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					             Chapter One
       Chemistry Is the Logic of
        Biological Phenomena
1.1 Distinctive Properties of Living Systems
1.2 Biomolecules: The Molecules of Life
1.3 A Biomolecular Hierarchy: Simple Molecules Are the
Units for Building Complex Structures
1.4 Properties of Biomolecules Reflect Their Fitness to the
Living Condition
1.5 Organization and Structure of Cells
1.6 Viruses Are Supramolecular Assemblies Acting as Cell
Parasites
1.1
Distinctive Properties of Living
Systems


   Complicated and
   highly organized
The Orion Nebula, a
tremendous cloud of gas in
which many hot, young stars
are evolving rapidly toward
cataclysmic cosmic explosions
called supernovea. Energy
released by nuclear explosions
in such supernovea brought
about the fusion of simple
atomic nuclei, forming the
more complex elements of
which the earth, its atmosphere,
and all living things are
composed.
• (a) Mandrill           (b) Tropical orchid
(Mandrillus sphinx), a   (Bulbophyllum blumei),
baboon native to West    New Guinea.
Africa.
   Some characteristic
    of living matter.
Kaleidoscopes
    of life
Biological structures serve
   functional purposes.
Microscopic complexity and organization are
   apparent in this colorized thin section
Living systems are actively engaged in energy
                transformations


     Food pyramid




          Carnivores, Herbivores, Photosynthesis
A prairie falcon acquires nutrients
  by consuming a smaller bird.
ATP and NADPH, two biochemically important
         energy-rich compounds.
                   Living systems have a
                remarkable capacity for self-
Living systems have a remarkable capacity for self-replication.




                        replication.
   Biological reproduction occurs with near-
    perfect fidelity (zebra).
The DNA double helix. Two complementary polynucleotide chains
running in opposite directions can pair through hydrogen bonding
between their nitrogenous bases. Their complementary nucleotide
sequences give rise to structural complementarity.
 1.2 Biomolecules:
The Molecules of Life
The chemical
composition of
living material,
such as this
jellyfish(水母),
differs from that
of its physical
environment,
which for this
organism is salt
water.
The elemental composition of living
matter differs markedly from the relative
abundance of elements in the earth’s.
Hydrogen, oxygen, carbon, and nitrogen
constitute more than 99% of the atoms in
the human body, with most of the H and
O occurring as H2O.
Elements essential to animal life and health
               水母
Biomolecules Are Carbon
      Compounds
Aliphatic(脂肪族的, 脂肪质的)
Metabolites and Macromolecules
The major precursors for the formation of
biomolecules are water, carbon dioxide, and three
inorganic nitrogen compounds—ammonium (NH4+),
nitrate (NO3-), and dinitrogen (N2). Metabolic
processes assimilate and transform these inorganic
precursors through ever more complex levels of
biomolecular order.
Some functional groups of biomolecules
1.3 · A Biomolecular Hierarchy:
   Simple Molecules Are the
  Units for Building Complex
           Structures
   Macromolecules are
composed of building blocks
  Proteins----amino acids
  Nucleic acids----nucleotides
  Polysaccharides----sugars
  Lipids----fatty acids, glycerol and choline etc.
         Prebiotic Evolution

The finding that all biological macromolecules in
all organism are made from the same three dozen
subunits has provided strong evidence that
modern organism are descended from a single
primordial cell line whose fundamental chemistry
would be recognizable even today.
  Biomolecules first arose by
     chemical evolution
Aleksandr I Oparin’s theory:
Electrical energy from lightning
discharges or heat energy from
volcanoes cause ammonia, methane ,
water vapor, and other compounds of
the primitive atmosphere to react,
forming simple organic compounds.
These compounds then dissolved in the
ancient seas, which over many millenia
became enriched with a large variety of
simple organic substances. In the warm
solution(the “primordial soup”), some
organic molecules had a greater
tendency than others to associate into
larger complexes.
Over millions of years, these in
turn assembled spontaneously to
form membranes and catalysts
(enzyme), which came together to
become precursors of earliest cells.
Chemical evolution can be
simulated in the laboratory.




  A spark-discharge
  apparatus
RNA or related precursors may have
been the first genes and catalysts

In modern organism, nucleic acids encode the
genetic information that specifies the structure
of enzymes, and enzymes have the ability to
catalyze the replication and repair of nucleic
acids, the mutual dependence of two classes of
biomolecules bring up the perplexing question:
which came first, DAN or proteins?
which came first, DAN or proteins?


The answer may be: neither.

The discover that RNA molecules can act as
catalysts in their own formation suggests that
RNA or similar molecules may have been the
first gene and the first catalyst.
One possible “RNA
world” scenario,
showing the transition
from the prebiotic RNA
world(shades of yellow)
to the biotic DNA world
(orange).
The “RNA world” hypothesis is
plausible but by no means
universally accepted. The hypothesis
does make testable prediction, and
to the extent that experimental tests
are possible within finite time, the
hypothesis will be tested and refined.
Biological evolution
began more than three
and half billion years
ago.
Ancient reefs in Australia contain fossil evidence of microbial life in the
sea of 3.5 billion years ago. Bits of sand and limestone became trapped
in the sticky extracellular coats of cyanobacteria, gradually building up
these stromatolites(岩层)found in Hamelin Bay, Western Australia.
Microscopic
examination of
sections of such
ancient rock reveals
microfossils of
filamentous
becteria(b),
interpreted as
shown in the
drawing(b).
1.4 · Properties of Biomolecules
  Reflect Their Fitness to the
        Living Condition
Biological Macromolecules
and Their Building Blocks
    Have a “Sense” or
       Directionality
   The macromolecules of cells are built of units—
    amino acids in proteins, nucleotides in nucleic
    acids, and carbohydrates in polysaccharides—that
    have structural polarity. That is, these molecules
    are not symmetrical, and so they can be thought of
    as having a “head” and a “tail.” Polymerization of
    these units to form macromolecules occurs by
    head-to-tail linear connections. Because of this,
    the polymer also has a head and a tail, and hence,
    the macromolecule has a “sense” or direction to its
    structure.
Biological Macromolecules Are
Informational
Biological Macromolecules Are
Informational
Biological
Macromolecules
Are Informational
Biomolecules Have
Characteristic Three-
Dimensional Architecture
 IgG, Immunoglobulin G is a major type of
G(

circulating antibody. Each of the spheres represents
an atom in the structure.
Weak Forces Maintain Biological
Structure and Determine
Biomolecular Interactions

Covalent bonds hold atoms together so that
molecules are formed. In contrast, weak chemical
forces or noncovalent bonds, (hydrogen bonds, van
der Waals forces, ionic interactions, and hydrophobic
interactions) are intramolecular or intermolecular
attractions between atoms.
Hydrogen bonds,
Van der Waals forces,
Ionic interactions,
Hydrophobic interactions
Structural Complementarity Determines
Biomolecular Interactions
This principle of structural complementarity is the
very essence of biomolecular recognition.
Structural complementarity is the significant clue
to understanding the functional properties of
biological systems. Biological systems from the
macromolecular level to the cellular level operate
via specific molecular recognition mechanisms
based on structural complementarity: a protein
recognizes its specific metabolite, a strand of DNA
recognizes its complementary strand, sperm
recognize an egg. All these interactions involve
structural complementarity between molecules.
Biomolecular Recognition Is Mediated by
Weak Chemical Forces
Weak Forces Restrict Organisms to a
Narrow Range of Environmental
Conditions---The central role of weak
forces in biomolecular interactions restricts
living systems to a narrow range of
physical conditions.
Enzymes
The sensitivity of cellular constituents to
environmental extremes places another
constraint on the reactions of metabolism.
Metabolic Regulation Is
Achieved by Controlling the
Activity of Enzymes
Thousands of reactions mediated by an equal
number of enzymes are occurring at any given
instant within the cell. Metabolism has many
branch points, cycles, and interconnections.
This metabolic regulation is achieved through
controls on enzyme activity so that the rates of
cellular reactions are appropriate to cellular
requirements.
A glance at
a metabolic
pathway
map
1.5 · Organization and
Structure of Cells

     prokaryotic
     eukaryotic
All living cells fall into one of two broad
categories—prokaryotic and eukaryotic. The
distinction is based on whether or not the cell has
a nucleus. Prokaryotes are single-celled
organisms that lack nuclei and other organelles;
the word is derived from pro meaning “prior to”
and karyot meaning “nucleus.” Eukaryotic cells
have true nuclei and other organelles such as
mitochondria, with the prefix eu meaning “true.”
Structural Organization of Prokaryotic Cells
A dividing Escherichia coli (E. coli ) cell
Dividing Saccharomyces cerevisiae
(baker’s yeast ) cell
Structural Organization of eukaryotic Cells
Nuclear
 pores
          Nuclear
           pores




nucleus
chromosome
Structure of
a mitochondrion
Structure of
a chloroplast
Portion of a skeletal muscle cell(artificial color)
Collenchyma (厚
角组织)cells
of a plant stem
Human sperm
cells (artificial
color)
Mature human
erythrocytes
(artificial color)
Human embryo at
the two-celled
stage cells
1.6 · Viruses Are Supramolecular
Assemblies Acting as Cell Parasites


Virus
Virions, nonliving particles(outside of the host cells)
Bacteriophages, simply phages, specific for the
becteria.
HIV
SARS :Coronavirus
(a) a bacterial virus, bacteriophage T4; (b) an
animal virus, adenovirus (inset at greater
magnification); (c) a plant virus, tobacco
mosaic virus.
New Words Review
Orion Nebula    Prebiotic    Prior
Cataclysmic     Primitive    Erythrocytes
Kaleidoscopes   Apparatus    Virus
Carnivore                    Virion
Herbivore       Perplexing
                             Phenomena
Prairie         Hypothesis   Reflect
Fidelity        Plausible    Properties
Material        Microbial    Assembly
Elemental       Covalent     Fitness
Ammonium                     Complicated
Metabolite      Parasite
                             Tremendous
Hierarchy       instant      Atmosphere
Complementarity   Scenario
Complement        Microbial      Leukocyte
Complementary     Stromatolites  Erythrocytes
Composition       Filamentous    Embryo
Glycerol          Reveal         Bacteriophage
Polysaccharides   Directionality Tobacco mosaic virus
Nucleotide        Polarity
Amino acids       Carbohydrates
Spontaneously     Symmetrical
Catalyst          Architecture
Precursor         Immunoglobulin
simulated         Sphere
The End of
Chapter 1
        Topics of Discussion

1 What Are Distinctive Properties of Living
   System?
2 How Many Types of the Important
   Biomacromolecules?
3 What Are Features of Biomolecules?
4 Talk About the Organization and Structure
  of Cells.

				
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posted:2/17/2013
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