Download Life and Chemistry: Small Molecules

Life and Chemistry:
Small Molecules
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Life and Chemistry: Small Molecules
• Water and the Origin of Life’s Chemistry
• Atoms: The Constituents of Matter
• Chemical Bonds: Linking Atoms Together
• Water: Structure and Properties
• Acids, Bases, and the pH Scale
• Properties of Molecules
• Chemical evolution
• Amino Acids
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Please recall or learn from book
• Atom, Atom structure, Proton, Neutron, Electron
• Elements, Periodic table, Isotopes, Orbitals
• Molecules,Chemical
Molecules Chemical bonds & interactions
• Isomers, Optical isomers
• Chemical reactions, Reactants, Products, Bond
energy
• Mole, Molar
• pH, Buffers
ff
Ch t 2 in
Chapter
i “Life”
“Lif ” or in
i “Biology”
“Bi l ” or in
i “Cell
“C ll Biology”
Bi l ”
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Chemical Bonds: Linking Atoms Together
• A covalent bond is formed by sharing of a pair of
electrons between two atoms.
• In hydrogen molecules (H2), a pair of electrons
share a common orbital and spend equal amounts
of time around each of the two nuclei.
• The nuclei stay some distance from each other
due to mutually repelling positive charges.
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Chemical Bonds: Linking Atoms Together
• Covalent bonds are very strong.
• Each covalent bond has a characteristic length,
angle, and direction, which makes it possible to
predict the three
three-dimensional
dimensional structures of
molecules.
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Chemical Bonds: Polar covalent bonds
• Electrons are not always shared equally between
covalently bonded atoms.
• The attractive force that an atom exerts on electrons is
called electronegativity.
• When a molecule has nuclei with different
electronegativities an electron spends most of its time
electronegativities,
around the nucleus with the greater electronegativity.
resulting
g in a p
polar covalent bond.
• Water: A polar molecule
Electronegativity
O = 3.5
H = 2.1
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Chemical Bonds: Hydrogen bonds
• Hydrogen bonds may form within or between molecules
with polar covalent bonds.
• Atoms bound by Hydrogen bonds do not share electrons.
• Although hydrogen bonds are weak
weak, they tend to be
additive (10 hydrogen bond equal 1 covalent bond), and
p
biological
g
importance.
p
theyy are of profound
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Chemical Bonds: Ionic bonds
• Ions are formed when an atom loses or gains
electrons (becomes charged).
• Ionic bonds are formed by the electrical
attraction between ions with opposite charges.
0.9
Electronegativity
3.1
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Polar molecules in water
When salt is introduced
into water, the partial
charges of the water
molecules can easily
interfere with the ionic
bonds.
bonds
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Chemical Bonds: Hydrophilic molecules
• Substances that are ionic or polar often dissolve in water
due to hydrogen bonds, and are called hydrophilic.
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Chemical Bonds: Hydrophobic interactions
• Nonpolar molecules are called hydrophobic because they tend to
avoid water and aggregate with other nonpolar molecules. (Oil)
C
2.5 electronegativity
H
2.1
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Chemical Bonds: Hydrophobic & Van der Waals forces
• Nonpolar molecules are also attracted to each other via relatively weak
attractions called van der Waals forces, which are brief interactions
induced by random variations in electron distribution
• A single van der Waals interaction is weak but large non-polar
molecules' can form many interactions
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Chemical Bonds: Van der Waals forces
• A single van der Waals interaction is weak but large non-polar
molecules can form many interactions
Gecko foot
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Non-coovalentt
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Non-Covalent bonds
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The Molecule That Supports All of Life
• Water is the biological medium on Earth
• All living organisms require water more than any other substance
• 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
• The water molecule is a polar
molecule: The opposite ends have
opposite charges
• Polarity allows water molecules to
f
form
h d
hydrogen
bbonds
d with
ith eachh
other.
• Each molecule forms hydrogen
bonds with four other molecules.
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Water: Structure and Properties
Due to its shape
shape, polarity
polarity, and ability to form hydrogen bonds
bonds, water
has some unusual properties.
• Water expand upon freezing: Ice is held in a crystalline
structure by the orientation of water molecules’ hydrogen bonds.
• Ice is structured but not p
packed = Ice floats allowing
g life under the
ice.
Energy allows bond to break
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Water: Structure and Properties
• A calorie
l i (cal)
( l) iis th
the amountt off energy (h
(heat)
t) required
i d tto raise
i
the temperature of 1 g of water by 1°C
• 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 1
1ºC
C
• The specific heat of water is 1 cal/g/ºC
• Liquid water has a higher specific heat than most other small
molecules in liquid form (ethanol 0.6 cal/g/ºC).
• The high specific heat of water minimizes temperature
fluctuations to within limits that permit life
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Water: Structure and Properties
• The heat of vaporization is the amount of heat needed to
change a substance from liquid state to gaseous state.
• A lot of heat is required to change water to a gaseous
state because the hydrogen bonds of the liquid water
must be broken.
• Evaporation has a cooling effect by absorbing calories.
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Water: Cohesion & adhesion
• Water has a cohesive strength because of hydrogen
bonds.
• The cohesive strength of water molecules allows the
transport of water from the roots to the tops of trees.
http://moodle.huji.ac.il/hu10/mod
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Water: Structure and Properties
• Water has high
g surface tension,, which means that
the surface of liquid water is relatively difficult to
puncture.
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Acids, Bases, and the pH Scale
• Water has a slight tendency to ionize into a hydrogen ion and a
hydroxide ion
H2O ↔ H+ + OH–
• The H+ ion is formed as Hydronium ion.
The concentration of hydrogen ions is 1 x 10–77 moles per liter of
water.
• This ionization is very important for living creatures and the
chemical
h i l reactions
ti
th
they mustt perform
f
b
because th
the H+ ion
i iis so
reactive.
H
O
H
H
O
H
2H2O
H
O H
H
O
H
Hydroxide
y
Hydronium
ion (OH–)
ion (H3O+)
One in 500,000,000
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The pH Scale
•p
pH is the measure of hydrogen
y g ion concentration
• It is defined as the negative logarithm of the
hydrogen
y g ion concentration in moles p
per liter.
= -log10[H+].
• A pH 7 means the concentration of hydrogen ions
is 1 x 10–7 moles per liter of water.
• The pH scale indicates the strength of a solution
of an acid or base. The scale values range from 1
through 14.
14
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Acids, Bases, and the pH Scale
• Substances that dissolve in water and release
hydrogen ions (H+); are called acids.
• Substances that dissolve in water and capture
hydrogen ions are called bases.
• Most bases are substances that release
hydroxide ions (OH–) when dissolved in water.
H d id iions can bi
Hydroxide
bind
d with
ith a h
hydrogen
d
iion tto
form water: H2O ↔ H+ + OH–
• Acids donate H+; bases accept H+.
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Acids
• Acids
c ds release
e ease H+ ions
o s in so
solution.
ut o
• If the reaction is complete, it is a strong acid, such
as HCl.
HCl
HCl → H+ + Cl• The carboxyl group (—COOH) is common in
biological compounds. It functions as an acid
because
—COOH
COOH ↔ —COO
COO- + H+
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Bases
• Bases
ases accept H+ in so
solution.
ut o
• NaOH ionizes completely to Na+ and OH–. The
OH– absorbs H+ to form water
water. It is a strong
base.
• Th
The amino
i group ((—NH
NH2) is
i an iimportant
t t partt off
many biological compounds; it functions as a
weak base by accepting H+:
ƒ —NH2 + H+ ↔ —(NH3)+
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Acids, Bases, and the pH Scale
• Ionization of strong
g acids is virtually
y irreversible.
HCl → H+ + Cl• IIonization
i ti off weakk acids
id and
db
bases iis somewhat
h t
reversible.
• Many large molecules in biological systems
contain weak acid or base groups.
Figure 2.18 pH Values of Some Familiar Substances
Properties of Molecules
Figure 2.19 Buffers Minimize Changes in pH
• pH of blood is 7.4 and is normally very stable (pH
of 7 or 7,8 means death). Organisms are able to
maintain stable pH
• In the blood, this is achieved by the presence of
Bicarbonate and Carbonic acid. Together
g
they
y
form a buffer system
• Addition of reactants to one side of a reaction
drives the reaction in the direction that uses that
component.
p
H+ + HCO3- Ù H2CO3
Bicarbonate
Carbonic acid
Figure 2.19 Buffers Minimize Changes in pH
CO2+H2O Ù H+ + HCO3- Ù H2CO3
Bicarbonate
Carbonic acid
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Acids, Bases, and the pH Scale
•O
Organisms
ga s s regulate
egu ate (bu
(buffer)
e)p
pH a
and
d depe
depend
do
on it.
t
• A buffer is a mixture of a weak acid and its
corresponding base
base.
• Because buffers can react with both added bases
and
d acids,
id th
they make
k th
the overallll solution
l ti resistant
i t t
to pH change.
H+ + HCO3- Ù H2CO3
Bicarbonate
Carbonic acid
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Elements of life
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Elements of life
=99%
=0.9%
Required
q
in trace amounts
Found (not clear if required)
2
• Trace Elements are important
• Iodine is required for production of
thyroid hormones
• Goiter disease is caused by Iodine
deficiency when the thyroid gland
enlarges in attempt to increase
hormone production
Hyperthyroidism, Hypothyroidism
affects about 5% of the population
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Trace elements
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Organic Molecules
• 99% of live material is made of molecules composed of:
C,H,O,N
• The basis of most organic molecules is a carbon skeleton
• The properties of each molecule are determined by its
composition and spatial organization.
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Functional groups in organic chemistry
• Distinctive properties of organic molecules depend not
only on the carbon skeleton but also on the molecular
components attached to it
• A number of characteristic groups are often attached
to skeletons
k l
off organic
i molecules.
l
l
Th
These are called
ll d
functional groups
• Functional groups are most commonly involved in
chemical reactions
• The number and arrangement of functional groups
give each molecule its unique properties
Estradiol
Testosterone
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Functional groups in organic chemistry
• Important functional groups include:
ƒ Hydroxyl group
ƒ Carbonyl
y group
g p
ƒ Carboxyl group
ƒ Amino group
ƒ Sulfhydryl group
ƒ Phosphate group
ƒ Methyl group
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Hydroxyl group
EXAMPLE
STRUCTURE
In a hydroxyl group (—OH), a
hydrogen atom is bonded to
an oxygen atom, which in turn
is bonded to the carbon
FUNCTIONAL
skeleton of the organic
PROPERTIES
molecule. (Do not confuse
this functional group with the
hydroxide ion, OH–.)
NAME OF
Alcohols (their specific names
COMPOUND usually end in -ol)
Sugars
g
Ethanol, the alcohol
present in
alcoholic beverages
Is polar as a result of the
electrons spending more
time near the
electronegative
oxygen atom.
Can fform hydrogen
C
h d
bonds with water
molecules, helping
dissolve organic
compounds such as
sugars.
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Carbonyl group
STRUCTURE
EXAMPLE
Acetone, the simplest ketone
The carbonyl
y group
g p ( CO))
consists of a carbon atom
joined to an oxygen atom by
a double bond.
Propanal, an aldehyde
Ketones if the carbonyl group
FUNCTIONAL A ketone and an aldehyde may
is within a carbon skeleton
NAME OF
COMPOUND Aldehydes if the carbonyl
group is at the end of the
carbon skeleton
PROPERTIES be structural isomers with
different properties, as is the
case for acetone and propanal.
These two groups are also
found in sugars, giving rise to
two major groups of sugars:
aldoses (containing an
aldehyde) and ketoses
(containing a ketone).
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Carboxyl group
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Amino group
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Methyl group
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Phosphate group
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Sulfhydryl group
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Water and the Origin of Life’s Chemistry
• The
e ea
earliest
est cchemical
e ca ssignatures
g atu es o
of life
eo
on Earth
at
are about 4 billion years old.
• The presence of water
water, possibly brought by
comets striking the Earth, was critical in making
conditions suitable for life.
• Environmental conditions conducive to life
evolved during the Hadean period
period.
Figure 2.1 A Geological Time Scale
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Theories of the Origin of Life
• Living things are composed of the same elements
as the universe.
• The arrangement of these elements in biological
systems is unique.
• There are two theories for the origin of life during
the 600 million yyears of the Hadean:
ƒ Life from extraterrestrial sources
ƒ Chemical evolution
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Theories of the Origin of Life
• Cou
Could
d life
e have
a e co
come
e from
o outs
outside
de Earth?
at
• The composition of meteorites suggests that
some of life
life’s
s complex molecules could have
come from space.
• Th
There is
i no proof,
f however,
h
that
th t living
li i thi
things h
have
ever traveled to Earth by way of a comet or
meteorite.
meteorite
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Theories of the Origin of Life
• The theory of chemical evolution holds that conditions on
the primitive Earth led to the formation of the large
molecules unique to life.
• In the 1950s, Stanley Miller and Harold Urey set up an
experimental “primitive” atmosphere and used a spark to
simulate lightning.
Figure 3.1 Synthesis of Prebiotic Molecules in an Experimental Atmosphere
Methane
Ammonia
Hydrogen
Water
Nitrogen
g
Amino acids
N l i acids
Nucleic
id
Hydrogen
Water
Nitrogen
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Theories of the Origin of Life
• The
e results
esu ts o
of tthe
e Miller-Urey
e U ey e
experiments
pe e ts have
a e
undergone several interpretative refinements
(Volcanic eruptions contribute sulfur).
• The earliest stages of chemical evolution resulted
g
of monomers and p
polymers
y
that
in the emergence
probably have remained generally unchanged for
3.8 billion years.
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Amino acids
• General structure of amino acids
α
Amine
Carboxyl
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Amino acids
• Amino acids in water
α
H3N+Ù H+ +
Ù -COO- + H+
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Amino acids
• Condensation reaction releases water and
creates a peptide bond
Table 3.2 The Twenty Amino Acids Found in Proteins (Part 1)
Table 3.2 The Twenty Amino Acids Found in Proteins (Part 2)
Table 3.2 The Twenty Amino Acids Found in Proteins (Part 3)