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Chap 5 Campbell
Structure and Function of
Macromolecules
Condensation Reaction
Hydrolysis
The subunit for carbohydrates is sugar (sacharride)
Carbons could be
straight chained or
cyclical
• Starch is a storage polysaccharide composed
entirely of glucose monomers.
– Most monomers are joined by 1-4 linkages between
the glucose molecules.
– One unbranched form of starch, amylose, forms a
helix.
– Branched forms, like amylopectin, are more complex.
Fig. 5.6a
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• Plants store starch within plastids, including
chloroplasts.
• Plants can store surplus glucose in starch and
withdraw it when needed for energy or carbon.
• Animals that feed on plants, especially parts rich
in starch, can also access this starch to support
their own metabolism.
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• Animals also store glucose in a polysaccharide
called glycogen.
• Glycogen is highly branched, like amylopectin.
• Humans and other vertebrates store glycogen in the liver
and muscles but only have about a one day supply.
Insert Fig. 5.6b - glycogen
Fig. 5.6b
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• While polysaccharides can be built from a
variety of monosaccharides, glucose is the
primary monomer used in polysaccharides.
• One key difference among polysaccharides
develops from 2 possible ring structure of
glucose.
– These two ring forms differ in whether the hydroxyl
group attached to the number 1 carbon is fixed above
(beta glucose) or below (alpha glucose) the ring
plane.
Fig. 5.7a
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• Starch is a polysaccharide of alpha glucose
monomers.
Fig. 5.7
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• Structural polysaccharides form strong building
materials.
• Cellulose is a major component of the tough wall
of plant cells.
– Cellulose is also a polymer of glucose monomers, but
using beta rings.
Fig. 5.7c
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Fig. 5.8
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• The enzymes that digest starch cannot hydrolyze
the beta linkages in cellulose.
– Cellulose in our food passes through the digestive
tract and is eliminated in feces as “insoluble fiber”.
– As it travels through the digestive tract, it abrades the
intestinal walls and stimulates the secretion of
mucus.
• Some microbes can digest cellulose to its
glucose monomers through the use of cellulase
enzymes.
• Many eukaryotic herbivores, like cows and
termites, have symbiotic relationships with
cellulolytic microbes, allowing them access to
this rich source of energy.
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
This Tiny Crustacean Menace Could Fuel the
World
By Clay Dillow Posted 03.09.2010 at 2:58 pm 11
Comments
Gribbles via BBC
They don't exactly look like the saviors of our energy economy,
but that's exactly what some researchers think they could be.
Gribbles -- tiny crustacean pests with a knack for digesting
wood -- have long been considered a marine parasite for the
destruction they cause to wooden hulls and piers. But the
enzymes gribbles use in to break wood fibers down into sugars
could make them the next biofuels breakthrough.
Essentially, gribbles are blessed with a digestive process
unparalleled (to our knowledge) by other wood-consuming
insects and animals. Their digestive enzymes can break down
woody cellulose and even lignin -- the normally indigestible part
of woody plants -- creating sugars that are more or less ideal
for fermenting into alcohol-based fuels.
A biofuel factory based on the gribble's digestive biology could yield energy-dense sugars for biofuel
production in an efficient manner. But of course there's a give-and-take in the equation that involves feeding
woody plant materials -- like trees -- into the process as fuel. But by pushing forward with more efficient
means to convert woody cellulose into fuels -- and perhaps by engineering woodier trees -- we reduce the
amount of organic matter we need to feed in to get the combustible stuff out.
The gribble -- thorn in the side of harbormasters, plague of the age of sail -- might just be good for
something after all.
Chiton forms the exoskeleton
of arthropods such as insects
and also the cell walls of fungi
• Glycerol consists of a three carbon skeleton with
a hydroxyl group attached to each.
• A fatty acid consists of a carboxyl group attached
to a long carbon skeleton, often 16 to 18 carbons
long.
Fig. 5.10a
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Fat = 1 glycerol + 3 fatty acids
• The many nonpolar C-H bonds in the long
hydrocarbon skeleton make fats hydrophobic.
• The C-H bonds store a lot of energy.
• In a fat, three fatty acids are joined to glycerol
by an ester linkage, creating a triacylglycerol.
Fig. 5.10b
Unsaturated fatty
acids are liquid at
room temperature
Hydrogenating them
makes them saturated
Saturated fatty
acids are solid
at room temp
• The three fatty acids in a fat can be the same or
different.
• Fatty acids may vary in length (number of
carbons) and in the number and locations of
double bonds.
– If there are no
carbon-carbon
double bonds,
then the molecule
is a saturated fatty
acid - a hydrogen
at every possible
position.
Fig. 5.11a
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– If there are one or more carbon-carbon double bonds,
then the molecule is an unsaturated fatty acid formed by the removal of hydrogen atoms from the
carbon skeleton.
– Saturated fatty acids
are straight chains,
but unsaturated fatty
acids have a kink
wherever there is
a double bond.
Fig. 5.11b
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• Fats with saturated fatty acids are saturated fats.
– Most animal fats are saturated.
– Saturated fat are solid at room temperature.
– A diet rich in saturated fats may contribute to
cardiovascular disease (atherosclerosis) through
plaque deposits.
• Fats with unsaturated fatty acids are unsaturated
fats.
– Plant and fish fats, known as oils, are liquid are room
temperature.
• The kinks provided by the double bonds prevent the
molecules from packing tightly together.
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Trans-double bonds
straighten the fatty
acid chain and make
them act like saturated
fats
What is trans fat, how does it get into our food, and
what are its effects on human health?
Traditionally, animal fats like butter and lard (saturated
fats) were used as spreads and for baking. Vegetable
oils (unsaturated fats) were cheaper, but as liquids they
were not a suitable alternative. Unsaturated fats have a
structure with kinks; these kinks result in a liquid state
at room temperature. In the early 20th century, a
chemical process called hydrogenation was developed
that converts vegetable oils into saturated, more solid
fats (margarine and vegetable shortening). When it was
discovered that eating saturated fats increases the risk
for coronary heart disease, the food industry turned to
partial hydrogenation. This process lowerd the content
of saturated fat in vegetable shortening and margarine,
but also dramatically increased the amount of a certain
kind of fat - trans fat - in our diets. While suppliers
praised processed vegetable oils as healthy unsaturated
and cholesterol-free substitutes for animal fats, there is
now strong evidence that introducing trans-fatty acids
into our diets does more harm than good.
The Skinny On Trans Fat
It's found almost everywhere, but even a small amount of
trans fat can drive up cholesterol levels, says a nutrition expert at
Tufts University.
Boston [08.15.02] -- Found in over 42,000 food products and
considered more potent than saturated fat, trans fat is difficult to avoid.
While the average American consumes close to 5 grams of the
substance a day, researchers say even one gram--which can drive up
LDL cholesterol levels--is too much in a healthy diet. To help better
educate consumers, nutrition experts including Tufts' Alice
Lichtenstein are working on new ways to inform the public about
the dangers of trans fat and ways to avoid it.
"Anything above zero will increase the LDL cholesterol levels,"
Lichtenstein, a nutritional biochemist at Tufts University and a
member of the National Academy of Sciences, told the San Jose
Mercury News. "If you double the trans intake, you [nearly] double
the rise in LDL cholesterol. So the recommendation is to minimize
it."
• The major function of fats is energy storage.
– A gram of fat stores more than twice as much energy
as a gram of a polysaccharide.
– Plants use starch for energy storage when mobility is
not a concern but use oils when dispersal and packing
is important, as in seeds.
– Humans and other mammals store fats as long-term
energy reserves in adipose cells.
• Fat also functions to cushion vital organs.
• A layer of fats can also function as insulation.
– This subcutaneous layer is especially thick in whales,
seals, and most other marine mammals.
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Hydrophobic
tails
Steroids are lipids characterized by
four fused rings
Examples are cholesterol, testosterone
and estrogen
• Cholesterol, an important steroid, is a
component in animal cell membranes.
• Cholesterol is also the precursor from which all
other steroids are synthesized.
– Many of these other steroids are hormones, including
the vertebrate sex hormones.
• While cholesterol is clearly an essential
molecule, high levels of cholesterol in the blood
may contribute to cardiovascular disease.
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2003
1. A polypeptide is a polymer of amino
acids connected in a specific sequence
• Amino acids consist of four components attached
to a central carbon, the alpha carbon.
• These components include a
hydrogen atom, a carboxyl
group, an amino group, and
a variable R group
(or side chain).
– Differences in R groups
produce the 20 different
amino acids.
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Amino
group
Acid group
R groups determine
type of amino aci
Peptide bonds form forming a polypeptide
2. A protein’s function depends on
its specific conformation
• A functional proteins consists of one or more
polypeptides that have been precisely twisted,
folded, and coiled into a unique shape.
• It is the order of amino acids that determines what
the three-dimensional conformation will be.
Fig. 5.17
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• The primary structure
of a protein is its unique
sequence of amino
acids.
– Lysozyme, an enzyme
that attacks bacteria,
consists on a polypeptide
chain of 129 amino
acids.
– The precise primary
structure of a protein is
determined by inherited
genetic information.
Fig. 5.18
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Fig. 5.19
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
• The secondary structure of a protein results
from hydrogen bonds at regular intervals along
the polypeptide backbone.
– Typical shapes
that develop from
secondary structure
are coils (an alpha
helix) or folds
(beta pleated
sheets).
Fig. 5.20
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• The structural properties of silk are due to beta
pleated sheets.
– The presence of so many hydrogen bonds makes
each silk fiber stronger than steel.
Fig. 5.21
• Tertiary structure is determined by a variety of
interactions among R groups and between R
groups and the polypeptide backbone.
– These interactions
include hydrogen
bonds among polar
and/or charged
areas, ionic bonds
between charged
R groups, and
hydrophobic
interactions and
van der Waals
interactions among
hydrophobic R
Fig. 5.22
groups. This causes the protein to fold up into a 3D structure
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• While these three interactions are relatively
weak, disulfide bridges, strong covalent bonds
that form between the sulfhydryl groups (SH) of
cysteine monomers, stabilize the structure.
Fig. 5.22
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HYDROPHILLIC
• Quarternary structure results from the
aggregation of two or more polypeptide subunits.
– Collagen is a fibrous protein of three polypeptides
that are supercoiled like a rope.
• This provides the structural strength for their role in
connective tissue.
– Hemoglobin is a
globular protein
with two copies
of two kinds
of polypeptides.
Fig. 5.23
Fig. 5.24
Animation 5.9.5
How biotech is driving computing
The most super of supercomputers are folding proteins, not crunching numbers. That's because the life sciences have
overtaken physics as the source of the most challenging computing problems.
By Chris Taylor, Business 2.0 Magazine senior editor
August 31 2006: 4:32 PM EDT
SAN FRANCISCO (Business 2.0 Magazine) -- Pop quiz: What new technology has the United States and Japan engaged in the virtual equivalent of the Space Race?
The surprising answer: It's biotech.
Some background, in case you haven't been keeping up with current computing news: Japanese researchers have cobbled together a $9 million supercomputer
called MDGrape-3 that last month broke the petaflop barrier for the first time.
Sign up for the Future Boy e-mail newsletter
Prosthetic
group
• A protein’s conformation can change in response
to the physical and chemical conditions.
• Alterations in pH, salt concentration,
temperature, or other factors can unravel or
denature a protein.
– These forces disrupt the hydrogen bonds, ionic
bonds, and disulfide bridges that maintain the
protein’s shape.
• Some proteins can return to their functional
shape after denaturation, but others cannot,
especially in the crowded environment of the
cell.
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Fig. 5.25
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• In spite of the knowledge of the threedimensional shapes of over 10,000 proteins, it is
still difficult to predict the conformation of a
protein from its primary structure alone.
– Most proteins appear to undergo several intermediate
stages before reaching their “mature” configuration.
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• The folding of many proteins is protected by
chaperonin proteins that shield out bad influences.
Fig. 5.26
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• A new generation of supercomputers is being
developed to generate the conformation of any
protein from its amino acid sequence or even its
gene sequence.
– Part of the goal is to develop general principles that
govern protein folding.
• At present, scientists use X-ray crystallography
to determine protein conformation.
– This technique requires the formation of a crystal of
the protein being studied.
– The pattern of diffraction of an X-ray by the atoms of
the crystal can be used to determine the location of
the atoms and to build a computer model of its
structure.
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Fig. 5.27
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• The sugar-phosphate backbones of the two
polynucleotides are on the outside of the helix.
• Pairs of nitrogenous
bases, one from each
strand, connect the
polynucleotide chains
with hydrogen bonds.
• Most DNA molecules
have thousands to
millions of base pairs.
Fig. 5.30
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4. We can use DNA and proteins as
tape measures of evolution
• Genes (DNA) and their products (proteins)
document the hereditary background of an
organism.
• Because DNA molecules are passed from
parents to offspring, siblings have greater
similarity than do unrelated individuals of the
same species.
• This argument can be extended to develop a
molecular genealogy between species.
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• Two species that appear to be closely-related
based on fossil and molecular evidence should
also be more similar in DNA and protein
sequences than are more distantly related species.
– In fact, the sequence of amino acids in hemoglobin
molecules differ by only one amino acid between
humans and gorilla.
– More distantly related species have more differences.
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
ATP is a nucleotide
used to transfer
energy
DNA is used to
store genetic
information
(heredity)
RNA is used in the
synthesis of
proteins
Do Lab simulation
• Go to this site:
• http://midpac.edu/~biology/Intro%20Biolog
y/PH%20Biology%20Lab%20Simulations/
bioprop/intro.html
• Do the lab simulation on Properties of
Biological Molecules, then take the practice
test – print out the test to turn in.