CHAPTER-THREEOUT LINES o Structure and function of Amino Acids o Introduction to Amino acids (essential and non- essential amino acids) o Structure of Amino Acids o Peptide Bond Formation (Peptide linkage) o Structure and function of Proteins 1. Primary Structure of Proteins 2. Secondary Structure of Proteins 3. Tertiary Structure of Proteins 4. Quaternary Structure of Proteins o Denaturation of Proteins o Uses of proteinsIntroduction ~ Proteins are of paramount importance in biological systems. + Proteins are macromolecules found abundantly in our body « Termed as the work horses of the body «+ Made up of chain of amino acids in the body. « Are found in every cell in the body. All the major structural and functional aspects of the body are carried out by protein molecules * Involved in most of the body function & life process. & » All proteins are polymers of amino acids ~ Proteins are composed of a number of amino acids linked by peptide bonds. Proteins can be broken down (hydrolyzed) to their constituent iQ acids by a variety of methods. - Lori si2026o Serve as transporters of metabolite (Hemoglobin, Albumin, Transferin) known as transport. proteins. o Serve as storage materials (Myoglobin, Ferritin) © Protect the body from infection & toxins and Serve as defense weapons (antibodies, Immunoglobulins). o Form body structures (Collagen, Keratin & elastin) o Aid body cell movement (Actin, Myosin) © Serve as chemical messengers (Insulin, Glucagon) © Catalyze biological reactions takes place in the body catalyzed by proteins, acts_as biological catalyst (Enzyme proteins) o Provide energy to the body (Protein diets) o_ Regulate cell division, development and growth (Cyclins, Cyclin dependen Thases) and ragulates metabolic pathw af insulin).INTRODUCTION TO AMINO ACIDS o There are approximately 300 amino acids present in various animals, plants, and microbial systems, but only 20 amino acids are coded by DNA to appear in proteins. © Cells produce proteins with strikingly different properties and activities by joining the same 20 amino acids in many different combinations and sequences. o This indicates that the properties of proteins are determined by the physical and chemical properties of their monomer units, the amino acids. © Almost all of the naturally occurring amino acids in proteins are L- o Amino acids are the most essential components of all living cell.AMINO ACID: STRUCTURE & FUNCTION Definition: « Amino acids are the basic structural units of proteins consisting of: > an amino group, (-NH2) » acarboxyl (-COOH) group >» a hydrogen (H) atom and i a (variable) distinctive (R) group. ~ All of the substituent's in amino acid are attached (bonded) to the same central a- Carbon atom. » This carbon atom is called o- Carbon atom because it is bonded to the carboxyl (acidic) group.AMINO ACIDS-BUILDING BLOCKS OF PROTEINSGENERAL STRUCTURE OF AMINO ACIDS [OO ae tise Amino group Carboxyl group a- Carbon R__ R group Fig. Structure of standard amino acids (except proline) eSTEREOISOMERS IN AMINO ACIDS © Stereochemistry mainly emphasizes the configuration of amino acids at the a carbon atom, having either D or Lisomers. © Out of the 20 amino acids, proline is not an. amino acid rather an a_- imino acid. o Except for glycine (achiral), all amino acids contain at least one asymmetric carbon atom (the a- Carbon atom) and have two stereoisomers L- and D-form. © Only L-forms make up proteins in our body. coo- coo- + * H3N H H = NH3 \ lj ‘CH3 CH3 L-Alanine D-AlanineGENERAL STRUCTURE...CON’T. o The 20 different amino acid found in proteins differ only by the chemical group attached to the a-carbon, known as the side chain/ R group © So vary in structure, size, and electric charge, and which influence the solubility of the amino acids in water. o The common amino acids of proteins have been assigned three letter abbreviations and one-letter symbols (Table 1), which are used as shorthand to indicate the composition and sequence of amino acids polymerized in proteins.© Conventions Associated with the Common Amino Acids Found in Proteins. Names and abbreviations of the common amino acids. Amino Acid Alanine Arginine Asparagine Aspartic acid Glutamic acid Glutamine Isoleucine Leucine Lysine Methionine Phenylalanine Proline Serine Threonine ‘Tryptophan ‘Tyrosine Valine <4 SHewszAr TapPEPTIDE BCo A peptide bond forms when the carboxylic acid group (R-C[O]OH) of one amino acid reacts with the amine group (R-NH,) of another. o The resulting molecule is an amide with a. C_N bond (R-C(O)-NH-R). o This condensation reaction results in a dipeptide, and the release of a water molecule - with a hydroxyl (OH) leaving the carboxyl group, and the hydrogen atom from the amine - with the carboxy] group releasing a hydroxide, and the amine releasing a hydrogen atom. o Normally, when we refer to this process in biology, we call it a «dehydration synthesis», since we are building a higher order structure at the expense of a loss of water. 6PEPTIDE BOND FORMATION...PEPTIDE BOND FORMATION....PEPTIDE BOND FORMATION.... - An amine groupPEPTIDE BOND FORMATION.... OTM el N Ce INN CNTR I] oar) (ena erat ane Ma rane Can you identify the carboxyl group?PEPTIDE BOND FORMATION° 0 f orn | or] | H fe) in H | | Tee xz fe} i S) | rs) | Fd | ad ° i s) I rs) | 3 I xCLASSIFICATION OF AMINO ACIDS BASED ON THEIR CHEMICAL STRUCTURE o The 20 different AAs found in proteins differ only by the chemical group attached to the a-carbon, known as the side chain/ R- group. o Five chemical categories: e Amino Acids with Non polar, Aliphatic R-Groups. e Amino Acids with Polar, uncharged R-groups. e Amino Acids with Aromatic R groups. e Amino Acids with Positively charged amino acids (Basic). e Amino Acids with Negatively charged amino acid(Acidic). —_—_CLASSIFICATION OF AMINO ACID...CON’T. 1. Amino acids with non polar side chain » Does not bind or give proton « Does not participate in hydrogen bond » They promote hydrophobic interaction « Methionine, one of the two sulfur- containing amino acids, has a slightly nonpolar thioether group in its side chain. - Proline has an aliphatic_side chain with a distinctive cyclic structure that reduces flexibility of polypeptide regions containing proline.CLASSIFICATION OF AMINO ACIDS... Nonpolar, aliphatic R groups coo- coo- coo coo- + + [LH + H3N—C—H = -H3N—C—H ee H3N—C—H I HIN ‘CH H cH I Au H2C CH cis “cH, Glycine Alanine Proline coo- coo- coo- * + + H3N—C—H H3N—C—H hi—o—H ae Pee eeu CH cH cH. cH ZR He He CH; “CH; cH § CHs Leucine Isoleucine = Methionine estionin: FIGURE 1. NON-POLAR ALIPHATIC AMINO ACIDSCLASSIFICATION OF AMINO ACIDS... o 2. Amino acids with polar, uncharged side chain (R) «Can participate in hydrogen bond. «The R group is more soluble in water (hydrophilic), than those of the nonpolar amino acids, because, they contain functional groups that form hydrogen bonds with water. ~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.CLASSIFICATION OF AMINO ACIDS... Polar, uncharged R groups coo” coo Asi—e—a H3N—c—H CH20H H == OH cus Serine Threonine coo” H3N—cC—H Tai H2N AS Asparagine coo Cysteine coo + H3N—C—H Sia i” c zs, HN oO GlutamineCLASSIFICATION OF AMINO ACIDS... 3. Amino acids with aromatic R-group ¥ Phenylalanine, tyrosine, and tryptophan v All can participate in hydrophobic interaction v The hydroxyl group of tyrosine can form hydrogen bonds, and it is an important functional group in some enzymes. v Tyrosine and tryptophan are significantly more polar than phenylalanine because of the tyrosine hydroxyl group and the nitrogen of the tryptophan indole ring. 6CLASSIFICATION OF AMINO ACIDS... Aromatic R groups coo- coo” coo™ H;N— cH H,N— ¢—H H,N—C—H CH, es O Sh Phenylalanine Tyrosine Tryptophan °CLASSIFICATION OF AMINO ACIDS... 4. Positively charged (basic) R group » Have most hydrophilic R group » The amino acids in which the R groups have significant positive charge at pH 7.0 are: lysine, which has a second primary amino group at the ¢ position on its aliphatic chain; arginine, which has a positively charged anidinium group; and histidine, which has an aromatic imidazole group. — Histidine is the only common amino acid having. an ionizable side chain with pKa near neutrality. » histidine residues facilitate many enzyme-catalyzed. reactions by serving as proton donors/acceptors.. » This class of amino acids consists of those amino acids which have one_COOH group and two — > Thus they are diamino monocarboxylic acids. 6 >CLASSIFICATION OF AMINO ACIDS... Positively charged R groups goo" coo" goo" Hai—¢—H HaN—¢—H HaN—C—H ot e cHe cH c_NH cH, CH, | Ton | | c—N ae : *NH3 G=NH Lysine Arginine Histidine 6CLASSIFICATION OF AMINO ACIDS... 5. Negatively charged (acidic) R group * The amino acids aspartic and glutamic acids are proton donors. They are negatively charged at physiologic pH. They form ionic or electrostatic_bond with positively charged molecules. These amino acids have two -COOH groups and one — NH2 group. » They are therefore monoaminodicarboxylic acids.CLASSIFICATION OF AMINO ACIDS... Negatively charged R groups coo- coo- HN—C—H H;N—C—H CHa CHa coo- CHa coo™ Aspartate GlutamateCLASSIFICATION OF AMINO ACIDS BASED ON NUTRITIONAL REQUIREMENTS OR SYNTHESIS nn the functional property of amino acids for the organism: 1. Essential amino acids v Not synthesized in the human body and vy Must be obtained from the diet to meet metabolic needs. v There are 10 essential amino acids. Il. Nonessential amino acids v Not obtained from diet, y Can be biosynthesized in adequate amounts within the organism. v There are 10 nonessential amino acidsTHE ESSENTIAL AND NON ESSENTIAL AMINO ACIDS | Essential amino acids Non essentialaminoacids _ Phenylalanine Alanine Isoleucine Aspartate Threonine Glutamate Methinonine Serine Arginine Glycine Lysine Tyrosine Histidine Proline Tryptophan Cysteine | leucine GlutamineESSENTIAL AMINO ACIDS Try This VIP MaLL : ‘Tryptophan Threonine Histidine Valine Isoleucine » Phenylalanine Methionine Lysine LeucineNON ESSENTIAL AMINO ACIDS Ah, Almost All Girls Go Crazy After Guys Take Proposal Seriously. » Alanine » Arginine » Asparagine » Aspartic acid » Glutamine » Glycine = cysteine » Tyrosine » Proline eo » Serine© Apart from being the monomeric component of proteins and peptides, amino acids serve variety of functions. © Amino acids are building block of proteins, synthesis of variety of proteins © Biosynthesis of purines, pyrimidines,and urea © Prominentrole in the neuroendocrine synteny as hormone, hormone releasing factor, neurotransmitters. Promote production of hormone. © Required to maintain proper nitrogen balance and promote normal cellular structure. © Required to maintain proper health of human body and vital organs A. Some amino acids are converted to carbohydrates and are called as glucogenic amino acids. B. Specific amino acids give rise to specialized products, e.g. * Tyrosine forms hormones such as thyroid hormones, epinephrine and norepinephrine and a pigment called Melanin. + Tryptophan can synthesize a vitamin called niacin, serotonin, and melatonin. + Glycine, Arginine and Methionine used to synthesize Creatinine. eoGlycine and cysteine help in synthesis of Bile salts. oGlutamate, cysteine and Glycine synthesize glutathione. oHistidine changes to histamine on Decarboxylation. oSerotonin is formed from tryptophan. oGlycine is used for the synthesis of haem. oCystine and Methionine are sources of Sulphur. 6STRUCTURE AND FUNCTION OF PROTEINS © The word protein is derived from Greek word, proteious meaning primary. So, proteins are the major components of any living organism. © Proteins are the most abundant biological macro molecules occurring in all cells. © Proteins are linear polymers of amino acids that are functionally diverse. o Besides Carbon, Hydrogen and Oxygen, they also contain Nitrogen, and sometimes, Sulfur and Phosphorous. © The sequence of amino acids, determines the way a protein folds in to a unique three dimensional structure which is its native conformation.PROTEINS... © Protein containing foods are essential for living organism, because: » protein is the most important biological molecules in building up and maintenances of the structure of body, > giving as much energy as carbohydrates in the course of metabolism in the body. © Proteins are most important constituent of cell membranes and lasm.CLASSIFICATION OF PROTEIN ON THEIR LEVEL OF ORGANIZATION (STRUCTURE) a There are 4 levels of protein structure « Primary structure: the sequence of amino acid in polypeptide chain. « Secondary structure: regular chain organization pattern. Coiling of peptide chains, present in zig zig manner. Duc to_ hydrogen bonding. + Tertiary structure: Twisting or folding of polypeptide chains or 3D complex folding. « Quaternary structure: association between polypeptides. arrangements of multiple folded proteins in multi-subunit complex. eoPRIMARY STRUCTURE OF PROTEIN 1. primary structure » The primary structure of proteins is defined as a linear sequence of amino acids joined together by peptide bonds to form a polypeptide chain. Pro—Val-Thr—Gly—Lys—Cys—Glu » Peptide bonds and disulfide bonds are responsible for maintaining the primary structure.SECONDARY STRUCTURE OF PROTEIN 2. secondary structure a The secondary structure of a protein is defined as Spatial arrangement_of amino acids close to one another in_ primary structure. a Is the pegular arrangement of amino acid residues in a segment of a polypeptide chain, in which each residue is spatially related to its neighbors in the same way. 4 The polypeptide back bone form regular arrangement of amino acids that are located near each other, this arrangement is called secondary structure of the polypeptide. 4 H-bonds are responsible for stabilizing the secondary structure. 4 2 main types of secondary structure: » The ozhelix >» The B-sheet 6THE ot-HELIX (ALPHA HELIX) o The most common polypeptide helices that are found in nature. © Itis a spiral structure consisting of: >» Tightly packed, » Coiled polypeptide backbone core, » The side chains of the component amino_acids extending outward from the central axis to avoid interfering sterically with each other. o It is stabilized by hydrogen bonds between the peptide bond of carboxyl oxygen C= O and an amide hydrogen N —H of every fourth amino acid. ~ C = O--------— H-N o The helix can either coil to the right or the left.THE G-HELIX... oa-helices can wind around each other to form ‘coiled coils’ that are extremely stable and found in fibrous structural proteins such as keratin, myosin (muscle fibers) etc . o Examples of proteins that contains o-helix are » The a- keratins — fibrous protein — nearly entirely o- helical » Hemoglobin — globular protein — 80% a-helicalTHE Gt-HELIX... @ carbon Amino terminus | © Hydrogen oxen Nitrogen | _ @Rgroup sarge (a) Carboxylterminus (b) FIG: THE - @-HELIXTHE B- PLEATED SHEET B-pleated sheet © -sheet another type of secondary structure where the peptide b : : : © The surface of B-sheet appear “pleated “ and therefore called “B-pleated sheets” © Extended stretches of 5 or more [Link] are called B-strands B-strands organized next to each other make B-sheets o In B-pleated sheet, polypeptide chains line up side by side toform sheet . © Composed of two or more peptide chains (B-strands) or segments of polypeptide chain that is almost fully extended. o Form rigid structures with the H-bond _ © Inf -sheets the Hydrogen bonds are perpendicular to the polypeptide backbone. °THE B- PLEATED SHEET... o A f-sheet can be formed from two or more polypeptide chains that are arranged either parallel or antiparallel to each other. olf the polypeptide strands run in the same direction it is parallel if it is in opposite direction anti parallel. o If adjacent strands are oriented in the same direction (N-end to C-end), the structure is termed as parallel {-sheet, if adjacent strands run opposite to each other, it is an antiparallel B-sheet.THE B- PLEATED SHEET... (A) anti-Parallel (B) Parallel ®TERTIARY STRUCTURE OF PROTEIN [Link] structure o Refers to three dimensional, folded and biologically active conformation of a protein. o It is the folding pattern of the secondary structural element in to a three dimensional conformation. © Tertiary refers both to the folding of domains and the final arrangement_of domains ina polypeptide. o The structure reflects the overall shape of the molecule. © The three -dimensional tertiary structure of a protein is stabilized by_interactions between side_chain, functional group, covalent, isulfide bonds, hydrogen bonds, Ionic_ interaction, and hydrophobic interactions. Therefore e[Link] STRUCTURE... o Is Spatial arrangement of secondary structures into domains. © Regions of a polypeptide chain that can fold stably and independently are called domains . © Protein segments may fold independently, producing more than one compact unit “domain” © Many proteins are organized into multiple ‘domains’ © Domains are compact _globular_units that_are connected_by a flexible — mpect gicbuler,» segment of the polypeptide © Each domain contributes a specific function to the overall protein. © Tertiary structure is the complete three dimensional structure of a polypeptide chain. © There are two general classes of proteins based on tertiary structure: fibrous and globular proteins. }[Link] STRUCTURE... Models of three different protein domains Cytochrome bss. NAD-binding Variable domain of IgG 6 domain of lactic H Heavy chain dehydrogenase ney[Link] STRUCTURE... Different domains within a protein often have different functionsQUATERNARY STRUCTURE OF PROTEIN 4, Quaternary Structure © Spatial arrangement_of subunits and their inter-molecular : : © Refers to a complex or an assembly of two or more separate peptide chains that are held together by non-covalent interactions. E.g, hydrogen bonds, ionic bonds, and hydrophobic interactions. © The arrangement of these polypeptide subunits is called the quaternary structure of the protein. o Subunits are held together by non-covalent _interactions) o Each unit of this protein is called a subunit and the protein is an oligomeric protein _ o Subunits (monomers) can be identical or different. eo —_—_—QUATERNARY STRUCTURE...QUATERNARY STRUCTURE... B Quaternary structure of hemoglobin-interaction between different subunits Alpha subunits: gray and light blue Beta subunits: red and dark bluePROTEIN FOLDING AND DENATURATION o All proteins begin their existence on a ribosome as a linear sequence of amino acid residues. o This polypeptide must fold during and following synthesis to take up its native conformation. © Modest changes in the protein’s environment can bring about structural changes that can affect function. o We now explore the transition that occurs between the folded and unfolded states. © Not all proteins fold spontaneously as they are synthesized in the cell. ©PROTEIN FOLDING UProtein folding - process_by which proteins attain the proper structure, and therefore proper function (enzyme activity). O There are proteins that help in folding of protein structure these are chaperones. UThey participate in folding of over half of mammalian protein. UProtein_ folds in to stable _three-dimensional structure known as native conformation. ©PROTEIN FOLDING... conzp © The three dimensional structure of a protein >» Must have binding site for one specific molecule or group of molecules Must exhibit degrees of flexibility and rigidity appropriate to its function. v » Must have a structure that can be degraded when it is damaged or no longer needed in the cell.PROTEIN DENATURATION © loss of protein structure results in loss of function. o Aloss of three-dimensional structure sufficient to cause loss of function is called denaturation. © The three-dimensional structure and the function of proteins can be destroyed by denaturation. © under most conditions, denatured proteins exist in a set of partially folded states that are poorly understood. © Proteins can be denatured not only by heat but by extremes of pH, © by certain miscible organic solvents such as alcohol or acetone °PROTEIN DENATURATION... ” The process in which a protein loses its native conformation and function is referred to as protein denaturation. ” Proteins are denatured and their shapes changed by heat, chemicals, mechanical agitation ” Primary structure is unchanged by protein denaturation. » It may be reversible by protein refolding: Normal protein Heat, acids, salts, ‘and mechanical agitation Denatured proteinFACTORS THAT AFFECT DENATURATION ~ Physical factors © Temperature, pressure, mechanical force, ultrasonic yibration and ionizing radiation causes the protein to lose its biological activity. Chemical factors © Acids and alkalis, organic solvents (acetone, ethanol), detergents (cleaning agents), certain amides urea, hydrochloride, alkaloids, and heavy metal salts (Hg, Cu, Ba, Zn, Cd...) Cause the denaturation.USES OF PROTEINS o Proteins are an important parts of a healthy diet. o They have multiple function. o Made up of building blocks called amino acids © your body uses amino acids to build and repair muscles, tissues, bones and to make hormones and [Link] enzymes. © They can_act as energy source inaduecate_carbohydrates and fates. © It drives metabolic reaction, maintain acid-hase (PH), fluids and electrolyte balance and keeps the immune system, making antibodies . © Transport and stores nutrients. © Mainly used for Structural support, biochemical catalysts, hormone, enzymes, building blocks, and initiators of cellular death. © Enabling wound healing, tissue regeneration and nerve function)