Download Chapter 3 – The Molecules of Cells

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.
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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!
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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 + 2 O2 → 2 H2O + CO2 + Energy
Organic Chemistry
The unique properties of an organic compound
depend upon the size and shape of its carbon
skeleton and the groups of atoms that are
attached to that skeleton.
Of the six groups of atoms that are essential to
life, five serve as functional groups.
Functional groups affect a molecule’s function
by participating in chemical reactions in
characteristic and predictable ways.
carbon skeleton: the chain of carbon atoms in an organic molecu
Hydroxyl group – polar, consists of a
Hydrogen bonded to an Oxygen
Carbonyl group – polar, Carbon linked
by a double bond to an Oxygen
Carboxyl group – polar, a Carbon
double-bonded to both an Oxygen
and a Hydroxyl group
Amino group – polar, composed of a
Nitrogen bonded to 2 Hydrogen atoms
and the Carbon skeleton
Phosphate group – polar, consists of a
Phosphorus atom bonded to 4 Oxygen
atoms
Methyl group – nonpolar and not
reactive,Carbon bonded to 3 Hydrogen
Same structure, but
different functional
groups
Estradiol – female
sex hormone
Methyl group
Female Lion
Hydroxyl group
Carbonyl group
Testosterone –
male sex hormone
Male Lion
Besides water, all biological molecules are
organic, or carbon-based.
There are many organic molecules, but most
of the human body 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 incredible diverse.
The proteins in you and a fungus are made
with the same twenty 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.
An unlinked monomer has a hydroxyl group
(--OH) at one end, and a hydrogen atom (--H)
at the other end.
Hydrogen
atom
Hydroxyl
group
Dehydration Reaction
polymer
Hydrogen
atom
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
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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 enter a
cell otherwise.
Hydrolysis
Water
molecule
Hydrogen
atom
Hydroxyl
group
shorter
monomer
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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
Hydrogen
atom
monomer
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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
Carbohydrates
are polymers made up of
Carb
ohydr
carbon, hydrogen
hydrogen, and oxygen
oxygen atoms.
carbon
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.
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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.
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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 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!
Cellulose
1
2
3
4
Polysaccharide: Chitin
Chitin is a structural polysaccharide used by
animals.
Animals that use chitin for external skeletons
include insects and crustaceans.
Fungi also have chitin in their cell walls for
structural support.
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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Animal
s
Plants
Glycogen
Starch
Chitin
Cellulose
Storag
e
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
non-polar.
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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.
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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.
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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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Who You Calling Fat?!
• 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.
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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
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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.
Cholester
ol
Testosteron
e
Estroge
n
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.
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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).
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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.
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Every protein has four
levels of structure:
• Primary
• Secondary
• Tertiary
• Quaternary
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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 pleated sheet or an alpha helix
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Secondary Structure
• The many hydrogen
bonds within the
polypeptide chain
of silk fibers make
spider fiber as
strong as steel;
uses of silk proteins
include fishing line,
surgical thread and
bulletproof vests!
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.
• Not all proteins consist of 2 or more
polypeptide chains, but those that do have a
quaternary structure.
• Each polypeptide chain in the association has
its own primary, secondary, and tertiary
structures.
Quaternary Structure
Primary structure
Secondary
structure
Quaternary structure
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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
Protein shape determines function
• When exposed to excessive heat, or changes
in salinity or pH, a protein can denature.
• Denaturation causes the
Properly-folded
protein
polypeptide chains in a
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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Proteins gone bad
• So what happens is a protein folds incorrectly?
• Many diseases, such as Alzheimer’s and
Parkinson’s involve an accumulation of
misfolded proteins
• Prions are infectious agents composed of
proteins
• Prion diseases are currently untreatable and
always fatal
Prions
• Prions infect and propogate by refolding
abnormally into a structure that is able to
convert normally-folded molecules into
abnormally-structured form
• This altered form accumulates in infected
tissue, causing tissue damage and cell death
• Prions are resistant to denaturation due to
their extremely stable, tightly packed
structure
Prions
• Prions are implicated in a number of diseases
in a variety of mammals:
– Bovine Spongiform Encephalopathy (“Mad Cows
Disease”) – spread by feed containing ground-up
infected cattle
– Creutzfeldt-Jakob Disease – degenerative
neurological disorder spread by skin grafts or
human growth hormone products; Kuru is a
similar disease spread by cannibalism among the
Fore tribe of Papua New Guinea
Prions
• Chronic Wasting Disease – found in deer,
moose, elk in U.S. and Canada
• Fatal Familial Insomnia – very rare, inherited
prion disease (50 families worldwide have the
responsible gene mutation); insoluble protein
causes plaques to develop in the thalamus,
the region of brain responsible for the
regulation of sleep; fatal within several
months
Proteins gone bad (or maybe not…)
• Sickle cell anemia is caused by a genetic
mutation of hemoglobin (not a prion); causes a
sickling of the red blood cell
• Those with 2 copies of the mutated gene have
a reduced life expectancy; those with only 1
copy have “Sickle trait” – cells only sickle under
reduced oxygen load
• Sickle cell disease common in tropical and
subtropical regions where malaria is common;
provides a selective advantage against malaria!
Sickle Cell Anemia
• Remember natural
selection is a pessimistic
process
• Those with the sickle cell
mutation survive malaria
infestation better than
those without
• “Heterozygous
advantage”
Normal red blood cell
Sickle blood cells
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
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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:
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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 contains the nucleotide uracil (U) instead
of the nucleotide thymine (T).
RNA contains:
• adenine (A)
• uracil (U)
• cytosine (C)
• guanine (G)
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RNA
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RNA
• RNA exists as a long,
single strand of
nucleotides.
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DNA
• In deoxyribonucleic acid, a hydroxyl group on
the sugar is replaced with a hydrogen atom.
• DNA contains the nucleotide thymine (T)
instead of the nucleotide uracil (U).
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 (adenine and
guanine) pair with smaller bases (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)