1. CELL CHEMISTRY – CHPT 2 Chemical composition of living things is unique Four most abundant elements in life: –Hydrogen, oxygen, carbon, nitrogen Life systems depend upon/evolved in water Biomolecules have characteristic bonds (linkages between atoms/elements): –Covalent: strong bonds holding monomers in macromolecular polymers –Noncovalent: weaker bonds – hydrogen, ionic, van der Waals interactions, hydrophobic interactions

2. 50-60% 3-4% 8-10% 25-30% Carbon, hydrogen, nitrogen and oxygen together constitute >99% (dry weight) of life molecules (mostly macromolecules) ; these are >1% in the earth’s crust

3. Differences in chemical abundance comparing living organisms and the earth’s crust What are the consequences for living organisms?

4. 30 SMALL MOLECULE PRECURSORS OF MACROMOLECULES 20 amino acids – monomers of proteins 5 aromatic bases make nucleotides- the monomers of nucleic acids: – 2 purines – adenine and guanine – 3 pyrimidines – cytosine, uracil, thymine 2 sugars: – D-glucose (photosynthesis product and glycolysis substrate) – ribose/deoxyribose (nucleotide sugars) 3 membrane phospholipids: –fatty acid - palmitate, –the tri-alcohol – glycerol, –the amine - choline

5. Water is typically ~70% of cells ~30 precursor molecules but ~3000 kinds of molecules total in a cell

6. CARBON Over 50% of organism’s dry weight – primary element upon which life is based. Very diverse forms & quite stable molecules. –Long chains, rings, combinations of these –Bonds a variety of other elements i.e.: oxygen, hydrogen, nitrogen, sulfur Forms covalent bonds sharing pairs of electrons: –Single, double, triple

8. Covalent bonds have shared pairs of electrons Free radicals (highly reactive) may form when a covalent bond is broken such that each atom retains one of the two shared electrons comprising the bond. They may also form when an atom or molecule accepts a single electron transferred during an oxidation - reduction reaction.

9. Normally complete rotation around C-C single bonds (unless large/charged side groups attached to both) Double bonds are more rigid – do not allow complete rotation Rigidity has enormous structural/functional significance

10. Bond Strength: amount of energy required to break 1 mole (6 x 10 23 molecules) One calorie = amount of energy to raise the temperature of 1 gm (1 cm 3 ) of water 1 degree C One kilocalorie = 1000 calories Know approximate strengths!

11. Bonds are oriented at precise angles as a result of repulsions of the outer electron orbitals dipolar symmetrical Ball-and-stick models show bond angles but not lengths well Space-filling models show outer contours and are proportional in dimensions to the radius of different atoms

12. WATER Most abundant component of cells – 70% Organisms evolved in water and all aspects of cell structure/function adapted to physical/chemical properties of water –Modeling of molecule structure depends on interactions with water –Solvent of cells (hydrophilic substances dissolve, hydrophobic substances avoid water) Polar, electrophilic oxygen more attracts shared electrons, producing electrical asymmetry. –Forms important hydrogen bonding with other molecules Liquid at most environmental temperatures in spite of low MW

13. Water as an electrical dipole. Delta represents a partial weak charge. Size and direction of the charge separation is the dipole moment Hydrophilic substances readily dissolve in water (ions, salts, nonionic molecules with hydroxyl, aldehyde, or ketone groups. Hydrophobic substances do not dissolve in water (nonpolar substances which associate with each other, avoiding interactions with water).

14. Dotted lines represent the transient hydrogen bonds between water molecules that provide a cohesiveness Hydrogen bonds are weaker than covalent bonds and in this case are formed between the negative oxygen atoms and positive hydrogens

15. The bonding in ice crystals indicates tighter packing, more ordered interactions

16. = high for water, due to the hydrogen bonding providing cohesiveness; high specific heat (amt heat input to change temp) buffers against rapid temperature changes

17. 4 KINDS OF NON-COVALENT BONDS 1.Hydrogen bond 2.Ionic bond 3.van der Waals interaction 4.Hydrophobic bond These are transient because they are weaker than covalent bonds (~1-5 kcal/mol) Important in stabilizing 3D structure of large molecules because large numbers of these bonds work together

19. Energy (kcal/ Einstein); Einstein = a mole of photons Bond Energy (kcal/mole) 140 120 100 80 60 40 20 200 400 600 800 1000 Wavelength (nm) 140 120 100 80 60 40 20 Ultraviolet Visible Infrared Covalent double/triple bonds Covalent single bonds Ionic bonds Hydrogen bonds RELATIONSHIP BETWEEN ENERGY AND WAVELENGTH

20. Hydrogen bond: a weak associations between an electronegative atom and a hydrogen atom covalently bound to another atom. There is a characteristic length to the bond, depending on the specific atoms.

21. Atoms which attract electrons more have a greater electronegativity Differences in electronegativity determine bond polarities H 2 O NaCl

22. 11+ 11n 17+ 17n 11+ 11n 17+ 17n Sodium atom, Na (0.9) Chlorine atom, Cl (3.0) Sodium cation, Na+ Chlorine anion, Cl- An ionic bond forms when a dipolar bond breaks and electrons stay with the more electronegative atom. Here the chlorine atom is much more electronegative than the sodium atom.

23. HYDROPHOBIC INTERACTIONS Occur between nonpolar molecules or parts of molecules Based on avoidance of water and charged molecules Since energy is required to force hydrophobic-hydrophilic interactions, association of two hydrophobic molecules is less costly.

24. Hydrophobic molecules associate with each other and avoid interaction with water or charged molecules

25. A van der Waal bond is a non-specific attraction due to transient dipoles between 2 atoms 3-4 o apart (here 2 oxygen molecules). It is a weak force (~1 kcal/mol). Because atoms repel each other if close, it is a measure of the size of the electron cloud surrounding an atom.

26. Where are the covalent bonds?

27. 1. Which is more flexible/variable in shape - a small or large organic molecule? Why is size a factor? 2. Why are the atomic spheres depressed at their intersections in spacing-filling models? 3. What force is a measure of the electron cloud? 4. What is the importance of double/triple bonding to the determination of the three-dimensional shape? 5. Why is the three-dimensional shape of a molecule critical to its function? 6. What is the significance to the cell of differing internal and external chemicals & proportions? 7. Generally, how do molecules within cells differ in size from those outside? REVIEW QUESTIONS: