Reginald H. Garrett
Charles M. Grisham
www.cengage.com/chemistry/garrett
CHAPTER 1
Chemistry is the Logic of
Biological Phenomena
Dr. J.K. Lu
2-18-2014
Reginald Garrett & Charles Grisham • University of Virginia
Outline
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1.1
1.2
1.3
1.4
1.5
1.6
On Life and Chemistry...
Distinctive Properties of Living Systems
Biomolecules: Molecules of Life
Biomolecular Hierarchy
Properties of Biomolecules
Organization and Structure of Cells
Viruses as Cell Parasites
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“Living things are composed of lifeless
molecules”
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(Albert Lehninger)
“Chemistry is the logic of biological
phenomena”
(Garrett and Grisham)
Distinctive Properties of Living
Systems
Life
a complex phenomena, impossible to
define in a precise fashion
Life possesses the properties of
replication, catalysis, and mutability
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- Norman Horowitz
Organisms are complicated and
highly organized
Biological structures serve
functional purposes
Living systems are actively
engaged in energy
transformations
Living systems have a
remarkable capacity for selfreplication
Living organisms objective 1: Complexity & Organization
Living Organisms Objective 2: Nutrient required
2
Cellular Architecture
1.1 – What Are the Distinctive Properties of
Living Systems?
Solar energy flows from photosynthetic organisms through food
chains to herbivores and on to carnivores at the apex of the food
pyramid.
Food pyramid
Figure 1.2 The food pyramid. Photosynthetic organisms at the base
capture light energy. Herbivores and carnivores derive their energy
ultimately from these primary producers.
Two biochemical important energyrich compound
Living Organisms Objective 3: Biological reproduction
The Fidelity of Self-Replication Resides
Ultimately in the Chemical Nature of DNA
Diverse living organisms share common chemical features
Figure 1.5 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.
BIOCHEMISTRY
Bioechemistry is…
A study of the molecular basis of life
“The study of life on the molecular level”
- D. Voet & J. Voet
(NOTE: Why YOU need to study “ Biochemistry” ?!)
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Goals of Biochemistry
Describe structure, organization, function
of cells in molecular terms:
- Structural Chemistry
- Metabolism
- Molecular Genetics
Chemical mechanisms of many central processes
of life now understood
common molecular patterns and principles
biochemistry is profoundly influencing medicine
Advanced molecular biology, biotechnology
Biochemistry at Revolution in
biological sciences
e.g. Designing Molecules (medical applications)
6-Mercaptopurine
3'-Azido-2',3'-dideoxythymidine (AZT)
Isoproterenol
What property unites H, O, C and N and
renders these atoms so appropriate to
the chemistry of life?
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As: Their ability to form covalent bonds
by electron-pair sharing
Biomoecules
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Elements: hydrogen, oxygen, carbon,
nitrogen(lightest elements of the
periodic table capable of forming a
variety of strong covalent bonds
Compounds: carbon-based compounds
1.2 Biomolecules:The Molecules of Life
What are the bond energies of covalent
bonds?
Bond
H-H
C-H
C-C
C-O
Example of the
versatility of
C-C bonds in
building complex
structures
Energy kJ/mol
436
414
343
351
- essential metals: Na+, K+, Mg+2, Ca+2, ClFig. 1-7, p. 6
Table 1-4, p. 13
Fig. 1-14, p. 13
1.2 Biomolecules: The Molecules of Life
H, O, C and N make up 99+% of atoms in the
human body
ELEMENT
Oxygen
Hydrogen
Carbon
Nitrogen
PERCENTAGE
63
25.2
9.5
1.4
Table 1-2, p. 7
Elements found
In organisms
Biomolecular hiearchchy
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Fig1-36 The three stages of the
evolution of life
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Fig 1-37 Apparatus for emulating the
synthesis of organic compounds on
the prebiotic Earth
Simple compounds: H2O, CO2, NH4+, NO3-,
N2
Metabolites
Building blocks: amino acids, nucleiotide,
monosaccharides
Macromolecules: protein,nucleic acids,
polysaccharides
1.3 A Biomolecular Hierarchy
Simple Molecules are the Units for
Building Complex Structures
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Molecular organization
In the cell is hierarchy
Metabolites and Macromolecules
Organelles
Membranes
The Unit of Life is the Cell
1.4 Properties of Biomolecules Reflect Their
Fitness to the Living Condition
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Macromolecules and Their Building Blocks
Have a “Sense” or Directionality
Macromolecules are Informational
Biomolecules have Characteristic ThreeDimensional Architecture
Weak Forces Maintain Biological Structure
and Determine Biomolecular Interactions
Fig. 1-9a, p. 10
Fig. 1-9b, p. 10
Fig. 1-9c, p. 10
Biological Molecules: Macromolecules
The molecular basis of life
Monomers/Polymers (Figure 1.7)
v Sugar/Polysaccharide
v Nucleotide/Nucleic Acids
v Amino acid/Polypeptides (Figure 1.6)
Revolves around the organization
and interrelationship between the 4
building blocks of life
Fig. 1-9, p. 10
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1.4 Properties of Biomolecules
Reflect Their Fitness to the Living
Condition
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3-Dimensional architecture and
intermolecular interactions (via
complementary surfaces of
macromolecules are based on weak
forces
Information content: sequence of
monomer building blocks and 3Dimensional architecture
Weak Forces
q van der Waals: 0.4-4.0
kJ/mole
q Hydrogen bonds: 12-30
kJ/mole
q Ionic bonds: 20 kJ/mole
q Hydrophobic interactions:
< 40 kJ/mole
Ionic bonds in biological molecules
Protein strand
Two Important Points About Weak
Forces
Structural complementary
Biomolecular Recognition is
Mediated by Weak Chemical Forces
Weak Forces Restrict Organisms
to a Narrow Range of
Environmental Conditions
Biochemistry 2/e - Garrett & Grisham
Denaturation and renaturation of the intricate
Structure of a protein
Copyright © 1999 by Harcourt Brace & Company
Metabolism is the organized release or capture of small amounts
Of energy in processes whose overall change in energy is large
Biochemistry as a Biological
Science
Enzyme catalyze metabolic reactions
A Biomolecular Hierarchy
Simple Molecules are the Units for Building
Complex Structures
- Metabolites and Macromolecules
- Organelles
- Membranes
“The Unit of Life is the Cell” !
Carbonic anhydrase
Organization and Structure of
Cells
Prokaryotic cells
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A single (plasma) membrane
no nucleus or organelles
Eukaryotic cells
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much larger in size than prokaryotes
103-104 times larger!
Nucleus plus many organelles
ER, Golgi, mitochondria, etc.
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Fig 1-4 Phylogenetic tree.
Figure 1-1 Scale drawings
of some prokaryotic cells.
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Figure 1-2 Schematic
drawing of a prokaryotic cell.
1.5 What is the Organization and Structure of Cells?
Fig. 1-5 Schematic diagram of an animal cell
accompanied by electron micrographs of its
organelles.
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Fig. 1-9 Drawing of a plant cell accompanied
by electron micrographs of its organelles
1.5 What is the Organization and Structure of
Cells?
Figure 1.22
Electron
micrograph of a
chloroplast.
Figure 1.22 Electron micrograph of a Golgi body.
1.5 What is the Organization and Structure of
Cells?
Figure 1.22
Electron
micrograph of a
nucleus
1.5 What is the Organization and
Structure of Cells?
1.5 What is the Organization and
Structure of Cells?
1.5 What is the Organization and
Structure of Cells?
1.6 What Are Viruses?
1.6 What are Viruses?
Figure 1.23 Viruses are genetic elements enclosed in a protein coat. Viruses are
not free-living organisms and can reproduce only within cells. Viruses show an
almost absolute specificity for their particular host cells, infecting and multiplying
only within those cells. Viruses are known for virtually every kind of cell. Shown
here are examples of (a) an animal virus, adenovirus; (b) bacteriophage T4 on
E.coli; and (c) a plant virus, tobacco mosaic virus.
Figure 1.24 The virus life cycle. Viruses are mobile bits of genetic information
encapsulated in a protein coat.
Function of organelles of eukaryotes
v
v
v
v
v
v
v
Mitochondria
Endoplasmic reticulum
Golgi complex
Nucleus
Lysosomes
Chloroplasts
peroxisomes
Figure 1-12Embryonic development of a fish,
an amphibian (salamander), a bird (chick), and
a mammal (human).
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Fig. 1-11 Evolutionary tree indicating the
lines of descent of cellular life on Earth.