Rudolf Žitný, Ústav procesní a zpracovatelské techniky ČVUT FS 2010

This course is approximately at this level

CHEMISTRY E182019 CH12

BIOCHEMISTRY

BIOCHEMISTRYCH12

LIVINGmatter

Biomolecules - polymers (except lipids)

Carbohydrates

Nucleotides

Cells (membrane, protoplasm,..are formed from biomolecules)

Nutrition proteinse.g.Casein

Viruses

e.g.Starch

Structural proteins(connective) e.g.Collagen

CelluloseAmylose

Enzymes (catalytic proteins)

e.g.Invertase, Trypsin,...

Eukaryotic cell (large cells withinner structure: nucleus, organelles)

Prokaryotic cell(small and simple)

Multicellular Organisms(organs tissue eukaryotic cells)

Plants Animals Fungi

Unicellular microorganisms

Bacteriae.g.E.coli...

Lipids ProteinsNucleic acidsDNA RNA

Yeastse.g.Baker's yeasts

Amino acids(20 -amino acids)

Tyrosine

ValineIsoleucine

Hystidine

Proline

SerineGlutamicacid

Cysteine

Methionine

PhenylalanineAspartic ac.

Asparagine

Threonine

TryptophanGlycine

Glutamine

Leucine

LysineArginine

Alanine

Hormones (regulation)e.g. Norepinephrine

Peptidese.g.Fats

Monosaccharides

OligosaccharidesGlucose

e.g.Maltose

Sacharose

Lactose

Fructose

Glycogen

Adenine

Thymine

Uracil

Cytosine

Guanine

Transport proteins (oxygenin the blood) Hemoglobin

Contractile proteins (inmuscles) e.g.Myosin

Toxins (defend organisms,e.g.bacteria) e.g.Botulinus

Vitamins cannotbe synthesized by thebody ascorbic acid

Lipids are derivatives ofCarboxylic acidsPhosphoric acidsGlycerol (alcohol)Terpenes

Steroids

Eukaryotic cellCH12

POST

POWERPLANT

STORE

PROTEINSYNTHESIS

WASTESLibraryR&D

What ismissing in thiseukaryotic city

?RibosomesRNAprotein

RibosomesRNAprotein

Golgi apparatusPacking&targeting

Golgi apparatusPacking&targeting

MitochondrionEnergy production

MitochondrionEnergy production

Lysosomewastes digestion

Lysosomewastes digestion

Nucleus DNARNA

Nucleus DNARNA

Endoplasmic Ret.Transport nets

Endoplasmic Ret.Transport nets

VacuoleVacuole

ProteinsCH12

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,Phenylalanine

- CH2C6H5 (phenyl group)

I, Ile, Isoleucine - CH(CH3)CH2CH3 Y,Tyr,Tyrosine B CH2C6H4OH (phenyl group)

S, Ser, Serine + CH2OH W,Try,Tryptophan CH2(C=CH)NHC6H4

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 (sulphuric group)

E, Glu,Glutamic acid +A

CH2CH2COOH M,Met,Methionine - CH2CH2SCH3

N, Asn, Asparagine + CH2CONH2 P,Pro,Proline (CH2)3NHCOOH (=molecule)

H2N-CHR-COOH R-group R-group

Proteins are linear chains of -amino acids

ProteinsCH12 H2N-CHR-COOH All proteins are in fact polyamides, copolymers of amino acids, formed by the polycondensation reaction of amino acids:

O

C

H

R2

N

H

C

O

CN

H H

R1H

C C

O

N

H

H

Rc

HOC

OH

Rn

N

H N=...

C C

Amide groupAmide group

N-Amine endN-Amine end C- Carboxyl endC- Carboxyl endAmidic (peptide) bond C-NAmidic (peptide) bond C-N

O

CN

H H

R1H

HOC

O

CN

H H

R1H

HOC

H2O

Proteins = structuresCH12

Primary structure the 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 structure describes the partitioning of a polypeptide chain into a combination of helices, pleated sheets and turns.

C

C

OO

C

O

O

N

N

N

Hydrogenbond

-helix

O

C

OC

C

C

C

C

N

H

H

H

N

H

H

EnzymeCH12

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.

E+SESE+P

E+FEF Inhibition

SE

FE

F+

S -waiting

E -enzyme S -substrate

activatedcomplex

E+P -productsE S+

Lock & key

Inhibition

EnzymeCH12

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

dtk S E k ESS S

[ ][ ][ ] [ ]

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

dtk F E k EFF F

[ ][ ][ ] [ ]

Activated complex ES decomposes into a constant number of molecules P

d P

dtk ESP

[ ][ ]

product

Enzyme fermentation processCH12

Changes of [ES] correspond to the three reactions E+SES, ESE+S, ESE+P:

d ES

dtk S E k k ESS S P

[ ][ ][ ] ( )[ ]

Mass balances (constraints)

[ES]+[EF]+[E]=[E]0

[EF]+[F]=[F]0,

Enzyme E and inhibitor F are not consumed (destroyed)

Result is 6 equations for 6 unknowns, problem is closed and can be solved

(for example numerically)

Enzyme fermentation processCH12

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

dtk S E ES k ESS S

[ ][ ]([ ] [ ]) [ ] 0

d ES

dtk S E ES k k ESS S P

[ ][ ]([ ] [ ]) ( )[ ] 0

If the rate of the activated complex changes is negligible (d[ES]/dt0), the concentration [ES] can be eliminated

Simplified case without inhibition and fast formation of activated complex

d S

dt

k E S

k SP

M

[ ] [ ] [ ]

[ ]

0

Michaelis Mentene rate equation

Enzyme fermentation processCH12

Michaelis Mentene rate equation

CarbohydratesCH12 (C H2O)6n

Saccharide Formula Properties, occurrence

Glucose C6H12O6blood sugar - short term energy storage (sufficient for several minutes of life)

Fructose C6H12O6sugar occurring in fruits, the sweetest of all sugars

Ribose C5H10O5encountered in RNA (ribonucleic acid); there are only 5 carbons in a molecule!

Sucrose C12H22O11cane sugar, formed by a condensation reaction between glucose and fructose

Lactose C12H22O11milk 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,...

CarbohydratesCH12

-glucose or-D-glucopyranose

hexagonal ring

-glucose or-D-glucopyranose

hexagonal ring

-fructose or-D-fructofuranose

pentagonal ring

-fructose or-D-fructofuranose

pentagonal ring

Carbohydrates polycondensation of glucoseCH12

-link amylose (STARCH)

-link CELLULOSE

LipidsCH12

Chains of carboxylic acids

H

H

H C

C

C

OH

OH

OH

HO-C-(C17H35)

O

HO-C-(C17H35)

O

H

H

(C17H35)-C-OH

O

+

+

+

H2O

H2O

H2O H

H

H C

C

C

O-C-(C17H35)

O

H

H

(C17H35)-C-O

OO-C-(C17H35)

O

glycerol Stearic acid

condensation

Ester group

Tristearylglycerol

Nucleic acids DNA/RNACH12

C

N

N

C

C

C

HO

H

H

H

O

U T C

N

N

C

C

C

HO

H

H

O

CH3

C C

N

N

C

C

C

HO

H

H

NH2

AC

N

N

C

C

C

NH

N

NH2

HC

H

G C

N

N

C

C

C

NNH2

N

O

HC

H

H