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

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?

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

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

Amino acid R groups (side chains) differences in R groups produce the 20 different amino acids 8 are essential: body cannot synthesize them

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

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

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

Forming a Polypeptide Peptide bond: links between amino acids Growth of polypeptide is from N to C-terminus Fig. 5.16 Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

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

Protein shape determines function Amino acid order determines the shape (conformation) of a protein Conformation determines function Amino acids  conformation  function

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

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

Primary (1o) Structure

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

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

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

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

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 http://peptaibol.cryst.bbk.ac.uk/images/alamet.gif

Tertiary (3o) Structure: Proline kink Forms a natural kink in the polypeptide backbone Helps to shape tertiary structure Video (0:58): https://www.youtube.com/watch?v =qt4iUa5OZQc http://www.blopig.com/blog/wp-content/uploads/2013/09/blog_pic.png

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 https://www.youtube.com/watch?v=qBRFIMcxZNM

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

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

Types of Quaternary (4o) Structure Fibrous Globular Fig. 5.23 Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Quaternary (4o) Structure: Fibrous Water insoluble Threadlike Example: collagen 3 polypeptides supercoiled like a rope provides structural strength for role in connective tissue

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

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

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.

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

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

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.

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

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