Chapter 1 The Facts of Life: Chemistry is the Logic of Biological Phenomena

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Chapter 1The Facts of Life Chemistry is the
Logic of Biological Phenomena
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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?

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On Life and Chemistry

• Living things are composed of lifeless
  molecules. (Albert Lehninger)
• Chemistry is the logic of biological phenomena.
  (Garrett and Grisham)

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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
  self-replication

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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
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Covalent Bond Formation by H, C, N, and O Makes
Them Suitable to the Chemistry of Life
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The Fidelity of Self-Replication Resides
Ultimately in the Chemical Nature of DNA
All due to complementary forces!!
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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

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1.3 What is the Structural Organization of
Complex Biomolecules?
Examples of the versatility of C-C bonds in
building complex structures
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1.3 What is the Structural Organization of
Complex Biomolecules?
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1.3 What is the Structural Organization of
Complex Biomolecules?
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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

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1.4 Properties of Biomolecules Reflect Their
Fitness to the Living Condition
Amino acids build proteins
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1.4 Properties of Biomolecules Reflect Their
Fitness to the Living Condition
Polysaccharides are built by joining sugars
together
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1.4 Properties of Biomolecules Reflect Their
Fitness to the Living Condition
Nucleic acids are polymers of nucleotides
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1.4 Properties of Biomolecules Reflect Their
Fitness to the Living Condition
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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

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Biomolecules Have Characteristic
Three-Dimensional Architecture
Antigen-binding domain of immunoglobulin G (IgG).
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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 lt40 kJ/mol
• These interactions influence profoundly the
  nature of biological structures

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Van der Waals Forces Are Important to
Biomolecular Interactions
Van der Waals packing is enhanced in molecules
that are structurally complementary.
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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.
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1.4 Properties of Biomolecules Reflect Their
Fitness to the Living Condition
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1.4 Properties of Biomolecules Reflect Their
Fitness to the Living Condition
Some biologically important H bonds
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1.4 Properties of Biomolecules Reflect Their
Fitness to the Living Condition
Ionic bonds in the Mg-ATP complex
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1.4 Properties of Biomolecules Reflect Their
Fitness to the Living Condition
Ionic bonds contribute to the stability of
proteins
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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

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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.
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Biomolecular Recognition is Mediated by Weak
Chemical Forces
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Biomolecular Recognition is Mediated by Weak
Chemical Forces
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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.
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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
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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
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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

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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.

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How Many Genes Does a Cell Need?
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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.
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1.5 What is the Organization and Structure of
Cells?
This figure diagrams a cell in the leaf of a
higher plant
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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.

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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.
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1.6 What are Viruses?
The virus life cycle. Viruses are mobile bits of
genetic information encapsulated in a protein
coat.
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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.