NOTES FOR BIOLOGY
CHEMICAL FOUNDATIONS FOR CELLS
>>>>>>>An understanding of chemistry is
important because the interaction between atoms is one of the lowest levels of
biological organization.
>>>>>The basic unit of all forms of matter is
the atom
---atom is the smallest unit of matter that retains the
physical and chemical properties of the element.
--element is a substance that can’t be broken down into
other substances by chemical reactions.
-elements
are composed of atoms
>>>>>>>Atoms are made up of subatomic
particles. The 3 most stable subatomic particles are: neutrons, protons, and
electrons (see fig 2.2)
---Protons are positively charged particles found at the
core, or nucleus, of the atom.
---Neutrons are uncharged particles found at the core, or
nucleus, of the atom.
---Electrons are light, negatively charged particles that
orbit around the nucleus in electron shells
|
charge location |
NEUTRON uncharged at the core of the atom known as the nucleus |
PROTON +1 charge at the core of the atom known as the nucleus |
ELECTRON -1 charge orbiting around the nucleus in electron shells |
>>>The Atomic Nucleus
---atomic number is the number of protons in an atom of a
particular element (see table 2-1)
-The
atomic number is constant for a given element
The mass number or atomic weight of an element is the number
of protons plus the number of neutrons
The atoms of a particular element may have different numbers
of neutrons
This
difference results in isotopes
---Isotopes are atoms of the same element which have
different atomic weights
—Radioisotopes are isotopes which are unstable and breakdown
or decay by emitting energy and particles.
>>>The Electron Orbitals
---Electron orbitals are the
three-dimensional space around the nucleus of an atom where an electron will be
found 90% of the time. (See fig 2.6)
---The electron orbitals of an
atom are arranged in electron shells based on their energy level.
Each electron shell occupies a specific distance from the
nucleus. The further away, the higher the energy level.
(See fig 2.7)
The chemical behavior of an atom is determined by the number
of electrons in the outermost electron shell.
An atom with an incomplete (partially full) electron shell
is reactive whereas an atom with a full electron shell is non-reactive or
inert.
If an atom has a vacancy in the outer electron shell, it
will try to fill that vacancy or get rid of the “extra” electrons so the outer
shell is full.
CHEMICAL BONDS: JOINING ATOMS TO MAKE MOLECULES
>>>>>>>A reactive atom will try to fill
the valence shell by interacting with other atoms. This interaction may result
in two atoms forming a chemical bond.
---Chemical bond is an attraction that holds two atoms
together.
---Molecule is two or more atoms held together by chemical
bonds. The smallest unit that retains the physical and
chemical properties of a compound.
Similar
atoms > (molecule) > element
Different
atoms > molecule > compound
---compound is composed of 2 or more elements in a fixed
ratio
-example:
table salt, NaCl
-compounds
are composed of molecules
---Mixture is composed of 2 or more elements and/or
compounds in proportions that can vary.
-example: our atmosphere, nitrogen, helium, carbon dioxide, etc.
>>>Formation of ions
If an atom has an almost empty or an almost full outer
electron shell it is more likely to form an ion (See fig. 2.9)
---Ion is a charged atom or molecule
---Anion
is a negatively charged atom or molecule
---Cation is a positively charged atom or molecule
---Ionic bond is formed by the attraction between oppositely
charged ions after the completion of an electron transfer
Ionic
compounds are called salts and usually form crystals as a solid.
Ionic
bonds are strong in crystals but break easily in water.
>>>Sharing Electrons
>>>>>>>Covalent bond is a bond formed
when two atoms share electrons.
An atom may have to share only one pair of electrons to fill
the outer shell. Some atoms may have to share two (or more) pairs of electrons
or may have to share with more than one atom to fill the outer electron shell.
---Single covalent bond shares a single pair of electrons
---Double covalent bonds share two pairs of electrons
---Triple covalent bonds share three pairs of electrons
>>>Non-polar Covalent Bonds versus Polar Covalent
Bonds
---Nonpolar covalent bond is a
covalent bond in which the sharing of the electron pair is equal.
---Polar covalent bond is a covalent bond in which the
sharing of the electron pair is unequal.
When polar covalent bonds form, the molecules which result
may also be polar.
-positive charge at one end negative charge at the other.
>>>Hydrogen bonds form between polar molecules
---Hydrogen bond is formed by the charge attraction when a
hydrogen atom which is covalently bonded to one atom is attracted to a second
atom. (See fig. 2.11a)
A weak attractive force about 20 times easier to break than a
covalent bond.
A charge attraction between oppositely charged polar molecules.
Weak bonds are often as important as strong bonds in
biological systems.
Reversible
binding
Can form between molecules or within large molecules.
Can help stabilize three-dimensional shape of large molecules.
>>>WATER AND LIFE
Cells are 70-95% water.
Water covers 70% of the surface of the
earth.
Some of the most biologically important polar covalent bonds
are the bonds in water molecules.
Because
of these polar covalent bonds, water is a polar molecule (See fig 2.12)
This polarity along with the hydrogen bonding ability make
water a very
versatile
solvent.
Polar and ionic substances which are hydrophilic are easily
dissolved in water.
---Hydrophilic describes the property of having an affinity
for water.
The polarity of water molecules makes water a poor solvent
for molecules which do not have charged regions
Nonpolar substances are
hydrophobic.
---Hydrophobic describes the property of not having an
affinity for water.
-hydrophobic
molecules clump together in water because of hydrophobic
interaction
>>>Water helps to moderate the effects of changes
in temperature.
---Temperature is a measure of the molecular motion in a element, compound or mixture
|
Temperature scale |
Temperature at which water melts |
Temperature at which water boils |
Temperature of the human body |
|
Celsius |
0 oC |
100 oC |
37 oC |
|
Fahrenheit |
32 oF |
212 oF |
98.6 oF |
Three
properties of water help keep temperature stable:
1)
High specific heat
2)
High heat of vaporization
3)
High heat of fusion
---Specific heat is the amount of energy that must be
absorbed or lost for one gram of matter to change its temperature by one degree
Celsius.
-specific
heat of water 1 calorie/gram
-specific
heat of alcohol 0.6 calorie/gram
-specific
heat of table salt 0.2 calorie/gram
-specific
heat of rock 0.02 calorie/gram
---Calorie (cal) is the amount of energy it takes to raise
the temperature of one gram of water by one degree Celsius.
Water has a high heat of vaporization and cools surfaces as
it evaporates.
---Vaporization (evaporation) is the transformation of
matter from a liquid to a gas.
---Heat of vaporization is the quantity of heat a liquid
must absorb for 1 gram to be converted to the gaseous state.
-Leads
to cooling of the surface of a liquid when during evaporation.
Water has a high heat of fusion and freezes much slower than
other liquids.
When
water freezes, it forms an unusual solid, Ice
>>>Water Molecules Tend To Stick Together
Water
has cohesive behavior which is the result of hydrogen bonding between the water
molecules and the other molecules and includes cohesion, and surface tension.
---Cohesion is the attraction of a molecule to the same kind
of molecule.
This
is the phenomenon that holds water together.
---Surface tension is the force that increases the ability
of a surface of a liquid to stretch without breaking. (See fig. 2-11)
Water
has a greater surface tension than most liquids because of the arrangement of
the hydrogen bonds at the surface.
Causes
water to bead
Water molecules can dissociate. That means that the hydrogen
atom of one water molecule leaves its electron behind and forms a hydrogen ion
(H+) and a hydroxide ion (
H
(
O H+
'
=> _
H
O
'
H
In pure water the number of H+ ions = the number of
If the solution is acidic, then the number of H+ ions is
greater than the number of
Conversely if the number of
---Acid is a substance which increases the concentration of
H+ in a solution.
---Base is a substance which reduces the concentration of H+
in a solution.
>>>The pH Scale
The degree of acidity is expressed on the pH scale.
---pH scale is a scale used to measure the acidity of
solutions. The scale ranges from 0 to 14. (See fig. 2-10)
For
a neutral solution pH =7
For an
acidic solution pH =5
For a
basic solution pH = 9
Because the pH scale is a logarithmic scale, a change of one
pH unit represents a tenfold change in the concentration of H+.
Most biological solutions are between pH 6 and pH 8
>>>Buffers Help Maintain A
Constant pH
---Buffers are substances that prevent large sudden changes
in pH.
Buffers
are combinations of H+ donor and H+ acceptors
Buffers function by accepting H+ ions from solution when
they are in excess, and
donating H+ ions to the solution when the supply is depleted.
Example:
Bicarbonate buffer