LECTURE - 2
Water & Carbon
Quiz Answers



The Carboxyl functional group:
The most predominant color on a world map is blue.
The Central dogma of Molecular Biology is:



DNA → RNA → PROTEIN
Epigenetics: The structural adaptation of chromosomal regions so as
to register, signal or perpetuate altered activity states.
The best part of California is the people!
Outline

Water
 Structure
 Important

properties
Carbon
 Structure
 Important
properties
 Functional Groups
Water

•
•
•
•
The molecule that supports all life (as we know it)
It is the biological medium on Earth
All living organisms require water
Most cells are surrounded by water, and cells
themselves are about 70–95% water
The abundance of water is the main reason the
Earth is habitable
Water is a polar molecule

Polar covalent bonds allow for extensive hydrogen
bonding
 Polar
– the opposite ends have opposite charges
Four Important Properties of Water
1.
2.
3.
4.
Cohesive behavior
Ability to moderate temperature
Expansion upon freezing
Versatility as a solvent
#1 - Cohesion

Cohesion


Hydrogen bonds hold water molecules together
Adhesion

An attraction between different substances
Example of Cohesion & Adhesion
Water molecules bind together to form the water column (cohesion)
They also bind to the cell walls to help resist gravity (adhesion)
#1 - Cohesion

Surface tension
 Related

to cohesion
A measure of how hard it is to break the surface of a
liquid
#2 – Moderation of Temperature



Kinetic energy is the energy of motion
Heat = the total amount of kinetic energy due to
molecular motion
Temperature measures the intensity of heat due to
the average kinetic energy of molecules
#2 – Moderation of Temperature

Measuring temperature
 Celsius
scale to indicated temperature
0
degrees Celsius is freezing, 100 degrees is boiling
 Room Temp is about 20 - 25 degrees
 Why would most biochemical experiments be run at 37
degrees?

Calorie
 The
amount of heat it takes to raise the temperature of
1g of water by 1 degree celcius
#2 – Moderation of Temperature


Specific Heat - The amount of heat that must be
absorbed or lost for 1g of substance to change its
temperature 1 degree C.
Water has a high specific heat.
#2 – Moderation of Temperature

Water has a High Specific Heat
 allows
it to minimize temperature fluctuations
 Heat is absorbed when hydrogen bonds break
 Example:
 Heat
Liquid water  steam
is released when hydrogen bonds form
vapor in clouds  raindrops
 Formation of raindrops or ice actually raises the surrounding
air temperature by a slight amount!
 Water
#2 - Moderation of Temperature



Oceans stabilize the temperature of the air.
Water absorbs heat from warmer air and releases
stored heat to cooler air
Water can absorb or release a large amount of
heat with only a slight change in its own
temperature
#2 – Moderation of Temperature

Oceans can absorb heat during the day and
release it back at night while the ocean temp
remains relatively constant.
70s (°F)
80s
90s
100s
San Bernardino
100°
Riverside 96°
Santa Ana
Palm Springs
84°
106°
Burbank
90°
Santa Barbara 73°
Los Angeles
(Airport) 75°
Pacific Ocean 68°
San Diego 72°
40 miles
#2 – Moderation of Temperature


Evaporation is transformation of a substance from
liquid to gas
Heat of vaporization



The heat a liquid must absorb for 1 g to be converted
to gas – water has a high heat of vaporization
As a liquid evaporates, its remaining surface cools, a
process called evaporative cooling
Evaporative cooling of water helps stabilize
temperatures in organisms and bodies of water
# 3 – Expansion Upon Freezing

Ice Floats on Water
 As
H-bonds stabilize, the resulting crystal becomes less
dense.
 H-bonds are breaking and re-forming in liquid water,
therefore there are more molecules per volume
#3 – Expansion Upon Freezing
Hydrogen bond
Ice:
Hydrogen bonds
are stable
Liquid water:
Hydrogen bonds
break and re-form
#3 – Expansion Upon Freezing

Major benefit of Ice floating on water – Insulation
 Insulates
living organisms under ice pack in lakes and
frozen seas.
 Snow insulates seeds and roots under ground in winter.
#4 – Solvent Properties

Water is a versatile solvent due to its polarity
 It
can easily for hydrogen bonds with other molecules
including ionic compounds
Figure 3.7
Na




Cl






Na

Cl








#4 – Solvent Properties

Large molecules such as proteins can dissolve in
water if they have ionic and polar regions
Figure 3.8
+


+
#4 – Solvent Properties



Hydrophilic - substance that has an affinity for
water.
Hydrophobic – substance that does not have an
affinity for water.
Some molecules are both.
#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 possible

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