Types of non-covalent interactions

1. The induced dipole (d,e) and the dispersion forces (f) depend on the distortion of the electron distribution in a nonpolar atom or molecule. The symbols q-, q+ denote a fraction of an electron or proton charge (a partial charge δ) Types of non-covalent interactions Biochemistry, Mathews, Van Holde, Ahern

2. Examples of different types of 2° Structure in a protein

3. Collagen In large animals, collagen may make up a third of the total protein mass. Collagen fibers form the matrix material in bone, on which the mineral bind; it makes up a major portion of tendons and is an important component in skin. Example of helical fibrous protein

4. Fibroin – spider silk! Stacked β sheets  This arrangement of alternating Gly and Ala or Ser makes this fibrous protein VERY strong and inextensible, but flexible – perfect for building. Dissolvable films of silk fibroin for ultrathin conformal bio-integrated electronics. Nature Materials 2010.

5. Globular Proteins Most of the synthesizing, transporting, and metabolizing that goes on in the cell is carried out by these proteins.

6. What is the main difference between globular and fibrous proteins? Aside from the difference in shape (elongated vs. spheroidal) and solubility (insoluble vs. soluble), fibrous proteins generally have only primary and secondary structure whereas globular proteins have tertiary and sometimes quaternary structure in addition to primary and secondary structure.

8. Bioenergetics in a cell 2nd Law of Thermodynamics: The entropy (disorder) of an isolated system will tend to increase to a maximum value. In an isolated system, disorder is the ruler!! BUT….we never deal with isolated systems in biology!!!! EVERY biological system is open to exchange with matter and energy in its environment.

9. So…….Energy and Entropy must be considered! • Gibbs Free Energy (G) describes BOTH. • (H) enthalpy – measures energy ∆ at constant pressure • (S) entropy – importance of randomization G = H – TS ∆G = ∆H – T∆S

10. What factors make processes favorable? • ↓ in energy (∆H is neg.) AND/OR • ↑ in entropy (∆S is pos.) MAKES ∆G NEGATIVE!!!

11. The criterion for a favorable process in a non-isolated system, at constant temperature and pressure, is that ∆G be negative When ∆G is negative, is the process endergonic or exergonic?? EXERGONIC!

12. Favorable processes are NOT necessarily rapid. A catalyst may increase the rate for some reactions but the favored direction is always determined by ∆G. • Entropy of an open system CAN decrease (water  ice) in entropy. BUT…..this is paid for by the expenditure of ENERGY. You’ve got to pay the piper for organization – there is a price for life!

13. So what is ∆G???? • It measures the maximum amount of useful work that can be obtained from a chemical process. • Things like: muscle contraction, cell motility, transport of ions and molecules, cell communication, tissue growth and MORE! • ∆H = total energy change in a reaction. Part of which (T∆S) is always lost as heat. This HEAT energy is NOT available to do other things.

14. ATP Cycle Exergonic:(Releases Energy) Cell Respiration Catabolism Endergonic: (Requires Energy) Active transport Cell Movements Anabolism ADP + Pi ENERGY ENERGY Synthesis of ATP from ADP and Pi requires energy Hydrolysis of ATP to ADP and Pi releases energy ATP The energy ATP releases is greater than the energy most other molecules could deliver

15. Phosphorylation • Transfers of a phosphate group from one molecule to another transfers the energy as well. • The molecule that receives the phosphate group is less stable and therefore more reactive. • This can include proteins like enzymes, transport proteins or any proteins that perform work.

16. Enzymes reduce the energy required to catalyze a reaction

17. An enzyme binds substrate(s), promotes the reaction, and releases product(s). An enzyme works by forcing the substrate(s) into a position or orientation that allows for collisions between molecules to occur or for atoms with a molecule to stretch and bend. This is the induced fit model

18. Two models Originally biochemists adopted the “Lock and Key” model of enzyme catalysis, but the Induced Fit is more accurate – BOTH the enzyme and the substrate change their conformation in order for catalysis to occur.

19. Hexokinase The binding of glucose to hexokinase induces a major conformational change in the enzyme. The enzyme is a single polypeptide chain, but its two major domains are shaded differently to distinguish them. Notice how the cleft between the domains closes around the glucose molecule!

20. Active site of the protease carboxy-peptidase A The zinc atom serves as a metal ion catalyst to promote hydrolysis. It does so by stabilizing the negative charge on the oxygen in the transition state. The bond cleaved is indicated by the red wedge.

21. Examples of each of the major classes of Enzymes

22. Allosteric Enzymes • Multisubunit proteins with multiple active sites. • Exhibit cooperativity in substrate binding and regulation of their activity by other effector molecules (activators or inhibitors). • Activators and inhibitors allow for feedback control • http://bcs.whfreeman.com/thelifewire/content/chp06/0602002.html • http://www.northland.cc.mn.us/biology/biology1111/animations/enzyme.swf

23. Inhibitors Prevents Cellular Respiration by blocking cytochromeoxidase in the mitochondria Was used in WWI as a chemical warfare agent – causes severe burns, blindness Good ol’ Penicillin – antibiotic inhibits transpeptidase and enzyme that helps build the cell wall