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Transcript of BASIC CELL BIOLOGY I CHEMISTRY of LIFE CLASSIFICATION OF THE ORGANIC COMPOUNDS, FUNCTIONAL GROUPS.
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BASIC CELL BIOLOGY
I CHEMISTRY of LIFE
CLASSIFICATION OF THE ORGANIC COMPOUNDS, FUNCTIONAL GROUPS
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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
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Lecture 4The principles of depicting molecular structure
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Lecture 4The principles of depicting molecular structureApproaches to depict the molecular structure
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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
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Lecture 4The principles of depicting molecular structureApproaches to depict the molecular
structure
Structural isomers
Simplified (schematic) structural formula
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Lecture 4The principles of depicting molecular structureApproaches to depict the molecular
structure
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Lecture 4The principles of depicting molecular structureApproaches to depict the molecular structure
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Lecture 4The principles of depicting molecular structure
Approaches to depict the molecular structure
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Lecture 4The principles of depicting molecular structureApproaches to depict the molecular
structure
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Lecture 4The principles of depicting molecular structure
Approaches to depict the molecular structure
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Lecture 4The principles of depicting molecular structure
Approaches to depict the molecular structure
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Lecture 4Functional groups
The groups of atoms within the molecule which posses distinct
chemical properties
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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
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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
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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
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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
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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
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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
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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)
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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-
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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
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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
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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
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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
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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
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C
O
O
CH3CH3
At condensation of alcohol and organic acid an esther is formed
Methylesther of acetic acid, Methylacetate
Lecture 4Functional groups
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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
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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:
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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
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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.
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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.
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CH CH
CH3
CH3H
H
Types of the organic compounds
Lecture 4
Spatial isomers
FREE ROTATION AROUND BOND - NO ISOMERS
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Types of the organic compounds
Lecture 4
Spatial isomers
FREE ROTATION AROUND BOND - NO ISOMERS
CH CH
H
HCH3
CH3
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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
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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)
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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
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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
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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
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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)
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Lecture 4
Types of the organic compounds
AMINO ACIDS: NON -POLAR
C
O
NH2 C
OHCH3
H
Alanine (Ala; A)
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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
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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)
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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
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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
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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)
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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)
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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)
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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-
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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
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Lecture 4
Types of the organic compounds
AMINO ACIDS: BASIC
Histidine (His; H)
C
O
CH
CH2
NH2
NH NH+
OH
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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
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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
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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
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Lecture 4
Types of the organic compounds
HETOROCYCLIC COMPOUNDS: NUCLEOSIDES AND NUCLEOTIDES
PHOSPHATE
P
O
OH
OH
OH
PHOSPHORIC ACID
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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
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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
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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
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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