Rudolf Žitný, Ústav procesní a zpracovatelské techniky ČVUT FS 2010

1. This course is approximately at this level CHEMISTRYE182019 CH12 BIOCHEMISTRY Rudolf Žitný, Ústav procesní a zpracovatelské techniky ČVUT FS 2010

2. BIOCHEMISTRY CH12

3. Golgi apparatus Packing&targeting Mitochondrion Energy production Endoplasmic Ret. Transport nets Vacuole Lysosome wastes digestion Ribosomes RNAprotein Nucleus DNARNA Eukaryotic cell CH12

4. Proteins CH12 Proteins are linear chains of -amino acids H2N-CHR-COOH R-group R-group

5. All proteins are in fact polyamides, copolymers of amino acids, formed by the polycondensation reaction of amino acids: All proteins are in fact polyamides, copolymers of amino acids, formed by the polycondensation reaction of amino acids: H H H H O O H H O O C C C C N N R R H H 1 1 Amide group Amide group Amide group N-Amine end N-Amine end N-Amine end C- Carboxyl end C- Carboxyl end C- Carboxyl end Amidic (peptide) bond C-N Amidic (peptide) bond C-N Amidic (peptide) bond C-N Proteins H2N-CHR-COOH CH12 All proteins are in fact polyamides, copolymers of amino acids, formed by the polycondensation reaction of amino acids: H2O

6. All proteins are in fact polyamides, copolymers of amino acids, formed by the polycondensation reaction of amino acids: All proteins are in fact polyamides, copolymers of amino acids, formed by the polycondensation reaction of amino acids: Amide group Amide group N-Amine end N-Amine end C- Carboxyl end C- Carboxyl end Amidic (peptide) bond C-N Amidic (peptide) bond C-N Proteins = structures CH12 Primary structurethe order of amino acids is a protein. For example, Gly-Leu-Pro-Cys-Asn-Gln-Ile-Tyr-Cys is the primary structure of the hormone oxytocin, the first biologically active protein prepared artificially by V.Vigneaud in 1953. Secondary structure of proteins is the -helix or -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. Tertiary structuredescribes the partitioning of a polypeptide chain into a combination of helices, pleated sheets and turns.

7. All proteins are in fact polyamides, copolymers of amino acids, formed by the polycondensation reaction of amino acids: All proteins are in fact polyamides, copolymers of amino acids, formed by the polycondensation reaction of amino acids: + E+P E S -products E S -enzyme -substrate activated complex F F E + E Inhibition S S - waiting Amide group Amide group N-Amine end N-Amine end C- Carboxyl end C- Carboxyl end Amidic (peptide) bond C-N Amidic (peptide) bond C-N Enzyme CH12 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+SESE+P Inhibition E+FEF

8. All proteins are in fact polyamides, copolymers of amino acids, formed by the polycondensation reaction of amino acids: All proteins are in fact polyamides, copolymers of amino acids, formed by the polycondensation reaction of amino acids: Amide group Amide group N-Amine end N-Amine end C- Carboxyl end C- Carboxyl end Amidic (peptide) bond C-N Amidic (peptide) bond C-N Enzyme CH12 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 ESE+S increases [S] proportionally to the concentration [ES]. 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: Activated complex ES decomposes into a constant number of molecules P product

9. All proteins are in fact polyamides, copolymers of amino acids, formed by the polycondensation reaction of amino acids: All proteins are in fact polyamides, copolymers of amino acids, formed by the polycondensation reaction of amino acids: Amide group Amide group N-Amine end N-Amine end C- Carboxyl end C- Carboxyl end Amidic (peptide) bond C-N Amidic (peptide) bond C-N Enzyme fermentation process CH12 Changes of [ES] correspond to the three reactions E+SES, ESE+S, ESE+P: Enzyme E and inhibitor F are not consumed (destroyed) Mass balances (constraints) [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)

10. All proteins are in fact polyamides, copolymers of amino acids, formed by the polycondensation reaction of amino acids: All proteins are in fact polyamides, copolymers of amino acids, formed by the polycondensation reaction of amino acids: Amide group Amide group N-Amine end N-Amine end C- Carboxyl end C- Carboxyl end Amidic (peptide) bond C-N Amidic (peptide) bond C-N Enzyme fermentation process CH12 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] : If the rate of the activated complex changes is negligible (d[ES]/dt0), the concentration [ES] can be eliminated Michaelis Mentene rate equation

11. All proteins are in fact polyamides, copolymers of amino acids, formed by the polycondensation reaction of amino acids: All proteins are in fact polyamides, copolymers of amino acids, formed by the polycondensation reaction of amino acids: Amide group Amide group N-Amine end N-Amine end C- Carboxyl end C- Carboxyl end Amidic (peptide) bond C-N Amidic (peptide) bond C-N Enzyme fermentation process CH12 Michaelis Mentene rate equation

12. All proteins are in fact polyamides, copolymers of amino acids, formed by the polycondensation reaction of amino acids: All proteins are in fact polyamides, copolymers of amino acids, formed by the polycondensation reaction of amino acids: Amide group Amide group N-Amine end N-Amine end C- Carboxyl end C- Carboxyl end Amidic (peptide) bond C-N Amidic (peptide) bond C-N Carbohydrates CH12

13. All proteins are in fact polyamides, copolymers of amino acids, formed by the polycondensation reaction of amino acids: All proteins are in fact polyamides, copolymers of amino acids, formed by the polycondensation reaction of amino acids: Amide group Amide group N-Amine end N-Amine end C- Carboxyl end C- Carboxyl ed Amidic (peptide) bond C-N Amidic (peptide) bond C-N Carbohydrates CH12 -glucose or -D-glucopyranose hexagonal ring -fructose or -D-fructofuranose pentagonal ring

14. All proteins are in fact polyamides, copolymers of amino acids, formed by the polycondensation reaction of amino acids: All proteins are in fact polyamides, copolymers of amino acids, formed by the polycondensation reaction of amino acids: Amide group Amide group N-Amine end N-Amine end C- Carboxyl end C- Carboxyl ed Amidic (peptide) bond C-N Amidic (peptide) bond C-N Carbohydrates polycondensation of glucose CH12 -link amylose (STARCH) -link CELLULOSE

15. All proteins are in fact polyamides, copolymers of amino acids, formed by the polycondensation reaction of amino acids: All proteins are in fact polyamides, copolymers of amino acids, formed by the polycondensation reaction of amino acids: Amide group Amide group N-Amine end N-Amine end C- Carboxyl end C- Carboxyl ed Amidic (peptide) bond C-N Amidic (peptide) bond C-N Lipids CH12 Ester group Chains of carboxylic acids Tristearylglycerol Stearic acid glycerol condensation

16. All proteins are in fact polyamides, copolymers of amino acids, formed by the polycondensation reaction of amino acids: All proteins are in fact polyamides, copolymers of amino acids, formed by the polycondensation reaction of amino acids: Amide group Amide group N-Amine end N-Amine end C- Carboxyl end C- Carboxyl ed Amidic (peptide) bond C-N Amidic (peptide) bond C-N Nucleic acids DNA/RNA CH12