Proteins PDF

BLOCHEMISTR structure, the of i study of the metabolism and function biomolecules 4 bromolecules: / anino acids protein - · carbohydrates · nucleic · acids - - monosaccharides uncheotides words · PROTEINS A. Amino Acids 1. General Properties HeN - " · -c00H "protein gen...

BLOCHEMISTR structure, the of i study of the metabolism and function biomolecules 4 bromolecules: / anino acids protein - · carbohydrates · nucleic · acids - - monosaccharides uncheotides words · PROTEINS A. Amino Acids 1. General Properties HeN - " · -c00H "protein geni" Gbisomers ↳ · Classifications smallest, achiral valineiv) isopropys + 4. isobutyl 2. H -> MHn H by R group (polarity i.nonpolar ↓ in Glycine (gly, G) H dominant amphoteric cool a. 20 mostly chiral · R 2. - + + + C00- HHz+ - Mr Alanine (ald, A) CHy lencine (len, 2) f 5. · Abutyl & Branched chain isoleucine 1 like, I) Ur G. 7.2. Phenylalanine CH2 HH-C -100H(pro,P) o (phe,F) / 10. · Proline ↳/ aromatic Le xanthoprotein test · only blue/violet yellow methionine (met, M) m · Saty 9. thioether G - - AAs 10 20 In Tryptophan (tip, wh CH2 Indole ⑭IX) dHopkinscet Lead acetate re (Fohl's test) ii. "imino acid" Ninhydrin test-general for #) 8. 10 AA polar 10.m serine of 1.*,cysteine 1. (Ms. 2) r tyrosine (Mr,Y) CH2 ophenolic o*Lemil onA 15. In 1.therine (sers) t Glutamine (gin, a) CHICHICONH2 (the Redox: - SH HS-OA-S-5-disulfide 14.MCOMHz Asparagine Cash, N) iii. acidic dicarboxylic acid "max-2 Aspartic acid (asp,D) 17. M 16. CHICHE COOH CHz CO0H basic"-diamines" iv. 2 + Histidine (his, H) 10N-, oimidazoleseacotest Ar 20. (CHz)s NH d HeN "NH 19. ↳ Lysine (Ms, K) CH2 c citz ciz NHz Arginine (arg, RC · no guanidine Sakagnihi test by dietary requirement b. · essential required in diet (cannotbe synthesized) pheu c. Glutamic acid (9M, E) Arg m HALL by metabolic fate exclusively glucogenic exclusively ketogenic · ~ · both glicolKetogenic - - FITTT Leucine, lysine 3) conization H H2N PH - C00H E -> + C00- NHe H -> NHz + -c00H + - · 0 H pKd(constant) pH<pka pH acidic few I "Protonated" ~ Determine the structure & d) = change of (pkdcoolt=2.4, 11.0 = HiTN - c deprotonated ala at a) b) pH -C00H ph) = 6.0 PH "N-c +1 Hs H2N Isoelectric pl c00- O-zwitterions -c -> - d3 H 11 = 2.0b) pH =3.0 H = d3 C) " pKAMAr=9.8) H pH 2.0 + (C00, NH-) (COOH, NH3 +) C) PH pkd > basic many H+ ex. 14 - C pHwhere 1 2.4 +1 the 9.8 0 AA is purely criterionic G I - average ola's flanking O compute or of the glutamic acid (p(a) 2.1,X.1,9.3) = 2.1 +1 (2.1 PF = 4.1 0 4.)) + # I - 1 = 3), average = - 2 smaller plas I arginine (pk9) 1.8,8.9,12.5) ↑1 of = +2 18 0.9 12.5 H-0 - pI=(8.9 12.5)/2 + 10.7 = average 2 - I larger pkds structure B. Protein H H2H - C - c: H p k as H H N-terminus I F-c-C00N condensationsnudrous Tc#. j- H A = j 0,1 peptide bond I c -c00 - renterminus -> a-dipeptide partialdouble bond character ~ stable levels 1. organization of Primary to of N- correct correct us sequence bonds notyetfunctional usually - acids from the C-terminus linear-peptide - ex. animo sequence -> structure sicklecell anemia -> HbA -> (normal) insulin analogs -> Abs functional 102 (sickle) altered DOA sequencing reagents: · · Sanger reagent Edman -> · · 2. reagent - 2.4-dinitrofmorobenzene phenylisothiocyanate cleave the N terminal AA cyanogen bromide (CNBr) ex. · - Y - tmpsin M - C A -> YM + Secondary 2-helix - -> t of CA cleavesbasic AAs(msine, ⑨- chymotrypsin E - cleave a terminal side orginine) AAs aromatic > via H local folding into helices/sheets bonding a pleated sheets me HcN 1241 100+ parallel CO0H t HHz Hom Hi antiparallel more common 3. Tertiary folding of complete - the peptide chain via residue interactions interactions a hydrophobic interactions b. electrostatic residue H bonds c. disulfide d. * acidic polar AAS + basic (WOHINH) Often functional (native) ↳ by:heat, Quaternary ex.zo -1 xfunction deviation from native - can be caused and ex. - - cys - denaturation * 4. nonpolar AAs - extreme pH, other chemicals - 2 or myoglobin - hemoglobin more tertiary I strand - strands 3 4 strands/subunits 4 classifications: a. b. globular by shape fibrous spherical threadlike H20 SOI H2O insOl. PlaSM proteins structural proteins by composition simple. AA only ex.globulins, albumins, gluten digestion of gluten ↳ "ginten free" Chistones) AA+ others ex.glycoproteins, nucleoprotein conjugated. metalloprotein (ex. heme Fe) celic disease - ↓ - prosthetic grow - fightly bond its protein to lipoprotein by function c. structural-nails, hair-Keratin storage -mnoglobin transport hemoglobin - regulatory defence - catalytic C. - skin, gum-collagen hormones collagen abundant most protein primaring gly, antibodies also haslas & pro enzymes Enzymes · · biologic catalysts most are proteins catalyst reactant -> ↳substrate) (enzumel · requires binding ⑰ Active site " 2 product -> s E S major theories d. Lock and key-rigid /absolute ⑰ s - b. Induced fit ⑦ E · - Es flexible conformational + S most enzymes change --> are ES & conjugated "I complex" Holoenzyme (active) A cofactor chmnorot;inactive) Apoenzyme I protein, inactive) inorganic organic metal ions coenzymes (from vitamins) classifications · · based on the reactions catalyzed commission system-Enzyme V EC #1:oxidoreductases (EC) voxidase dehydrogenase reductase redoxalcohol · dehydrogenase ethanol ECA1:transferases · acetaldehude -> transfer Ukinase vpolymerase transferase · (involve a substrates nexokinase qulose -> glucose Poy ATP ADP EC#3:hydrolases · hydrolusis - starts w/ substrate name incrase sucrose -> occasionally, end in - ECAX: Lysses · either addition or in glulose fructose (ex.trupsin, murosin) elimination carbonic H2C03 anhydrase - > H20 CO2 + EC #5:Isomerases Isomerization / rearrangement · 1.3 biphosphogrcerate 2 mutase - visomerase phosphoplncerate mutase biphosphoglycerate positional - functional EC #G:ligases · 2.3 -> /sunthase condensation no - vsynthetase - energy energy change change v carboxylase oxaloacetate AleMI - COA synthase >A a citrate Enzyme kinetics - product substrate ↑I ↑PV VMAX<- * in - - - - - - - (... mented plot michaelis km=michaelis constant - Lineweaver Bark plot (double reciprocal) Y/[V] vmax · Nkm ⑨ 1/ [S] External factors affecting 1. kinetics: a temperatures denaturation temp 3.pH optimum temp po" denaturation ↑ Affinity optimum pH binding by ease of as to an E eX. S ACK = in S2=Neostigmine my amtsk ↑ km - A types ofinhibition 1 competitive - the active site. targets no C I oim raxin Umaxf ·vmaxf a. noncompetitive - allosteric site maxin Kmi knf Uncompetitive allosteric maxi * ·Uma vmee 3. ID rate ↓ · · · km, Umax-different