An AP biology Mantra

Organisms are made of organic compounds whose…

• Shapes• Charges• Concentrations• Interactionsand • Reaction ratesrule the world.

And the most important of

these is shape.

Students will understand…the reason that only C H N O P S can form the

millions of organic molecules found in organisms.

Ch 3 Characteristics of an organic compound

• Covalently bonded• Contains at least C and H

simplest organic compounds are hydrocarbons made only with C & H

• Usually is built upon a chain of covalently bonded C’s known as a backbone

• Has atoms or groups of atoms bonded to the C backbone, and these are known as substituents

• Must have nonmetal atoms covalently bonded so that each meets its need for a valence octet.

Carbon can link to other C’s in a “carbon backbone”, as well as to side group—here in these hydrocarbons, the only side chain is H. The longest continuous chain of C’s is termed the backbone. Other chains of C attached as substituents are termed functional or alkyl groups.

C backbones are variable in• Length• Shape (branched,

linear, cyclic)• #, locations of double

and triple bonds(no C=C: saturated—as many H as

it can hold; 1 or more C=C, unsaturated—could bond more H’s if the double bonds were single bonds instead)

• Side groups (H or functional groups)

Whatever the shape of the backbone & whatever the nature of its side chains, these rules will help you assess whether a structural formula is drawn correctly. # covalent bonds allowed—in this priorityH 1 never violated C 4 never violatedO 2 hardly ever violatedP, N 3 unless part of a charged functional

group (the normally unbonded pair can form a coordinate covalent bond)

S 2 unless part of a charged functional group

Stop—take 10 minutes to examine the ball and stick models of atoms,

on your white boards identify them by color and H, P, S, O, N, and C or halogens.

Build an organic compound that contains at least one of each atom in CHNOPS. The model must meet the octet rule for each atom. Draw the full structural formula and write a molecular formula for the organic compound that you made.

Short sticks are used to represent single covalent bonds (2 shared valence electrons) between C and H or H and H, but long sticks are used elsewhere in single bonds. For multiple bonds, springs are used (2 springs = 1 double bond; 3 springs = 1 triple bond).

Which balls represent which elements?

Black C 4 holes needs to share 4 ve-Red S, O 2 holes needs to share 2 ve-Yellow H 1 hole (lots of them) 1 ve- sharedGreen halogens 1 hole (few of them) 1 ve-

sharedBlue P, N 3 or 4 holes

shares 3 ve- but can also use coordinate covalent bonds in charged ions (it donates BOTH of its normally lone pair to the bond in such a case)

Students will understand …the methods used to convey the 3D structures of

molecules, and they will be able to build physical models of small organic compounds given either shorthand, condensed or full structural formula representations.

Organic compounds can be represented in several ways

Full structures—show every atom and every covalent bond

Condensed structures—use the organization of the atoms in a word-like format to convey structure

Organic shorthand—the C backbone and H side chains are not shown, but functional groups (side chains that are not H but one of several groups of atoms) are shown

Ball and stick modelsSpace filling models

EthanolFull structure condensed organic shorthand

aka geometric structureCH3CH2OH

butyric acid

Full structure condensed organic shorthand

CH3(CH2)2COOH

Summary: different shapes, lengths, #s, and arrangements of CHONPS allows tremendous

molecular diversity

Another way that C compounds are able to generate millions of organic compounds

is isomerism.

Isomers are organic compounds having the same molecular formula, but a different structure. Since their shape differs, then so do their physiological functions!

Stop --move to your base groups—take 10 minutes or less

Build 2 very different models that have the formula C4H10O (stable if all holes are filled)—keep them for us to examine together—then draw the full, condensed, and organic structures for both. Draw these in your notebooks and also put a copy on the white board– show work to me and be prepared to present to the class if called on.

Isomers are compounds of the same molecular formula, but different atomic organization. Isomers have different shapes, so they also have different properties.

a) butane is linear, isobutane is branched—butane boils at a lower temperature.

b) cis-isomers: larger side chains (X) attached to C at ends of a C=C are on the same plane (double C=C bonds are stiff, whereas atoms rotate around single covalent bonds)

trans-isomers: different sized side chains attached Cs at either end of C=C are on the same plane of the double bond

Trans-fats are less healthy to eat.c) d (right) & l (left) hand mirror images form

stereoisomers (enantiomers) around chiral C (4 different side groups on the same C)

The broadest class of isomer is structural isomers.

This is the general term to describe molecules having the same molecular formula but different arrangements of the atoms and covalent bonds.

Geometric and stereoisomers are subgroups of structural isomers.

Examples for C4H10O—structural isomers

Example of how subtle rearrangements of atoms between isotopes affects shape and function:

C5H10O has more than 10 structural isomers—some toxins, others pleasant tasting food additives.

You can use the Merck index to look up properties of common organic compounds. Look under the index of chemical formulas.

Isoprenol is a flammable gas that causes severe eye irritation—industrial solvent

But, Valeraldehyde is a food flavoring or perfume scent

http://www.alibaba.com/promotion/promotion_c5h10o-promotion-list.html

More C5H10O isomers

• Pain reliever (analgesic)

• Industrial solvent

Examples for C4H10O isomers

Geometric isomers have different properties because of their shapes.Cis-fatty acids are healthier for eating than trans

fatty acids because they are less likely to clog blood vessels

9/2/2010 Which of these are cis isomers? Which are trans isomers? Which are not geometric isomers?

Build and draw (complete and shorthand structures) cis and trans isomers of CHOHCHOH

A third class of isomers is stereoisomers, also called

enantiomers. They are termed d or l according to how they

rotate a plane of polarized light shown through their crystals. d-isomers: right handed rotation of polarized light. l-isomers: left handed rotation of polarized light)

Even though visually, stereoisomers seem nearly identical—just mirror images—cells are very specific about which form use.

Cells use d-sugars but l-amino acids.

L-valine amino acid

For example, one stereoisomer of carvone tastes like spearmint, the

other like caraway seeds.

Huge molecules can be stereoisomers at more than one site. D and l configuration is described

for a particular, stated chiral C. In this small molecule, only C b is chiral (attached to 4

different side groups)

Still another way to increase diversity of organic compounds is to use functional groups

• http://www.chemistry-drills.com/functional-groups.php?q=simple

• A functional group is a covalently bonded group of atoms that tends to give organic compounds characteristic types of chemical reactions

• Molecules in the same class (like amino acids, sugars, fats, nucleotides) have similar cell functions because they have similar functional groups

• You need to recognize these functional groups• Carboxyl• Carbonyl• Amino (also called amine)• Phosphate• Sulfahydryl• Ester• hydroxyl

R means the rest of the molecule other than the R group of interest

Most functional groups render an organic compound polar covalent if they are asymmetric in their organization. This is because they often contain both highly electronegative O or N bonded to either C or H atoms that have lower electronegativity. For example, when a hydroxyl group replaces one H of nonpolar ethane (a hydrocarbon), polar ethanol is formed. Ethane is poorly soluble in water—is very hydrophobic—while ethanol is highly soluble in water—is very hydrophilic.

Finally, polymerization or use of conserved motifs (ch 5 topics) increases diversity

Simpler subunits are joined into chains(e.g., glucose chains form glycogen, starch, and

cellulose; amino acid subunits form chains called proteins; nucleotide chains form nucleic acids DNA & RNA)