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Organic chemistry – the chemistry of life
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Based on carbon
Takes place in water (aqueous solution)
In a narrow range of temperatures (on earth)
Is complex, vastly more complex than any
other chemical system known
• Dominated by large polymeric molecules
• Matter is made of combinations of elements
• Elements are substances that cannot be broken
down or converted into other substances by
chemical means, like carbon
• An atom is the smallest particle of an element that
still retains it’s chemical properties
• Groups of atoms linked together form molecules
including the molecules of life
• Atoms have a nucleus which is positively charged
due to the protons (neutrons have no charge)
which is surrounded by a cloud of electrons,
which have a negative charge.
• Atomic number = number of protons, and
determines the chemical behavior of the element
• Number of neutrons can vary and have no charge.
(12C, carbon has 6 protons and 6 neutrons.) They
contribute to the stability of the nucleus – too
many or too few and it may disintegrate by
radioactive decay. These are isotopes.
– Ex. 14C has 6 protons and 8 neutrons and is unstable.
• Atomic weight = number of protons plus neutrons
– Ex. 14C has an atomic weight of 14
Figure 2.2
• The mass of an atom is specified in daltons,
one dalton = mass of one hydrogen atom.
• One gram of hydrogen = 6 X 1023 atoms
• 6 X 1023 = Avogadro’s number = the
number of molecules in a mole of the any
substance
• molecular weight of any substance is the
mass of 6 X 1023 atoms = a mole of that
substance.
– 1 mole of carbon weighs 12 grams
Figure 2.3
Figure 2.4
• Electrons move continuously around the nucleus. They
move in discrete orbits or electron shells.
• The electrons in the closest shell are very strongly attracted
to the positive nucleus. This shell holds only 2 electrons.
• The next or second shell can hold up to eight electrons.
This shell is farther away from the positive nucleus and the
electrons are less tightly bound.
• The third shell holds up to eight electrons but the fourth
and fifth shells hold up to 18 electrons.
• An atom with the outermost shell full is stable and not
inclined to react with other atoms.
• Atoms with unfilled electron shells are less stable and have
a strong tendency to react with other atoms.
Figure 2.5
• Atoms with unfilled outer shells tend to
interact by exchanging or sharing electrons
in order to fill their outer shells.
• The number of electrons an atom needs to
complete its outer shell is its valence.
• When atoms gain or lose electrons, the bond
is ionic.
• When atoms share electrons, the bond is
covalent.
• Covalent bonds can be polar, when the
electrons are shared unequally.
Become ions
cation
anion
Packed together in a precise 3-D array. Salts are usually soluble in
water due to interaction of polar water molecules and charged ions.
The molecules of the
cell are held together
by covalent bonds.
These bonds do not
break in water. They
are stronger than ionic
bonds
Shared electrons form
a cloud around both
nuclei which is densest
in between them and
holds them together.
The repulsion of the
2 positive nuclei and
the attraction of the
positive nuclei and
the negative electron
cloud balance out at
a specific bond
length. Table 2-2
• Bond strength is measured in kilocalories per mole
(6 X 1023), the energy required to break the bond.
• Kilocalorie = the energy needed to raise the
temperature of one liter of water by one degree
centigrade.
• Covalent bonds are very strong. Breaking and
making these bonds requires specific catalysts
(enzymes) and is carefully controlled by the cell.
• Covalent bonds result in specific bond angles,
length, and bond energies. This precise geometry
is the basis for the 3-D shape of organic
molecules. Figure 2-9
• Noncovalent bonds are usually weaker on a one to
one basis. Panel 2-7 and Figure 2-12
6 electrons,
needs 2
A single bond allows
rotation, is longer and
not a strong as a
double bond
A double bond is
stronger, shorter, and
more rigid.
Bonds help to
determine the 3-D
shape of a molecule.
Non-covalent bonds
are weak but lots of
weak bonds together
can be relatively
strong.
Life hinges on the properties of water
• Properties of water are due to hydrogen bonds (non-covalent)
• The two bonds between oxygen and hydrogen are highly polar
because the oxygen is larger and more positive it attracts the electrons
more strongly. Therefore the oxygen side of water is more negative
and the hydrogen sides are more positively charged.
• The slightly positive hydrogen attracts negative ions or negative areas
on polar molecules. These are hydrogen bonds.
• Hydrogen bonds are much weaker than covalent bonds and are easily
broken by random thermal motions. The hydrogen bonds of water are
continually made and broken.
• Hydrogen bonds give water it’s life giving properties - stays liquid at
room temp, has a high boiling point, and high surface tension.
• Many hydrogen bonds together can be very strong and are important
for the folding of large molecules into their unique shape and for
interactions between molecules.
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• Molecules that are polar and ions are called
hydrophilic because they form hydrogen bonds
with water.
– Sugars, DNA, RNA, many proteins
• Molecules that are not polar do not dissolve in
water and are called hydrophobic.
– Hydrocarbons in cell membranes
• When a molecule with a hydrogen in a
highly polar covalent bond dissolves in
water, the hydrogen virtually give up its
electron and becomes a proton (H+).
• This proton can leave it’s electron behind
and become attracted to the oxygen atom in
another water molecule, forming a
hydronium ion (H30+).
• These protons are constantly jumping form
here to there.
• Substances that release protons when they
dissolve in water are acids.
• Substances that raise the concentration of
the hydroxyl ion (OH-) are bases (alkaline).
• The concentration of protons is expressed
by the pH scale. The pH inside the cell
must be closely regulated close to pH of 7.
• Water is neutral, pH = 7
A cell is formed from carbon compounds
organic molecules
• Carbon-carbon bonds are highly stable and
can form chains, branched chains, and rings.
• Carbon can also combine with other
molecules to add chemical groups with
specific chemical behavior and physical
properties.
Glycerol plus fatty
acids =
triacylglycerol (pg
58)
Amino acids
Peptide bonds
Nucleic acids
phospholipids
2 phosphoric acids minus water
Cells contain four major families of small organic molecules
small organic molecules:
*monomers for
macromolecules
*energy sources
*formed and
broken down into a
distinct set of
simple compounds
Simple sugars, monosaccharides,
carbohydrates
(CH2O)n
Glucose
Sugar polymers can be branched, contain different types of
bonds and different derivatives. The result is tremendous
variety and complexity, making the sequence and
arrangement of a particular carbohyrate very difficult to
determine compared to the sequence of proteins and DNA.
•cell membranes (recognition etc.)
•glycolipids and glycoproteins (ABO blood types)
•mechanical support
•cellulose in plants (cell wall)
chitin in insects (exoskeleton)
•energy (glucose) storage
•Glycogen (animals) and starch (plants)
Most fatty acids are linked to
other molecules by their
carboxylic acid group.
Different fatty acids differ
only in the length of their
hydrocarbon chains and the
number and position of the
carbon-carbon double bonds.
Serve as concentrated energy
reserve in cells. Can be
broken down to produce 6Xs
the usable energy weight for
weight as glucose. Are stored
in the cytoplasm of many
cells as droplets of
triacylglycerol.
Animal fats found in meat, butter, and cream are
usually saturated, and solid at room temperature.
Plant oils like corn oil contain more unsaturated
fatty acids. Peanut and olive oil contain
monounsaturated fatty acids.
Molecules with both
hydrophobic and
hydrophilic regions are
termed amphipathic
Amino acids have a carboxylic acid group and an
amino group linked to the alpha carbon. The chemical
variety results from the side chain attached to the alpha
carbon. These can be charged (5 ) or uncharged and
polar (hydrophilic) or non polar (hydrophobic).
Notice that the hydrogen atoms nearest to nitrogen are smaller
since their electrons are pulled in by the large nitrogen nucleus,
creating a smaller electron cloud around them.
Nucleotides can act as short-term carriers of chemical energy
ATP
adenosine triphosphate
Formed by oxidation of food. The phosphates are linked by phosphoanhydride
bonds which release large amounts of useful energy when broken. The terminal
phosphate is frequently split off by hydrolysis, releasing energy which drived
energy-requiring reactions in the cell
Ribonucleic acid (RNA) contains bases A, G, C, and U. Usually
occurs as single stranded molecules.
Deoxyribonucleic acid (DNA) contains bases A, G, C, and T and is
always doublestranded. The two polynucleotide strands are held
together by hydrogen bonds between bases.
Macromolecules are abundant in cells
Each polymer is built by
enzymes which covalently
bond monomers by
condensation reactions
Macromolecules contain a specific sequence of monomers covalently
linked. The diversity that results is demonstrated by proteins. 20
amino acids allow for 20200 possible 200 aa polypeptides.
Macromolecules are extremely
diverse and versatile
proteins serve as
enzymes to catalyze reactions
subunits to build structural
components of cells
molecular motors to produce
force and movement
Single covalent bonds allow rotation and therefore unlimited
conformations (shapes). However, macromolecules normally have
one stable conformation due to many non-covalant bonds forming
between different areas of the molecule.
ionic bonds
hydrogen bonds
van der Waals
attractions
hydrophobic forces
When two molecules fit closely and are attracted by many
non-covalent interactions, their binding affinity can be
strong. This is the basis for the specificity of binding of
macromolecules to other molecules, as in enzyme specificity
for their substrates, DNA double helix, multimolecular
structures like ribosomes.