KERTÉSZETI ÉS ÉLELMISZERIPARI EGYETEM

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Connection of biomolecules with organic chemistry

Judit Kosáry

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. All of atoms except carbon and hydrogen are called heteroatom (e.g. N, O, P and S).

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EN=2.1

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EN=2.5

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EN=3.0

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EN=3.5

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EN=2.2

S

EN=2.5

Position of biogenic elements in the periodical system and their electronegativity (EN)

Biomolecules

Biomolecules are organic molecules building up living organisms. Types of biomolecules: proteins, carbohydrates, nucleic acids and lipids (apolar biomolecules). Proteins, carbohydrates, nucleic acids are chiral biopolymers:

Type of biomolecule

Units

Bonds between units

Proteins

(-Amino acids

Peptide bond (a special carboxamide bond)

Carbohydrates

Simple sugars

O-Glycosidic bond (a special acetal bond)

Nucleic acids

______________________

Nucleotides

______________________

3’,5’-Phosphodiester bond

_____________________

Lipids (apolar biomolecules)

Simple lipids cannot be hydrolyzed by NaOH

Complex lipids can be hydrolyzed by NaOH

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

In the living organisms biomolecules takes part in organic chemical reactions, they are called biochemical processes. Therefore the types of organic reactions we have to know.

Organic reactions

The reactivity of organic molecules and their reaction mechanism chemical reactions are influenced by their electron density characterized by the electronegativity of the atoms in the organic molecule. There are two phases of an organic reaction: attack and stabilization. A reagent molecule attacks the substrate molecule and at least one of the covalent bonds is disappeared. The type of this split is determined by the distribution of the electron concentration of this covalent bond.

Radical mechanism:

In the case of a reaction of radical mechanism an A–B the ( covalent bond of the substrate (the attacked molecule) with symmetric electron density (ENA(ENB – (EN=0 or very small) splits by homolysis: AB (( A( + (B forming two free radicals (containing unpaired electron). This kind of split needs a high energy (heat and/or pressure) or a presence of a free radical as reagent. A typical radical type reaction is the thermal decomposition of hydrocarbons.

Ionic mechanism:

In the case of a reaction of ionic mechanism the distribution of the A–B ( covalent bond of the substrate is asymmetric (ENA(ENB), this bond has a polarized electron density: an electron deficiency ((() on atom A and an electron surplus ((Ө) on atom B. This bond splits by heterolysis. The electron pair of the original ( bond transforms to a non-bonding electron pair of the atom B of higher electronegativity: ((()A((B((Ө) (( A( + B|Ө forming ions. It does not need extra energy therefore easily be carried out. Theoretically the atom of the bond with an electron deficiency ((() can be attacked by a nucleophilic reagent and the atom of the bond with an electron surplus ((Ө) can be attacked by an electrophilic reagent, but there are other important parameters to determine the real attack.

During the second phase of an organic reaction the intermediate formed in the first phase (attack) is stabilized either by a rearrangement or by a transfer of a small part of the intermediate.

Types of reactions (in these cases A–B is the substrate and C–D is the reagent):

Addition (A): A=B + C–D ( C–A–B–D (2 molecules ( 1 molecule, the substrate contains a double bond) AN, AE, AR

Elimination (E): C–A–B–D ( A=B + C–D (1 molecule ( 2 molecules, one of the reaction products contains a double bond) Eionic, ER

Substitution) (S): A–B + C–D ( [A–C–D + B] (intermediate and leaving group) ( A–C (product) + B–D (by-product). During stabilization a small part from the intermediate and the leaving group gives the by-product. (2 molecules ( 2 molecules) SN, SE, SR

Catalyzed reactions

Diagram of catalyzed reactions in an example of exothermic reaction. Catalyst forms a complex with the substrate or the reagent opening a new reaction route with low activation energy

In the case of high activity energy the reagent cannot attack the substrate. In this case a catalyst forms a complex with the substrate or the reagent opening a new, two-step reaction route with low activation energy. The formation of the complex with secondary bonds needs low activation energy. The properties of the complex make the reaction easy, therefore this step needs also low activity energy. At the end of the reaction the catalyst is regenerated. In the case of an exothermic reaction energy released, and in the case of an endothermic reaction energy absorbed can be found. In the living organisms practically all of the reactions are catalyzed. The catalysts are special proteins and they are called enzymes.

Solubility in organic solvents

Solvent – organic solvent – polar and apolar solvents

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Columns(

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Noble gases

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Cl

Electron saving property (ESP) of some elements in the periodical system

When an element is next to electron octet of noble gases (e.g. it is in 7. column), it does not incline to give an electron (no cation or H-bond formation), and this element has a large electron saving property (ESP). The closer is the electron system of an atom to the noble gas configuration; the larger is its ESP. An atom with a large ESP is unable to lose electron concentration even for a hydrogen bond.

The parts of organic molecules

The carbon skeleton part contains only carbon and hydrogen atoms, therefore the electron concentration of this part of the molecule is symmetric (low reactivity). The electron density of the part of a molecule contains heteroatom(s) (e.g. N or O) with high electronegativity besides carbon and hydrogen is asymmetric. This part of the molecule can be easily attacked by nucleophilic or electrophilic reagent. This part (named functional group) of a molecule can determine the reactivity of the whole molecule.

Essential polar and apolar characters:

Polar character: H-bonds with water molecules (polarized bonds, e.g. methanol:

H3C–OH)

Apolar character: no H-bonds with water

a) non-polarized bonds (e.g. hydrocarbons or fats)

b) polarized bond with a heteroatom of large ESP (e.g. methyl chloride H3C–Cl)

In simple functional groups (the heteroatom directly connects to the carbon skeleton): amines – weak H-bonds, alcohols – strong H-bonds, ethers and chlorides – no H-bonds.

In combined functional groups (a central carbon atom (wearing at least two simple functional groups) connects to the carbon skeleton): with carboxylic acids (e.g. acetate) – strong H-bonds, with esters (e.g. ethyl acetate) – no H-bonds, with carboxamides (e.g. acetamide) – very strong H-bonds.

Polar and apolar characters of combined functional groups

Essential polar and apolar characters of simple functional groups

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 called isomers. When the atoms bond are in different order in isomers they are structural (constitutional) isomers. 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), 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 hybridization (sp3), the angle of the bonds is 109,5°, i.e. its geometry is tetrahedral. A carbon atom with four different substituents (often 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

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Other group

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

Group of highest oxidation number

|

Characteristic functional group–C–Smallest functional group

|

Other group

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

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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.

DL

||

DD

Diastereomers

Many biologically active molecules are chiral, including the naturally occurring proteins, carbohydrates and nucleic acids. As enzymes are 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.

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.

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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 2Cu2( ( Cu22(), therefore aldoses are called reducing sugars. Ketones cannot be oxidized because of the absence of CH in carbonyl group. But in forced conditions ketoses can be isomerized to aldoses by double oxo-enol-oxo tautomerism, therefore all of simple sugars are reducing sugars.

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Cyclization of simple sugars

The cyclization of sugars is caused by a reversible intramolecular reaction (nucleophilic addition) between the carbonyl and one of hydroxyl group of the straight-chain (open form) sugar. This hydroxyl group is connected to the chiral carbon atom of highest number. The cycle that contains an oxygen and the new hydroxyl groups is connected to chiral carbon atom can be in different positions forming stereoisomers. Aldopentoses and ketohexoses form five-membered rings with plane surface (furanosides). Aldohexoses form three dimensional six-membered rings (pyranosides), those are generally projected as planar, and D-hydroxy groups are under the ring and L-hydroxy groups are above the ring. Cyclization generates a new chiral center, in which the D-hydroxyl group is called the (-anomer and the L-hydroxy group is called the (-anomer.

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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).

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The most important disaccharides and the ring-formed fructose

Among polysaccharides starch and cellulose are the most important. The building unit of starch is maltose. Plants use starch as energy reserve. Its function is similar to that of glycogen in animals and people. There are two types of starch: amilose (a linear polymer containing only 1,4 glycosidic bonds) and amilopectin (a branched polymer containing both 1,4 and 1,6 glycosidic bonds). The building unit of cellulose is cellobiose. Cellulose is a structural components of primary cell walls of green plants and is the most wide-spread organic molecule in the world. The name of the polysaccharides containing only D-glucose molecules is glucan – starch is an (-glucan and cellulose is a (-glucan.

Proteins

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

Units of the polypeptide chain, the L-(-amino acids

They are the building blocks of proteins connected by peptide bonds. Standard (protein, proteinogenous) amino acids build up proteins, non-standard (non-protein, non-proteinogenous) amino acids can be important metabolic intermediates. The name of standard amino acids is used generally in their abbreviated form. The modified 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.

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a

n

i

n

(

A

l

a

)

v

a

l

i

n

(

V

a

l

)

l

e

u

c

i

n

(

L

e

u

)

H

2

N

C

H

C

O

O

H

C

H

C

H

3

C

H

2

C

H

3

H

2

N

C

H

C

O

O

H

C

H

2

N

C

O

O

H

H

i

z

o

l

e

u

c

i

n

(

I

l

e

)

f

e

n

i

l

a

l

a

n

i

n

(

P

h

e

)

p

r

o

l

i

n

(

P

r

o

)

A

h

i

d

r

o

f

ó

b

k

ö

l

c

s

ö

n

h

a

t

á

s

r

a

a

l

k

a

l

m

a

s

f

e

h

é

r

j

e

a

l

k

o

t

ó

a

m

i

n

o

s

a

v

a

k

Amino acids of hydrophobic character

A

z

i

o

n

o

s

k

ö

l

c

s

ö

n

h

a

t

á

s

r

a

a

l

k

a

l

m

a

s

f

e

h

é

r

j

e

a

l

k

o

t

ó

a

m

i

n

o

s

a

v

a

k

H

2

N

C

H

C

O

O

H

(

C

H

2

)

4

N

H

2

l

i

z

i

n

(

L

y

s

)

a

s

z

p

a

r

a

g

i

n

s

a

v

(

A

s

p

)

H

2

N

C

H

C

O

O

H

C

O

O

H

C

H

2

g

l

u

t

a

m

i

n

s

a

v

(

G

l

u

)

H

2

N

C

H

C

O

O

H

C

H

2

C

H

2

C

O

O

H

H

2

N

C

H

C

O

O

H

(

C

H

2

)

3

N

H

C

=

N

H

N

H

2

a

r

g

i

n

i

n

(

A

r

g

)

Amino acids with ionic character

H

2

N

C

H

C

O

O

H

C

H

2

O

H

H

2

N

C

H

C

O

O

H

O

H

C

H

3

C

H

H

2

N

C

H

C

O

O

H

C

H

2

H

2

N

C

H

C

O

O

H

C

H

2

C

O

N

H

2

H

2

N

C

H

C

O

O

H

C

H

2

C

H

2

C

O

N

H

2

O

H

t

i

r

o

z

i

n

(

T

y

r

)

t

r

e

o

n

i

n

(

T

h

r

)

s

z

e

r

i

n

(

S

e

r

)

a

s

z

p

a

r

a

g

i

n

(

A

s

n

)

g

l

u

t

a

m

i

n

(

G

l

n

)

t

r

i

p

t

o

f

á

n

(

T

r

p

)

h

i

s

z

t

i

d

i

n

(

H

i

s

)

H

2

N

C

H

C

O

O

H

C

H

2

N

H

H

2

N

C

H

C

O

O

H

C

H

2

N

N

H

A

h

i

d

r

o

g

é

n

k

ö

t

é

s

r

e

a

l

k

a

l

m

a

s

f

e

h

é

r

j

e

a

l

k

o

t

ó

a

m

i

n

o

s

a

v

a

k

Amino acids with hydrogen bonds

H

2

N

C

H

C

O

O

H

C

H

2

C

H

2

S

–

C

H

3

m

e

t

i

o

n

i

n

(

M

e

t

)

A

d

i

p

ó

l

u

s

-

d

i

p

ó

l

u

s

k

ö

l

c

s

ö

n

h

a

t

á

s

r

a

a

l

k

a

l

m

a

s

f

e

h

é

r

j

e

a

l

k

o

t

ó

a

m

i

n

o

s

a

v

H

2

N

C

H

C

O

O

H

C

H

2

S

H

c

i

s

z

t

e

i

n

(

C

y

s

)

A

d

i

s

z

u

l

f

i

d

k

ö

t

é

s

r

e

a

l

k

a

l

m

a

s

f

e

h

é

r

j

e

a

l

k

o

t

ó

a

m

i

n

o

s

a

v

Cysteine with disulphide bond and methionine with dipole-dipole interaction

N

a

O

H

H

2

O

S

N

i

e

t

i

l

é

n

-

k

l

ó

r

h

i

d

r

i

n

s

z

o

m

s

z

é

d

-

c

s

o

p

o

r

t

h

a

t

á

s

C

H

2

C

H

2

O

d

d

N

a

O

H

H

2

O

d

C

H

2

C

H

2

O

O

H

H

A

N

e

t

i

l

é

n

g

l

i

k

o

l

A

z

e

t

i

l

é

n

k

l

ó

r

h

i

d

r

o

n

r

e

a

k

c

i

ó

j

a

"

O

"

C

H

3

C

H

2

O

C

H

2

C

H

3

"

O

"

H

2

O

H

S

C

H

3

m

e

t

á

n

-

t

i

o

l

+

C

H

3

S

H

s

t

a

b

i

l

d

i

s

z

u

l

f

i

d

h

í

d

C

H

3

S

S

C

H

3

C

H

3

C

H

2

O

O

–

C

H

2

C

H

3

C

H

3

C

H

2

O

d

i

e

t

i

l

é

t

e

r

d

i

e

t

i

l

-

p

e

r

o

x

i

d

A

p

e

r

o

x

i

d

o

k

é

s

a

d

i

s

z

u

l

f

i

d

o

k

s

t

a

b

i

l

i

t

á

s

i

k

ü

l

ö

n

b

s

é

g

e

C

H

2

C

H

2

O

d

d

d

e

t

i

l

é

n

-

o

x

i

d

(

s

z

ö

g

f

e

s

z

ü

l

t

s

é

g

)

C

H

2

C

H

2

C

l

O

d

d

C

H

2

C

H

2

C

l

O

–

H

d

d

2

Formation of disulphide bond and peroxides

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.

N

a

O

H

C

u

2

+

C

H

R

C

N

C

H

C

N

O

O

R

H

H

i

b

o

l

y

a

s

z

í

n

û

k

o

m

p

l

e

x

A

b

i

u

r

e

t

r

e

a

k

c

i

ó

C

u

C

H

R

C

N

C

H

C

N

O

O

R

C

H

R

C

N

C

H

C

N

H

O

H

O

R

(

a

n

á

t

r

i

u

m

-

h

i

d

r

o

x

i

d

d

a

l

s

ó

t

k

é

p

e

z

h

e

t

)

i

m

i

d

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.

H

2

N

C

H

N

H

R

O

C

H

O

O

H

N

-

t

e

r

m

i

n

á

l

i

s

C

-

t

e

r

m

i

n

á

l

i

s

A

f

e

h

é

r

j

é

k

e

l

s

ô

d

l

e

g

e

s

s

z

e

r

k

e

z

e

t

e

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.

C

C

N

C

H

a

a

O

d

i

p

o

l

á

r

i

s

,

g

á

t

o

l

t

r

o

t

á

c

i

ó

j

ú

s

z

a

k

a

s

z

a

s

a

v

a

m

i

d

c

s

o

p

o

r

t

b

a

n

(

a

p

e

p

t

i

d

k

ö

t

é

s

b

e

n

)

O

a

a

C

C

N

C

H

a

c

e

t

a

m

i

d

C

H

3

C

O

N

H

2

d

N

a

O

H

n

a

g

y

o

n

n

e

h

e

z

e

n

k

i

s

C

H

3

C

O

N

H

2

C

H

3

C

O

N

H

H

A

s

a

v

a

m

i

d

c

s

o

p

o

r

t

j

e

l

l

e

m

z

é

s

e

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

1

/

2

O

2

(

a

z

a

s

z

k

o

r

b

i

n

s

a

v

k

ö

z

v

e

t

í

t

é

s

é

v

e

l

)

H

y

p

r

é

s

z

l

e

t

a

f

e

h

é

r

j

e

l

á

n

c

b

a

n

N

O

H

O

P

r

o

r

é

s

z

l

e

t

a

f

e

h

é

r

j

e

l

á

n

c

b

a

n

N

O

A

h

i

d

r

o

x

i

-

p

r

o

l

i

n

k

é

p

z

ô

d

é

s

e

a

p

e

p

t

i

d

l

á

n

c

b

a

n

Oxidation of proline to hydroxyproline in the peptide chain by L-ascorbate (vitamin C)

Tertiary structure: – Connections between remote parts of the peptide chain by secondary bonds between the side chains of amino acids – globular structures (folded to three dimensional structures, they contain all of the secondary structures) and fibrous structures (folded to fibres, they contain only one of the secondary structures).

Interactions:

· hydrophobic interactions – glycine (Gly), alanine (Ala), valine (Val), leucine (Leu), isoleucine (Ile), phenylalanine (Phe), proline (Pro)

· ionic interactions – aspartic acid (Asp) glutamic acid (Glu), lysine (Lys), arginine (Arg)

· hydrogen bonds – serine (Ser), threonine (Thr), tyrosine (Tyr), asparagine (Asn), glutamine (Glu), tryptophan (Trp), histidine (His)

· disulphide bond – cysteine (Cys)

· dipole-dipole interactions methionine (Met);

Quaternery structure:– Connection between several polypeptide chains usually called protein subunits by secondary bonds between the side chains of amino acids.

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

The classification of enzymes – enzymes can be identified by their number in Enzyme Nomenclature (Enzyme Catalogue EC). EC number is a combination of four numbers. The first number of the combination shows the type of the reaction catalyzed.

1. Oxidorecuctases – catalyze oxidation and reduction (dehydrogenases and oxigenases)

2. Transferases – catalyze subtitutions

3. Hydrolases – catalyze hydrolysis

4. Lyases – catalyze addition and elimination

5. Isomerases – catalyze tautomerism

6. Ligases – catalyze reactions using the energy of macroerg bonds

Coenzymes

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.

N

H

C

O

N

H

2

N

H

H

C

O

N

H

2

H

H

+

H

l

m

a

x

=

2

6

0

n

m

l

m

a

x

=

2

6

0

é

s

3

4

0

n

m

A

n

i

k

o

t

i

n

a

m

i

d

o

t

t

a

r

t

a

l

m

a

z

ó

k

o

e

n

z

i

m

e

k

r

e

d

u

k

á

l

ó

d

á

s

i

f

o

l

y

a

m

a

t

a

The process of reduction of coenzymes containing a nicotinamide structure

N

N

N

N

N

H

2

2

H

(

H

+

H

)

R

=

H

(

N

A

D

H

+

H

+

)

R

=

(

N

A

D

P

H

+

H

+

)

P

R

=

H

(

N

A

D

+

)

n

i

k

o

t

i

n

a

m

i

d

-

a

d

e

n

i

n

-

d

i

n

u

k

l

e

o

t

i

d

R

=

(

N

A

D

P

+

)

P

A

N

A

D

+

é

s

N

A

D

P

+

k

o

e

n

z

i

m

e

k

N

H

O

O

N

H

H

O

C

H

2

O

O

O

H

O

H

H

H

H

H

p

s

z

e

u

d

o

u

r

i

d

i

n

(

y

C

)

H

N

N

H

O

O

d

i

h

i

d

r

o

–

u

r

a

c

i

l

(

D

H

U

)

N

é

h

á

n

y

r

i

t

k

a

n

u

k

l

e

o

t

i

d

k

é

p

l

e

t

e

N

N

N

N

N

H

2

N

H

H

H

H

O

H

O

H

O

C

H

2

C

O

N

H

2

O

H

H

C

H

2

H

H

H

H

O

R

O

H

O

O

N

H

H

H

H

O

H

O

H

O

C

H

2

C

O

N

H

2

O

H

C

H

2

H

H

H

H

O

R

O

H

O

O

O

P

P

O

P

P

H

Coenzymes NAD( and NADPH(

N

N

N

N

H

H

A

f

l

a

v

i

n

t

t

a

r

t

a

l

m

a

z

ó

k

o

e

n

z

i

m

e

k

r

e

d

u

k

á

l

ó

d

á

s

i

f

o

l

y

a

m

a

t

a

2

H

The process of reduction of coenzymes containing flavines

N

N

N

H

N

C

H

2

H

C

O

H

H

C

O

H

H

C

O

H

H

2

C

H

3

C

H

3

C

O

O

N

N

N

N

N

H

2

C

H

2

H

H

H

H

O

H

O

H

O

2

H

N

N

N

H

N

C

H

2

H

C

O

H

H

C

O

H

H

C

O

H

H

2

C

H

3

C

H

3

C

O

O

O

H

H

N

N

N

N

N

H

2

O

C

H

2

H

H

H

H

O

H

O

H

O

F

A

D

(

f

l

a

v

i

n

-

a

d

e

n

i

n

-

d

i

n

u

k

l

e

o

t

i

d

)

F

A

D

H

2

N

N

N

H

N

C

H

2

H

C

O

H

H

C

O

H

H

C

O

H

H

2

C

H

3

C

H

3

C

O

O

O

–

R

P

R

=

R

=

H

(

B

2

v

i

t

a

m

i

n

)

r

i

b

o

f

l

a

v

i

n

F

M

N

(

f

l

a

v

i

n

m

o

n

o

n

u

k

l

e

o

t

i

d

)

A

f

l

a

v

i

n

t

t

a

r

t

a

l

m

a

z

ó

k

o

e

n

z

i

m

e

k

é

s

p

r

e

k

u

r

z

o

r

v

i

t

a

m

i

n

j

u

k

O

P

P

O

O

O

P

P

Flavin-containing coenzymes and their precursor vitamin

Ubiquinone (coenzyme Q) (its starting material is tyrosine and its reduced form is ubiquinol) is that kind of oxidoreductase coenzyme, which can work by both ionic and radical mechanism. The name of the human ubiquinone is CoQ10. The starting material of ubiquinone is tyrosine.

Redox reactions of ubiquinone

In various kinds of cytochromes the coenzyme effecting electron transfer is hem (by ferrous-ferric transformation).

The structure of hem

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

O

H

O

H

O

C

C

H

2

O

H

H

H

O

O

L

-

a

s

z

k

o

r

b

i

n

s

a

v

(

C

-

v

i

t

a

m

i

n

)

o

x

r

e

d

d

e

h

i

d

r

o

-

a

s

z

k

o

r

b

i

n

s

a

v

(

b

o

m

l

é

k

o

n

y

)

O

O

O

C

C

H

2

O

H

H

H

O

O

A

z

a

s

z

k

o

r

b

i

n

s

a

v

o

x

i

d

á

l

t

é

s

r

e

d

u

k

á

l

t

f

o

r

m

á

j

a

A

z

A

T

P

á

t

a

d

h

a

t

ó

c

s

o

p

o

r

t

j

a

i

N

N

N

N

N

H

2

O

O

H

O

H

H

H

H

H

P

–

O

–

P

–

O

–

P

–

C

H

2

Redox reactions of L-ascorbic acid

Transferases can catalyze several kinds of substitutions. The transferred 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).

H

N

N

H

C

O

S

C

H

2

C

H

2

C

H

2

C

H

2

C

O

O

H

C

O

2

A

T

P

A

D

P

N

H

C

O

N

C

O

O

H

C

H

2

C

H

2

C

H

2

C

H

2

S

H

O

O

C

b

i

o

t

i

n

(

H

-

v

i

t

a

m

i

n

)

k

a

r

b

o

x

i

-

b

i

o

t

i

n

A

b

i

o

t

i

n

k

e

l

e

t

k

e

z

é

s

e

é

s

f

o

r

m

á

i

Transfer coenzyme – carbon dioxide – biotin

C

H

C

O

O

H

C

H

2

C

H

2

S

C

H

3

H

2

N

+

O

O

H

O

H

H

H

H

H

–

O

–

C

H

2

N

N

N

N

N

H

2

P

P

i

P

i

M

e

t

A

T

P

N

N

N

N

N

H

2

O

O

H

O

H

H

H

H

H

C

H

2

H

3

C

H

2

N

S

C

H

2

C

H

2

C

O

O

H

C

H

S

-

a

d

e

n

o

z

i

l

-

m

e

t

i

o

n

i

n

(

S

A

M

)

C

H

3

N

N

N

N

N

H

2

O

O

H

O

H

H

H

H

H

C

H

2

H

2

N

S

C

H

2

C

H

2

C

O

O

H

C

H

S

-

a

d

e

n

o

z

i

l

-

h

o

m

o

c

i

s

z

t

e

i

n

(

S

A

H

)

O

P

P

P

O

A

S

A

M

k

e

l

e

t

k

e

z

é

s

e

é

s

k

ü

l

ö

n

b

ö

z

ô

f

o

r

m

á

i

Transfer coenzyme – methyl group – SAM

C

H

C

O

O

H

C

H

2

C

H

2

C

O

H

N

C

H

2

–

N

H

N

N

N

H

N

H

2

N

O

H

H

C

O

O

H

C

1

1

2

3

4

5

6

7

8

4

-

a

m

i

n

o

b

e

n

z

o

e

s

a

v

G

l

u

C

1

:

C

H

O

C

H

3

C

H

2

O

H

C

H

C

O

O

H

C

H

2

C

H

2

C

O

H

N

C

H

2

–

N

H

N

N

N

H

N

H

2

N

O

C

O

O

H

f

o

l

s

a

v

(

B

1

0

v

i

t

a

m

i

n

)

A

C

1

r

é

s

z

l

e

t

e

k

e

t

s

z

á

l

l

í

t

ó

k

o

e

n

z

i

m

é

s

p

r

e

k

o

e

n

z

i

m

v

i

t

a

m

i

n

j

a

C

H

2

t

e

t

r

a

h

i

d

r

o

-

f

o

l

s

a

v

(

T

H

F

)

Transfer coenzyme – C1 – THF

P

N

N

C

H

2

N

C

H

S

N

H

2

H

3

C

H

3

C

C

H

2

C

H

2

O

O

P

t

i

a

m

i

n

-

p

i

r

o

f

o

s

z

f

á

t

(

T

P

P

)

N

N

C

H

2

N

C

H

S

N

H

2

H

3

C

H

3

C

C

H

2

C

H

2

O

H

t

i

a

m

i

n

(

a

n

e

u

r

i

n

)

B

1

-

v

i

t

a

m

i

n

A

z

a

c

e

t

a

l

d

e

h

i

d

e

t

s

z

á

l

l

í

t

ó

k

o

e

n

z

i

m

é

s

p

r

e

k

u

r

z

o

r

v

i

t

a

m

i

n

j

a

H

N

N

H

C

O

S

C

H

2

C

H

2

C

H

2

C

H

2

C

O

O

H

C

O

2

A

T

P

A

D

P

N

H

C

O

N

C

O

O

H

C

H

2

C

H

2

C

H

2

C

H

2

S

H

O

O

C

b

i

o

t

i

n

(

H

-

v

i

t

a

m

i

n

)

k

a

r

b

o

x

i

-

b

i

o

t

i

n

A

b

i

o

t

i

n

k

e

l

e

t

k

e

z

é

s

e

é

s

f

o

r

m

á

i

P

O

P

N

N

C

H

2

N

C

S

N

H

2

H

3

C

H

3

C

C

H

2

C

H

2

O

C

H

3

C

H

O

H

"

a

k

t

í

v

a

c

e

t

a

l

d

e

h

i

d

"

Transfer coenzyme – acetaldehyde – TPP

K

o

e

n

z

i

m

-

A

c

i

s

z

t

e

a

m

i

n

b

-

a

l

a

n

i

n

O

O

O

H

H

H

H

H

C

H

2

O

N

N

N

N

N

H

2

P

2

,

4

-

d

i

h

i

d

r

o

x

i

-

3

,

3

-

d

i

m

e

t

i

l

-

v

a

j

s

a

v

P

N

N

N

N

N

H

2

O

O

O

H

H

H

H

H

C

H

2

O

C

H

3

–

C

O

–

S

K

o

A

a

c

e

t

i

l

k

o

e

n

z

i

m

A

"

a

k

t

í

v

e

c

e

t

s

a

v

"

C

H

2

O

H

C

C

H

–

O

H

C

H

3

C

H

3

C

=

O

N

H

C

H

2

C

H

2

C

O

O

H

p

a

n

t

o

t

é

n

s

a

v

(

r

é

g

e

n

B

9

-

v

i

t

a

m

i

n

)

(

ú

j

a

b

b

a

n

B

5

v

i

t

a

m

i

n

)

N

H

3

C

H

O

C

H

2

O

H

C

H

2

O

H

N

H

3

C

H

O

C

H

2

O

–

C

H

O

P

N

H

3

C

H

O

C

H

2

O

–

C

H

2

N

H

2

P

p

i

r

i

d

o

x

i

n

(

B

6

-

v

i

t

a

m

i

n

)

p

i

r

i

d

o

x

á

l

-

f

o

s

z

f

á

t

(

P

A

L

)

p

i

r

i

d

o

x

a

m

i

n

-

f

o

s

z

f

á

t

(

P

A

M

)

A

z

a

m

i

n

o

c

s

o

p

o

r

t

o

t

s

z

á

l

l

í

t

ó

k

o

e

n

z

i

m

é

s

p

r

e

k

u

r

z

o

r

v

i

t

a

m

i

n

j

a

O

P

P

O

C

H

2

C

C

H

–

O

H

C

H

3

C

H

3

C

=

O

N

H

C

H

2

C

H

2

C

=

O

N

H

C

H

2

C

H

2

S

H

O

C

H

2

C

C

H

–

O

H

C

H

3

C

H

3

C

=

O

N

H

C

H

2

C

H

2

C

=

O

N

H

C

H

2

C

H

2

S

–

C

–

C

H

3

O

P

P

O

A

k

o

e

n

z

i

m

-

A

k

ü

l

ö

n

b

ö

z

ô

f

o

r

m

á

i

Transfer coenzyme – acetyl group – coenzyme A

S

S

C

C

H

3

O

C

O

O

H

H

S

S

C

O

O

H

H

H

d

i

h

i

d

r

o

-

l

i

p

o

n

s

a

v

a

c

e

t

i

l

-

d

i

h

i

d

r

o

-

l

i

p

o

n

s

a

v

A

l

i

p

o

n

s

a

v

k

o

e

n

z

i

m

k

ü

l

ö

n

b

ö

z

ô

f

o

r

m

á

i

S

S

C

O

O

H

l

i

p

o

n

s

a

v

Transfer coenzyme – acetyl group – lipoic acid

N

H

3

C

H

O

C

H

2

O

H

C

H

2

O

H

N

H

3

C

H

O

C

H

2

O

–

C

H

O

P

N

H

3

C

H

O

C

H

2

O

–

C

H

2

N

H

2

P

p

i

r

i

d

o

x

i

n

(

B

6

-

v

i

t

a

m

i

n

)

p

i

r

i

d

o

x

á

l

-

f

o

s

z

f

á

t

(

P

A

L

)

p

i

r

i

d

o

x

a

m

i

n

-

f

o

s

z

f

á

t

(

P

A

M

)

A

z

a

m

i

n

o

c

s

o

p

o

r

t

o

t

s

z

á

l

l

í

t

ó

k

o

e

n

z

i

m

é

s

p

r

e

k

u

r

z

o

r

v

i

t

a

m

i

n

j

a

Transfer coenzyme – amino group – PAL

Lipids

There are two types of lipid (apolar – fatty soluble) biomolecules. Simple lipids cannot be hydrolyzed by sodium hydroxide and complex lipids contain ester group therefore they can be hydrolyzed by sodium hydroxide.

The two main types of simple lipids are the fatty acids and the terpenes. Fatty acids (C16 and C18) are building blocks of complex lipids (neutral triglycerides and phospholipids). Saturated fatty acids are palmitate (CH3(CH2)14–COOH) and stearate (CH3(CH2)16–COOH). Unsaturated fatty acids are the unsaturated versions of stearate (C18): oleate, linoleate and linolenate. The essential linoleate ((-6-fatty acid) and linolenate ((-3-fatty acid) are known as PUFA (polyunsaturated fatty acids) or vitamins F.

Formulas of oleate, linoleate and linolenate

Terpenes can be derived from isoprene (methylbutadiene) CH2=C(CH3)–CH=CH2 (C5H8). Monoterpenes contain two (C5H8)2 (C10), diterpenes four (C5H8)4 (C20), triterpenes six (C5H8)6 (C30) and tetraterpenes eight isoprene units (C5H8)8 (C40). The branched end of isoprene is called the head (fej in Hungarian) and the other part is called the tail (láb in Hungarian). There are different variations for connecting the isoprene units. Most frequent are head-to-tail connections, while and tail-to-tail and head-to-head variations are rare.

H

2

C

C

C

H

C

H

2

C

H

3

i

z

o

p

r

é

n

f

e

j

-

f

e

j

f

e

j

-

l

á

b

l

á

b

-

l

á

b

f

e

j

l

á

b

A

z

i

z

o

p

r

é

n

e

g

y

s

é

g

e

k

k

a

p

c

s

o

l

ó

d

á

s

i

f

a

j

t

á

i

Different variations of connecting isoprene units: head-to-head, head-to-tail and tail-to-tail

Only two representatives of polyisoprenoids are shown here: chloresterol as triterpene (C30) and (-carotene as tetraterpene (C40). Triterpenes and tetraterpenes generally contain two chains with head-to-tail connection and these chains are 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 cholesterol by uv light plays an important role in calcification of cartilage and bone.

A

B

C

D

C

H

3

C

H

3

A

B

C

D

g

o

n

á

n

v

á

z

s

z

t

e

r

á

n

v

á

z

k

o

l

e

s

z

t

e

r

o

l

c

i

k

l

o

a

l

k

á

n

o

k

C

H

3

C

H

2

C

H

3

C

H

3

C

H

3

C

H

3

O

C

H

3

C

H

3

H

O

C

H

3

C

H

3

C

H

3

l

i

m

o

n

é

n

k

á

m

f

o

r

m

e

n

t

o

l

N

é

h

á

n

y

m

o

n

t

e

r

p

é

n

k

é

p

l

e

t

e

O

H

H

C

H

3

C

H

3

C

H

3

H

O

C

H

3

C

H

3

C

H

3

A

C

D

h

n

h

n

B

C

H

3

H

O

C

H

3

C

H

3

C

H

3

C

H

2

D

3

-

v

i

t

a

m

i

n

(

k

o

l

e

k

a

l

c

i

f

e

r

o

l

)

C

H

3

C

H

3

C

H

3

C

H

3

C

H

3

C

H

3

C

H

3

C

H

3

C

H

3

C

H

3

o

x

.

b

-

j

o

n

o

n

b

-

k

a

r

o

t

i

n

b

-

j

o

n

o

n

C

H

2

O

H

C

H

3

C

H

3

C

H

3

C

H

3

C

H

3

r

e

t

i

n

o

l

(

A

-

v

i

t

a

m

i

n

)

C

H

3

C

H

3

C

H

3

C

H

3

C

H

O

C

H

3

1

1

-

c

i

s

z

-

r

e

t

i

n

á

l

A

g

o

n

á

n

v

á

z

,

a

s

z

t

e

r

á

n

v

á

z

é

s

a

k

o

l

e

s

z

t

e

r

o

l

k

é

p

l

e

t

e

Formulas of gonane and sterane skeletons, and of cholesterol

Tetraterpene carotenoides are organic pigments that are naturally occurring in the chloroplasts and chromoplasts of plants. There are two classes of carotenoides: carotenes are hydrocarbons and xanthophylls contain oxygen. Because of polyconjugated double bond system, carotenoids can absorb light energy for use in photosynthesis, and as antioxidants they protect chlorophyll from photodamage. Antioxidants can eliminate free radicals by reduction. In humans (-carotene and other 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

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.

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Hydrolysis of triglycerides by sodium hydroxide producing soap

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.

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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. The acyl groups are from fatty acids (C16-C18). Phosphoglycerides are surfactants and lecitines are the major component of animal cell membranes (in plants the major membrane lipid components are glycolipids).

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Formation of different kinds of phosphoglycerols: phosphatidyl ethanolamines (szerin-kefalinok in Hungarian), phosphatidyl serines (szerin-kefaninok in Hungarian) and phosphatidyl cholines (lecithines) (lecitinek in Hungarian) from phosphatidate

There many biomolecules containing phosphate in ester (e.g. phosphatidate acid) or anhydride (e.g. ATP) form, therefore their abbreviations are used.

Abbreviations of phosphates in esters and anhydrides

Membrane transport processes

A membrane is a layer of material which serves as a selective barrier between its two sides, and remains impermeable to specific particles, molecules, or substances. The structure of membranes can be illustrated by the fluid mosaic model. Through the bimolecular layer surfactant phospholipids membrane-integrated (transmembrane) proteins can make passage possible for specific molecules. Surface proteins can bind different regular molecules as receptors.

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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.

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. The unit consisting only of a nucleic base and sugar is called nucleoside. The name for a nucleoside monophosphate is nucleotide. The figure of adenosine-triphosphate (ATP) is only an illustration:

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Adenosine triphosphate (ATP)

Connection of biomolecules with organic chemistry (questions)

1. Definition and characterization of biogenic elements.

2. Definition of electronegativity (EN) and electron saving property (ESP).

3. What atoms build up carbon skeleton. Definition of heteroatoms. Heteroatoms of biomolecules.

4. Types of the mechanism of the organic reactions (scheme).

5. Types of organic reactions (scheme).

6. The properties of polar and apolar compounds. Lipids are polar or apolar compounds.

7. Definition and types of biomolecules. Units of different biomolecules.

8. Definition and nomenclature of carbohydrates.

9. Fehling reaction.

10. Importance of the cyclization of sugars (example).

11. The general figure of (-amino acids. Biomolecule containing (-amino acids. The structure of peptide bond.

12. The structural level of peptides (type of bonds).

13. Biuret reaction.

14. Definition and types of lipids (examples).

15. Definition and types of simple lipids (examples).

16. Definition and types of complex lipids. The biological function of different types.

17. What about surfactant molecules (scheme). Membrane transport.

18. Definition and types of compounds with coenzyme function (examples).

19. Redox coenzymes with ionic and radical mechanism (examples).

20. Definition and types of transfer coenzymes (examples).

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