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BASIC CELL
BIOLOGY
I CHEMISTRY of LIFE
CLASSIFICATION OF THE ORGANIC
COMPOUNDS, FUNCTIONAL GROUPS
CLASSIFICATION OF THE ORGANIC
COMPOUNDS, FUNCTIONAL GROUPS
• The principles of depicting molecular
structure
• Functional groups typically found in
biomolecules
•Condensation and hydrolysis reactions
of organic compounds
• Ethers and esters
•Alkanes, alkenes, alkynes, aromatic
compounds
•Alcohols and sugars
• Amino acids
• Nucleotides
The principles of depicting molecular structure
Lecture 4
Lecture 4
The principles of depicting molecular structure
Approaches to depict the molecular structure
Lecture 4
The principles of depicting molecular structure
Approaches to depict the molecular structure
By taking away a hydrogen atom from the molecule of methane (CH4)
a methyl radical is created (CH3-), which has highly reactive,
unsaturated valence
+
=
H2C= + =CH2 = H2C=CH2
Lecture 4
The principles of depicting molecular structure
Approaches to depict the molecular structure
Structural
isomers
Simplified
(schematic)
structural
formula
Lecture 4
The principles of depicting molecular structure
Approaches to depict the molecular structure
Lecture 4
The principles of depicting molecular structure
Approaches to depict the molecular structure
Lecture 4
The principles of depicting molecular structure
Approaches to depict the molecular structure
Lecture 4
The principles of depicting molecular structure
Approaches to depict the molecular structure
Lecture 4
The principles of depicting molecular structure
Approaches to depict the molecular structure
Lecture 4
The principles of depicting molecular structure
Approaches to depict the molecular structure
Lecture 4
Functional groups
The groups of atoms within the molecule
which posses distinct chemical properties
Functional groups
The rest of the molecule which is
connected to the functional group is
denoted by R - (radical)
Name
Methyl-CH3
Formula
R- CH3
The simplest
compound
H-CH3 = CH4
Methane
The type of
macromolecules
Hydrocarbons
Lecture 4
Representative
H3C-CH3
ethane
Lecture 4
Functional groups
The presence of the functional groups in the
molecule is denoted in their names by specific
endings
Name
Formula
The simplest
compound
Hydroxyl- R-OH
H3C-OH
-OH
methanol
The type of
macromolecules
Alcohols
Representative
CH3-CH2-OH
ethanol, vine spirit
Lecture 4
Functional groups
Functional groups may be involved in chemical
reactions
Name
Formula
The simplest
compound
Hydroxyl- R-OH
H3C-OH
-OH
methanol
R-O-R
H3C-O-CH3
dimethylether
The type of
macromolecules
Alcohols
Representative
CH3-CH2-OH
ethanol, vine spirit
Ethers
H3C-O-C2H5
methyl-ethyl ether
Lecture 4
Functional groups
Name
Formula
Carbonyl-CHO
The simplest
compound
O
R
C
O
H
Type of
Representative
comp.
Aldehydes
O
C
H
H 3C
H
H
methanal,
methylaldehyde
C
R
C
O
ethanal, ethyl aldehyde
(acetaldehyde)
Ketons
H3 C
R
C
H3 C
O
O
H3 C
dimethylketone
C
H
C
H3 C
H
O
CH2
methyl-ethyl ketone
Lecture 4
Functional groups
Names
Carboxyl
-COOH
Formula
The simplest
compound
O
R
O
C
H
OH
C
OH
Type of
comp.
Carboxyl
acids
(organic acids)
Mathanic acid
(formic acid)
O
H 3C
C
OH
Ethanic acid (acetic acid)
Esters
O
R
Representative
O
H3 C C
C
O
R
O CH3
Methyl ester of the acetic
acid
Methylacetate
Lecture 4
Functional groups
Oxidation of the methane
OH
H
H
C
H
H
H
C
O
O
H
H
Alcohol
H
H
C
H
Aldehyde
C
OH
Acid
Lecture 4
Functional groups
One molecule may contain several
identical or different functional
groups
H
H
CH
HC
C
OH OH OH
H
H
H
H
HC
C
Polyvalent alcohols
- polyols (glycerol)
OH
O
C
OH
Complex carbonic
acids (lactic acid)
Lecture 4
Functional groups
Name
Amino-NH2
Formula
- OPO
compound
compounds
N
H
Phosphates –
23
Type of
H-NH2=NH3
ammonia
H
R
The simplest
Organic
phosphates
O
R O
O
P
O
-
-
O
HO
Amines
O
-
-
H-SH = H2S
Hydrogen
sulphide
C
HC
H
CH
OH
OH
O
O
P
O-
phosphate
R-SH
H3C-NH2
methylamine
O
P
O
Sulphidryl
-SH
Representative
Mercaptans
(thiols)
Phosphog;lycerate
HS-CH2-CH2-OH
mercaptoethanol
O-
Lecture 4
Functional groups
Placement of the functional groups in the molecule
R
R
H3C
CH2
CH2
R
CH2
At the primary C atom
CH3
CH
H3C
CH2
At the secondary C atom
C
H3 C
CH2
H3C
CH2
OH
Primary (n-) butanol
OH
CH3
CH
H3C
CH3
At the tertiary C atom
OH
CH2
CH3
CH2
Secondary (izo-) butanol
C
H3 C
CH3
CH3
Tertiary (tret-) butanol
Functional groups
Lecture 4
Optical (mirror) symmetry / chirality (+/-) D/L
isomers - enantomers
The secondary C atom of lactic acid is connected to
three different functional groups and to H atom
Lecture 4
Functional groups
Functional groups may be involved in chemical
reactions
• condensation (associatioun which is
accompanied by release of water)
• hydrolysis (dissocciation by addition of
water)
R -OH + OH-R
R-O-R +H2O
R-O-R +H2O
R -OH + OH-R
Lecture 4
Functional groups
At condensation of two alcohol molecules an
ether is formed
R-O-R
H3C-O-CH3
H3C-O-C2H5
dimetil-ēteris
metil-etil - ēteris
Lecture 4
Functional groups
At condensation of alcohol and organic acid an
esther is formed
O
R
O
R
C
OH
HO
R
C
O
R
Lecture 4
Functional groups
At condensation of alcohol and organic acid an
esther is formed
O
H3C C
O CH3
Methylesther of acetic acid, Methylacetate
Lecture 4
Types of the organic compounds
Alcans– the simplest organic molecules, which
are formed only by H and C atoms.
General chemical composition: CnH2n+2
The simplest alcane: methane: CH4
Ethane
Propane
Butane
Pentane
H3C-CH3 ;
H3C-CH2-CH3;
H3C-(CH2)2-CH3;
H3C-(CH2)3-CH3;
C2H6
C3H8
C4H10
C5H12
Lecture 4
Types of the organic compounds
Alcane radicals are obtained by taking away one
hydrogen atom from the molecule. The names of the
radicals are derived by adding the ending -yl to the
corresponding names of the alcanes (dodecyl-).
STRUCTURAL ISOMERS:
TRIVIAL NAMES USED IN BIOLOGY:
n-pentane
iso-pentane
neo-pentane
H3 C
CH3
H3 C
CH2
CH2
CH2
CH3
CH
H3 C
CH3
CH2
H3 C
C
CH3
H3 C
pentane
2-methyl-butane
2,2-dimethyl-propane
INTERNATIONAL CHEMICAL NOMENCLATURE(IUPAC)
Lecture 4
Types of the organic compounds
Cyclic alkanes: CnH2n
Cyclohexane
H2C
CH2
CH2
H2C
CH2
CH2
Aromatic compounds (arens)
Benzol (benzene)
H
H
H
C
H
C
C
C
C
C
H
H
Conjugated (connected) double bounds in the bezene ring are not
fixed to a specific carbon atom. They may fluctuate from one atom to
another.
Lecture 4
Types of the organic compounds
Alkenes
If two hydrogen atoms are removed from
neighbouring carbon atoms in an alcane
molecule (dehydration), a double covalent
bond may be formed.
Hydrocarbons, which contain one or more
double bonds are called alkenes.
Their names are derived from the names of
corresponding alcanes by replacing ending ane with the ending -ene.
Types of the organic compounds
Alkynes
Lecture 4
If four hydrogen atoms are removed from
neighbouring carbon atoms in an alcane
molecule (dehydration), a triple covalent
bond may be formed.
Hydrocarbons, which contain one or more
triple bonds are called alkynes.
Their names are derived from the names of
corresponding alcanes by replacing ending ane with the ending -yne. Trivial names are
used too, e.g. - ethyne=acetylene.
Lecture 4
Types of the organic compounds
Spatial isomers
H 3C
HC
H
H
CH
CH 3
FREE ROTATION AROUND BOND - NO ISOMERS
Lecture 4
Types of the organic compounds
Spatial isomers
H
HC
H 3C
CH 3
CH
H
FREE ROTATION AROUND BOND - NO ISOMERS
Lecture 4
Types of the organic compounds
Spatial isomers
H
CH3
C
H3 C
H
C
H
C
H
trans- butilene
H3 C
C
CH3
cis- butilene
NO ROTATION AROUND DOUBLE BOND - ISOMERS
Lecture 4
Types of the organic compounds
CARBOHYDRATES (SUGARS)
General chemical formula (CH2O) = carbon + water.
Simple molecules (monomers) – monosaccharides:
a chain of 3 – 6 C atoms + one carbonyl (aldehyde-)
and several hydroxyl groups.
In the result of condensation reactions di-, tri- and
poly-saccharides are formed.
Lecture 4
Types of the organic compounds
CARBOHYDRATES (SUGARS)
C
OH
OH
HO
C
C
OH
HO
H2C
OH
H
C
OH H
C
H
H
C
OH H
C
H
C
OH H
OH
Ribose
H2C
HC
H
H
OH
O
HC
HC
HC
H2C
O
O
O
H
C
OH
H
HO
C
H
C
H
H
C
C
OH
H
H2C
OH
Deoxyribose
Galactose
Pentoses
Aldoses
C
O
HO
C
H
OH
H
C
OH
C
OH
H
C
OH
H2C
OH
H2C
OH
Glucose
Hexoses
Fructose
Ketose
Lecture 4
Tautomerisation of the carbohydrates
6
CH 2OH
O
1
H
4
HO
OH
H
HO
H
HO
H
O
H
OH
OH O
H
OH OH
OH
H
1
OH
OH
H
H
OH
a-D-glycopyranose
H
H
OH
6
CH 2OH
H
6
H
OH
D - glucose
4
HO
O
H
OH
H
H
OH
OH
1
H
b-D-glycopyranose
Tautomerisation of the carbohydrates
6
6 CH OH
HOH C
2
2
5
H
4
HO
OH
H3
O
1
OH
a-D-glycopyranose
5
H
H 2H
3
OH
a-D-ribofuranose
OH
2
CH 2OH
OH
H
1
b-D-fructofuranose
CH 2OH
O
H
H 2H
1
OH
OH
H
OH
2
CH 2OH
O
O
H HO
H
H
Lecture 4
3
OH
1
OH
H
a-D-2-deoxyribofuranose
5 C atoms + O atom = pyranose; 4 C atoms + O atoms =
furanose (riboses, fructose)
Lecture 4
Types of the organic compounds
AMINO ACIDS
H
H
C
H
O
H2 N
C
H
ACETIC ACID
OH
C
H
O
C
OH
GLYCINE ( Gly; G)
Lecture 4
Types of the organic compounds
AMINO ACIDS: NON -POLAR
H
H2 N
C
CH3
O
C
OH
Alanine (Ala; A)
Lecture 4
Types of the organic compounds
AMINO ACIDS; NON-POLAR
H
H2 N
H2 N
C
C
CH
H3 C
H
O
OH
Valine (Val; V)
C
C
CH2
CH3
H2 N
OH
CH3
Leucine (Leu; L)
C
CH
H3 C
CH
H3 C
H
O
O
C
OH
CH2
CH3
Isoleucine (Ile; I)
Lecture 4
Types of the organic compounds
AMINO ACIDS: NONOH
POLAR
H 2N
CH
CH 2
C
O
O
H2N CH C
CH2
OH
NH
Phenylalanine (Phe; F)
Typtophan (Trp; W)
Lecture 4
Types of the organic compounds
AMINO ACIDS: NONPOLAR
O
H2N CH C
OH
CH2
H
N HC
CH2
S
CH3
Methionine (Met; M)
H2 C
O
C
CH2 OH
CH2
Proline (Pro; P)
Lecture 4
Types of the organic compounds
AMINO ACIDS: POLAR
H
H2 N
C
CH2
O
C
OH
H
H2 N
C
CH
OH
HO
Serine (Ser; S)
O
C
OH
CH3
Threonine (Thr; T)
Lecture 4
Types of the organic compounds
AMINO ACIDS: POLAR
O
H2N CH C
OH
H
H2 N
C
CH2
O
C
CH2
CH2
OH
SH
Cysteine (Cys; C)
S
CH3
Methionine(Met; M)
Lecture 4
Types of the organic compounds
AMINO ACIDS: POLAR
OH
O
H 2N
H2N CH C
CH2
OH
OH
Tyrosine (Tyr; Y)
CH
CH 2
C
O
Phenylalanine (Phe; F)
Lecture 4
Types of the organic compounds
AMINO ACIDS: POLAR
O
H2N CH C
OH
O
H2N CH C
H2 C
H2 C
C
OH
CH2
O
H2 N
Asparagine (Asn; N)
C
H2 N
O
Glutamine (Gln; Q)
Lecture 4
Types of the organic compounds
AMINO ACIDS: ACIDIC
O
H2N CH C
H2N CH C
CH2
O
H2 C
OH
CH2
C
-
OH
C
O
O
Asparaginic acid (Asp; D)
O
-
O
Glutaminic acid (Glu; E)
Lecture 4
Types of the organic compounds
AMINO ACIDS: BASIC
H2N CH C
O
CH2
H2N CH C
H2 C
OH
CH2
NH
CH2
Lysine (Lys; K)
OH
CH2
CH2
H2N CH2
O
C
H2 N
+
NH2
Arginine (Arg; R)
Lecture 4
Types of the organic compounds
O
AMINO ACIDS: BASIC
H2 N
CH C
CH2
HN
OH
NH
+
Histidine (His; H)
Lecture 4
Types of the organic compounds
HETOROCYCLIC COMPOUNDS: BASES
PYRIMIDINES
NH 2
O
O
H 3C
3
NH
5
N
NH
NH
1
O
Cytosine
NH
O
Thymine
DNA
NH
Uracil
RNA
O
Lecture 4
Types of the organic compounds
HETOROCYCLIC COMPOUNDS: BASES
PURINES
N
3
9
NH
O
NH2
1
N
Adenine
N
N
9
NH
NH
1
N
Guanine
NH2
Lecture 4
Types of the organic compounds
HETOROCYCLIC COMPOUNDS: NUCLEOSIDES
AND NUCLEOTIDES
SUGARS
5
HO
CH2
OH
O
HO
CH2
OH
O
1
4
2
3
OH
H
Deoxyribose
OH
OH
Ribose
Lecture 4
Types of the organic compounds
HETOROCYCLIC COMPOUNDS: NUCLEOSIDES
AND NUCLEOTIDES
PHOSPHATE
O
HO
P
OH
OH
PHOSPHORIC ACID
Lecture 4
Types of the organic compounds
HETOROCYCLIC COMPOUNDS: NUCLEOSIDES
AND NUCLEOTIDES
O
Guanosine
N
NH
9
HO
N
N
1
2
N-glycosidic
bond
O
3
OH
OH
NH2
Lecture 4
Types of the organic compounds
HETOROCYCLIC COMPOUNDS: NUCLEOSIDES
AND NUCLEOTIDES
NH2
Deoxycytidine
HO
N
5
1
5
N
O
O
1
3
2
OH
H
N-glycosidic
bond
Lecture 4
Types of the organic compounds
HETOROCYCLIC COMPOUNDS: NUCLEOSIDES
AND NUCLEOTIDES
Deoxyadenosine 5’monophosphate; 5’-dAMP
NH2
N
OH
9
N
5
HO
P
O
O CH2
N
3
1
N
O
1
4
3
2
OH
H
Lecture 4
Types of the organic compounds
HETOROCYCLIC COMPOUNDS: NUCLEOSIDES
AND NUCLEOTIDES
Deoxyguanosine- 5’- triphosphate;
O
5’-dGTP
N
OH
HO
P
O

HO
O
P
O
OH
b
O
P
O
a
C
C
NH
HC
O
5
CH 2
9
N
O
HC
CH
3
CH
CH
OH
H
C
1
N
C
NH 2