Chapter 3: Molecular Families

I) Overview and Functional Groups

A) Deriving Families from Carbon

B) Functional Groups
-- small groups of atoms having specific
chemical properties
-- found in biological molecules
-- confer their chemical properties to
molecules that contain them

II) Alkanes
A) Introduction
-- made of C and H
-- defined by number of methyl groups (CH3)
-- insoluble; hydrophobic

Recognize Carbon Backbone

Know Prefixes (vocabulary)

Understand Free Bond Rotation

B) Isomers
1) Structural Isomers

- Ex:

Butane vs. Isobutane

2) Stereoisomers (Enantiomers) / Optical Isomers

Importance in biology arrangements specific

How important?

C) Solubility of Alkanes
methane 1C
ethane

2C

propane 3C
butane

4C

pentane 5C
17C
18C

How Determine Solubility?

1) Charges?
2) Opportunity to form H-bonds?
Methyl group
Electronegativities nearly same
nonpolar
Hydrophobic
Dont react strongly

However, if have enough methyl groups

III) Alcohols
-- defined by having hydroxyl group
A) Methyl Alcohol (CH3OH)
Hydroxyl group
contributes to water solubility
allows interaction with water and with
other OH groups
solubility of hydroxyl grp greater than
hydrophobicity of methyl grp

B) Ethyl Alcohol (C2H5OH; CH3CH2OH) only one tolerated by human body

C) Propyl Alcohol (C3H7OH; CH3CH2CH2OH)

Isopropyl Alcohol (isomer)

D) Butyl Alcohol (C4H9OH; CH3CH2CH2CH2OH)

E) Phases at Room Temperature

1C
2C
3C
11C
12C

IV) Carbohydrates

-- Ex: C6H12O6 (glucose)

A) Carbs defined by:

Ex: Triose
Aldehyde type

Ketone type

B) Simple Carbohydrates
1) Monosaccharides triose, tetrose, pentose, hexose
-- 3-carbon
-- 4-carbon
-- 5-carbon sugars 2nd most abundant
-- 6-carbon sugars most abundant in nature

2) Disaccharides 2 monosaccharides covalently linked

C) Oligosacchardies (trisaccharides, tetrasaccharides, penta- etc.)

D) Polysacchardies (complex carbohydrates)

-- Other examples of polysaccharides:

Cellulose
Chitin
Pectin

Consider Lactose Intolerance

E) Hexose Isomers and Structural Forms

-- open chain structure

Glucose

Galactose

Open-chain Ring
- both forms exist
- free bond rotation

Fructose

F) Dehydration Synthesis
-- forming larger molecules from smaller ones with production of H2O molecule
-- condensation reactions
-- with sugars, have glycosidic linkages

G) Chemically-modified Carbohydrates
-- may contain additional functional groups
-- modifies the form and function of a carbohydrate

V) Acids, Bases, pH, and Buffering

A) Acid
Strong Acid

Weak Acid

Strong Base

Weak Base

B) Base
ex: NH3 + H2O

C) pH
pH

every 1 unit of pH = 10-fold [H+]

pH = 7 [H+] is
pH = 2 [H+] is
pH = 12 [H+] is
Biological systems mostly pH

D) Importance of pH
if a biological molecule gains or loses H+, its properties can change
(ex: denature inhibits function)
-- many biological molecules contain Reversibly Dissociable Groups

pKa = pH at which reversible dissociable group is half-dissociated

E) Buffer a substance that can accept or release H+, thereby resisting changes in pH
-- has molecules containing reversibly dissociable functional groups

Bicarbonate Buffer System

Why do we need O2?

Where does CO2 come from? Why do we exhale it?

Metabolic Acidosis

VI) Lipids

A) Fatty Acids carboxylic acids found in fats

Examples:

Formic Acid

Acetic Acid

Long chain fatty acid (f.a.) 16+ carbons most common in nature

 Saturated vs Unsaturated

-Monounsaturated
vs
-Polyunsaturated

B) Fats
-- triglycerides; triacylglycerides
-- functions:

1)
2)
3)

Glycerol with Fatty Acid(s) attached

Monoglycerol
Diglycerol
Triglycerol

Attached fatty acids can be same or differ in #Cs and/or # double bonds

 Fats vs. Oils

Fats

Oils

18C saturated =

Stearic Acid melts at 69oC

18C monounsaturated = Oleic Acid melts at 13oC

(double bond at 9C)

18C polyunsaturated = Linoleic Acid melts at -9oC

(double bonds at 9C, 12C)

18C polyunsaturated = Linolenic Acid melts at -17oC

(double bonds at 9C, 12C, 15C)

 Arachidonic Acid
- body uses to synthesize: i) thromboxanes for platelet function/clumping
ii) leukotrienes for inflammatory response
iii) prostaglandins signal localized pain

Isomers of double bonds: Cis vs. Trans

Oleic acid
- behaves as unsaturated
(melts at low temp)

Elaidic acid
- behaves more as saturated
(melts at 44oC)

 Omega Fatty Acids

-- nomenclature
-- omega ( ) counting from the final carbon (CH3) end of fatty acid

-- omega-3-fatty acid has double bond after 3rd carbon from CH3 end (fish oils)
-- omega-6-fatty acid has double bond after 6th carbon from CH3 end (nuts, seeds)

D) Phospholipids

 Lecithin
- emulsifier (like soap or detergent)
- made by liver (part of bile)
- large fat droplets smaller fat droplets

Surfactant

E) Steroids

VII) Amino Acids

A) General Structure

B) Functional Groups
- amino, carboxyl, side chain
- as a family, amino acids are hydrophilic
- consider functional groups at different pHs

pH 7

pH 4

pH 10

Need to consider protonation at diff pHs esp. for electrophoresis

Still need to consider side chains/groups
Proteins can act as pH buffer bind or release H+

C) Peptide backbone formation

peptide bond

Dipeptides
Tripeptides
Oligopeptides
Polypeptides
Small proteins
Large proteins
What makes proteins different?

D) Levels of Protein Structure

1) Primary Structure

2) Secondary Structure

3) Tertiary Structure

4) Quartenary Structure

E) Bonds, Forces, Interactions

-- hold proteins in properly-folded form

F) Importance of Proper Folding

-- a.a. sequence determines overall fold in proper physical conditions
-- string of beads folds to achieve lowest free energy structure

Consider: Sickle cell anemia

G) Denaturation

-- bonds holding protein structure are delicate

Major Factors that can denature proteins:

-- breaks H-bonds
-- disrupts ionic bonds
-- disrupts hydrophobic
interactions
-- disrupts intramolecular
bonding