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CH12 CHEMISTRY E182019 BIOCHEMISTRY This course is approximately at this level Rudolf Žitný, Ústav procesní a zpracovatelské techniky ČVUT FS 2010 CH12 BIOCHEMISTRY LIVING matter Multicellular Organisms Unicellular microorganisms (organstissueeukaryotic cells) Plants Animals Yeasts Fungi e.g.Baker's yeasts Eukaryotic cell (large cells with (small and simple) Cells (membrane, protoplasm,.. are formed from biomolecules) Biomolecules - polymers (except lipids) Nucleic acids Lipids Carbohydrates e.g.Starch Cellulose DNA RNA e.g.Fats Amylose Glycogen Monosaccharides Glucose Fructose Oligosaccharides Viruses Proteins Enzymes (catalytic proteins) e.g.Invertase, Trypsin,... Nutrition proteins e.g.Casein Peptides Hormones (regulation) e.g. Norepinephrine Nucleotides Adenine Guanine e.g.Maltose Cytosine Sacharose Uracil Lactose Thymine Lipids are derivatives of Carboxylic acids Phosphoric acids Glycerol (alcohol) Terpenes e.g.E.coli... Prokaryotic cell inner structure: nucleus, organelles) Steroids Bacteria Vitamins cannot be synthesized by the body ascorbic acid Amino acids (20 -aminoLeucine acids) Alanine Arginine Lysine Asparagine Methionine Aspartic ac. Phenylalanine Cysteine Proline Glutamic Serine acid Glutamine Threonine Glycine Tryptophan Hystidine Tyrosine Isoleucine Valine Structural proteins (connective) e.g.Collagen Transport proteins (oxygen in the blood) Hemoglobin Contractile proteins (in muscles) e.g.Myosin Toxins (defend organisms, e.g.bacteria) e.g.Botulinus CH12 Eukaryotic cell Golgi apparatus Packing&targeting Mitochondrion Energy production Endoplasmic Ret. Transport nets Vacuole POWER PLANT POST STORE PROTEIN SYNTHESIS Library R&D Ribosomes RNAprotein Nucleus DNARNA What is missing in this eukaryotic city ? WASTES Lysosome wastes digestion CH12 Proteins Proteins are linear chains of -amino acids H2N-CHR-COOH R-group R-group G, Gly, Glycine - H D,Asp,Aspartic acid + A CH2COOH A, Ala, Alanine - CH3 K,Lys,Lysine + B (CH2)4NH2 V, Val, Valine - CH(CH3)2 R,Arg,Arginine + B (CH2)3NH(C=NH)NH2 L, Leu, Leucine - CH2CH(CH3)2 F,Phe,Phenylalanin e - CH2C6H5 I, Ile, Isoleucine - CH(CH3)CH2CH3 Y,Tyr,Tyrosine B CH2C6H4OH (phenyl group) S, Ser, Serine + CH2OH W,Try,Tryptophan T, Thr, Threonine + CH(CH3)OH H,His,Histidine + B CH2(C=CH)NH(N=CH) Q, Gln, Glutamine + CH2CH2CONH2 C,Cys,Cysteine B CH2SH E, Glu,Glutamic acid + A CH2CH2COOH M,Met,Methionine - CH2CH2SCH3 N, Asn, Asparagine + CH2CONH2 P,Pro,Proline (phenyl group) CH2(C=CH)NHC6H4 (sulphuric group) (CH2)3NHCOOH (=molecule) Proteins CH12 H2N-CHR-COOH All proteins are in fact polyamides, copolymers of amino acids, formed by the polycondensation reaction of amino acids: H2O H H O N C C H R1 H H O N C C H R1 O H H H O N C C H R1 H O N C C H R2 H O H O N C C H Rn N=... H O N C C H Rc O Amide group N-Amine end Amidic (peptide) bond C-N C- Carboxyl end H CH12 Proteins = structures Primary structure the order of amino acids is a protein. For example, Gly-Leu-Pro-Cys-Asn-Gln-Ile-Tyr- O -helix Cys is the primary structure of the hormone oxytocin, the first biologically active protein prepared artificially by V.Vigneaud in N 1953. pleated sheet formed by a single polypeptide chain. The precise geometry of these spatial structures is given by regular distances between NH and CO groups in the backbone of a particular protein. Hydrogen and oxygen in these polar groups are attracted by the van der Waals force, by the hydrogen bond. Hydrogen bond O C C H C H Secondary structure of proteins is the -helix or - N C H N C O C N H C Tertiary structure describes the partitioning of a polypeptide chain into a combination of helices, pleated sheets and turns. C O C N H O CH12 Enzyme The decomposition of primary structure of proteins is called hydrolysis, and the protein that is able to cleave a polypeptide chain is protease - an enzyme. Enzymes are proteins that catalyse chemical reactions. Lock & key E+SESE+P + E -enzyme S -substrate E+P -products ES activated complex Inhibition E+FEF E + F E F Inhibition S S - waiting CH12 Enzyme kinetics of the fermentation process, rate equation Concentrations [S], [P], [E], [F], [ES], [EF] (S-substrate, P-product, E-free enzymes, F-inhibitor, ES, EF-activated complexes). The number of molecules S (substrate) is diminished by the number of molecules which adhere to a free enzyme E. This amount is directly proportional to the concentration of S and to the number of free enzyme sites [E]. On the other hand, the reverse reaction ESE+S increases [S] proportionally to the concentration [ES]. d[ S ] k S [ S ][ E ] k S [ ES ] dt The number of molecules F is diminished by the enzyme lock EF. There is always a certain probability that the locked molecules F will escape and this probability is given by a constant k-F: d[ F ] k F [ F ][ E ] k F [ EF ] dt Activated complex ES decomposes into a constant number of molecules P d [ P] dt k P [ ES ] product CH12 Enzyme fermentation process Changes of [ES] correspond to the three reactions E+SES, ESE+S, ESE+P: d [ ES ] k S [ S ][ E ] ( k S k P )[ ES ] dt Mass balances (constraints) Enzyme E and inhibitor F are not consumed (destroyed) [ES]+[EF]+[E]=[E]0 [EF]+[F]=[F]0, Result is 6 equations for 6 unknowns, problem is closed and can be solved (for example numerically) CH12 Enzyme fermentation process Simplified case without inhibition and fast formation of activated complex Assuming that the inhibitor concentration [F] is negligible, system can be reduced to the two following equations for two unknowns [S] and [ES] : d[ S ] k S [ S ]([ E ]0 [ ES ]) k S [ ES ] dt d [ ES ] k S [ S ]([ E ]0 [ ES ]) ( k S k P )[ ES ] dt If the rate of the activated complex changes is negligible (d[ES]/dt0), the concentration [ES] can be eliminated Michaelis Mentene rate equation d[ S ] k P [ E ]0 [ S ] dt k M [S ] CH12 Enzyme fermentation process Michaelis Mentene rate equation CH12 Carbohydrates (C H2O)6n Saccharide Formula Properties, occurrence Glucose C6H12O6 blood sugar - short term energy storage (sufficient for several minutes of life) Fructose C6H12O6 sugar occurring in fruits, the sweetest of all sugars Ribose C5H10O5 encountered in RNA (ribonucleic acid); there are only 5 carbons in a molecule! Sucrose C12H22O11 cane sugar, formed by a condensation reaction between glucose and fructose Lactose C12H22O11 milk sugar, formed by a condensation reaction between galactose and glucose Amylose n~1000 main component of STARCH - long term storage of glucose in plants Glycogen n~1000 mid-term energy storage in animals (an equivalent of starch) Cellulose n~1000 glucose polymer produced by plants (structural component); wood, paper,... CH12 Carbohydrates CH2OH H OH O H OH H H H OH H OH -glucose or -D-glucopyranose hexagonal ring O CH2OH H OH OH CH2OH OH H -fructose or -D-fructofuranose pentagonal ring Carbohydrates polycondensation of glucose CH12 CH2O HH H 4 OH O H CH2O HH H 1 H OH H H OH 3 H 2 O 4 OH O H H O CH2O H O H OH H H OH H H H CH2O HH H OH O O H OH H OH O H OH O H H H H O O O H H O O H OH H H OH OH H H H H H OH H OH CH2O HH CH2O HH O O -link amylose (STARCH) CH2O H CH2O H -link CELLULOSE H OH CH12 Lipids Chains of carboxylic acids H H O (C17H35)-C-OH + H2O H2O H O O H C OH + HO-C-(C17H35) OH C H Ester group H O (C17H35)-C-O O C OH + HO-C-(C17H35) H H C O-C-(C17H35) C H C O O-C-(C17H35) H H2O glycerol Tristearylglycerol Stearic acid condensation Nucleic acids DNA/RNA CH12 O H C N C O U N H NH2 O H C H C N C H O CH3 C T N H C C N C C H O C N H O NH2 H C C N C C H H A N H N C N C C H C C N G N NH2 N C C C N H H T C A G H