BIOCHEMISTRY POST-LAB DISCUSSIONS

EXPERIMENT 1:DIFFERENCES BETWEEN ORGANIC AND INORGANIC COMPOUNDS AND TESTS FOR ELEMENTS FOUND IN ORGANIC COMPOUNDS

1. Organic compounds are the result of activities of living beings while inorganic compounds are created either due to natural processes unrelated to any life form or the result of human experimentation in the laboratory.2. Inorganic compounds can make salt, while organic cannot.3. Organic compounds contain carbon, while inorganic do not.4. Organic compounds have carbon-hydrogen bonds, while inorganic do not.

5. Inorganic compounds contain metal atoms, whereas organic compounds do not.6. Organic compounds are biological and inorganic are mineral in nature.7. Organic compounds are part of a class of chemical compounds the molecules of which contain carbon and hydrogen, while inorganic compounds mostly comprise of metal containing compounds even if they happen to exist in living organisms.

SUGAR (CH22O11) vs. SALT (NaCl) organic compounds have lower melting and boiling points than inorganic compounds Sugar: 146oC, Salt: 801oCCHLOROFORM (CHCl3) vs. SALT Solution (NaCl) organic slow; inorganic quickAgNO3(aq) + NaCl(aq) → AgCl(s) + NaNO3(aq)

DETECTION OF ELEMENTS:HYDROGEN & OXYGENC2H5OH + 3O2 2CO2 + 3H2OCARBONCa(OH)2 + CO2 = CaCO3 + H2ONITROGENUrea ------> NH3 + CO2

If you add sodium hydroxide solution to an unknown organic compound, and it gives off ammonia on heating then it is an amide.You can recognize the ammonia by smell and because it turns red litmus paper blue.

SULFURWhen proteins containing sulfur are decomposed by sodium hydroxide, sodium sulfide is formed; the latter is converted into lead sulfide by lead saltsThe presence of sulfur-containing amino acids such as cysteine can be determined by converting the sulfur to an inorganic sulfide through cleavage by base. When the resulting solution is combined with lead acetate, a black precipitate of lead sulfide results.

Comparison between Organic and Inorganic compounds

Properties Inorganic compounds Organic compounds

A. Elements Involved All elements C,H,O,N.& S

B. Physical Properties

1. physical state

2. combustibility

3.melting point

4.boiling point

5.Solubility in water

6.solubility in organic solvents

7.conductivility in the fused state

Solid

Non-combustible

Very high

Non-volatile/very high

Soluble

Insoluble

conductivity

Solid, liquid, gas

Usually combustible

Very low

Relatively low

Insoluble

Soluble

nonconductor

C. Structure of the solid

1.crystalline type

2.units of structure

Bonding between units

Ionic crystals

+ and – ions

Electrostatic/ionic

Molecular crystals

Molecules

Van der waals forces/covalent

EXPERIMENT 2:STRUCTURES OF HYDROCARBONS

BONDING PATTERN OF

CARBON

ARRANGEMENT OF BONDS AROUND CARBON

BOND ANGLES

4 SINGLE TETRAHEDRAL 109.5O

2 SINGLE1 DOUBLE

TRIGONAL PLANAR

120O

2 DOUBLE LINEAR 180O

1 SINGLE1 TRIPLE

LINEAR 180O

HydrocarbonsHydrocarbons

C C

C C

C C

C

C

C

C

C

C

H

H

H

H

H

H

C C C C C

H

H

H

H

H H

H

H

H

H

H

H

Alkanes Alkenes

Alkynes Aromatics

C C C C C

H

H

H

H

H

H

H

H

H

H

C C C C CH

H

H

H

H

H

H

H

Drawing structures

of Hydrocarbons

The First ten Straight-chain AlkanesHydrocarbon/molecular formula

Condensed structural formula No. of carbon atoms

Methane-CH4 CH4 1

Ethane –C2H6 CH3-CH3 2

Propane C3H8 CH3 – CH2 – CH3 3

Butane C4H10 CH3-(CH2)2-CH3 4

Pentane C5H12 CH3-(CH2)3-CH3 5

Hexane C6H14 CH3-(CH2)4-CH3 6

Heptane C7H16 CH3-(CH2)5-CH3 7

Octane C8H18 CH3-(CH2)6-CH3 8

Nonane C9H20

Decane C10H22

CH3-(CH2)7-CH3

CH3-(CH2)8-CH3

910

14

• Molecular formula describes the numbers of different kinds of atoms in a molecule,

• Structural formula represents a two-dimensional model of how the atoms are bonded to each other. Each dash represents a bonding pair of electrons.

16

structural and condensed formulasThis is a full structural or displayed formula. All the bonds are shown including all the hydrogen atoms

shows the exact way in which the atoms are connected to each other.

This is a form of a condensed structural formula

shortcut method in presenting molecular formula

Drawing structures: it’s all good

CH3

CH

CH

CH3

CH3

CH3

CH3

CHCH

CH3

2-butene

This is called the “condensed structure”

C C C C

H

H

H

H H H

H

H

CH3 CH CH CH3

On a test, choose a method that shows all Hs

CH3CH=CHCH3

Using brackets can also shorten some formulas: CH3(CH2)4CH3 vs. CH3CH2CH2CH2CH2CH3

Background: formulas for HCs

• Alkanes= CnH2n+2, enes= CnH2n, ynes= CnH2n-2

• Remember enes, then think of what would happen if bond was single or triple instead.

Q - how many hydrogens in each of these:6 carbon alkaneAlkene: C22H

14448 (2x5 - 2 = 10 - 2)CH3 CH3

Numbering carbonsQ- draw penteneA- Where’s the bond?

We number C atoms

• Always give double bond the lowest number

• Q - Name these

C C C CCH3

H

H

H

H H H

HCH31

C2

C3

C4

C5

H

H

H

H H H

HCH35

C4

C3

C2

C1

H

H

H

H H H

H

Ethene

3-nonyne

2-buteneCH3

CH

CH

CH3

CH3 CH3

C2H4

1-pentene

2-butene

propene

1-butyne

CH3 CH CH2

CH3 CH CH CH3

CH3 CH CH C

CH3 CH3

CH3

2,4-dimethyl-2-pentene

CH C CH2 CH3

Draw the structures of the following:2,2-dimethyloctane

1,3-dimethylcyclopentane

1,1-diethylcyclohexane

6-ethyl-5-isopropyl-7-methyl-1-octene

Hydrocarbons: IUPAC names

Naming Hydrocarbons (nomenclature)

Basic names of hydrocarbons• Hydrocarbon names are based on: • 1) class • 2) # of C, • 3) side chain type and • 4) position • 5) name will end in -ane, -ene, or -yne• 6) the number of carbons is given by a “Prefix”

1 meth- 2 eth- 3 prop- 4 but- 5 pent- 6 hex- 7 hept- 8 oct- 9 non- 10 dec-

• Actually, all end in a, but a is dropped when next to a vowel. E.g. a 6 C alkene is hexene

Q - What names would be given to these:7C, 9C alkane2C, 4C alkyne1C, 3C alkene

heptane, nonaneethyne, butynedoes not exist, propene

CH3 CH3

CH3

CH3Naming hydrocarbons and side chain• Names are made up of:

side chains, root

• Root is the longest possible HC chain• Must contain multiple bonds if present• Add -yl to get name of side chain• Common side chains include:

CH3- methyl CH3CH2- ethyl

CH3CH2CH2- propyl (CH3)2CH- isopropyl

• 2,3-dimethylpentane

CH3 C H3

C H3

C H3

CH3CH

CH3

* “iso” (branched) is not an IUPAC

convention• Br- (bromo), Cl- (chloro), F- (fluoro), I- (iodo)

ene

Rules in Naming HydrocarbonsB. Alkenes

CH3 CH2 C

CH2

CH2 C

CH2

CH3

CH3

CH3

Rule 1: choose the correct ending

ene

Rule 2: longest carbon chain

Rules in naming hydrocarbons

CH3 CH2 C

CH2

CH2 C

CH2

CH3

CH3

CH3

1-hexene ene

Rule 3: attach prefix (according to # of C)

Rules in Naming Hydrocarbons

CH3 CH2 C

CH2

CH2 C

CH2

CH3

CH3

CH3

Rule 4: Assign numbers to each carbon

1-hexene

Rules in Naming Hydrocarbons

CH3 CH2 C

CH2

CH2 C

CH2

CH3

CH3

CH3

Rule 4: Assign numbers to each carbon

CH3 CH2 C2

CH21

CH23

C4

CH25

CH3

CH3

CH36

CH3 CH2 C

CH2

CH2 C

CH2

CH3

CH3

CH3

1-hexene 1-hexene

Rules in Naming Hydrocarbons

CH3 CH2 C2

CH21

CH23

C4

CH25

CH3

CH3

CH36

Rule 5: Determine name for side chains

CH3 CH2 C

CH2

CH2 C

CH2

CH3

CH3

CH3

1-hexene 1-hexene

Rules in Naming Hydrocarbons

ethyl

methyl

methyl

CH3 CH2 C

CH2

CH2 C

CH2

CH3

CH3

CH3

CH3 CH2 C2

CH21

CH23

C4

CH25

CH3

CH3

CH36

1-hexene2-ethyl-4-methyl-4-methyl-1-hexene

Rules in Naming Hydrocarbons

ethyl

methyl

methylRule 6: attach name of branches

Rule 7: list alphabetically

CH3 CH2 C

CH2

CH2 C

CH2

CH3

CH3

CH3

CH3 CH2 C2

CH21

CH23

C4

CH25

CH3

CH3

CH36

1-hexene2-ethyl-4-methyl-4-methyl-1-hexene

Rules in Naming Hydrocarbons

ethyl

methyl

methyl

Rule 8,9: group similar branches

CH3 CH2 C

CH2

CH2 C

CH2

CH3

CH3

CH3

CH3 CH2 C2

CH21

CH23

C4

CH25

CH3

CH3

CH36

1-hexene2-ethyl-4-methyl-4-methyl-1-hexene

Rules in Naming Hydrocarbons

ethyl

methyl

methyl

Rule 8,9: group similar branches

CH3 CH2 C

CH2

CH2 C

CH2

CH3

CH3

CH3

CH3 CH2 C2

CH21

CH23

C4

CH25

CH3

CH3

CH36

2-ethyl-4,4-dimethyl-1-hexene

Rules in Naming Hydrocarbons

ethyl

methyl

methyl

Naming Multiple bonds: C. Alkenes; Alkynes

• Give 1st bond (1st point of difference) lowest #• include di, tri, tetra, penta, etc. before ene/yne• Comma between #s, hyphen between #-letter• You need to know ene and yne

2,3-heptadieneCH3CH3

CH3

CH2CCCCCCCH3

2,4,6-nonatriyne

C C C C

H

H

H

H

H

H

CH3CH2CH2CH=C=CH2

CH2CCH

CHCH2

2-butyne

1,2-hexadiene1,2,4-pentatriene

C

C

C

CC H

HHH

H

H

HH H

H

D.Naming Cyclic structures• Cyclic structures are circular• Have “cyclo” in name• Benzene is not a cyclic structure

• cyclopentaneQ- Draw these (note: carbons in a double bond

should be consecutive- 1 and 2, 5 and 6, etc.): cyclobutene 1,3-cyclopentadiene cyclopropane

CH2

CH

CH2

CHCC

C CCH

H H

H

H H

CH2

CH2

CH2

CH3 CH3

CH3

CH3

Practice exercise:Name the following hydrocarbons

CH3 CH2

CH CH3

CH2CH2

CH3

CH3 CH

CH

CH3

CH

CH3

CH2 CH2 CH3

CH2 CH3

CH3CH2CH CH CH CH2CH CH3

CH3

CH2CH3

CH3 CH3

3-methylhexane4-ethyl-2,3-dimethylheptane

5-ethyl-2,4,6-trimethyloctane

3-ethyl-2-methylpentane

3-ethyl-1,5,5-trimethylcyclohexene

CH3

CHCH

CH2CH3

CH3

CH2CH3

CH3 CH3

CH3CH3

Name the structures below

More practice

4-bromo-7-methyl-2-nonene

5-fluoro-7,7-dimethyl-2,4-octadiene

BrBr Br

Cl

CH3 C CH2C CH CH CH CH3

CH3

CH3

F

2,5-dibromo-6-chloro-1,3-cycloheptadiene

b) same

c) 5-ethyl-4-methyl-2-heptyne

a) 3,3-dimethyl-1-pentene

CH2 CH C CH2 CH3

CH3

CH3

CH3 C CH CH2

CH3

CH2 CH3

CH CH CH2

CH2 CH3

CC

CH3CH3

CH3

For more lessons, visit www.chalkbored.com

Aromatic compounds: Benzene

• -originally referred to certain compounds that had a pleasant odor and similar chemical and physical properties.

• It has the formula of C6H6

• Have several double bonds to fulfill the bonding requirements for carbon, thus making it unsaturated.

• Is a colorless liquid with a distinct gasoline like odor• it is insoluble in water but soluble in alcohol and ether• It is toxic when taken internally, contact with the skin is

harmful and continued inhalation of benzene vapors deceases red and white blood cell counts.

• benzene is now considered mildly carcinogenic, and care must be taken with its use,

44

You need to recognize the benzene structure in structural formulas

This is the general layout with a perfect hexagon. In this particular diagram you do not see the double bonds.

45

Two Lewis structures for the benzene ring.

46

Shorthand notation for benzene rings.

Benzene formula

CC

CC

C

C

H

H

H

H

H

H

CHCH

CHCH

CH

CH

There are 2 naming methods1) Numbering carbons2) ortho, meta, para (stomp)

Aromatic nomenclature

CH3

Ortho

Para

ST Meta

CH3

CH3

CH3

CH3

CH3CH3

1,2-dimethylbenzeneorthodimethylbenzene

1,3-dimethylbenzenemetadimethylbenzene

1,4-dimethylbenzeneparadimethylbenzene

Benzene is very stable (does not generally undergo addition)

49

Some common mono-substituted benzene molecules

Toluene, sometimes you see this on marker pens ”contains no toluene”

Has the condensed structural formula C6H5CH3

EXPERIMENT 3:PROPERTIES OF HYDROCARBONS

ODORAlkane: Gasoline odor; Alkene: sweet odor; Alkyne: sweet odorIGNITION TESTAromatic hydrocarbons burn with a yellow, sooty flame due to their high carbon content. Aliphatic hydrocarbons burn with flames that are yellow, but less sooty.SOLUBILITYAlcohol: miscible; Alkane, ene, & yne: immiscible

SOLUBILITY OF HYDROCARBONS IN EACH OTHER: “Like dissolves Like”REACTIVITY OF BROMINE WITH HYDROCARBONS:Bromine is slightly soluble in water, but it is highly soluble in organic solvents such as carbon disulfide, aliphatic alcohols, and acetic acid.

Pentene is an unsaturated hydrocarbon (One that does not have many possible side branches) It reacts readily with halogens to form new substances.In this case, bromine reacts with pentene in an addition reaction, this changes pentene into 1,1-dibromopentane.Thus, removing bromine from the solution, hence the distinct orange color is removed.

BROMINE SUBSTITUTION REACTION WITH ALKANESAlkanes react slowly or not at all with Bromine at room temperature in the dark, but in the presence of sunlight, substitution is fairly rapid.

POTASSIUM PERMANGANATE TEST FOR UNSATURATED HYDROCARBONShexane + KMnO4 ===> no reaction toluene + KMnO4 ===> benzoic acid When alkenes like 1-pentene are oxidised with cold, alkaline KMnO4, dihydroxy compounds (diols or glycols) are formed. The KMnO4 gets decolorized.

KMnO4 reacts with unsaturated hydrocarbons but not with saturated hydrocarbons and aromatic hydrocarbons.PURPLE dilutes to LIGHT PURPLE = saturatedPURPLE to BROWN = unsaturatedPREPARATION OF ETHYNE AND TEST FOR FLAMMABILITYCaC2+2H2O=C2H2+Ca(OH)2

ACETYLENE: FLAMMABLE

EXPERIMENT 4:PREPARATION AND

PROPERTIES OF ESTERS AND SOAPS

PREPARATION OF SOME ESTERCH3COOH + CH3CH2OH → CH3COOCH2CH3 + H2O ACETIC ACID + ETHANOL ETHYL ACETATE + WATER

C6H4(OH)(COOH ) + CH3OH C6H4(OH)(COOCH3) + H2OSALICYLIC ACID + METHANOL METHYL SALICYLATE + WATER

CH3COOH + CH3(CH2)3CH2OH CH3COOCH2(CH2)3CH3 + H2OACETIC ACID + PENTANOL PENTYL ACETATE + WATER

C6H5COOH + CH3CH2OH C6H5COOCH2CH + H2O BENZOIC ACID + ETHANOL ETHYL BENZOATE + WATER

Saponification and Soap• Hydrolysis with a strong base• Triglycerides split into glycerol

and the salts of fatty acids • The salts of fatty acids are

“soaps”• KOH gives softer soaps

Properties of TriglyceridesHydrogenation

• Unsaturated compounds react with H2

• Ni or Pt catalyst• C=C bonds C–C bonds

Hydrolysis• Split by water and acid or enzyme catalyst• Produce glycerol and 3 fatty acids

Saponification

3+ Na+ -O C (CH2)14CH3

O

CH

CH2 OH

OH

CH2 OH

CH

CH2

CH2 O

O

O

C (CH2)16CH3

O

C

O

(CH2)16CH3

(CH2)16CH3C

O

+ 3 NaOH

salts of fatty acids (soaps)

Hydrogenation

CH

CH2

CH2 O

O

O

C

O

(CH2)5CH CH(CH2)7CH3

C

O

(CH2)5CH CH(CH2)7CH3

C

O

+

(CH2)5CH CH(CH2)7CH3

H23Ni

Product of Hydrogenation

Hydrogenation converts double bonds in oils to single bonds. The solid products are used to make margarine and other hydrogenated items.

CH

CH2

CH2 O

O

O

C (CH2)14CH3

O

C (CH2)14CH3

O

C (CH2)14CH3

O

HydrolysisTriglycerides split into glycerol and three fatty acids (H+ or enzyme catalyst)

CH

CH2

CH2 O

O

O

C (CH2)14CH3

O

C (CH2)14CH3

O

C (CH2)14CH3

O H2O+3

3+ HO C (CH2)14CH3

O

CH

CH2 OH

OH

CH2 OH

H+

SALTING OUT SOAPThe soap is separated from the saltwater and glycerin obtained from the saponification.FORMATION OF FATTY ACIDSCH3(CH2)16CO2

-Na+ + HCl → CH3(CH2)16CO2H + Na+ + Cl-

FORMATION OF SOAP SCUM2 CH3(CH2)16CO2

-Na+ + Mg2+ → [CH3(CH2)16CO2

-]2Mg2+ + 2 Na+

EXPERIMENT 5:PROPERTIES OF

ALCOHOLS, ALDEHYDES, AND

KETONES

• Common examples of alcohols with one, two, and three hydroxyl groups per molecule. The IUPAC name is given above each structural formula, and the common name is given below.

4C alcohols

1-butanol 2-butanol

CH2CH2CH3 CH2

OH

CHCH2CH3 CH3

OH

CHCH3 CH2

OH

CH3

1-isobutanol,

2-methyl-1-propanol

2-isobutanol,

2-methyl-2-propanol

CCH3 CH3

CH3

OH

• The carbonyl group (A) is present in both aldehydes and ketones, as shown in (B). (C) The simplest example of each, with the IUPAC name above and the common name below each formula.

4C aldehydes

butanal

isobutanal,

2-methylpropanal

CH

O

CH2CH2CH3

CH

O

CHCH3

CH3

4C ketones

2-butanone, (butanone)

C

O

CH2CH3 CH3

The end….thank you…