Biochemistry Notes PDF

## UNIT-1 ### Amino Acids * Monomers of proteins * Present in cytoplasm of cell. * Present in inactive form in cytoplasm. * They are activated during protein synthesis. * C, H, N, O - main elements in aa * H NH2 - C - COOH | R General structure H NH2 - C - COO- | R Ionic form (exists in cell) * x aa → 2 functional groups attached to C (NH2, COOH) * There are 20 std aa + 2aa are repeatedly present in protein. * Organic compounds. ### Table of amino acids | S.No. | Single letter code | Three letter code | Name of amino acid | |---|---|---|---| | 1 | A | Ala | Alanine | | 2 | B | - | - | | 3 | C | Cys | Cysteine | | 4 | D | Asp | Aspartic Acid/Aspartate | | 5 | E | Glu | Glutamic acid | | 6 | F | Phe | Phenylalanine | | 7 | G | Gly | Glycine | | 8 | H | His | Histidine | | 9 | I | Ile | Isoleucine | | 10 | J | - | - | | 11 | K | Lys | Lysine | | 12 | L | Leu | Leucine | | 13 | M | Met | Methionine | | 14 | N | Asn | Asparagine | | 15 | O | Pyr | Pyrrolysine [22nd aa] | | 16 | P | Pro | Proline | | 17 | Q | Gln | Glutamine | | 18 | R | Arg | Arginine | | 19 | S | Ser | Serine | | 20 | T | Thr | Threonine | | 21 | U | Sec | Selenocysteine [21st aa] | | 22 | V | Val | Valine | | 23 | W | Trp | Tryptophan | | 24 | X | Any | - | | 25 | Y | Tyr | Tyrosine | | 26 | Z | - | - | V E R ↓ ↓ ↓ ↓ Val - Glu - Glu - Arg - Leu - Ala ↓ ↓ ↓ BIKA LAKSHMI DA M Asp - Ala - Met - Ile - Lys - Ala - Leu - Ala - Lys - Ser - His - Met - Ile ### Classification * There are different ways of classification of aas based on structure, functional groups & mutritional requirements. 1. Based on structure 2. Based on side chain 3. Based on nutritional requirement #### I) Classification based on structure: | Amino acid | 3 letter code | Single letter code | Structure | |---|---|---|---| | (i) Glycine | Gly | G | H H - C - COO- NH3+ | | (ii) Alanine | Ala | A | H CH3 - C - COO- NH3+ | | (iii) Valanine | Val | V | CH3 CH3 - CH - C - COO- H NH3+ CH3 | | (iv) Leucine | Leu | L | CH3 CH3 - CH2 - CH - C - COO- H NH3+ | | (v) Isoleucine | Ile | I | CH3 CH3 - CH2 - CH - C - COO- CH3 NH3+ | #### @aa with OH group containing side chain | (vi) Serine | Ser | S | H CH2 - C - COO- OH NH3+ | | (vii) Threonine | Thr | T | H CH3 - CH - C - COO- OH NH3+ | * Ser, Thr, Tyr & are OH group containing aas * C with 4 different functional groups is called chiral carbon. #### ③ aa Sulphur containing aa | (viii) Cysteine | Cys | C | H CH2 - C - COO- SH NH3+ | #### Kystine H CH2 - C - COO- S S H CH2 - C - COO- NH3+ #### (ix) Methionine | Met | M | H CH2 - CH2 - C - COO- S-CH3 NH3+ | #### ④ Acid aa & their amides | (x) Aspartic Acid | Asp | D | H COO- - CH2 - C - COO- NH3+ | | (xi) Aspargine (Amide of Asp) | Asn | N | H NH2 - C - CH2 - C - COO- NH3+ | | (xii) Glutamic Acid | Glu | E | H COO- - CH2 - CH2 - C - COO- NH3+ | | (xiii) Glutamine (Amide of Glu) | Gln | Q | H NH2 - C - CH2 - CH2 - C - COO- NH3+ | #### ⑤ Basic aas | (xiv) Lysine | Lys | K | H CH2 - CH2 - CH2 - CH2 - C - COO- NH3+ NH3+ | | (xv) Arginine (more basic than Lys) | Arg | R | H CH2 - CH2 - CH2 - C - COO- C = NH2 NH3+ | | (xvi) Histidine (contain vamidazole ring) | His | H | H - CH - C - COO- HN N NH3+ | #### ⑥ Aromatic aa | (xvii) Phenylalanine | Phe | F | H CH2 - C - COO- NH3+ | | (xviii) Tyrosine | Tyr | Y | H OH - CH2 - C - COO- NH3+ | | (xix) Tryptophan | Trp | W | H CH2 - C - COO- NH3+ | #### ④ Amino Acid | (xx) Proline | Pro | P | H CH2 CH2 CH2 N H2 C - COO- | ### Genetic Code * Contains codons * 43 = 64 codons (Total) * Singlet codon is disproved because 41 = 4. Only for 1 aa. * Doublet codon is also disproved. 42 = 16. Only for 16 aas. * Triplet codon is correct. * 43 = 64 codons/ combinations. Triplet (3 nucleotides as 1 codon) * Stop codons → 3 → UAA, UAG, UGA (ochre, amber, opal) * terminate” * Degeneracy/Redundancy → Single aa is coded by more than 1 codon. * Initial”/start codons → 2 (AUG, GUG) (met/met) * AUG codes for Methionine always. * GUG codes for Valine generally. But when GUG acts as start codon it codes for Methionine. * Single codon containing aa → 2. They are Methionine & Tryptophan. * Met is Met [Methionine formyl] in prokaryotes. * Met in Eukaryotes. * Met in Prokaryotes. * Basicity order → His > Arg > Lys. * Unambiguous/Specificity → One codon always codes for specific aa. * No comma/punctuation b/w the coding triplets. * Wobble hypothesis → Degeneracy occurs at 3rd position while two base of codon doesn’t change. 3rd base is called Wobble base. ### I) Classificat" based on side chains * aa with hydrophobic side chain * mon polar, H2O hating * Eg: - G, A, V, L, I, P, M, F, W * Gly, Ala, Val, Leu, Ile, Pro, Met, Phe, Tsp. * No met charge side chain nullifies due to hydrophobicity. * These type of aa are present inside the globular protein to protect themselves. * aa with uncharged polar side chain * No met charge * H2O loving * Present exterior/on surface of globular proteins * Eg: - S,T, C, N, Q, Y * Ser, Thr, Cys, Asn, Gln, Tyr * 6aa * Tys is both hydrophilic & hydrophobic in nature * L↳ so vamphiphilic in mature. * aa with charged polar side chain * have met charge * (i) +vely charged → H, R, K * basic, more NH3 groups * (ii) -vely charged → D, E * Is acidic, more COOH groups * In +vely charged aa - They have both charges. * In -vely charged aa - They have both charges. * But +ve is more * Due to met charge. They are present on the surface of globular proteins. * Cation & Anode +ve * Cathode & anion - ve * Histidine can be found in interior of few proteins like myoglobin & Hb. <start_of_image>circle with interior aa - made of hydrophobic aa surface aa - polar ### 1) Classificat based on nutritional requirements * Essential aa * The aa which cannot be synthesized by body. Eg: - H. V ITTALLMP * His, Val, Ile, Thr, Trp, Arg, Leu, Lys, Met, Phe * Non essential aa - The body can synthesize these aa. * Eg: - Ala, Cysteine Aspartic Acid, Glutamic Acid, Glycine, Aspergine, Broline, Glutamine, Serine, Tyrosine. * Semi essential an - The body can synthesize partially. * Eg: - R, H * 21st aa * Selenocysteine (Sec) * It contains Selinium in place of sulphur atom of cysteine. H CH2 - C - COO- SeH | NH3+ Selenocysteine H CH2 - C - COO- | SH | NH3+ Cysteine * It is coded by mon - universal codon / partially universal codon. * It is coded by stop codon - UGA (opal) * Genetic code partially universal because sometimes stop codons code for few as. Eg: - UGA for Selenocysteine. UAG for pyrrolysine. * 22nd amino acid * Pyrrolysine (Pyr) → (C12H21N3O3 * coded by stop codon UAG, Amber H2 - CH2 - CH2 - CH2 - COO- | NH3+ lysine H NH2 - CH2 - CH2 - CH2 - C - COO- C=O N CH3 Pyrrolysine * Physical properties of aa * 1. Solubility - Mostly soluble in water & insoluble in organic solvents. * 2. Melting point - aa melt rat higher temperature (>200oc) * 3. Taste - with sweet taste - Gly, Ala, Val * Tasteless aa → Leu * Bitter taste → Arg, Ile. * Monosodium glutamate (MSG) → It is a salt of glutamate / glutamic acid. * flavouring ragent of food industry to ↑ taste & flavour * ↑ in conc of MSG results in Chinese Restaurant syndrome. * 4. Optical vactivity - All aa shows optical visomerism except Glycine * 5. aas with vampholytes → aa have both acidic (COOH) & basic (NH2) igroups. * They can donate H+/protons or vaccept protons. COO - NH3+ ↓ Hence these aas vare vampholytes. * Zwitter ion: dipolar ions called as Zwitter ion. * The word Zwitter derived from German word which means hybrid. * The aa rarely exist in a meutral form with carboxylic group (COOH) & amino group (NH3). * In strong vacidic pH (low pH) then aa is +vely charged (cation) while in strong valkaline pH(high pH) then aa is -vely charged (vanion) H | NH2 - C - COO- | R -ve charge (wathode) ↓ moves to vanode OH basic H PH>PI ↓ R-C-COO- | NH3+ ↓ No met charge H+ acidic H | NH3+ - C - COOH | R ↓ +ve charge (anode) ↓ moves to valhode * Isoelectric PH * It vis defined as the pH vat which a molecule exists as Zwitter ion that means they show both tve & -ve ions. * No met charge → Zwitter ion * (PI=pH) * Generally PH is 6-7 #### 11. Chemical prop of aa * React of aa are due to 2 functional groups * 1. aas due to the presence of carboxylic groupe & when reacts with valkali forms its salts & alcohols (R-OH)forms esters. * H3+ N - C - COO- | R aa -H2O H | H3+ N - C - COONa | R salts H3+ N - C - COO- | R aa -H2O H | NH3+ - C - COOR | R ester eg: Alcohol like CH2OH, C2H5OH, etc. * 2. Decarboxylat":- a a undergo decarboxylation to produce amines. H | H3+ N - C - COO- | R -CO2 H | NH3 - C - H | R amine H | NH3 - C - H + CO2 | R * This react is significant in the living cells. Que to the format of many biologically imp amines. Amines include histamine, tyramine, 8-amino butyric acid (GABA) from histidine, tyrosine, glutamate respectively. * 3. React with ammonia : * The carboxylic group of racidic aa reacts with ammonia to form their amides. * H | COO- - CH2 - C - COO- + NH3 → NH2 - C - CH2 - C - COO- | Aspartic vacid | NH3+ | NH3+ Aspergine * H | COO- - CH2CH2 - C - COO- + NH3 → | Glutamic acid | NH3+ | NH2 - C - CH2 - CH2 - C - COO- | NH3+ Glutamine * 4. aas due to the presence of NH3 group reacts with vacids to form their salts H | NH3+ - C - COO- + HCl → CH3+ N - C - COO- | R aa | R Salts * 5. Reaction with Ninhydrin: The xaas react with Ninhydrin to form purple blue/pink colour complex. This react is used for qualitative determinat of aas & proteins. C |=O C | OH Ninhydrin + H | H3+ N - C - COO- | R NH3 CO2 → C |=O C | OH Reduced Ninhydrin +R-CHO H | H | + N | H | H + OH Reduced Ninhydrin (liberated NH3) OH → C |=O C | OH C |=O Ninhydrin (excess) C |=O C=N-C C | O | O H Blue coloured complex. ### PROTEINS * GK word proteus - means 1st place * laa binds with other a a by peptide bond. * Proteins vare the most abundant vorganic molecules of the living system. They occur in every part of the wells & about 50% of cellular dry wt vis proteins. * →50-55% * N -13-19% * 0 19-24% * H 6-7.3% * S → 0-4% composit of protein * High molecular wt polypeptides vare proteins. * 15-20aa oligopolypylides * <50aa → polypeptide * >50aa → 11 * with 3D structure * protein. * All proteins vare polypeptides. But vall polypeptides are not proteins. ### 3 Structure of proteins:- * Proteins vare polymers of L-x-aas. * Structural classificat" of proteins (Scops)/ Structural levels of proteins (SLOPS) * 4 structures. #### (i) 1o structure : linear varrangement of aas forming polypeptide 0000 * avg mol ut of aa → 110D. * Tetrapeptide bond b/w llaa is 4. * Dipeptide bond b/w lla a vis 10. * Pentapeptide bond those saa. H | H2N - C - COOH + H2N - C - COOH | R1 | aa1 R2 aa2 -H2O H | NH2 - C - C - NH - C - COOH | | R1 R2 ↓ dipeptide bond →aa binds with other a a by peptide bond. H | NH2 - C - C - NH - C - C - NH - C - COOH | | | R1 R2 R3 ↓ →2H2O molecules are released in tripeptide bond formation. →cis is not favourable. Trans is more favourable #### (ii) 2o structure :- spatial arrangement of aas by twisting / folding the polypeptide chain. → 2 types * → xchelices Right handed * → Left handed * → p helices → x helices vare most common 2o structure → Right handed x helices are more istable than left handed x helices → x & B helices stabilised by Hbond → 3. Gaa/per torn → Ritch of turn - 5.4Ao → Hydrogen bond b/w C=O of 1aa & NH of other aa. → Dist b/w 2 aas in x helices is 1.5A/0.15mm →5.4 - 1.5A →36 → l = 10-15a a in x helices. → Corey & Paul in 1951. →H bonds occur vat (i+4) aaa. 00000000 C = O Hbond loop ↓ 13 vatoms 3.613 → Bchelices stabilized by H bonds → proposed by Corry & Paul → S bonds are also present when a a like Cys/Met vare present. → It is disulphide bonds → due to oxidat → present only in extra vellular proteins. Because of oxidising environment outside the cell. → Inside the well there is reduced environment so oxidat doesnt occur & mo sulphide bond format in intracellular proteins. Hbond parallel ← bond vantiparallel vaa run in same side/orientat ### ③ 3o structure Interchain bonds & intrachain bonds are present. * H, disulfide bonds, hydrophobic bonds/vinteract's, hydrophilic bonds, dipole interact's, Wanderwaals interact's are present in globular form of protein * Hydrophilic vaa vare outside * Hydrophobic aa are present interior to protein * biologically active structure. ### ④ Quaternary structure (4o):- * Some proteins vare composed of 2/ more sub units of polypeptide types → 2 types * Homo 2/ more subunits with similar structure * Helero diff subunits * contain mon covalent interact’s (disulfide, H bond, hydrophobic etc). * Haemoglobin is example of heteromer structure * 688 containing protein * have 2x chains & 2B chains * have 4 monomers 2x subunits 2B subunits * Domain The fundamental unit of 3 structure which act vas funct al unit is called domain. It is a part of polypeptide chain that can fold independently. * Protein may contain 2/ more domains. * Eg: - If a protein has 20aa & made into 3 fragments 100 aa - contain vdomain. Then It can independently fold & become functal. 50aa} not 5000} not vactive because no domain * 19) Calculate the length of polypeptide (in nm) chain containing 105aa if it exist in & helical form * A) 1 b/w 2 aa = 1.5A * 105→? * 105 x 1.5 = 157.5 * 1575A = 15.75nm * 20) A protein x was fused with GFP (Green Fluorescent protein) then length of protein x is 1000 aa & the mol wt of GFP vis 27K Da. What is the total vapprox mol wt of ra fission protein in Da. * A) x + GFP → 1000 aa * ↓ * wt = 27 x 1000 Da = 27000 Da * mol w * mol wt of laa = 110 Pa * 110 x 1000aa = 110000 mol not * 110 × 1000aa + 27000 * = 137000 Da * = 137000 Da * 30) If 1 Arg has mol wt of 174 Da then what would be the mol mass (in Da) of a circular polymer of 38 Arg. * 1 →174 Da * 38 →? * 174 x 38 = 6612 Da * 18 x 38 = 684 * 6612 Da - 684 H2O = 5928 Da * 5928 Da ### 61. Ramachandran Plot * The geometry of the protein backbone (dipeptid bond) reveals several vimp features:- * The peptide bond is planar in mature & this bond format is endergonic process [AG=+21KJ] → means taking E →AG = +21 KJ ЗАТР * The delocalisation of the Ip of eis von Niatom gives partial double bond (partial dipeptide bond) H H2N - C - COOH+HN R1 R2 C-COOH } -H2O H H2N - C - C - N - C - COOH R1 H R2 H * For a pair of a a linked b/w a peptide bond 6 ratoms lies in the same plance plane Cx, C=O group from the 1st aa, NH, Ca ratom from the 2nd aa. * The peptide C-N bond has partial double bond character. -N C -N * The bond length is only 1.35Ao which is usually shorter than C-N bond I of 1.45Ao. * The peptide bond has approx 40% double bond character. As a result the rotato of the bond vis restricted ie, w-angle → wrangle of rotato around the peptide bond usually has the value w = 180o (trans) occassally wrangle vis 0o (cis). * There are 2 conformat’s possible for a planar peptide bond. * In the trans confirmat the 2Cx vatoms are in the opp sides of the peptide bond & in cis confirmation the Ca atoms vare in the same side of the peptide bond. H | C-N-H | R1 | R2 Trans * side chains doesn’t come close. So favourable R1 C-N-C | R2 Cis * Not favourable * Almost vall peptide bonds in proteins are trans. * The trans form is favour over the cis confirmat because in the cis form Cx & the side chains of neighboring residues (aas) vare in too close proximity results in steric hindrance. * Rotat ’ sabout bonds vis described vas dihedral / tortion angles. * Fortion vangle blo Ca-C→ →psi * Cx-N→ pi The tortion angle b/w C, of vone aa & N of vanother aa vis 3 O= CJNFC-R angle Ca H R * In principle 4 & & can have any value b/w -180 & +180o (because trans is max 180) but many values vare prohibited by steric interference b/w ratoms. * The permitted values for & & & were 1st determined by G.N.Ramachandran. * The permitted values for 4 & & are usually indicated on a 2D map (also known as Ramachandran plot). +180 120- 60 B L left handed Khelix -60- RH -120 -180 ←←← Ø Puallowed +180 * 1. White Region → Sterically disallowed vregion for vall ramino acids except glycinerdue to lack of side chain. * 2. Red Region → Allowed region mainly & helices & B pleated sheets. * (i) 4 = -ve 2 most viegular right handed x helices * =-ve (ii) 4 = +ve 2 P pleaded sheets vare present → Parallel →Parallel ẞ→ Ψ=+113o Ø=-119o →Antiparallel B→ ψ = 135o Ø=-139o (iii) 4= +ve? left handedothelices vare present Ø = +ve 4=+57o 4= +47o (iv) 4 = - ve? 2 No regular 2o structure is possible Ø = +ve * Ramachandran plot is used to predict the 2’ structure in peptide / protein. * It is useful to identify the combinat of 4 & $values that can give stable 2o structure. ### CARBOHYDRATES * Polyhydroxy valdehydes/ketones * Saccharon-sugar * Cx(H2O)y General formula * Fund’s * E source 4 cal/gm * present in plasma membrane & give structural stability to vell * storage vof E. * Classificat * 1. Monosaccharide - simplest sugar which cannot be hydrolysed * 2. Disaccharide * 3. Oligosaccharide-Aisaccharide, trisaccharides, tetraachary * 4. Polysaccharide * Glycosidic bond is present * If the hydrolysis react is + ve → There is glycosidic bond so mot minosare. * can be any carbohydrat 2 * except monosaccharide * If the hydrolysis react is - ve → No glycosidec bond → So it is monosaccharide. * Based on mo. of Catoms. Carbohydrates are classified into : | Ex :- Aldoses | Eg:-Ketoses | |---|---| | 2- Diose | Glycoaldehyde | DHA(dehydroxy acetone) | | 3- Triose | Glyceraldehyde | - | | 4-Jetrose | Erythrose | Erythriulose | | 5- Pentose | Ribose | Ribulose | | 6-Hexose | Glucose, Mannose, Galactose | Fructose, Sucrose | | 7-Heptose | Heptose | Sedopeptidose | * Carbohydrate + lipids → Glycolipid * “ + protein → Glycoprotein * Glyceraldehyde is fundamental istruc for aa structive * Classificat" based on type of functal group * If monomer has CHO vas functal group saldon * If monomer has ketose functal group (C=0) → Ketose ### 8/11/24 Classificat ### MONOSACCHARIDES simplest sugars, not hydrolysed * Numbering:- The least mo. should be given to the funct'al group vattached to C. * CHO H - C - OH CH2OH D-glyceraldehyde CHO H + C - OH CH2OH L-glyceraldehyde * 99.9% carbohydrates show Diforms. * These vare visomeric forms) * The OH should be last but one c' called vas penaltimate C. * Monosaccharides consists of single polythroxy valdehyde/ketone. * The most rabundant monomer in mature is D-glucose. * Numbering of C:- The C number are sequentially with valdehyde/ketone group being on (with lowest possible mumber. CHO CHO H-C-OH CH2OH H-C-OH CH2OH * All monosaccharides except DHA shows sterioisomerism due to the presence of 1/more chiral Cvatoms & thus shows optically ractive & forms isterio isomers. * To calculate stereoisomers = 2n * n = No. of chiral Carbons. <start_of_image> CH2OH | C=O | H-C-OH | H DHA (Norchiralc) * As mo of schieral C number 1 the mo. of possible visomers also 1 * Glyceraldehyde is the reference molecule for carbohydrate. * No. of whiral C in glyceraldehyde vis 1. * 21= 21 = 2 (stereoisomers). * fycose has 4 chiral Chassymmetric C * 24 = 16 (stereoisomers). * D & Lisomers -These are mirror images of each other. If OH group is on right side of last but one 'c' (penultimate c) - D form →If OH is present on LHS of penultimate C7 CHO H-C-OH | CH2OH D-form CHO OH-C-H | CH2OH L-form L form CHO H-C-OH | CH2OH D-glyceraldehyde (3c) ✓ Threose (4C) CHO (OH) C-H | H-C-H | CH2OH Dform Erythrose (4C) CHO | HOSH | H-C- OH Dform | CH2OH → Add new cat and posit only because mo change in D& I forms CHO | H-C-H | OH-C-H | H-C-H | CH2OH D-Lyxose (5c) CHO | H-C-OH | HO-C-H | H-C-H | CH2OH D-xylose SC CHO | H-C-OH |

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