Chemistry of Amino Acids and Proteins - I AAU 2024 PDF

Chemistry of Amino Acids and Proteins - I 1  Outline of the topic  General structure of Amino Acids  Classification of Amino acids  Function of Amino Acids  Acid-Base property of amino acids  Peptide bond structure and functional peptides  Protein structure  Biol...

Chemistry of Amino Acids and Proteins - I 1  Outline of the topic  General structure of Amino Acids  Classification of Amino acids  Function of Amino Acids  Acid-Base property of amino acids  Peptide bond structure and functional peptides  Protein structure  Biological functions of proteins  Protein classification 2  Objectives of the topic At the end of this session, you will be able to Describe general structure of amino acids List the biochemical functions of amino acids Categorize amino acids by different basis of classification Explain acid-base property of amino acids Explain peptide bond and its character Mention functional peptides Give details of protein structure Elucidate biological functions of proteins Classify proteins 3 What are Proteins? Unbranched Polymers of amino acids linked head to tail Major constituent of most cells Usually form multi-molecular complexes They are folded into specific conformations Their conformation and functional-group chemistry controls function Responsible for most of our phenotype (define what an organism is, what it looks like, how it behaves, etc.) Made from almost 20 different types of standard amino- acids Special condition: Selenocysteine incorporated during co- translation in human 4  Amino acids  Structure:  central carbon H O  amino group H | ||  Carboxyl group —N— —C— C—OH H | Side chain (R group)  variable group R  confers unique chemical functionality  Chiral/ Optically active  Acid–base properties  Capacity to polymerize 5  Classification of Amino Acids Amino acids can be classified based on  Side chain character  Nutritional value  Metabolic fate  Presence/ absence in proteins 6 Amino Acid Classification by Side Chain Character  Hydrophobic side chain: stabilize protein structure by hydrophobic interactions.  Tyrosine can form hydrogen bonding. 7 Classification...  Reversible formation of a disulfide bond by the oxidation of two molecules of cysteine 8  Classification… Acidic side chain: H+ (proton) donor 9  Classification … Basic side chains: H+ acceptors  Histidine side chain pKa= 6.0  10% protonated at pH= 7  Serving as a proton donor/ acceptor in many enzymatic reactions  Identification of carbon atoms in amino acids 10  Names and Codes of Amino Acids Name One Three R-Group Properties letter Letter Glycine G Gly Hydrophobic Alanine A Ala Hydrophobic Valine V Val Hydrophobic Leucine L Leu Hydrophobic Isoleucine I Ile Hydrophobic, two chiral carbons Proline P Pro Cyclic, not terribly hydrophobic Phenylalanine F Phe Hydrophobic, bulky Tyrosine Y Tyr Less hydrophobic (than Phe), bulky Tryptophan W Trp Hydrophobic, bulky (indole ring) Cysteine C Cys Hydrophobic, highly reactive (S-S link) Methionine M Met Hydrophobic (start a.a.) Serine S Ser Hydrophilic, reactive Threonine T Thr Hydrophilic, reactive, two chiral carbons Lysine K Lys Highly hydrophilic, positively charged Arginine R Arg Highly hydrophilic, positively charged Histidine H His Highly hydrophilic, positive or neutral Aspartate D Asp Highly hydrophilic, negatively charged Glutamate E Glu Highly hydrophilic, negatively charged Asparagine N Asn Polar, Uncharged Glutamine Q Gln Polar, Uncharged 11 Amino Acid Classification Based on Nutritional Value  Basedupon whether the AAs can be synthesized in human body or not  Indispensable or essential amino acids: 9 amino acids  Not synthesizable in the body in adequate amounts  Val, Ile, Thr, Trp, Leu, Lys, Met, Phe and His.  Dispensable or non-essential AAs o Can be synthesizable in the body from the essential ones  Conditionally essential amino acids: During illness or stress  Tyrosine, cysteine, arginine, glutamine, glycine, proline, and serine. 12  CLASSIFICATION BASED ON METABOLIC FATE  Based upon the catabolic fate of Carbon skeleton of amino acids Ketogenic Mixed Glucogenic Type  Ketogenic Catabolically give intermediates Leu IIe convertible into Acetyl-CoA or Acetoacetyl-CoA Lys Tyr Ala, Arg Asp,  Glucogenic Asn Glu, Gln 14 of them give rise to intermediates of Ser, Met Pro, Trp glycolysis or Kreb’s cycle Gly His, Thr Val, Cys  Mixed type Carbon-skeleton of which is catabolized to Phe produce glycolytic intermediates or acetyl CoA derivatives 13 Some Common Biological Functions of Amino Acids  Formation of peptides and proteins  Stabilize 3D structure of proteins by forming multiple bonds  Specific AAs at the active site are vital for enzyme catalysis  Some AAs as source of glucose  Cys and Met are sources of S in the body (e.g. for Fe-S center formation)  Carbon skeleton and Nitrogen of AAs used for nucleic acid synthesis  Gly and Met help in the detoxification mechanisms  Met can act as a methyl group donor in methylation reactions 14 Amino Acids as Precursors of Biologically Important Derivatives  Gycine is a precursor for  Heme  Creatine  Tyrosine is the precursor for number of hormones:  Thyroxine & Triiodothyronine  Epinephrine & nor-epinephrine  Skin pigment melanin  Tryptophan can give rise to Niacin Serotonin  Histidine can be converted to Histamine 15 Uncommon Amino Acids – Found in proteins Hydroxylysine and hydroxyproline - Mainly in collagen - Found in connective tissues Tyroxine and Triiodotyronine - Produced from degradation of thyroglobulin - Act as hormones for growth & development N-methylarginine and N-acetyllysine - found in histone proteins 16 Uncommon Amino Acids – Found in proteins Methylhistidine, -N-methyllysine, & N,N, N-trimethyllysine - Methylated amino acids in myosin -Carboxyglutamic acid - In blood clotting proteins & Ca2+ containing proteins e.g. Prothrombin 17 Uncommon Amino Acids – Found in proteins Desmosine - Derivative of four Lys residues - Found in fibrous protein elastin Selenocysteine - Derived from serine - Introduced during protein synthesis - Role in antioxidant activity e.g. Gluthione peroxidase active site 18  Amino Acids not found in proteins GABA (decarboxylation of glutamic acid) - a potent neurotransmitter. Histamine (decarboxylation of histidine) & Serotonin (from tryptophan) - function in smooth muscle contraction, as nurotransmitter, vascular permeability, etc -Alanine - for synthesis of carnosine (for muscle endurance) 19  Amino Acids not found in proteins Epinephrine Ornithine & Citrulline - in urea cycle, Arg synthesis. Dopa (3,4-dihydroxyphenylalanine): Precursor of melanin S-adenosyl methionine (SAM): a methyl donor in transmethylation rxn 20 Acid-Base Properties of Amino Acids  Ammonium form acts as an acid, the carboxylate as a base. 21  pI of Neutral Amino Acids  The PI can be calculated as the average of pKa1 and pKa2 22 pI of Amino Acids - Alanine 23 Amino Acids with Ionizable Side Chains Lysine 24 pI of Amino Acids – With Acidic, Neutral and Basic Side Chains 25 pKa and PI Values of Common Amino Acids 26  Peptide Bond & Functional Peptides 27  Peptide Bonds (Amide bond) Condensation rxn Formation of dipeptide, tripeptides, etc....  Forms N-terminal and C-terminal Acid-base behavior of a peptide can be predicted from its free -amino and -carboxyl groups as well as the nature and number R groups.  Have characteristic characteristic pI  pKa value for an ionizable R group can Serylglycyltyrosylalanylleucine change somewhat when an amino acid or becomes a residue in a peptide. Ser–Gly–Tyr–Ala–Leu 28  Planar peptide groups in a polypeptide chain Amide nitrogen are non-basic because their unshared electron pair is delocalized by interaction with the carbonyl group. Rotation around C-N bond is restricted due to the double bond nature Peptide groups are therefore planar Planar Structure of peptide 29  Biologically Active Peptides  Glutathione – Formed from -glutamic acid, Cysteine & Glycine – It protects the cell membrane from damage,  e.g., prevents hemolysis of erythrocytes Slightly larger peptides/ Oligopeptides  Insulin – contains two polypeptide chains one having 30 and the other has 21amino acid residues  Corticotropin – is a 39-residue hormone of the anterior pituitary gland – stimulates the adrenal cortex 30  Commercial peptide: Example O O O H2N CH C NH C CH C OCH3  Aspartame/ L-Aspartyl- CH2 CH2 L-phenylalanine methyl Methyl ester ester/ Neurasweet C OH  Artificial sweetener O Aspartic Acid Phenylalanine 31  Structure and Classification of Proteins 32  Protein structure  The 3-D structure mainly depends on types, number and sequence of amino acids  twisted, folded, coiled into unique shape Pepsin  Structure determines the function of a protein  Native, folded structure of the protein depends on several factors Collagen (1) interactions with solvent molecules (2) the pH and ionic composition of the solvent (3) the sequence of amino acid in a protein. Hemoglobin 33 Primary structure of proteins  Describes sequence and number of amino acids in chain ◦ Determined by gene (DNA sequence) ◦ Contain all information necessary for folding into its “native” structure  Amino acid sequence of Lysozyme 34  Primary structure... Does Amino Acid Sequence determine protein function? Oxytocin Ile Gln Tyr Asn - Initiates contractions of the uterus during childbirth Cys Cys Pro-Leu-GlyNH 2 - Plays a role in the release of milk during lactation S S Vasopressin (ADH) Phe Gln Tyr Asn - Regulate the amount of water Cys Cys present in the body Pro-Arg-GlyNH2 S S 35  Primary structure... Change in amino acid sequence may cause problem! Hemoglobin – 574 amino acids 36 Secondary structure of proteins: Local folding  Formed by H-bonding  Describes about folding pattern along short sections of polypeptide  The Development of regular patterns of hydrogen bonding result in distinct folding patterns 37 Secondary structure: Examples  -helix  Peptide carbonyl H-bonded to peptide N- H group four residues farther  One turn of the helix represents 3.6 amino acid residues (13 atoms from the O to the H of the H-bond - 3.613 helix)  All of the H-bonds lie parallel to the helix axis  All of the carbonyl groups are pointing in one direction along the helix axis 38 Secondary (2°) structure: Examples e.g. Myoglobin – 153 AAs - Eight stretches of  -helix forming a box to contain the heme prosthetic grp. Other forms of Helix 310 helix - 3.0 residues per turn (with 10 atoms in the ring formed by making the hydrogen bond three residues up the chain) 27 ribbon 39 Secondary (2°) structure: Examples  -Pleated Sheet  Each strip of paper as a single peptide strand  Peptide backbone makes a zigzag pattern along the strip  –carbons lying at the folds of the pleats.  Formation of interstrand H- bonds  Side chains oriented perpendicular to the plane of the sheet,  Side chains extending out from the plane on alternating sides 40  Secondary (2°) structure: Examples Two types Parallel pleated sheet - Typically large structures Usually > five strands Antiparallel pleated sheet - Usually having hydrophobic side chain on one side, so it requires alternating hydrophobic & hydrophilic residues arrangement in primary structure 41  Secondary (2°) structure: Examples -Turn/ tight turn/ -bend - A tight loop formed by the carbonyl O of the 1st is H-bonded with amide N of the 4th residue down the chain - Proline & glycine, occur frequently in -turn sequences - Abundant in globular structures 42  Secondary (2°) structure: Examples -Bulge  A small piece of non-repetitive structure that can occur by itself  Most often occurs as an irregularity in antiparallel -structures  Occurs between two normal – structure H-bonds and comprises 2 residues on one strand and one residue on the opposite strand  Bulges thus cause changes in the direction of the polypeptide chain, but to a lesser degree than -turns. 43 Super Secondary Common motifs: Examples 44 Super-secondary structures commonly found in some DNA- binding proteins 45 Tertiary (3°) structure: All things hold together  Shows the whole molecule folding pattern ◦ Describes about overall 3-D structure of a polypeptide ◦ Determined by interactions between R groups ◦ Bonds that determine 3D-structure are:  Hydrogen bond  Hydrophobic interactions  Disulfide bridges  Ionic bonds  Van der Waals Force 46 Bonds determining 3° structure of proteins 47 Examples of some domains -Barrel Bundle Saddle 48  Quaternary (4°) structure  Formed from more than one polypeptide chain  Organized by the same types of bonds as tertiary structure  Most intracellular enzymes are oligomers C) Immunoglobulin49  Advantages of Quaternary Association Stability - Favorable reduction of the protein’s surface-to-volume ratio - Interactions stabilizes the protein energetically - Shield hydrophobic residues from solvent water Genetic Economy and Efficiency - Less DNA is required to code for a monomer 50  Advantages of … Bringing Catalytic Sites Together  Monomer may not constitute a complete enzyme active site  May also carry out different but related reactions on different subunits e.g. Tryptophan synthase (22) -subunit: - subunit : Cooperativity - Regulate catalytic activity by subunit interactions - Some proteins are inactive when oligomers e.g. Insulin hexamer formation in solution - Ligand binding at one site changes affinity of Hb the other site for O2 51 Examples of Proteins with Quaternary Structure 52  Summary of Levels of Protein Structure aa sequence peptide bonds determined by DNA H bonds of carbonyl O and Amide H of peptide R groups Hydrophobic, Ionic, Disulfide bridges, H-bond Multiple polypeptides All bond types like tertiary53 Classification of Proteins – Based on Function  a. Enzymes:  e.g. Glucokinase  b. Regulatory Proteins  Regulating other proteins  Eg. Insulin  Regulation of gene expression e.g. Transcription activators c. Transport Proteins e.g. Hb: Serum albumin: Fatty acid transport Membrane transporters (channels): e.g. AA & Glucose transporters 54  Functional classes … d. Storage Proteins: e.g. Casein: Major source of Calcium phosphate in mammalian infants E.g. Ferritin: for Hb synthesis e. Contractile and Motile Proteins፡ For cell motility, muscle contraction , cell division e.g. Actin & Myosin: muscle contraction Dynein and Kinesin (Motor proteins): drive the movement of vesicles, granules, and organelles along microtubules 55  Functional classes … f. Structural Proteins - Provide strength & protection to cells & tissues e.g. -keratin: hair, horns, and fingernails Collagen: bone, connective tissue, tendons, cartilage, Elastin: an important component of ligaments Collagen and proteoglycans: in ECF that cushion and lubricate g. Scaffold Proteins (Adapter Proteins) eg. Can act as a scaffold onto which a set of different proteins assembled Anchoring (or targeting) proteins: bind other proteins, causing them to associate with other structures in the cell 56  Functional classes … h. Protective proteins - active role in cell defense & protection - Eg. Immunoglobulins or antibodies by lymphocytes - thrombin and fibrinogen: 57  Protein Classification Based on Nutritional Value ◦ Complete or high quality proteins:  Contain all the necessary essential amino acids; eggs, meat, etc. ◦ Incomplete or low-quality proteins:  Deficient in one or more essential amino acids  Eg. corn deficient with Lys, Met, Try  Protein Classification Based on composition: Simple Vs Conjugated ◦ Simple proteins: only amino acids ◦ Conjugated proteins: amino acids + something else. 58  Types of Conjugated Proteins i. Glycoproteins - Mostly Proteins destined for an extracellular location e.g. Fibronectin (adhesive glycoproteins) and proteoglycans for ECM IgG: circulate in plasma - Many glycosylated membrane proteins on extracellular segment ii. Lipoproteins: Primarily in the transport of lipids iii. Nucleoproteins: for storage & transmission of genetic information e.g. Ribosomes, Chromosomes 59  Types of Conjugated Proteins iv. Phosphoproteins: Esterified with phosphates by ser, thr or tyr e.g. Casein: bring phosphorous to growing infant v. Metalloproteins: - metal storage proteins (e.g. ferritin) - metal containing enzymes e.g SOD vi. Hemoproteins - Subclass of metalloproteins - Having heme prosthetic grp vii. Flavoproteins - Containing flavin (vitamin B2 derivative) E.g. oxidoreductases 60 Protein Classification Based on Shape (Architecture) - Fibrous proteins, “long & thin” - Simple, regular linear structure - Polypeptides organized nearly parallel along a single axis - Insoluble proteins in water or in dilute salt solution e.g -Keratins in Collagen - Serve structural role in cells (e.g. Hair, wool, skin, nail) - Often assembled into large cables or threads - Globular Proteins, “Spherical Shape” - Roughly spherical - Compactly folded with hydrophobic interior - Usually very soluble in aqueous solution - Most soluble cellular proteins e.g. Insulin, Hb, Enzymes, Abs, Carrier proteins 61 - Membrane Proteins - Hydrophobic side chains oriented outward for interaction with membrane - Hence, insoluble in aqueous but solubilized by detergents - Have fewer hydrophilic amino acids than cytosolic proteins 62 Common Fibrous and Globular Proteins: Occurrence & Use 63  Example of Fibrous proteins: -Keratin  Major components of hair & nails  A fibrous structural protein coiled into a right-handed helix  -helix strands are wound into a “superhelix”.  One complete superhelix turn for each 35 turns of the -helix.  -helix stabilized by H-bonds between amide N–H groups and C=O groups four residues away a-helical segments in their chains 64 Your hair 65  Examples of Fibrous Proteins: Collagen  Constituent of connective tissues  Tendons, cartilage, bones, teeth, skin, & blood vessels A Triple Helix  Rigid, inextensible fibrous  High tensile strength  Helps for running and jumping that put severe stresses on joints and skeleton  Collagen is just like rope -- enables your skin to be strong and flexible.  Most common collagen types  Type I - bones, tendons, and skin – two 1 (I) & one 2 (I)  Type II – Cartilage  Type III - Blood vessels 66  Examples of Fibrous Proteins: Collagen Tropocollagen: Basic structural unit of collagen Three intertwined polypeptide chains each >1000 AAs Mainly composed of Glycine (one in three) & proline Sequence are repeats of a Gly-x-y motif, where x is frequently Pro y is frequently Pro or Hyp In the triple helix, every third residue faces or contacts the crowded center of the structure. So only glycine fit Contain 4-hydroxyproline (Hyp), 3-hydroxyproline, & 5- hydroxylysine (Hyl) Important for intermolecular and intramolecular cross linkage Hydroxylation require ascorbic acid 67 Examples of Fibrous Proteins: Collagen - Collagen triple helices are 300 nm long, - 40-nm gaps occur between adjacent collagen molecules in a row - Pattern repeats every five rows (5 X 68 nm = 340 nm) Hole regions: 40-nm gaps are important for  Attachment of sugars to 5-hydroxylysine  plays a role in organizing fibril assembly  Plays a role in bone formation.  Microcrystals of hydroxyapatite (Ca5(PO4)3OH) embedded in a matrix of collagen fibrils. 68