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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
Lecture 4The principles of depicting molecular structure
Lecture 4The principles of depicting molecular structureApproaches to depict the molecular structure
Lecture 4The principles of depicting molecular structure
=
H2C= + =CH2 = H2C=CH2
By taking away a hydrogen atom from the molecule of methane (CH4) a methyl radical is created (CH3-), which has highly reactive, unsaturated valence
Approaches to depict the molecular structure
Lecture 4The principles of depicting molecular structureApproaches to depict the molecular
structure
Structural isomers
Simplified (schematic) structural formula
Lecture 4The principles of depicting molecular structureApproaches to depict the molecular
structure
Lecture 4The principles of depicting molecular structureApproaches to depict the molecular structure
Lecture 4The principles of depicting molecular structure
Approaches to depict the molecular structure
Lecture 4The principles of depicting molecular structureApproaches to depict the molecular
structure
Lecture 4The principles of depicting molecular structure
Approaches to depict the molecular structure
Lecture 4The principles of depicting molecular structure
Approaches to depict the molecular structure
Lecture 4Functional groups
The groups of atoms within the molecule which posses distinct
chemical properties
Lecture 4Functional groups
The rest of the molecule which is connected to the functional group is
denoted by R - (radical)
Name Formula The simplestcompound
The type ofmacromole-
cules
Represen-tative
Methyl-
-CH3
R- CH3 H-CH3 = CH4
Methane
Hydrocarbons H3C-CH3
ethane
Lecture 4Functional groups
The presence of the functional groups in the molecule is denoted in their names by
specific endings
Name Formula The simplestcompound
The type ofmacromole-
cules
Representative
Hydroxyl-
-OH
R-OH H3C-OH
methanol
Alcohols CH3-CH2-OH
ethanol, vine spirit
Lecture 4Functional groups
Functional groups may be involved in chemical reactions
Name Formula The simplestcompound
The type ofmacromole-
cules
Representative
Hydroxyl-
-OH
R-OH H3C-OH
methanol
Alcohols CH3-CH2-OH
ethanol, vine spirit
R-O-R H3C-O-CH3
dimethylether
Ethers H3C-O-C2H5
methyl-ethyl ether
Lecture 4Functional groups
Name Formula The simplestcompound
Type of
comp.
Representative
Carbonyl-
-CHO
methanal,methylaldehyde
Aldehydes
ethanal, ethyl aldehyde(acetaldehyde)
dimethylketone
Ketons
methyl-ethyl ketone
CO
R
R
CO
CH3
CH2CH3
CO
CH3
CH3C
H
O
H
C
H
O
HC
H
O
R C
H
O
CH3
Lecture 4Functional groups
Names Formula The simplestcompound
Type of
comp.
Representative
Carboxyl-COOH
Mathanic acid(formic acid)
Carboxylacids(organic acids)
Ethanic acid (acetic acid)
Esters
Methyl ester of the aceticacidMethylacetate
C
O
O
R
R
C
O
O
CH3CH3
C
OH
O
R C
OH
O
H C
OH
O
CH3
Lecture 4Functional groups
C
OH
O
HC
H
O
HC H
OH
H
H
C H
H
H
H
Oxidation of the methane
Alcohol Aldehyde Acid
Lecture 4Functional groups
One molecule may contain several identical or different
functional groups
C CCH
OH
H
OH
OH
H
C CHCH
OH
H
OH
HH
OH
Polyvalent alcohols - polyols
(glycerol)
Complex carbonic acids (lactic acid)
Lecture 4Functional groups
Name Formula The simplest
compound
Type of
compounds
Representative
Amino--NH2
H-NH2=NH3
ammoniaAmines H3C-NH2
methylamine
Phosphates –- OPO3
2-
phosphate
Organicphosphates
Phosphog;lycerateSulphidryl-SH
R-SH H-SH = H2SHydrogensulphide
Mercaptans(thiols)
HS-CH2-CH2-OHmercaptoethanol
R N
H
H
P
O
O
O-O-
RP
O
OH
O-O-
CO OH
CH
CH
OH
H O P
O
O-
O-
Lecture 4Functional groups
P l a c e m e n t o f t h e f u n c t i o n a l g r o u p s i n t h e m o l e c u l e
A t t h e p r i m a r y C a t o m A t t h e s e c o n d a r y C a t o m A t t h e t e r t i a r y C a t o m
P r i m a r y ( n - ) b u t a n o l S e c o n d a r y ( i z o - ) b u t a n o l T e r t i a r y ( t r e t - ) b u t a n o l
CH 3
C H 2
C H 2
C H 2
RCH 3
C HC H 2
C H 3
R
CH 3
CC H 3
R
C H 3
CH 3
C HC H 2
C H 3
O H
CH 3
CC H 3
O H
C H 3
CH 3
C H 2
C H 2
C H 2
O H
Lecture 4Functional groups
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 4Functional 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 +H2OR-O-R
+H2OR -OH + OH-R
R-O-R H3C-O-CH3
dimetil-ēteris
H3C-O-C2H5
metil-etil - ēteris
Lecture 4Functional groups
At condensation of two alcohol molecules an ether is formed
C
O
O
R
R
R C
OH
O
OH R
Lecture 4Functional groups
At condensation of alcohol and organic acid an esther is formed
C
O
O
CH3CH3
At condensation of alcohol and organic acid an esther is formed
Methylesther of acetic acid, Methylacetate
Lecture 4Functional groups
Types of the organic compoundsLecture 4
Ethane H3C-CH3 ; C2H6Propane H3C-CH2-CH3; C3H8Butane H3C-(CH2)2-CH3; C4H10Pentane H3C-(CH2)3-CH3; C5H12
Alcans– the simplest organic molecules, which are formed only by H and C atoms. General chemical composition: CnH2n+2
The simplest alcane: methane: CH4
Types of the organic compoundsLecture 4
TRIVIAL NAMES USED IN BIOLOGY:n-pentane iso-pentane neo-pentane
pentane 2-methyl-butane 2,2-dimethyl-propaneINTERNATIONAL CHEMICAL NOMENCLATURE(IUPAC)
CH3CH2CH2CH2CH3
CH3CHCH2CH3
CH3
CH3
C CH3
CH3
CH3
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:
Types of the organic compoundsLecture 4
Cyclic alkanes: CnH2n Aromatic compounds (arens)Cyclohexane Benzol (benzene)
Conjugated (connected) double bounds in the bezene ring are notfixed to a specific carbon atom. They may fluctuate from one atom toanother.
CH2
CH2
CH2
CH2
CH2
CH2
C
C
C
C
C
C
H
H
H
H
H
H
Types of the organic compoundsLecture 4
AlkenesIf 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 Lecture 4
AlkynesIf 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.
CH CH
CH3
CH3H
H
Types of the organic compounds
Lecture 4
Spatial isomers
FREE ROTATION AROUND BOND - NO ISOMERS
Types of the organic compounds
Lecture 4
Spatial isomers
FREE ROTATION AROUND BOND - NO ISOMERS
CH CH
H
HCH3
CH3
Types of the organic compounds
Lecture 4
CH3
C C
HH
CH3CH3
C C
CH3H
H
Spatial isomers
trans- butilene cis- butilene
NO ROTATION AROUND DOUBLE BOND - ISOMERS
Types of the organic compounds
Lecture 4
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.
CARBOHYDRATES (SUGARS)
Types of the organic compounds
Lecture 4
CARBOHYDRATES (SUGARS)
Ribose DeoxyriboseGalactose Glucose FructosePentoses Hexoses
Aldoses Ketose
CH
C
C
C
CH2 OH
O
H OH
H OH
H OH
CH
C
C
C
CH2 OH
O
H H
H OH
H OH
CH
C
C
C
C
CH2 OH
O
H OH
OH H
OH H
H OH
CH
C
C
C
C
CH2 OH
O
H OH
OH H
H OH
H OH
CH2
C
C
C
C
CH2 OH
OH
O
OH H
H OH
H OH
OH
O
H
OHOH H
H
OH
H
OH
D - glucose
-D-glycopyranose
-D-glycopyranose
OCH2OH
H
OHOH
H
H
H
OH
OH
6
14
OCH2OH
HH
OHOH
H
H
OH
H
OH
6
14OH
O
H OH
OH H
H OH
H OH
1
6
Tautomerisation of the carbohydratesLecture 4
5 C atoms + O atom = pyranose; 4 C atoms + O atoms = furanose (riboses, fructose)
H
OH
CH2OHOH
OH
HH
HOH2C O
1
2
6
OCH2OH
H
OHOH
H
H
H
OH
OH
1
2
5
6
3
4
H
OH
HH
OH
H
CH2OHO
12
3OH
OH
HH
OH
H
CH2OHO
12
3
5-D-glycopyranose
-D-fructofuranose
-D-2-deoxyribofuranose
-D-ribofuranose
Tautomerisation of the carbohydrates Lecture 4
Lecture 4
Types of the organic compounds
AMINO ACIDS
C
O
H C
OHH
H
C
O
NH2 C
OHH
H
ACETIC ACID GLYCINE ( Gly; G)
Lecture 4
Types of the organic compounds
AMINO ACIDS: NON -POLAR
C
O
NH2 C
OHCH3
H
Alanine (Ala; A)
Lecture 4
Types of the organic compounds
AMINO ACIDS; NON-POLAR
Valine (Val; V)
Isoleucine (Ile; I)
Leucine (Leu; L)
C
O
NH2 C
OHCH
H
CH3 CH3
C
O
NH2 C
OHCH2
H
CH
CH3CH3
C
O
NH2 C
OHCH
H
CH3 CH2
CH3
Lecture 4
Types of the organic compounds
AMINO ACIDS: NON-POLAR C
O
CH
CH2
NH2
NH
OHCH2
CHNH2 C
O
OH
Phenylalanine (Phe; F) Typtophan (Trp;
W)
Lecture 4
Types of the organic compounds
AMINO ACIDS: NON-POLAR
C
O
CHNH
CH2CH2
CH2OH
Methionine (Met; M)
Proline (Pro; P)
CO
CH
CH2
NH2OH
CH2
S
CH3
Lecture 4
Types of the organic compounds
AMINO ACIDS: POLAR
Serine (Ser; S) Threonine (Thr; T)
C
O
NH2 C
OHCH2
H
OH
C
O
NH2 C
OHCH
H
OH CH3
Lecture 4
Types of the organic compounds
AMINO ACIDS: POLAR
Cysteine (Cys; C)
C
O
NH2 C
OHCH2
H
SH
CO
CH
CH2
NH2OH
CH2
S
CH3
Methionine(Met; M)
Lecture 4
Types of the organic compounds
AMINO ACIDS: POLAR
Tyrosine (Tyr; Y)
C
O
CH
CH2
NH2
OH
OH
CH2
CHNH2 C
O
OH
Phenylalanine (Phe; F)
Lecture 4
Types of the organic compounds
AMINO ACIDS: POLAR
Asparagine (Asn; N)
CO
CH
CH2
NH2OH
C
NH2
O
CO
CH
CH2
NH2OH
CH2
CONH2
Glutamine (Gln; Q)
Lecture 4
Types of the organic compounds
AMINO ACIDS: ACIDIC
Asparaginic acid (Asp; D)
Glutaminic acid (Glu; E)
C
OO-
CO
CH
CH2
NH2OH
CO
CH
CH2
NH2OH
CH2
COO-
Lecture 4
Types of the organic compounds
AMINO ACIDS: BASIC
Lysine (Lys; K)
Arginine (Arg; R)
CH2
CO
CH
CH2
NH2OH
CH2
CH2NH2
CH2
CO
CH
CH2
NH2OH
CH2
NH
CNH2
+NH2
Lecture 4
Types of the organic compounds
AMINO ACIDS: BASIC
Histidine (His; H)
C
O
CH
CH2
NH2
NH NH+
OH
Lecture 4
Types of the organic compounds
HETOROCYCLIC COMPOUNDS: BASES
N
NH
NH2
O
NH
NH
O
O
NH
NH
O
O
CH3
1
35
PYRIMIDINES
Cytosine Thymine UracilDNA RNA
Lecture 4
Types of the organic compounds
HETOROCYCLIC COMPOUNDS: BASESPURINES
Adenine Guanine
N
N
NH
N
NH2
9 13
N
NH
NH
N
NH2
O
19
Lecture 4
Types of the organic compounds
HETOROCYCLIC COMPOUNDS: NUCLEOSIDES AND NUCLEOTIDES
SUGARS
OHO
CH2OH
OHOH
OHO
CH2OH
HOH
1
3
5
2
4
Deoxyribose Ribose
Lecture 4
Types of the organic compounds
HETOROCYCLIC COMPOUNDS: NUCLEOSIDES AND NUCLEOTIDES
PHOSPHATE
P
O
OH
OH
OH
PHOSPHORIC ACID
Lecture 4
Types of the organic compounds
HETOROCYCLIC COMPOUNDS: NUCLEOSIDES AND NUCLEOTIDES
NO
OH
OHOH
N
NHN
NH2
O
1
3 2
9
N -glycosidicbond
Guanosine
Lecture 4
Types of the organic compounds
HETOROCYCLIC COMPOUNDS: NUCLEOSIDES AND NUCLEOTIDES
Deoxycytidine
NO
OH
HOH
N
NH2
O1
1
5
3 2
5
N -glycosidicbond
Lecture 4Types of the organic compounds
HETOROCYCLIC COMPOUNDS: NUCLEOSIDES AND NUCLEOTIDES
Deoxyadenosine 5’- monophosphate; 5’-dAMP
NO
CH2
HOH
N
NN
NH2
OP
O
OH
OH9 1
3
1
3
5
24
N
CH
CH
O
CH
CH
CH2O
HOH
P
O
OH
P
O
O
OH
OH
OH
O
O
P
C
C
C
N
NH
CCH
N
NH2
O
9 1
3
5
Lecture 4Types of the organic compoundsHETOROCYCLIC COMPOUNDS: NUCLEOSIDES AND NUCLEOTIDES
Deoxyguanosine- 5’- triphosphate; 5’-dGTP