Lecture #2 - SMALL MOLECULES: STRUCTURE AND BEHAVIOR

Dr. Hirsh – 9/4/01

All figure references are from Purvis, 6th ed.

Chemical Reactions

Fig 2.13:  Propane (C3H8)+oxygen-> CO2 +H2O.

Concepts here: conservation of mass; release of energy: heat: oxidation of C  -> release of energy:
 This is an analogy to oxidative metabolism in life: (carbohydrate+ oxygen),life’s coupling of reaction to other energy absorbing reactions to limit heat production, use resulting energy for life processes.

I.    Atoms: The Constituents of Matter

A.  An element is made up of only one kind of atom: most common elements in living creatures: C, H, O, N, P, S; traces of many others

B.    The number of protons identifies the element (also known as the atomic number).  The atomic number also equals the number of electrons.  The atomic mass # = the number neutrons+protons.  Electrons virtually w/o mass, so don’t affect the calculation.

C.    Isotopes differ in number of neutrons: H, vs 3H: here the superscript 3 before the symbol indicates a mass of 3, where a typical Hydrogen atom has one proton and no neutrons with a mass of 1.  3H is radioactive and decays (emits particles).  Its half-life,  t-half is 13 yrs;  for 32P, 60 days; for 14C, ~5750 yrs.  Obviously half-lives vary significantly among atoms and isotopes.

Explanation of carbon dating:

http://www.museum.mq.edu.au/eegypt2/carbdate.html

Note the key fact that carbon-14 is created in the upper atmosphere, creating a constant supply.  Also note that the concept of a half-life does not mean that all of something is gone in two half-lives!

FIG: TYPES OF BONDS: FAVORABLE; ENTROPIC CONSIDERATIONS

D.    Electron behavior determines chemical bonding: outer shell determines reactivity: Periodic table: empty->filled outer shell, L->R.  Non reactive if filled: inert on R side.

FIG: METHANE

Carbon with 4 bonds to 4 Hydrogens; satisfies the Hydrogen atoms, which need 1 electron to fill their s shell (2 electrons) and satisfies the Carbon atom, which needs 4 electrons to fill its outer shell

II.  Chemical Bonds: Linking Atoms Together: Bonding is energtically favorable! 

A.      Covalent bonds consist of shared pairs of electrons: most stable

B.      Hydrogen bonds may form between molecules

C.      Ions form bonds by electrical attraction

E.     Polar and nonpolar substances interact best among themselves

To form bond: must overcome activation energy: sketch.  Entropic consideration also a factor – will forming a bond increase randomness (entropy) or decrease it?  Systems favor increased entropy, but also favor decreased energy which is created through bonding.

Outer orbital determines geometry of covalent bonds: tetahedral arrangement of CH4
Double bonds between carbon atoms do not allow rotation between the carbons; this makes protein bonds stiff due to the protein bond’s partial double bond character [to be discussed Lecture 3].

Sketch: each line 1pr electrons.  Unequal sharing: H2O: electronegativity.

Electronegativity = propensity to hold electrons

O, Cl, N highest; Na, K lowest in life systems. Carbon in the middle – can interact with both

Table 2.3: CO vs CH


H bonds between & within molecules: CO--NH: weak compared to covalent bonds

Ionic bonds: between atoms w/ greatly different electronegativities. Note low strength of these bonds.

Weak interactions within large molecules (such as globular proteins) increase degrees of freedom [entropy] within a molecule, thus favorable.

Organization within molecules = low entropy, requires work (energy); thus assembling molecules has an “entropic cost”.

Non polar molecules interact (hydrophobic): repel polar substances (see water below).

III. Chemical Reactions: Atoms Change Partners

Fig 2.13:  Propane (C3H8)+oxygen-> CO2 +H2O. conservation of mass; release of energy: heat: oxidation of C-> release of energy: analogy to oxidative metabolism: (carbohydrate+ oxygen) coupling of reaction to limit heat production, use resulting energy for life processes.

Exothermic reactions generate wasted energy as heat; life’s problem is how to capture this energy. Energy is produced when elements transition from a reduced state  -> oxidized state.

Catalysis: activation energy – reactions are generally not spontaneous even if they are favorable because they must obtain sufficient energy in the system to overcome the activation energy barrier.  Catalysts lower the required activation energy, not the beginning or ending energy levels.

Enzyme = biological catalyst

Metabolism – take reduced Carbon, oxidize it to form partially oxidized (or fully oxidized) products.  Couple these oxidizing reactions to harness Energy in small steps (oxidative phosphorylation), manufacture ATP.

IV.       Water: Structure and Properties

Water: key molecule of life.

A.      Water has a unique structure and special properties: Fig 2.15

High thermal capacity: especially for ice & gas phase transitions; great change in bonds.  It takes energy to change state because of bond interactions that must be made or broken.

            Extensive bonding in liquid water -> cohesive strength allows water columns to be pulled.  -> surface tension; interface w/ relatively hydrophobic air.

B.    Most biological substances are dissolved in water -> solution

Hydrophobic interactions:  gasoline (organic compound) into water.  Cannot create bonds with water, water forms an “ice-like” structure around the organic comound = clathrate.  Clathrate requires lots of bonds -> lots of entropy cost -> unfavorable.

Globular polypeptides have charged groups on their exterior for favorable interaction with water molecules; hydrophobic groups are interiorized, avoid unfavorable entropic costs.

  V.       Acids, Bases, and the pH Scale

A.      Acids donate H+, bases accept H+ ;        HCL, NaOH; -CO2-

B. Water is a weak acid

C.  pH is the measure of hydrogen ion concentration (negative log of H+ concentration)

D. Buffers minimize pH change: most effective near their equilibrium point.  carbonic acid -> H+ + bicarbonate (HCO3-); reversible – pKa ~ pH 7

Importance in vitro: never mix anything in water w/o buffer in the solution first!

VI.       The Properties of Molecules

A.      Functional groups give specific properties to molecules: Fig 2.20

B.      Isomers have different arrangements of the same atoms: Fig 2.21

C.      Amino acid general configuration