Chapter 2 Small Molecules…

Biology 101

Tri-County Technical College

Pendleton, SC

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

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

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

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

Isotopes• Isotopes of same element have same number of

protons but differ in the number of neutrons in nucleus

• 12C; 13C; 14C• 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

Isotope Visual

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

Shells, cont.

• For our course ONLY: 1st shell = 2; 2nd shell = 8; and 3rd shell = 8 electrons– 3rd 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

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

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

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

Charge…

• Ion is atom that has lost or gained an electron(s)• Chalk talk time on sodium and chlorine• Ions may have multiple charges (Ca2+; Fe3+)• Groups of covalently bonded atoms that carry

charge are called complex ions– NH4

+ 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

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

Ion Visual

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

Water Visual

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

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 iceliquid gas are important in living systems

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 1oC– Takes large amount of energy to just break

hydrogen bonds that hold liquid water together

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

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

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 1023 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 1017 molecules of solute per mole

• Many molecules present in living systems exist in micromolar (um) to millimolar (mM) [ ]s

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

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 (H3O+)

• For simplicity: H2OH+ + OH-

• Ionization of water very important for all living creatures

pH Scale• Stands for “potential of hydrogen”• pH value defined as negative logarithm of the

hydrogen ion [ ] in moles per liter (molar concentration)

• pH = -log10[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

pH Scale Visual

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 (HcCO3) and bicarbonate ion (HCO3

-)

• 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

Scan for carbon units…

• Organic (text) defined as containing carbon atoms– What does one do with CO2?

• We shall define an organic molecule as one containing both carbon and hydrogen

• H2O; CO2; CH4; C6H12O6

• You have been cautioned…enough said

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

Isomers• C6H12O6 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