unit 2: smells molecular structure and...
TRANSCRIPT
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Chemistry of
covalent
bonds
Unit 2: SMELLS
Molecular Structure and
Properties
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How do elements combine that have
similar electronegativities?
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Combine in fixed ratios.
Hydrogen peroxide
Glucose C6H12O6
*the combination of two or more different kinds of atoms.
Property of almost all elements – the ability to
combine with other elements and form
compounds*
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In a compound, the different elements lose
their individual chemical properties.
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Compounds and Chemical Formula
Compounds often have common names such as
water or salt - but are also named by their formula
which tell what elements make up the compound
and in what proportion.
For example, a molecule of
water is made up of two
hydrogen atoms for every one
oxygen atom. H2O
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Law of conservation of mass
Mass is not created or destroyed during a chemical reaction or physical change – but it can change form.
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Compounds can be
separated based on their size
and charge.
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The reactions/actions of elements
that share electrons
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How compounds form -
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Electron arrangement determines
the chemical properties of an atom
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e- move around
the nucleus in
specific energy
levels
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Each energy level
(shell) is
numbered starting
closest to the
nucleus.
This is called the energy
level’s “quantum number”
Max. # of e- in each energy level calculated
by the formula: 2n2 (where n is the quantum number)
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Each atomic orbital and the electrons in it are associated with
a specific amount of energy, and the farther an electron is
from the nucleus the greater its
energy (very important).
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*The electrons in the outermost (highest) E level.
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It is the outermost electrons that determine the chemical properties of the element. (very important)
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These outermost electrons are the one’s that are
involved in bonding.
Chemistry of an element depends almost entirely
on the number of its valence electrons.
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Chemical Bonding
A chemical bond results from strong electrostatic interactions between two atoms.
The nature of the atoms determines the kind of bond.
Atoms bond to achieve
stability – reach a stable
OCTET
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Predicting types of bonds
How do you predict what type of bond will from between atoms?
Notice the location of the elements in the Periodic Table. As a rule, elements on the right (non-metals) share electrons with each other (covalent bonds) and elements on the left tend to donate electrons to elements on the right (ionic bonds).
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What factors determine if an atom forms a covalent or ionic bond with another atom?
The number of electrons
in an atom, particularly the
number of the electrons
furthest away from the
nucleus determines the
atom’s reactivity and
hence its tendency to form
covalent or ionic bonds.
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If enough energy is applied, either by another
element or by external photons, electrons can be
pushed so far that they escape the attraction of the
nucleus
Losing an electron is called ionization
Ionic Bonding
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Losing/gaining an electron is called ionization
An ion is an atom that has either a net positive or net
negative charge.
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cation
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It is possible that, as two
atoms come close, one
electron is transferred to the
other atom.
The atom that gives up an
electron acquires a +1
charge and the other atom,
which accepts the electron
acquires a –1 charge.
The two atoms are attracted
to each (opposite charges
attract) resulting in an IONIC
bond.
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3 Biologically Important Properties
of Ionic Compounds
Ionic compounds are soluble in water.
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In aqueous
solution, an
ionic compound
dissociates
into its ions.
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The
dissociated
ions in
aqueous
solution give
the solution the
ability to
conduct
electricity.
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Metallic Bonds
Metallic bonds occur when metal atoms share electrons.
Electrons in the outer shells float together loosely and form a “sea” electrons.
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This also explains why metals are
good conductors
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The outer electrons are so weakly bound to metal
atoms that they are free to roam across the entire
metal. Having “lost” their outer electrons, individual
metal atoms are more like positive ions in a swarm
of communal electrons.
Metallic bonding
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Lesson 1: Sniffing Around
Molecular Formulas
What does chemistry have to do with
smell?
Smell appears to be related to molecular
formula and chemical name.
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Lesson 2: Molecules in Two
Dimensions
Structural Formulas
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Key Question
How can molecules with the same molecular
formula be different?
You will be able to:
• describe the difference between
structural formulas and molecular
formulas
• recognize isomers
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Molecular formula: The chemical formula
of a molecular substance, showing the types of
atoms in each molecule and the ratios of those
atoms to one another.
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Covalent Bonds
A chemical bond that involves sharing a pair
of electrons between neutral atoms in a
molecule in order to achieve an octet in the
valence shell.
In covalent bonding the attraction for electrons is similar for two atoms.
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COVALENT bonds result from a strong
interaction between NEUTRAL atoms
Each atom donates an electron resulting in a
pair of electrons that are SHARED between
the two atoms
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For example, consider a hydrogen molecule, H2. When the two hydrogen, H, atoms are far apart from each other they are not attracted to each other. As they come closer each “feels” the presence of the other.
The electron on each H atom occupies a volume that covers both H atoms and a COVALENT bond is formed.
Once the bond has been formed, the two electrons are shared by BOTH H atoms.
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COVALENT bonds result from a strong interaction
between atoms of similar electronegativity and
electron affinity.
Each atom
donates an
electron
resulting in a
pair of
electrons that
are SHARED
between the
two atoms
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Generally, elements with similar electronegativity form covalent bonds
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Atoms can bond forming single, double,
triple and even quadruple covalent bonds.
ethene
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O
H
H
Structural formulas indicate kind, number and arrangement of bonds using a line to represent a shared e- pair
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One word of warning: hydrogen behaves with a divided personality. While it is traditionally placed in the periodic table above lithium, and can form ions (as in the case of acids), it typically forms covalent bonds. And remember: As with all generalizations, there are exceptions.
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3 Biologically Important Properties
of Covalent Compounds
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Because the angles formed between covalently
bonded atoms are specific and defined -
biological molecules formed with covalent
bonds have definite and predicable shapes.
glucose
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matter Anything that has mass and takes up space.
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Bond energy.
Covalent bonds represent chemical potential energy
that can be used in biological reactions. An example of
this are the phosphoanhyride bonds of ATP.
A covalent bond STORES energy
– so breaking those bonds
releases energy that can be used
for the needs of living organisms.
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Polarity
polar covalent bonds are extremely important because
of the unique properties exhibited by molecules with
these kinds of bonds. (this is particularly true for living
organisms)
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The structure of
covalent
molecules:
Structural
Formulas
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Structural formulas indicate kind, number and arrangement of bonds using a line to represent a shared e- pair
remember
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Drawing structural
formulas
• First identify the valence electrons.
• Draw Lewis dot structures
• Apply the octet rule to determine where and
how many bonds will form.
• Replace shared electrons with line.
• Leave dots for lone pairs of electrons
• Represent the correct geometry.
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• First identify the valence electrons.
• Draw Lewis dot structures
• Apply the octet rule to determine where and
how many bonds will form.
• Replace shared electrons with line.
• Leave dots for lone pairs of electrons
• Represent the correct geometry.
Let’s try some!
Drawing structural
formulas
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Bonded pair: A pair of electrons that are shared
in a covalent bond between two atoms.
Lone pair: A pair of valence electrons not involved
in bonding within a molecule. The two electrons
belong to one atom.
After bonding, each atom has a
total of eight valence electrons
surrounding it. (H exception)
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Draw the Lewis dot structure for the two
covalently bonded molecules shown here.
Explain how you arrived at your answer.
a. O2 b. NH3
Draw the molecular structure for the two
covalently bonded molecules shown here.
Explain how you arrived at your answer.
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from the text:
The HONC 1234 rule and the octet rule both help you figure out Lewis dot structures and structural formulas.
Both the HONC 1234 rule and the octet rule can be satisfied by using double and triple bonds appropriately.
It is not possible to create a triple-bonded oxygen compound, according to the HONC rule.
There are exceptions to the bonding rules laid out here.
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A Puzzling Activity
Each puzzle piece contains the correct
number of valence electrons for that atom. It
also contains the appropriate number of tabs
for bonding.
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Structural formulas show how the atoms in a molecule are connected.
A molecular formula can be
associated with more than one structural formula.
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Isomers
The structural formula for certain molecules can differ.
Compounds with the same molecular formula but different structural formulas
are isomers.
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C4H8O2
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chemical compounds
which have a common
chemical formula, but not a
common structure.
This gives isomers different chemical properties
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C5H12
structural isomers
• show a different arrangement in covalent bonds
• Usually occur in differences in the arrangements of the carbon
skeleton.
• Locations of double bonds may vary also
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Differ in covalent arrangement
OR
location of double bond
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Geometric isomer
• differences in arrangements of atoms around a double bond.
(double-bonded carbons do not exhibit rotation).
• When molecules/functional groups are found on the same side
of a double bond, this is known as the "Cis" configuration
• When atoms/functional groups are located on opposite sides
of a double bond, this is called the "trans" configuration
trans-2-butene cis-2-butene
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Example in the biological
world
This is a schematic diagram of
a rod cell. The stacked disks
contain rhodopsin, the complex
of opsin protein and 11-cis-
retinal.
The nerve fires a signal to the
brain as a result of retinal
isomerization passed along to a
connecting nerve cell, creating
an electrical impulse
interpreted as visual
information by the brain.
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Upon absorption of a
photon in the visible
range, 11-cis-retinal
can isomerize to all-
trans-retinal.
Note how the size
and shape of the
molecule change as
a result of this
isomerization.
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optical isomers
when 4 different
atoms/functional
groups occur
around a single
carbon
This results in molecules which are "mirror images"
of each other, but NOT IDENTICAL.
The resulting molecules do not function the same.
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Amino acids & proteins often show this feature.
Biological systems usually can identify and use the correct form,
the other is usually ignored.
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dextro = right
levo = left
The two forms of an enantiomer are known as the "L"
form or the "D" form
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Example in the biological
world
Laboratory tests after the
thalidomide disaster showed
that the 'S' enantiomer was
teratogenic but the 'R' isomer
was an effective sedative. It is
now known that even when a
selective sample of
thalidomide is created, it can
cause racemizing. This
means that both enantiomers
are formed in a roughly equal
mix in the blood. So, even if a
drug of only the 'R' isomer
had been created, the
disaster would not have been
averted.
Thalidomide
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phocomelia
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polarity Electron position in a covalently bonded molecule
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Polar covalent bonds are a particular type of covalent
bond.
In a polar covalent bond, the electrons shared by the atoms spend
a greater amount of time, on the average, closer to one nucleus
(in this example- Oxygen) than the other nucleus (in this case
Hydrogen). This is because of the geometry of the molecule and
the great electronegativity difference between the two atoms.
Polar covalent bonds
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Chlorine is clearly to the right of carbon. Carbon is however fairly central. Electrons in a bond between these two elements are shared (covalent), but they are not shared equally. The shared electrons (one from Cl, one from C) would spend more of their time under the influence of chlorine, being farther right, but are not completely lost to carbon (as they would be to sodium).
Consider, carbon (C) and chlorine (Cl).
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The electrons
being shared are
held closer to the
Cl than to the C
giving the
molecules
slightly charged
areas.
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In a polar covalent bond, the electrons shared
by the atoms spend a greater amount of time,
on average, closer to one of the nucleus’ of
one of the atoms.
This is because of the geometry of the molecule and
the great electronegativity difference between the two
atoms.
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The result of this
pattern of unequal
electron association is
a charge separation in
the molecule, where
one part of the
molecule has a partial
negative charge and
the other has a partial
positive charge.
(You should note this molecule is not an ion because there is no exchange of electrons, but there is a simple charge
separation in this electrically neutral molecule.)
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Polar covalent bonds are extremely important in
biological systems because they allow the
molecules to form another kind of weak bond….
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The biological importance of
polar covalent bonds is that
these kinds of bonds can
lead to the formation of a
weak bond called a
hydrogen bond.
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Hydrogen bonds
How are they formed? a hydrogen bond is
formed when a charged part of a molecule
having polar covalent bonds forms an
electrostatic (as in positive attracted to
negative) interaction with a substance of
opposite charge. Molecules that have
nonpolar covalent bonds do not form
hydrogen bonds.
Important. Hydrogen bonds are extremely important in
biological systems. Their presence explains many of the
properties of water. They are used to stabilize and
determine the structure of large macromolecules like proteins and nucleic acids. They are involved in the
mechanism of enzyme catalysis.
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Strength. Hydrogen bonds are classified as weak
bonds because they are easily and rapidly formed and
broken under normal biological conditions.
What classes of compounds can form hydrogen
bonds? Under the right environmental conditions, any
compound that has polar covalent bonds can form
hydrogen bonds.
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Polar/nonpolar
lab
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Water
Water is the most abundant
molecule in the body. Water
forms the internal ocean that
baths every cell of the human
body. It makes up around 65%
of the body weight. The water
molecule is composed of one
atom of oxygen and two atoms
of hydrogen held together by
covalent bonds.
The polarity of water plays a critical role
in all living and nonliving systems
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The shape of the water
molecule and the
atoms in it give water a
special property called
polarity. This means
that one end of the
molecule is slightly
positive while the other
end is slightly negative.
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Special properties of water
Water exhibits some very special and unique
properties that make it a critical compound.
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Special Properties of Water.
Polar: H bonding, adhesion and cohesion.
High specific heat.
Universal Solvent.
High Surface Tension.
Has capillary action.
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Po
larity
pro
pe
rties
Polarity gives
water several
special
properties that
are very
useful for
living
organisms :
COHESION
ADHESION
HYDROGEN
BONDING
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Universal Solvent
In a solution one or more substances are dissolved. The dissolved
substances are called solutes. The water which dissolves the
solutes is called the solvent.
Notice how the
negative ends of water
attract sodium
and the positive ends
attract chloride.
Water is so effective at dissolving substances that
it is referred to as the universal solvent.
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Water is an example of
a molecule that has
polar covalent bonds
and engages in
hydrogen bonding.
hydrogen bond
They are simply a special type of powerful dipole-
dipole attraction.
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Hydrogen bonds are caused by dipole
attraction between two molecules containing
hydrogen bonded to small electronegative
elements (N, O or F).
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Hydrogen Bonding
The dipole forces are attracted.
A low-energy bond forms.
This attractive force is what
gives water its cohesive and adhesive properties.
Molecules that have nonpolar covalent bonds
form hydrogen bonds.
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Cohesion
Water attracted to other water.
This is caused by hydrogen bonds that form between
the slightly positive and negative ends of neighboring
molecules. This is the reason why water is found in
drops; perfect spheres.
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Surface Tension Surface tension is the name we give to the
cohesion of water molecules at the surface of a body of water.
Water Strider
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Can You Float A Paper Clip?
water has the ability to support small objects. The hydrogen bonds between neighboring molecules cause a “film” to develop at the surface.
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Breaking The Surface Tension What happened when you added a drop of
detergent?
Why?
The detergent has phosphate in it. The phosphate attracts to the water molecules and breaks the surface tension.
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adhesion
Water can also be
attracted to other
materials. This is
called adhesion.
(Remember adhesive
tape picks up things)
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What do you observe when you placed a drop of water onto a piece of wax paper?
Why do you think it is this shape?
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007 Science
You only
Live Twice
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What is happening?! Water is not attracted to wax paper
(there is no adhesion between the drop and the wax paper). Each molecule in the water drop is attracted to the other water molecules in the drop. This causes the water to pull itself into a shape with the smallest amount of surface area, a bead (sphere). All the water molecules on the surface of the bead are 'holding' each other together or creating surface tension.
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Capillary Action
Capillary action
is related to the
adhesive
properties of
water.
Capillary action is when water moves up a cylinder.
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the water molecules are attracted to the straw molecules.
When one water molecule moves closer to the straw molecules the other water molecules (which are cohesively attracted to that water molecule) also move up into the straw.
What is happening with the straw demonstration?
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Capillary action is limited by gravity and the size of
the straw. The thinner the straw or tube the higher
up capillary action will pull the water.
This explains how a meniscus forms in a cylander.
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Apply these properties to answer WHY the
meniscus is different.
glass plastic
(wax)
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Plants and Capillary Action Plants take advantage of capillary action to
pull water from the soil into themselves.
From the roots water is drawn through the plant by another force, transpiration.
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Specific Heat
Water has a high heat capacity.
Specific heat (a measure of heat capacity),
is the heat required to raise the temperature
of 1 gram of water 1°C.
Water, with its high heat capacity, changes
temperature more slowly than other
compounds that gain or lose energy.
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• Water’s resistance to sudden changes in temperature
makes it an excellent habitat (organisms adapted to narrow
temperature ranges may die if the temperature fluctuates widely).
• The heat retaining properties of water provide a much
more stable environment than is found in terrestrial
situations. AND Fluctuations in water temperature occur
very gradually (seasonal extremes are small).
Water As a Habitat
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Hydrogen bonds are extremely
important in living systems
Hydrogen bonds are
responsible for the
unique properties of
water and they loosely
pin biological
polymers like proteins
and DNA into their
characteristic shapes.
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Hydrogen bonds are classified as weak bonds
because they are easily and rapidly formed
and broken under normal biological
conditions.
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An electron density plot for the H2 molecule
shows that the shared electrons occupy a
volume equally distributed over BOTH H atoms.
Electron Density for the H2 molecule
non-polar In addition to polar covalent
bonds, there are nonpolar
covalent bonds.
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In biological systems, if a molecules has a predominance of
nonpolar covalent bonds, that substance is hydrophobic. (very important)
Nonpolar covalent bonds
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The hydrophobic effect is another unique
property of water caused by the hydrogen
bonds.
The hydrophobic effect is particularly important
in the formation of cell membranes.
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Hydrophilic properties are very important because
they allow molecules to be soluble in water.
(because most living organisms are mostly water – this is
a good thing)
Hydrophilic properties (between polar molecules)
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amphipathic molecules
Molecules with a polar/ionized region at one end
and a non-polar region at the other end
hydrophilic hydrophobic
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If amphipathic molecules are
mixed with water, the molecules
form clusters with the polar
(hydrophilic) regions at the
surface, where they will come
into contact with water, and the
non-polar (hydrophobic) regions
nestled in the center of the
cluster away from contact with
water. The arrangement will
increase the overall solubility in
water.
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Hydrophilic:
Hydrophobic:
Example: mix salad oil with water—shake to break H bonds
but as these bonds reform between water molecules, they
push the oil molecules out of the way-the oil tends to
cluster together in drops or as a layer on the water’s
surface-thereby exposing less surface area to the water
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Bond strength
In biological systems, covalent bonds are called strong
bonds. This means that they are not normally broken
under biological conditions unless by enzymatic
catalysis.
This is in opposition to weak bonds such as ionic bonds
which are easily broken under normal biological
conditions of temperature and pressure.
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Van der Waals interactions
probably the
most basic type
of interaction.
Any two
molecules
experience Van
der Waals
interactions.
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due to the spatial orientation of the molecules,
the attractive forces outweigh the repulsive
ones.
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Even macroscopic surfaces experience
VDW interactions
VDW forces are electrostatic in nature
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strongest
weakest
covalent
ionic
hydrogen
Van der Waals