Download Organic Chemistry

Organic Chemistry
•Organic chemistry is the study of carbon-based
molecules.
•Nearly all of the compounds that a cell makes are
composed of carbon bonded to other carbon atoms and
to atoms of other elements.
Organic Chemistry
•Carbon is unparalleled in its ability to form large,
diverse molecules.
•Recall that carbon has six electrons:
– 2 in its innermost shell and 4 in its outermost shell
C
Carbon completes its outer
shell by sharing electrons with
other atoms in 4 covalent
bonds.
Organic Chemistry
•The diversity of carbon molecules is the driving force
behind the myriad of molecules and chemical processes
required for life, and explains the great diversity of life on
Earth!
Organic Chemistry
•Carbon can share its electrons with four hydrogen
atoms, creating CH4 or methane.
•Methane is an example of an organic compound and is
the simplest of all organic compounds.
H
H
C
H
H
Organic Compunds
• When Carbon shares electrons with Hydrogen atoms,
a hydrocarbon results
• Hydrocarbons are the major components of petroleum
• Petroleum (crude oil) consists of the partially
decomposed remains or organisms that lived millions
of years ago
• This is why the burning of fossil fuels increases carbon
dioxide into our atmosphere
CH4 + 2O2 → 2H2O + CO2 + Energy
Organic Chemistry
•The unique properties of an organic compound depend
upon the size and shape of its carbon skeleton (the
chain of carbon atoms in an organic molecule) and the
groups of atoms that are attached to that skeleton.
•Functional groups are smaller portions of a larger
molecule affect a molecule’s function by participating in
chemical reactions in characteristic and predictable
ways.
•Of the six functional groups of atoms that are
essential to life, five are polar and one is nonpolar.
Same carbon
skeleton, but
different
functional
groups
Estradiol
female sex
hormone
Testosterone
male sex
hormone
Female Lion
Male Lion
• Besides water, all biological molecules are organic, or
carbon-based.
• There are many organic molecules, but most of the
organism is made up of just four types:
carbohydrates, lipids, proteins and nucleic acids.
• Carbohydrates, lipids, proteins and nucleic acids are
called macromolecules, and are the building blocks
of cells and their chemical machinery.
• Cells make most of these large molecules by joining
together smaller molecules, or monomers, into
chains called polymers.
Polymer
Monomer
Nucleic Acid
Cellular structure
Chromosome
DNA strand
Nucleotide
• The key to the great diversity of macromolecules is in
the arrangement of its monomers.
• DNA is built up of only four monomers (nucleotides),
and proteins are made with only twenty monomers
(amino acids), but both macromolecules are
incredibly diverse.
• The DNA and proteins in you and a fungus are made
with the same 4 nucleotides and 20 amino acids!
• A cell links monomers together to form polymers by
way of a dehydration reaction.
• A dehydration reaction is so named because it results
in the removal of a water molecule from the 2 reacting
monomers.
• An unlinked monomer has a hydroxyl group (--OH) at
one end and a hydrogen at the other end, with will
react with another unlinked monomer or a polymer
that is increasing in size.
Hydroxyl
group
Dehydration Reaction
polymer
monomer
Hydroxyl
group
By removing the hydroxyl group of the polymer, and
the hydrogen atom of the monomer that is being
added, a water molecule is released.
Dehydration Reaction
Water
molecule
• Just as removing a water molecule links monomers
together (to form polymers), the addition of a water
molecule breaks a polymer chain apart (releasing a
monomer).
• The process of breaking up polymers is called
hydrolysis.
• Hydrolysis is essentially the reverse of a dehydration
reaction.
• Hydrolysis is necessary to break down polymers that
are too large to be used by the organism.
– digestion of food
Hydrolysis
Water
molecule
Hydrogen
atom
Hydroxyl
group
shorter
polymer
monomer
Hydrolysis
• Note that the addition of a water molecule results in
the reinstatement of a hydroxyl group at the detached
end of the polymer, and the hydrogen atom at the
detached end of the newly formed monomer.
Hydroxyl
group
shorter
polymer
Hydrogen
atom
monomer
Enzymes
• Both dehydration reactions and hydrolysis require the
help of enzymes to make and break bonds
• Enzymes are specialized proteins that speed up the
chemical reactions in cells
• Enzymes are extremely important – without them,
many reactions cannot take place. If you lack lactase,
you cannot hydrolyze the bond in lactose (lactose
intolerant)
• Carbohydrates are polymers made up of carbon,
hydrogen, and oxygen atoms.
• Carbohydrates play important roles in the energy
storage and structural support of organisms, and are
themselves an excellent source of energy.
• The monomers that make up carbohydrates are called
monosaccharides.
• A monosaccharide is a small sugar, that can link
together to form larger, more complex sugars.
• Monosaccharides generally contain carbon, hydrogen
and oxygen in a ratio of 1:2:1.
• Glucose, the sugar that carries energy to the cells of
your body, is a monosaccharide with the chemical
formula of C6H12O6.
• When two monosaccharides are linked together by
dehydration synthesis, they form a disaccharide.
• Examples of disaccharides include the table sugar
sucrose, the milk sugar lactose, and maltose which is
formed by linking two glucose molecules together.
Recall that all polymers are built by a
dehydration reaction.
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Monosaccharides can also be linked together to
form polysaccharides.
A polysaccharide is a large polymer consisting of
hundreds or thousands of monosaccharides
linked by dehydration reactions.
Polysaccharides function as storage molecules
or structural compounds.
The most common types of polysaccharides are
starch, glycogen, cellulose, and chitin.
Polysaccharide: Starch
Starch (amylose) is an energy storage
polysaccharide used by plants.
Starch consists entirely of repeating glucose
monomers.
glucose glucose
glucose glucose
glucose
glucose
glucose
glucose
glucose
glucose
glucose glucose
glucose
glucose
glucose
glucose
glucose glucose
glucose
glucose
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Through the process of photosynthesis, plants
produce glucose as an energy source.
Often, a plant produces more glucose than is
readily needed, so the plant stores this energy
as long chains of glucose molecules, or starch!
Starch is found in potatoes and grains,
such as wheat, corn and barley.
Polysaccharide: Glycogen
Glycogen is an energy storage polysaccharide
used by animals.
Glycogen also consists entirely of repeating
glucose monomers, but is much longer and
more branched than starch.
Glycogen is broken down into glucose as energy
is needed.
Polysaccharide: Cellulose
Cellulose is a structural polysaccharide used by
plants.
Cellulose is the most abundant organic
compound on Earth, forming the cell walls of all
plant cells.
Polysaccharide: Cellulose
Cellulose consists of long chains of glucose
molecules linked in such a way that they can not
be broken down easily.
Humans are unable to digest cellulose and it
makes up the fiber in our diets.
Certain microbes can digest cellulose, and
reside in the guts of herbivores, such as cows,
sheep, and even termites!
Polysaccharide: Chitin
Chitin is a structural polysaccharide used by
animals.
Animals that use chitin for external skeletons
include insects and crustaceans.
Chitin attaches to proteins forming a tough and
resistant protective material.
Chitin forms the
exoskeleton of
crustaceans such
as crabs and
lobsters, as well
as insects and
spiders!
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Animals
Plants
Glycogen
Starch
Chitin
Cellulose
Storage
Structure
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Lipids
• For short-term energy storage, animals convert
glucose into glycogen.
• For long-term storage, however, organisms usually
convert sugars into fats, or lipids.
• Lipids are a diverse group of molecules that includes
oils, fats, waxes, phospholipids, and steroids.
• All lipids are insoluble in water because they are nonpolar.
Lipids
• Lipids are important for energy storage because
they contain many more energy-rich C-H bonds
than carbohydrates.
• A gram of lipids contains twice as much energy
as a gram of polysaccharides, such as starch.
Lipids: Fats
• Fats are made up of 2 smaller molecules:
glycerol and fatty acids.
• A fat molecule contains 1 glycerol and 3 fatty
acids.
• For this reason, fats are called triglycerides.
triglycerides
Lipids: Fats
• A fatty acid consists of a long chain of carbon
and hydrogen atoms.
• The arrangement of these atoms can vary,
affecting the fat molecule’s physical properties.
• Fats whose fatty acids contain the maximum
number of hydrogen atoms that can fit are called
saturated fats.
Lipids: Fats
• Fats whose fatty acids contain double bonds
between some of the carbon atoms are called
unsaturated fats because they contain fewer
than the maximum amount of hydrogen atoms.
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Lipids: Fats
• The double bonds (C=C) in unsaturated fats cause
kinks, or bends, in the carbon chains of the fatty
acids.
• These kinks prevent the molecules from packing
tightly together so unsaturated fats (like corn oil)
remain liquid at room temperature.
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Lipids: Fats
• In contrast, saturated fats have no double bonds
(or kinks).
• The molecules can then pack more tightly
together, so saturated fats (like butter) are solid
at room temperature.
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• Triglycerides (fats and oils):
– Store energy
– Insulate (blubber, etc)
– Provide cushioning
– Prevent dehydration
– Help to maintain internal temperature
Lipids: Phospholipids
• Phospholipids are structurally similar to fats,
but contain only 2 fatty acids attached to a
glycerol molecule.
• Each phospholipid molecule has a polar, or
hydrophilic end, and a non-polar, or
hydrophobic end.
• Phospholipids are the main component of
cellular membranes.
Lipids: Phospholipids
• The polar, or hydrophilic end of a
phospholipid is “water-loving” and
water soluble.
• The non-polar, or hydrophobic
end of a phospholipid is “waterfearing” and water insoluble.
insoluble
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Lipids: Phospholipids
• The membranes of all cells are composed of two
layers of phospholipids, called a bi-layer.
• The polar, hydrophilic ‘heads’ face outward and
are in contact with the aqueous environment on
either side of the membrane.
• The non-polar, hydrophobic ‘tails’ cluster
together in the middle of the membrane.
Lipids: Phospholipids
Hydrophilic head
Hydrophobic
tails
Water (outside of cell)
Water (inside of cell)
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Lipids: Steroids
• A steroid is a type of lipid that does not contain
fatty acids.
• Instead, steroids are composed of 4 carbon
rings fused together.
3
1
4
2
4 Carbon
rings
Lipids: Steroids
• Cholesterol is a common steroid found in animal
cell membranes.
• Cholesterol is also part of some sex hormones
like testosterone, estrogen and progesterone.
Cholesterol
Testosterone
Estrogen
Proteins
• Proteins are a very diverse group of organic
molecules. The many shapes of protein molecules
allow them to perform a variety of functions.
• In living organisms, they are used for transport,
structure, metabolism, communication, and even to
detect stimuli such as light.
• The protein hemoglobin carries oxygen in your blood,
and the protein keratin helps support your skin, hair
and nails.
Amino Acids
• Like other organic polymers, proteins are made of
many monomers bonded together.
• These monomers are called amino acids, and there
are 20 different kinds found in protein molecules.
• Every amino acid molecule contains an amino group
(--NH2) and a carboxyl group (--COOH).
Amino acids are linked together via dehydration
synthesis.
The bonds between
amino acid
monomers are called
peptide bonds.
Peptide bond
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Proteins
• A polypeptide contains hundreds or thousands of
amino acids linked together by peptide bonds.
• The unique combination of amino acids in a protein
molecule determines its specific shape, or structure.
• The shape of a protein determines its specific
function.
Proteins have different levels
of structure.
Primary Structure
• The primary structure of a protein describes its
unique sequence of amino acids.
• The primary structure is determined by the cell’s
genetic information (DNA).
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Secondary Structure
• The secondary structure of a protein describes
its folding pattern.
• Chains of polypeptides may fold into shapes like
a beta pleated sheet or an alpha helix
• Theses secondary structures are stabilized by
hydrogen bonds between spatially nearby amino
acids
Tertiary Structure
• The tertiary structure of a protein describes its
overall 3-dimensional shape.
• This includes all of the pleated sheets and alpha
helixes and is the active form of the protein.
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Quaternary Structure
• The quaternary structure of a protein describes
the complex association of multiple
polypeptide chains.
• Each polypeptide chain in the association has its
own primary, secondary, and tertiary structures.
Quarternary Structure
Polypeptide
chain
• Collagen is formed by several
polypeptide chains in a rope-like
arrangement
• Gives connective tissue, bone,
tendons, and ligaments its strength!
• Hemoglobin is another example of a
quarternary structure protein
(transports oxygen in blood)
Collagen
Quaternary Structure
Te
r
y
it ar
c
u
r
st
re
u
t
Primary structure
Secondary
structure
Quaternary structure
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Protein shape determines function
• When exposed to excessive heat, or changes in
salinity or pH, a protein can denature.
• Denaturation causes the
Properly-folded
polypeptide chains in a
protein
protein to unravel, and
lose their specific shape.
• When this happens, a
protein will no longer
function normally.
Denaturatio
n
Denature
d protein
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Enzymes
• Enzymes are proteins that increase the rate of
chemical reactions and so are called catalysts.
• Like other proteins, the structure of enzymes
determines what they do.
• Since each enzyme has a specific
shape, it can only catalyze a
specific chemical reaction.
• The digestive enzyme pepsin, for
example, breaks down proteins in
your food, but can’t break down
lipids or carbohydrates.
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Nucleic Acids
• Nucleic acids are molecules, like DNA, that
store genetic information - the instructions cells
need to build proteins.
• A nucleic acid contains information on what type
of amino acids are needed to make a protein
and in what order they should be linked to give
the protein its structure, and function.
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Nucleotides
• The monomers that are linked together to form a
nucleic acid polymer are called nucleotides.
Chromosome
Every
chromosome in
our cells
contains nucleic
acids
Polymer = nucleic acid
Nucleic acids are
polymers
Monomer = nucleotide
Many nucleotide
monomers make
up each nucleic
acid
Nucleotides
• Every nucleotide has three parts:
– 5-carbon sugar
– Phosphate group
– Nitrogenous base
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Nucleotides
• Nucleotides can encode information because
they contain more than one type of nitrogenous
base.
• There are 5 different nitrogenous bases:
Nucleotides
Pyrimidines
Cytosine
Thymine
Uracil
Purines
Adenine
Guanine
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Nucleic Acids
• There are two types of nucleic acids:
– RNA
– DNA
Nucleic Acids
• There are two types of nucleic acids:
– RNA = ribonucleic acid
– DNA = deoxyribonucleic acid
• Both are nucleotide polymers but they differ in
both their structures and their functions.
RNA
• Ribonucleic acid contains the sugar ribose.
• RNA is composed of 4 nucleotides
RNA contains:
• adenine (A)
• uracil (U)
• cytosine (C)
• guanine (G)
RNA
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RNA
• RNA exists as a long, single
strand of nucleotides.
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DNA
• Deoxyribonucleic acid contains the sugar
deoxyribose.
• DNA also is composed of 4 nucleotides
DNA contains:
• adenine (A)
• thymine (T)
• cytosine (C)
• guanine (G)
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DNA
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DNA
• DNA exists as a two
strands of nucleotides
wound around each other
to form a double helix.
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The Double Helix
• DNA’s double helix results from hydrogen bonds
formed between its nitrogenous bases.
• Large nitrogenous bases or purines (adenine
and guanine) pair with smaller bases
pyramidines (thymine and cytosine).
• Adenine bonds with thymine (A-T) and
guanine bonds with cytosine (G-C).
The Double Helix
• Because of its A-T, G-C pairing, each DNA
strand is complimentary to the other.
• If the sequence of one
strand is ATCGAT, the
sequence of the other
strand must be TAGCTA
because A always bonds
to T, and C always bonds
to G.
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DNA Double Helix
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DNA Double Helix
• The 2 DNA chains are held in a double helix by
hydrogen bonds between their paired bases
• Most DNA molecules have thousands or millions
of base pairs
– (A and T would be considered a base pair; as
would C and G)
Hydrogen
bonds
(dotted
lines)