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Protein Structure & Function

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The document discusses the levels of protein structure from primary to quaternary structure. It defines the primary structure as the amino acid sequence. Secondary structure forms from hydrogen bonding between amino acids and includes alpha helices and beta pleated sheets. Tertiary structure results from folding influenced by interactions between amino acid side chains. Quaternary structure occurs when multiple polypeptide chains interact to form a protein complex. Examples including hemoglobin and glyceraldehyde-3-phosphate dehydrogenase are provided to illustrate the different levels of structure.

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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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Protein Structure & 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.