Biochemistry Corr.

Judit Kosáry (2013)

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
Columns 1 … 4 5 6 
Periodes EN

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)

Definition for Exam 1-4

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 Units

Bonds between un
Proteins -Amino acids
Peptide bond (a spe
carboxamide bon
Carbohydrates Simple sugars O-Glycosidic bond
special acetal bon
Nucleic acids Nucleotides 3’,5’-Phosphodies
_____________________ _____________________ bond
_ _ ________________
_
Lipids (apolar Simple lipids cannot be Complex lipids ca
 2

biomolecules) hydrolyzed by NaOH hydrolyzed by NaOH

Characteristic data of the structure of proteins,
carbohydrates and nucleic acids; characterization of lipids

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 (sp 3), 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
 3

|
Other group

The application of Fischer’s convention on the L-enantiomer

CHO CHO CHO CHO CH2OH

HO C H HO C H H C OH H C OH HO C H
CH2OH CH2OH CH2OH CH2OH CHO
L-glicerinaldehid D-glicerinaldehid

Az aszimmetria-centrumok Fischer-féle ábrázolása

COOH COOH H2N COOH

C H CH
R
H2N C H
NH2 R
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).
 4

COOH
H C OH
HO C H
HO C–H
H C–OH
COOH

COOH COOH
D D
H C OH H C OH
L D
H C OH HO C H
COOH COOH
mezo-borkôsav (+)-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
H rotáció H H H
H3C CH3
etán H H H H H
fedô állás nyitott állás
(kedvezôtlen) (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 transz-1,2-dibróm-etilén
kevésbé stabil stabilabb
A simple example for geometric isomers: cis- and trans-1,2-dibromoethylene

Exam 2
 5

Carbohydrates
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.

CHO CHO CHO CHO

HO O
H C OH H C OH H C OH H C OH
O CH2OH H C OH H C OH HO C H
HO
CH2OH H C OH H C OH
HO CH D-glicerinaldehid CH2OH H C OH
D-eritróz
CH2OH D-ribóz CH2OH
L-aszkorbinsav aldózok D-glükóz
(C-vitamin)

CH2OH CH2OH CH2OH CH2OH CH2OH

C O C O C O C O C O
CH2OH H C OH HO C H HO C H HO C H
H C OH H C OH H C OH H C OH
dihidroxi-aceton
CH2OH CH2OH H C OH H C OH
D-ribulóz D-xilulóz CH2OH H C OH
ketózok D-fruktóz CH2OH
D-szeduheptulóz
A legfontosabb egyszerû cukrok és a C-vitamin képlete
 6

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
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 2Cu 2  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.


 O O O H
H C H C H C

H C OH H C OH H C OH

HO C H HO C H HO C H
O H O
H C OH H C OH H C OH

H C OH H C H C

CH2OH CH2OH CH2–OH

CH2OH
O 
H OH
H H
OH H
HO

H OH
- D-glükopiranozid
Az egyszerû cukrok ciklizálódása
Cyclization of simple sugars
 7

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 chiral center, in which the D-hydroxyl group is called the -anomer and the L-
hydroxy group is called the -anomer.
CH2OH H
H CH2OH CH2OH
H O H O O
HO HO 
H H H H
OH H HO H H HO OH
HO OH  OH OH
H H H
H OH  OH
- D-glükopiranozid - 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

CH2OH
O
CH2OH CH2OH H H OH
CH2OH
O OH H H
H O O O
HH H H
H H H
OH H  O OH H OH H H OH
HO OH HO H
H OH H OH H OH
maltóz cellobióz
CH2OH
O
H H CH2OH
H
OH H  O
HO H OH
CH2OH H
OH H H
HOCH2 H OH O HO O O
O H

H HO OH H H OH
H CH2OH H H

OH H H OH
szaharóz laktóz

CH2OH OH
HOCH2 O
O O CH2 
H H HO
H H
OH H O CH2OH
HO
H H H H
H
OH
OH H
H OH HO OH
- D-fruktofuranóz
H OH
genciobióz
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.

Exam 1
Proteins
Proteins (polypeptides) are biopolymers made of -L-
amino acids connected by peptide bonds (a special type of
carboxamide bond).
 9

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 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 COOH H2N COOH H2N COOH

CH CH CH
glicin (Gly)
CH3 CH CH2
alanin (Ala) CH3 CH3 CH
valin (Val) CH3 CH3
leucin (Leu)
H2N COOH H2N COOH
CH CH
CH2 H
CH N COOH
CH2 CH3
CH3
izoleucin (Ile) fenilalanin (Phe) prolin (Pro)

A hidrofób kölcsönhatásra alkalmas fehérjealkotó aminosavak

Amino acids of hydrophobic character

H2N COOH H2N COOH H2N COOH H2N COOH

CH CH CH CH
CH2 CH2 (CH2)4 (CH2)3
COOH CH2 NH2 NH
aszparaginsav (Asp) COOH lizin (Lys) C=NH
glutaminsav (Glu) NH2
arginin (Arg)
Az ionos kölcsönhatásra alkalmas fehérjealkotó aminosavak
Amino acids with ionic character
 10

H2N COOH H2N COOH H2N COOH

CH CH CH
CH2OH CH CH2
CH3 OH
szerin (Ser) treonin (Thr)

H2N COOH H2N COOH

CH CH OH
tirozin (Tyr)
CH2 CH2
CONH2 CH2
aszparagin (Asn) CONH2
glutamin (Gln)
H2N COOH H2N COOH
CH CH
CH2 CH2

NH
N
N
H
triptofán (Trp) hisztidin (His)
A hidrogénkötésre alkalmas fehérjealkotó aminosavak
Amino acids with hydrogen bonds

H2N COOH
CH
H2N COOH CH2
CH
CH2
CH2SH
cisztein (Cys) S–CH3
metionin (Met)
A diszulfidkötésre alkalmas A dipólus-dipólus kölcsönhatásra
   
fehérjealkotó

CH
Cl
2 CH
O–H
aminosav2
Na
alkalmas
CH
OH  Cl
fehérjealkotó
CH 2 2
aminosav
CH
O
CH 2 2

O  SNi
etilén-oxid
Cysteine with disulphide bondH and
etilén-klórhidrin
O methionine with dipole-dipole interaction
2 (szögfeszültség)
szomszéd-csoport hatás

  NaOH
CH2 CH2 H O CH2 CH2 O H AN
H2O
O etilénglikol

Az etilénk lórhidron reak ciója

"O"
CH3 S H + H S CH3 CH3 S S CH3
metán-tiol stabil diszulfid híd
H2O

CH3CH2 O CH2CH3 "O" CH3CH2 O O–CH2CH3 2 CH3CH2 O

dietiléter dietil-peroxid
A perox idok és a diszulfidok stabilitási k ülönbsége
 11

Formation of disulphide bond and peroxides

Formulas: Glu, Asp, Met, Cys, Ser

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 O
H2N
CH N CH OH
R H

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.

O
CH3 C
NH2
acetamid
O O
 C  C
O C C C
CH3 C N C N
N H
H H
H
dipoláris, gátolt
rotációjú szakasz
kis  O
CH3 C a savamidcsoportban
NH2 (a peptidkötésben)

NaOH nagyon
nehezen
A savamidcsoport jellemzése
 12

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, 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 O
N 1/2 O2 N
(az aszkorbinsav
közvetítésével)
HO
Pro részlet a Hyp 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
 13

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.
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.
 14

O O O H O H
NaOH Cu2+
CH C N CH C N CH C N CH C N
R H R H R R imid
Cu
O O (a nátrium-hidroxiddal sót képezhet)

CH C N CH C N
R R
ibolyaszínû komplex
A biuret reakció
Exam 6
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.

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’.
v1 v2
E+S ES E+P
v-1
v1= k1[E].[S] v-1= k-1[ES] v2= k2[ES]
 15

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 Michael-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.

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.
 16

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.

The types of reversible inhibitions: competitive inhibition, mixed inhibition, non-

competitive 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
 17

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.

H
H
H
H H
CONH2 CONH2

+ H
N N

max = 260 nm max = 260 és 340 nm

A nikotinamidot tartalmazó koenzimek redukálódási folyamata

The process of reduction of coenzymes containing a nicotinamide structure
 O
O
HN NH
HN
18 HOCH2O O O
O N
H H H
H H
dihidro–uracil (DHU)
OH OH
pszeudo uridin (C)
Néhány ritka nukleotid képlete

H H H
CONH2 CONH2

CH2 O N CH2 O N
O H H O H H H
H H 2H (H + H ) H H
P P
OH OH NH2 OH OH NH2
O N O N
N N
P P N
N N N
O O
CH2 O CH2 O
H H H H
H H H H
OH OR OH OR
R = H (NAD+ ) nikotinamid-adenin-dinukleotid R = H (NADH + H+ )
R = P (NADP+ ) R = P (NADPH + H+ )

A NAD+ és NADP+ koenzimek

Coenzymes NAD and NADPH

H
N N
2H

N N
H
A flavint tartalmazó koenzimek redukálódási folyamata
The process of reduction of coenzymes containing flavines
 19

O H O
H3C N H3C N
NH 2H NH

H3C N N O H3C N N O
CH2 CH2 H
NH2 NH2
HCOH HCOH
N N
HCOH N HCOH N
HCOH N HCOH N
N N
H2C O P O P O CH2 O H2C O P O P O CH2 O
H H H H
H H H H
OH OH OH OH
FAD (flavin-adenin-dinukleotid) FADH2

O
H3C N
NH

H3C N N O
CH2
R = P FMN (flavin mononukleotid)
HCOH 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 CoQ 10. 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).
 20

The structure of hem

The coenzyme of direct oxygenases is ascorbic acid (vitamin C).

O O
HO O
ox
O O
red
HO O
C H HO C H
HO
CH2OH CH2OH
L-aszkorbinsav dehidro-aszkorbinsav
(C-vitamin) (bomlékony)
Az aszkorbinsav oxidált és redukált formája

NH2
N
N

N N
P–O–P–O–P–CH2 O
H H
H H
Redox reactions
OHof L-ascorbic
OH acid

Transferases can catalyze

Az ATPseveral kinds
átadható of substitutions. The transferred
csoportjai

groups can be different carbon skeletons: C1 – CO2 (biotin that is vitamin H), only
methyl group (SAM – S-adenosylmethionine, its starting material is methionine),
methyl group, aldehyde group, etc. (THF – tetrahydrofolate, its starting material is
folic acid i.e. vitamin B9 – earlier vitamin B10; C2 – acetaldehyde (TPP – thiamine
pyrophosphate, its staring material is aneurine, i.e. vitamin B1), acetyl group in a
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
prosthetic group therefore it is often called lipoamide); and other groups: phosphate
group (ATP or other nucleoside triphosphate molecules), amino group (PAL –
pyridoxal phosphate, its reacted form is PAM – pyridoxamine phosphate, and its
starting material is pyridoxine i.e. vitamin B6).
 21

O O
ATP ADP
C HOOC C
HN NH N NH

CO2
CH2 CH2 CH2 CH2
S CH2 CH2 COOH S CH2 CH2 COOH
biotin karboxi-biotin
(H-vitamin)
A biotin keletkezése és formái
Transfer coenzyme – carbon dioxide – biotin

NH2
H2N COOH N
N
CH
N PPi Pi
CH2 N
P O P O P –O–CH2 O
CH2 H H
H H
S +
CH3 OH OH
Met ATP

H2N COOH H2N COOH

CH NH2 CH3 CH NH2
CH2 N CH2 N
N N
CH2 CH2
N N N N
S S CH2
H3C CH2 O O
H H H H
H H H H

OH OH OH OH
S-adenozil-metionin (SAM) S-adenozil-homocisztein (SAH)
A SAM keletkezése és különbözô formái
Transfer coenzyme – methyl group – SAM
 22

CH2

O H C1
4 N CH2–NH COHN COOH
HN 3 5
6 CH C1: CHO
2
1 8 7 CH2 CH3
H2N N N 4-aminobenzoesav
CH2 CH2OH
H
COOH
tetrahidro-folsav (THF)

Glu
O
N CH2–NH COHN COOH
HN CH
CH2
H2N N N
folsav (B10 vitamin) CH2
COOH
A C1 részleteket szállító koenzim és prekoenzim vitaminja

Transfer coenzyme – C1 – THF

H3C CH2CH2O P O P
N H3C CH2CH2O P O P
H3C CH2 N N
S
N CH H3C CH2 N S
NH2 N C
tiamin-pirofoszfát (TPP) NH2 H3C C OH
H "aktív acetaldehid"
H3C CH2CH2OH
N
H3C CH2 N S
N CH
NH2
tiamin (aneurin) B1-vitamin
Az acetaldehidet szállító koenzim és prekurzor vitaminja

O Transfer coenzyme – acetaldehydeO– TPP

ATP ADP
C HOOC C
HN NH N NH

CO 2
CH2 CH2 CH2 CH2
S CH2 CH2 COOH S CH2 CH2 COOH
biotin
karboxi-biotin
(H-vitamin)
A biotin keletkezése és formái
 CH2OH CHO CH2NH2

HO CH2OH HO CH2O– P HO CH2O– P

23
H3C N H3C N H3C N
piridoxin piridoxál-foszfát piridoxamin-foszfát
(B6-vitamin) (PAL) (PAM)
Az aminocsoportot szállító koenzim és prekurzor vitaminja

NH2 NH2
N N
N N

N N N N
O P O P O CH2 O P O P O CH2
O O
CH2 H H CH2 H H
H H H H
CH3 C CH3 CH3 C CH3 2,4-dihidroxi-
CH–OH O OH CH–OH 3,3-dimetil- O OH
C=O P C=O vajsav P
NH NH
CH2 CH2 CH2OH
-alanin
CH2 CH2 CH3 C CH3

C=O C=O CH–OH

NH NH C=O
CH2 CH2 NH
ciszteamin CH2
CH2 CH2
SH S–C–CH3 CH2

O COOH
Koenzim-A
CH3–CO–SKoA pantoténsav
acetil koenzim A (régen B9-vitamin)
"aktív ecetsav" (újabban B5 vitamin)
A koenzim-A különbözô formái

Transfer coenzyme – acetyl group – coenzyme A

COOH
COOH
HS SH
S S
liponsav dihidro-liponsav
COOH
HS S C CH3
O
acetil-dihidro-liponsav
A liponsav koenzim különbözô formái
Transfer coenzyme – acetyl group – lipoic acid
 24

CH2OH CHO CH2NH2

HO CH2OH HO CH2O– P HO CH2O– P

H3C N H3C N H3C N

piridoxin piridoxál-foszfát piridoxamin-foszfát
(B6-vitamin) (PAL) (PAM)
Az aminocsoportot szállító koenzim és prekurzor vitaminja

Transfer coenzyme – amino group – PAL

Exam 3
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
 25

(C5H8)6 (C30) and tetraterpenes eight isoprene units (C 5H8)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.

H2C C CH CH2
CH3 fej
izoprén láb fej-fej

fej-láb láb-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 (formulas): 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 connected in a tail-to-tail
combination in the middle of the molecule. The chain of the triterpene squalene is
cyclized to cholesterol. The ring system of cholesterol is called the sterane skeleton
(without methyl groups gonane skeleton). Cholesterol can be the starting material for
different kinds of steroids – among them sexual hormones. Vitamin D formed from
CH3
CH3
CH3
cholesterol by uv light plays an important role in calcification of cartilage and bone.
O
CH3 CH3
H
CH3 CH2 OH
kámfor mentol
limonén
Néhány monterpén k éplete

CH3 CH3
CH3 CH3

C D CH3
CH3 C D CH3

A B A B
HO
gonánváz szteránváz koleszterol

cikloalkánok

A gonánv áz, a szteránv áz és a k oleszterol k éplete

CH3 CH3 CH3 CH3

CH3 CH3

CH3 C D CH3 h CH3

CH2
A B
HO h HO
D3-vitamin (kolekalciferol)

Formulas of gonane and sterane skeletons, and of cholesterol

CH3 CH3 CH3
CH3
CH3

Tetraterpene carotenoides are organic pigments that are naturally occurring in

CH3 ox.
-karotin
CH3 CH3 CH3 CH3

-jonon
the chloroplasts and chromoplasts of plants. There are two classes of carotenoides:
-jonon

CH3
carotenes are hydrocarbons and xanthophylls contain oxygen. Because of
CH3 CH3 CH3 CH3
CH2OH
CH3 CH3

polyconjugated double bond system, carotenoids can absorb light energy for use in
CH3
CH3 CH3

photosynthesis, and as antioxidants they protect chlorophyll from photodamage.

retinol (A-vitamin) 11-cisz-retinál CHO

Antioxidants can eliminate free radicals by reduction. In humans -carotene and other
 26

carotenoids can be converted to retinol (vitamin A) by an oxidative splitting. Retinal

synthesized from retinol is essential for vision.

The conjugated double bond system of -carotene

Exam 4
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 CH2 O H
O
RCOOCH + 3 NaOH 3 R C + CH O H
O Na
RCOOCH2 CH2 O H
szappan
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.
 27

O O O
CH3 (CH2)14–C O O
O Na poláros
O zsír O
nátrium-palmitát felület
poláros O O
O O
apoláros
A mosóhatás
Selective adsorption of surfactants to fat

There are different types of phospholipids and type of phosphoglycerides is

their major class. Phosphoglycerols can be derived from phosphatidate (phosphatidic
acid) that is a phosphate ester of diacylglycerols producing phosphatidyl
ethanolamines, phosphatidyl serines, and phosphatidyl cholines.
P ThePacyl groups are
from fatty acids (C16-C18). Phosphoglycerides are surfactants and lecitines are the
major component of animal cell membranes (in plants the P
major Pmembrane lipid
components are glycolipids). P P P

RCOOCH2 RCOOCH2
RCOOCH RCOOCH NH2
CH2–O– P CH2 O P O–CH2–CH
foszfatidsavak szerin-kefalinokCOOH

RCOOCH2
RCOOCH
RCOOCH2 CH2 O P O–CH2CH2 NH2
RCOOCH kolamin-kefalinok
CH2 O P O –CH2CH2 N(CH3)3
apoláros rész 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.
 28

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)
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)

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
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.
 29

Exam 5
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 D-ribose 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.

O O NH2 NH2 O
7
6
1 6 CH3 1 5 N N
HN 5 HN N N HN
8
2 2
4
N 4 N H2N N N
O 3N O N O N 3 9
H H
H H H
uracil timin citozin adenin guanin
(RNS) (DNS)

pirimidin bázisok purin bázisok

a kapcsolódási hely ( ) feltüntetésével

5' 5'
HOCH2 O HOCH2 O
1' OH 4' 1' OH
4'
pentózok H H H H
H 2' H
H
3' 2' H
3'
OH OH OH H
- D-ribofuranozid - D-2'-dezoxiribofuranozid

A nukleinsavak építô elemei

The structure of nucleoside units

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.
 30

O O NH2
CH3
HN HN N

O N O N O N
ROCH2 ROCH2 O ROCH2 O
O
H H H H H H
H H H H H H

OH OH OH H OH Q

R = H uridin (U) R = H dezoxitimidin (dT) R = H, Q = H dezoxicitidin (dC)

R = P uridin monofoszfát R = P dezoxitimidin- R = P O P , Q = OH
(UMP) -monofoszfát (dTMP) 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
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.
 31

The 3’,5’-phosphodiester bond in the polynucleotide chain (R=H DNA, R=OH RNA)

P O CH2 O Bázis B bázis

5'-láncvég H H
H cukor egység
H
3' P 5' 3' (ribóz, dezoxiribóz)
O OH
A nukleozid egység sematikus ábrázolása
P
5' A G
O CH2 O Bázis
H H 5'-láncvég 3'
H P 5'
H P 5' 3' 3'-láncvég
O OH A nukleinsav szekvencia sematikus
3'-láncvég
ábrázolása
A nukleinsavak elsôdleges szerkezete
(a P a megfelelô foszforsav egységet 5'-láncvég AGC ......... 3'-láncvég
jelenti) 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 C-G) and the character of one base
determines the another base, therefore they are called
complementary base pairs.
 32

O NH2 O N
H2N
H3C
H N N
N N N H N
R
N
N N N N
O O H2N
R R R
T A C 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 left-
handed 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.
 33

 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;
 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 nucleotide 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

N N
P O P O P O CH2 O
H H
H H
OH OH
adenozin-trifoszfát (ATP)

Az ATP képlete
Adenosine triphosphate (ATP) formula!
 34

O O
a) savanhidridek – foszforsavanhidrid (pl. ATP) O P O P O O P O P O
H O O H

O C O P
O O
vegyes savanhidrid C O P O pl. H C O H
O H CH2 O P
glicerinsav 1,3-difoszfát

b) különleges észterek – enolészter pl. PEP (foszfo-enol-piruvát) COOH

CH O P
CH2
– tiolészter pl. acetil-koenzim-A O
CH3 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
 35

discussed because the metabolism of nucleic acids is in mitochondria and its role is
peripheral in the nutrition.

Scheme of the degradation of the nutritive materials

Scheme of the biosynthesis of biomolecules

Catabolism
Exam 7
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
 36

coenzyme A by oxygen to CO2 (citric acid cycle) and H2O (with the form of
macroerg bonds) (terminal oxidation – respiratory chain) takes place.

Biomolecule Enzyme Intermediate

Polysaccharides Glycosidases/ Sugars/
Phosphorylases Sugar phosphates
Proteins Proteases/Peptidase Amino acids
s
Neutral Lipases Fatty acids and
triglycerides glycerol
(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-1-
phosphate 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
 37

(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.

Exam 8
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 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 1,6-bisphosphate 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 (C 3) 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.
 38

Glycolysis and the possibilities for the further degradation of

pyruvate

The oxidative step of the glycolysis is the formation of

1,3-bisphosphoglycerate (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.
 39

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 3-
phosphoglycerate. The rearrangement of 3-phosphoglycerate to
2-phosphoglycerate is in fact a combination of two transfer
reactions by means of a cofactor 2,3-bisphosphoglycerate, 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

 40

Fructose can enter the glycolysis in an alternative way called fructose 1-

phosphate 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
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

 41

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

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.
 42

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.
 43

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.
 44

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

Exam 9
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 NAD and the product is 3-ketoacyl CoA
(its earlier name is -ketoacyl CoA; that is the origin of the
 45

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
Exam 10
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
 46

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.

Transamination and oxidative deamination of glutarate

 47

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 ammonia is converted to
urea (in Hungarian karbamid) in the urea cycle (another name
is ornithine cycle) connected to the biosynthesis of arginine
(Arg).
 48

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

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
 49

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 + P i 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

Exam 11
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
 50

elimination followed by water addition. The enzyme is a lyase (aconitase after the
name of the unsaturated 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
 51

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
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 acetyl-
CoA 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.

Exam 12
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
 52

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 3-
phosphate 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

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 oxidation-reduction 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.
 53

Scheme of terminal oxidation

The direction of electron transport: - values  E’0  + values

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-

Formation of the peroxide anion: O2 + 2e  O22-
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  H2O + O2
Elimination of toxic oxygen-containing byproducts

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 F O
subunit.
 54

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. 2,4-
nitrophenol) 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 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
 55

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-3-
methylgutaryl 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 acetyl-
CoA from 3-hydroxy-3-methylgutaryl CoA. The ketone bodies are: acetoacetate,
acetone (produced by the irreversible decarboxylation of acetoacetate) and D-3-
hydroxybutyrate that is produced by the reversible reduction of acetoacetate
accompanied with a NAD  (NADH+H) conversion.
 56

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

Exam 14/1
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.
 57

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).
 58

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. 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 P i  36 ATP + 36 H2O. In the case of the malate-
aspartate shuttle the number of ATP molecules is 38.

Exam 13
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 5-phosphate, erythrose-4-phosphate). The
 59

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 5-posphate 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

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 5-
phosphate (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
 60

transketolases and D in the case of transaldolase. The pentose phosphate pathway is

regulated by the level of NADP.

The pentose phosphate pathway (only until ribose and

xylulose)

The stoichiometry of the pentose phosphate cycle

 61

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 via the glycerol 3-phosphate shuttle. From six
glucose 6-phosphate molecules twelve reduced coenzymes (NADPH+H), six carbon
dioxide molecules and six ribose 5-phosphate 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 non-
carbohydrate precursors called gluconeogenesis. In plants glucose is synthesized by
photosynthesis. During the germination of seeds glucose can be synthesized by
different ways.

Exam 14/2
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 6-phosphate and
 62

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 6-phosphatase 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 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.
 63

Gluconeogenesis

The summary of the process of gluconeogenesis is given in a separate scheme

with the names of intermediates (lactate in Hungarian is tejsav).
 64

The process of gluconeogenesis

Photosynthesis
Exam 15
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.
 65

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.

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
 66

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 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
 67

excited P-680* and P-700 and through several complexes: a primary electron
acceptor that contains pheophytin (PEA), different plastoquinones Q A, 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.
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.

Exam 16
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.
 68

The Calvin cycle (until glycerinaldehyde-3-phosphate)

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 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 3-phosphate 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.
 69

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.

Exam 17
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 acetyl-
CoA 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
 70

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).

The glyoxylate cycle

The scheme of the biosynthesis of glucose by the glyoxylate cycle

Exam 18
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.
 71

Thee 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.
 72

Biosynthesis of glucans

The biosynthesis of lipids

The staring material of both fatty acids and terpenes is acetyl-CoA.

Exam 19.
The biosynthesis of fatty acids
The biosynthesis of fatty acids till the C 16 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
 73

macroerg thiolester. There are two acetyl-CoA molecules at the start of the
biosynthesis. One of the acetyl-CoA molecules is joined to the ACP, to the site of the
prospective long fatty acid (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
(acyl-malonyl-ACP condensing enzyme). The driving force of the synthesis of
acetoacetyl-ACP 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
L-enantiomer, 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 C 2 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.
 74

Biosynthesis of fatty acids

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)
(On the example of -oxidation)

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
 75

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 acyl-CoA 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

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).
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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 acetyl-
CoA, 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
3-hydroxy-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 3-
hydroxy-3-methylgutaryl CoA is reduced by a reductase to mevalonate accompanied
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 (C 10). 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.
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Biosynthesis of the monoterpene geranyl pyrophosphate

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
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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 3-
phosphoglycerate (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.

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.
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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.

The scheme of the biosynthesis of pyrimidine nucleotides

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Biosynthesis of purine nucleotides

The starting material of purine nucleotides is PRPP synthesized from ribose 5-
phosphate (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).

The formation of 2’-deoxyribose from ribose

Exam 20
The biosynthesis of DNA (replication)
During the
The genetic information is stored and expressed by DNA.
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
 81

(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).

The scheme of the replication

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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)

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
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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 hydrolis 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).

Exam 21
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 be transferred;
therefore it is the template recognizing site of tRNA. The third nucleotide member of
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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
 85

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.

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.

Topics in Biochemistry

1. Definition of biomolecules. Proteins – structures, biochemical functions and

figures of some representatives.
 86

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.
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.