Protein Structure and Function

1. Protein Structure and Function Protein Structure Chapter 3.2 - 3.3

2. Objectives • Be familiar with how polymers are assembled and dismantled • Understand that most organic macromolecules are polymers of smaller units called monomers • Understand what an isomer is and be able to apply your understanding • Describe the properties of a Protein • Understand how proteins are structured. Be able to explain each level of organization affects the shape and specificity of the protein

3. POLYMER PRINCIPLES. • Most macromolecules are polymers built from smaller units called monomers. • Polymerization reactions are carried out through the elimination of water (condensation or dehydration synthesis) or the addition of water (hydrolysis). • An immense variety of polymers can be built from a small set of monomers.

5. Diversification of Monomers • Isomers: variation in the structure of organic molecules with the same molecular formula • Structural isomers: differ in the covalent arrangement of their atoms. • Geometric isomers: differ in their spatial arrangement around a C=C bond. • Enantiomers (optical isomer): structures thatare mirror images of each other. Are built around an asymmetric (chiral) carbon atom.

7. PROTEINS: MOLECULAR TOOLS OF THE CELL. • A Polypeptide is a structural term used to describe a polymer of amino acids • Amino acids: the monomer building block of Proteins • Protein is a functional term applied to one or more polypeptides that perform a task within a cell • Functions of proteins may include: • Structural, Storage, Transport, Hormonal, Receptor, Contractile, Defensive, Enzymatic

8. STRUCTURE OF AMINO ACID. • Hydrogen atom. • Carboxyl group. • Amino group. • Variable R group.

10. Peptide Bond: The covalent bond between two amino acids formed via condensation synthesis.

11. FUNCTION DEPENDS ON SPECIFIC CONFORMATION. • Primary level of organization • Sequence of amino acids, numbered from the amino end • Secondary level of organization • H bond interactions between the amino acid • Tertiary level of organization • “R” group interactions • Quaternary level of organization • subunit interactions

12. Protein Structure • Primary level of organization • Defined as the sequence of amino acids • Numbered from the amino end • Each protein has a unique combination of amino acids

13. Proteins are Flexible • Leads to complex three dimensional shapes

15. So what. Why should we care? • Flexibility within the polypeptide chain allows for potential interactions between various regions of the polypeptide and/or with other polypeptides. • This leads to diverse chemical structures, each potentially capable of performing a different role within the cell.

16. Protein Structure • Secondary level of organization • H bond interactions between the amino and carbonyl groups of amino acids •  helix, H bonds between every 4th AA • Pleated sheet, H bonds between protein regions lying parallel to each other

17. Pleated sheet: H bonds between protein regions lying parallel to each other; drawn as arrows in models •  helix: H bonds between every 4th AA

18. Protein Structure • Tertiary level of organization • “R” group interactions, bonds • Disulfide bridges • Ionic bonds • H bonds • Hydrophobic interaction between nonpolar AA • reinforced by van der Waals

20. Protein Structure • Quaternary level of organization • Multiple polypeptides may come together to create a protein with a quaternary structure • Each polypeptide involved is called a subunit

22. Summary of protein structure can be found in Table 3.2 (p.61)

23. Changes in Protein Conformation • Denaturation: loss of a protein’s shape • Principally influenced by • pH: Disrupts H-bond interactions • Temperature: May break disulfide bonds • Protein folding is sometimes assisted by molecular chaperone proteins