1. Protein Structure Amino Acids Polypeptide Levels of Structure
©The Law of Science

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?

3. Amino acid structure four components attached to a central carbon
amino group
carboxylic acid (carboxyl) group
hydrogen atom
variable R group (or side chain) H |
H2N – C – COOH
| R

4. Amino acid structure
Amphiprotic: containing both acidic and basic functional groups H |
H2N – C – COOH R
The ionized form is observed in aqueous solutions because the acidic group can donate H+ ion to the basic group
+H2O H |
+H3N – C – COO-
| R

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. 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
Polar
Acidic
basic H |
H2N – C – COOH
| R

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. Forming a Polypeptide Condensation reaction to join 2 amino acid
Requires:
Carboxyl group
Amine
Fig. 5.16
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9. Forming a Polypeptide Peptide bond: links between amino acids
Growth of polypeptide is from N to C-terminus
Fig. 5.16
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10. Polypeptide Structure
Questions:
What groups make up the polypeptide backbone?
What groups are “hanging off” the backbone?
Which direction does
the polypeptide grow?
Fig. 5.16
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11. Protein shape determines function
Amino acid order determines the shape
(conformation) of a protein
Conformation determines function
Amino acids  conformation  function

12. Levels of protein structure
Primary (1o)
Secondary (2o)
Tertiary (3o)
Quaternary (4o)
organizes folding within a single polypeptide
interactions between two or more polypeptides that make a protein

13. 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. 5.18
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14. Primary (1o) Structure

15. 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.
Fig. 5.19
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16. Secondary (2o) Structure
results from hydrogen bonds at regular intervals along the polypeptide backbone
typical shapes:
alpha helix (coils)
beta pleated sheets (folds)
Fig. 5.20
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17. Tertiary (3o) Structure
Interactions between:
R groups and R
groups
R groups and
backbone
Fig. 5.22
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18. Tertiary (3o) Structure
Types of interaction include all the different types of intermolecular forces of attraction
Between polar / charged
amino acids:
Hydrogen bonds
Dipole-dipole
Ion-dipole
Between nonpolar amino
acids:
Hydrophobic interactions (often in interior of protein)
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
Fig. 5.22

19. Tertiary (3o) Structure: Proline kink
Proline is the only amino acid in which the R group is attached to the amino group
Doesn’t fit into alpha helical structure

20. Tertiary (3o) Structure: Proline kink
Forms a natural kink in the
polypeptide backbone
Helps to shape tertiary structure
Video (0:58):
=qt4iUa5OZQc

21. Tertiary (3o) Structure: function
All proteins will have a tertiary structure since this is where we would first see a protein’s function
Conformation determines function
Amino acids  conformation  function

22. Categories of Protein Function
Example
Structural support
Collagen
Storage
Albumin (egg white)
Transport
Hemoglobin
Hormonal
Insulin
Receptor
Nerve cell receptors
Contractile
Actin and myosin
Defensive
Antibodies
Enzymatic
Digestive enzymes

23. Quaternary (4o) Structure
Some, but not all, proteins will have a fourth
level of structure that involves:
Interactions (aggregations) between two or more polypeptide chains
Each chain is often referred to as a subunit
Not found in all proteins
Protein function would be evident at this level

24. Types of Quaternary (4o) Structure
Fibrous
Globular
Fig. 5.23
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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. Quaternary (4o) Structure: Globular
Water soluble
Compact, spherical
Example: hemoglobin

27. Levels of Protein Structure
Fig. 5.24
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28. 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.

29. Example of conformational change
Carrier protein
Fig. 8.14
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30. 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.
Fig. 5.25
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

31. their functional shape after denaturation
Renaturation: some proteins can return to
their functional shape after denaturation
But others cannot, especially in the crowded environment of the cell.

32. Protein Denaturation Video
protein_denaturation.html

33. HW Question Contrast secondary and tertiary levels of
protein structure.
Compare conformational change and denaturation. Use an example.