Proteins. Department of Biochemistry Faculty of medicine University of Szeged
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1 Proteins
2 Classification Function Structure Connecting peptide parts
3 Synthesis Transcription - nucleus Translation - cytoplasma Posttranslation changes (folding) - endoplasmatic reticulum
4 Amino acids
5 Amino acids
6 Amino acids
7 Structure Primer= order of the aminoacids Secunder= the conformation of the peptide chain alfa-helix, beta-sheet, beta-turn, random coil
8 Structure Suprasecunder: the location of the domains inside the tertier structure Tertier= shape of the peptide chain globular, fibrillar
9 Structure Quaterner= location of the subunits (peptide chains)
10 Folding, Denaturation Protein folding: formation of the native conformation - chaperons features and roles Denaturation: loss of native structure - reasons - reversible (tertier, quaterner structure) - irreversible (secunder)
11 Bioenergetics
12 Termodynamics Isolated system Closed system Open system: material-, energy- and informationtransport, if the entropy level is low - Energy source: C-atom (oxidation)
13 Free entalpy-change A + B C + D G = Go + RT ln ( [C] [D] / [A] [B] ) = Go + RT lnk G = Gproducts - Gstarting materials +: endergon; 0: balance; -: exergon
14
15 Linked reactions
16 Role of the enzymes: the decrease of the activation energy
17 Macroerg compounds Macroerg binding (>30kJ) containing molecules Carbamil-phosphate phosphoenol-piruvate
18 Macroerg compounds 1,3-bifosphoglycerate Creatine-phosphate
19 Macroerg compounds Cyclic adenosine-monophosphate Adenosine-triphosphate
20 Enzymes
21 General features Biocatalisator Definers of velocity, specificity, direction of the reaction Conditions of the optimal work: temperature, ph, ions
22 Models of substrate binding A: Lock and key model B: Induced fit C: Fluktuation
23 Types of enzyme catalysis Kovalent catalysis - temporary kovalent binding (side chains) instabile intermedier - eg.: trypsin, etc.
24 Types of enzyme catalysis Acid-basis - H+ absorbation/adsorbation (acidic and basical side chains) - eg.: ribonuclease
25 Types of enzymecatalysis Metal ione-catalysis - temporary binding to a metal ion deformation, tension of the binding - carbonic acid-anhydrase Entropy-effect - temporary decrease of the entropy the chance of the proper collision is elevated
26 Enzyme classes Nomenclature: 1. class - 2. subclass - 3. group - 4. concrete enzyme 1.: Oxydoreductases - oxidases, oxigenases, reductases, etc. - eg.:glycerine aldehide-3-phosphatedehydrogenase 2.: Transferases - kinases, transaldolases, transketolases, transferases - eg.: hexokinase, glucokinase
27 Enzyme classes Hidrolases - phosphatases, esterases, etc. - eg.: glucose-6-phoszphatase Liases - C-C, C-O, C-N, C-S, C-O liases, subtypes - eg.: aldolase
28 Enzyme classes Isomerases - cis-trans isomerases, intramolecular isomerases, etc. - eg.: triose phosphate-isomerase Ligases - C-O, C-S, C-N, C-C, P-ester, N-Me binding producers - eg.: piruvate-carboxylase
29 Coenzymes Necessary for the enzyme s work, but not protein Role: energytransfer, chargetransfer, acilgroup transfer Prostetic group
30 Nutritients with coenzyme-function Metal ions and atoms - eg.: Fe2+ - cytocrome-oxydase, Mg2+ - glucokinase, Se glutatione-peroxydase Vitamins - eg.: B1-vitamine (tiamin) tiamin-pirophosphate aldehids piruvate acid-dehydrogenase Folic acid (B9) - tetrahidrofolate (THF) one C atomic groups timidilate synthase
31 Coenzymes of oxydoreductases 1. Nicotinamide-adenin-dinucleotide (-phosphate; NAD + & NADP + ; vitamine B 3, niacin) eg. -alcohol dehydrogenase -lactate dehydrogenase
32 2. a) Flavin-mononucleotide (FMN; vitamine B 2, riboflavin) eg. -NADH dehydrogenase 2. b) Flavin-adenin-dinucleotide (FAD) eg. -succinate dehydrogenase -acyl-coa-dehydrogenase Faculty riboflavin medicine
33 3. Lipoic acid (dithio octanic acid) eg. -pyruvate dehydrogenase Dihydro lipoic acid 4. Tetrahydrobiopteryn (THB, BH 4 ) eg. -tyrosine hydroxylase -nitrogen monoxide synthase
34 5. Coenzyme Q (Q9 or Q10 coenzyme, ubiquinone) eg. mtchrial respiratory chain Complex I & II
35 1. S-adenosyl-methionine (SAM) eg. -choline acetyl transferase Coenzymes for transferases 2. Tetrahydrofolate (THF, FH 4 ; folate, pteroylglutamate, vitamine B 9 ) methylmethylenemethenylformylformimino- THF Eg.: thymidilate synthase -purine nucleotide synthesis
36 3. biotin (vitamine H) eg. -pyruvate carboxylase -acetyl-coa carboxylase -propionyl-coa carboxylase 4. Thiamine pirophosphate (TPP; thiamine, vitamine B 1 ) eg. -Pyruvate dehydrogenase
37 5. Coenzyme A (CoA; panthotenic acid, vitamine B 5 ) adenosine panthotenic acid thioethanolamine eg. -fatty acid/ketone body/cholesterol synthesis -pyruvate dehydrogenase 6. Pyridoxal phosphate (PLP; adermine, vitamine B 6 ) eg. -transaminase reactions: - Alanine aminotransferase (ALT) - Aspartate aminotransferase (AST)
38 7. adenosine-triphosphate (ATP) eg. -hexokinase 9. cytidine triphosphate (CTP) eg. -CTP:phosphocholine cytidil transferase 8. cyclic adenosine monophosphate (camp) 10. uridine triphosphate (UTP) eg. -UDP glucuronyl transferase
39 phosphoadenosine-5 -phosphosulfate (PAPS; active sulfate) eg. -sulfotransferases 12. Cobalamine (vitamine B12) eg. -methyl malonyl CoA mutase -homocystein methyl transferase
40 Coenzymes for lyases 1. thiamine PP 2. pyridoxal P (see at transferases) 3. biotin Coenzymes for isomerases 1. NADH (see at oxidoreductases) 2. cobalamine (see at transferases) 3. pyridoxal phosphate (see at transferases) Coenzymes for ligases 1. Nucleoside triphosphates (ATP, GTP, UTP, CTP; see at transferases) 2. NADH (see at oxidoreductases)
41 Multienzyme system Meaning: Entirety of closely working enzymes that catalyses different steps of the same reaction chain. Closely placed in the space eg.: fatty acid synthase S A B C P E1 E2 E3 E4
42 Kinetics of the enzyme reaction 0 order: the velocity of the reaction is not affected by the concentration 1st order: the velocity affected by the starting concentration 2nd order: the velocity is affected by the concentration of two materials
43 The kinetics of the enzyme reaction Michaelis-Menten model: the velocity of the reaction depends on the S concentration - saturation curve k 1 E + S ES E + P K -1 Conditions: -. At the beginning the [P] is small, thus velocity (v) of the backforming is minimal, k 2 process occurs irreversible - [S]>>[E] - free [S] = initial [S] (for the initial [S] to [P] is minimal) k 2
44 The kinetics of the enzyme reaction v of ES production V of ES elimination k 1 [E][S] = k -1 [ES] + k 2 [ES] k 1 [E][S] = (k -1 + k 2 )[ES] [E][S] = (k -1 + k 2 )[ES] k 1 K M = [S], where the v is the half of v max Briggs-Halden formula: v = v max [S] [S] + K M
45 The kinetics of the enzyme reactionthe direct linearisation
46 The kinetics of the enzyme reaction Linewaver-Burk form Take the reciproke 1 K M + [S] v [S]v max
47 Regulation of the enzyme-function Kovalens modification Limited proteolysis Gene induction Allosterical regulation Compartmentalisation Inhibition
48 Modulation of the enzyme activity Competitive - substrate (S) & inhibitor (I) contest for the same site - K M, v max ø - pl.: phrosphofructokinase ATP E + S ES E + P + I EI
49 Modulation of the enzyme activity nonkompetitive - inhibitor inhibits the catalysis by binding to another site - KM ø, vmax - eg.: metal ions (Zn 2+ carbonic acid anhydrase) E + S ES E + P + I + I EI + S EIS
50 Modulation of the enzyme activity uncompetitive - inhibitor binds to an alternative form of the enzyme - KM, vmax E + S ES E + P + I EIS
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