BIO 2, Lecture 4

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BIO 2, Lecture 4

• THE CHEMISTRY OF LIFE II THE SPECIAL PROPERTIES
  OF WATER AND CARBON

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WATER
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• Water is lifes universal solvent
• All living organisms require water
• Most cells are surrounded by water, and cells
  themselves are about 7095 water
• The abundance of water is the main reason the
  Earth is habitable
• Oh, ugly bags of mostly water

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• The water molecule is a polar molecule One side
  is slightly positively charged and one is
  slightly negative charged
• Polarity allows water molecules to form hydrogen
  bonds with each other
• Hydrogen bonds are weak and constantly break and
  reform, giving water its fluidity

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• Water has 4 special properties that facilitate an
  environment for life
• Cohesive behavior
• Ability to moderate temperature
• Expansion upon freezing
• Versatility as a solvent

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COHESIVE BEHAVIOR

• Collectively, hydrogen bonds hold water molecules
  together, a phenomenon called cohesion
• Cohesion helps the transport of water against
  gravity in plants
• Adhesion is an attraction between different
  substances, for example, between water and plant
  cell walls

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Adhesion
Water-conducting cells
Direction of water movement
Cohesion
150 µm
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• Surface tension is a measure of how hard it is to
  break the surface of a liquid
• Surface tension increases with cohesion

The high surface tension of water allows some
organisms to crawl across it
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MODERATES TEMPERATURE

• 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

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• The specific heat of a substance is the amount of
  heat that must be absorbed or lost for 1 g of
  that substance to change its temperature by 1ºC
• The specific heat of water is 1 cal/g/ºC, which
  is very high
• Water resists changing its temperature because of
  its high specific heat

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• Waters high specific heat can be traced to
  hydrogen bonding
• Heat is absorbed when hydrogen bonds break
• Heat is released when hydrogen bonds form
• The high specific heat of water minimizes
  temperature fluctuations to within limits that
  permit life
• Cyclical nature of the ice ages may be partly
  explained by this property of water

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• Ice floats in liquid water because hydrogen bonds
  in ice are more stable and ordered, making ice
  less dense
• Water reaches its greatest density at 4C
• If ice sank, all bodies of water would eventually
  freeze solid, making life impossible on Earth

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Hydrogen bond
Liquid water Hydrogen bonds break and re-form
Ice Hydrogen bonds are stable
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• 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
• An aqueous solution is one in which water is the
  solvent

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• Water is a versatile solvent due to its polarity,
  which allows it to form hydrogen bonds easily
• When an ionic compound is dissolved in water,
  each ion is surrounded by a sphere of water
  molecules called a hydration shell

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Na








Na




Cl
Cl








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• Water can also dissolve compounds made of
  nonionic polar molecules
• Even large polar molecules (including some
  proteins or parts of proteins) can dissolve in
  water if they have ionic and/or polar regions

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• A hydrophilic substance is one that has an
  affinity for water
• A hydrophobic substance is one that does not have
  an affinity for water
• Oil molecules are hydrophobic because they have
  relatively non-polar bonds

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• Hydrogen bonds are weak and constantly break and
  reform between water molecules
• When they break, the proton of the hydrogen atom
  from one of the water molecules is transferred to
  the other molecule
• The water molecule with the extra proton is now a
  hydronium ion (H3O), though it is often
  represented as H
• The water molecule that lost the proton is now a
  hydroxide ion (OH)

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• Water is in a state of dynamic equilibrium in
  which water molecules dissociate (hydrogen bonds
  break) at the same rate at which they are being
  reformed

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• In any aqueous solution at 25C the product of
  H and OH is constant and can be written as
  
  HOH 1014
• The pH of a solution is defined by the negative
  logarithm of H concentration, written as pH
  log H
• For a neutral aqueous solution
  H is 107 (7)
  7

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• Concentrations of H and OH are equal in pure
  water and are both very low
• Only 1 in 10 million water molecules are
  dissociated at any one time
• Adding certain solutes, called acids and bases,
  modifies the concentrations of H and OH
• Biologists use the pH scale to describe whether a
  solution is acidic or basic

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• An acid is any substance that increases the H
  concentration of a solution
• Acids typically dissociate (fully or partly) in
  water, forming H and an anion
• As H increases, OH- decreases
• A base is any substance that reduces the H
  concentration of an aqueous solution
• Bases dissociate (fully or partly) in water into
  OH- and a cation (e.g. NaOH) as OH- increases,
  H decreases
• Alternatively, they may accept (bind up) H from
  the solution, thereby reducing pH directly

First shell
Second shell
Third shell
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pH Scale
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1
Battery acid
Gastric juice, lemon juice
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H
H
H
Vinegar, beer, wine, cola
OH
H
3
H
OH
Increasingly Acidic H gt OH
H
H
H
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Tomato juice
Acidic solution
Black coffee
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Rainwater
6
Urine
OH
Saliva
OH
Neutral H OH
7
Pure water
OH
H
H
OH
OH
Human blood, tears
H
H
H
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Seawater
Neutral solution
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10
Increasingly Basic H lt OH
Milk of magnesia
OH
OH
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OH
OH
H
Household ammonia
OH
OH
OH
H
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Basic solution
Household bleach
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Oven cleaner
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• 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 as well as on land

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0
More acidic
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2
Acid rain
Acid rain
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4
5
Normal rain
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7
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9
10
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12
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More basic
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• 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

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• A buffer solution contains a weak acid and its
  conjugate base
• HA H2O H3O A-
• When an acid is added to the solution, the
  dissociated H is consumed to drive the
  equilibrium backwards
• When a base is added, the loss of H drives the
  equilibrium forward
• Thus, the pH changes less than it would if the
  acid or base had been added to a solution of pure
  water

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CARBON
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• Although cells are 7095 water, the rest
  consists mostly of carbon-based 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

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• Although cells are 7095 water, the rest
  consists mostly of carbon-based 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

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• Organic chemistry is the study of compounds that
  contain carbon
• Organic compounds range from simple molecules to
  colossal ones
• Most organic compounds contain hydrogen atoms in
  addition to carbon atoms

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• Vitalism, the idea that organic compounds arise
  only in living organisms, was disproved when
  chemists synthesized these compounds in the
  laboratory from non-living substances
• Mechanism is the view that all natural phenomena
  (including life) are governed by the same
  physical and chemical laws

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• 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

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• 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

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• Carbon chains form the skeletons of most organic
  molecules
• Carbon chains vary in length and shape

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• Hydrocarbons are organic molecules consisting of
  only carbon and hydrogen
• Many organic molecules, such as fats, have
  hydrocarbon components
• Hydrocarbons require a lot of energy (from
  sunlight) to make and therefore also store a lot
  of potential energy

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• 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

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2-methyl butane
Pentane
(a) Structural isomers
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cis isomer The two Xs are on the same side.
trans isomer The two Xs are on opposite sides.
(b) Geometric isomers
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L isomer
D isomer
(c) Enantiomers
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• Enantiomers are 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

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• Distinctive properties of organic molecules
  depend not only on the carbon skeleton but also
  on the molecular components attached to it
• A small number of characteristic groups, or
  functional groups, are often attached to
  skeletons of organic molecules

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• The seven 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

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• One phosphate molecule, adenosine triphosphate
  (ATP), is the primary energy-transferring
  molecule in the cell
• ATP consists of an organic molecule called
  adenosine attached to a string of three phosphate
  groups

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