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BASIC CELL BIOLOGY

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

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BASIC CELL BIOLOGY

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

  2. 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

  3. Lecture 4 The principles of depicting molecular structure

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

  5. 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

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

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

  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 Functional groups The groups of atoms within the molecule which posses distinct chemical properties

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

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

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

  17. Lecture 4 Functional groups

  18. Lecture 4 Functional groups

  19. Lecture 4 Functional groups Oxidation of the methane Alcohol Aldehyde Acid

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

  21. Lecture 4 Functional groups

  22. Lecture 4 Functional groups

  23. 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

  24. 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

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

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

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

  28. 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

  29. 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:

  30. Lecture 4 Types of the organic compounds

  31. 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.

  32. 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.

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

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

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

  36. 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.

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

  38. Lecture 4 Tautomerisation of the carbohydrates a-D-glycopyranose D - glucose b-D-glycopyranose

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

  40. Lecture 4 Types of the organic compounds • AMINO ACIDS ACETIC ACID GLYCINE ( Gly; G)

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

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

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

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

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

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

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

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

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

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

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