1. Insulin: Weight = 5733, 51 amino acids Glutamine Synthetase: Weight = 600,000, 468 amino acids

2. Amino Acids & Dehydration Synthesis Amino acid structure: Functional groups Peptide bonds

7. Sample amino acid structures: carboxyl group-bluealpha carbon-gray amino group-greenR groups-beige

8. The twenty essential amino acids. Note R groups in blue

9. Amino Acids w/ various R groups

10. Nonpolar amino acids

11. Neutral Amino Acids

12. Ionic amino acids

13. Amino acids are joined together in proteins by peptide bonds. A peptide bond forms between the carboxyl group of one amino acid (amino acid 1 in the figure preceding) and the amino group of the adjacent amino acid (amino acid 2).

14. Dehydration synthesis

17. Dehydration synthesis animation

18. Dehydration Synthesis

19. Dehydration Synthesis : Amino acid 1 Amino acid 2 Dipeptide (Peptide bond) Amino group

20. Protein Structure Amino acid structure Dehydration synthesis

21. Insulin: Weight = 5733, 51 amino acids Glutamine Synthetase: Weight = 600,000, 468 amino acids

22. Four ‘levels’ of protein structure

23. Four levels of protein structure

24. Primary structure: Visualized as a straight chain of aa’s, but with a specific sequence, As determined by its gene

25. Secondary structure: alpha helix or beta pleated sheet

26. Tertiary structure: coiled chains of aa’s are folded & wound around themselves

27. Close up of 2 o & 3 o Protein Structure

28. Quarternary structure: separate polypeptide chains are combined

29. Levels of Protein Structure

30. Four Levels of Protein Structure (note change in scale from 2 o to 3 o )

31. Collagen molecule

32. Actin molecule

33. Myosin molecule

34. Hemoglobin molecule

35. Antibody molecule

36. (purple) Reverse transcriptase of HIV1 w/ a fragment of DNA (colors)

38. Protein Synthesis: Transcription & Translation

39. Transcription: Making a copy of the blueprint

40. Morse Code Key

41. Using the Genetic Code: DNA :: mRNA :: Protein Get from ‘language’ of DNA (A,G,C,orT) to ‘language’ of protein (aa’s) DNA’s ‘language’ is a triplet code in which 3 nucleotide bases (a codon) specify 1 amino acid in protein.

42. DNA (1 gene) :: mRNA :: polypeptide

47. Steps in Transcription

49. Transcription: Note the free nucleotides

50. DNA unzips

51. Complementary base pairing

52. mRNA- final product of Transcription mRNA moves off to ribosome

53. Transcription: Getting the plan straight (copying the gene)

54. Transcription animation

57. Translation Building the protein from the plan

58. Using the Genetic Code: DNA :: mRNA :: Protein Get from ‘language’ of DNA (A,G,C,orT) to ‘language’ of protein (aa’s) DNA’s ‘language’ is a triplet code in which 3 nucleotide bases (a codon) specify 1 amino acid in protein.

59. Structure of a Ribosome

60. Structure of a tRNA

63. Translation : purple = mRNA blue = ribosome yellow = tRNA (note anticodon) white = amino acids red = peptide bond

68. Translation initiation

69. Translation initiation (cont)

70. Translation- elongation

71. Translation- termination

72. A Polysome: With more than one ribosome translating an mRNA at one time, it is possible to produce many polypeptides simultaneously from a single mRNA.

73. Protein Synthesis

75. In a prokaryotic cell, transcription and translation are coupled; that is, translation begins while the mRNA is still being synthesized. In a eukaryotic cell, transcription occurs in the nucleus, and translation occurs in the cytoplasm.

76. Protein synthesis in eukaryotes

77. Antibiotic Mechanism

78. Antibiotic Mechanism

79. Collagen molecule

80. Actin molecule

81. Myosin molecule

82. Antibody molecule

83. Hemoglobin molecule

84. Enzymes

85. Definitions: Catalyst = An additive that speeds up a chemical reaction without itself being consumed or changed by the reaction Enzyme = A protein that acts as a catalyst, usually in a biological context. –All enzymes are proteins, not all proteins are enzymes

86. Enzyme mechanism of action: An enzyme improves the odds of ‘useful’ collisions between substrate molecules.

88. Steps in enzyme function

89. Enzyme-substrate animation

94. S = substrate E = enzyme P = product ES = enzyme- substrate complex

98. Lock & Key Model: Enzymes are very specific and it was suggested by Emil Fischer in 1890 that this was because the enzyme had a particular shape into which the substrate(s) fit exactly. This is often referred to as "the lock and key" hypothesis. An enzyme combines with its substrate(s) to form a short- lived enzyme-substrate complex.

99. Induced fit hypothesis: In 1958 Daniel Koshland suggested a modification to the "lock and key" hypothesis. Enzymes are rather flexible structures. The active site of an enzyme could be modified as the substrate interacts with the enzyme. The amino acids side chains which make up the active site are molded into a precise shape which enables the enzyme to perform its catalytic function. In some cases the substrate molecule changes shape slightly as it enters the active site. A suitable analogy would be that of a hand changing the shape of a glove as the glove is put on.

101. Enzyme Animation

102. Enzyme Websites: Enzyme notes in ppt format, few diagrams: http://www.hcc.mnscu.edu/programs/dept/chem/V.28/page_id_2897.html animation of enzyme action http://web.ukonline.co.uk/webwise/spinneret/other/hienz.htm written outline- enzymes by Worthington http://www.worthington-biochem.com/introBiochem/introEnzymes.html asd

103. Enzyme & Cell Regulation Gene activation Feedback loops for enzyme activity

104. Various possible routes of feedback in the production-regulation of a given protein

105. Changing the conformation (shape) of an enzyme’s active site changes its ability to act as a catalyst

106. Zymogens: Enzyme Precursors

107. Competitive Enzyme Inhibition

108. Allosteric Modulation of an Enzyme

110. Genes can be either inducible or repressible. Many genes are normally blocked by the action of a repressor protein. This prevents the RNA polymerase enzyme from binding to the gene and transcribing the structural gene. Such genes are induced by the arrival of an inducer molecule which binds to the repressor protein and rendering it inactive. This allows transcription from the structural gene and the production of a protein. Other genes are normally active and able to be constantly transcribed, because the repressor protein is produced in an inactive form. On the arrival and binding of the corepressor molecule the complex can act as a functional repressor and block the structural gene by binding at the operator site.

111. Steps in Transcription

112. DNA Technology

117. Bases: A- adenine G- guanine T- thymine C- cytosine

120. Other translation animations: Add an amino acid to tRNA- http://www.phschool.com/science/biology_place/biocoach/translation/addaa.html Initiation of Translation- http://www.phschool.com/science/biology_place/biocoach/translation/init.html Elongation of Polypeptide- http://www.phschool.com/science/biology_place/biocoach/translation/elong1.html Termination of Polypeptide- http://www.phschool.com/science/biology_place/biocoach/translation/term.html