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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
(organstissueeukaryotic 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
RNAprotein
Nucleus
DNARNA
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+SESE+P
+
E -enzyme
S -substrate
E+P -products
ES
activated
complex
Inhibition
E+FEF
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 ESE+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+SES, ESE+S, ESE+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]/dt0), 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