals are on the same side). ✓Anti-parallel ß-pleated sheet: formed of one or more polypeptide chains running in opposite directions (N and C terminals are alternating)  Tertiary structure ❑ The final arrangement of single polypeptide chain resulting from spatial relationship of more distant AAS residues. ❑ Two forms of tertiary structures: 2. Bonds responsible for tertiary structure are: a) Hydrogen bonds: within the chain or between chains. b) Hydrophobic bonds: between nonpolar side chains (R) of neutral amino acids. c)Electrostatic bonds (salt bonds):between oppositely charged groups in the side chains of amino acids e.g. Σ-amino group of lysine and carboxyl group of aspartate. d) Disulfide bonds: between cysteine residues within the chain.  Quaternary structure Many proteins are composed of several polypeptide chains. Each polypeptide chain is called: subunit. 1. Each subunit has its own primary, secondary and tertiary structure. 2. Bonds responsible for quaternary structure: a) Hydrogen bond. b) Hydrophobic bond. c) Electrostatic bond 3. Example of proteins having quaternary structure: a) Insulin: 2 subunits. b) Lactate dehydrogenase enzyme: 4 subunits. c) Globin of hemoglobin: 4 subunits.