H-B Woodlawn Biology - Jim’s Discussion Notes
THE STRUCTURE AND FUNCTION OF MACROMOLECULES
· Cells join smaller organic
molecules together to form larger molecules.
· These larger molecules, macromolecules, may be composed of
thousands of atoms and weigh over 100,000 daltons.
· The four major classes of
macromolecules are: carbohydrates, lipids, proteins, and nucleic acids.
1. Most
macromolecules are polymers
· Three of the four classes of
macromolecules form chainlike molecules called polymers.
· Polymers consist of many similar or identical building blocks linked by
covalent bonds.
· The repeated units are small
molecules called monomers.
· Some monomers have other
functions of their own.
· The chemical mechanisms that
cells use to make and break polymers are similar for all classes of
macromolecules.
· Monomers are connected by
covalent bonds via a condensation
reaction or dehydration reaction.
· One monomer provides a
hydroxyl group and the other provides a hydrogen and together these form water.
· This process requires energy
and is aided by enzymes.
· The covalent bonds
connecting monomers in a polymer are disassembled by hydrolysis.
· In hydrolysis, as the
covalent bond is broken a hydrogen atom and hydroxyl group from a split water
molecule attaches where the covalent bond used to be.
· Hydrolysis reactions
dominate the digestive process, guided by specific enzymes.
2. An immense variety of polymers can be built from
a small set of monomers
· Each cell has thousands of
different macromolecules.
· These molecules vary among
cells of the same individual; they vary more among unrelated individuals of a
species, and even more between species.
· This diversity comes from
various combinations of the 40-50 common monomers and other rarer ones.
· These monomers can be
connected in various combinations, like the 26 letters in the alphabet can be
used to create a great diversity of words.
· Biological molecules are
even more diverse.
· Carbohydrates include both sugars and polymers.
· The simplest carbohydrates
are monosaccharides or simple sugars.
· Disaccharides, double
sugars, consist of two monosaccharides joined by a condensation reaction.
· Polysaccharides are polymers
of monosaccharides.
1. Sugars, the smallest
carbohydrates serve as a source of fuel and carbon sources
· Monosaccharides generally have molecular formulas that are some multiple of CH2O.
· For example, glucose has the
formula C6H12O6.
· Most names for sugars end in
-ose.
· Monosaccharides have a
carbonyl group and multiple hydroxyl groups.
· If the carbonyl group is at
the end, the sugar is an aldose, if not, the sugars is a ketose.
· Glucose, an aldose, and
fructose, a ketose, are structural isomers.
· Monosaccharides are also
classified by the number of carbons in the backbone.
· Glucose and other six carbon
sugars are hexoses.
· Five carbon backbones are
pentoses and three carbon sugars are trioses.
· Monosaccharides may also
exist as enantiomers.
· For example, glucose and galactose,
both six-carbon aldoses, differ in the spatial arrangement around asymmetrical
carbons.
· Monosaccharides,
particularly glucose, are a major fuel for cellular work.
· They also function as the
raw material for the synthesis of other monomers, including those of amino
acids and fatty acids.
· Two monosaccharides can join
with a glycosidic linkage to form a dissaccharide via dehydration.
· Maltose, malt sugar, is
formed by joining two glucose molecules.
· Sucrose, table sugar, is
formed by joining glucose and fructose and is the major transport form of
sugars in plants.
· While often drawn as a
linear skeleton, in aqueous solutions monosaccharides form rings.
2. Polysaccharides, the
polymers of sugars, have storage and structural roles
· Polysaccharides are polymers of hundreds to thousands of monosaccharides joined by
glycosidic linkages.
· One function of
polysaccharides is as an energy storage macromolecule that is hydrolyzed as
needed.
· Other polysaccharides serve
as building materials for the cell or whole organism.
· 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.
· 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.
· 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.
· 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 structures 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.
· Starch is a polysaccharide
of alpha glucose monomers.
· 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.
· While polymers built with
alpha glucose form helical structures, polymers built with beta glucose form
straight structures.
· This allows H atoms on one
strand to form hydrogen bonds with OH groups on other strands.
· Groups of polymers form
strong strands, microfibrils, which are basic building material for plants (and
humans).
· 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.
· Another important structural
polysaccharide is chitin, used in
the exoskeletons of arthropods (including insects, spiders, and crustaceans).
· Chitin is similar to
cellulose, except that it contains a nitrogen-containing appendage on each
glucose.
· Pure chitin is leathery, but
the addition of calcium carbonate hardens the chitin.
· Chitin also forms the
structural support for the cell walls of many fungi.
· Lipids are an exception
among macromolecules because they do not have polymers.
· The unifying feature of lipids is that they all have little or
no affinity for water.
· This is because their
structures are dominated by nonpolar covalent bonds.
· Lipids are highly diverse in
form and function.
1. Fats
store large amounts of energy
· Although fats are not
strictly polymers, they are large molecules assembled from smaller molecules by
dehydration reactions.
· A fat is constructed from two kinds of smaller molecules, glycerol
and fatty acids.
· 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.
· The many nonpolar C-H bonds
in the long hydrocarbon skeleton make fats hydrophobic.
· In a fat, three fatty acids
are joined to glycerol by an ester linkage, creating a triacylglycerol.
· 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.
· 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.
· Fats with saturated fatty
acids are saturated fats.
· Most animal fats are
saturated.
· Saturated fats 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.
· 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.
2. Phospholipids are major components of cell membranes
· Phospholipids have two fatty acids attached to glycerol and a phosphate group at the
third position.
· The phosphate group carries
a negative charge.
· Additional smaller groups
may be attached to the phosphate group.
· The interaction of
phospholipids with water is complex.
· The fatty acid tails are
hydrophobic, but the phosphate group and its attachments form a hydrophilic
head.
· When phospholipids are added
to water, they self-assemble into aggregates with the hydrophobic tails
pointing toward the center and the hydrophilic heads on the outside.
· This type of structure is
called a micelle.
· At the surface of a cell
phospholipids are arranged as a bilayer.
· Again, the hydrophilic heads
are on the outside in contact with the aqueous solution and the hydrophobic
tails from the core.
· The phospholipid bilayer forms
a barrier between the cell and the external environment.
· They are the major component
of membranes.
3. Steroids include cholesterol and certain hormones
· Steroids are lipids with a carbon skeleton consisting of four fused carbon
rings.
· Different steroids are
created by varying functional groups attached to the rings.
· 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.
· Proteins are instrumental in
about everything that an organism does.
· These functions include
structural support, storage, transport of other substances, intercellular
signaling, movement, and defense against foreign substances.
· Proteins are the
overwhelming enzymes in a cell and regulate metabolism by selectively
accelerating chemical reactions.
· Humans have tens of
thousands of different proteins, each with their own structure and function.
· Proteins are the most
structurally complex molecules known.
· Each type of protein has a
complex three-dimensional shape or conformation.
· All protein polymers are
constructed from the same set of 20 monomers, called amino acids.
· Polymers of proteins are
called polypeptides.
· A protein consists of one or more polypeptides folded and coiled into
a specific conformation.
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.
· The twenty different R
groups may be as simple as a hydrogen atom (as in the amino acid glutamine) to
a carbon skeleton with various functional groups attached.
· The physical and chemical
characteristics of the R group determine the unique characteristics of a
particular amino acid.
· One group of amino acids has
hydrophobic R groups.
· Another group of amino acids
has polar R groups, making them hydrophilic.
· The last group of amino
acids includes those with functional groups that are charged (ionized) at
cellular pH.
· Some R groups are bases,
others are acids.
· Amino acids are joined
together when a dehydration reaction removes a hydroxyl group from the carboxyl
end of one amino acid and a hydrogen from the amino group of another.
· The resulting covalent bond
is called a peptide bond.
· Repeating the process over
and over creates a long polypeptide chain.
· At one end is an amino acid
with a free amino group the (the N-terminus) and at the other is an amino acid
with a free carboxyl group the (the C-terminus).
· The repeated sequence
(N-C-C) is the polypeptide backbone.
· Attached to the backbone are
the various R groups.
· Polypeptides range in size
from a few monomers to thousands.
2. A protein’s function depends on its specific conformation
· A functional protein
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.
· A protein’s specific
conformation determines its function.
· In almost every case, the
function depends on its ability to recognize and bind to some other molecule.
· For example, antibodies bind
to particular foreign substances that fit their binding sites.
· Enzymes recognize and bind
to specific substrates, facilitating a chemical reaction.
· Neurotransmitters pass
signals from one cell to another by binding to receptor sites on proteins in
the membrane of the receiving cell.
· The folding of a protein
from a chain of amino acids occurs spontaneously.
· The function of a protein is
an emergent property resulting from its specific molecular order.
· Three levels of structure:
primary, secondary, and tertiary structure, are used to organize the folding
within a single polypeptide.
· Quaternary structure arises
when two or more polypeptides join to form a protein.
· 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.
· Even a slight change in
primary structure can affect a protein’s conformation and ability to function.
· In individuals with sickle
cell disease, abnormal hemoglobins, oxygen-carrying proteins, develop because
of a single amino acid substitution.
· These abnormal hemoglobins
crystallize, deforming the red blood cells and leading to clogs in tiny blood
vessels.
· 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).
· 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.
· 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 groups.
· 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.
· Quaternary 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.
· 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.
· In spite of the knowledge of
the three-dimensional 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.
· The folding of many proteins
is protected by chaperonin proteins
that shield out bad influences.
· 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.
· The amino acid sequence of a
polypeptide is programmed by a gene.
· A gene consists of regions
of DNA, a polymer of nucleic acids.
· DNA (and their genes) is
passed by the mechanisms of inheritance.
1. Nucleic acids store and transmit hereditary information
· There are two types of
nucleic acids: ribonucleic acid (RNA)
and deoxyribonucleic acid (DNA).
· DNA provides direction for
its own replication.
· DNA also directs RNA
synthesis and, through RNA, controls protein synthesis.
· Organisms inherit DNA from
their parents.
· Each DNA molecule is very
long and usually consists of hundreds to thousands of genes.
· When a cell reproduces
itself by dividing, its DNA is copied and passed to the next generation of
cells.
· While DNA has the
information for all the cell’s activities, it is not directly involved in the
day to day operations of the cell.
· Proteins are responsible for
implementing the instructions contained in DNA.
· Each gene along a DNA
molecule directs the synthesis of a specific type of messenger RNA molecule
(mRNA).
· The mRNA interacts with the
protein-synthesizing machinery to direct the ordering of amino acids in a
polypeptide.
· The flow of genetic
information is from DNA -> RNA -> protein.
· Protein synthesis occurs in
cellular structures called ribosomes.
· In eukaryotes, DNA is
located in the nucleus, but most ribosomes are in the cytoplasm with mRNA as an
intermediary.
2. A nucleic acid strand is a polymer of nucleotides
· Nucleic acids are polymers
of monomers called nucleotides.
· Each nucleotide consists of
three parts: a nitrogen base, a pentose sugar, and a phosphate group.
· The nitrogen bases, rings of
carbon and nitrogen, come in two types: purines
and pyrimidines.
· Pyrimidines have a single
six-membered ring.
· The three different pyrimidines,
cytosine (C), thymine (T), and uracil (U) differ in atoms attached to the ring.
· Purine have a six-membered
ring joined to a five-membered ring.
· The two purines are adenine
(A) and guanine (G).
· The pentose joined to the
nitrogen base is ribose in nucleotides
of RNA and deoxyribose in DNA.
· The only difference between
the sugars is the lack of an oxygen atom on carbon two in deoxyribose.
· The combination of a pentose
and nucleic acid is a nucleoside.
· The addition of a phosphate
group creates a nucleoside monophosphate or nucleotide.
· Polynucleotides are synthesized by connecting the sugars of one nucleotide to the
phosphate of the next with a phosphodiester link.
· This creates a repeating
backbone of sugar-phosphate units with the nitrogen bases as appendages.
· The sequence of nitrogen
bases along a DNA or mRNA polymer is unique for each gene.
· Genes are normally hundreds
to thousands of nucleotides long.
· The number of possible
combinations of the four DNA bases is limitless.
· The linear order of bases in
a gene specifies the order of amino acids - the primary structure of a protein.
· The primary structure in
turn determines three-dimensional conformation and function.
3. Inheritance is based on replication of the DNA double helix
· An RNA molecule is a single polynucleotide
chain.
· DNA molecules have two
polynucleotide strands that spiral around an imaginary axis to form a double helix.
· The double helix was first
proposed as the structure of DNA in 1953 by James Watson and Francis Crick.
· 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.
· Because of their shapes,
only some bases are compatible with each other.
· Adenine (A) always pairs
with thymine (T) and guanine (G) with cytosine (C).
· With these base-pairing
rules, if we know the sequence of bases on one strand, we know the sequence on
the opposite strand.
· The two strands are complementary.
· During preparations for cell
division each of the strands serves as a template to order nucleotides into a
new complementary strand.
· This results in two
identical copies of the original double-stranded DNA molecule.
· The copies are then
distributed to the daughter cells.
· This mechanism ensures that
the genetic information is transmitted whenever a cell reproduces.
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.
· 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 differs by only one amino acid between
humans and gorilla.
· More distantly related
species have more differences.