1.2 The Chemicals of Life

Hydrocarbons• Nonpolar and form straight or branched chains and

ring shaped structures. • Names reflect the number of carbons, the number

and location of any double or triple bonds and any functional groups.

• Names based on the number of carbons in the longest carbon chain:1 carbon......meth 6 carbons....hex2 carbons....eth 7 carbons....hept3 carbons....prop 8 carbons....oct4 carbons....but 9 carbons....non5 carbons....pent 10 carbons..dec

Organic Chemistry• The study of carbon compounds• Most organic compounds are classified as

hydrocarbons.• Hydrocarbons (hydrogens bonded to

carbons) can be classified as– Saturated

• Single bonds between carbons• Do not react with H

– Unsaturated• Double or triple bonds between carbons• React with H

Organic Compounds

1. Hydrocarbons

2. Derivatives of halogen acids (water and ammonia)

3. Carbonyl compounds (C=O)

Naming Organic CompoundsNomenclature

• The system developed for naming these compounds is the IUPAC.

• Hydrocarbons are studied and named based on bond, atom arrangement, and number of atoms.

1. Alkanes (Paraffins) CnH2n+2

• Saturated

• Named according to the number of Carbon atoms

• Names end in ‘-ane’

# of Carbon Atoms Structure Name

1 CH4 Methane

2 CH3CH3 Ethane

3 CH3CH2CH3 Propane

4 CH3 (CH2) 2CH3 Butane

5 CH3 (CH2)4CH3 Pentane

6 CH3 (CH2) 4CH3 Hexane

7 CH3 (CH2)5CH3 Heptane

8 CH3 (CH2)7CH3 Octane

9 CH3 (CH2) 7CH3 Nonane

10 CH3 (CH2)8CH3 Decane

• Most organic compounds have side chains or branches known as alkyl’s and the main chain is the parent.

• When naming alkyl side chains the same nomenclature seen for the alkanes is used, but the ‘-ane’ ending becomes a ‘-yl’ ending.

Naming branched alkanes1. Find the longest continuous carbon chain

(parent), this is not always a straight line.

2. Number the parent chain, starting at the end closest to the branch.

3. Identify the branch and its numerical position

4. Attach the number and name of the branch to the name of the parent

5. When more than one branch exists arrange them in alphabetical order

Ex. CH3CH2CHCH2CH2CH2CH3

CH2CH2CH3

2. Alkenes (Olefins)• Unsaturated• Name ends in ‘-ene’ with one double bond• ‘-adiene’ with 2 double bonds• ‘-atriene’ with 3 double bonds• Ex. CH3CH2CH3 Propane• CH2=CHCH3 Propene• When numbering the carbons in the longest chain,

the first carbon is the one closest to the double bond.

• Ex. CH3CH=CHCH2CH3 2 pentene• CH3CH=CHCH=CH2 1,3 pentadiene

3. Alkynes• Unsaturated with at least 1 triple bond

• Name ends in ‘-yne’ with 1 triple bond

• Name ends in ‘-adiyne’ with 2 triple bonds

• Name ends in ‘-atriyne’ with 3 triple bonds

• Ex. CH3CH2CH3 Propane

• CH = CCH3 Propyne

• When numbering the carbons, the chain is numbered to give the lowest number to the triple bondCH3CH2C=CH 1-butyne

4. Cyclic Hydrocarbons• When naming cyclic hydrocarbons the

prefix ‘cyclo-’ is added to the name of the alkane or alkene.

• Cyclohexane Cyclohexene

• Benzene is a special form of cycloheane with 3 double bonds

Benzene• When side chains are attached to benzene

their names become prefixes to benzene when benzene is the parent

--CH3methylbenzene

• When benzene is attached to a chain with more than 7 carbons it is now called ‘phenyl-’ or if it is attached to a chain with a functional group.

CH3

CH(CH2)5CH3 2-phenyloactane

Structural Isomers• Isomers = 2 or more different compounds

with the same molecular formula

• Structural Isomers = compounds with the same molecular formula whose atoms bond in different orders

• Ex. Structural isomers for C4H10

a. CH3CH2CH2CH3 butane

b. CH3CHCH3 Methylpropane

CH3

CH3

• CH3CH2CH2-- or CH3CH

propyl (n-propyl) isopropyl

n= normal (straight)

iso= isometric

sec = secondary

t = tertiary

CH3CH2CH2CH2 –

Butyl (n-butyl)

Isobutyl t-butyl

Example• In monosaccharides, the number of isomers

that are possible can be determined by the number of chiral carbon atoms.

•In a monosaccharide that contains n chiral centers, there are 2n possible isomers. This idea is illustrated below for a monosaccharide that contains 2 chiral carbon atoms; 22 = 4 isomers.

                                                                                   

Exercise• How many isomers are there of

• How many chiral carbon atoms are there in

General Chemistry Online: Isomer Construction Set

Stereoisomers

• Compounds that have the same structure but differ in the arrangement of atoms in space

• A example of stereoisomers are geometric isomers. Geometric isomers only occur in two types of compounds:

1. Alkenes2. Cyclic compounds

Geometric Isomers• Stereoisomers that differ by

having similar compounds on the same side or opposite sides of a rigid molecule (double bond, cyclic compound)

• When single bonds exist between carbons, they can move, spin, rotate and flex to adjust their conformation. Carbons attached by double bonds or attached in a cyclic compound are unable to alter their conformation.

• Two like groups on the same side of a rigid bond are said to be CIS. Like groups on opposite sides are said to be TRANS.

• These molecules are said to be Chiral moleculeshttp://cwx.prenhall.com/petrucci/medialib/media_portfolio/text_images/083_Chirality.MOV

Exercise 1:

• Which molecules are mirror images of each other?

Hint: Look at the Chiral carbon atoms

Exercise 2• Which molecule is a mirror image of this

one:

Functional Groups

• Site of chemical reactivity in a molecule

• Include pi bonds (double or triple bonds) or an electronegative/electropositive atom

Common Functional Groups

• Carbon with H,O, S and P attachments

• More reactive than the hydrocarbon (C and H only) of a molecule

• Site of chemical reactions functional groups

Functional Groups in Biomolecules(Table 1, pp. 25, Nelson Biology 12)

Group Structure Formula Found in

Hydroxyl

Carboxyl

Amino

Sulfydryl

Phosphate

Carbonyl

1. Alcohols• Structure: contains a hydroxyl group (-OH)

bonded to a sp3 hybridized carbon• Function: used in alcoholic beverages, gas-

line anti-freeze or as bacteriocidal agent• Naming: From the parent chain of alkanes

of alkenes, the ‘e’ is replaced with the ending ‘-ol’

• Example: CH3OH Methanol CH2=CHCH2OH 2-propenol

Note: More than one OH group is designated by di-, tri-, etc…

2. Aldehydes • Structure: Carbonyl compound that

contains at least one hydrogen attached to a carbonyl carbon

• Functon: Found in living systems in the form of sugars and hormones

• Naming: From the parent chain of alkanes or alkenes, the ‘e’ is replaced with the ending ‘-al’

• Example:

3. Ketones• Structure: Carbonyl compound that

contains two alkyl/aryl groups attached to the carbonyl carbon

• Function: See aldehydes

• Naming: From the parent chain of alkanes or alkenes, the ‘e’ is replaced with the ending ‘-one’

• Example:

4. Amines• Structure: N bonded to 3 other atoms, H, C or

combination of the two• Function: Found in many proteins and nucleic

acids. Adrenaline stimulates nervous system. Can be extracted from plants as decongestants

• Naming: The alkyl or aryl group is named then given the ending ‘-amine’

• Example

5. Amides• Structure: N bonded to a carbonyl carbon

• Function: in living systems, found in urea

• Naming: from the parent chain of alkanes or alkenes, the ‘e’ is replaced with the ending ‘-amide’

• Synthesized from carboxylic acids and ammonia or amine

6. Thiol

• Structure: Sulfhydryl group (SH)

• Function: amino acids

• Naming: From the parent chain of alkanes or alkenes, the ‘e’ is replaced with the ending ‘-thiol’

• ethanethiol

7. Ether• Structure: O molecule bonded between 2

carbons. Can be open chain or cyclic (ROR)

• Function: made from reactions involving alcohols

• Naming: Identify alkyl group to the left of O and alkyl group to the right and end with the suffix ‘-ether’

• Methyl ethyl ether

8. Esters

• Structure: C bonded to 2 O atoms, one of which is bonded to an alkyl group

• Naming: Name alkyl group attached to O. Then name parent carboxylic acid with ending changed to ‘-oate’

• Methyl ethanoate

9. Carboxylic Acid

• Structure: contains a carboxylic group (COOH), made of a carbonyl group and a hydroxyl group

• Naming: parent alkane is name, ‘e’ is replaced with ‘-oic acid’

• Methanoic acid

Exercise• Identify and name the functional groups in

this molecule

Functional Groups Video

http://www.zerobio.com/videos/functional_circle2.html

Linkage Bonds• Organic macromolecules are composed of

many tiny subunits that are linked together• Carbohydrates, lipids, proteins and nucleic

acids are all assembled in the same way• To link subunits a covalent bond is

formed between two subunits in which:1. One molecule contains a hydroxyl group

(OH)2. One molecule contains a hydrogen (H)

• The hydroxyl group combines with the hydrogen in a process called a dehydration reaction where water is removed.

• Energy is required to position the two subunits and to apply enough stress on the bonds to break them. This process is called catalysis.

• When macromolecules are broken, water is added to separate the linkage groups hydrolysis reaction.

Macromolecules

Carbohydrates

Lipids

Proteins

Nucleic Acids

MacromoleculesDehydration Synthesis (Condensation Reaction)

Two subunits link together through the removal of a water molecule.

Dehydration synthesis is an anabolic reaction that absorbs energy.

MacromoleculesHydrolysis Reaction

Two subunits break apart through the addition of a water molecule.

Hydration synthesis is a catabolic reaction that releases energy.

Carbohydrates• Produced through plants and algae through the

process of photosysnthesis • Carbohydrates are used for energy, building materials

and for cell identification and communication.• Carbohydrates contain carbon, hydrogen and oxygen

in a 1:2:1 ratio. General formula – (CH2O)n, n represents the # of C atoms.

• Carbohydrates are classified into 3 groups:

1. Monosaccharides

2. Oligosaccharides

3. Polysaccharides

Monosaccharides• Simple sugars, ex. glucose, galactose, fructose• 5 or more carbons – linear in dry state, form ring

structure when dissolved in water.• α – glucose, 50% chance OH group of C 1 will be

below plane of ring.• β – glucose, 50% chance OH group of C 1 will be

above plane of ring.

How many of the structures shown below are ketoses?

                                                                     

EXERCISE

MONOSACCHARIDESQUIZ: Select the formula that represents a monosaccharide

C4H8O4 C5H10O10 C6H6O12 C6H6O6

Oligosaccharides• 2 or 3 simple sugars attached by covalent

glycosidic linkages, formed by condensations (dehydration synthesis) reactions.

• Ex. Maltose, Sucrose

Polysaccharides• 100s – 1000s of

monosaccharides held together by glycosidic linkages.

• Used for energy storage and structural support.

• Starch and Glycogen – storage

• Cellulose and Chitin – structure

Condensation and HydrolysisCondensation/Hydrolysis

Dehydration Synthesis-Hydrolysis

Lipids• Hydrophobic molecules (“water fearing”)

of C H O that are generally nonpolar• Used for storing energy, building

membranes and chemical signals.

• Includes fats, phospholipids, steroids (e.g., cholesterol and sex hormones) and waxes (waterproof coating on plants and animals).

Molecular Structures of Fat

Fats• Triglycerides = glycerol and 3 fatty acids formed by ester linkage (esterification)

Saturated Fats• Usually come from animals.• Solid at room temperature due to increased

van der Waals attractions• In animals, they are used for long-term energy

storage, insulation, protection and helps dissolve fat soluble vitamins.

• NO double bonds between carbon atoms.

LipidsUnsaturated Fats• Usually comes from plant oils.• Liquid at room temperature.• One or more double bonds

between carbon atoms.• Rigid kinks reduce the number

of van der Waals attractions

Lipids

Esterification of a Triglyceride• The hydroxyl group of one glycerol reacts with the

carboxyl group of three fatty acids.• The resulting bond is an ester linkage.

Triglycerides

Phospholipids• Composed of one glycerol, two fatty acids

and a highly polar phosphate group.• Form cellular membranes (phospholipid

bilayer).• The phospholipid bilayer is virtually

impermeable to macromolecules, relatively impermeable to charged ions, and quite permeable to small, lipid soluble molecules.

• O2 and CO2 diffuse through with very little resistance.

• Larger molecules pass through the membrane using carrier proteins (facilitated diffusion).

Steroids (Sterols) • Composed of 4 fused hydrocarbon rings & functional groups.• Ex. Cholesterol, testosterone, estrogen,

progesterone.

Waxes•Long chain fatty acids linked to alcohols or carbon ring.•Firm, pliable consistency, used as a waterproof coating.

Proteins• Proteins are made of one or

more amino acid polymers that have been coiled together.

• Of the 20 amino acids that make up proteins, we must consume 8, as we can not make these essential amino acids on our own: trp, met, val, thre, phe, leu, ile, lys.

• The bonds that hold amino acids together are called peptide bonds.

Amino Acids• Amphiprotic (posses both acidic, carboxyl,

and basic, amino groups).

• May be polar, nonpolar or charged depending on the R group

• Sequence determines the final shape (conformation) of protein.

Proteins

The Four Levels of Protein Folding• Primary Structure: The sequence of amino acids in a polypeptide chain, which is

determined by the nucleotide sequence of a particular gene. • Secondary Structure: The folding and coiling of the polypeptide chain as it grows into a

pleated sheet or helix• H bond between C=O group and N-H group 4 bonds away forms a helix.• When 2 parts of the chain lie parallel forms a pleated sheet

• Tertiary Structure: The polypeptide chain undergoes additional folding due to side chain interactions.

• Attraction and repulsion between polypeptide and its environment.• Stabilized by R group interactions.• Proline forms natural kink• Disulfide bridge forms between 2 cysteines and are strong stabilizers

• Quaternary Structure: Two or more polypeptide chains come together, such as in collagen and haemoglobin.

•Temperature and pH changes can cause a protein to unravel (denature). A denatured protein is unable to carry out its biological function.

•Chaperone Proteins aid a growing polypeptide to fold into tertiary structure

•Globular Protein – one or more polypeptide chains that take on a rounded shape.

Rediscovering Biology - Animation Archive

Nucleic Acids

• Nucleic acids are found in DNA (stores hereditary info.), RNA (ribonucleic acid), ATP and nucleotide coenzymes (NAD+, NADP+ and FAD) used in energy transformations.

• DNA and RNA are nucleotide polymers.• Nucleotides consist of a nitrogenous base, a five-

carbon sugar and a phosphate group.• The nitrogenous bases are: adenine (A), guanine

(G), cytosine (C), thymine (T) and uracil (U).

Nucleic Acids• Cytosine, thymine and uracil are single-ringed pyramidines,

while adenine and guanine are larger double-ringed purines.

• In DNA, A bonds with T with 2 hydrogen bonds, and G bonds with C with 3 hydrogen bonds.

• The two strands are antiparallel (one strand is upside down compared to the other).

Purines always bond with a pyramidine.