2. BASIC CELL BIOLOGY I CHEMISTRY of LIFE CLASSIFICATION OF THE ORGANIC COMPOUNDS, FUNCTIONAL GROUPS

3. 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

4. Lecture 4 The principles of depicting molecular structure

5. Lecture 4 The principles of depicting molecular structure Approaches to depict the molecular structure

6. Lecture 4 The principles of depicting molecular structure  = H 2 C= + =CH 2 = H 2 C=CH 2 By taking away a hydrogen atom from the molecule of methane (CH 4 ) a methyl radical is created (CH 3 -), which has highly reactive, unsaturated valence Approaches to depict the molecular structure

7. Lecture 4 The principles of depicting molecular structure Approaches to depict the molecular structure Structural isomers Simplified (schematic) structural formula

8. Lecture 4 The principles of depicting molecular structure Approaches to depict the molecular structure

9. Lecture 4 The principles of depicting molecular structure Approaches to depict the molecular structure

10. Lecture 4 The principles of depicting molecular structure Approaches to depict the molecular structure

11. Lecture 4 The principles of depicting molecular structure Approaches to depict the molecular structure

12. Lecture 4 The principles of depicting molecular structure Approaches to depict the molecular structure

13. Lecture 4 The principles of depicting molecular structure Approaches to depict the molecular structure

14. Lecture 4 Functional groups The groups of atoms within the molecule which posses distinct chemical properties

15. Lecture 4 Functional groups The rest of the molecule which is connected to the functional group is denoted by R - (radical)

16. Lecture 4 Functional groups The presence of the functional groups in the molecule is denoted in their names by specific endings

17. Lecture 4 Functional groups Functional groups may be involved in chemical reactions

18. Lecture 4 Functional groups

19. Lecture 4 Functional groups

20. Lecture 4 Functional groups Oxidation of the methane AlcoholAldehydeAcid

21. Lecture 4 Functional groups One molecule may contain several identical or different functional groups Polyvalent alcohols - polyols (glycerol) Complex carbonic acids (lactic acid)

22. Lecture 4 Functional groups

23. Lecture 4 Functional groups

24. Lecture 4 Functional 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

25. 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-RR-O-R +H 2 O R -OH + OH-R

26. Lecture 4 Functional groups At condensation of two alcohol molecules an ether is formed

27. Lecture 4 Functional groups At condensation of alcohol and organic acid an esther is formed

28. Methylesther of acetic acid, Methylacetate Lecture 4 Functional groups

29. Types of the organic compounds Lecture 4 Alcans– the simplest organic molecules, which are formed only by H and C atoms. General chemical composition: C n H 2n+2 The simplest alcane: methane: CH 4

30. Types of the organic compounds Lecture 4 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:

31. Types of the organic compounds Lecture 4

32. Types of the organic compounds Lecture 4 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.

33. Types of the organic compounds Lecture 4 Alkynes 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.

34. Types of the organic compounds Lecture 4 Spatial isomers FREE ROTATION AROUND BOND - NO ISOMERS

35. Types of the organic compounds Lecture 4 Spatial isomers FREE ROTATION AROUND BOND - NO ISOMERS

36. Types of the organic compounds Lecture 4 Spatial isomers trans- butilenecis- butilene NO ROTATION AROUND DOUBLE BOND - ISOMERS

37. Types of the organic compounds Lecture 4 General chemical formula (CH 2 O) = 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)

38. Types of the organic compounds Lecture 4 CARBOHYDRATES (SUGARS)

39. D - glucose  -D-glycopyranose  -D-glycopyranose Tautomerisation of the carbohydrates Lecture 4

40. 5 C atoms + O atom = pyranose; 4 C atoms + O atoms = furanose (riboses, fructose)  -D-glycopyranose  -D-fructofuranose  -D-2-deoxyribofuranose  -D-ribofuranose Tautomerisation of the carbohydrates Lecture 4

41. Types of the organic compounds AMINO ACIDS ACETIC ACIDGLYCINE ( Gly; G)

42. Lecture 4 Types of the organic compounds AMINO ACIDS: NON -POLAR Alanine (Ala; A)

43. Lecture 4 Types of the organic compounds AMINO ACIDS; NON-POLAR Valine (Val; V) Isoleucine (Ile; I)Leucine (Leu; L)

44. Lecture 4 Types of the organic compounds AMINO ACIDS: NON- POLAR Phenylalanine (Phe; F) Typtophan (Trp; W)

45. Lecture 4 Types of the organic compounds AMINO ACIDS: NON- POLAR Methionine (Met; M) Proline (Pro; P)

46. Lecture 4 Types of the organic compounds AMINO ACIDS: POLAR Serine (Ser; S) Threonine (Thr; T)

47. Lecture 4 Types of the organic compounds AMINO ACIDS: POLAR Cysteine (Cys; C)Methionine(Met; M)

48. Lecture 4 Types of the organic compounds AMINO ACIDS: POLAR Tyrosine (Tyr; Y ) Phenylalanine (Phe; F)

49. Lecture 4 Types of the organic compounds AMINO ACIDS: POLAR Asparagine (Asn; N) Glutamine (Gln; Q)

50. Lecture 4 Types of the organic compounds AMINO ACIDS: ACIDIC Asparaginic acid (Asp; D) Glutaminic acid (Glu; E)

51. Lecture 4 Types of the organic compounds AMINO ACIDS: BASIC Lysine (Lys; K) Arginine (Arg; R)

52. Lecture 4 Types of the organic compounds AMINO ACIDS: BASIC Histidine (His; H )

53. Lecture 4 Types of the organic compounds HETOROCYCLIC COMPOUNDS: BASES PYRIMIDINES CytosineThymineUracil DNA RNA

54. Lecture 4 Types of the organic compounds HETOROCYCLIC COMPOUNDS: BASES PURINES Adenine Guanine

55. Lecture 4 Types of the organic compounds HETOROCYCLIC COMPOUNDS: NUCLEOSIDES AND NUCLEOTIDES SUGARS DeoxyriboseRibose

56. Lecture 4 Types of the organic compounds HETOROCYCLIC COMPOUNDS: NUCLEOSIDES AND NUCLEOTIDES PHOSPHATE PHOSPHORIC ACID

57. Lecture 4 Types of the organic compounds HETOROCYCLIC COMPOUNDS: NUCLEOSIDES AND NUCLEOTIDES Guanosine

58. Lecture 4 Types of the organic compounds HETOROCYCLIC COMPOUNDS: NUCLEOSIDES AND NUCLEOTIDES Deoxycytidine

59. Lecture 4 Types of the organic compounds HETOROCYCLIC COMPOUNDS: NUCLEOSIDES AND NUCLEOTIDES Deoxyadenosine 5’- monophosphate; 5’-dAMP

60. Lecture 4 Types of the organic compounds HETOROCYCLIC COMPOUNDS: NUCLEOSIDES AND NUCLEOTIDES Deoxyguanosine- 5’- triphosphate; 5’-dGTP