Aulanni’am Biochemistry Laboratory Chemistry Departement Brawijaya University

1. Chemical Foundations Aulanni’am Biochemistry Laboratory Chemistry Departement Brawijaya University Aulani " Biokimia" Presentasi1

2. The Chemicals of Life Aulani " Biokimia" Presentasi1

3. The Chemicals of Life Macromolecules Aulani " Biokimia" Presentasi1

4. Covalent bonds • Formed when two different atoms share electrons in the outer atomic orbitals • Each atom can make a characteristic number of bonds (e.g., carbon is able to form 4 covalent bonds) • Covalent bonds in biological systems are typically single (one shared electron pair) or double (two shared electron pairs) bonds Aulani " Biokimia" Presentasi1

5. The making or breaking of covalent bonds involves large energy changes In comparison, thermal energy at 25ºC is < 1 kcal/mol Aulani " Biokimia" Presentasi1

6. Covalent bonds have characteristic geometries Aulani " Biokimia" Presentasi1

7. Covalent double bonds cause all atoms to lie in the same plane Aulani " Biokimia" Presentasi1

8. Electrons are shared unequally in polar covalent bonds Atoms with higher electronegativity values have a greater attraction for electrons Aulani " Biokimia" Presentasi1

9. water molecule has a net dipole moment caused by unequal sharing of electrons Aulani " Biokimia" Presentasi1

10. Asymmetric carbon atoms are present in most biological molecules • Carbon atoms that are bound to four different atoms or groups are said to be asymmetric • The bonds formed by an asymmetric carbon can be arranged in two different mirror images (stereoisomers) of each other • Stereoisomers are either right-handed or left-handed and typically have completely different biological activities • Asymmetric carbons are key features of amino acids and carbohydrates Aulani " Biokimia" Presentasi1

11. Stereoisomers of the amino acid alanine Aulani " Biokimia" Presentasi1

12. Different monosaccharides have different arrangements around asymmetric carbons Aulani " Biokimia" Presentasi1

13.  and glycosidic bonds link monosaccharides Aulani " Biokimia" Presentasi1

14. Noncovalent bonds • Several types: hydrogen bonds, ionic bonds, van der Waals interactions, hydrophobic bonds • Noncovalent bonds require less energy to break than covalent bonds • The energy required to break noncovalent bonds is only slightly greater than the average kinetic energy of molecules at room temperature • Noncovalent bonds are required for maintaining the three-dimensional structure of many macromolecules and for stabilizing specific associations between macromolecules Aulani " Biokimia" Presentasi1

15. Multiple weak bonds stabilize large molecule interactions Aulani " Biokimia" Presentasi1

16. The hydrogen bond underlies water’s chemical and biological properties Molecules with polar bonds that form hydrogen bonds with water can dissolve in water and are termed hydrophilic Aulani " Biokimia" Presentasi1

17. Hydrogen bonds within proteins Aulani " Biokimia" Presentasi1

18. Ionic bonds • Ionic bonds result from the attraction of a positively charged ion (cation) for a negatively charged ion (anion) • The atoms that form the bond have very different electronegativity values and the electron is completely transferred to the more electronegative atom • Ions in aqueous solutions are surrounded by water molecules, which interact via the end of the water dipole carrying the opposite charge of the ion Aulani " Biokimia" Presentasi1

19. Ions in aqueous solutions are surrounded by water molecules Aulani " Biokimia" Presentasi1

20. van der Waals interactions are caused by transient dipoles When any two atoms approach each other closely, a weak nonspecific attractive force (the van der Waals force) is created due to momentary random fluctuations that produce a transient electric dipole Aulani " Biokimia" Presentasi1

21. Hydrophobic bonds cause nonpolar molecules to adhere to one another Nonpolar molecules (e.g., hydrocarbons) are insoluble in water and are termed hydrophobic Since these molecules cannot form hydrogen bonds with water, it is energetically favorable for such molecules to interact with other hydrophobic molecules This force that causes hydrophobic molecules to interact is termed a hydrophobic bond Aulani " Biokimia" Presentasi1

22. Multiple noncovalent bonds can confer binding specificity Aulani " Biokimia" Presentasi1

23. Phospholipids are amphipathic molecules Aulani " Biokimia" Presentasi1

24. Phospholipids spontaneously assemble via multiple noncovalent interactions to form different structures in aqueous solutions Aulani " Biokimia" Presentasi1

25. Chemical equilibrium • The extent to which a reaction can proceed and the rate at which the reaction takes place determines which reactions occur in a cell • Reactions in which the rates of the forward and backward reactions are equal, so that the concentrations of reactants and products stop changing, are said to be in chemical equilibrium • At equilibrium, the ratio of products to reactants is a fixed value termed the equilibrium constant (Keq) and is independent of reaction rate Aulani " Biokimia" Presentasi1

26. Equilibrium constants reflect the extent of a chemical reaction • Keq depends on the nature of the reactants and products, the temperature, and the pressure • The Keq is always the same for a reaction, whether a catalyst is present or not • Keq equals the ratio of the forward and reverse rate constants (Keq = kf/kr) • The concentrations of complexes can be estimated from equilibrium constants for binding reactions Aulani " Biokimia" Presentasi1

27. Biological fluids have characteristic pH values • All aqueous solutions, including those in and around cells, contain some concentration of H+ and OH- ions, the dissociation products of water • In pure water, [H+] = [OH-] = 10-7 M • The concentration of H+ in a solution is expressed as pH pH = -log [H+] • So for pure water, pH = 7.0 • On the pH scale, 7.0 is neutral, pH < 7.0 is acidic, and pH > 7.0 is basic • The cytosol of most cells has a pH of 7.2 Aulani " Biokimia" Presentasi1

28. The pH Scale Aulani " Biokimia" Presentasi1

29. Hydrogen ions are released by acids and taken up by bases • When acid is added to a solution, [H+] increases and [OH-] decreases • When base is added to a solution, [H+] decreases and [OH-] increases • The degree to which an acid releases H+ or a base takes up H+ depends on the pH Aulani " Biokimia" Presentasi1

30. [A-] pH = pKa + log — [HA] The Henderson-Hasselbalch equation • The Henderson-Hasselbalch equation relates the pH and Keq of an acid-base system • The pKa of any acid is equal to the pH at which half the molecules are dissociated and half are neutral (undissociated) • It is possible to calculate the degree of dissociation if both the pH and the pKa are known Aulani " Biokimia" Presentasi1

31. Cells have a reservoir of weak bases and weak acids, called buffers, which ensure that the cell’s pH remains relatively constant The titration curve for phosphoric acid (H3PO4), a physiologically important buffer Aulani " Biokimia" Presentasi1

32. Biochemical energetics • Living systems use a variety of interconvertible energy forms • Energy may be kinetic (the energy of movement) or potential (energy stored in chemical bonds or ion gradients) Aulani " Biokimia" Presentasi1

33. The change in free energy determines the direction of a chemical reaction • Living systems are usually held at constant temperature and pressure, so one may predict the direction of a chemical reaction by using a measure of potential energy termed free energy (G) • The free-energy change (G) of a reaction is given by G = Gproducts – Greactants • If G < 0, the forward reaction will tend to occur spontaneously • If G > 0, the reverse reaction will tend to occur • If G = 0, both reactions will occur at equal rates Aulani " Biokimia" Presentasi1

34. The G of a reaction depends on changes in enthalpy (bond energy) and entropy • TheGof a reaction is determined by the change in bond energy (enthalpy, or H) between reactants and products and the change in the randomness (entropy, or S) of the system G = H - TS • In exothermic reactions (H < 0), the products contain less bond energy than the reactants and the liberated energy is converted to heat • In endothermic reactions (H > 0), the products contain more bond energy than the reactants and heat is absorbed Aulani " Biokimia" Presentasi1

35. Entropy • Entropy is a measure of the degree of randomness or disorder of a system • Entropy increases as the system becomes more disordered and decreases as it becomes more structured • Many biological reactions lead to an increase in order and thus a decrease in entropy (S < 0) • Exothermic reactions (H < 0) that increase entropy(S > 0)occur spontaneously (G < 0) • Endothermic reactions (H > 0) may occur spontaneously if S increases enough so thatT Soffsets the positiveH Aulani " Biokimia" Presentasi1

36. Many cellular processes involve oxidation-reduction reactions • Many chemical reactions result in the transfer of electrons without the formation of a new chemical bond • The loss of electrons from an atom or molecule is termed oxidation and the gain of electrons is termed reduction • If one atom or molecule is oxidized during a chemical reaction then another molecule must be reduced • Many biological oxidation-reduction reactions involve the removal or addition of H atoms (protons plus electrons) rather than the transfer of isolated electrons Aulani " Biokimia" Presentasi1

37. The oxidation of succinate to fumarate Aulani " Biokimia" Presentasi1

38. An unfavorable chemical reaction can proceed if it is coupled to an energetically favorable reaction • Many chemical reactions are energetically unfavorable (G > 0) and will not proceed spontaneously • Cells can carry out such a reaction by coupling it to a reaction that has a negative Gof larger magnitude • Energetically unfavorable reactions in cells are often coupled to the hydrolysis of adenosine triphosphate (ATP), which has a Gº = -7.3 kcal/mol • The useful free energy in an ATP molecule is contained is phosphoanhydride bonds Aulani " Biokimia" Presentasi1

39. The phosphoanhydride bonds of ATP Aulani " Biokimia" Presentasi1

40. ATP is used to fuel many cell processes The ATP cycle Aulani " Biokimia" Presentasi1

41. Activation energy and reaction rate • Many chemical reactions that exhibit a negative G°´ do not proceed unaided at a measurable rate • Chemical reactions proceed through high energy transition states. The free energy of these intermediates is greater than either the reactants or products Aulani " Biokimia" Presentasi1

42. Example changes in the conversion of a reactant to a product in the presence and absence of a catalyst Enzymes accelerate biochemical reactions by reducing transition-state free energy Aulani " Biokimia" Presentasi1

43. thank you Aulani " Biokimia" Presentasi1