Here are sample responses: Secondary structure involves hydrogen bonding between amino acids along the polypeptide backbone, forming regular structures like alpha helices and beta sheets. Tertiary structure involves interactions between R groups of amino acids, forming the overall 3D shape of the protein. Conformational change alters a protein's shape but does not disrupt its function, allowing it to perform its role. For example, a carrier protein may change shape to bind a substrate. Denaturation permanently alters a protein's shape through environmental changes like heat, disrupting its function. Boiling an egg is an example - it denatures the proteins.

1. Protein Structure
Amino Acids, Polypeptide
Levels of Structure

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. 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. 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. 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 H
|
 Polar
H2N – C – COOH
 Acidic |
 basic 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. Nonpolar amino acids has
hydrophobic R groups
 Hydrophobic R groups
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 5.15a

9. Polar amino acids
 Polar R groups
 hydrophilic
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 5.15b

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 charge
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 5.15c

11. Forming a Polypeptide
 Condensation reaction
to join 2 amino acid
 Requires:
 Carboxyl group
 Amine
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 5.16

12. Forming a Polypeptide
 Question: What is name
of the new functional
group formed?
 Peptide bond: links
between amino acids
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 5.16

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. 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. 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. 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. Primary (1o) Structure

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. 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 proteins
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 5.20

20. Tertiary (3o) Structure
Interactions between:
 R groups and R
groups
 R groups and
backbone
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 5.22

21. Tertiary (3o) Structure
Types 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. 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. Quaternary (4o) Structure
 aggregation of
two or more
polypeptide
subunits
 forms 2 types of
proteins: globular
and fibrous
 not found in all
proteins
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 5.23

24. Quaternary (4o) Structure: Globular
 Water soluble
 Compact, spherical
 Example: hemoglobin

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. Levels of Protein Structure
Fig.
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings 5.24

27. Protein Folding
 Occurs spontaneously
 Aided by chaperone proteins (chaperonin)
 Provide ideal environment for folding
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 5.26

28. Tutorial: Protein Folding
 http://www.wiley.com/legacy/college/boyer/0470003790/ani
mations/protein_folding/protein_folding.htm

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

33. Protein Denaturation Video
http://highered.mcgraw-hill.com/sites/0072943696/student_view0/chapter2/animation__protein_denaturation.html

34. HW Question
 Contrast secondary and tertiary levels of
protein structure. [2 marks]
 Compare conformational change and
denaturation. Use an example. [3 mark]