basic cell biology i chemistry of life classification of the organic compounds, functional groups

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


=

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


structure

Lecture 4The principles of depicting molecular structureApproaches to depict the molecular structure


structure

Lecture 4Functional groups

The groups of atoms within the molecule which posses distinct

chemical properties


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


The presence of the functional groups in the molecule is denoted in their names by

specific endings



cules

Representative

Hydroxyl-

-OH

R-OH H3C-OH

methanol

Alcohols CH3-CH2-OH

ethanol, vine spirit


Functional groups may be involved in chemical reactions



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



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


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


C

OH

O

HC

H

O

HC H

OH

H

H

C H

H

H

H

Oxidation of the methane

Alcohol Aldehyde Acid


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)


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-


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


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


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


At condensation of two alcohol molecules an ether is formed

C

O

O

R

R

R C

OH

O

OH R


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


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


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:


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


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


Lecture 4

Spatial isomers

FREE ROTATION AROUND BOND - NO ISOMERS

CH CH

H

HCH3

CH3


Lecture 4

CH3

C C

HH

CH3CH3

C C

CH3H

H

Spatial isomers

trans- butilene cis- butilene

NO ROTATION AROUND DOUBLE BOND - ISOMERS


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)


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


AMINO ACIDS

C

O

H C

OHH

H

C

O

NH2 C

OHH

H

ACETIC ACID GLYCINE ( Gly; G)

Lecture 4


AMINO ACIDS: NON -POLAR

C

O

NH2 C

OHCH3

H

Alanine (Ala; A)

Lecture 4


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


AMINO ACIDS: NON-POLAR C

O

CH

CH2

NH2

NH

OHCH2

CHNH2 C

O

OH

Phenylalanine (Phe; F) Typtophan (Trp;

W)

Lecture 4


AMINO ACIDS: NON-POLAR

C

O

CHNH

CH2CH2

CH2OH

Methionine (Met; M)

Proline (Pro; P)

CO

CH

CH2

NH2OH

CH2

S

CH3

Lecture 4


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


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


AMINO ACIDS: POLAR

Tyrosine (Tyr; Y)

C

O

CH

CH2

NH2

OH

OH

CH2

CHNH2 C

O

OH

Phenylalanine (Phe; F)

Lecture 4


AMINO ACIDS: POLAR

Asparagine (Asn; N)

CO

CH

CH2

NH2OH

C

NH2

O

CO

CH

CH2

NH2OH

CH2

CONH2

Glutamine (Gln; Q)

Lecture 4


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


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


AMINO ACIDS: BASIC

Histidine (His; H)

C

O

CH

CH2

NH2

NH NH+

OH

Lecture 4


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


HETOROCYCLIC COMPOUNDS: BASESPURINES

Adenine Guanine

N

N

NH

N

NH2

9 13

N

NH

NH

N

NH2

O

19

Lecture 4


HETOROCYCLIC COMPOUNDS: NUCLEOSIDES AND NUCLEOTIDES

SUGARS

OHO

CH2OH

OHOH

OHO

CH2OH

HOH

1

3

5

2

4

Deoxyribose Ribose

Lecture 4



PHOSPHATE

P

O

OH

OH

OH

PHOSPHORIC ACID

Lecture 4



NO

OH

OHOH

N

NHN

NH2

O

1

3 2

9

N -glycosidicbond

Guanosine

Lecture 4



Deoxycytidine

NO

OH

HOH

N

NH2

O1

1

5

3 2

5

N -glycosidicbond

Lecture 4Types of the organic compounds


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

basic cell biology i chemistry of life classification of the organic compounds, functional groups

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