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Reginald H. Garrett
Charles M. Grisham
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Chapter 1
The Facts of Life:
Chemistry is the Logic of
Biological Phenomena
Reginald Garrett & Charles Grisham • University of Virginia
Outline and Key Questions
• What Are the Distinctive Properties of Living
Systems?
• What Kinds of Molecules Are Biomolecules?
• What is the Structural Organization of Complex
Biomolecules?
• How Do the Properties of Biomolecules Reflect Their
Fitness to the Living Condition?
• What is the Organization and Structure of Cells?
• What are Viruses?
On Life and Chemistry…
• “Living things are composed of lifeless molecules.”
(Albert Lehninger)
• “Chemistry is the logic of biological phenomena.”
(Garrett and Grisham)
1.1 – What Are the Distinctive Properties of Living
Systems?
• 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
Energy-rich molecules
Organisms capture energy in the form of special
energized molecules such as ATP and NADPH.
Steady state – the appearance of consistency over
time, but not at equilibrium
Equilibrium – the appearance of consistency over time
due to equal and opposite forces
Covalent Bond Formation by H, C, N, and O
Makes Them Suitable to the Chemistry of Life
The Fidelity of Self-Replication Resides
Ultimately in the Chemical Nature of DNA
All due to complementary forces!!
1.3 What is the Structural Organization of
Complex Biomolecules?
• Simple Molecules are the Units for
Building Complex Structures
•
•
•
•
Metabolites and Macromolecules
Organelles
Membranes
The Unit of Life is the Cell
1.3 What is the Structural Organization of
Complex Biomolecules?
Examples of the versatility of C-C bonds in building complex structures
1.3 What is the Structural Organization of
Complex Biomolecules?
1.3 What is the Structural Organization of
Complex Biomolecules?
1.4 – Properties of Biomolecules Reflect Their
Fitness to the Living Condition
• Macromolecules and their building blocks have a
“sense” or directionality
• Macromolecules are informational
• Biomolecules have characteristic three-dimensional
architecture
• Weak forces maintain biological structure and
determine biomolecular interactions
1.4 – Properties of Biomolecules Reflect Their
Fitness to the Living Condition
Amino acids build proteins
1.4 – Properties of Biomolecules Reflect Their
Fitness to the Living Condition
Polysaccharides are built by joining sugars
together
1.4 – Properties of Biomolecules Reflect Their
Fitness to the Living Condition
Nucleic acids are polymers of nucleotides
1.4 – Properties of Biomolecules Reflect Their
Fitness to the Living Condition
1.4 – Properties of Biomolecules Reflect Their
Fitness to the Living Condition
• Covalent bonds hold atoms together so that
molecules are formed
• Weak forces profoundly influence the structures and
behaviors of all biological molecules
• Weak forces create interactions that are constantly
forming and breaking under physiological conditions
• Energies of weak forces range from 0.4 to 30 kJ/mol
• Weak forces include:
• van der Waals interactions
• Hydrogen bonds
• Ionic interactions
• Hydrophobic interactions
Biomolecules Have Characteristic ThreeDimensional Architecture
Antigen-binding domain of immunoglobulin G (IgG).
1.4 – Properties of Biomolecules Reflect Their
Fitness to the Living Condition
• Know these important numbers
•
•
•
•
Van der Waals Interactions: 0.4-4.0 kJ/mol
Hydrogen Bonds: 12-30 kJ/mol
Ionic Interactions: 20 kJ/mol
Hydrophobic Interactions: <40 kJ/mol
• These interactions influence profoundly the nature of
biological structures
Van der Waals Forces Are Important to
Biomolecular Interactions
Van der Waals packing is enhanced in molecules that are
structurally complementary.
Van der Waals Forces Are Important to
Biomolecular Interactions
The van der Waals
interaction energy
profile as a function of
the distance, r, between
the centers of two
atoms.
1.4 – Properties of Biomolecules Reflect Their
Fitness to the Living Condition
1.4 – Properties of Biomolecules Reflect Their
Fitness to the Living Condition
Some
biologically
important
H bonds
1.4 – Properties of Biomolecules Reflect Their
Fitness to the Living Condition
Ionic bonds in the Mg-ATP complex
1.4 – Properties of Biomolecules Reflect Their
Fitness to the Living Condition
Ionic bonds
contribute to
the stability of
proteins
1.4 – Properties of Biomolecules Reflect Their
Fitness to the Living Condition
Two Important Points about
Weak Forces
• Biomolecular recognition is mediated by weak
chemical forces
• Weak forces restrict organisms to a narrow range of
environmental conditions
Biomolecular Recognition is Mediated by
Weak Chemical Forces
Structural complementarity: The antigen on the right (gold) is a
small protein, lysozyme, from hen egg white. The antibody
molecule (IgG) (left) has a pocket that is structurally
complementary to a surface feature (red) on the antigen.
Biomolecular Recognition is Mediated by
Weak Chemical Forces
Biomolecular Recognition is Mediated by
Weak Chemical Forces
Biomolecular Recognition is Mediated by
Weak Chemical Forces
Large energy changes can cause problems for the cell.
Small, step reaction are necessary to prevent things like
denaturation.
1.4 – Properties of Biomolecules Reflect Their
Fitness to the Living Condition
Combustion of
glucose in a
calorimeter yields
energy in its least
useful form, heat
1.4 – Properties of Biomolecules Reflect Their
Fitness to the Living Condition
Cells release
the energy of
glucose in a
stepwise
fashion,
capturing it
in the
formation of
ATP
1.4 – Properties of Biomolecules Reflect Their
Fitness to the Living Condition
The Time Scale of Life:
• The processes of life have durations ranging over 33
orders of magnitude
• From 10-15 sec (for electron transfer reactions)
• To 1018 sec (the period of evolution, from the first
appearance of organisms to today)
• The processes and lifetimes described in Table 1.5
will be discussed throughout the text and course
1.5 What is the Organization and Structure
of Cells?
• Prokaryotic cells
• A single (plasma) membrane
• No nucleus or organelles
• Eukaryotic cells
• Much larger in size than prokaryotes
• 103-104 times larger!
• Nucleus plus many organelles
• ER, Golgi, mitochondria, etc.
How Many Genes Does a Cell Need?
The Structural Organization of Eukaryotic Cells Is
More Complex Than That of Prokaryotic Cells
This figure diagrams
a rat liver cell, a
typical higher animal
cell.
1.5 What is the Organization and Structure
of Cells?
This figure
diagrams a cell in
the leaf of a higher
plant
Cellular Features
• Tables 1.7, 1.8 and 1.9 outline the major features of
prokaryotic, eukaryotic, and plant cells. It is
important that if you are not familiar with these
general features that you carefully read these tables.
1.6 What Are Viruses?
Viruses are genetic elements enclosed in a protein coat.
Viruses are not free-living organisms and can reproduce only
within cells. (a) adenovirus; (b) bacteriophage T4 on E.coli; (c)
a plant virus, tobacco mosaic virus.
1.6 What are Viruses?
The virus life cycle. Viruses are mobile bits of genetic
information encapsulated in a protein coat.
Questions
• You should be able to complete questions 1-14 and
16-17 at the end of the chapter. While they will not
be graded, they would be excellent practice.