Biochemistry 3: Amino Acids, Peptides, and Proteins FOR PHYSIO Students PDF

AMINO ACIDS PEPTIDES PROTEINS BIOMOLECULES Proteins Carbohydrates Lipids Nucleic acids  Most of them are polymers – comprised of repeating units called Monomers Such polymeric macromolecules in living systems are highly ordered chemical entities, with specific sequences of...

AMINO ACIDS PEPTIDES PROTEINS BIOMOLECULES Proteins Carbohydrates Lipids Nucleic acids  Most of them are polymers – comprised of repeating units called Monomers Such polymeric macromolecules in living systems are highly ordered chemical entities, with specific sequences of monomeric subunits giving rise to discrete structures and functions  Three interrelated principles: (1) the unique structure of each macromolecule determines its function (2) noncovalent interactions play a critical role in the structure and thus the function of macromolecules (3) the monomeric subunits in polymeric macromolecules occur in specific sequences, representing a form of information on which the ordered living state depends The water molecule and its ionization products, H+ and OH– , profoundly influence the structure, self-assembly, and properties of all cellular components, including proteins, nucleic acids, and lipids. The noncovalent interactions responsible for the strength and specificity of “recognition” among biomolecules are decisively influenced by water’s properties as a solvent, including its ability to form hydrogen bonds with itself and with solutes KEY PRINCIPLES of proteins In every living organism, proteins are constructed from a common set of 20 amino acids (AA) So-called proteinogenic AA 20 have the standard genetic code Additional 2 (selenocysteine in eukaryotes and pyrrolysine) incorporated by special translation mechanism – stop codon UGA In proteins, AA are joined in characteristic linear sequences through a common amide linkage – the peptide bond carbonyl carbon-to-nitrogen bond Individual proteins can be separated from the thousands of other proteins present in a cell based on differences in their chemical and functional properties arising from their distinct AA sequence  Proteins are responsible for many of the essential functions of life Their function comes from their structure, which is determined by their sequence Amino acids The amino acids have an amino and a carboxylic acid group that are joined to the same carbon atom. This carbon atom is referred to as the α carbon. AAs differ from each other in their side chains, or R groups, which vary in structure, size, and electric charge, and which influence the solubility of the amino acids in water  A chiral centre is an atom that has four different The α-carbon atom is a chiral center groups bonded to it in such a manner that it has a non-superimposable mirror image Because of the tetrahedral arrangement of the bonding orbitals around the α-carbon atom, the four different groups can occupy two unique spatial arrangements, and thus amino acids have two possible stereoisomers Optically active Interact with light differently Since they are nonsuperposable mirror images of each other, the two forms represent a class of stereoisomers called enantiomers A review of isomers Amino Acids Can Be Classified by R Group Five main classes based on the properties of their R groups (20AAs) [particularly their polarity, or tendency to interact with water at biological pH?] The polarity of the R groups varies widely, from nonpolar and hydrophobic (water-insoluble) to highly polar and hydrophilic (water- soluble) A few amino acids are somewhat difficult to characterize or do not fit perfectly in any one group, particularly glycine, histidine, and cysteine ‘Knowledge of the chemical properties of the common amino acids is central to an understanding of biochemistry’ hydrophobic Nonpolar, Aliphatic R Groups The R groups in this class of amino acids are nonpolar and hydrophobic The side chains of alanine, valine, leucine, and isoleucine tend to cluster together within proteins, stabilizing protein structure through the hydrophobic effect Glycine has the simplest structure very small side chain makes no real contribution to interactions driven by the hydrophobic effect Methionine, one of the two sulfur-containing AA, has a slightly nonpolar group in its side chain Proline has an aliphatic side chain with a distinctive cyclic structure Aliphatic = hydrocarbon chain Aromatic R Groups Phenylalanine, tyrosine, and tryptophan, with their aromatic side chains, are relatively nonpolar (hydrophobic) All can contribute to the hydrophobic effect The hydroxyl group of tyrosine can form hydrogen bonds, and it is an important functional group in some enzymes Tyrosine and tryptophan are significantly more polar than phenylalanine because of the tyrosine hydroxyl group and the nitrogen of the tryptophan indole ring Polar, Uncharged R Groups The R groups of these AA are more soluble in water (hydrophilic) because they contain functional groups that form hydrogen bonds with water This class of AA include serine, threonine, cysteine, asparagine, and glutamine The polarity of serine and threonine is contributed by their hydroxyl groups and that of asparagine and glutamine by their amide groups Cysteine is an outlier here because its polarity, contributed by its sulfhydryl group, is quite modest Cysteine is a weak acid and can make weak hydrogen bonds with oxygen or nitrogen Asparagine and glutamine – ionized forms are aspartate and glutamate Cysteine is readily oxidized to form a covalently linked dimeric amino acid called cystine, in which two cysteine molecules or residues are joined by a disulfide bond Positively Charged (Basic) R Groups The most hydrophilic R groups are those that are either positively or negatively charged The amino acids in which the R groups have significant positive charge at pH 7.0 Lysine has a second primary amino group at the 5th position on its aliphatic chain Arginine has a positively charged guanidinium group Histidine has an aromatic imidazole group May be positively charged (protonated form) or uncharged at pH 7.0 or deprotonated His residues facilitate many enzyme-catalyzed reactions by serving as proton donors/acceptors Nitrogenous analogue of carbonic acid C=O vs C=NH, OH vs NH2 Negatively Charged (Acidic) R Groups The two amino acids having R groups with a net negative charge at pH 7.0 are aspartate and glutamate, each of which has a second carboxyl group Non Standard Amino Acids These Amino acids do not take part in protein synthesis but play an important role in the body Modification of common amino acids: 4-hydroxyproline (found in collagen) pyrrolysine Free metabolites: Citrulline – intermediate in urea cycle Ornithine – intermediate in arginine biosynthesis Taurine L-DOPA – a precursor to the neurotransmitters dopamine, norepinephrine (noradrenaline), and epinephrine (adrenaline), which are collectively known as catecholamines (from glutamate) GABA – an inhibitory neurotransmitter, soothes firing neurons, ease anxiety (from tyrosine) AA can act as Acids or Bases Amino groups, carboxyl groups, and ionizable R groups = Weak acids and basis Zwitterion occurs at neutral PH Ion that contains 2 functional groups Both + and – charges The net formal charge is zero Polymerisation of amino acids – formation of peptide bonds Amino acids are polymerised in cells to make polypeptides and proteins They react by condensation polymerisation (for every monomer added to the growing polymer chain, one molecule of water is also produced or “lost” – dehydration) Broken through? Some terminology 2 AAs = dipeptide 3 AAs = tripeptides 3-10 AAs = oligopeptides > 10 AAs = polypeptides (mol. Weight < 10kDa) PROTEINS – large polypeptides of 300-1000 AAs ❯❯ Key Convention: When an amino acid sequence of a peptide, polypeptide, or protein is displayed, the amino-terminal end is placed on the left, the carboxyl-terminal end on the right. The sequence is read left to right, beginning with the amino-terminal end. ❮❮ Biologically Active Peptides and Polypeptides Occur in a Vast Range of Sizes and Compositions Av. Mol. Weight of AA is about 128 Mol. Weight of water is 18  Some proteins consist of a single polypeptide chain, but others, called multisubunit proteins have two or more polypeptides associated noncovalently Some Proteins Contain Chemical Groups Other Than Amino Acids Some proteins contain permanently associated chemical components in addition to amino acids - conjugated proteins The non–amino acid part is called its prosthetic group lipoproteins contain lipids glycoproteins contain sugar groups metalloproteins contain a specific metal Some proteins contain more than one prosthetic group Usually the prosthetic group plays an important role in the protein’s biological function Conjugated proteins Classification of proteins: physiochemical properties 1. Simple proteins 2. Compound proteins 3. Derived proteins Simple proteins Albumin - soluble proteins, coagulated by heat (serum albumin) Globulin – insoluable (serum globulin) Globins - rich in histidine, not basic, they unite with heme to form haemoglobin Prolamins - soluble in 70 to 80% ethanol but insoluble in water and absolute alcohol (gliadin of wheat and zein of maize) Histone - very strongly basic proteins, rich in arginine, with DNA they form nucleoproteins or nucleohistones which occur in nuclei forming chromatin material Protamines -present in sperm cells, smaller size, basic protein Compound proteins Nucleoproteins (histones+ DNA,RNA) Phosphoproteins (casein of milk, vitellin of egg) Lipoproteins Proteo/Glycoproteins Chromoproteins (hemoglobin, rhodopsin, cytochromes) Metalloproteins (ferritin-Fe, carbonic anhydrase-Zn, ceruloplasmin- Cu) Derived proteins Primary derived - NATIVE PROTEINS – if its amino acid composition and molecular conformation are unchanged from that found in the natural state Secondary derived - formed as intermediates during the hydrolysis of proteins Proteases, peptides (formed during the digestion process) Classification based on Function Catalytic proteins (enzymes) Transport proteins (Transferrin, ceruloplasmin) Structural proteins (collagen, elastin) Immune proteins (γ-globulins) Contractile proteins (actin, myosin) Genetic proteins (histones) Storage proteins (ovalabumin, casein,gluten) Key principles of protein structure Protein structures are stabilised by noncovalent interactions and forces Protein segments can adopt regular secondary structures such as the alpha helix and the beta-sheet conformation Tertiary structure describes the well-defined, three-dimensional fold adopted by a protein Tertiary structure is determined by AA sequence In principle, proteins can assume an uncountable number of special arrangements = conformations A limited number of conformations predominate under biological conditions Native = proteins in any functional, folded conformations Chemical or structural functions relate to unique 3-D shape Proteins - folds  The structure of proteins The spatial arrangement of atoms in a protein or any part of a protein is called its conformation Four levels of protein structure are commonly defined: - Primary - Secondary - Tertiary - Quaternary The structure of proteins: primary structure  The primary structure of peptides and proteins refers to the linear number and order of the amino acids present (bonded by covalent bonds – peptide and disulfide) The most important element of primary structure is the sequence of amino acid residues The primary structure bonds are: Rigid & planar C-N partial double bond prevents rotation, limiting the range of conformations The group can take one of two major configurations: Cis (proline) or Trans (majority)  The structure of proteins: secondary structure Describes the spatial arrangement of the main-cmain atoms in a segment of a polypeptide chain The alpha helix is a spiral structure Tightly packed coiled polypeptide backbone, with extending side chains The beta sheet is a zigzag structure + loops fall at the surface of proteins and contain a lot of polar and small residues form the shapes of active sites two special amino acids- proline and glycine interesting conformational properties-- glycine being very flexible, and proline being restricted, but being able to form cis peptide bonds often found within loop regions of proteins α-helix The formation of the α-helix is spontaneous It is stabilized by H-bonding between amide hydrogens and carbonyl oxygens of peptide bonds A complete turn of the helix contains an average of 3.6 aminoacyl residues, and the distance it rises per turn is 0.54 nm The R groups of each aminoacyl residue in an α helix face outward e.g. the keratins- entirely α-helical, Myoglobin- 80% helical Proline and glycine occur infrequently in alpha helix β-sheets β-sheets are composed of 2 or more different regions of stretches of at least 5- 10 amino acids The folding and alignment of stretches of the polypeptide backbone aside one is stabilized by H-bonding between amide hydrogens and carbonyl oxygens Unlike the compact backbone of the α helix, the peptide backbone of the β sheet is highly extended β-sheets are said to be pleated in which the R groups of adjacent residues point in opposite directions β-sheets are either parallel or antiparallel Proline and glycine often occur in beta-turns Right handed are most common Left haded are really not observed in proteins The structure of proteins: tertiary structure Tertiary structure refers to the complete three-dimensional structure of the polypeptide units of a given protein Arrangement of secondary structure within a single polypeptide Secondary structures of proteins often constitute distinct domains Domain is the basic unit of structure and function Tertiary structure describes the relationship of different domains to one another within a protein OR the final arrangement of domains in a polypeptide  The interactions of different domains is governed by several forces These include hydrogen bonding, hydrophobic interactions, electrostatic interactions and van der Waals forces The spontaneous folded state of globular proteins is a balance between the opposing energetics of H-bonding between hydrophilic R-groups and the aqueous environment and the repulsion from the aqueous environment by the hydrophobic R-groups Classifying Proteins Four major types based on polypeptide chains Fibrous proteins arranged in long strands or sheets Fibrous proteins usually consist largely of a single type of secondary structure, and their tertiary structure is relatively simple provide support, shape, and external protection E.g. collagen Globular proteins folded into a spherical or globular shape Globular proteins often contain several types of secondary structure most enzymes and regulatory proteins E.g. myoglobin Membrane proteins Intrinsically disordered proteins Fibrous proteins Hydrophobic residues: Ala, Val, Leu, Met, Phe, Ile Cross-links stabilised by disulfide bonds (which residues?)  The structure of collagen Found in connective tissue Secondary structure – left-handed, repeating tripeptide unit (usually Gly, Proline and 4-hydroxyproline) 4-hydroxyproline permits the sharp twisting of the collagen helix to establish the rigid structure Tertiary and quaternary structure – right- handed twisting of 3 separate polypeptides Covalent cross-links in collagen fibrils Links create uncommon AA residues (e.g.HyLys) Vit. C is required for the hydroxylation of proline and lysine in collagen Globular proteins - myoglobin Myoglobin provided early clues about the complexity of globular protein structure Contain a heme prostetic group that can reversibly bind to oxygen Supplies oxygen to myocytes The structure of proteins: quarternary structure Many proteins contain 2 or more different polypeptide chains that are held in association by the same non-covalent forces that stabilize the tertiary structures of proteins Two subunits- dimeric Three subunits- trimeric Proteins with multiple polypeptide subunits are oligomeric proteins Hemoglobin and alcohol dehydrogenase Loss of Protein Structure Results in Loss of Function A loss of three-dimensional structure sufficient to cause loss of function is called denaturation  DENATURATION- takes place when some or all of the cross-linkages which keep the protein intact are broken down  Denaturation is not reversible except in certain cases May be brought about by: 1. Heat 2. X-rays 3. Ultrasonic waves - Shaking or stirring for a long time, Extremes of pH, Salts of heavy metals, Urea, Alcohol & acetone Disorders associated with defects in protein folding Amyloidose diseases Amyloid fiber – protein secreted in a misfolded state and converted to an insoluble extracellular fiber E.g. Alzheimer disease, Huntington‘s disease and Parkinson‘s disease, type 2 diabetes (normally islet amyloid co-secreted with insulin, fibre is toxic to beta cells) Cystic fibrosis Caused by defects in the membrane-bound protein cystic fibrosis transmembrane conductance regulator (deletion of a Phe) Helps to maintain the balance of salt and water on the lung surface The prion disease Misfolded brain protein (Creutzfeldt-Jakob disease) Essential vs. non essential AAs Classified based on nutritional aspects 11 are nonessential amino acids because the body can synthesize them 9 are essential amino acids because we cannot synthesize them These must be obtained from the diet Sometimes during infancy, growth, and in diseased states the body cannot synthesize enough of some of the nonessential amino acids: called conditionally essential amino acids  Essential and Non essential AA Phenylketonuria – mutation in the enzyme phenylalanine hydroxylase https://aminoco.com/blogs/amino-acids/conditionally-essential-amino-acids Sources of Dietary Protein Complementing Protein Sources the Vegan Way Protein Digestibility Corrected Amino Acid Score (PDCAAS) Protein intake The Acceptable Macronutrient Distribution Range (AMDR) for protein for adults is between 10 and 35 % of kilocalories 10 to 15% of total daily energy intake RDA for healthy adult population - 0.8 to 1.0 g/kg/day determined by assessing nitrogen balance athletes – 1.2 - 1.8 g/kg /day 2 groups vegetable (beans, soy) animal (meat, milk and dairy products, egg whites) intake of vegetable and animal protein in the ratio 2/1 protein give us energy too (4 kcal = 17 kJ/1g) there is no storage form of protein source of nitrogen (-NH2)