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Life and Chemistry: Large Molecules

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Title: Life and Chemistry: Large Molecules


1
Life and Chemistry Large Molecules
2
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

3
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

4
Theories of the Origin of Life
  • Could life have come from outside Earth?
  • The composition of meteorites suggests that some
    of lifes 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.

5
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.

6
Figure 3.1 Synthesis of Prebiotic Molecules in
an Experimental Atmosphere
7
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.

8
Macromolecules Giant Polymers
  • There are four major types of biological
    macromolecules
  • Proteins
  • Carbohydrates
  • Lipids
  • Nucleic acids

9
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.

10
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.

11
Table 3.1 The Building Blocks of Organisms
12
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

13
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.

14
Figure 3.3 Condensation and Hydrolysis of
Polymers (Part 1)
15
Figure 3.3 Condensation and Hydrolysis of
Polymers (Part 2)
16
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.

17
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.

18
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 (SS).
  • 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.

19
Table 3.2 The Twenty Amino Acids Found in
Proteins (Part 1)
20
Table 3.2 The Twenty Amino Acids Found in
Proteins (Part 2)
21
Table 3.2 The Twenty Amino Acids Found in
Proteins (Part 3)
22
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.

23
Figure 3.5 Formation of Peptide Linkages
24
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 NCCNCC.
  • Enormous numbers of different proteins are
    possible.

25
Proteins Polymers of Amino Acids
  • A proteins secondary structure consists of
    regular, repeated patterns in different regions
    in the polypeptide chain.
  • This shape is influenced primarily by hydrogen
    bonds arising from the amino acid sequence (the
    primary structure).
  • The two common secondary structures are the a
    helix and the b pleated sheet.

26
Proteins Polymers of Amino Acids
  • The a helix is a right-handed coil.
  • The peptide backbone takes on a helical shape due
    to hydrogen bonds.
  • The R groups point away from the peptide
    backbone.
  • Fibrous structural proteins have a-helical
    secondary structures, such as the keratins found
    in hair, feathers, and hooves.

27
Proteins Polymers of Amino Acids
  • b pleated sheets form from peptide regions that
    lie parallel to each other.
  • Sometimes the parallel regions are in the same
    peptide, sometimes the parallel regions are from
    different peptide strands.
  • This sheetlike structure is stabilized by
    hydrogen bonds between N-H groups on one chain
    with the CO group on the other.
  • Spider silk is made of b pleated sheets from
    separate peptides.

28
Figure 3.6 The Four Levels of Protein Structure
(Part 1)
29
Figure 3.6 The Four Levels of Protein Structure
(Part 2)
30
Figure 3.6 The Four Levels of Protein Structure
(Part 3)
31
Proteins Polymers of Amino Acids
  • Tertiary structure is the three-dimensional shape
    of the completed polypeptide.
  • The primary determinant of the tertiary structure
    is the interaction between R groups.
  • Other factors can include the location of
    disulfide bridges, which form between cysteine
    residues.

32
Figure 3.4 A Disulfide Bridge
33
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

34
Proteins Polymers of Amino Acids
  • It is now possible to determine the complete
    description of a proteins tertiary structure.
  • The location of every atom in the molecule is
    specified in three-dimensional space.

35
Figure 3.7 Three Representations of Lysozyme
36
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
    three-dimensional shape of the finished protein.
  • Hemoglobin is an example of such a protein it
    has four subunits.

37
Figure 3.8 Quaternary Structure of a Protein
38
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.

39
Figure 3.9 Noncovalent Interactions between
Proteins and Other Molecules
40
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 proteins normal three-dimensional
    structure is called denaturation.

41
Figure 3.11 Denaturation Is the Loss of Tertiary
Protein Structure and Function
42
Proteins Polymers of Amino Acids
  • Chaperonins are specialized proteins that help
    keep other proteins from interacting
    inappropriately with one another.
  • When a protein fails to fold correctly, serious
    complications can occur.
  • Some chaperonins help folding some prevent
    folding until the appropriate time.

43
Figure 3.12 Chaperonins Protect Proteins from
Inappropriate Folding
44
Carbohydrates Sugars and Sugar Polymers
  • Carbohydrates are carbon molecules with hydrogen
    and hydroxyl groups.
  • They act as energy storage and transport
    molecules.
  • They also serve as structural components.

45
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

46
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 121 ratios of the monomers.

47
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
    b-glucose, exist in equilibrium when dissolved in
    water.

48
Figure 3.13 Glucose From One Form to the Other
49
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.

50
Figure 3.14 Monosaccharides Are Simple Sugars
(Part 1)
51
Figure 3.14 Monosaccharides Are Simple Sugars
(Part 2)
52
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.

53
Figure 3.15 Disaccharides Are Formed by
Glycosidic Linkages
54
Carbohydrates Sugars and Sugar Polymers
  • Oligosaccharides contain more than two
    monosaccharides.
  • Many proteins found on the outer surface of cells
    have oligosaccharides attached to the R group of
    certain amino acids, or to lipids.
  • The human ABO blood types owe their specificity
    to oligosaccharide chains.

55
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.

56
Figure 3.16 Representative Polysaccharides (Part
1)
57
Figure 3.16 Representative Polysaccharides (Part
2)
58
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.

59
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.

60
Figure 3.17 Chemically Modified Carbohydrates
(Part 1)
61
Figure 3.17 Chemically Modified Carbohydrates
(Part 2)
62
Figure 3.17 Chemically Modified Carbohydrates
(Part 3)
63
Figure 3.17 Chemically Modified Carbohydrates
(Part 4)
64
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.

65
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)

66
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.

67
Figure 3.18 Synthesis of a Triglyceride
68
Lipids Water-Insoluble Molecules
  • Saturated fatty acids have only single
    carbon-to-carbon 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.

69
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.

70
Figure 3.19 Saturated and Unsaturated Fatty Acids
71
Lipids Water-Insoluble Molecules
  • Phospholipids have two hydrophobic fatty acid
    tails and one hydrophilic phosphate group
    attached to the glycerol.
  • 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.

72
Figure 3.20 Phospholipid Structure
73
Figure 3.21 Phospholipids Form a Bilayer
74
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.

75
Figure 3.22 b Carotene is the Source of Vitamin
A
76
Lipids Water-Insoluble Molecules
  • Steroids are signaling molecules.
  • 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.

77
Figure 3.23 All Steroids Have the Same Ring
Structure
78
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.

79
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.

80
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.

81
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.

82
Figure 3.24 Nucleotides Have Three Components
83
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.

84
Figure 3.25 Distinguishing Characteristics of
DNA and RNA
85
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.

86
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.

87
Figure 3.26 Hydrogen Bonding in RNA
88
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.

89
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.

90
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.

91
Nucleic Acids Informational Macromolecules That
Can Be Catalytic
  • Nucleotides have other important roles
  • The ribonucleotide ATP acts as an energy
    transducer in many 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.

92
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.

93
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.

94
Figure 3.28 Disproving the Spontaneous
Generation of Life (Part 1)
95
Figure 3.28 Disproving the Spontaneous
Generation of Life (Part 2)
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