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Biochemistry
Judit Kosáry (2016-1)
The lecture gives a basic knowledge about the basic rules of living organisms
(bioaffinity, biocatalysis, bioregulation), the role of different biomolecules (proteins,
nucleic acids, carbohydrates, lipids) in living organisms, enzymes, the metabolism of
biomolecules (catabolism, anabolism), generation and storage of metabolic energy,
membrane transports.
Biogenic elements
Building biomolecules: carbon (C), hydrogen (H), oxygen (O), nitrogen (N)
(and P és S). They are in the first and second periods (high charge concentration on
their surface unit), their atoms are not susceptible to deformation and they form with
own atoms and other biogenic elements strong -bonds.
Electronegativity can be characterized the atoms connected by a -bond. The
atom with higher electronegativity can collect a part of the electron density of the
-bond, this causes an electron surplus (Ө) on it. This effect causes an electron
deficiency () on the atom with lower electronegativity.
EN
1
…
4
5
6
Columns

EN
Periodes

1
H
EN=2.1
2
C
N
O
EN=2.5
EN=3.0
EN=3.5
3
P
S
EN=2.2
EN=2.5
Position of biogenic elements in the periodical system and their electronegativity (EN)
Biomolecules
Biomolecules are organic molecules building up living organisms. Types of
biomolecules: proteins, carbohydrates, nucleic acids and lipids (apolar biomolecules).
Proteins, carbohydrates, nucleic acids are chiral biopolymers:
Type of biomolecule
Proteins
Units
-Amino acids
Bonds between units
Peptide bond (a special
carboxamide bond)
Carbohydrates
Simple sugars
O-Glycosidic bond (a
special acetal bond)
Nucleic acids
Nucleotides
3’,5’-Phosphodiester bond
______________________ ______________________ _____________________
Lipids (apolar
Simple lipids cannot be Complex lipids can be
biomolecules)
hydrolyzed by NaOH
hydrolyzed by NaOH
Characteristic data of the structure of proteins, carbohydrates and nucleic
acids; characterization of lipids
2
Rules of biochemistry at the molecular level
1. Bioaffinity – there is at least one biological surface to interact with a biomolecule.
2. Biocatalysis – in living organisms practically all of reactions are catalyzed and the
biocatalysts are called enzymes (mostly proteins).
3. Bioregulation – all of biochemical processes are regulated.
Isomerism in biomolecules
When two molecules have some differences in their structure but their
molecular formula (the composition of elements) is the same, they are isomers. When
the atoms bond in different order in isomers they are structural (constitutional)
isomers. There are different types of structural isomers. In biomolecules tautomerism
(the difference between two isomers is in the position of one hydrogen atom and a
double bond) can be found frequently (e.g. aldoses and ketoses in carbohydrate
chemistry).
The stereoisomers have the same molecular formula and sequence of bonded
atoms (constitution), but their atoms have differences in their three-dimensional
orientation in space. There are different types of stereoisomers: optical isomers
(enantiomers and diastereomers), geometrical isomers and conformers.
Conformational isomers (conformers) differ by rotations around one or more single
bonds (e.g. chair and sofa conformations of glucopyranoside).
Optical isomerism
In the case of saturated carbon atoms, due to hibridization (sp3), the angle of
the bonds is 109,5°, i.e. its geometry is tetrahedral. A carbon atom with four different
substituents (marked by a star) is called a chiral carbon atom (on the basis of the
Greek word kheir– hand). In the case of a single chiral atom two isomers, called
enantiomers are possible. Enantiomers (antipodes) are related as mirror images. The
chemical and physical properties of the enantiomers are the same, because the
microenvironment of the atoms is the same. The only difference is in their optical
rotation, which is opposite. An enantiomer can be identified by the direction in which
it rotates the plane of monochromatic and monopolarized light. If it rotates the light
clockwise, that enantiomer is labeled (+), while its mirror-image is labeled (−).
Group of highest oxidation number
|
Smallest functional group–C–Characteristic functional group
|
Other group
The application of Fischer’s convention on the D- enantiomer
Group of highest oxidation number
|
Characteristic functional group–C–Smallest functional group
|
Other group
The application of Fischer’s convention on the L-enantiomer
3
CHO
CHO
HO C H
HO C H
CH2OH
CHO
CHO
H C OH
H C OH
CH2OH
CH2OH
L-glicerinaldehid
CH2OH
D-glicerinaldehid
CH2OH
HO C H
CHO
Az aszimmetria-centrumok Fischer-féle ábrázolása
COOH
C
R
H
NH2
COOH
H2N C H
R
H2N
COOH
CH
R
Az L-aminosavak térbeli, Fischer-féle és a speciális, a Fischer-féle konvención alapuló ábrázolása
The modified Fischer convention for the L--amino acids
Distinction of enantiomers can be carried out by application of the Fischer
convention that is based on the simplest aldose glyceraldehyde. When the
characteristic group is on right side in Fischer projection, the enantiomer is called
right-handed (D – after Latin word dexter) and the other enantiomer is the left-handed
variation (L – after Latin word laevus). D and L are typically typeset in SMALL CAPS.
Nowadays, except for sugars and amino acids, for the definition of chirality the R/S
notation is used. This is defined by the Cahn-Ingold-Prelog priority rules based on
atomic number. In the case of glyceraldehyde the D enantiomer is the clockwise (+)
and L-enantiomer is the anti-clockwise (–) enantiomer. For the L--amino acids a
modified Fischer convention is used because it is better for illustration of the peptide
bond.
Diastereomers contain at least two centers of chirality, and one of the centers
has the same and the other has the opposite position. Diastereomers are not mirror
images and therefore their chemical and physical properties of are different, the
microenvironment of the atoms being different. This fact can serve as a basis for the
separation of enantiomers from their mixtures (called racemic mixtures) by forming
diastereomers. This process is called resolution.
D
L
|
|
D
D
Diastereomers
In compounds containing two chirality centers and the carbon atoms have the
same substituents of opposite chirality therefore the direction of the optical rotation of
two carbon atoms is opposite (resultant optical rotation is zero) – this variation is
called meso form (e.g. meso-tartarate).
H
C
OH
HO
C
H
HO
C–H
H
4
C–OH
COOH
D
H
H
C
L
COOH
COOH
H
OH
C
OH
HO
COOH
mezo-borkôsav
D
D
C
OH
C
H
COOH
(+)-borkôsav
Borkôsav (tartarát) diasztereomerek
Meso-tartarate and (+)-tartarate are diastereomers
Many biologically active molecules are chiral, including the naturally
occurring proteins, carbohydrates and nucleic acids. As enzymes are mostly proteins
and proteins are chiral, they preferentially catalyze the transformation of only one of
the enantiomers of a chiral substrate. Naturally occurring proteins are made of L-amino acids, carbohydrates, di-, oligo- and polysaccharides are all made of D-sugars.
Nucleic acids contain also D-sugars: ribose or deoxyribose.
Geometrical isomerism
In the case of free rotation in saturated hydrocarbons in eclipsed structure –
hydrogen or other atoms are in disturbing each other; in the open structure – hydrogen
or other atoms are in the in a rotated position, causing minimal disturbance, therefore
this structure is preferred.
H
HH
H3C
CH3
etán
H
H
H H
rotáció
H
fedô állás
(kedvezôtlen)
H
H
H H
nyitott állás
(kedvezô)
konformációk
Az etán konformációi
Conformations of ethane:eclipsed and open structures
When there is a barrier to rotation (e.g. a ring system or a double bond) the
large substituents can be on the same or on opposite sides. When large substituents are
on the opposite side (trans isomer) the disturbance is less and therefore this isomer is
more advantageous than when they are on the same side (cis isomer). Now in organic
chemistry E-Z notation based on the Cahn-Ingold –Prelog rules is used.
H
H
H
Br
C C
C C
Br
Br
Br
H
cisz-1,2-dibróm-etilén
kevésbé stabil
transz-1,2-dibróm-etilén
stabilabb
A simple example for geometric isomers: cis- and trans-1,2-dibromoethylene
Carbohydrates
5
Carbohydrates (saccharides) are organic compounds of the general formula
Cn(H2O)n. The ratio of hydrogen and oxygen is 2:1 as in the water. Formerly
carbohydrates were viewed as hydrates of carbon and this is the origin of their name.
In simple sugars (monosaccharides) the general formula is CnH2nOn (generally C3-C7).
They are polyhydroxy carbonyl (oxo) compounds. The carbonyl group may be
aldehyde (aldose) or ketone (ketose). In ketoses the carbonyl group is always at
position 2 of the sugar. The sugars are named not only based on the type of their
carbonyl group but by the number of the carbon atoms (on the basis of Greek name of
numbers): triose (C3 – C3H6O3), tetrose (C4 – C4H8O4), pentose (C5 – C5H10O5),
hexose (C6 – C6H12O6), heptose (C7 – C7H14O7), e.g. glyceraldehyde is an aldotriose,
glucose is an aldohexose and fructose is a ketohexose. The secondary hydroxy groups
of sugars are stereocenters and the chirality of the sugar is based on the configuration
of the chiral carbon atom of highest number (e.g. C5 in hexoses). The different aldoses
and ketoses with the same number of carbon atoms are diastereomers except one,
which is their enantiomer. In the living organisms sugars are generally in D- and not
L-enantiomer form It is known that only one kind of enantiomers can connect to
different biological surfaces. Sugars are usually metabolized as their phosphate esters.
HO
O
O
HO
HO CH
CHO
CHO
CHO
CHO
H C OH
H C OH
H C OH
H C OH
CH2OH
H C OH
H C OH
CH2OH
H C OH
H C OH
CH2OH
H C OH
D-glicerinaldehid
D-eritróz
CH2OH
D-ribóz
L-aszkorbinsav
aldózok
HO C H
CH2OH
D-glükóz
(C-vitamin)
CH2OH
CH2OH
CH2OH
CH2OH
CH2OH
C O
C O
C O
C O
C O
HO C H
HO C H
HO C H
CH2OH
dihidroxi-aceton
H C OH
H C OH
H C OH
H C OH
CH2OH
CH2OH
H C OH
H C OH
CH2OH
H C OH
D-fruktóz
CH2OH
D-ribulóz
D-xilulóz
ketózok
A legfontosabb egyszerû cukrok és a C-vitamin képlete
H C OH
D-szeduheptulóz
The most important straight-chain simple sugars and a sugar derivative L-ascorbic
acid (ascorbate, glyceraldehyde, erithrose, ribose, glucose, dihydroxyacetone,
ribulose, xylulose, fructose, sedoheptulose
In sugars the different functional groups retain their original properties,
therefore aldohexoses can be easily oxidized and carbonyl group can react with one of
hydroxyl groups.
Detection of sugars by oxidation: according to the condition of chemical
oxidizability (i.e. the presence of a hydrogen connected to a carbon that is in a
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polarized bond) only aldehydes can be easily oxidized to carboxylic acids. The
example of acetaldehyde is presented:
The Fehling reaction of acetaldehyde forming acetate and Cu2O as red precipitate
During the reaction the oxidation of aldehyde is combined with the reduction
of the oxidizing reagent (on this case 2Cu2  Cu22), therefore aldoses are called
reducing sugars. Ketones cannot be oxidized because of the absence of CH in
carbonyl group. But in forced conditions ketoses can be isomerized to aldoses by
double oxo-enol-oxo tautomerism, therefore all of simple sugars are reducing sugars.

H C

O
H C OH
HO C H
H C
O
H C
O H
H C OH
H C OH
HO C H
O
H
HO C H
H C OH
H C OH
H C OH
H C OH
H C
H C
CH2–OH
CH2OH
CH2OH
CH2OH
H
HO
O
H
OH
O
H

OH
H
OH
H
- D-glükopiranozid
Az egyszerû cukrok ciklizálódása
Cyclization of simple sugars
The cyclization of sugars is caused by a reversible intramolecular reaction
(nucleophilic addition) between the carbonyl and one of hydroxyl group of the
straight-chain (open form) sugar. This hydroxyl group is connected to the chiral
carbon atom of highest number. The cycle that contains an oxygen and the new
hydroxyl groups is connected to chiral carbon atom can be in different positions
forming stereoisomers. Aldopentoses and ketohexoses form five-membered rings with
plane surface (furanosides). Aldohexoses form three dimensional six-membered rings
(pyranosides), those are generally projected as planar, and D-hydroxy groups are
under the ring and L-hydroxy groups are above the ring. Cyclization generates a new
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chiral center, in which the D-hydroxyl group is called the -anomer and the Lhydroxy group is called the -anomer.
CH2OH
O H
H
H
OH H
HO
H
OH 
OH
H
CH2OH
O
HO
H
H
HO
H
OH
H
 OH
- D-glükopiranozid
H
HO
HO
CH2OH
O

H
H
OH
OH
H
H
- D-glükopiranozid
A gyûrüs glükóz ábrázolási lehetôségei és glikozidos kötésének térállása
Representations of - and -D-glucopyranoside
The cyclized sugars contain a hemiacetal or hemiketal structure (in sugars the
new hydroxyl group is called the glycosidic hydroxyl) that can be easily reacted with a
hydroxyl group of another sugar. The product is a disaccharide. A ring-formed sugar
can be reacted with a variety of hydroxyl groups; the general name of the product is
glycoside that is a special form of an acetal. Because of the reversibility of this
cyclization the disaccharides containing glycosidic hydroxyl group (maltose,
cellobiose, lactose, gentiobiose) are reducing compounds. In saccharose (sucrose) the
glycosidic bond is formed between two glycosidic hydroxyl groups therefore it is not a
reducing sugar. The connection between two sugars in disaccharides is shown by their
names (e.g. maltose is D-glucopyranosyl-[1,4-]-D-glucopyranose).
8
H
HO
CH2OH
O
H
OH H
HH
 O
OH
H
CH2OH
O
H
OH H
H
H
H
OH
HO
H
CH2OH
O
H
OH H
H
HO
HOCH2
H
H

OH O
O

H HO
CH2OH
CH2OH
O
H
OH H
HO
H
H
OH
H
O
OH
H
H
laktóz
CH2OH
O
H
OH H
H
CH2OH
O
H
OH H
OH
H
OH
H
szaharóz
HO
OH
H
H
cellobióz
H
H
H
O
maltóz
CH2OH
O
H
OH H
OH
OH
H
OH
CH2OH
O
H
OH H
HOCH2
O CH2
H H
OH HO
genciobióz
O
H
OH
H
H
OH
H
H
OH
O
H HO
OH

CH2OH
OH
H
- D-fruktofuranóz
Az ismertebb diszacharidok és a ciklizált fruktóz képlete
The most important disaccharides and the ring-formed fructose
Among polysaccharides starch and cellulose are the most important. The
building unit of starch is maltose. Plants use starch as energy reserve. Its function is
similar to that of glycogen in animals and people. There are two types of starch:
amilose (a linear polymer containing only 1,4 glycosidic bonds) and amilopectin (a
branched polymer containing both 1,4 and 1,6 glycosidic bonds). The building unit of
cellulose is cellobiose. Cellulose is a structural components of primary cell walls of
green plants and is the most wide-spread organic molecule in the world. The name of
the polysaccharides containing only D-glucose molecules is glucan – starch is an glucan and cellulose is a -glucan.
Proteins
Proteins (polypeptides) are biopolymers made of -L-amino acids connected
by peptide bonds (a special type of carboxamide bond).
Units of the polypeptide chain, the L--amino acids
They are the building blocks of proteins connected by peptide bonds. Standard
(protein, proteinogenous) amino acids build up proteins, non-standard (non-protein,
non-proteinogenous) amino acids can be important metabolic intermediates. The name
of standard amino acids is used generally in their abbreviated form. The modified
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Fischer conventions of the formulas of twenty standard amino acids and their
abbreviations are presented in schemes. Ten of amino acids (Val, Leu, Ile, Phe, Lys,
Thr, Trp, Met, Arg, His) are called essential amino acids, because the human body
cannot synthesize them from other compounds at the level needed for normal growth,
therefore they must be obtained from food. (Notice: while large quantities of the
essential amino acids are needed, there are other essential compounds, e.g. vitamins,
which we need only in small quantities). Often selenocysteine and taurine are also put
on the list of standard amino acids, while Arg, His are classified as semiessential
amino acids by several authors.
H2N CH2 COOH
H2N
glicin (Gly)
CH
COOH
H2N
CH3
alanin (Ala)
CH
COOH
CH3
H2N
COOH
CH
CH2
CH3
CH
CH3
CH3
leucin (Leu)
COOH
CH2
CH
CH2
CH
COOH
CH
CH
valin (Val)
H2N
H2N
H
N
COOH
CH3
CH3
izoleucin (Ile)
prolin (Pro)
fenilalanin (Phe)
A hidrofób kölcsönhatásra alkalmas fehérjealkotó aminosavak
Amino acids of hydrophobic character
H2N
CH
COOH
H2N
CH
COOH
H2N
CH
COOH
H2N
CH
COOH
CH2
CH2
(CH2)4
(CH2)3
COOH
CH2
NH2
NH
aszparaginsav (Asp)
COOH
lizin (Lys)
glutaminsav (Glu)
C=NH
NH2
arginin (Arg)
Az ionos kölcsönhatásra alkalmas fehérjealkotó aminosavak
Amino acids with ionic character
10
H2N
CH
H2N
COOH
CH
COOH
H2N
CH
CH2OH
CH3
szerin (Ser)
CH
COOH
CH2
OH
treonin (Thr)
H2N
CH
H2N
COOH
CH
COOH
CH2
CH2
CONH2
CH2
OH
tirozin (Tyr)
CONH2
aszparagin (Asn)
glutamin (Gln)
H2N
CH
H2N
COOH
CH
COOH
CH2
CH2
NH
N
N
H
triptofán (Trp)
hisztidin (His)
A hidrogénkötésre alkalmas fehérjealkotó aminosavak
Amino acids with hydrogen bonds
H2N


H
CH
2N
2
Cl

CH2
CH2COOH
CH
OH  Cl
Na
O–H
CH2SH
cisztein (Cys)
etilén-klórhidrin
Cysteine with
CH3
CH2
CH2
O
CH2
COOH

CH2
H
+
A dipólus-dipólus kölcsönhatásra
AN
H O fehérjealkotó
CH2 CH2 O
H
alkalmas
aminosav
H
S
CH3
metán-tiol
CH3CH2 O CH2CH3
dietiléter
SNi
szomszéd-csoport hatás
metionin (Met)
H2O
etilénglikol

disulphide
bond
and
methionine
with
dipole-dipole
Az etilénklórhidron reakciója
S

CH2
O

etilén-oxid
S–CH3 (szögfeszültség)
H2O
A diszulfidkötésre alkalmas


NaOH
CH2 CHaminosav
fehérjealkotó
2
O
CH
"O"
H2O
"O"
CH3CH2
CH3
S
S
interaction
CH3
stabil diszulfid híd
O O–CH2CH3
dietil-peroxid
A peroxidok és a diszulfidok stabilitási különbsége
Formation of disulphide bond and peroxides
2 CH3CH2
O
11
Structural levels of proteins
Primary structure: The sequence of amino acids. On one end of every polypeptide
chain, called the amino terminal or N-terminal, there is a free amino group. The other
end, with its free carboxyl group, is called the carboxyl terminal or C-terminal.
O
H2N
O
CH
N
R
H
CH
OH
N-terminális
C-terminális
A fehérjék elsôdleges szerkezete
Primary structure of proteins with the N- and C-terminals of the chain
Peptide bonds are special carboxamide bonds with strong hydrogen bonds
caused by a partial delocalization in the functional group. Because of this
delocalization the peptide bond is planar and rigid. This partial delocalization is
illustrated by the molecule acetamid.
CH3
C
O
NH2
acetamid
CH3
C
O
O
N H
H
kis  O
CH3 C
NH2
 C
C
O
N
C
 C
C
H
N
C
H
dipoláris, gátolt
rotációjú szakasz
a savamidcsoportban
(a peptidkötésben)
NaOH nagyon
nehezen
A savamidcsoport jellemzése
Partial delocalization and hindered rotation of acetamid illustrated by mesomeric
structures
Secondary structure:– Structures established by hydrogen bonds between peptide
bonds: righ-handed -helix, -sheet – between antiparallel chains, collagen structures
– there are three of left-handed extended helix structures rolled into a cable form of a
right-handed helix in tropocollagen units containing Gly-Pro-Hyp triplets,
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hydroxyproline is synthesized by a direct oxidation of proline in peptide chain by
means of L-ascorbate).
-helix structure
a -sheet structure
collagen structure
O
N
O
N
1/2 O2
(az aszkorbinsav
közvetítésével)
HO
Hyp részlet a
Pro részlet a
fehérjeláncban
fehérjeláncban
A hidroxi-prolin képzôdése a peptidláncban
Oxidation of proline to hydroxyproline in the peptide chain by L-ascorbate (vitamin
C)
Tertiary structure: – Connections between remote parts of the peptide chain by
secondary bonds between the side chains of amino acids – globular structures (folded
to three dimensional structures, they contain all of the secondary structures) and
fibrous structures (folded to fibres, they contain only one of the secondary structures).
Interactions:
 hydrophobic interactions – glycine (Gly), alanine (Ala), valine (Val), leucine
(Leu), isoleucine (Ile), phenylalanine (Phe), proline (Pro)
 ionic interactions – aspartic acid (Asp) glutamic acid (Glu), lysine (Lys), arginine
(Arg)
 hydrogen bonds – serine (Ser), threonine (Thr), tyrosine (Tyr), asparagine (Asn),
glutamine (Glu), tryptophan (Trp), histidine (His)
 disulphide bond – cysteine (Cys)
 dipole-dipole interactions methionine (Met);
Quaternery structure:– Connection between several polypeptide chains usually called
protein subunits by secondary bonds between the side chains of amino acids.
13
Simple proteins contain only protein chains. Complex proteins contain other
kinds of biomolecules or metal ions: glycoproteins (often in membranes),
nucleoproteins (in ribosomes), lipoproteins (e.g. LDL – a cholesterol transferring
lipoprotein), metalloproteins (e.g. some enzymes as lactate dehydrogenase contain
zinc), chromoproteins (e.g. red hemoglobin), phosphoproteins (e.g. casein), etc.
Biological function of proteins
 Enzyme proteins – catalysts of biochemical reactions, they are vital to metabolism
 Structural proteins – e.g. collage fibers as fibrin
 Contractile (mechanical) proteins – e.g. muscle proteins
 Transport proteins – e.g. hemoglobin transports oxygen
 Proteins for supply – e.g. myoglobin supplies oxygen
 Immune protection – etc. immunoglobulins
 Toxins (poisons) – e.g. snakes poison
Biuret reaction is a colorimetric protein assay methods that use cupric ions as
colouring agent. Cupric ions form a complex of faint blue-violet color with the imide
tautomer of at least two (according to several authors four) peptide bonds. The
intensity of the color produced is proportional to the number of peptide bonds
participating in the reaction; therefore the biuret reaction is an often used analytical
method for the quantitative determination the total protein concentration. The reaction
was named after the organic compound biuret (NH2-CO-NH-CO-NH2) that is the
simplest compound to give a colored (light blue) complex.
O
CH C
R
O H
O
NaOH
N CH C N
H R
H
R
Cu
O
CH C
R
CH C
O
O H
N CH C N
Cu2+
R imid
(a nátrium-hidroxiddal sót képezhet)
N CH C N
R
ibolyaszínû komplex
A biuret reakció
Enzymes
Enzymes are globular proteins generally with quaternary structure. As
biocatalysts they give an alternative reaction for the product synthesis with lower
activity energy than the original reaction of really high activity via forming a complex
with substrate. Since enzymes are selective for their substrates and speed up only a
few reactions from among many possibilities, the set of enzymes made in a cell
determines which metabolic pathways occur in that cell. Enzymes are known to
catalyze about 4,000 biochemical reactions. Activity of enzyme is affected by
temperature, chemical environment (e.g., pH and salt concentration), and the
concentration of substrate.
14
Reaction diagram without and with enzyme
Enzyme reactions are reversible. The sum of the rate of the dissociation of the
enzyme substrate complex (v-1) and the rate of the synthesis of product and
regeneration of the enzyme (v2) from this complex can be equal to the rate of forming
enzyme substrate complex (v1), this status is called ‘steady state’.
E+S
v1= k1[E].[S]
v1
v-1
ES
v2
v-1= k-1[ES]
E+P
v2= k2[ES]
A saturation curve can be found when the concentration of the product [P] is
plotted against reaction time. Also a saturation curve can be found for the relation
between the substrate concentration [S] and rate (v0). This rate (v0) is the rate of
enzyme reaction at the first period of the reaction. This can be characterized by the
modified Michaelis-Menten plot that is called the equation of enzyme kinetics. As the
substrate concentration increases, more and more of the free enzyme is converted into
the substrate-bound ES form. At the maximum rate (Vmax) of the enzyme, all the
enzyme active sites are bound to substrate, and the amount of ES complex is the same
as the total amount of enzyme. The amount of substrate needed to achieve a given rate
of reaction is also important. This is given by the Michaelis constant (KM), which is
the substrate concentration required for an enzyme to reach one-half its maximum
rate.
15
Diagrams and equal of enzyme kinetics
Only the active site of an enzyme takes part in the catalytic reaction while
other parts of the enzyme assure the active conformation of the active site, that
contains two important parts. The substrate binding site can be characterized by KM
for a given substrate, and this can show how tight the binding of the substrate is to the
enzyme. The parameters and/or compounds decreasing the binding of the substrate
can increase the value of KM. For a given substrate the catalytic site can be
characterized by Vmax. The parameters and/or compounds decreasing the
transformation of the substrate-enzyme complex to the product can decrease the value
of Vmax.
The double reciprocal plot
The KM and Vmax values are the important kinetic constants of the kinetics of
enzymes for a given substrate. The determination of these constants is given by a
double reciprocal plot (Lineweaver-Burk plot) that yields a straight line with an
intercept of 1/Vmax and a slope of KM/Vmax.
Certain compounds can alter the activity of enzymes. Enzyme activity can be
decreased by various inhibitors or can be increased by activators. The effect of such
compounds can be reversible or irreversible. Reversible inhibitors are classified
according to their linkage to the active site. Compounds of similar structure to the
substrate can bind to the substrate binding site and are called competitive inhibitors.
Compounds which disturb the function of the catalytic site are called non-competitive
inhibitors. Compounds that can disturb the function of both the substrate binding and
catalytic sites are called mixed inhibitors.
16
The types of reversible inhibitions: competitive inhibition, mixed inhibition, noncompetitive inhibition
The classification of enzymes – enzymes can be identified by their number in
Enzyme Nomenclature (Enzyme Catalogue EC). EC number is a combination of four
numbers. The first number of the combination shows the type of the reaction
catalyzed.
1. Oxidorecuctases – catalyze oxidation and reduction (dehydrogenases and
oxigenases)
2. Transferases – catalyze subtitutions
3. Hydrolases – catalyze hydrolysis
4. Lyases – catalyze addition and elimination
5. Isomerases – catalyze tautomerism
6. Ligases – catalyze reactions using the energy of macroerg bonds
Oxidoreductases and transferases need reagents (compounds with coenzyme
function) for the catalyzed reactions. Compounds with coenzyme function (henceforth
they are called as coenzymes) are connected to enzymes either by secondary bonds
(they are really coenzymes – they can be regenerated also in other reactions) or by
covalent bonds (prosthetic groups – they can be regenerated only in their original
place). Compounds with coenzyme function have two forms (unreacted and reacted) –
only lipoic acid has three forms. The starting materials for coenzymes are water
soluble vitamins and in a few cases essential amino acids).
In primary metabolism oxidoreductases are always dehydrogenases, because
the reoxidation of reduced coenzymes is connected with the producing of energy in
form of macroerg bonds. The mechanism of these oxidoreductase coenzymes can be
ionic (hydrogen molecules are transported as hydride anions and protons) or radical
(one hydrogen molecule is transported in form of two hydrogen atoms).
In the oxidative degradative processes of catabolism NAD (its starting
material is nicotinamide i.e. vitamin B3) – its reduced form is (NADH+H)
(nicotinamide adenine dinucleotide) involve an ionic, while FAD (its starting material
is riboflavine i.e. vitamin B2) – its reduced form is FADH2 (flavin adenine
dinucteotide) and FMN – its reduced form is FMNH2 (flavin mononucleotide) a
radical mechanism. FMN takes part only in terminal oxidation. In reductive
biosyntheses of anabolism the coenzyme is (NADPH+H) in both mechanisms. The
difference between NAD NADP is the presence of a phosphoryl group on the C-2
hydroxyl group of ribose in NADP. Flavin-containing coenzymes are always
prosthetic groups.
17
H
H
H
H O
H
O
CONH2
HN
HN
N
CONH2
NH
+ H
O
N
H
(DHU)
= 260dihidro–uracil
nm
HOCH2O
O
O
N
H
H
H
H
max = 260 és 340 nm
max
OH OH
pszeudo
uridin (C)
A nikotinamidot tartalmazó koenzimek redukálódási
folyamata
Néhány ritka nukleotid képlete
The process of reduction of coenzymes containing a nicotinamide structure
H
H
H
CONH2
CONH2
CH2
O
H
P
O
H
H
OH OH NH2
N
H
N
P
H
H
H
OH OH NH2
N
H
O
P
N
N
O
CH2
2H (H + H )
O
H
H
H
H
H
R = H (NADH + H+ )
R = P (NADPH + H+ )
A NAD+ és NADP+ koenzimek
Coenzymes NAD and NADPH
H
N
2H
N
N
OH OR
OH OR
R = H (NAD+ ) nikotinamid-adenin-dinukleotid
R = P (NADP+ )
N
H
N
N
O
CH2
H
H
N
O
O
H
P
O
CH2
N
O
N
H
A flavint tartalmazó koenzimek redukálódási folyamata
The process of reduction of coenzymes containing flavines
18
O
H3C
H3C
N
H
NH
N
N
O
H3C
N
H3C
N
N
CH2
H
NH
2H
O
CH2
NH2
HCOH
HCOH
H2C O P O P O CH2
H
HCOH
H2C O
H
H
N
N
HCOH
N
N
O
NH2
HCOH
N
N
HCOH
O
P
O
H
H
N
N
O
P O CH2
H
H
OH OH
H
OH OH
FADH2
FAD (flavin-adenin-dinukleotid)
O
H3C
N
H3C
N
NH
N
CH2
HCOH
O
R = P FMN (flavin mononukleotid)
R = H (B2 vitamin) riboflavin
HCOH
HCOH
H2C O–R
A flavint tartalmazó koenzimek és prekurzor vitaminjuk
Flavin-containing coenzymes and their precursor vitamin
Ubiquinone (coenzyme Q) (its starting material is tyrosine and its reduced
form is ubiquinol) is that kind of oxidoreductase coenzyme, which can work by both
ionic and radical mechanism. The name of the human ubiquinone is CoQ10. The
starting material of ubiquinone is tyrosine.
Redox reactions of ubiquinone
In various kinds of cytochromes the coenzyme effecting electron transfer is
hem (by ferrous-ferric transformation).
19
The structure of hem
The coenzyme of direct oxygenases is ascorbic acid (vitamin C).
O
O
HO
ox
O
HO
HO C H
CH2OH
L-aszkorbinsav
(C-vitamin)
red
O
O
O
HO C H
CH2OH
dehidro-aszkorbinsav
(bomlékony)
Az aszkorbinsav oxidált és redukált formája
Redox reactions of L-ascorbic acid
NH2
N
Transferases can catalyze several
N kinds of substitutions. The transferred
groups can be different carbon skeletons: C1 – CO2 (biotin that is vitamin H), only
methyl group (SAM – S-adenosylmethionine,
N itsNstarting material is methionine),
methyl group, aldehyde
group,
etc.
(THF
–
tetrahydrofolate, its starting material is
P–O–P–O–P–CH2
O
folic acid i.e. vitamin B9 – earlier vitamin B10; C2 – acetaldehyde (TPP – thiamine
H
H i.e. vitamin B ), acetyl group in a
pyrophosphate, its staring material is aneurine,
1
H
H
macroerg thiolester bond (coenzyme A, its starting material is pantothenic acid i.e.
vitamin B5; and lipoic acid that is connected
to the -amino group of a lysine as a
OH OH
prosthetic group therefore it is often called lipoamide); and other groups: phosphate
group (ATP or other nucleoside triphosphate molecules), amino group (PAL –
Az ATP
átadható
csoportjai
pyridoxal phosphate, its reacted
form
is PAM
– pyridoxamine phosphate, and its
starting material is pyridoxine i.e. vitamin B6).
20
O
HN
C
ATP
O
ADP
HOOC
NH
CH2
S
CH2
biotin
(H-vitamin)
CH2
CH2
N
C
NH
CO2
COOH
CH2
CH2
CH2
CH2
COOH
S
karboxi-biotin
A biotin keletkezése és formái
Transfer coenzyme – carbon dioxide – biotin
NH2
H2N
COOH
CH
CH2
O
P
P
P –O–CH2
O
CH2
H
OH
CH3
Met
Pi
PPi
N
H
H
+
OH
ATP
COOH
N
N
CH2
S
CH3
NH2
CH
CH2
H3C
N
O
H
S
H2N
N
N
CH2
H
H
N
N
O
H2N
COOH
NH2
CH
CH2
CH2
S
N
N
CH2
H
H
H
OH OH
S-adenozil-metionin (SAM)
N
N
O
H
H
OH
H
OH
S-adenozil-homocisztein (SAH)
A SAM keletkezése és különbözô formái
Transfer coenzyme – methyl group – SAM
21
CH2
O
H
4
5
6
8 7
1
N
H2N
CH2–NH
N
HN 3
2
C1
CH
4-aminobenzoesav
N
COOH
COHN
H
C1:
CHO
CH2
CH3
CH2
CH2OH
COOH
tetrahidro-folsav (THF)
Glu
O
N
H2N
CH2–NH
N
HN
COOH
COHN
CH
CH2
N
CH2
folsav (B10 vitamin)
COOH
A C1 részleteket szállító koenzim és prekoenzim vitaminja
Transfer coenzyme – C1 – THF
H3C
CH2CH2O
N
H3C
CH2 N
NH2
O
P
H3C
H3C
CH2 N
C
N
tiamin-pirofoszfát (TPP)
H3C
O
S
CH2CH2OH
CH2 N
CH
N
P
NH2 H3C C OH
H "aktív acetaldehid"
N
H3C
CH2CH2O
N
S
CH
N
P
S
NH2
tiamin (aneurin) B1-vitamin
Az acetaldehidet szállító koenzim és prekurzor vitaminja
Transfer coenzyme – acetaldehyde – TPP
O
HN
C
S
ATP
O
ADP
HOOC
NH
CH2
CH2
biotin
(H-vitamin)
CH2
CH2
N
C
CO 2
COOH
S
NH
CH2
CH2
CH2
CH2
COOH
karboxi-biotin
A biotin keletkezése és formái
P
H3C
H3C
N
piridoxin
(B6-vitamin)
H3C
N
N
piridoxamin-foszfát
(PAM)
piridoxál-foszfát
(PAL)
22
Az aminocsoportot szállító koenzim és prekurzor vitaminja
NH2
N
P O P
O CH2
CH3
H
CH–OH
O
C=O
NH
P
CH2
P O P
O
H
H
C CH3
H
OH
CH3
O
H
C CH3
CH–OH
C=O
NH
C=O
NH
C=O
NH
OH
CH3
C CH3
CH–OH
C=O
NH
CH2
CH2
S–C–CH3
CH2
O
CH3–CO–SKoA
acetil koenzim A
"aktív ecetsav"
COOH
pantoténsav
(régen B9-vitamin)
SH
Koenzim-A
(újabban B5 vitamin)
A koenzim-A különbözô formái
Transfer coenzyme – acetyl group – coenzyme A
COOH
COOH
S
HS
S
liponsav
H
CH2OH
CH2
ciszteamin
H
H
2,4-dihidroxiO
3,3-dimetilvajsav
P
CH2
-alanin
CH2
CH2
O CH2
CH2
CH2
CH2
N
N
O
CH2
N
N
N
N
O
NH2
N
SH
dihidro-liponsav
COOH
HS
S C CH3
O
acetil-dihidro-liponsav
A liponsav koenzim különbözô formái
Transfer coenzyme – acetyl group – lipoic acid
23
CH2OH
HO
H3C
piridoxin
(B6-vitamin)
CH2O– P
HO
H3C
N
CH2NH2
CHO
CH2OH
N
piridoxál-foszfát
(PAL)
CH2O– P
HO
H3C
N
piridoxamin-foszfát
(PAM)
Az aminocsoportot szállító koenzim és prekurzor vitaminja
Transfer coenzyme – amino group – PAL
Lipids
There are two types of lipid (apolar – fatty soluble) biomolecules. Simple
lipids cannot be hydrolyzed by sodium hydroxide and complex lipids can be
hydrolyzed by sodium hydroxide.
The two main types of simple lipids are the fatty acids and the terpenes. Fatty
acids (C16 and C18) are building blocks of complex lipids (neutral triglycerides and
phospholipids). Saturated fatty acids are palmitate (CH3(CH2)14–COOH) and stearate
(CH3(CH2)16–COOH). Unsaturated fatty acids are the unsaturated versions of stearate
(C18): oleate, linoleate and linolenate. The essential linoleate (-6-fatty acid) and
linolenate (-3-fatty acid) are known as PUFA (polyunsaturated fatty acids) or
vitamins F.
Formulas of oleate, linoleate and linolenate
Terpenes can be derived from isoprene (methylbutadiene)
CH2=C(CH3)–CH=CH2 (C5H8). Monoterpenes contain two (C5H8)2 (C10), diterpenes
four (C5H8)4 (C20), triterpenes six (C5H8)6 (C30) and tetraterpenes eight isoprene units
(C5H8)8 (C40). The branched end of isoprene is called the head (fej in Hungarian) and
the other part is called the tail (láb in Hungarian). There are different variations for
connecting the isoprene units. Most frequent are head-to-tail connections, while and
tail-to-tail and head-to-head variations are rare.
24
H2C
C CH CH2
CH3
izoprén
fej
fej-fej
láb
láb-láb
fej-láb
Az izoprén egységek kapcsolódási fajtái
Different variations of connecting isoprene units: head-to-head, head-to-tail and
tail-to-tail
Only two representatives of polyisoprenoids are shown here: chloresterol as
triterpene (C30) and -carotene as tetraterpene (C40). Triterpenes and tetraterpenes
generally contain
two chains with head-to-tail connection and these chains are
CH3
CH3
CH3of the molecule. The chain of the
connected in a tail-to-tail combination
in the middle
O
triterpene squalene is cyclized to cholesterol. The ring system of cholesterol is called
the sterane skeleton (withoutCHmethyl
3 CH3 groups gonane skeleton). Cholesterol can be the
H
starting material for different kinds of steroids – among
them sexual hormones.
CH2
CH3
OH
Vitamin D formed from cholesterol
by
uv
light
plays
an
important
role in calcification
mentol
kámfor
limonén
of cartilage and bone.
Néhány monterpén képlete
CH3
CH3
CH3
C
A
D
CH3
B
A
C
CH3
CH3
CH3
D
B
HO
gonánváz
szteránváz
koleszterol
cikloalkánok
A gonánváz, a szteránváz és a koleszterol képlete
Formulas ofCH
gonane
and sterane
skeletons, and of cholesterol
CH3
3
CH
3
CH3
CH3
CH3
Tetraterpene carotenoides areCHorganic
pigments that are naturally occurring
CH3 in
h
3
CH3 C
D
the chloroplasts and
chromoplasts of plants. There areCH
two
classes
of
carotenoides:
2
carotenes Aare hydrocarbons
and
xanthophylls
contain
oxygen. Because of
B
polyconjugated
double h
bond system, carotenoids
can absorb light energy for use in
HO
HO
photosynthesis, and as antioxidants they protect
chlorophyll
from photodamage.
D3-vitamin
(kolekalciferol)
Antioxidants can eliminate free radicals by reduction. In humans -carotene and other
carotenoids can be converted to retinol (vitamin A) by an oxidative
CH3splitting. Retinal
CH
CH
CH
CH
3
3
3
synthesized3 from retinol
is essential for vision.
-jonon
CH3
CH3
CH3
CH3
ox.
-karotin
CH3
CH3
CH3
CH2OH
CH3
CH3
CH3
-jonon
CH3
CH3
CH3
CH3 CH3
25
The conjugated double bond system of -carotene
Complex lipids have generally ester group(s) (sometimes carboxamides)
therefore they can be attacked by nucleophilic reagents e.g. sodium hydroxide. There
are four categories of complex lipids: fruit esters, waxes, neutral triglycerides (fats and
oils) and phospholipids (membrane lipids that can form the lipid bilayers of cell
membranes).
Fruit esters (synthesized from short-chained carboxylic acids and
short-chained alcohols) are flavour components of fruits, e.g. aroma of pineapple is
methyl butyrate (CH3CH2CH2–COOCH3). Waxes (synthesized from long-chain
carboxylic acids and long-chain alcohols) are not only water-repellent materials on the
surface of leaves and fruits but bees use beeswax (H3C(CH2)14–COO(CH2)29CH3
myricyl palmitate) to form the walls and caps of the comb.
Neutral triglycerides (triacylglycerols)are triesters of glycerol with fatty acids
(C16-C18)- They serve as are highly concentrated energy stores in fat cells (adipose
cells), as water-repellent materials (e.g. on the skin) and as heat-insulators in humans
and animals. Fats are solid and their fatty acid parts are palminate, stearate and oleate.
Oils are liquids and their major fatty acid part is linoleate. Surfactant (detergent) soaps
(sodium salts of fatty acids) can be produced by the hydrolysis of fats with sodium
hydroxide.
RCOOCH2
RCOOCH + 3 NaOH
3 R C
CH2 O H
O
+ CH O H
O Na
szappan
RCOOCH2
CH2 O H
glicerol
A szappanfôzés összfolyamata
Hydrolysis of triglycerides by sodium hydroxide
Surfactant molecules (o) contain both polar (o) and apolar () parts that are
suitable for selective adsorption. In this way the apolar surface of the fat (zsír in
Hungarian) can be changed to quasi-polar and fats can produce an emulsion in water.
O
O
CH3 (CH2)14–C
O
nátrium-palmitát
O
O
Na
zsír
O
poláros
apoláros
O
O
O
O
A mosóhatás
O
O
poláros
felület
26
P
Selective adsorption of surfactants to fat
P
P
P
There are different types of phospholipids and type of phosphoglycerides
P is
P
P
their major class. Phosphoglycerols can be derived from phosphatidate (phosphatidic
acid) that is a phosphate ester of diacylglycerols producing phosphatidyl
P
ethanolamines, phosphatidyl serines, and phosphatidyl cholines. The acyl groups are
from fatty acids (C16-C18). Phosphoglycerides are surfactants and lecitines are the
major component of animal cell membranes (in plants the major membrane lipid
components are glycolipids).
RCOOCH2
RCOOCH2
RCOOCH
RCOOCH
CH2 O
CH2–O– P
foszfatidsavak
NH2
O–CH2–CH
szerin-kefalinok COOH
P
RCOOCH2
RCOOCH
CH2 O
RCOOCH2
RCOOCH
CH2 O
apoláros rész
P
O–CH2CH2 NH2
kolamin-kefalinok
P
O –CH2CH2 N(CH3)3
poláros rész
lecitinek
A foszfolipidek származtatása a foszfatidsavból
Formation of different kinds of phosphoglycerols: phosphatidyl ethanolamines
(szerin-kefalinok in Hungarian), phosphatidyl serines (szerin-kefaninok in Hungarian)
and phosphatidyl cholines (lecithines) (lecitinek in Hungarian) from phosphatidate
There many biomolecules containing phosphate in ester (e.g. phosphatidate
acid) or anhydride (e.g. ATP) form, therefore their abbreviations are used.
Abbreviations of phosphates in esters and anhydrides
Membrane transport processes
A membrane is a layer of material which serves as a selective barrier between
its two sides, and remains impermeable to specific particles, molecules, or substances.
The structure of membranes can be illustrated by the fluid mosaic model. Through the
bimolecular layer surfactant phospholipids membrane-integrated (transmembrane)
27
proteins can make passage possible for specific molecules. Surface proteins can bind
different regular molecules as receptors.
áthatoló fehérje
felületi fehérje
irányított, bimolekuláris
foszfolipid réteg
A membránok felépítése
Fluid mosaic model of the structure of membranes – place of a transmembrane
(membrane-integrated) protein (áthatoló fehérje in Hungarian) and a surface protein
(felületi fehérje in Hungarian)
The scheme of an Eukaryotic cell (from book of Ádám and Fehér)
Some compounds are allowed to pass through the membrane, whereas others
are retained. The driving force for the passage is a difference in the concentrations of
28
the molecule on the two sides of the membrane and the molecules pass from the
higher to lower concentration without the investment of energy (called passive
diffusion). The transfer can be carried out in a simple way for small molecules (e.g.
water) or by a facilitated diffusion by special transfer molecules.
There are different kinds of passive diffusion with the aid of transmembrane
proteins. In symport transport there are two molecules bound to the same part of
membrane and the concentration gradient from higher to lower concentration is valid
for the sum of the concentrations of both molecules. In antiport transport there are two
molecules bound to the opposite sides of membrane and the concentration gradient
from higher to lower concentration has to be valid for both of them. In this way the
position of two molecules is exchanged during the passive diffusion. The name of this
kind of proteins is translocases.
Passage from a lower to a higher concentration needs a change in the
conformation of the integrated protein by energy investment (by the hydrolysis of a
macroerg bond). The process is similar to the antiport because generally the position
of two molecules is exchanged.
Nucleic acids
Nucleic acids are biopolymers consisting of nucleotide units connected by
3’,5’-phosphodiester bonds. A nucleotide unit contains a nucleic acid base either
containing a pyrimidine ring (thymine (T) and cytosine (C) for DNA or uracil (U) and
cytosine (C) for RNA) and or a purine skeleton (adenine (A) and guanine (G) for both
DNA and RNA). The connection of sugars i.e. D-2’-deoxyribose for DNA and Dribose for RNA to nucleic bases is shown by an arrow (). This point is 3-N for
pyrimidine and 9-N for purine bases. Nucleic acids are N-glycosides. The numbering
of sugar is distinguished from that of the base with comma. The phosphate is
connected to the 5’-hydroxyl group of sugars forming ester group.
1
6
HN
O
N
H
timin
(DNS)
H
uracil
(RNS)
O
NH2
7
5
N
6
1
N
N
N
H
citozin
3
4
N
9
H2N
) feltüntetésével
5'
5'
HOCH2
O
4'
H
3'
1'
OH
H
2'
H
OH OH
- D-ribofuranozid
HOCH2
4'
H
O
H
3'
1'
OH
2'
H
H
OH H
- D-2'-dezoxiribofuranozid
A nukleinsavak építô elemei
The structure of nucleoside units
N
guanin
purin bázisok
a kapcsolódási hely (
H
N
H
N
HN
adenin
pirimidin bázisok
pentózok
O
8
2
4
3N
CH3
HN
5
2
O
NH2
O
O
N
H
29
The unit consisting only of a nucleic base and sugar is called nucleoside. The
name for a nucleoside monophosphate is nucleotide. The name of nucleosides are
uridine, thymidine, cytidine, adenosine, guanosine. Nucleotides of DNA are
distinguished from RNA by the abbreviation of ‘deoxy’: UMP, dTMP, CMP, dCMP,
AMP, dAMP, GMP, dGMP.
ROCH2
O
N
ROCH2
O
H
CH3
HN
HN
O
H
H
H
OH
O
ROCH2
H
N
O
H
H
OH H
R = H dezoxitimidin (dT)
R = H uridin (U)
R = P uridin monofoszfát R = P dezoxitimidin-monofoszfát (dTMP)
(UMP)
OH
N
N
O
H
H
NH2
O
O
H
H
OH
H
Q
R = H, Q = H dezoxicitidin (dC)
R = P O P , Q = OH
citidin-difoszfát (CDP)
Néhány pirimidinvázas nukleozid, nukleotid, nukleozid-difoszfát
és nukleozid-trifoszfát képlete
The formulas of some nucleosides, nucleotides, nucleoside diphosphates and
nucleoside triphosphates containing a pyrimidine ring
The formulas of some nucleosides, nucleotides, nucleoside diphosphates and
nucleoside triphosphates containing a purine skeleton
The nucleotide units are connected by 3’, 5’-phosphodiester bonds. In each
unit there is one acidic hydrogen atom at the phosphate part therefore the biopolymer
30
itself is called nucleic acid. The 5’ terminal of the polymer chain (strand) contains a
phosphate ester and its 3’ terminal contains a hydroxyl group.
The 3’,5’-phosphodiester bond in the polynucleotide chain (R=H DNA, R=OH RNA)
P O CH2
O
5'-láncvég
H
H
H
3'
O
B bázis
Bázis
H
P 5'
OH
3'
cukor egység
(ribóz, dezoxiribóz)
A nukleozid egység sematikus ábrázolása
P
5'
O CH2
H
H
A
Bázis
O
H
H
O
OH
3'-láncvég
A nukleinsavak elsôdleges szerkezete
(a P a megfelelô foszforsav egységet
jelenti)
5'-láncvég
P 5'
G
3'
P 5'
3' 3'-láncvég
A nukleinsav szekvencia sematikus
ábrázolása
5'-láncvég AGC ......... 3'-láncvég
A nukleinsav szekvenciájának legegyszerûbb
ábrázolása
A polinukleotid lánc ábrázolási lehetôségei
Various modes to represent the polynucleotide chain
In DNA two of antiparallel polynucleotide strands form a double helical
structure described by the Watson - Crick Model. On the surface of helix is the chain
containing the sugar and phosphate. Inside the helix two nucleic bases (a pyridine and
a purine base) form a pair connected by hydrogen bonds (two for T-A and three for CG) and the character of one base determines the another base, therefore they are called
complementary base pairs.
31
O
H3C
H
N
N
R
N
N
N
O
N
R
T
O
NH2
H2N
R
A
N
H N
N
N
N
N
O
C
R
H2N
G
A komplementer bázispárok
Complementary pairs of bases.)
In most of the cases RNA contains only one strand, but it can form a double
helix with a DNA during its biosynthesis. There can be a double helical section in an
RNA chain when it contains an antiparallel complementary sequence – this folded
form is called palindromic structure (e.g. in tRNA). There can be double palindromic
structures in DNA, as well. Nucleic acids are in the nucleus of the cell, therefore the
double helix needs to assume various more compact forms. The double helix of DNA
is wrapped around clusters of histones (small proteins with a basic character) by lefthanded superhelical turns to form nucleosomes, which are coiled to form solenoids
that are further compact formations for DNA. Solenoids are able to become
increasingly even more packed formations – these are chromosomes.
Scheme of the Watson-Crick Model of DNA
The biological function of DNA is to preserve genetic information for the
biosynthesis of proteins. Different types of RNA include tRNA (transfer), mRNA
(messenger), rRNA (ribosomal) and snRNA (small nuclear) provide the conditions for
the biosynthesis of proteins (translation). Details are given in the section of the
metabolism of the biomolecules of the genetic information.
 mRNA transports information from DNA about a protein sequence to the
ribosome (the site of protein synthesis in the cell);
 tRNA transports amino acids to the ribosome connected to its 3’ terminal as
esters;
32


rRNA is the catalytic component of the ribosome containing not only RNA but
several proteins;
snRNA makes ripening of different types of RNA by splicing.
Macroerg bonds
The phosphoric acid anhydride (pyrophosphate) derivatives of nucleotides are
the nucleoside diphosphates (NDP) and nucleoside triphosphates (NTP). Their
anhydride bonds (one in NDP and two in NTP) are called macroerg bonds (they have
a high phosphoryl-transfer potential) because their synthesis requires energy while
their hydrolysis generates an energy of about 30,6 kJ/mol. The most important NTP is
adenosine triphosphate. There are different types of macroerg bonds. They are formed
from an acid and a compound with acidic character. Anhydrates can be synthesized
from two molecules of phosphates (phosphoric acid anhydrides e.g. ATP) or from a
carboxylate and a phosphate (mixed anhydrides e.g. glycerate 1,3-bisphosphate).
There are other compounds with acidic character that can form esters with an acid. An
ester from phosphate and an enol (e.g. phosphoenolpyruvate – PEP) or a thiolester
from a carboxylate and a thiol (e.g. acetyl coenzyme A – acetyl-CoA)
(H3C–COSCoA) contain also macroerg bonds.
NH2
N
N
P
O
P
O
N
N
O
P O CH2
H
H
H
H
OH OH
adenozin-trifoszfát (ATP)
Az ATP képlete
Adenosine triphosphate (ATP)
33
O
a) savanhidridek – foszforsavanhidrid (pl. ATP)
O P O P O
H O
O
vegyes savanhidrid
O
pl.
P
O
P
O
O H
P
O C O
O
C O P O
O
H C O H
CH2 O
O H
P
glicerinsav 1,3-difoszfát
b) különleges észterek – enolészter pl. PEP (foszfo-enol-piruvát)
COOH
CH O
– tiolészter pl. acetil-koenzim-A
CH3
P
CH2
O
C
S KoA
A makroerg kötések
Compounds containing macroerg bonds: phosphoric acid anhydride, mixed
anhydrides e.g. glycerate 1,3-bisphosphate, enolester e.g. phosphoenolpyruvate,
thiolester e.g. acetyl coenzyme A
Metabolism
The whole range of organic reactions of biomolecules in the living organisms
are called metabolism.
Primary metabolism – the metabolism of biomolecules.
Phases of primary metabolism:
Catabolism – oxidative degradation of biomolecules combined
with the generation of energy in form of macroerg bonds (e.g. ATP). The
intermediates of catabolism are the starting materials of anabolism. The terminal
products of the catabolism are CO2 and H2O.
Anabolism – reductive biosynthesis of biomolecules by means
of the energy produced during catabolism. In autotrophic plants glucose molecules are
synthesized from CO2 and H2O by the energy of the light. The other biomolecules are
synthesized from ammonia and the metabolites of glucose degradation. The starting
materials of anabolic reactions of heterotrophic living organisms (animals and human
beings) derive from the oxidative degradation of the nutritive materials (foods).
Secondary metabolism: the metabolism of different molecules of the living
organisms which are generally needed for their functioning. Secondary metabolites are
synthesized from the different intermediates of biomolecules. The most important
types of secondary metabolites are coenzymes, regulating (e.g. hormones), attracting
(e.g. the sweet sucrose, the fruit esters as scent agents etc.) and repelling agents (e.g.
alkaloids and toxins).
The processes of basic biochemistry take place inside the cell: in the cytosol
(cytoplasm), mitochondria and ribosomes – and we are focused on human
biochemistry (except photosynthesis). Only the metabolism of nutritive materials is
34
discussed because the metabolism of nucleic acids is in nucleus of the cell and its role
is peripheral in the nutrition.
Scheme of the biosynthesis of biomolecules
Catabolism
The first phase of the degradation of nutrients (and nucleic acids) is the
hydrolysis of the combined functional groups of biopolymers in the cytosol. Then in
the second phase (at first in the cytosol then in the mitochondria) the oxidative
degradation of the intermediates (sugars – especially glucose, amino acids, fatty acids
and glycerol) leads to a synthesis of a common intermediate acetyl coenzyme A
(H3C-COSCoA with a macroerg thiolester) (the intermediates of some amino acids
are the members of citric acid cycle). In the third phase (in the mitochondria)
oxidative degradation of acetyl coenzyme A by oxygen to CO2 (citric acid cycle) and
H2O (with the form of macroerg bonds) (terminal oxidation – respiratory chain) takes
place.
35
Biomolecule
Polysaccharides
Enzyme
Glycosidases/
Phosphorylases
Proteases/Peptidases
Lipases
Intermediate
Sugars/
Sugar phosphates
Amino acids
Fatty acids and glycerol
Proteins
Neutral triglycerides
(triacylglycerols)
Nucleic acids
Nucleases
Nucleotides
The first phase of the degradation of biomolecules
In the hydrolytic phase of the degradation of biopolymers different types of
hydrolase enzymes take part. Exohydrolase enzymes start the hydrolysis at one end of
the biopolymers (e.g. with polysaccharose chains at the non-reducing end; in proteins
amino peptidase enzymes at N-terminal and carboxypeptidase enzymes at C-terminal).
Endohydrolase enzymes start hydrolysis in the middle of the biopolymers (in
polysaccharide chains in a random way, in proteins between special amino acid units:
pepsin – before aromatic amino acids; trypsin – after basic amino acids; chymotrypsin – after aromatic amino acids). Hydrolase enzymes often need an
activating step (phosphorylation or hydrolysis) before action.
Hydrolases of amylose (one of the two components of starch): -amylase is an
endohydrolase; -amylase an exohydrolase; that starts the hydrolysis of amylose at the
non-reducing end splitting off maltose molecules; maltase hydrolyzes maltose to two
glucose molecules. Cellulose is hydrolyzed by cellulase (only in certain
microorganisms) to cellobiose, that is hydrolyzed by -glucosidase to glucose. Lactose
is hydrolyzed by lactase (-galactosidase) to glucose and galactose, sucrose is
hydrolyzed by invertase to glucose and fructose.
The addition of a phosphate group from an inorganic phosphate (phosphoric
acid) to a substrate can be catalyzed by phosphorylases. The name ‘phosphorylase’ is
generally used for glycogen phosphorylase that catalyzes the release of glucose-1phosphate from the reducing end of glycogen molecule with an inorganic phosphate
(Pi). Glucose-1-phosphate is converted to glucose-6-phosphate to enter glycolysis. The
details of this reaction are given in the section of biosynthesis of polysaccharides.
The degradation of carbohydrates to acetyl coenzyme A
After the hydrolysis of carbohydrates the product is mostly glucose. Other
sugars (except fructose) can be formed directly or in NDP-sugar phase to glucose (e.g.
galactose). The first phase of the degradation of glucose is glycolysis from glucose (C6
stage) to pyruvate (pyruvic acid) (C3 stage) in the cytosol. Pyruvate is a common
starting material for the two kinds of anaerobic degradations (alcoholic and lactic acid
fermentations) of glucose in the cytosol and its aerobic degradation (at first to acetyl
coenzyme A then to carbon dioxide and water) in the mitochondria. Different
biochemical processes are characterized not only by their participants but also by their
stoichiometry. Stoichiometry (stoichiometry of reactions) is the quantitative
relationships of the reactants and products in a balanced chemical reaction.
Glycolysis
The steps of glycolysis are reversible – except three of them. The first and the
third reactions are catalyzed by kinases (hexokinase and phosphofructokinase – PFK).
A kinase (transferase) can phosphorylate a molecule coupled with the hydrolysis of a
36
macroerg phosphoric acid anhydride bond of a NTP (mostly ATP) but the product has
not a macroerg bond (in the case of sugars the product is a phosphate ester of a sugar),
therefore this kind of reaction is irreversible. The details of the third irreversible step
of glycolysis will be given later.
The phosphorylation of glucose to glucose 6-phosphate by hexokinase is often
called the ‘activation of glucose’. It is not a real activation step, because – as it was
mentioned earlier – this ester does not contain a macroerg bond. But the phosphoric
acid unit of sugars can help the formation of a connection between sugars and
enzymes by ionic interactions. The isomerization of glucose 6-phosphate to fructose
6-phosphate catalyzed by an isomerase is a double oxo-enol-oxo tautomerism that was
presented earlier.
The last step of C6 stage of glycolysis is the synthesis of fructose 1,6bisphosphate from fructose 6-phosphate catalyzed by PFK. PFK is the key enzyme in
the control of glycolysis because its activity can be inhibited by ATP that is the end
product of oxidative phosphorylation part of the respiratory chain. In the case of high
ATP concentration glycolysis is stopped but at low ATP concentration glycolysis is
started. This control system is called feedback and its mechanism is called allosteric
mechanism. There are also other regulating agents of PFK.
In the second stage (C3) of glycolysis the cleavage of fructose 1,6-bisphosphate
catalyzed by aldolase results in a mixture of glyceraldehyde 3-phosphate and
dihydroxyacetone phosphate (DHAP). Glyceraldehyde 3-phosphate is on the direct
pathway of glycolysis. The conversion of DHAP to glyceraldehyde 3-phosphate is
catalyzed by an isomerase. It is noticed that at equilibrium 96% of triose phosphate is
DHAP.
37
Glycolysis and the possibilities for the further degradation of pyruvate
The oxidative step of the glycolysis is the formation of 1,3bisphosphoglycerate (its earlier name is 1,3-diphosphoglycerate) containing a
macroerg mixed anhydride bond from glyceraldehyde 3-phosphate catalyzed by
glyceraldehyde 3-phosphate dehydrogenase with a covalent catalysis. The coenzyme is
NAD that is reduced to (NADH+H). This step is one of the two energy producing
steps of glycolysis. In the course the synthesis of the macroerg mixed anhydride bond
during the oxidation at first a macroerg thiolester intermediate is formed in the
enzyme-substrate complex (ES) that is attacked by an inorganic phosphate.
The stoichiometry of glycolysis
The energy of 1,3-bisphosphoglycerate is converted to the synthesis of an ATP
molecule from ADP and an inorganic phosphate (Pi) accompanied by the formation of
38
3-phosphoglycerate. The rearrangement of 3-phosphoglycerate to 2-phosphoglycerate
is in fact a combination of two transfer reactions by means of a cofactor 2,3bisphosphoglycerate, and catalyzed by a mutase that is a transferase.
During the elimination of a water molecule from 2-phosphoglycerate to
phosphoenolpyruvate (PEP) a macroerg thiolester bond is formed (the catalyst is
enolase). The energy of this thiolester bond is converted to the energy of a phosphoric
acid anhydride (ADP+PiATP), and enolpyruvate is transformed immediately to
pyruvate by an irreversible oxo-enol tautomerism (the catalyst is pyruvate kinase).
This reaction is the third irreversible step of glycolysis because direct conversion of
pyruvate to enolpyruvate is impossible it can be carried out only in a roundabout way
(see gluconeogenesis).
The entrance of fructose to the glycolysis
Fructose can enter the glycolysis in an alternative way called fructose 1phosphate pathway because the affinity of hexokinase is about twenty times lower
than that of glucose, and the glucose concentration is generally higher in cells than
that of fructose. The phosphorylation of fructose by ATP to fructose 1-phosphate is
catalyzed by fructosekinase and the elimination of fructose 1-phosphate to DHAP and
glyceraldehyde is catalyzed by fructose 1-phosphate aldolase. DHAP is the
intermediate of the glycolysis but glyceraldehyde can enter the glycolysis only after a
phosphorylation glyceraldehyde 1-phosphate by ATP catalyzed by triose kinase. It is
noticed that there are some tissues (e.g. adipose tissue) in which hexokinase can
phosphorylate fructose to fructose 6-phosphate because of the high fructose
concentration in them.
The possibilities for the further degradation of pyruvate
According to the stoichiometry of glycolysis during the degradation of one
molecule of glucose to two molecules of pyruvate one molecule reduced coenzyme
(NADH+H) and two molecules of ATP (exactly two macroerg bonds) are formed. In
39
a fermentation process only the reduced coenzyme is used for the reduction of
pyruvate (to ethanol and CO2 in alcoholic fermentation and to L-lactate in lactic acid
fermentation). That means that the benefit of the combination of glycolysis and
fermentation (that is the anaerobic degradation of glucose) is only 2ATP/glucose.
The stoichiometry of the lactic acid and alcoholic fermentations of glucose
Ethanol is formed from pyruvate in yeast and several other microorganisms in
two steps. The decarboxylation of pyruvate to acetaldehyde is catalyzed by pyruvate
decarboxylase then the reduction of acetaldehyde by (NADH+H) formed in
glycolysis to ethanol is catalyzed by alcohol dehydrogenase.
L-Lactate from pyruvate can be formed by the reduction of (NADH+H) not
only in certain microorganisms but in the muscle of animals and human beings. It is a
fast but ‘non-economic’ method for releasing of energy during the degradation of
glucose.
There is another possibility for the further degradation of pyruvate. This takes
place in mitochondria and the result of this complex process using oxygen (6
O2/glucose) is 36-38ATP/glucose. This process is called the aerobic degradation of
glucose. After the irreversible penetration of pyruvate to the mitochondria the first
step of this complex process is the formation of acetyl coenzyme A from pyruvate
catalyzed by pyruvate dehydrogenase complex.
The structure of mitochondria
Mitochondria have an outer membrane (in Hungarian külső membrán) and a
highly folded inner membrane (in Hungarian belső membrán) with a large surface.
The intermembrane space is between the folds of the membranes. The inside of the
mitochondria is the matrix that is bound by the inner membrane. The outer membrane
is permeable to small molecules and ions. In contrast penetration through the inner
membrane is only possible by membrane transport processes of transmembrane
proteins. The site of the dehydrogenation of pyruvate, the citric acid cycle and the
fatty acid oxidation occurs in the matrix. The site of terminal oxidation (respiratory
chain) is in the inner membrane.
Membranes of mitochondria
40
The oxidative decarboxylation of pyruvate to acetyl coenzyme A catalyzed by pyruvate
dehydrogenase multienzyme complex
The oxidative decarboxylation of pyruvate to acetyl coenzyme A with a
macroerg thiolester bond is catalyzed by the pyruvate dehydrogenase multienzyme
complex. Coenzyme is NAD.
The reaction catalyzed by pyruvate dehydrogenase
There are different steps, three enzyme subunits (pyruvate dehydrogenase,
dihydrolipoyl transacetylase, dihydrolipoyl dehydrogenase), three coenzymes (TPP,
coenzyme A, NAD) and two prosthetic groups (lipoic acid, FAD) participating in the
oxidative decarboxylation of pyruvate. The first step is the decarboxylation of
pyruvate combined with the synthesis of active acetaldehyde. Active acetaldehyde is
derivative of coenzyme TPP that seems to be a secondary alcohol but really it can
react as a carbonyl compound (it can be oxidized to acyl group), because the carbon
atom between N+ and S is a reactive carbon atom with acidic (dissociable) proton.
Active acetaldehyde is oxidized by lipoic acid to an acetyl group that is immediately
connected to one of the thiol groups of the reduced lipoic acid (acetyl dihydrolipoic
acid with a macroerg thiolester bond). The acetyl group is transferred to a coenzyme A
and lipoic acid is regenerated from dihydrolipoic acid by a cascade reductive system
containing FAD as prosthetic group and the coenzyme NAD producing
(NADH+H). The product acetyl coenzyme A with a macroerg thiolester bond is the
starting material of the citric acid cycle.
41
The stoichiometry of the reaction catalyzed by pyruvate dehydrogenase
The degradation of lipids to acetyl coenzyme A
Degradation in the cytosol
After the hydrolysis of complex lipids by lipases the ways of the oxidative
degradation of fatty acids and glycerol are different. The oxidative degradation of
alcohols is related to the degradation of carboxylic acids
Glycerol 3-phosphate (its earlier name is -glycerol phosphate) is formed by
the phosphorylation of glycerol with ATP catalyzed by a kinase. Glycerol 3-phosphate
can be oxidized by NAD and the product is DHAP which is an intermediate of
glycolysis.
The decomposition of triglycerides and glycerol
Fatty acids are activated before oxidative degradation by transformation to acyl
coenzyme A with the aid of a macroerg thiolester bond. The first step is the reaction
of the fatty acid and ATP to acyl-AMP that contains a macroerg mixed acid anhydride
bond. The reaction needs the energy of another macroerg phosphoric acid anhydride
provided by the hydrolysis of the by-product pyrophosphate to two molecules of
phosphoric acid. Acyl coenzyme A is formed from the reaction of acyl-AMP and
coenzyme A.
42
The activation of fatty acids to acyl coenzyme A
Acyl coenzyme A enters the matrix of mitochondria in form of acyl carnitine
formed in a reaction catalyzed by carnitine acyltransferase I at the cytoplasmic side of
the inner membrane then it takes part in an antiport membrane transport process
against L-carnitine that transfers the acyl group to coenzyme A in a reaction catalyzed
by carnitine acyltransferase II at the matrix side of the inner membrane
The membrane transport of fatty acids from cytosol to the matrix of mitochondria
-Oxidation of fatty acids to acetyl coenzyme A molecules
Degradation in the mitochondrial matrix – -oxidation
The oxidative degradation of the saturated acyl CoA named -oxidation
contains a recurring sequence of four reactions and the first three of these reactions
closely resembles the last reactions (from succinate to oxaloacetate) of the citric acid
cycle. The coenzyme (prosthetic group) of the oxidation of acyl CoA to enoyl CoA
containing a trans double bond between C-2 and C-3 is FAD. The coenzyme of the
second oxidation step after the hydration of enoyl CoA to L-3-hydroxyacyl CoA is
43
NAD and the product is 3-ketoacyl CoA (its earlier name is -ketoacyl CoA; that is
the origin of the name of the degradation). The last step of the -oxidation is the
cleavage 3-ketoacyl CoA by the thiol group of a molecule of coenzyme A resulting in
a molecule of acetyl-CoA and an acyl CoA shortened by two carbon atoms. The
reaction is called thiolysis and is catalyzed by -ketothiolase (or simply thiolase). At
the end of -oxidation each carbon atom of the original fatty acids is transformed to
acetyl coenzyme A.
At the end product of the -oxidation of fatty acids having an odd number of
carbon atoms (these are minor species) is, instead of acetyl-CoA, one molecule of
propionyl CoA. This is converted to succinyl CoA (an intermediate of citric acid
cycle) in two steps (a carboxylation followed by an intramolecular rearrangement).
Unsaturated fatty acids contain cis double bonds. In the case of one double
bond (oleate) an isomerization of cis double bond to a trans double bond is catalyzed
by an isomerase. When there is another double bond in the fatty acid (linoleate and
linolenate) the result of the hydration step is a D-hydroxyl derivative that is converted
to L- hydroxyl derivative by an epimerase.
The oxidative degradation of terpenes to acetyl-CoA is carried out by similar
processes as described for -oxidation.
Degradation of L-amino acids to acetyl coenzyme A or intermediates of citric acid
cycle
After the hydrolysis of proteins by different kinds of peptidases and proteases
there are four levels of the degradation of amino acids. Three of them (transamination,
oxidative deamination of glutamate, urea cycle) are connected with the removing of
the -amino groups (the details are given later) and produce -keto carboxylic acids
while the fourth level is the oxidative degradation of -keto carboxylic acids to
pyruvate (Ala, Thr, Gly, Ser, Cys, Trp), acetyl-CoA (Trp, Leu, Ile), acetoacetyl-CoA
(Phe, Tyr, Trp, Leu, Lys), -ketoglutarate (Glu, Gln, His, Arg, Pro), succinyl CoA
(Met, Val, Ile), fumarate (Tyr, Phe, Asp) and oxaloacetate (Asp, Asn). There are also
other direct degradation modes (oxidative deamination or elimination of an ammonia
or water molecule).
Transamination
In transamination reactions (catalyzed by aminotransferases) the amino group
of amino acids is transported to -ketoglutarate (that is an intermediate of citric acid
cycle) – the products are -keto carboxylic acids (from the amino acid) and glutamate
(from -ketoglutarate) by means of the coenzyme pyridoxal phosphate (PAL) that is
in fact a prosthetic group. The first step of this process is the formation of aldimines
(Schiff bases). Then by the rearrangement of aldimines ketimines are synthesized by
an aldimine-ketimine tautomerism. -Keto carboxylic acids and pyridoxamine
phosphate (PAM) are produced by the hydrolysis of ketimines. The regeneration of
PAM to PAL is carried out by a transformation of -ketoglutarate to glutamate. In this
way the amino groups from all of the amino acids are transferred to glutamate
molecules.
Aldimines are the starting materials of biogenic amines by decarboxylation
followed by hydrolysis. Aldimines from some amino acids (e.g. serine) transfer their
side chain to a tetrahydrofolate (THF) coenzyme producing glycine from the amino
acids.
44
Transamination and oxidative deamination of glutarate
Other reactions from aldimines derived from amino acids
Oxidative deamination of glutarate
Glutarate molecules produced from amino acids are oxidized to an imino acid
derivative which is hydrolyzed to -ketoglutarate and ammonia. The reaction is
catalyzed by glutamate dehydrogenase accompanied by NAD  (NADH+H)
conversion. In plants the reverse process (reductive amination) of this reaction gives a
possibility for the assimilation of ammonia using (NADPH+H).
The urea cycle
A part of ammonia (as NH4+) is used for the biosynthesis of nitrogen
derivatives. Since ammonia is a toxic for animals and human beings therefore surplus
45
ammonia is converted to urea (in Hungarian karbamid) in the urea cycle (another
name is ornithine cycle) connected to the biosynthesis of arginine (Arg).
The urea cycle and its connection with the citric acid cycle
The stoichiometry of the urea cycle
From five reactions of the urea cycle two are mitochondrial and three
cytoplasmic. In the mitochondria CO2, NH3 and 2ATP produce carbamoyl phosphate,
2ADP and Pi. Then carbamoyl phosphate reacts with ornithine and produces citrulline
and Pi. The cycle is continued in the cytosol. The second amino group of urea is
derived from aspartate that reacts with citrullin by means of converting an ATP to
AMP and PPi and the product is argininosuccinate. From argininosuccinate arginine
and fumarate are formed in an elimination reaction. Aspartate can be recovered from
fumarate in citric acid cycle (fumarate  malate  oxaloacetate followed by a
transamination to aspartate). Arginine can be hydrolyzed to ornithine (being the final
step of the cycle) and urea (in two steps with isourea as intermediate). According to
the stoichiometry of the urea cycle the synthesis of an urea molecule needs the energy
of three macroerg bonds.
Degradation of the common intermediate (acetyl coenzyme A) to CO2 and H2O
46
During the further degradation of acetyl coenzyme A the formation of carbon
dioxide and water molecules takes place in separate reactions. These biochemical
processes are localized in mitochondria. In the citric acid cycle two molecules of
carbon dioxide and a CoA molecule are formed from one acetyl-CoA molecule,
meanwhile four reduced coenzymes: 3 (NADH+H), FADH2 and one macroerg bond
(GDPGTP) are produced in the mitochondrial matrix. In the respiratory chain
(terminal oxidation) in the inner membrane of mitochondria the reduced coenzymes
reduce an oxygen molecule to water by electron transport and at the same time the
energy of nutrients are built into macroerg bonds of ATP (ADP + Pi ATP). Finally
all of the carbon atoms of the nutrients are oxidized to CO2, at the same time the
hydrogen (formed during the regeneration of coenzymes) and oxygen atoms of
nutrients produce water molecules.
The stoichiometry of the citric acid cycle
Citric acid cycle
The other names of this cycle are: tricarboxylic acid cycle (TCA cycle), Krebs
cycle, or sometimes Szentgyörgyi-Krebs cycle. Acetyl-CoA reacts with the staring
material (oxaloacetate) of the cycle in an addition reaction catalyzed by citrate
synthase followed by the hydrolysis of the intermediate (citryl CoA) to citrate and
CoA. In this reaction the nucleophilic attack of the acetyl group at the carbonyl group
of oxaloacetate is carried out by the methylen part of the enol tautomer that is
temporarily formed in the reaction under the influence of the strong hydrogen bond of
a His of the enzyme.
Nucleophilic attack of the enol tautomer of acetyl-CoA at the carbonyl group of
oxaloacetate
It was proved by a labeled compound that in the further reaction citric acid
reacts as an asymmetric molecule because of the asymmetric association with the
enzyme. That is the reason why the carbon dioxide molecules are derived from carbon
atoms of oxaloacetate and the regenerated oxaloacetate contains the carbon atoms of
acetyl-CoA. The problem is shown by the illustration of both forms of oxaloacetate in
the scheme of citric acid cycle.
The next step of the citric acid cycle is a rearrangement of citrate to
L-isocitrate that is carried out by a combination of a water elimination followed by
water addition. The enzyme is a lyase (aconitase after the name of the unsaturated
47
intermediate cis-aconitate). The products of the oxidation of isocitrate combined with
decarboxylation are -ketoglutarate, carbon dioxide and (NADH+H) in a reaction
catalyzed by isocitrate dehydrogenase. The second carbon dioxide molecule is
produced in the oxidative decarboxylation of -ketoglutarate to succinyl CoA with a
macroerg thiolester bond catalyzed by -ketoglutarate dehydrogenase multienzyme
complex. The structure of this enzyme is similar to that of pyruvate dehydrogenase
using three coenzymes (TPP, coenzyme A, NAD) and two prosthetic groups (lipoic
acid, FAD). The reduced coenzyme is again (NADH+H) and CoA comes from the
acetyl-CoA.
The citric acid cycle
Succinyl CoA is hydrolyzed by succinate CoA synthetase that is a ligase. The
energy of the macroerg bond is transmitted to a GDP+Pi  GTP conversion. The next
three steps of the cycle are similar to the first steps of -oxidation of fatty acids.
Succinate is oxidized to fumarate by succinate dehydrogenase accompanied by a FAD
 FADH2 conversion. In a hydration reaction catalyzed by fumarase fumarate is
converted to L-malate which is oxidized to oxaloacetate (the staring material of the
cycle) by malate dehydrogenase. The reaction is accompanied with a NAD 
(NADH+H) conversion.
The enzymes of the citric acid cycle are working as large enzyme complexes
attached to the inner membrane of mitochondria. The cycle is regulated by feedback.
The essential regulating effect is the ATP/ADP ratio but other intermediates play also
an important role. The citric acid cycle is in close cooperation with other biochemical
processes. Its intermediates participate as starting materials in many biochemical
48
reactions therefore it is often called ‘the pool of biointermediates’. Glycolysis can
work under both anaerobic and aerobic condition while the citric acid cycle can work
only in an aerobic mode, because the regeneration of the reduced coenzymes takes
place in the terminal oxidation which needs the presence of oxygen.
There are many bacteria and plants that can synthesize glucose from acetylCoA in a biosynthetic process called the glyoxylate cycle. As far as the synthesis of
isocitrate the steps of glyoxylate cycle are the same as those of the citric acid cycle.
The details are given later.
Terminal oxidation (Respiratory chain)
The name ‘terminal oxidation’ means that this metabolic pathway is the last
oxidation step in the catabolic pathway (in the oxidation of the carbon atoms of
biomolecules or other organic compounds). Now this name is preferred.
The name ‘respiratory chain’ means that this metabolic pathway can be
connected directly to respiration, the direct oxygen consumption of living organisms.
This name is preferred in medical biochemistry.
There are two partial processes in terminal oxidation. The electron transport
chain is a special chain to transfer electrons from a higher-energy molecule (the
donor) with lower standard oxidation-reduction potential (E’0) to a lower-energy
molecule (the acceptor) with higher standard oxidation-reduction potential in order to
regenerate reduced coenzymes. Oxidative phosphorylation is the metabolic pathway
that uses energy released by the oxidation of nutrients to produce macroerg bonds
(ADP+Pi  ATP). Instead of terminal oxidation the name ‘oxidative
phosphorylation’ is often used for the whole metabolic pathway.
The electron transport chain
The enzyme complexes of the terminal oxidation are in the inner membrane of
mitochondria. There are three large enzyme complexes (NADH-Q reductase,
cytochrome reductase and cytochrome oxidase) and two small ones (coenzyme Q and
cytochrome c). Coenzyme Q (ubiquinone) can move between the two walls of the
inner membrane, therefore it can receive hydrogen atoms from the intermembrane
space through the outer part of the inner membrane of mitochondria (e.g. glycerate 3phosphate redox shuttle). NADH-Q reductase contains as prosthetic group FMN. The
driving force of electron transport is the electron-transfer potential of reduced
coenzymes to oxygen. The direction of the electron transport is determined by the
standard oxidation-reduction potential values (E’0) of the participants. The direction is
from negative to positive values of the standard oxidation-reduction potentials. It
means that the direction is from participants with high-potential electrons to those
with low-potential electrons. The standard oxidation-reduction potentials are given in
V (volts). The standard oxidation-potential of H:H2 is defined to be 0 V. The
standard oxidation-reduction potentials of the coenzymes are: (NADH+H) (-0.32 V)
and (NADPH+H) (-0.32 V), FADH2 (-0.22). If necessary (NADPH+H) reduces
NAD to (NADH+H) catalyzed by NADPH dehydrogenase, in this way it can take
part in the electron transport.
(NADPH+H) + NAD  NADP + (NADH+H)
Reaction catalyzed by NADPH dehydrogenase
49
There are three of transitions of electron transport involved in the energy
producing oxidative phosphorylation and in these transitions there are large
differences between the standard oxidation-reduction potential of electrons of the
participants. These differences result in proton pumps (3×3 protons) connected with a
change of the conformation in the membrane proteins. The proton pumps transfer
protons not only from the inner membrane but from the matrix (via the dissociation of
water molecules) to the intermembrane space causing a significant difference in the
pH between the intermembrane space (acidic region) and the matrix (basic region).
This difference in pH starts the oxidative phosphorylation to produce a macroerg bond
by an ADP+Pi  ATP conversion (three ATP molecules in the case of NADH+H).
These transitions are: NADH-Q reductase – coenzyme Q, cytochrome reductase –
cytochrome c, cytochrome oxidase – oxygen molecule. As the standard oxidationreduction potential of FADH2 is more positive than that of NADH-Q reductase, it can
join later (at coenzyme Q) in the electron transport therefore it produces only two ATP
molecules by the electron transport. From (NADH+H) to coenzyme Q hydrogen
atoms (protons and electrons) take part together in the electron transport chain. From
coenzyme Q to oxygen molecules only electrons take part in the electron transport
chain; and the protons take part in the proton pump.
The direction of electron transport: - values in E’0  + values in E’0
NADH-Q reductase (-0.30 V), coenzyme Q (+0.04 V), cytochrome reductase
(cytochrome b + 0.07 V and cytochrome c1 +0.23 V), cytochrome c (+0.25 V),
cytochrome oxidase (cytochrome a +0.29 V and cytochrome aa3 +0.55 V), oxygen
(+0.82 V).
The terminal oxidation pathway and the participants of the electron transport with
their standard oxidation-reduction potentials (E’0)
To avoid forming free radicals four electrons and four protons are connected to
oxygen molecules almost simultaneously producing two molecules of water. There are
special enzymes to eliminate the toxic byproducts i.e. the superoxide anion by
superoxide dismutase and hydrogen peroxide by catalase.
Formation of the superoxide anion: O2 + e  O2 Ө
Formation of the peroxide anion: O2 + 2e  O22 Ө
Formation of hydrogen peroxide: 2 H + O22Ө  H2O2
Elimination of superoxide anion by superoxide dismutase: 2 O2Ө  O22Ө + O2
Elimination of hydrogen peroxide by catalase: 2 H2O2  2H2O + O2
Elimination of toxic oxygen-containing byproducts
50
Oxidative phosphorylation
According the Mitchell’s chemiosmotic hypothesis in the oxidative
phosphorylation the difference in the pH between the intermembrane space (acidic
region) and the matrix (basic region) activates the ATP-synthesizing enzyme complex
ATP synthase, also known as FOF1-ATPase. The production of macroerg bonds by
ADP+Pi  ATP conversions is catalyzed by the F1 subunit of FOF1-ATPase and at the
same time the difference in the pH values between the intermembrane space and the
matrix is eliminated by the contribution of the FO subunit.
The stoichiometry of the terminal oxidation
There are so called uncoupling materials eliminating the connection between
electron transport and oxidative phosphorylation. Such compounds (e.g. 2,4nitrophenol) are able to transfer protons back to the matrix without forming macroerg
bonds. The FO subunit of FOF1-ATPase is involved in this uncoupling activity. The O
letter in FO subunit means that the antibiotic oligomycin is also an uncoupling agent.
Uncoupling agents are toxic materials, because they eliminate the energy producing
function of terminal oxidation.
Oxidative phosphorylation and uncoupling agents
Connection between the catabolic processes
There are complex systems regulating connections between catabolic and
anabolic pathways as well as within the catabolic processes. Now some processes
supporting the well-balanced metabolism are presented.
Anaplerotic reactions
There are special reactions named anaplerotic reactions serving to maintain the
level of oxaloacetate not only for the citrate acid cycle in mitochondria, but also for
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other metabolic pathways (e.g. gluconeogenesis) in the cytosol. The activity of the
enzymes in these reactions can be regulated by the feedback of acetyl-CoA. The
processes are activated by a low acetyl-CoA concentration. In the cytosol
phosphoenolpyruvate (in a reversible reaction) and in the mitochondria pyruvate (in an
irreversible reaction) can be carboxylated by carbon dioxide to oxaloacetate. It was
mentioned earlier that both membranes of the mitochondria are permeable for
pyruvate.
For the activation of carbon dioxide direct carboxylation reactions always need
the energy of a macroerg phosphoric acid anhydride bond (ATP for pyruvate and GTP
for phosphoenolpyruvate), and the coenzyme biotin to transfer the carboxylic group.
Carboxylation of the biotin-enzyme complex always needs the presence of magnesium
ions. The reaction of carboxybiotin-enzyme complex with pyruvate needs the presence
of manganese ions. Since the membranes of mitochondria are not permeable for
oxaloacetate it can pass through only in its reduced form (L-malate). There exist
cytoplasmic and mitochondrial malate dehydrogenase (MDH) enzymes to help the
transfer and regenerate oxaloacetate. These reactions play an important role in glucose
biosynthesis from pyruvate (gluconeogenesis). The details of this process are given
later.
Oxaloacetate synthesis from pyruvate catalyzed by pyruvate carboxylase
Oxaloacetate synthesis from phosphoenolpyruvate catalyzed by PEP carboxykinase
and its passing through the membranes of mitochondria
There are other mechanisms which regulate the level of acetyl-CoA in
mitochondria. In the case of a low oxaloacetate level of so-called ketone bodies (e.g.
in the liver in illness diabetes mellitus) can be formed from acetyl-CoA molecules.
From two molecules of acetyl-CoA acetoacetyl-CoA is synthesized. This compound
takes part in an addition reaction with the third acetyl-CoA to produce 3-hydroxy-3methylgutaryl CoA (its earlier name is -hydroxy--methylgutaryl CoA). This
compound is the starting material of the biosynthesis of terpenes – (details see later).
In the synthesis of ketone bodies acetoacetate is formed by the elimination of acetylCoA from 3-hydroxy-3-methylgutaryl CoA. The ketone bodies are: acetoacetate,
52
acetone (produced by the irreversible decarboxylation of acetoacetate) and D-3hydroxybutyrate that is produced by the reversible reduction of acetoacetate
accompanied with a NAD  (NADH+H) conversion.
The biosynthesis of ketone bodies
In the case of a low concentration of acetyl-CoA ketone bodies can be a source
of acetyl-CoA. In this way they can be used as energy sources (by means of the citrate
acid cycle and terminal oxidation). The macroerg thiolester bond of acetoacetyl-CoA
is derived from a succinyl CoAsuccinate conversion. Acetoacetyl-CoA can react
with acetyl-CoA according to the last step of -oxidation of fatty acids catalyzed by
thiolase producing two molecules of acetyl-CoA.
Regeneration of acetyl-CoA from acetoacetate
Redox shuttles
Redox shuttles can regenerate coenzyme NAD from the reduced
(NADH+H) formed in the cytosol (e.g. in glycolysis). These hydrogen atoms can be
transported to the mitochondria, to the terminal oxidation for producing energy by
redox shuttles. These cytoplasmic (cytosolic) coenzymes reduced in this way are often
called extra mitochondrial (NADH+H) molecules. There are two redox shuttles for
transferring the extra mitochondrial (NADH+H) molecules: the glycerol 3-phosphate
(its earlier name is -glycerolphosphate) and the malate-aspartate redox shuttle.
53
The glycerol 3-phosphate shuttle
The starting material of glycerol 3-phosphate shuttle is dihydroxyacetone
phosphate (DHAP) that is an intermediate of the glycolysis. This compound is
reduced by (NADH+H) in a reaction catalyzed by cytoplasmic glycerol 3-phosphate
dehydrogenase to glycerol-3-phosphate that can pass the outer membrane of
mitochondria. In the intermembrane space glycerol-3-phosphate is oxidized by
mitochondrial glycerol 3-phosphate dehydrogenase to DHAP, but the coenzyme of
this reaction is FAD. DHAP returns to the cytosol and can repeat this process. At the
outer side of the inner membrane the hydrogen atoms of the reduced FADH2
coenzyme enter the electron transport by coenzyme Q – that means the formation of
only two instead of three ATP molecules from ADP. This seems to be a loss in
transporting of reducing equivalents, but in reality it is an active membrane transport,
since the hydrogen atoms of the reduced FADH2 coenzyme can enter the electron
transport even at high mitochondrial concentration of reduced coenzyme
(NADH+H).
Malate-aspartate redox shuttle
In the case of the malate-aspartate redox shuttle oxaloacetate is reduced by
extra mitochondrial (NADH+H) to L-malate by cytoplasmic malate dehydrogenase
(MDH) for which the membranes of mitochondria are permeable. In the matrix
mitochondrial MDH regenerates oxaloacetate forming reduced (NADH+H). It means
that there is no loss in transporting of reducing equivalents in this case. Since the inner
membrane of mitochondria is not permeable for oxaloacetate only for aspartate and ketoglutarate, therefore oxaloacetate leaves the mitochondria in a roundabout way.
54
Oxaloacetate and glutamate give -ketoglutarate and aspartate in a transamination
reaction. They leave the mitochondria by antiport membrane transport processes by
the help of translocases. Oxaloacetate is regenerated by the transamination reaction of
-ketoglutarate and aspartate producing glutamate for which membranes of
mitochondria is permeable by an antiport membrane transport process. The pairs in
the antiport membrane processes are aspartate and glutamate, as well as ketoglutarate and oxaloacetate. This reversible redox shuttle can work only in when
the (NADH+H)/NAD ratio is higher in the cytosol than in the mitochondrial matrix
(e.g. in tissues of high capacity as the human heart and liver).
The stoichiometry of aerobic oxidative degradation of glucose
During the oxidative degradation of glucose when the glycerol 3-phosphate
shuttle is used, the overall reaction is: C6H12O6 + 6 O2  6 CO2 + 6 H2O
accompanied by the reaction: 36 ADP + 36 Pi  36 ATP + 36 H2O. In the case of the
malate-aspartate shuttle the number of ATP molecules is 38.
The pentose phosphate pathway
The pentose phosphate pathway (earlier called the direct oxidation of glucose
or the phosphogluconate pathway or the hexose monophosphate shunt) is an
alternative cytoplasmic oxidative degradation of glucose resulting in (NADPH+H)
from NADP as well as different intermediates (e.g. ribose 5-posphate, ribulose 5phosphate, erythrose-4-phosphate). The reduced coenzyme (NADPH+H) is the
coenzyme of reductive biosyntheses for all kinds of living organisms. Except plants
(using the energy of photons for glucose biosynthesis) and some microorganisms
(using other chemical energy) the living organisms use pentose phosphate pathway for
the biosynthesis of (NADPH+H). Moreover (NADPH+H) is an antioxidant
reducing agent in living organisms (e.g. it can regenerate hemoglobin containing
ferrous ion from methemoglobin containing ferric ion by reduction). Ribose 5posphate is one of the starting materials of the biosynthesis of nucleic acids. Ribulose
5-posphate is the starting material of the synthesis of ribulose 1,5-bisposphate being
the starting material of Calvin cycle. Erythrose-4-phosphate is used in the synthesis of
aromatic amino acids.
Reactions catalyzed by transketolases and transaldolases
55
The starting material of the pentose phosphate pathway is glucose 6-phosphate
that is oxidized to 6-phosphoglucono--lactone (the coenzyme is NADP reduced to
NADPH+H) catalyzed by glucose 6-phosphate dehydrogenase. After the hydrolysis
of this lactone to 6-phosphogluconate this molecule is oxidized by NADP (which is
reduced to NADPH+H) and ribulose 5-phosphate and carbon dioxide are produced.
From ribulose 5-phosphate by isomerisation ribose 5-phosphate and xylulose 5phosphate (by epimerization that is a change in the chirality) are formed. In the next
steps of the pathway by means of transferase enzymes transketolases and a
transaldolase from six ribulose 5-phosphate molecules five glucose 6-phosphate
molecules are formed in a complicated system. Both transaldolase and transketolases
can perform transformations of aldoses to ketoses and inversely by transferring C-2
(transketolases) or C-3 (transaldolase) fragments from a ketose to an aldose. The
chirality of the new hydroxyl group from the aldehyde group is L in the case of
transketolases and D in the case of transaldolase. The pentose phosphate pathway is
regulated by the level of NADP.
56
The pentose phosphate pathway
The stoichiometry of the pentose phosphate cycle
In the pentose phosphate cycle during the degradation of one glucose molecule
twelve reduced coenzymes (NADPH+H) (equivalent to 36 ATP molecules) and six
carbon dioxide molecules are produced. On the basis of equivalents between reduced
coenzyme (NADPH+H) and macroerg phosphoric acid anhydride bond of ATP the
pentose phosphate cycle is equivalent to the aerobic oxidative degradation of glucose
57
via the glycerol 3-phosphate shuttle. From six glucose 6-phosphate molecules twelve
reduced coenzymes (NADPH+H), six carbon dioxide molecules and six ribose 5phosphate molecules are produced. From six ribose 5-phosphate molecules (C5) five
glucose 6-phosphate molecules (C6) were formed by sugar transformation reactions.
Stoichiometry of the pentose phosphate cycle
Anabolism
In the following the reductive biosynthetic pathways of different biomolecules
are presented, at first the anabolic reactions of glucose.
Biosynthesis of glucose
In animals the maintenance of glucose level can be maintained (beyond the
direct use of the glucose content of foods) by the biosynthesis glucose from noncarbohydrate precursors called gluconeogenesis. In plants glucose is synthesized by
photosynthesis. During the germination of seeds glucose can be synthesized by
different ways.
Gluconeogenesis
Gluconeogenesis (or ‘de novo’ synthesis of glucose) is a glucose biosynthesis
from non-carbohydrate precursors (pyruvate, L-lactate, DHAP, glycerol, some amino
acids degradation of which gives pyruvate or an intermediate of the citric acid cycle –
these are glucogenic amino acids). Animals cannot synthesize glucose from fatty
acids. In the liver glucose is synthesized from lactate formed by glycolysis and lactic
acid fermentation in skeletal muscles when the rate of glycolysis exceeds the
metabolic rate of the citric acid cycle and the terminal oxidation (respiratory chain)
(anaerobe period of muscle activity). This regeneration of glucose used up by muscles
is called the Cori cycle. Gluconeogenesis helps to maintain the glucose level in blood
and brain.
The gluconeogenesis is not a simple reversal of glycolysis. It was shown
earlier that there are three irreversible steps of glycolysis: The glucose  glucose 6phosphate and fructose 6-phosphate  fructose 1,6-bisphosphate reactions catalyzed
by kinase enzymes. These reactions utilize the energy of a macroerg phosphoric acid
anhydride bond of an ATP molecule, but sugar phosphates do not contain macroerg
bonds. The reverse reactions are hydrolyses catalyzed by phosphatases (glucose 6phosphatase and fructose 1,6-bisphosphatase) to glucose and fructose 6-phosphate and
Pi.
The third irreversible step of glycolysis is the phosphoenolpyruvate 
pyruvate conversion because of the irreversibility of oxo-enol tautomerism. Pyruvate
formed in the cytoplasm and entered to the mitochondria is carboxylated to
oxaloacetate (by pyruvate carboxylase) as it was described in the section for
anaplerotic reactions. The pass of oxaloacetate from mitochondria to the cytosol in
form of malate and the conversion of the regenerated oxaloacetate to PEP is the
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reverse process catalyzed by PEP carboxykinase which were also described earlier.
This reaction is reversible, because during the decarboxylation of oxaloacetate first
enolpyruvate is formed that is immediately (before the irreversible tautomerism)
phosphorylated by GTP. In the scheme of gluconeogenesis the mitochondrial reactions
are in a frame.
Gluconeogenesis
The summary of the process of gluconeogenesis is given in a separate scheme
with the names of intermediates (lactate in Hungarian is tejsav).
59
The process of gluconeogenesis
Photosynthesis
Practically all energy consumed by living organisms arises from solar energy
that is trapped by the process of photosynthesis. Only a few microorganisms can use
other chemical energy. For the biosynthesis of one glucose molecule the energy of
twelve photons is used:
6 H2O + 6 CO2 12 h  C6H12O6 + 6 O2
Water and carbon dioxide molecules are incorporated in separate processes. As
a result of photolysis the hydrogen atoms of water are transported separately as
protons and electrons in the light phase (electron transport) of photosynthesis to
NADP molecules to produce reduced (NADPH+H) molecules by the energy of
absorbed light. Photosynthesis in green plants takes place in the chloroplasts. The
absorption of four photons is accompanied by the synthesis of two macroerg
phosphoric acid anhydride bonds of two ATP molecules and the formation of one
oxygen molecule.
The stoichiometry of the light phase of photosynthesis
The assimilation of carbon dioxide molecules to ribulose 1,5-bisphosphate by
the contribution of (NADPH+H) and ATP molecules take place in the dark phase of
the photosynthesis (Calvin cycle). This phase can be carried out without the presence
of light.
60
The stoichiometry of the dark phase of photosynthesis
Photosynthesis in green plants takes place in chloroplasts in which there is a
so-called thylakoid membrane system the structure of which resembles to that of the
of mitochondria. There are two photosystems in chloroplasts that can trap the energy
of photons in a complicated system containing chlorophylls (molecules containing a
porphyrin skeleton and a coordinated magnesium ion). The stroma that is similar to
the matrix of mitochondria contains all of the enzymes of the dark phase of the
photosynthesis.
Chlorophyll a and b
The light phase of the photosynthesis
The light phase of photosynthesis can be illustrated by a Z-scheme that shows
the standard oxidation-reduction potentials of the participants of the electron transport
from water to the coenzyme NADP. As it was mentioned earlier the direction of the
electron transport is determined by the standard oxidation-reduction potential (E’0) of
the participants (from the negative to the positive values), the Z-scheme illustrates that
the standard oxidation-reduction potential of photosystems can be changed to the
61
negative region by the energy of the photons absorbed. The energy of absorbed
photons is the driving force for the electron transport from water molecules (E’0
+0.80) to NADP (E’0 -0.32).
The Z-scheme of photosynthesis
At first photosystem I (PS-I) absorbs light of 700 nm wavelength (P-700).
Affected by the photon the standard oxidation-reduction potential of PS-I changes
from about +0.5 V to about -1.3 V. One of the electrons of chlorophyll of PS-I from
excited PS-700* enters the electron transport cascade and through different complex
iron-sulphur proteins (clusters). One of them is the ferredoxin reducing system (FRS)
and the other is ferredoxin (Fd), ferredoxin-NADP reductase (Fd-N-Ox). Finally the
electron reduces NADP to (NADPH+H). Clusters are proteins containing sulphur
both in covalent (in cysteine) and ionic (between inorganic sulphur and iron) bonds.
The electron deficiency of PS-I is eliminated by excitation of photosystem II
(PS-II) by light of 680 nm wavelength (P-680). The standard oxidation-reduction
potential of PS-II is changed from about +1.0 V to about -0.80 V by the second
photon. One of electrons of chlorophyll in PS-II enters electron transport between
excited P-680* and P-700 and through several complexes: a primary electron acceptor
that contains pheophytin (PEA), different plastoquinones QA, QB, QH2 – (this reduced
plastoquinone is called plastoquinone pool PQ), then to the cytochrome bf complex,
and plastocyanin (PC). Because of the proton pump between cytochrome b and
cytochrome f this electron transport is accompanied by yielding one macroerg bond in
an ADP+Pi  ATP conversion. This reaction is catalyzed by CFOCF1-ATPase.
Electron deficiency in PS-II is stopped by exciting the photolysis of water to
protons, electrons and oxygen. The electrons enter PS-II by the mediation of a cluster
complex containing manganese. This cluster can prevent the formation of oxygen
molecules from the generating of dangerous oxygen radicals. Protons of water can
reach the coenzyme reduced by electrons with the help of a proton gradient. This last
part of the light phase of the photosynthesis is called the Hill reaction.
62
When the reduced coenzyme level is high, there is an alternative pathway for
electrons from P-700* through another ferredoxin to the cytochrome bf complex. In
this way the energy of one photon leads to a formation one macroerg bond of ATP:
h  ATP. This process is the cyclic photophosphorylation. During the light phase
from two photons one reduced coenzyme (equivalent to the energy of three macroerg
bond of ATP) and one macroerg bond of ATP is formed: 2 h  4 ATP that means:
h  2 ATP. Cyclic photophosphorylation provides the synthesis of only a half of
ATP molecules, but it is an easy way to produce extra ATP molecules.
The dark phase of the photosynthesis (Calvin cycle)
In the dark phase of photosynthesis the fixation (assimilation) of carbon
dioxide to ribulose 1,5-bisphosphate by the contribution of (NADPH+H) and ATP
molecules leads to the biosynthesis of glucose and this process is connected with the
regeneration of ribulose 5-phosphate: it is phosphorylated by the extra ATP of cyclic
photophosphorylation to restore ribulose 1,5-bisphosphate.
The Calvin cycle
The enzyme for carbon dioxide assimilation to ribulose 1,5-bisphosphate is
ribulose 1,5-bisphosphate carboxylase (its short name is Rubisco) which is also an
oxygenase. The addition of CO2 is (through an enediol intermediate) between C-2 and
C-3 results in two glycerate 3-phosphate molecules but only one of them contains the
assimilated carbon dioxide as a carboxylic group. Similarly to the glycolysis only
glycerate 1,3-bisphosphate is able to take part in a oxidation-reduction reaction. In this
case glycerate 3-phosphate is phosphorylated by ATP (formed in the light phase)
catalyzed by a kinase, then glycerate 1,3-bisphosphate containing a macroerg mixed
acid anhydride bond is reduced by (NADPH+H) (formed in the light phase) to
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glyceraldehyde 3-phosphate. Glucose is synthesized by the steps of gluconeogenesis
but only in the ratio of the absorbed carbon dioxide. From the other glyceraldehyde 3phosphate molecules ribulose 5-phosphate is regenerated by similar transformations
catalyzed by transketolases and a special aldolase presented earlier in the pentose
phosphate pathway. Ribulose 1,5-bisphosphate is synthesized by the phosphorylation
by ATP (formed in the cyclic photophosphorylation in the light phase). The traditional
photosynthesis is called C3 photosynthesis, because the intermediates of the
assimilation of carbon dioxide contain three carbon atoms.
Rubisco is also an oxygenase; therefore it catalyzes the addition of an oxygen
molecule to ribulose 1,5-bisphosphate resulting in glycerate 3-phosphate and
phosphoglycolate (H2O3P-O-CH2–COOH). From phosphoglycolate glycine can be
synthesized. Generally the rate of carboxylase reaction is four times that of oxygenase
reaction. The name of this disadvantageous reaction is photorespiration.
There is another variation of photosynthesis in tropical plans because of the
extreme circumstances. The light and dark phases are working separately and carbon
dioxide is stored temporarily in L-malate produced by the carboxylation of PEP
followed by reduction. Because malate contains four carbon atoms, this variation is
called C4 photosynthesis.
Glucose biosynthesis in different seedlings
The seedlings in the ground are unable to photosynthesize therefore they use
the stored biomolecules of the seeds for glucose biosynthesis. There are different
kinds of seeds. Cereals are rich in polysaccharides (e.g. starch) and glucose is
produced by their hydrolysis. From the seeds that are rich in proteins (e.g. bean) after
the hydrolysis of proteins glucose can be synthesized from glucogenic amino acids by
gluconeogenesis. From oilseeds (e.g. sunflower seeds) that are rich in oil glucose can
be synthesized after the oxidative degradation of fatty acids from acetyl-CoA
molecules by the glyoxylate cycle.
The glyoxylate cycle
There are many bacteria and plants that can synthesize glucose from acetylCoA in a biosynthetic process called the glyoxylate cycle. In plants the glyoxylate
cycle occurs in organelles called glyoxysomes. Until the synthesis of isocitrate the
steps of glyoxylate cycle are the same that of the citric acid cycle that is degradation
process (the addition of acetyl-CoA to the starting material oxaloacetate,
rearrangement of citric acid to isocitrate).
In the glyoxylate cycle isocitrate takes part in an elimination reaction
producing succinate and glyoxylate. From succinate oxaloacetate can be synthesized
in three steps following the citric acid cycle which can be then serve as starting
material for the biosynthesis of glucose by gluconeogenesis.
From glyoxylate oxaloacetate (the starting material of glyoxylate cycle) is
regenerated by the addition of another molecule of acetyl-CoA followed by the
oxidation of the product L-malate. These reactions are catalyzed first by malate
synthase that resembles citrate synthase in the citric acid cycle, then by malate
dehydrogenase similarly to the last step of the citric acid cycle accompanied by a
NAD  (NADH+H) conversion. In the glyoxylate cycle succinate (C4) can be
derived from two molecules of acetyl-CoA (C2).
64
The glyoxylate cycle
The scheme of the biosynthesis of glucose by the glyoxylate cycle
The biosynthesis of polysaccharides
After the activation of the glycosidic hydroxyl group of sugars O-glycosides
can be synthesized in the cytosol. It is illustrated by the example of glucose. Glucose
6-phosphate (the first intermediate of glycolysis) is converted to glucose 1-phosphate
by means of a combination of two transfer reactions assisted by the cofactor glucose
1,6-bisphosphate. The reaction is catalyzed by a mutase (glucose-phosphate mutase or
phosphoglucose mutase) a transferase. A reverse process is carried out after the
degradation of glycogen by phosphorylase.
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The reaction catalyzed by glucose-phosphate mutase
The active NDP-sugar derivatives (that are sugar donors for the biosynthesis of
O-glycosides) are produced from sugar 1-phosphate and nucleoside triphosphate
(NTP) molecules. NDP- sugars contain a phosphoric acid anhydride macroerg bond
and the energy of the other macroerg bond of NTP is used for the biosynthesis of the
active sugar derivative. The hydroxyl component can be an alcoholic or glycosidic
hydroxyl group of another sugar or an aglycon molecule. The formation of the
glycosidic bond does not need extra energy; the byproduct of the reaction is NDP.
Biosynthesis of O-glycosides of glucose
In the case of glucose the starting material is NDP-glucose. For sucrose
biosynthesis UDP-glucose is the starting material. For the biosynthesis of glucans the
starting material for amylose is ADP-glucose and for cellulose that is GDP-glucose.
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Biosynthesis of glucans
The biosynthesis of lipids
The staring material of both fatty acids and terpenes is acetyl-CoA.
The biosynthesis of fatty acids
The biosynthesis of fatty acids till the C16 stage is takes place in the cytosol.
Acetyl-CoA is transported from mitochondria to cytosol by a combination of reactions
presented earlier.
The way of acetyl-CoA from the mitochondria to the cytosol
The biosynthesis is catalyzed by a multienzyme complex (fatty acid synthase)
that contains six active sites and an acyl carrier protein (ACP). ACP binds the acyl
group of the fatty acid of increasing number of carbon atoms by a macroerg thiolester.
There are two acetyl-CoA molecules at the start of the biosynthesis. One of the acetylCoA molecules is joined to the ACP, to the site of the prospective long fatty acid
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(catalyzed by acetyl transacylase). The other acetyl-CoA is connected to the site of the
new acetyl-CoA units and carboxylated to malonyl-CoA by the coenzyme biotin (as
prosthetic group) aided by the energy of ATP  ADP conversion (catalyzed by
acetyl-CoA carboxylase) followed by a transacylation reaction from coenzyme A to
ACP. ATP plays role in the formation of carboxybiotin.
The formation of malonyl-CoA is often named the ‘activation of acetyl-CoA’.
In fact it is not a real activation step, because the number of macroerg bonds does not
increase. But the electron distribution of malonyl-CoA can help its connection to an
acyl-ACP accompanied by a decarboxylation catalyzed by -acyl-ACP-synthase (acylmalonyl-ACP condensing enzyme). The driving force of the synthesis of acetoacetylACP is the elimination of carbon dioxide.
The next three steps (reduction of the -keto group, dehydration, and reduction
of the unsaturated double bond) of fatty acid biosynthesis are similar to the steps of
the -oxidative degradation of fatty acids in the opposite direction, but with several
differences: the steps of the biosynthesis are in a chain connected to ACP (instead of
CoA); the coenzyme of both reductive reactions is (NADPH+H) (instead of NAD
and FAD); in hydration the D-epimer (enantiomer) is formed instead of the Lenantiomer, therefore an epimerization is also needed. The end product of the first
elongation cycle is butyryl-ACP that reacts with a second malonyl-CoA. Elongation
may continue until palmitoyl-ACP that is hydrolyzed to ACP and palmitate from
which palmitoyl-CoA is synthesized in two steps. Further C2 units can be attached to
the chain by the fatty acid elongation system in the endoplasmic reticulum membrane
(in closed vesicles called microsomes) with reactions similar to those of cytoplasmic
ACP.
Biosynthesis of fatty acids
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Unsaturated fatty acids are synthesized from the saturated fatty acids in
microsomes catalyzed by a monooxygenase. Monooxygenases can use molecular
oxygen for the oxidation but only one of oxygen atoms oxidizes the saturated C–C
bonds to double bonds, the other oxygen is reduced by (NADPH+H) using an
electron transport chain containing NADH-cytochrome b5 reductase (with
FAD/FADH2 content), cytochrome b5 reductase (with Fe2/Fe3 content) and
desaturase (with Fe2/Fe3 content). This process cannot be carried out in mammals
therefore linoleate and linolenate are essential fatty acids. In mammals these fatty
acids are the starting materials for other unsaturated fatty acids of biological
importance (e.g. arachidonate for the biosynthesis of prostaglandin hormones)
Formation of unsaturated fatty acids
The biosynthesis of triacylglycerols and phosphoglycerides
Triacylglycerols (triglycerides) and phosphoglycerides are synthesized in the
endoplasmic reticulum membrane and their common intermediates are phosphatidates
(phosphatidic acids) containing different fatty acid components. The starting material
of phosphatidates is glycerol 3-phosphate that is synthesized by the reduction of
DHAP. This reaction in the opposite way described in the section of redox shuttles. In
the biosynthetic process the phosphoric acid unit of glycerol 3-phosphate can help the
formation of a link between the substrate and enzyme by ionic interactions.
The hydroxyl groups of glycerol 3-phosphate can react with different acylCoA molecules to produce phosphatidates. In the case of the biosynthesis of
triacylglycerols phosphatidates are hydrolyzed by special phosphatases to produce
diacylglycerols that react with a third acyl-CoA. The enzymes of this process are
associated in a triacylglycerol synthetase complex.
The biosynthesis of triglycerides
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In the case of the biosynthesis of phosphoglycerides there are different
possibilities to introduce another ester group to phosphatidates. One of these
possibilities is the activation phosphatidates by forming a macroerg phosphoric acid
anhydride bond by the reaction with CTP. This reaction is similar to the activation of
glucose 1-phosphate to NDP-glucose that was described in the section of the
biosynthesis of polysaccharides. CDP-diacylglycerols can produce phosphatidyl
ethanolamines with ethanolamine, phosphatidyl serines with serine, and phosphatidyl
cholines with choline (lecitines). The byproduct of the reactions is CDP. Another
variation is that the hydroxyl compound is activated by phosphorylation followed by a
reaction with CTP. In this case the CDP derivative of the hydroxyl compounds is
reacted with diacylglycerols (e.g. in the synthesis of lecitines diacylglycerols are
reacted with CDP-choline).
Variations for the biosynthesis of phosphatidyl cholines (lecitines)
The biosynthesis of lecitine
The biosynthesis of terpenes
The starting material of the cytoplasmic biosynthesis of terpenes is acetylCoA, and the first phase is the synthesis of isopentenyl pyrophosphate from three
acetyl-CoA molecules. As it was mentioned in connection with the synthesis of ketone
bodies acetoacetyl-CoA is synthesized from two molecules of acetyl-CoA. This
compound takes part in an addition reaction with a third acetyl-CoA to produce 3hydroxy-3-methylgutaryl CoA (its earlier name is -hydroxy--methylgutaryl CoA).
In an addition reaction a nucleophilic attack of acetyl group on the carbonyl group of
acetoacetyl-CoA is carried out by the methylene part of the enol tautomer that is
temporarily formed in the reaction under the influence of the strong hydrogen bond of
a His of the enzyme. Acetyl-CoA reacted with oxaloacetate similarly in the first step
of the citric acid cycle.
In the mitochondrial synthesis of ketone bodies 3-hydroxy-3-methylgutaryl
CoA takes part in an elimination reaction. In the cytoplasmic synthesis of terpenes 3hydroxy-3-methylgutaryl CoA is reduced by a reductase to mevalonate accompanied
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by 2 (NADPH+H)  2 NADP conversion in an irreversible reaction. After
phosphorylation to 5-pyrophosphomevalonate by 2 ATP molecules accompanied by a
decarboxylation isopentenyl pyrophosphate is formed.
Isopentenyl pyrophosphate and its isomer dimethylallyl pyrophosphate
condense to form the monoterpene geranyl pyrophosphate (C10). The intermediate of
this reaction is an allylic carbonium ion (named active isoprene) formed from
dimethylallyl pyrophosphate. Geranyl pyrophosphate can then be transformed to other
terpenes.
Biosynthesis of the monoterpene geranyl pyrophosphate
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Biosynthesis of amino acids
The biosynthesis of proteins from L--amino acids is connected with the
metabolism of nucleic acids. There are different pathways for the biosynthesis of
amino acids but some common features can be found. The starting materials of the
carbon skeletons of amino acids are the intermediates of glycolysis, pentose phosphate
pathway and citric acid cycle. On the basis of the starting materials five biosynthetic
families of amino acids can be distinguished. The name of these families is based on
the compound (generally amino acid) which can be the starting material of the other
members of the family.
The starting material of the glutamate amino acid family (Glu, Gln, Pro, Arg)
is -ketoglutarate (from the citric acid cycle). The starting material of the aspartate
amino acid family (Asp, Asn, Met, Lys, Thr, Ile) is oxaloacetate (from the citric acid
cycle). The starting material of the serine amino acid family (Ser, Cys, Gly) is 3phosphoglycerate (from the glycolysis). The starting material of the pyruvate amino
acid family (Ala, Val, Leu) is pyruvate (from the glycolysis). The starting materials of
the aromatic amino acid family (Phe, Tyr, Trp) are phosphoenolpyruvate (from the
glycolysis) and erythrose 4-phosphate (from the pentose phosphate pathway). The
starting material of histidine is ribose 5-phosphate (from the pentose phosphate
pathway). Generally the last step of the biosynthesis of amino acids is the
transamination reaction of an -keto carboxylic acids but there are several exceptions.
The metabolism of the biomolecules of genetic information
As it was mentioned earlier the metabolism of nucleic acids is in separated
place from the metabolism of other biomolecules in the nucleus of the cell. The
metabolism of nucleic acids is the subject of another science (genetics) therefore now
only a short summary is given.
Hydrolysis of nucleic acids
Nucleases (DNase an RNase enzymes) hydrolyze nucleic acids (DNA and
RNA) to nucleotides. There are exonucleases and endonucleases. Exonucleases can be
specific for the 3' or 5' end of the strand. From DNase enzymes restriction
endonucleases (that cleave DNA chain at specific sites) are often used in genetic
engineering. During further hydrolytic processes nucleosides then nucleic bases are
formed.
Oxidative degradation of pyrimidine nucleic bases
During the oxidative degradation of pyrimidine nucleic bases (through the
intermediates uracil and then dihydrouracil) ammonia and succinate are formed.
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Oxidative degradation of pyrimidine nucleic bases
Oxidative degradation of purine nucleic bases
As first intermediates xanthines (hypoxanthine and xanthine) then uric acid (in
Hungarian hugysav) are formed by oxidative deamination of purine nucleic bases
followed by an oxidative degradation to urea and glyoxylate.
Oxidative degradation of purine nucleic bases
Biosynthesis of pyrimidine nucleotides
The pyrimidine ring is synthesized from carbamoyl phosphate (formed in the
urea cycle) and aspartate through the intermediate orotate (orotic acid) that reacts with
PRPP (5-phosphoribosyl 1-pyrophosphate) to form the starting material of pyrimidine
nucleotides (orotate monophosphate). The amino group of CTP is synthesized from
UTP and glutamine accompanied by an ATP  ADP + Pi conversion. Thymine is
synthesized by the methylation of uracil (coenzyme is THF) in their nucleoside
monophosphate form.
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The scheme of the biosynthesis of pyrimidine nucleotides
Biosynthesis of purine nucleotides
The starting material of purine nucleotides is PRPP synthesized from ribose 5phosphate (formed in the pentose phosphate pathway). The first step of this
complicated process is the synthesis of 5’-phosphoribosylamine (a -glycoside). It is
the amino group of 5’-phosphoribosylamine which is incorporated into the purine
skeleton. The sources of the different atoms of the purine skeleton are shown below.
The scheme of the biosynthesis of purine nucleotides
Biosynthesis of the precursors of DNA
The reduction of ribose derivatives to 2’-deoxyribose derivatives proceeds in
their nucleoside diphosphate form by (NADPH+H).
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The formation of 2’-deoxyribose from ribose
The biosynthesis of DNA (replication)
The genetic information is stored and expressed by DNA. During the
semiconservative biosynthesis of DNA a new polynucleotide chain in a 5’ to 3’
direction is synthesized from precursor dNTP molecules (dATP, dGTP, dTTP, dCTP)
with the hydrolysis of two macroerg phosphoric acid anhydride bonds to the
antiparallel complementary original polynucleotide chain (template strand) in the
course of dividing of the cell. Two identical DNA molecules are produced from a
single double-stranded helical DNA molecule. DNA replication begins at specific
locations in the genome, called origins.
Building a new nucleotide unit in replication
The process of replication is more or less different in prokaryotes and
eukaryotes but common features can be found. The break-down of the superhelical
structure of DNA is carried out by the enzyme DNA gyrase (topoisomerase I) and
unwinding of the double helix is catalyzed by helicase. Opening of the helical
structure demands the energy of phosphoric acid anhydride macroerg bonds (ATP 
ADP + Pi). The construct formed by two separated strands is named the replication
fork and fixed by single strand binding (Ssb) proteins. At first a short RNA primer is
created on the template strand catalyzed by an RNA polymerase (primase). Elongation
of the DNA chain is continued by DNA polymerase III holoenzyme. At the end of
elongation instead of DNA polymerase III another enzyme (DNA polymerase I)
continues the biosynthesis of DNA strand by removing the RNA primer and replacing
it by a DNA section. This is one of the 3’ (5’->3’) exonuclease activities of DNA
polymerase I. At the end of the process the end of two DNA chains are connected by
DNA ligase using the energy of phosphoric acid anhydride macroerg bond (formed
from NAD in prokaryotes and ATP in eukaryotes).
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The scheme of the replication
As the direction of the biosynthesis is 5’3’, it can be carried out directly only
along the 3’5’ template strand (called leading strand). On the other strand (called
lagging strand 5’3’) the direction of biosynthesis is the opposite to the direction of
the sequence, therefore the synthesis of RNA primers are started at several places to
the opposite direction (5’3’) followed by elongation of DNA. When the short DNA
chains (called Okazaki fragments) reach the next RNA primers the elimination of
primers, they replace them by DNA sections and the connection of DNA sections is
repeated several times. In the double helix there are double replication forks forming a
bubble.
The reaction catalyzed by DNA-ligase
During the replication all of the new nucleotide units is controlled (and
corrected if it is necessary) by DNA polymerase I. This is the other 3’ (5’->3’)
exonuclease activity of DNA polymerase I. The 5’ terminal nucleotide unit is also
controlled (and corrected if it is necessary). This is the 5’ (3’->5’) exonuclease activity
of DNA polymerase I. There are also other possibilities for the correction of the DNA
strands after replication.
The biosynthesis of RNA (transcription)
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The biosynthesis of RNA with the participation of DNA is called transcription
and consists of the copying of DNA into messenger RNA during gene expression. The
technique of transcription is similar to the replication but the new strand is RNA. The
precursor molecules are ATP, GTP, UTP and CTP. As only one of the strands of
DNA is used as template (leading strand 3’5’) the direction of the biosynthesis and
the sequence of the strand is the same. The sequence of new RNA is antiparallel and
complementary to the original DNA. When the gene transcribed encodes for a protein,
the result of transcription is an mRNA, which is used for the biosynthesis of a protein
in the process of translation. Alternatively, the transcribed gene can encode other
RNA types (rRNA, tRNA, snRNA).
In transcription only a part of the DNA takes part therefore there are several
potential starting sites on it. In eukaryotes transcription is catalyzed by RNA
polymerase. Initiation of transcription requires the presence of a core promoter
sequence on the DNA that is recognized by the  subunit of the enzyme. The
transcription is continued to the terminal signal sequence on the DNA, that is a
palindrome sequence followed by a polyA sequence, therefore the new RNA contains
a palindrome folded structure and a tail of polyU at 3’ terminal. Specific proteins
called transcription factors play important roles in the transcription.
In most often the products of transcription are RNA precursors (pre-RNA
molecules) that are modified later. The only exceptions are the prokaryotic mRNA
molecules on which the translation (the protein biosynthesis) can be started before the
termination of transcription. There are different changes in the pre-mRNA structure of
eukaryotes. A polyA tail is attached to the 3’ terminal catalyzed by polyadenylate
polymerase using ATP molecules. Another reaction is when a cap (7-methylguanosine
pyrophosphate) is connected to the 5’ terminal of pre-mRNA to prevent the molecule
from the hydrolysis by RNases. Then a splicing is carried out that is the removal of
not to be translated sections called introns from the pre-mRNA strand and connecting
the remaining fragments called exons by the help of snRNA molecules). The terminals
of both pre-tRNA and pre-rRNA molecules in eukaryotes are hydrolyzed to tRNA
molecules. The pre-rRNA molecules can also hydrolyze themselves (this is ribozyme
function that is some kind of enzyme function).
The biosynthesis of proteins (translation)
The sites of protein biosynthesis are ribosomses that contain both rRNA
molecules and proteins. The information of the amino acid sequence contains the
mRNA that forms a complex with ribosome. The information is in the sequence of
nucleotide triplets (called codons). A codon is the sequence of three nucleotide units
starting from a fixed point. The genetic codon is universal (it can be used in all kinds
of living organisms) and there are no commas and no overlapping in it. The genetic
codon is degenerate what means that for most of amino acids have not only one
codon. The codon AUG is both the start codon and the codon of methionine (Met).
Stop codons are UUA, UGA and UAG.
Amino acids are transferred to the ribosome in ester form that can react with
an amino group (aminoacyl tRNA). At first an amino acid is connected to AMP by a
phosphoric acid anhydride macroerg bond of ATP and catalyzed by aminoacyl tRNA
synthetase. Then aminoacyl AMP is reacted with the 3’ hydroxyl group (with CCA
terminus) of tRNA to produce aminoacyl tRNA. The DHU loop of tRNA is connected
to the enzyme aminoacyl tRNA synthetase. The anticodon section of tRNA contains
an antiparallel and complementary sequence of the genetic codon of the amino acid to
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be transferred; therefore it is the template recognizing site of tRNA. The third
nucleotide member of the anticodon can be different nevertheless tRNA molecules
can recognize such a codon. The phenomenon is called wobble in base pairing.
Formation of aminoacyl tRNA
The structure of tRNA
There are two sites in the initiation complex of ribosome and mRNA: site P
(for the growing peptide chain connected to tRNA) and site A (for the new amino acid
unit in aminoacyl tRNA form). At the start of the protein biosynthesis (initiation step)
a Met-tRNA (in prokaryotes formylMet-tRNA) is connected to site P and the next
aminoacyl tRNA to the A site (on the basis of the next codon). The connection of the
aminoacyl tRNA to the site needs the energy of a phosphoric acid anhydride macroerg
bond (hydrolysis of GTP to GDP and an inorganic phosphate) catalyzed by a GTPase.
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Formation of peptide bond (O-N acyl transfer reaction)
The next step is elongation of the chain that is the formation of a carboxamide
(peptide) bond between the ester group of aminoacyl tRNA connected to site P and the
amino group of aminoacyl tRNA connected to the A site. This step is often called O-N
acyl transfer reaction. The free tRNA leaves site P and tRNA containing dipeptide
chain is moved from site A to P site by protein elongation factors using the energy of a
phosphoric acid anhydride macroerg bond of the hydrolysis of GTP (to GDP and an
inorganic phosphate) catalyzed by a GTPase. At the same time the position of mRNA
is changed in the complex, in this way the next codon is moved to site A and the
elongation can be continued. Each new amino acid unit in the peptide chain is
controlled (and corrected if it is necessary) by a special mechanism during translation.
When a stop codon is found at site A elongation stops and the new peptide chain is
hydrolyzed from the tRNA by the help by release factors. Proteins biosynthesis is
regulated in different ways in prokaryotes and eukaryotes. Parallel with translation the
formation of secondary, tertiary and quaternary structures of proteins proceeds.
There can be different post-translational modifications on the protein structure
e.g. cleavage the N-terminal methionine, different changes in the side chains of amino
acid units (e.g. the oxidation of proline to hydroxyproline described earlier), etc.
Literature
1. Stryer, L.: Biochemistry (3rd Edition) W.H. Freeman & Company New York
1988.
2. Ádám, G. and Fehér, O. (Eds): Élettan biológusoknak (Physiology for biologists).
Tankönyvkiadó, Budapest, 1990, pp 20.
Topics in Biochemistry
1. Definition of biomolecules. Proteins – structures, biochemical functions and
figures of some representatives.
2. Definition of biomolecules. Carbohydrates – structures, biochemical functions and
figures of some representatives.
3. Definition of biomolecules. Simple lipids – structures, biochemical functions and
figures of some representatives.
4. Definition of biomolecules. Complex lipids – structures, biochemical functions
and figures of some representatives.
5. Definition of biomolecules. Nucleic acids – structures, biochemical functions and
figures of some representatives.
79
6. Enzymes – structure and function (equations)
7. Degradation of biomolecules. The first step – hydrolysis.
8. Degradation of biomolecules. Glucose to the general intermediate (scheme).
9. Degradation of biomolecules. Fatty acids to the general intermediate (scheme).
10. Degradation of biomolecules. Amino acids to the general intermediate (scheme).
11. Degradation of biomolecules. Formation of CO2 during the degradation of the
general intermediate (scheme).
12. Degradation of biomolecules. Formation of H2O during the degradation of the
general intermediate (scheme).
13. Degradation of biomolecules. The alternative degradation of glucose – biological
functions in autotrophic and heterotrophic living organisms (scheme of some
starting steps and the stoichiometry of the reaction).
14. The principle of redox shuttles and gluconeogenesis (discussion on the scheme of
glycolysis).
15. Photosynthesis. The role of photons (Z-scheme).
16. Photosynthesis. Assimilation of CO2 (scheme of some starting steps and the
stoichiometry of the reaction).
17. Biosynthesis of glucose in seeds (wheat, bean, sunflower). The glyoxylate cycle.
18. Biosynthesis of the glycosidic bond.
19. Biosynthesis of fatty acids and triglycerides.
20. Biosynthesis of DNA and RNA
21. Biosynthesis of proteins.