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Chapter 3: WATER
The Molecule That Supports All of Life
•
Water is the biological medium on Earth
•
All living organisms require water more than any other substance for
life processes
•
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
–
Why?
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
The polarity of water molecules results in hydrogen
bonding
•
The water molecule is a
polar molecule: The
opposite ends have
opposite charges
•
Polarity allows water
molecules to form hydrogen
bonds with each other
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Hydrogen
bonds
Four emergent properties of water contribute to
Earth’s fitness for life
•
Four of water’s properties that facilitate an environment for life:
Cohesive behavior – it sticks together
Ability to moderate temperature – it regulates the temperature on
the Earth
Expansion upon freezing – causes ice to float, allowing it to
insulate the temperatures of the water below the ice
Versatility as a solvent – many biologically important molecules
are soluble, or able to dissolve, in water
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Cohesion
•
Collectively, hydrogen bonds hold water molecules together, a
phenomenon called cohesion
•
Cohesion helps the transport of water against gravity in plants
•
Adhesion of water to plant cell walls also helps to counter gravity
•
Surface tension is a measure of how hard it is to break the surface of
a liquid
•
Surface tension is related to cohesion as the water is held together, the
surface is harder to break
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Moderation of Temperature
•
Water absorbs heat from warmer air and releases stored heat to cooler
air, thus regulating the temperature
–
Think of the shore!!!
•
Water can absorb or release a large amount of heat with only a slight
change in its own temperature
•
The specific heat of a substance is the amount of heat that must be
absorbed or lost for 1 gram of that substance to change its temperature
by 1ºC
•
Water’s high specific heat minimizes temperature fluctuations to within
limits that permit life
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Note how the ocean moderates the temperature of
the coast!
Santa Barbara 73°
Los Angeles
(Airport) 75°
70s (°F)
80s
San Bernardino
100°
Riverside 96°
Santa Ana
Palm Springs
84°
106°
Burbank
90°
Pacific Ocean
90s
100s
San Diego 72°
40 miles
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Evaporative Cooling
•
Evaporation is transformation of a substance from liquid to gas
•
Heat of vaporization is the heat a liquid must absorb for 1 gram to be
converted to gas
•
As a liquid evaporates, its remaining surface cools, a process called
evaporative cooling
•
Evaporative cooling of water helps stabilize temperatures in organisms
(sweating) and bodies of water
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Insulation of Bodies of Water by Floating Ice
•
Ice floats in liquid water because hydrogen bonds in ice are more
“ordered,” making ice less dense
•
If ice sank, all bodies of water would eventually freeze solid, making
life impossible on Earth
•
Marine organisms would not survive as the water would freeze, and the
food chains would be destroyed, the temperature would not be
regulated, and fresh water is REQUIRED for life!
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
The Solvent of Life
•
A solution is a liquid that is a homogeneous mixture of substances
•
A solvent is the dissolving agent of a solution
•
The solute is the substance that is dissolved
•
Water is a versatile solvent due to its polarity
•
An aqueous solution is one in which water is the solvent
•
Water is an effective solvent because it readily forms hydrogen bonds
•
When an ionic compound is dissolved in water, each ion is surrounded
by a sphere of water molecules, a hydration shell
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
So, in salt water, NaCl is the solute and water is the solvent
–
Na+
+
+
–
–
+
–
–
Na+
–
+
+
Cl–
Cl–
+
–
+
+
–
–
–
–
Water can also dissolve compounds made of nonionic
polar molecules
•
Even large polar molecules such as proteins can dissolve in water if
they have ionic and polar regions
Lysozyme molecule
in a nonaqueous environment.
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Lysozyme molecule in an
aqueous environment.
Hydrophilic and Hydrophobic Substances
•
A hydrophilic substance is one that has an affinity for water – philic =
loves water
•
A hydrophobic substance is one that does not have an affinity for
water – phobic = ‘scared’ of, or doesn’t like water
–
Oil is a VERY hydrophobic substance
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Solute Concentration in Aqueous Solutions
MOLARITY
•
As you might imagine, since water makes up the majority of the mass
of a cell, most biochemical reactions occur in water
•
Chemical reactions depend on collisions of molecules and therefore on
the concentration of solutes in an aqueous solution
•
Molecular mass is the sum of all masses of all atoms in a molecule
•
Numbers of molecules are usually measured in moles, with one mole
being 6.02 x 1023 molecules – this is known as Avogadro’s number
•
Molarity is the number of moles of solute per liter of solution
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Dissociation of water molecules leads to acidic and
basic conditions that affect living organisms
•
A hydrogen atom in a hydrogen bond between two water molecules
can shift from one to the other:
–
The hydrogen atom leaves its electron behind and is transferred
as a proton, or hydrogen ion (H+)
–
The molecule with the extra proton is now a hydronium ion (H3O+)
–
The molecule that lost the proton is now a hydroxide ion (OH-)
Hydronium
ion (H3O+)
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Hydroxide
ion (OH–)
Effects of changes in pH
•
The process can be described in a simplified way as the separation of
a water molecule into a hydrogen ion (H+) and a hydroxide ion (OH-)
•
Though statistically rare, 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
•
Concentrations of H+ and OH- are equal in pure water
•
Adding certain solutes, called acids and bases, modifies the
concentrations of H+ and OH-
•
An acid is any substance that increases the H+ concentration of a
solution
•
A base is any substance that reduces the H+ concentration of a
solution
•
Biologists use something called the pH scale to describe how acidic or
basic (the opposite of acidic) a solution is
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
The pH Scale
1
The pH of a solution is
determined by the relative
concentration of hydrogen
(H+) ions
•
Acidic solutions have pH
values less than 7
•
Basic solutions have pH
values greater than 7
Increasingly Acidic
[H+] > [OH–]
•
pH Scale
0
Neutral
[H+] = [OH–]
Battery acid
2 Digestive (stomach)
juice, lemon juice
3 Vinegar, beer, wine,
cola
4 Tomato juice
5 Black coffee
Rainwater
6 Urine
7 Pure water
Human blood
8
Most biological fluids have pH
values in the range of 6 to 8
Seawater
Increasingly Basic
[H+] < [OH–]
•
9
10
Milk of magnesia
11
Household ammonia
12
Household bleach
13
Oven cleaner
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14
Buffers
•
The internal pH of most living cells must remain close to pH 7
•
Buffers are substances that minimize changes in concentrations of H+
and OH- in a solution
•
Most buffers consist of an acid-base pair that reversibly combines with
H+
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
The Threat of Acid Precipitation
•
Acid precipitation refers to rain, snow, or fog with a pH lower than 5.6
•
Acid precipitation is caused mainly by the mixing of different pollutants
with water in the air
•
Acid precipitation can damage life in lakes and streams
•
Effects of acid precipitation on soil chemistry are contributing to the
decline of some forests
•
The LA basin routinely has fogs made up of moisture with a pH of 2.2-4
•
The lowest recorded rainfall was in Wheeling, WV pH = 1.5
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
0
1
2
3
4
5
6
7
8
9
10
11
12
13
14
More
acidic
Acid
rain
Normal
rain
More
basic
Chapter 4: Carbon—The Backbone of Biological
Molecules
•
Although cells are 70–95% water, the rest consists mostly of carbonbased compounds
•
Carbon is unparalleled in its ability to form large, complex, and diverse
molecules
•
Proteins, DNA, carbohydrates, and other molecules that distinguish
living matter are all composed of carbon compounds
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Organic chemistry is the study of carbon
compounds
•
Organic compounds range from simple molecules to colossal ones
•
Most organic compounds contain hydrogen atoms in addition to carbon
atoms
•
Vitalism, the idea that organic compounds arise only in organisms,
was shown to be false when chemists synthesized many organic
compounds in the laboratory
•
Mechanism is the view that all natural phenomena are governed by
physical and chemical laws
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Carbon atoms can form diverse molecules by
bonding to four other atoms
•
An atom’s electron configuration is the key to its characteristics
•
Electron configuration determines the kinds and number of bonds an
atom will form with other atoms
•
With four valence electrons, carbon can form four covalent bonds with
a variety of atoms
•
This tetravalence makes large, complex molecules possible
•
In molecules with multiple carbons, each carbon bonded to four other
atoms has a tetrahedral shape
•
However, when two carbon atoms are joined by a double bond, the
molecule has a flat shape
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Basic structures of Carbon containing molecules
Molecular
Formula
Structural
Formula
Methane
PowerPoint Lectures for
Ethane
Biology, Seventh Edition
Neil Campbell and Jane Reece
Ethene
(ethylene)
Lectures
by Chris
Romero
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Ball-and-Stick
Model
Space-Filling
Model
Carbon can form bonds with atoms of many different elements
•
The electron configuration of carbon gives it covalent compatibility with
many different elements
•
The valences (number of H atoms an atom can bind with) 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)
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Nitrogen
(valence = 3)
Carbon
(valence = 4)
Ethane
Propane
Butane
2-methylpropane
(commonly called isobutane)
Length
Molecular Diversity
Arises from Carbon
Skeleton Variation
•
•
Branching
Carbon chains
form the
skeletons of most
organic molecules
1-Butene
Double bonds
2-Butene
Carbon chains
vary in length and
shape
Cyclohexane
Rings
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Benzene
Hydrocarbons
•
Hydrocarbons are
organic molecules
consisting of ONLY
carbon and hydrogen
•
Many organic
molecules, such as
fats, have
hydrocarbon
components
•
Hydrocarbons can
undergo reactions
that release a large
amount of energy
Mammalian adipose
cells
A fat molecule
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Fat droplets (red) 100 µm
Isomers
•
Isomers are compounds with the
same molecular formula but different
structures and properties:
–
Structural isomers have
different covalent arrangements
of their atoms
–
Geometric isomers have the
same covalent arrangements
but differ in spatial
arrangements
–
Enantiomers are isomers that
are mirror images of each other
Structural isomers differ in covalent partners, as shown in
this example of two isomers of pentane.
cis isomer: The two Xs
are on the same side.
trans isomer: The two Xs
are on opposite sides.
Geometric isomers differ in arrangement about a double
bond. In these diagrams, X represents an atom or group of
atoms attached to a double-bonded carbon.
L
isomer
D
isomer
Enantiomers differ in spatial arrangement around an
asymmetric carbon, resulting in molecules that are mirror
images, like left and right hands. The two isomers are
designated the L and D isomers from the Latin for left and
right (levo and dextro). Enantiomers cannot be
superimposed on each other.
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Enantiomers and medicine
•
Enantiomers are very
important in the
pharmaceutical industry
•
Two enantiomers of a
drug may have different
effects
•
Differing effects of
enantiomers demonstrate
that organisms are
sensitive to even subtle
variations in molecules
L-Dopa
(effective against
Parkinson’s disease)
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D-Dopa
(biologically
Inactive)
Functional groups are the parts of molecules
involved in chemical reactions
•
Distinctive properties of organic molecules depend not only on the
carbon skeleton but also on the molecular components attached to it
•
Certain groups of atoms are often attached to skeletons of organic
molecules
•
The functional groups of compounds are the most Important
determinant in the chemistry of life
•
Functional groups are the components of organic molecules that are
most commonly involved in chemical reactions
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Chemistry Determines Organism Characteristics
estradiol
testosterone
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Functional Groups of organic molecules
•
The six functional groups that are most important in the chemistry of
life:
–
Hydroxyl group
–
Carbonyl group
–
Carboxyl group
–
Amino group
–
Sulfhydryl group
–
Phosphate group
–
Methyl group
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
STRUCTURE
(may be written HO—)
Ethanol, the alcohol present in
alcoholic beverages
NAME OF COMPOUNDS
Alcohols (their
specific names
PowerPoint
Lectures
for
usually end in -ol)
Biology,
Seventh Edition
Neil Campbell and Jane Reece
Lectures by Chris Romero
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
FUNCTIONAL PROPERTIES
Is polar as a result of the
electronegative oxygen atom
drawing electrons toward itself.
Attracts water molecules, helping
dissolve organic compounds such
as sugars.
Acetone, the simplest ketone
STRUCTURE
EXAMPLE
Acetone, the simplest ketone
NAME OF COMPOUNDS
Ketones if theLectures
carbonyl group
PowerPoint
for is
within a carbon skeleton
Biology,
Seventh Edition
Aldehydes
if the carbonyl
group
is
Neil Campbell
and Jane
Reece
at the end of the carbon skeleton
Lectures by Chris Romero
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Propanal, an aldehyde
FUNCTIONAL PROPERTIES
A ketone and an aldehyde may
be structural isomers with
different properties, as is the case
for acetone and propanal.
STRUCTURE
EXAMPLE
Acetic acid, which gives vinegar
its sour taste
NAME OF COMPOUNDS
Carboxylic acids, or organic acids
PowerPoint Lectures for
Biology, Seventh Edition
FUNCTIONAL PROPERTIES
Has acidic properties because it is
a source of hydrogen ions.
The covalent bond between
oxygen and hydrogen is so polar
that hydrogen ions (H+) tend to
dissociate reversibly; for example,
Neil Campbell and Jane Reece
Acetic acid
Lectures by Chris Romero
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Acetate ion
In cells, found in the ionic form,
which is called a carboxylate group.
STRUCTURE
EXAMPLE
Glycine
Because it also has a carboxyl
group, glycine is both an amine and
a carboxylic acid; compounds with
both groups are called amino acids.
NAME OF COMPOUNDS
Amine
PowerPoint Lectures for
Biology, Seventh Edition
FUNCTIONAL PROPERTIES
Acts as a base; can pick up a
proton from the surrounding
solution:
Neil Campbell and Jane Reece
(nonionized) (ionized)
Lectures by Chris Romero
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Ionized, with a charge of 1+,
under cellular conditions
STRUCTURE
EXAMPLE
(may be written HS—)
Ethanethiol
NAME OF COMPOUNDS
PowerPoint
Lectures for
Biology,
Seventh Edition
Thiols
Neil Campbell and Jane Reece
Lectures by Chris Romero
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
FUNCTIONAL PROPERTIES
Two sulfhydryl groups can
interact to help stabilize protein
structure.
STRUCTURE
EXAMPLE
Glycerol phosphate
NAME OF COMPOUNDS
PowerPoint Lectures for
Organic phosphates
Biology, Seventh Edition
Neil Campbell and Jane Reece
FUNCTIONAL PROPERTIES
Makes the molecule of which it
is a part an anion (negatively
charged ion).
Can transfer energy between
organic molecules.
Lectures by Chris Romero
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Methyl
STRUCTURE
Methylated compounds
EXAMPLE
Addition of a methyl group
to DNA, or to molecules
bound to DNA, affects
expression of genes.
5-Methyl cytidine
5-Methyl cytidine is a
component of DNA that has
been modified by addition of
the methyl group.
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Arrangement of methyl
groups in male and female
sex hormones affects
their shape and function.
NAME OF
COMPOUND
FUNCTIONAL
PROPERTIES