1. Chapter 2 Small Molecules… Biology 101 Tri-County Technical College Pendleton, SC

2. I Love Chaos Theory  Quirks, smurks, gluons, nutrinos, and on and on  Let’s keep it short and sweet  ATOM is smallest unit of a chemical element  Consists of a nucleus and one or more electrons  ELEMENT is pure substance that contains only one type of atom

3. Beam me up Scotty…. Atom consists of dense, positively charged nucleus around which one or more negatively charged electrons move Nucleus contains proton(s) [+ charge]; neutron(s) [no charge] Atoms and their components have MASS Mass measures the quantity of matter present Proton and neutron have value of 1 each; electrons such small mass, they are ignored

4. Scan for carbon units…oh yeah! C, H, N, O, P, and S make up 98% of all living matter An element is distinguished from all other elements by number of protons in its nucleus This number, its atomic number, does NOT change Every element except hydrogen has one or more neutrons in its nucleus Mass number of atom = total number of protons and neutrons in its nucleus

5. More Atomic Theory Atomic mass (atomic weight) is average of mass numbers of representative sample of element (with all isotopes in their normally occurring proportions) Valence = bonding capacity of atom and is generally equal to number of unpaired electrons in atom’s outermost shell Valence shell = outermost energy shell containing valence electrons involved in chemical reactions of the atom

6. Isotopes Isotopes of same element have same number of protons but differ in the number of neutrons in nucleus 12 C; 13 C; 14 C Radioisotopes are unstable and give off energy (alpha, beta, gamma) as radiation Such decay transforms the nucleus into another atom Used in medicine (radiation therapy) and in science in radioactive dating and other experiments

7. Isotope Visual

8. Electron Shells Given orbital can only be occupied by at most 2 electrons Orbitals constitute series of electron shells (energy levels) First (innermost) shell consists of only ONE orbital (can only hold 2 electrons) Second shell = 4 orbitals= 8 electrons –1 s and 3 p orbitals

9. Shells, cont. For our course ONLY: 1 st shell = 2; 2 nd shell = 8; and 3 rd shell = 8 electrons –3 rd will hold more so you have been informed!! KEY: atoms are most stable (happy) when their outer shell is filled Can be obtained by sharing electrons with other atoms or by gaining or losing one or more electrons from outermost shell

10. Key terms and concepts Molecule defined as two or more atoms linked by chemical bonds Tendency of atoms in stable molecules to have eight electrons in outermost orbit is called the octet rule Useful concept but limited… For our course, an atom would like to have its outermost shell FULL

11. Care to bond? Covalent bond occurs when two atoms share electrons Chalk talk time on covalent bonds with examples Strongest bond we study; quite stable Represent with single, unbroken line Electronegativity is attractive force atom exerts on electrons Closer two atoms are in electronegativity, more EQUAL their sharing of electrons will be

12. Bonding II When electrons shared equally, bond is called nonpolar covalent bond Atoms with differing electronegativities share electrons unequally (just like kids) Results in a polar covalent bond (delta + and -) Produces polar molecules or polar regions of larger molecules Polar bonds very important to chemistry of life

13. Charge… Ion is atom that has lost or gained an electron(s) Chalk talk time on sodium and chlorine Ions may have multiple charges (Ca 2+ ; Fe 3+ ) Groups of covalently bonded atoms that carry charge are called complex ions –NH 4 + SO2/4- PO3/4- Ionic bonds formed by electrical attraction between ions bearing opposite charge Ions can interact with polar molecules as well as other ions

14. More on ions… In solids, ionic bonds are strong because ions are close together In solvents, ionic bond much weaker Water is main biological solvent Hydrophilic versus hydrophobic and chalk talk time

15. Ion Visual

16. Hydrogen Bonding Bonding that occurs between hydrogen atom of one polar molecule and the highly electronegative atom of another polar molecule Water is a polar molecule –Many properties of water dependent on hydrogen bonding Are very weak bonds but tend to be SO many of them, they influence structure and properties of substances

17. Water Visual

18. Chemical Reactions Occur when atoms combine or change bonding partners Chalk-talk time on reactants/products Matter/energy cannot be created nor destroyed Energy is capacity to do work (work is movement of mass through space) CRs do not create/destroy energy; but changes in energy usually accompany them

19. Water as Polar Molecule Shape of water molecule (tetrahedron), its polar nature, and its capacity to form hydrogen bonds give it unique properties Ice floats; excellent solvent, cohesive, adhesive, and energy changes that accompany its transitions from ice  liquid  gas are important in living systems

20. Five Unique Properties of Water Ice floats Melting and freezing –Excellent moderator of temperature change Heating and cooling –has a high heat capacity –specific heat of substance is amount of heat energy required to raise 1 g by 1 o C –Takes large amount of energy to just break hydrogen bonds that hold liquid water together

21. Properties, cont. Evaporation and Cooling –Has high heat of vaporization requiring lots of energy to change from liquid to gas –Evaporation has cooling effect on environment –Our sweating Cohesion and surface tension –Columns of water can “stretch” –Evaporates from leaves (transpiration/MSG) Has high surface tension meaning surface exposed to air is difficult to break

22. Solving the Solution Solution is produced when substance is dissolved in water (aqueous) or another liquid Solution = solvent + solute(s) Qualitative analysis deals with substances dissolved in solvent and chemical reactions that occur there Concentrations [ ]s = amount of substance in given amount of solution

23. Mighty Mole..and more Mole is amount of ion or compound in grams whose weight is equal to its molecular weight (1 mole sugar=342g) Avogadro’s number = 6.02 x 10 23 molecules per mole 1 mole of substance dissolved in water to make 1 liter is called a 1 molar (1M) solution a 1um (micromolar) solution has 6.02 x 10 17 molecules of solute per mole Many molecules present in living systems exist in micromolar (um) to millimolar (mM) [ ]s

24. Who’s on first…? Acid releases H + ions (protons) in solution Base will accept H + ions Terms “acidic” and “basic” refer only to solutions Acidity/alkalinity of solution depends on relative [ ]s of H + and OH - ions in it Acid and base refer to compounds and ions If donates a proton = acid Accept a proton(s) = base

25. Disassociation of Water Water will ionize into a hydrogen ion (H + ) and a hydroxide ion (OH - ) Two actually participate—one becomes a hydroxide ion and the other a hydronium ion (H 3 O + ) For simplicity: H 2 O  H + + OH - Ionization of water very important for all living creatures

26. pH Scale Stands for “potential of hydrogen” pH value defined as negative logarithm of the hydrogen ion [ ] in moles per liter (molar concentration) pH = -log 10 [H + ] In practical terms, lower pH means higher H + [ ] or greater acidity Water is neutral at pH 7; less than 7 = acidic; more than 7 = basic **Scale is logarithmic

27. pH Scale Visual

28. Buffers and Bicarbonate System Buffer is chemical system that maintain relative constant pH even when substantial amounts of acid or base are added Buffer is mixture of weak acid and its corresponding base –Carbonic acid (H c CO 3 ) and bicarbonate ion (HCO 3 - ) Buffers minimize effect of added acid/base Law of mass action states addition of component one one side of reversible reaction drives reaction in direction that uses up that component

29. Scan for carbon units… Organic (text) defined as containing carbon atoms –What does one do with CO 2 ? We shall define an organic molecule as one containing both carbon and hydrogen H 2 O; CO 2 ; CH 4 ; C 6 H 12 O 6 You have been cautioned…enough said

30. Functional Groups Functional groups are groups of atoms that make up part of larger molecule and have particular chemical properties –Shape, polarity, reactivity, and solubility Chalk-talk time on hydroxyl, carbonyl (aldehyde/ketone), carboxyl, amino, phosphate, sulfhydryl Will see next test and on the final exam…enough said

31. Isomers C 6 H 12 O 6 is glucose unless I tell you differently… Can also be fructose and galactose Structural isomers have same chemical formula but different structural arrangements Optical isomers are mirror images of each other –Amino acids and many sugars –D-amino acids(dextro) and L-amino acids (levo) –Only L-amino acids commonly found in most organisms