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Protein StructureAmino Acids, PolypeptideLevels of Structure
Monomer   The single unit that makes up a protein is an    amino acid   Question: Based on its name, which 2    function...
Amino acid structure   four components attached to a central carbon:     amino group                             H     ...
Amino acid structure                                                 H   Amphiprotic: containing both                 |  ...
Amino acid R groups (side chains)   differences in R groups produce the 20    different amino acids   8 are essential: b...
Amino acid R groups (side chains)   Physical and chemical characteristics of the R    group determine the unique characte...
Activity   Given the 20 amino acids, group them into    the 4 categories based on the properties of    their R groups   ...
Nonpolar amino acids hashydrophobic R groups    Hydrophobic R groupsCopyright © 2002 Pearson Education, Inc., publishing ...
Polar amino acids    Polar R groups    hydrophilicCopyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummi...
Acidic and Basic Amino Acids    Amino acids with charged (ionized) functional     groups at cellular pH can be either:   ...
Forming a Polypeptide    Condensation reaction     to join 2 amino acid    Requires:      Carboxyl group      AmineCop...
Forming a Polypeptide    Question: What is name     of the new functional     group formed?    Peptide bond: links     b...
Protein shape determines function    Amino acid order determines the shape     (conformation) of a protein    Conformati...
Protein binding examples   Antibodies bind to particular foreign    substances that fit their binding sites.   Enzymes r...
Levels of protein structure   Primary (1o)                      organizes folding within   Secondary (2o)               ...
Primary                  (1o) Structure   unique sequence of amino    acid   sequence determined by    DNA   a slight c...
Primary   (1o) Structure
Example: Sickle Cell Anemia    abnormal hemoglobin develop because of a single     amino acid substitution (change)    c...
Secondary                            (2o) Structure                                                           results fro...
Tertiary                    (3o) StructureInteractions between: R groups and R  groups R groups and  backboneCopyright ©...
Tertiary                    (3o) StructureTypes of interaction: Hydrogen bonds Ionic bonds Hydrophobic interactions    ...
Tertiary     (3o) Structure:       Proline kink    Proline is the only amino acid in which the R     group is attached to...
Quaternary                               (4o) Structure   aggregation of    two or more    polypeptide    subunits   for...
Quaternary      (4o) Structure: Globular   Water soluble   Compact, spherical   Example: hemoglobin
Quaternary            (4o) Structure:   Fibrous   Water insoluble   Threadlike   Example: collagen     3 polypeptides ...
Levels of Protein Structure                                                                       Fig.Copyright © 2002 Pea...
Protein Folding    Occurs spontaneously    Aided by chaperone proteins (chaperonin)    Provide ideal environment for fo...
Tutorial: Protein Folding   http://www.wiley.com/legacy/college/boyer/0470003790/ani    mations/protein_folding/protein_f...
Conformational Change   Changing the shape of a protein   Reversible   Does not disrupt a proteins function but    rath...
Example of conformational change      Carrier protein                                                                    ...
Denaturation    A change in the shape of the protein that     disrupts protein function.    Alterations in the environme...
Denaturation   Renaturation: some proteins can return to    their functional shape after denaturation   But others canno...
Protein Denaturation Videohttp://highered.mcgraw-hill.com/sites/0072943696/student_view0/chapter2/animation__protein_denat...
HW Question   Contrast secondary and tertiary levels of    protein structure. [2 marks]   Compare conformational change ...
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Protein structure

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Protein structure

  1. 1. Protein StructureAmino Acids, PolypeptideLevels of Structure
  2. 2. Monomer The single unit that makes up a protein is an amino acid Question: Based on its name, which 2 functional groups would be found in an amino acid? An amino acid is sometimes referred to as a residue
  3. 3. Amino acid structure four components attached to a central carbon:  amino group H  carboxylic acid (carboxyl) group |  hydrogen atom H2N – C – COOH |  variable R group (or side chain) R Question: Determine which functional group is acidic and basic. Explain how you know.
  4. 4. Amino acid structure H Amphiprotic: containing both | acidic and basic functional groups H2N – C – COOH | The ionized form is observed in R aqueous solutions because the +H2O acidic group can donate H+ ion to H the basic group | +H N 3 – C – COO- | R
  5. 5. Amino acid R groups (side chains) differences in R groups produce the 20 different amino acids 8 are essential: body cannot synthesize them
  6. 6. Amino acid R groups (side chains) Physical and chemical characteristics of the R group determine the unique characteristics of an amino acid Amino acids are classified into 4 groups based on their R groups:  Nonpolar H |  Polar H2N – C – COOH  Acidic |  basic R
  7. 7. Activity Given the 20 amino acids, group them into the 4 categories based on the properties of their R groups The 4 categories are:  Nonpolar  Polar  Acidic  basic
  8. 8. Nonpolar amino acids hashydrophobic R groups  Hydrophobic R groupsCopyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 5.15a
  9. 9. Polar amino acids  Polar R groups  hydrophilicCopyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 5.15b
  10. 10. Acidic and Basic Amino Acids  Amino acids with charged (ionized) functional groups at cellular pH can be either:  Acidic: carboxylic acid, negative charge  Basic: amino, positive chargeCopyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 5.15c
  11. 11. Forming a Polypeptide  Condensation reaction to join 2 amino acid  Requires:  Carboxyl group  AmineCopyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 5.16
  12. 12. Forming a Polypeptide  Question: What is name of the new functional group formed?  Peptide bond: links between amino acidsCopyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 5.16
  13. 13. Protein shape determines function  Amino acid order determines the shape (conformation) of a protein  Conformation determines function  Function depends on its ability to recognize and bind a molecule Amino acids  conformation  function  binding
  14. 14. Protein binding examples Antibodies bind to particular foreign substances that fit their binding sites. Enzymes recognize and bind to specific substrates, facilitating a chemical reaction. Neurotransmitters pass signals from one cell to another by binding to receptor sites on proteins in the receiving cell.
  15. 15. Levels of protein structure Primary (1o) organizes folding within Secondary (2o) a single polypeptide Tertiary (3o) interactions between two Quaternary (4o) or more polypeptides that make a protein
  16. 16. Primary (1o) Structure unique sequence of amino acid sequence determined by DNA a slight change in primary structure can affect a protein’s conformation and ability to function Fig. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings 5.18
  17. 17. Primary (1o) Structure
  18. 18. Example: Sickle Cell Anemia  abnormal hemoglobin develop because of a single amino acid substitution (change)  causes hemoglobin to crystallize, deforming the red blood cells and leading to clogs in blood vessels.Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 5.19
  19. 19. Secondary (2o) Structure  results from hydrogen bonds at regular intervals along the polypeptide backbone  typical shapes:  alpha helix (coils)  beta pleated sheets (folds)  not found in all proteinsCopyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 5.20
  20. 20. Tertiary (3o) StructureInteractions between: R groups and R groups R groups and backboneCopyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 5.22
  21. 21. Tertiary (3o) StructureTypes of interaction: Hydrogen bonds Ionic bonds Hydrophobic interactions  often in interior of protein Covalent bonds  Disulfide bridge: formed between the sulfhydryl groups (SH) of cysteine amino acids Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 5.22
  22. 22. Tertiary (3o) Structure: Proline kink  Proline is the only amino acid in which the R group is attached to the amino group  Forms a natural kink in the polypeptide  Helps to shape tertiary structure
  23. 23. Quaternary (4o) Structure aggregation of two or more polypeptide subunits forms 2 types of proteins: globular and fibrous not found in all proteinsCopyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 5.23
  24. 24. Quaternary (4o) Structure: Globular Water soluble Compact, spherical Example: hemoglobin
  25. 25. Quaternary (4o) Structure: Fibrous Water insoluble Threadlike Example: collagen  3 polypeptides supercoiled like a rope  provides structural strength for role in connective tissue
  26. 26. Levels of Protein Structure Fig.Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings 5.24
  27. 27. Protein Folding  Occurs spontaneously  Aided by chaperone proteins (chaperonin)  Provide ideal environment for foldingCopyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 5.26
  28. 28. Tutorial: Protein Folding http://www.wiley.com/legacy/college/boyer/0470003790/ani mations/protein_folding/protein_folding.htm
  29. 29. Conformational Change Changing the shape of a protein Reversible Does not disrupt a proteins function but rather is what defines the protein’s function Change occurs in response to the physical and chemical conditions.
  30. 30. Example of conformational change  Carrier protein Fig. 8.14 Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings http://bio1151b.nicerweb.com/Locked/media/ch07/07_15FacilitatedDiffusionB.jpg
  31. 31. Denaturation  A change in the shape of the protein that disrupts protein function.  Alterations in the environment (pH, salt concentration, temperature etc.) disrupt bonds and forces of attraction.Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 5.25
  32. 32. Denaturation Renaturation: some proteins can return to their functional shape after denaturation But others cannot, especially in the crowded environment of the cell.
  33. 33. Protein Denaturation Videohttp://highered.mcgraw-hill.com/sites/0072943696/student_view0/chapter2/animation__protein_denaturation.html
  34. 34. HW Question Contrast secondary and tertiary levels of protein structure. [2 marks] Compare conformational change and denaturation. Use an example. [3 mark]

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