LECTURE – 2 CONT.
Functional Groups
Outline

Water
 Structure
- Review
 Important properties
 #4

Solvent properties
Carbon
 Structure
 Important
properties
 Functional Groups
#4 – Solvent Properties

Water can disassociate into hydronium and
hydroxide ions
+
2 H2O
Hydronium
ion (H3O+)

Hydroxide
ion (OH)
#4 Solvent Properties: Acids & Bases


The dissociation of water molecules has a great
effect on organisms
Changes in concentrations of H+ and OH– can
drastically affect the chemistry of a cell
#4 Solvent Properties: Acids & Bases

Acid –
 donates
a proton
 Increases the number of Hydronium Ions in an aqueous
solution

Base –
 Accepts
a proton
 Reduces the number of Hydronium Ions in an aqueous
solution
#4 – Solvent Properties: The pH scale

pH is a measure of the relative concentration of
protons.
< pH < 7 is an Acid ([H30+] > 10-7M)
 7 < pH < 14 is a Base ([H30+] < 10-7M)
 pH 7 is neutral ([H30+] = [OH-] = 10-7M)
0
Figure 3.10
H+
H+
 H+
H+ OH
+
OH H H+
+
H H+
Acidic
solution
Increasingly Acidic
[H+] > [OH]
pH Scale
0
1
Battery acid
2
Gastric juice, lemon juice
3
Vinegar, wine,
cola
4
Tomato juice
Beer
Black coffee
5
6
OH
OH
H+ H+ OH

OH OH +
+
H
H
H+
Neutral
+
[H ] = [OH]
8
OH
OH H+ OH

OH OH

H+ OH
Basic
solution
Increasingly Basic
[H+] < [OH]
Neutral
solution
OH
7
Rainwater
Urine
Saliva
Pure water
Human blood, tears
Seawater
Inside of small intestine
9
10
Milk of magnesia
11
Household ammonia
12
13
Household
bleach
Oven cleaner
14
#4 – Solvent Properties: Buffers

Buffers are substances that minimize changes in
concentrations of H+ and OH– in a solution.



They resist a change in pH when a small amount of
acid or base is added to a solution.
Most buffers consist of an acid-base pair that
reversibly combines with H+
Buffers work within a specific pH range.
#4 – Solvent Properties: Buffers


Carbonic Acid – contributes to pH stability in blood
and other biological solutions.
H2CO3 is formed when CO2 reacts with water.
Carbon
Carbon

The backbone of life
Living organisms consist mostly of
carbon-based compounds.
 Really good at forming large,
complex, and diverse molecules.
 Proteins, DNA, carbohydrates, and
other molecules - all composed of
carbon compounds.

Carbon
Electron configuration determines the kinds and
number of bonds an atom will form with other
atoms
 Four valence electrons – Four covalent
 Allows for the formation of large, complex
molecules

Carbon bonds determine molecular
shape
Figure 4.3
Name and
Comment
Molecular
Formula
(a) Methane
CH4
(b) Ethane
C2H6
(c) Ethene
(ethylene)
C2H4
Structural
Formula
Ball-andStick Model
Space-Filling
Model
Diversity of carbon molecules
Carbon chains form the skeletons of most organic molecules
Carbon chains vary in length and shape


Figure 4.5
(c) Double bond position
(a) Length
Ethane
Propane
(b) Branching
Butane
1-Butene
2-Butene
(d) Presence of rings
2-Methylpropane
(isobutane)
Cyclohexane
Benzene
Valence Electrons

Figure 4.4

The electron configuration of carbon gives it covalent
compatibility with many different elements
The valences of carbon and its most frequent partners
(hydrogen, oxygen, and nitrogen) are the “building code”
that governs the architecture of living molecules
Hydrogen
(valence  1)
Oxygen
(valence  2)
Nitrogen
(valence  3)
Carbon
(valence  4)
Isomers

Compounds with the same molecular formula but
different structures and properties



Structural isomers have different covalent
arrangements of their atoms (constitutional)
Cis-trans isomers have the same covalent bonds but
differ in spatial arrangements
Enantiomers are isomers that are mirror images of
each other (they are chiral)
Isomers – Three types
Figure 4.7
(a) Structural isomers
(b) Cis-trans isomers
cis isomer: The two Xs
are on the same side.
trans isomer: The two Xs
are on opposite sides.
(c) Enantiomers
CO2H
CO2H
H
NH2
CH3
L isomer
NH2
H
CH3
D isomer
Isomers - Enatomers
Figure 4.8
Drug
Condition
Ibuprofen
Pain;
inflammation
Albuterol
Effective
Enantiomer
Ineffective
Enantiomer
S-Ibuprofen
R-Ibuprofen
R-Albuterol
S-Albuterol
Asthma
http://www.youtube.com/watch?v=L5QbBYj_zVs
Functional Groups
The components of organic molecules that are
most commonly involved in chemical reactions
 The number and arrangement of functional
groups give each molecule its unique
properties

The importance of functional groups
Female lion
CH3
OH
HO
Estradiol
Male lion
CH3
CH3
O
Testosterone
OH
7 most biologically important functional
groups
Figure 4.9a
Hydroxyl
STRUCTURE
(may be written
HO—)
EXAMPLE
Ethanol
Alcohols
(Their specific
names usually
end in -ol.)
NAME OF
COMPOUND
• Is polar as a result
of the electrons
spending more
time near the
electronegative
oxygen atom.
FUNCTIONAL
PROPERTIES
• Can form hydrogen
bonds with water
molecules, helping
dissolve organic
compounds such
as sugars.
Figure 4.9b
Carbonyl
STRUCTURE
Ketones if the carbonyl
group is within a
carbon skeleton
NAME OF
COMPOUND
Aldehydes if the carbonyl
group is at the end of the
carbon skeleton
EXAMPLE
Acetone
Propanal
• A ketone and an
aldehyde may be
structural isomers
with different properties,
as is the case for
acetone and propanal.
• Ketone and aldehyde
groups are also found
in sugars, giving rise
to two major groups
of sugars: ketoses
(containing ketone
groups) and aldoses
(containing aldehyde
groups).
FUNCTIONAL
PROPERTIES
Figure 4.9c
Carboxyl
STRUCTURE
Carboxylic acids, or organic
acids
EXAMPLE
Polar; can form H-bonds
NAME OF
COMPOUND
FUNCTIONAL
PROPERTIES
Weak acids; reversible dissociation in H2O
Acetic acid
Nonionized
Ionized
• Found in cells in the ionized
form with a charge of 1– and
called a carboxylate ion.
Figure 4.9d
Amino
STRUCTURE
Amines
NAME OF
COMPOUND
EXAMPLE
•
FUNCTIONAL
PROPERTIES
Acts as a base; can
pick up an H+ from the
surrounding solution
(water, in living
organisms):
Glycine
Nonionized
•
Ionized
Found in cells in the
ionized form with a
charge of 1.
Figure 4.9e
Sulfhydryl
STRUCTURE
Thiols
NAME OF
COMPOUND
•
Two sulfhydryl groups can
react, forming a covalent
bond. This “cross-linking”
helps stabilize protein
structure.
FUNCTIONAL
PROPERTIES
•
Cross-linking of cysteines
in hair proteins maintains
the curliness or straightness
of hair. Straight hair can be
“permanently” curled by
shaping it around curlers
and then breaking and
re-forming the cross-linking
bonds.
(may be
written HS—)
EXAMPLE
Cysteine
Figure 4.9f
Phosphate
STRUCTURE
Organic phosphates
NAME OF
COMPOUND
EXAMPLE
•
Contributes negative
charge to the molecule
of which it is a part
(2– when at the end of
a molecule, as at left;
1– when located
internally in a chain of
phosphates).
FUNCTIONAL
PROPERTIES
•
Molecules containing
phosphate groups have
the potential to react
with water, releasing
energy.
Glycerol phosphate
Figure 4.9g
Methyl
STRUCTURE
Methylated compounds
NAME OF
COMPOUND
EXAMPLE
•
Addition of a methyl group
to DNA, or to molecules
bound to DNA, affects the
expression of genes.
FUNCTIONAL
PROPERTIES
•
Arrangement of methyl
groups in male and female
sex hormones affects their
shape and function.
5-Methyl cytidine
LECTURE - 3
Biological Macromolecules
Outline


Monomers & Polymers
Four basic classes of biological macromolecules
 Carbohydrates
 Lipids
 Proteins
 Nucleic

Acids
Form follows function
Polymers

Polymer is a large molecule build from similar
building blocks
 Legos!


Building blocks are monomers
Carbohydrates, Proteins, Nucleic acids are polymers
Polymer Synthesis


Usually, monomers are joined via a dehydration
reaction.
Broken apart via hydrolysis.
Polymer Diversity


Thousands of different
macromolecules
They vary
 Cell
to cell
 Individuals
 Species…

Can build an immense variety of
polymers with a small set of
monomers
 legos
4 Classes of Macromolecules
1.
2.
3.
4.
Carbohydrates
Lipids
Nucleic Acids
Proteins
#1 Carbohydrates
#1 Carbohydrates


Fuel & building blocks
Monosaccharides
 Single
sugars
 One carbon ring

Polysaccharides
 Polymers
built from many sugar building blocks
#1 Carbohydrates: Simple Sugars

General Characteristics of Sugars
 Generally
have some multiple of CH2O
 Have a carbonyl group (C=O)
 Multiple hydroxyl groups (-OH)
 Aldoses & Ketoses
 Trioses (C3H6O3), Pentoses (C5H10O5) & Hexoses
(C6H12O6)
Glucose
Glyceraldehyde
(Fischer Projections)
Ribose
#1 Carbohydrates: Simple Sugars

Aldoses vs. Ketoses
Aldoses – Carbonyl group at the end of carbon skeleton
(aldehyde sugar)
 Ketoses – Carbonyl group within the carbon skeleton
(ketones)

Figure 5.3a
Ketose (Ketone Sugar)
Aldose (Aldehyde Sugar)
Trioses: 3-carbon sugars (C3H6O3)
Glyceraldehyde
Dihydroxyacetone
#1 Carbohydrates: Simple Sugars

Most sugars exist as ring structures.
Figure 5.4
1
2
6
6
5
5
3
4
4
5
1
3
4
2
3
6
Glucose
(a) Linear and ring forms
6
5
4
1
3
2
(b) Abbreviated ring structure
1
2
#1 Carbohydrates: Glucose vs.
Fructose
Glucose
Fructose
#1 Carbohydrates: Disaccharide

2 monosaccarides joined by a glycosidic linkage
Figure 5.5
1–4
glycosidic
1
linkage 4
Glucose
Glucose
(a) Dehydration reaction in the synthesis of maltose
Maltose
(important for
making beer)
1–2
glycosidic
1 linkage
2
Glucose
Fructose
(b) Dehydration reaction in the synthesis of sucrose
Sucrose
(Table sugar)
#1 Carbohydrates: Polysaccarides

Hundreds to 1000s of monosaccarides held
together via glycosidic linkages.
#1 Carbohydrates: Polysaccarides

Storage and structural roles
 Storage
- Carbohydrate “bank” - stored sugars can
later by released by hydrolysis for use in metabolism.
 Structure – Strong structural components are built from
polysaccharides.

Structure and function are determined by its
sugar monomers and the positions of glycosidic
linkages
#1 Carbohydrates: Polysaccarides;
Storage - Starch

Starch – Plants version of storage
polysaccharides
 Consists
entirely of glucose monomers
 Plants store surplus starch as granules within
chloroplasts and other plastids
amylose
 Most
starches are built from 1-4 linkages – more
complex starches can be linked differently
#1 Carbohydrates: Polysaccarides;
Storage - Starch
#1 Carbohydrates: Polysaccarides;
Storage - Starch



Starches are stored in plasteds
Animals have enzymes that can hydrolyze starches
Major sources:
 Potatoes
 Grains
Chloroplast
Starch granules
 Wheat
 Maize
 Corn
 Rice
1 m
#1 Carbohydrates: Polysaccarides;
Storage - Glycogen

Animals store glucose as
a polysaccharide called
glycogen.
Made up of glucose
monomers – like
Amylopectin but more
extensively branched.
 In vertebrates it is mostly
stored in the liver and
muscle cells.
 Glycogen stores don’t
last long.
Mitochondria
Glycogen granules

0.5 m
#1 Carbohydrates: Polysaccarides;
Structure
Cellulose is a major component of the tough
wall of plant cells
 Cellulose is a polymer of glucose.
 The glycosidic linkages differ from starch.
 The difference is based on two ring forms for
glucose: alpha () and beta ()

Figure 5.7a
1
4
 Glucose
(a)  and  glucose ring structures
1
4
 Glucose
Figure 5.7b
1
4
(b) Starch: 1–4 linkage of  glucose monomers
1
4
(c) Cellulose: 1–4 linkage of  glucose monomers
Figure 5.8
Cellulose
microfibrils in a
plant cell wall
Cell wall
Microfibril
10 m
0.5 m
Cellulose
molecules
 Glucose
monomer
#1 Carbohydrates: Polysaccarides;
Structure




Enzymes that digest starch by hydrolyzing 
linkages can’t hydrolyze  linkages in cellulose
Cellulose in human food passes through the
digestive tract as insoluble fiber
Some microbes use enzymes to digest cellulose
Many herbivores, from cows to termites, have
symbiotic relationships with these microbes
#1 Carbohydrates: Polysaccarides;
Structure
Figure 5.9a


Chitin, another
structural
polysaccharide, is
found in the
exoskeleton of
arthropods
Chitin also provides
structural support for
the cell walls of many
fungi
Chitin forms the exoskeleton
of arthropods.
#2 Lipids
Lipids - do not form polymers
 Lipids is having little or no affinity for water

 Hydrophobic
Consist mostly of hydrocarbons (nonpolar
covalent bonds)
 Fats, phospholipids, and steroids

#2 Lipids - Fats
Constructed from two types of smaller
molecules: glycerol and fatty acids
 Glycerol -a three-carbon alcohol with a
hydroxyl group attached to each carbon
 A fatty acid consists of a carboxyl group
attached to a long carbon skeleton

Figure 5.10
Fatty acid
(in this case, palmitic acid)
Glycerol
(a) One of three dehydration reactions in the synthesis of a fat
Ester linkage
(b) Fat molecule (triacylglycerol)
#2 Lipids – Fats; Saturated vs
Unsaturated

Saturated fatty acids (saturated fats)
 solid
at room temperature
 Most animal fats are saturated

Unsaturated fatty acids (unsaturated fats, or
oils)
 liquid
at room temperature
 Plant fats and fish fats are usually unsaturated
Figure 5.11
(a) Saturated fat
Structural
formula of a
saturated fat
molecule
Space-filling
model of stearic
acid, a saturated
fatty acid
(b) Unsaturated fat
Structural
formula of an
unsaturated fat
molecule
Space-filling model
of oleic acid, an
unsaturated fatty
acid
Cis double bond
causes bending.
#2 Lipids – Fats; Saturated vs
Unsaturated

Saturated fats – Not so good for you
 The
“tails” lack double bonds so they are more flexible
 Flexibility
 May
allows them to clump together
contribute to cardiovascular disease through
plaque deposits
#2 Lipids – Fats; Trans fats



Hydrogenation is the process of converting
unsaturated fats to saturated fats by adding
hydrogen
Hydrogenating vegetable oils also creates
unsaturated fats with trans double bonds
These trans fats may contribute more than saturated
fats to cardiovascular disease
#2 Lipids – Fats; Unsaturated Fats

Certain unsaturated fatty acids are not
synthesized in the human body.
 Essential
fatty acids
Must be supplied in the diet
 Include omega-3 fatty acids
 Required for normal growth, thought to provide
protection against cardiovascular disease

#2 Lipids – Fats – what are they for?
The major function of fats is energy storage
 Humans and other mammals store their fat in
adipose cells
 Adipose tissue also cushions vital organs and
insulates the body

#2 Lipids – Phospholipids
Two fatty acids and a phosphate group are
attached to glycerol.
 The two fatty acid tails are hydrophobic; the
phosphate group and its attachments form a
hydrophilic head

Hydrophobic tails
Hydrophilic head
Figure 5.12
Choline
Phosphate
Glycerol
Fatty acids
Hydrophilic
head
Hydrophobic
tails
(a) Structural formula
(b) Space-filling model
(c) Phospholipid symbol
Figure 5.13
Hydrophilic
head
Hydrophobic
tail
WATER
WATER
#2 Lipids – Steroids

Lipids characterized by a carbon skeleton
consisting of four fused rings
#2 Lipids – Steroids; Cholesterol

An a component in animal cell membranes



Plays a roll in cell/cell signaling and helps maintain
membrane integrity
Essential in animals
High levels in the blood may contribute to
cardiovascular disease
#3 Nucleic Acids

Two types of nucleic acids
Deoxyribonucleic acid (DNA)
 Ribonucleic acid (RNA)



DNA provides directions for its own replication
DNA directs synthesis of messenger RNA (mRNA) and,
through mRNA, controls protein synthesis
Figure 5.25-1
DNA
1 Synthesis of
mRNA
mRNA
NUCLEUS
CYTOPLASM
Figure 5.25-2
DNA
1 Synthesis of
mRNA
mRNA
NUCLEUS
CYTOPLASM
mRNA
2 Movement of
mRNA into
cytoplasm
Figure 5.25-3
DNA
1 Synthesis of
mRNA
mRNA
NUCLEUS
CYTOPLASM
mRNA
2 Movement of
mRNA into
cytoplasm
Ribosome
3 Synthesis
of protein
Polypeptide
Amino
acids
#3 Nucleic Acids

Polymers called polynucleotides
 Made
of monomers called nucleotides
Nucleotide consists of a nitrogenous base, a
pentose sugar, and one or more phosphate
groups
 The portion of a nucleotide without the
phosphate group is called a nucleoside

Figure 5.26ab
Sugar-phosphate backbone
5 end
5C
3C
Nucleoside
Nitrogenous
base
5C
1C
5C
3C
3 end
(a) Polynucleotide, or nucleic acid
Phosphate
group
(b) Nucleotide
3C
Sugar
(pentose)