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Proteins: Structure and Function

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Proteins: structure & function Based on a presentation by Timothy G. Standish
The Genetic Code S E C O N D B A S E A GGU GGC GGA GGG Gly* AGU AGC AGA AGG Arg G CGU CGC CGA CGG Arg G UGU UGC UGA UGG C GAU GAC GAA GAG AAU AAC AAA AAG Glu CAU CAC CAA CAG A UAU UAC UAA UAG Stop Tyr GUU GUC GUA GUG Val AUU AUC AUA AUG start Ile CUU CUC CUA CUG Leu U UUU UUC UUA UUG Leu Phe Met/ GCU GCC GCA GCG Ala ACU ACC ACA ACG Thr CCU CCC CCA CCG Pro C UCU UCC UCA UCG Ser U C A G U U C A G U C A G U C A G Gln † His Trp Cys T H I R D B A S E F I R S T B A S E Asp Lys Asn † Stop Ser Neutral Non-polar Polar Basic Acidic † Have amine groups * Listed as non-polar by some texts
Different Amino Acid Classes Polar Basic Acid ? Acid Amine OH O H H 2 N C C R Generic Non-polar C C C OH H H O H + N H H 2 N C NH C C Histidine H H 2 N C C H H O OH O C OH C Aspartic acid C C C OH H H O HS H H 2 N Cysteine OH H H O H H H 2 N C C C Alanine
Non-Polar Amino Acids OH O H H 2 N C C H Glycine Leucine OH O H H 2 N C C H 3 C CH 3 H C H H C Methionine OH O H H 2 N C C H 3 C H H C H H C S Alanine OH H H O H H H 2 N C C C Valine OH O H H 2 N C C H 3 C CH 3 H C Phenylalanine OH H H O H H 2 N C C C Tryptophan OH O H H 2 N C C NH H C H Isoleucine OH O H H 2 N C C H 3 C H H C H H 3 C C Proline OH O H H 2 N + C C H 2 C CH 2 H 2 C
Polar Amino Acids Cysteine C C C OH H H O HS H H 2 N Serine OH O H H 2 N C C HO CH 3 H C Threonine OH O H H 2 N C C H H C OH H C H Tyrosine HO H H O H H 2 N C C C OH Asparagine H H 2 N C C H H O OH O C NH 2 C Glutamine H H 2 N C C H H O OH O C NH 2 C C H H
Acidic Amino Acids Aspartic acid H H 2 N C C H H O OH O C OH C Glutamic acid H H 2 N C C H H O OH O C OH C C H H
Basic Amino Acids Histidine C C C OH H H O H + N H H 2 N C NH C C Lysine OH O H H 2 N C C + H 3 N H H C H H C C H H H H C Arginine OH O H H 2 N C C H H C H H C C H H H N + H 2 N NH 2 C
Levels Of Protein Organization ,[object Object],[object Object],[object Object],[object Object]
Levels Of Protein Organization Primary Structure Met- Gly -Ala-Pro- His -Ile- Asp - Glu -Met- Ser - Thr -...
Glyceraldehyde-3-Phosphate Dehydrogenase Primary Structure ,[object Object],[object Object]
Protein Secondary Structure ,[object Object],[object Object],[object Object],[object Object],[object Object]
Protein Secondary Structure:  Helix + - C O OH C N H H H C HO H C H O C N H H H C H H C H N C O C H N O C C O C H N C H N C O C O C O C O C H N H N C H N
Protein Secondary Structure:  Helix + - C O OH C N H H H C HO H C H O C N H H H C H H C H N C O C H N O C C O C H N C H N C O C O C O C O C H N H N C H N
Protein Secondary Structure:  Helix R groups stick out from the  helix influencing higher levels of protein organization R R R R R R R R R R R R R R
Protein Secondary Structure:  Helix
Yeast Cytochrome C Oxidase Subunit IV Leader ,[object Object],[object Object],[object Object],ML S L R QS I R FF K PA T R T L CSS R Y LL Neutral Non-polar Polar Basic Acidic R Y P L T C S R L S T I K P R F A F M R Q L L S S First 12 residues are sufficient for transport to the mitochondria
Protein Secondary Structure:  Pleated Sheet N H C O C H C C N O N H C O C H C C N O N H C O C H C C N O N H C O C H C C N O N H C O C H C C N O N H C O C H C C N O N H C O C H C C N O N H C O C H C C N O
Protein Secondary Structure:  Pleated Sheet N H C O C H C C N O N H C O C H C C N O N H C O C H C C N O N H C O C H C C N O N H C O C H C C N O N H C O C H C C N O N H C O C H C C N O N H C O C H C C N O N H C O C H C C N O N H C O C H C C N O N H C O C H C C N O N H C O C H C C N O
Protein Secondary Structure:  pleated sheet
Protein Secondary Structure: α helices and  pleated sheets
Levels Of Protein Organization Tertiary Structure ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
G-3-P Dehydrogenase Tertiary Structure Picture source: SWISS-PROT
Levels Of Protein Organization Quaternary Structure ,[object Object],[object Object],[object Object],[object Object],[object Object]
G-3-P Dehydrogenase from Bacillus stearothermophilus Skarzynski, T., Moody, P. C. E., Wonacott, A. J.: Structure of Holo-Glyceraldehyde-3-Phosphate Dehydrogenase from Bacillus Stearothermophilus at 1.8 Angstroms Resolution. J.Mol.Biol. 193 pp. 171 (1987) Picture source: SWISS-PROT
The Globin Gene Family ,[object Object],[object Object],Fe    
Haemoglobin ,[object Object],Picture source: SWISS-PROT
 
Protein denaturation ,[object Object],[object Object],[object Object],[object Object]
Protein denaturation

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Proteins: Structure and Function

  • 1. Proteins: structure & function Based on a presentation by Timothy G. Standish
  • 2. The Genetic Code S E C O N D B A S E A GGU GGC GGA GGG Gly* AGU AGC AGA AGG Arg G CGU CGC CGA CGG Arg G UGU UGC UGA UGG C GAU GAC GAA GAG AAU AAC AAA AAG Glu CAU CAC CAA CAG A UAU UAC UAA UAG Stop Tyr GUU GUC GUA GUG Val AUU AUC AUA AUG start Ile CUU CUC CUA CUG Leu U UUU UUC UUA UUG Leu Phe Met/ GCU GCC GCA GCG Ala ACU ACC ACA ACG Thr CCU CCC CCA CCG Pro C UCU UCC UCA UCG Ser U C A G U U C A G U C A G U C A G Gln † His Trp Cys T H I R D B A S E F I R S T B A S E Asp Lys Asn † Stop Ser Neutral Non-polar Polar Basic Acidic † Have amine groups * Listed as non-polar by some texts
  • 3. Different Amino Acid Classes Polar Basic Acid ? Acid Amine OH O H H 2 N C C R Generic Non-polar C C C OH H H O H + N H H 2 N C NH C C Histidine H H 2 N C C H H O OH O C OH C Aspartic acid C C C OH H H O HS H H 2 N Cysteine OH H H O H H H 2 N C C C Alanine
  • 4. Non-Polar Amino Acids OH O H H 2 N C C H Glycine Leucine OH O H H 2 N C C H 3 C CH 3 H C H H C Methionine OH O H H 2 N C C H 3 C H H C H H C S Alanine OH H H O H H H 2 N C C C Valine OH O H H 2 N C C H 3 C CH 3 H C Phenylalanine OH H H O H H 2 N C C C Tryptophan OH O H H 2 N C C NH H C H Isoleucine OH O H H 2 N C C H 3 C H H C H H 3 C C Proline OH O H H 2 N + C C H 2 C CH 2 H 2 C
  • 5. Polar Amino Acids Cysteine C C C OH H H O HS H H 2 N Serine OH O H H 2 N C C HO CH 3 H C Threonine OH O H H 2 N C C H H C OH H C H Tyrosine HO H H O H H 2 N C C C OH Asparagine H H 2 N C C H H O OH O C NH 2 C Glutamine H H 2 N C C H H O OH O C NH 2 C C H H
  • 6. Acidic Amino Acids Aspartic acid H H 2 N C C H H O OH O C OH C Glutamic acid H H 2 N C C H H O OH O C OH C C H H
  • 7. Basic Amino Acids Histidine C C C OH H H O H + N H H 2 N C NH C C Lysine OH O H H 2 N C C + H 3 N H H C H H C C H H H H C Arginine OH O H H 2 N C C H H C H H C C H H H N + H 2 N NH 2 C
  • 8.
  • 9. Levels Of Protein Organization Primary Structure Met- Gly -Ala-Pro- His -Ile- Asp - Glu -Met- Ser - Thr -...
  • 10.
  • 11.
  • 12. Protein Secondary Structure:  Helix + - C O OH C N H H H C HO H C H O C N H H H C H H C H N C O C H N O C C O C H N C H N C O C O C O C O C H N H N C H N
  • 13. Protein Secondary Structure:  Helix + - C O OH C N H H H C HO H C H O C N H H H C H H C H N C O C H N O C C O C H N C H N C O C O C O C O C H N H N C H N
  • 14. Protein Secondary Structure:  Helix R groups stick out from the  helix influencing higher levels of protein organization R R R R R R R R R R R R R R
  • 16.
  • 17. Protein Secondary Structure:  Pleated Sheet N H C O C H C C N O N H C O C H C C N O N H C O C H C C N O N H C O C H C C N O N H C O C H C C N O N H C O C H C C N O N H C O C H C C N O N H C O C H C C N O
  • 18. Protein Secondary Structure:  Pleated Sheet N H C O C H C C N O N H C O C H C C N O N H C O C H C C N O N H C O C H C C N O N H C O C H C C N O N H C O C H C C N O N H C O C H C C N O N H C O C H C C N O N H C O C H C C N O N H C O C H C C N O N H C O C H C C N O N H C O C H C C N O
  • 19. Protein Secondary Structure:  pleated sheet
  • 20. Protein Secondary Structure: α helices and  pleated sheets
  • 21.
  • 22. G-3-P Dehydrogenase Tertiary Structure Picture source: SWISS-PROT
  • 23.
  • 24. G-3-P Dehydrogenase from Bacillus stearothermophilus Skarzynski, T., Moody, P. C. E., Wonacott, A. J.: Structure of Holo-Glyceraldehyde-3-Phosphate Dehydrogenase from Bacillus Stearothermophilus at 1.8 Angstroms Resolution. J.Mol.Biol. 193 pp. 171 (1987) Picture source: SWISS-PROT
  • 25.
  • 26.
  • 27.  
  • 28.