Transcript Life and Chemistry: Large Molecules

Life and Chemistry:
Large Molecules
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Life and Chemistry: Large Molecules
• Theories of the Origin of Life
• Macromolecules: Giant Polymers
• Condensation and Hydrolysis Reactions
• Proteins: Polymers of Amino Acids
• Carbohydrates: Sugars and Sugar Polymers
• Lipids: Water-Insoluble Molecules
• Nucleic Acids: Informational Macromolecules That
Can Be Catalytic
• All Life from Life
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Theories of the Origin of Life
• Living things are composed of the same elements
as the inanimate universe.
• The arrangement of these elements in biological
systems is unique.
• There are two theories for the origin of life during
the 600 million years of the Hadean:
 Life from extraterrestrial sources
 Chemical evolution
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Theories of the Origin of Life
• Could life have come from outside Earth?
• The composition of meteorites suggests that
some of life’s complex molecules could have
come from space.
• There is no proof, however, that living things have
ever traveled to Earth by way of a comet or
meteorite.
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Theories of the Origin of Life
• The theory of chemical evolution holds that
conditions on the primitive Earth led to the
formation of the large molecules unique to life.
• In the 1950s, Stanley Miller and Harold Urey set
up an experimental “primitive” atmosphere and
used a spark to simulate lightning.
• Within days, the system contained numerous
complex molecules.
Figure 3.1 Synthesis of Prebiotic Molecules in an Experimental Atmosphere
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Theories of the Origin of Life
• The results of the Miller-Urey experiments have
undergone several interpretative refinements.
• The earliest stages of chemical evolution resulted
in the emergence of monomers and polymers that
probably have remained generally unchanged for
3.8 billion years.
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Macromolecules: Giant Polymers
• There are four major types of biological
macromolecules:
 Proteins - silk, hair, tendons
 Carbohydrates - starch, cellulose, chitin,
glycogen
 Lipids - fats, oils, waxes
 Nucleic acids - DNA, RNA, ATP
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Macromolecules: Giant Polymers
• These macromolecules are made the same way
in all living things, and are present in all
organisms in roughly the same proportions.
• An advantage of this biochemical unity is that
organisms acquire needed biochemicals by eating
other organisms.
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Macromolecules: Giant Polymers
• Macromolecules are giant polymers.
• Polymers are formed by covalent linkages of
smaller units called monomers.
• Molecules with molecular weights greater than
1,000 daltons (atomic mass units) are usually
classified as macromolecules.
Table 3.1 The Building Blocks of Organisms
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Macromolecules: Giant Polymers
• The functions of macromolecules are related to
their shape and the chemical properties of their
monomers.
• Some of the roles of macromolecules include:
 Energy storage
 Structural support
 Transport
 Protection and defense
 Regulation of metabolic activities
 Means for movement, growth, and development
 Heredity
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Condensation and Hydrolysis Reactions
• Macromolecules are made from smaller
monomers by means of a condensation or
dehydration reaction in which an OH from one
monomer is linked to an H from another
monomer.
• Energy must be added to make or break a
polymer.
• The reverse reaction, in which polymers are
broken back into monomers, is a called a
hydrolysis reaction.
Figure 3.3 Condensation and Hydrolysis of Polymers (Part 1)
Figure 3.3 Condensation and Hydrolysis of Polymers (Part 2)
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Proteins: Polymers of Amino Acids
• Proteins are polymers of amino acids. They are
molecules with diverse structures and functions.
• Each different type of protein has a characteristic
amino acid composition and order.
• Proteins range in size from a few amino acids to
thousands of them.
• Folding is crucial to the function of a protein and is
influenced largely by the sequence of amino
acids.
• 50% or more of the dry weight of animals and
bacteria
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Proteins: Polymers of Amino Acids
• An amino acid has four groups attached to a
central carbon atom:
 A hydrogen atom
 An amino group (NH3+)
 The acid is a carboxyl group (COO–).
 Differences in amino acids come from the side
chains, or the R groups.
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Proteins: Polymers of Amino Acids
• Amino acids can be classified based on the
characteristics of their R groups.
 Five have charged hydrophilic side chains.
 Five have polar but uncharged side chains.
 Seven have nonpolar hydrophobic side chains.
 Cysteine has a terminal disulfide (—S—S—).
 Glycine has a hydrogen atom as the R group.
 Proline has a modified amino group that forms
a covalent bond with the R group, forming a
ring.
Table 3.2 The Twenty Amino Acids Found in Proteins (Part 1)
Table 3.2 The Twenty Amino Acids Found in Proteins (Part 2)
Table 3.2 The Twenty Amino Acids Found in Proteins (Part 3)
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Proteins: Polymers of Amino Acids
• Proteins are synthesized by condensation
reactions between the amino group of one amino
acid and the carboxyl group of another. This forms
a peptide linkage.
• Proteins are also called polypeptides. A
dipeptide is two amino acids long; a tripeptide,
three. A polypeptide is multiple amino acids long.
Figure 3.5 Formation of Peptide Linkages
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Proteins: Polymers of Amino Acids
• There are four levels of protein structure: primary,
secondary, tertiary, and quaternary.
• The precise sequence of amino acids is called its
primary structure.
• The peptide backbone consists of repeating units
of atoms: N—C—C—N—C—C.
• Enormous numbers of different proteins are
possible.
Figure 3.6 The Four Levels of Protein Structure (Part 3)
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Proteins: Polymers of Amino Acids
• Other factors determining tertiary structure:
 The nature and location of secondary
structures
 Hydrophobic side-chain aggregation and van
der Waals forces, which help stabilize them
 The ionic interactions between the positive
and negative charges deep in the protein,
away from water
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Proteins: Polymers of Amino Acids
• It is now possible to determine the complete
description of a protein’s tertiary structure.
• The location of every atom in the molecule is
specified in three-dimensional space.
Figure 3.7 Three Representations of Lysozyme
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Proteins: Polymers of Amino Acids
• Quaternary structure results from the ways in
which multiple polypeptide subunits bind together
and interact.
• This level of structure adds to the threedimensional shape of the finished protein.
• Hemoglobin is an example of such a protein; it
has four subunits.
Figure 3.8 Quaternary Structure of a Protein
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Proteins: Polymers of Amino Acids
• Shape is crucial to the functioning of some
proteins:
 Enzymes need certain surface shapes in order
to bind substrates correctly.
 Carrier proteins in the cell surface membrane
allow substances to enter the cell.
 Chemical signals such as hormones bind to
proteins on the cell surface membrane.
• The combination of attractions, repulsions, and
interactions determines the right fit.
Figure 3.9 Noncovalent Interactions between Proteins and Other Molecules
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Proteins: Polymers of Amino Acids
• Changes in temperature, pH, salt concentrations,
and oxidation or reduction conditions can change
the shape of proteins.
• This loss of a protein’s normal three-dimensional
structure is called denaturation ( i.e. an egg).
Figure 3.11 Denaturation Is the Loss of Tertiary Protein Structure and Function
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Enzymes
• Enzymes are proteins that act as a catalyst
(increase the rate of a chemical reaction).
• Enzymes have an active site ( example of a lock
and key)
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Carbohydrates: Sugars and Starches
• Carbohydrates are carbon molecules with
hydrogen and hydroxyl groups.
• They act as energy storage and transport
molecules.
• They also serve as structural components and
building material (i.e. chitin and cellulose).
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Carbohydrates: Sugars and Sugar Polymers
• There are four major categories of carbohydrates:
 Monosaccharides
 Disaccharides, which consist of two
monosaccharides
 Oligosaccharides, which consist of between
3 and 20 monosaccharides
 Polysaccharides, which are composed of
hundreds to hundreds of thousands of
monosaccharides
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Carbohydrates: Sugars and Sugar Polymers
• The general formula for a carbohydrate monomer
is multiples of CH2O, maintaining a ratio of 1
carbon to 2 hydrogens to 1 oxygen.
• During the polymerization, which is a
condensation reaction, water is removed.
• Carbohydrate polymers have ratios of carbon,
hydrogen, and oxygen that differ somewhat from
the 1:2:1 ratios of the monomers.
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Carbohydrates: Sugars and Sugar Polymers
• All living cells contain the monosaccharide
glucose (C6H12O6).
• Glucose exists as a straight chain and a ring, with
the ring form predominant.
• The two forms of the ring, a-glucose and bglucose, exist in equilibrium when dissolved in
water.
Figure 3.13 Glucose: From One Form to the Other
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Carbohydrates: Sugars and Sugar Polymers
• Different monosaccharides have different
numbers or different arrangements of carbons.
• Most monosaccharides are optical isomers.
• Hexoses (six-carbon sugars) include the
structural isomers glucose, fructose, mannose,
and galactose.
• Pentoses are five-carbon sugars.
Figure 3.14 Monosaccharides Are Simple Sugars (Part 1)
Figure 3.14 Monosaccharides Are Simple Sugars (Part 2)
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Carbohydrates: Sugars and Sugar Polymers
• Monosaccharides are bonded together covalently
by condensation reactions. The bonds are called
glycosidic linkages.
• Disaccharides have just one such linkage:
sucrose, lactose, maltose, cellobiose.
• Maltose and cellobiose are structural isomers.
Figure 3.15 Disaccharides Are Formed by Glycosidic Linkages
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Carbohydrates: Sugars and Sugar Polymers
• Polysaccharides are giant polymers of
monosaccharides connected by glycosidic
linkages.
• Cellulose is a giant polymer of glucose joined by
b-1,4 linkages.
• Starch is a polysaccharide of glucose with a-1,4
linkages.
Figure 3.16 Representative Polysaccharides (Part 1)
Figure 3.16 Representative Polysaccharides (Part 2)
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Carbohydrates: Sugars and Sugar Polymers
• Starches vary by amount of branching.
• Some plant starch, such as amylose, is
unbranched. Others, such as amylopectin, are
moderately branched.
• Animal starch, called glycogen, is a highly
branched polysaccharide.
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Carbohydrates: Sugars and Sugar Polymers
• Carbohydrates are modified by the addition of
functional groups:
 Glucose can acquire a carboxyl group (—COOH),
forming glucuronic acid.
 Phosphate added to one or more hydroxyl (—OH)
sites creates a sugar phosphate such as fructose
1,6-bisphosphate.
 Amino groups can be substituted for —OH groups,
making amino sugars such as glucosamine and
galactosamine.
Figure 3.17 Chemically Modified Carbohydrates (Part 1)
Figure 3.17 Chemically Modified Carbohydrates (Part 2)
Figure 3.17 Chemically Modified Carbohydrates (Part 3)
Figure 3.17 Chemically Modified Carbohydrates (Part 4)
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Typical Hamburger
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Lipids: Water-Insoluble Molecules
• Lipids are insoluble in water.
• This insolubility results from the many nonpolar
covalent bonds of hydrogen and carbon in lipids.
• Lipids aggregate away from water, which is polar,
and are attracted to each other via weak, but
additive, van der Waals forces.
• Hydrophobic end- water hating
• Hydrophilic end - water loving
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Lipids: Water-Insoluble Molecules
• Roles for lipids in organisms include:
 Energy storage (fats and oils)
 Cell membranes (phospholipids)
 Capture of light energy (carotinoids)
 Hormones and vitamins (steroids and modified
fatty acids)
 Thermal insulation
 Electrical insulation of nerves
 Water repellency (waxes and oils)
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Lipids: Water-Insoluble Molecules
• Fats and oils store energy.
• Fats and oils are triglycerides, composed of
three fatty acid molecules and one glycerol
molecule.
• Glycerol is a three-carbon molecule with three
hydroxyl (—OH) groups, one for each carbon.
• Fatty acids are long chains of hydrocarbons with
a carboxyl group (—COOH) at one end.
Figure 3.18 Synthesis of a Triglyceride
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Lipids: Water-Insoluble Molecules
• Saturated fatty acids have only single carbon-tocarbon bonds and are said to be saturated with
hydrogens.
• Saturated fatty acids are rigid and straight, and
solid at room temperature. Animal fats are
saturated.
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Lipids: Water-Insoluble Molecules
• Unsaturated fatty acids have at least one
double-bonded carbon in one of the chains —the
chain is not completely saturated with hydrogen
atoms.
• The double bonds cause kinks that prevent easy
packing. Unsaturated fatty acids are liquid at room
temperature. Plants commonly have unsaturated
fatty acids.
Figure 3.19 Saturated and Unsaturated Fatty Acids
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Lipids: Water-Insoluble Molecules
• Phospholipids - similar to fats, except one or two
of the fatty acids are replaced by a phosphate
group which is connected to a nitrogen group.
• As a result, phospholipids orient themselves so
that the phosphate group faces water and the tail
faces away.
• In aqueous environments, these lipids form
bilayers, with heads facing outward, tails facing
inward. Cell membranes are structured this way.
Figure 3.20 Phospholipid Structure
Figure 3.21 Phospholipids Form a Bilayer
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Lipids: Water-Insoluble Molecules
• Carotenoids are light-absorbing pigments found
in plants and animals.
• One, b-carotene, is a plant pigment used to trap
light in photosynthesis.
• In animals, this pigment, when broken into two
identical pieces, becomes vitamin A.
Figure 3.22 b –Carotene is the Source of Vitamin A
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Lipids: Water-Insoluble Molecules
• Steroids are signaling molecules.
• Classified as a lipid because they are insoluble in
water.
• Steroids are organic compounds with a series of
fused rings.
• The steroid cholesterol is a common part of
animal cell membranes.
• Cholesterol is also is an initial substrate for
synthesis of the hormones testosterone and
estrogen.
Figure 3.23 All Steroids Have the Same Ring Structure
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Lipids: Water-Insoluble Molecules
• Some lipids are vitamins: small organic molecules
essential to health.
• Vitamin A is important for normal development,
maintenance of cells, and night vision.
• Vitamin D is important for absorption of calcium in
the intestines.
• Vitamin E, an antioxidant, protects membranes.
• Vitamin K is a component required for normal
blood clotting.
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Lipids: Water-Insoluble Molecules
• Waxes are highly nonpolar molecules consisting
of saturated long fatty acids bonded to long fatty
alcohols via an ester linkage.
• A fatty alcohol is similar to a fatty acid, except for
the last carbon, which has an —OH group instead
of a —COOH group.
• Waxy coatings repel water and prevent water loss
from structures such as hair, feathers, and leaves.
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Nucleic Acids: Informational Macromolecules
That Can Be Catalytic
• Nucleic acids are polymers that are specialized
for storage and transmission of information.
• Two types of nucleic acid are DNA
(deoxyribonucleic acid) and RNA (ribonucleic
acid).
• DNA encodes hereditary information and transfers
information to RNA molecules.
• The information in RNA is decoded to specify the
sequence of amino acids in proteins.
• Largest biological molecules.
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Nucleic Acids: Informational Macromolecules
That Can Be Catalytic
• Nucleic acids are polymers of nucleotides.
• A nucleotide consists of a pentose sugar, a
phosphate group, and a nitrogen-containing base.
• In DNA, the pentose sugar is deoxyribose; in RNA
it is ribose.
Figure 3.24 Nucleotides Have Three Components
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Nucleic Acids: Informational Macromolecules
That Can Be Catalytic
• DNA typically is double-stranded.
• The two separate polymer chains are held
together by hydrogen bonding between their
nitrogenous bases.
• The base pairing is complementary: At each
position where a purine is found on one strand, a
pyrimidine is found on the other.
• Purines have a double-ring structure.
Pyrimidines have one ring.
Figure 3.25 Distinguishing Characteristics of DNA and RNA
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Nucleic Acids: Informational Macromolecules
That Can Be Catalytic
• The linkages that hold the nucleotides in RNA and
DNA are called phosphodiester linkages.
• These linkages are formed between carbon 3 of
the sugar and a phosphate group that is
associated with carbon 5 of the sugar.
• The backbone consists of alternating sugars and
phosphates.
• In DNA, the two strands are antiparallel.
• The DNA strands form a double helix, a molecule
with a right-hand twist.
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Nucleic Acids: Informational Macromolecules
That Can Be Catalytic
• Most RNA molecules consist of only a single
polynucleotide chain.
• Instead of the base thymine, RNA uses the base
uracil.
• Hydrogen bonding between ribonucleotides in
RNA can result in complex three-dimensional
shapes.
Figure 3.26 Hydrogen Bonding in RNA
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Nucleic Acids: Informational Macromolecules
That Can Be Catalytic
• DNA is an information molecule. The information
is stored in the order of the four different bases.
• This order is transferred to RNA molecules, which
are used to direct the order of the amino acids in
proteins.
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Nucleic Acids: Informational Macromolecules
That Can Be Catalytic
• Closely related living species have DNA base
sequences that are more similar than distantly
related species.
• The comparative study of base sequences has
confirmed many of the traditional classifications of
organisms.
• DNA comparisons confirm that our closest living
relatives are chimpanzees: We share more than
98 percent of our DNA base sequences.
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Nucleic Acids: Informational Macromolecules
That Can Be Catalytic
• Certain RNA molecules called ribozymes can act
as catalysts.
• The discovery of ribozymes provided a solution to
the question of whether proteins or nucleic acids
came first when life originated.
• Since RNA can be informational and catalytic, it
could have acted as a catalyst for its own
replication as well as for the synthesis of proteins.
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Nucleic Acids: Informational Macromolecules
That Can Be Catalytic
• Nucleotides have other important roles:
 The ribonucleotide ATP supplies energy for
biochemical reactions.
 The ribonucleotide GTP powers protein
synthesis.
 cAMP (cyclic AMP) is a special ribonucleotide
that is essential for hormone action and the
transfer of information by the nervous system.
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All Life from Life
• Should we expect to see new life forms arise from
the biochemical environment?
• During the Renaissance, most people thought that
some forms of life arose directly from inanimate or
decaying matter by spontaneous generation.
• In 1668, Francisco Redi did an experiment to test
this hypothesis.
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All Life from Life
• The invention of the microscope unveiled a vast
new biological world which some scientists
believed arose spontaneously from their rich
chemical environment.
• Louis Pasteur completed experiments to disprove
this idea.
• Environmental and planetary conditions that exist
on Earth today prevent life from arising from
nonliving materials, as it might have during the
Hadean.
Figure 3.28 Disproving the Spontaneous Generation of Life (Part 1)
Figure 3.28 Disproving the Spontaneous Generation of Life (Part 2)