1. Proteins -Amino acids -Structure -Protein domains -Physicochemical properties -Folding and chaperones -Connective tissue proteins

2. AMINO ACIDS

3. Amino acids: general structure

4. Nonpolar alifatic

5. Aromatic

6. Polar uncharged

7. Positively charged

8. Negatively charged

9. Proteins consist of amino acids and have carboxyl- and amino-terminal ends

10. STRUCTURE OF PROTEINS

11. Primary structure: sequence of amino acids VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLS FPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAV AHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLL VTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR

12. Amino acid alignment of same proteins from different organisms

13. Protein globule is the functional structure (tertiary structure)

14. Secondary structure: alfa-helix

15. Secondary structure: beta-sheet

16. Tertiary structure: position of all protein atoms in space

17. Quaternary structure: association of two or more molecules

18. hemoglobin

19. DOMAINS: DISTINCT COMPACT PARTS IN PROTEIN STRUCTURE

20. Domains of pyruvate kinase Domain 2 (catalytic) Domain 3 (regulatory) Domain 1

21. FOLDING AND CHAPERONES

22. There is no universal way for protein folding (each protein follows its own folding pathway) But there is one general rule: - Hydrophobic amino acids form hydrophobic core inside protein globule

23. Forces that fold protein

24. Folding: example of stages

25. Chaperones Chaperones are the proteins that help other proteins to fold properly. Functions of chaperones: 1.To prevent aggregation of newly synthesized proteins. 2.To assist in folding of unfolded proteins (due to changes of temperature, pH)

26. Prions: “infective” proteins

27. CONNECTIVE TISSUE PROTEINS

28. Keratin

29. Keratin of hairs

31. Hydrophobic interactions stabilises supercoiled alfa-helix in keratin

32. Disulfide bonds

33. FIBRILLAR PROTEINS: - COLLAGEN

34. Collagen

35. Collagen triple helix: Gli – Х – Pro

36. Vitamin C is necessary for hydroxylation of proline in collagen

37. Lysine and hydroxy-lysine make cross-bridges in collagen to hold helices together

38. Conjugated proteins - Classification -Functions

40. HEMOPROTEINS: HEMOGLOBIN AND MYOGLOBIN

41. Heme = protoporphyrin + Fe 2+

42. Physiological functions Myoglobin stores oxygen in muscles. It releases oxygen only when oxygen concentration is very low (hypoxia) Hemoglobin transfers oxygen from lungs to tissues. It releases oxygen when oxygen concentration is in physiological range.

43. Complex between ligand and protein

44. О 2 is bound to heme group

45. Oxygen saturation curves for myoglobin (hyperbolic) and hemoglobin (sigmoidal): different ability to transfer oxygen Lungs: both proteins are saturated with oxygen. Tissues: - myoglobin is 90% saturated (gives back only 10%) - hemoglobin is 50% saturated (gives back 50%)

46. COOPERATIVITY OF OXYGEN BINDING

47. Myoglobin consists of single polypeptide chain, while functional hemoglobin molecule contains four polypeptide chains (which are very similar to myoglobin ones) Myoglobin (single chain) Hemoglobin (four subunits) Hemoglobin (one subunit)

48. Oxygen binding leads to structural (conformational) changes in binding site, which are transmitted to neighboring subunits through contacts between subunits

49. Binding of oxygen molecule by the first subunit enhances oxygen binding to other subunits This feature is called cooperativity

50. 2,3-BISPHOSPHOGLYCERATE AND COOPERATIVITY

51. 2,3-BPG is produced from one of the glycolysis intermediates The presence of 2,3- BPG indicates sites of high energy production and, therefore, oxygen demand

52. 2,3-BPG binds to the central cavity of hemoglobin molecule

53. Effects of 2,3-BPG: 2,3-BPG weakens oxygen binding. Therefore: High 2,3-BPG in tissue → weak oxygen binding → better oxygen supply This plays role in adaptation to highlands and intensive work

54. HEMOGLOBIN ISOFORMS: - ADULT - FETAL

55. Protein isoforms

56. Synthesis of different isoforms during embryonic development

57. Fetal vs. adult hemoglobin

58. PHYSIOLOGICAL REGULATION OF OXYGEN BINDING: EFFECTS OF PH AND CO2

59. Effects of pH and CO2 Tissues with high energy demand (high glycolysis): - high CO2 -low pH

60. Nucleic acids -Nitrogen bases -Nucleotides -DNA and RNA

61. DNA and RNA contain nitrogen bases

62. Nucleotides vs. nucleosides

63. How is this nucleoside / nucleotide called?

64. There are some other nitrogen bases Alkaloids Products of nitrogen bases breakdown

65. Some bases are not included in nucleic acids structure: alkaloids H H caffeine theobromine theophilline

66. Nitrogen bases which are formed during metabolism from adenine and guanine hypoxanthine xanthine Uric acid

67. Elevation of uric acid causes gout Uric acid forms insoluble salts Causes: increased production OR decreased excretion

68. DNA contains minor (modified) bases: regulation of gene expression by methylation

69. RNA contains minor bases: recognition, stability, regulation mRNA tRNA

70. FUNCTIONS

71. ATP as energy carrier high energy bond (macroergic bond, high energy phosphate) = good leaving group, high transfer potential (correct meaning)

72. Nucleotide moieties of coenzymes: coenzyme A

73. Nucleotide moieties of coenzymes: NAD

74. Nucleotide moieties of coenzymes: FAD

75. Regulatory functions of cyclic nucleotides cAMP has positive effect on energy-production pathways (glycolysis). One of the mechanisms of caffeine action is inhibition of cAMP breakdown. This leads to prolongation of cAMP stimulatory action. cGMP mediates muscle relaxation caused by NO. Effect of nitroglycerin on heart muscle relaxation is mediated by cGMP formation.

76. Summary Nucleotides consist of nitrogen base (A,T,G,C,U) + (deoxy)ribose + phosphate Nucleotides are the building blocks of nucleic acids (DNA, RNA) Nucleotides perform signaling functions (cAMP, cGMP) Nucleotides play role in catalysis (parts of coenzymes). Nucleotides are energy carriers (ATP, GTP)

77. NUCLEIC ACIDS: DNA

78. Conventional order of sequence description is from 5`- to 3`- end: 5` ATG 3` Nucleotides (in DNA or RNA) are joined by phosphodiester bonds

79. DNA is a double helix

80. DNA STRUCTURE AND DRUGS

81. Intercalation – insertion between planar bases of double helix

82. Intercalating drugs: bacteriostatics proflavin

83. Intercalating drugs for cancer cisplatin Mechanism of intercalation

84. NUCLEIC ACIDS: RNA

85. Differences between RNA and DNA: pentose Lack of OH-group makes DNA more chemically stable: DNA is more suitable for storing genetic information

86. RNA functions in protein synthesis: ribosomal RNA perform catalytic functions

87. RNA is the major structural component of ribosomal subunits 30S 50S rRNA: rRNA (brown) + proteins (blue):

88. RNA functions in protein synthesis: transfer RNA (tRNA) Real conformation in 3D

89. RNA functions in protein synthesis: messenger RNA (mRNA)

90. Other functions of RNA: Catalysis (ribozymes): ribosome, RNAse P, hammerhead ribozyme. Regulation of gene expression (RNA interference): small interfering RNAs

91. RNA as catalyst: ribozymes RNase P plays role in: - tRNA processing - regulation of transcription